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Nanamiya H, Tanaka D, Hiyama G, Isogai T, Watanabe S. Detection of four isomers of the human cytomegalovirus genome using nanopore long-read sequencing. Virus Genes 2024; 60:377-384. [PMID: 38861195 DOI: 10.1007/s11262-024-02083-6] [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: 04/09/2024] [Accepted: 06/01/2024] [Indexed: 06/12/2024]
Abstract
Human cytomegalovirus has a linear DNA genome with a total length of approximately 235 kb. This large genome is divided into two domains, "Long" and "Short". There are four isomers of the cytomegalovirus genome with different orientations of each domain. To confirm the presence of four types of isomers, it is necessary to identify the sequence of the junction between the domains. However, due to the presence of repeat sequences, it is difficult to determine the junction sequences by next-generation sequencing analysis. To solve this problem, long-read sequencing was performed using the Oxford Nanopore sequencer and the junctions were successfully identified in four isomers in strain Merin and ATCC-2011-3. Nanopore sequencing also revealed the presence of multiple copies of the "a" sequence (a-seq) in the junctions, indicating the diversity of the junction sequences. These results strongly suggest that long-read sequencing using the nanopore sequencer would be beneficial for identifying the complex structure of the cytomegalovirus genome.
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Affiliation(s)
- Hideaki Nanamiya
- Fukushima Translational Research Foundation, Capital Front Bldg., 7-4, 1-35, Sakae-Machi, Fukushima, 960-8031, Japan.
- Translational Research Center, Fukushima Medical University, 1, Hikarigaoka, Fukushima, 960-1295, Japan.
| | - Daisuke Tanaka
- Translational Research Center, Fukushima Medical University, 1, Hikarigaoka, Fukushima, 960-1295, Japan
| | - Gen Hiyama
- Translational Research Center, Fukushima Medical University, 1, Hikarigaoka, Fukushima, 960-1295, Japan
| | - Takao Isogai
- Translational Research Center, Fukushima Medical University, 1, Hikarigaoka, Fukushima, 960-1295, Japan
| | - Shinya Watanabe
- Translational Research Center, Fukushima Medical University, 1, Hikarigaoka, Fukushima, 960-1295, Japan
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2
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Gustavsson E, Grünewald K, Elias P, Hällberg BM. Dynamics of the Herpes simplex virus DNA polymerase holoenzyme during DNA synthesis and proof-reading revealed by Cryo-EM. Nucleic Acids Res 2024; 52:7292-7304. [PMID: 38806233 PMCID: PMC11229320 DOI: 10.1093/nar/gkae374] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2023] [Revised: 04/16/2024] [Accepted: 04/25/2024] [Indexed: 05/30/2024] Open
Abstract
Herpes simplex virus 1 (HSV-1), a double-stranded DNA virus, replicates using seven essential proteins encoded by its genome. Among these, the UL30 DNA polymerase, complexed with the UL42 processivity factor, orchestrates leading and lagging strand replication of the 152 kb viral genome. UL30 polymerase is a prime target for antiviral therapy, and resistance to current drugs can arise in immunocompromised individuals. Using electron cryo-microscopy (cryo-EM), we unveil the dynamic changes of the UL30/UL42 complex with DNA in three distinct states. First, a pre-translocation state with an open fingers domain ready for nucleotide incorporation. Second, a halted elongation state where the fingers close, trapping dATP in the dNTP pocket. Third, a DNA-editing state involving significant conformational changes to allow DNA realignment for exonuclease activity. Additionally, the flexible UL30 C-terminal domain interacts with UL42, forming an extended positively charged surface binding to DNA, thereby enhancing processive synthesis. These findings highlight substantial structural shifts in the polymerase and its DNA interactions during replication, offering insights for future antiviral drug development.
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Affiliation(s)
- Emil Gustavsson
- Department of Cell and Molecular Biology, Karolinska Institutet, 171 77 Stockholm, Sweden
- Centre for Structural Systems Biology, Deutsches Elektronen-Synchrotron DESY, Notkestraße 85, Building 15, 22607 Hamburg, Germany
| | - Kay Grünewald
- Centre for Structural Systems Biology, Deutsches Elektronen-Synchrotron DESY, Notkestraße 85, Building 15, 22607 Hamburg, Germany
- Leibniz-Institute of Virology, Martinistraße 52, 20251 Hamburg, Germany
- Department of Chemistry, University of Hamburg, Martin-Luther-King-Platz 6, 20146 Hamburg, Germany
| | - Per Elias
- Institute of Biomedicine, Department of Medical Biochemistry and Cell Biology, Sahlgrenska Academy, University of Gothenburg, Box 440, 405 30 Gothenburg, Sweden
| | - B Martin Hällberg
- Department of Cell and Molecular Biology, Karolinska Institutet, 171 77 Stockholm, Sweden
- Centre for Structural Systems Biology, Deutsches Elektronen-Synchrotron DESY, Notkestraße 85, Building 15, 22607 Hamburg, Germany
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3
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Uribe FR, González VPI, Kalergis AM, Soto JA, Bohmwald K. Understanding the Neurotrophic Virus Mechanisms and Their Potential Effect on Systemic Lupus Erythematosus Development. Brain Sci 2024; 14:59. [PMID: 38248274 PMCID: PMC10813552 DOI: 10.3390/brainsci14010059] [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: 11/07/2023] [Revised: 12/24/2023] [Accepted: 01/03/2024] [Indexed: 01/23/2024] Open
Abstract
Central nervous system (CNS) pathologies are a public health concern, with viral infections one of their principal causes. These viruses are known as neurotropic pathogens, characterized by their ability to infiltrate the CNS and thus interact with various cell populations, inducing several diseases. The immune response elicited by neurotropic viruses in the CNS is commanded mainly by microglia, which, together with other local cells, can secrete inflammatory cytokines to fight the infection. The most relevant neurotropic viruses are adenovirus (AdV), cytomegalovirus (CMV), enterovirus (EV), Epstein-Barr Virus (EBV), herpes simplex virus type 1 (HSV-1), and herpes simplex virus type 2 (HSV-2), lymphocytic choriomeningitis virus (LCMV), and the newly discovered SARS-CoV-2. Several studies have associated a viral infection with systemic lupus erythematosus (SLE) and neuropsychiatric lupus (NPSLE) manifestations. This article will review the knowledge about viral infections, CNS pathologies, and the immune response against them. Also, it allows us to understand the relevance of the different viral proteins in developing neuronal pathologies, SLE and NPSLE.
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Affiliation(s)
- Felipe R. Uribe
- Millennium Institute on Immunology and Immunotherapy, Laboratorio de Inmunología Traslacional, Departamento de Ciencias Biológicas, Facultad de Ciencias de la Vida, Universidad Andrés Bello, Santiago 8370146, Chile; (F.R.U.); (V.P.I.G.)
| | - Valentina P. I. González
- Millennium Institute on Immunology and Immunotherapy, Laboratorio de Inmunología Traslacional, Departamento de Ciencias Biológicas, Facultad de Ciencias de la Vida, Universidad Andrés Bello, Santiago 8370146, Chile; (F.R.U.); (V.P.I.G.)
| | - Alexis M. Kalergis
- Millennium Institute on Immunology and Immunotherapy, Facultad de Ciencias Biológicas, Pontificia Universidad Católica de Chile, Santiago 8330025, Chile;
- Departamento de Endocrinología, Facultad de Medicina, Pontificia Universidad Católica de Chile, Santiago 8331150, Chile
| | - Jorge A. Soto
- Millennium Institute on Immunology and Immunotherapy, Laboratorio de Inmunología Traslacional, Departamento de Ciencias Biológicas, Facultad de Ciencias de la Vida, Universidad Andrés Bello, Santiago 8370146, Chile; (F.R.U.); (V.P.I.G.)
| | - Karen Bohmwald
- Instituto de Ciencias Biomédicas, Facultad de Ciencias de la Salud, Universidad Autónoma, Santiago 8910060, Chile
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4
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Xu H, Akinyemi IA, Haley J, McIntosh MT, Bhaduri-McIntosh S. ATM, KAP1 and the Epstein-Barr virus polymerase processivity factor direct traffic at the intersection of transcription and replication. Nucleic Acids Res 2023; 51:11104-11122. [PMID: 37852757 PMCID: PMC10639065 DOI: 10.1093/nar/gkad823] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2023] [Revised: 09/09/2023] [Accepted: 09/20/2023] [Indexed: 10/20/2023] Open
Abstract
The timing of transcription and replication must be carefully regulated for heavily-transcribed genomes of double-stranded DNA viruses: transcription of immediate early/early genes must decline as replication ramps up from the same genome-ensuring efficient and timely replication of viral genomes followed by their packaging by structural proteins. To understand how the prototypic DNA virus Epstein-Barr virus tackles the logistical challenge of switching from transcription to DNA replication, we examined the proteome at viral replication forks. Specifically, to transition from transcription, the viral DNA polymerase-processivity factor EA-D is SUMOylated by the epigenetic regulator and E3 SUMO-ligase KAP1/TRIM28. KAP1's SUMO2-ligase function is triggered by phosphorylation via the PI3K-related kinase ATM and the RNA polymerase II-associated helicase RECQ5 at the transcription machinery. SUMO2-EA-D then recruits the histone loader CAF1 and the methyltransferase SETDB1 to silence the parental genome via H3K9 methylation, prioritizing replication. Thus, a key viral protein and host DNA repair, epigenetic and transcription-replication interference pathways orchestrate the handover from transcription-to-replication, a fundamental feature of DNA viruses.
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Affiliation(s)
- Huanzhou Xu
- Division of Infectious Diseases, Department of Pediatrics, University of Florida, Gainesville, FL 32610, USA
| | - Ibukun A Akinyemi
- Child Health Research Institute, Department of Pediatrics, University of Florida, Gainesville, FL 32610, USA
| | - John Haley
- Department of Pathology and Stony Brook Proteomics Center, Stony Brook University, Stony Brook, NY 11794, USA
| | - Michael T McIntosh
- Child Health Research Institute, Department of Pediatrics, University of Florida, Gainesville, FL 32610, USA
- Department of Molecular Genetics and Microbiology, University of Florida, Gainesville, FL 32610, USA
| | - Sumita Bhaduri-McIntosh
- Division of Infectious Diseases, Department of Pediatrics, University of Florida, Gainesville, FL 32610, USA
- Department of Molecular Genetics and Microbiology, University of Florida, Gainesville, FL 32610, USA
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Wu X, Zhou X, Wang S, Mao G. DNA damage response(DDR): a link between cellular senescence and human cytomegalovirus. Virol J 2023; 20:250. [PMID: 37915066 PMCID: PMC10621139 DOI: 10.1186/s12985-023-02203-y] [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: 05/22/2023] [Accepted: 10/04/2023] [Indexed: 11/03/2023] Open
Abstract
The DNA damage response (DDR) is a signaling cascade that is triggered by DNA damage, involving the halting of cell cycle progression and repair. It is a key event leading to senescence, which is characterized by irreversible cell cycle arrest and the senescence-associated secretory phenotype (SASP) that includes the expression of inflammatory cytokines. Human cytomegalovirus (HCMV) is a ubiquitous pathogen that plays an important role in the senescence process. It has been established that DDR is necessary for HCMV to replicate effectively. This paper reviews the relationship between DDR, cellular senescence, and HCMV, providing new sights for virus-induced senescence (VIS).
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Affiliation(s)
- Xinna Wu
- Affiliated Zhejiang Hospital, Zhejiang University School of Medicine, Hangzhou, 310030, China
| | - Xuqiang Zhou
- College of Life Science, Zhejiang Chinese Medical University, Hangzhou, 310053, China
| | - Sanying Wang
- Zhejiang Provincial Key Lab of Geriatrics & Geriatrics Institute of Zhejiang Province, Department of Geriatrics, Zhejiang Hospital, Hangzhou, 310030, China.
| | - Genxiang Mao
- Affiliated Zhejiang Hospital, Zhejiang University School of Medicine, Hangzhou, 310030, China.
- Zhejiang Provincial Key Lab of Geriatrics & Geriatrics Institute of Zhejiang Province, Department of Geriatrics, Zhejiang Hospital, Hangzhou, 310030, China.
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Pseudorabies Virus: From Pathogenesis to Prevention Strategies. Viruses 2022; 14:v14081638. [PMID: 36016260 PMCID: PMC9414054 DOI: 10.3390/v14081638] [Citation(s) in RCA: 37] [Impact Index Per Article: 18.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2022] [Revised: 07/21/2022] [Accepted: 07/25/2022] [Indexed: 11/16/2022] Open
Abstract
Pseudorabies (PR), also called Aujeszky’s disease (AD), is a highly infectious viral disease which is caused by pseudorabies virus (PRV). It has been nearly 200 years since the first PR case occurred. Currently, the virus can infect human beings and various mammals, including pigs, sheep, dogs, rabbits, rodents, cattle and cats, and among them, pigs are the only natural host of PRV infection. PRV is characterized by reproductive failure in pregnant sows, nervous disorders in newborn piglets, and respiratory distress in growing pigs, resulting in serious economic losses to the pig industry worldwide. Due to the extensive application of the attenuated vaccine containing the Bartha-K61 strain, PR was well controlled. With the variation of PRV strain, PR re-emerged and rapidly spread in some countries, especially China. Although researchers have been committed to the design of diagnostic methods and the development of vaccines in recent years, PR is still an important infectious disease and is widely prevalent in the global pig industry. In this review, we introduce the structural composition and life cycle of PRV virions and then discuss the latest findings on PRV pathogenesis, following the molecular characteristic of PRV and the summary of existing diagnosis methods. Subsequently, we also focus on the latest clinical progress in the prevention and control of PRV infection via the development of vaccines, traditional herbal medicines and novel small RNAs. Lastly, we provide an outlook on PRV eradication.
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Wang Y, Wei Y, Wu H, Feng L, Huang L. Specific inhibition of the interaction between pseudorabies virus DNA polymerase subunits UL30 and UL42 by a synthetic peptide. Vet Microbiol 2022; 272:109517. [PMID: 35908441 DOI: 10.1016/j.vetmic.2022.109517] [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: 06/19/2022] [Revised: 07/14/2022] [Accepted: 07/17/2022] [Indexed: 11/30/2022]
Abstract
Pseudorabies virus (PRV) is a ubiquitous and economically important swine alphaherpesvirus that causes devastating swine diseases worldwide. PRV-encoded DNA-dependent DNA polymerase, comprised of the catalytic subunit UL30 and the accessory subunit UL42, is essential for viral replication. PRV UL30 and UL42 act as a heterodimer with UL30 harboring inherent DNA polymerase activity and UL42 conferring processivity on the DNA polymerase holoenzyme. The formation of PRV UL30/UL42 heterodimer holoenzyme through protein-protein interactions is indispensable for viral replication. In work described here, we defined the key domains that mediate PRV UL30/UL42 interaction, and found that the 41 carboxy-terminal amino acids region of PRV UL30 is critical for its interaction with UL42. Intriguingly, a synthetic peptide corresponding to these 41 carboxy-terminal amino acid residues efficiently disrupted PRV UL30/UL42 interaction through competitively binding to UL42. These findings suggest that the peptides from the PRV DNA polymerase UL30/UL42 subunit interface may represent potential targets for designing a novel intervention strategy against PRV infection. This work further strengthens the concept that the herpesvirus DNA polymerase catalytic subunits utilize their extreme carboxy-terminal domains as a conserved mechanism to associate with their cognate accessory subunits, providing us the opportunity of designing novel antiviral agents against herpesvirus infection through disruption of the herpesvirus DNA polymerase subunit interactions.
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Affiliation(s)
- Yiping Wang
- Division of Swine Digestive System Infectious Diseases, State Key Laboratory of Veterinary Biotechnology, Harbin Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Harbin 150069, China
| | - Yanwu Wei
- Division of Swine Digestive System Infectious Diseases, State Key Laboratory of Veterinary Biotechnology, Harbin Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Harbin 150069, China
| | - Hongli Wu
- Division of Swine Digestive System Infectious Diseases, State Key Laboratory of Veterinary Biotechnology, Harbin Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Harbin 150069, China
| | - Li Feng
- Division of Swine Digestive System Infectious Diseases, State Key Laboratory of Veterinary Biotechnology, Harbin Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Harbin 150069, China.
| | - Liping Huang
- Division of Swine Digestive System Infectious Diseases, State Key Laboratory of Veterinary Biotechnology, Harbin Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Harbin 150069, China.
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Oleanolic Acid Derivative AXX-18 Exerts Antiviral Activity by Inhibiting the Expression of HSV-1 Viral Genes UL8 and UL52. Viruses 2022; 14:v14061287. [PMID: 35746758 PMCID: PMC9227917 DOI: 10.3390/v14061287] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2022] [Revised: 06/10/2022] [Accepted: 06/11/2022] [Indexed: 12/10/2022] Open
Abstract
Two-thirds of the world’s population is infected with HSV-1, which is closely associated with many diseases, such as Gingival stomatitis and viral encephalitis. However, the drugs that are currently clinically effective in treating HSV-1 are Acyclovir (ACV), Ganciclovir, and Valacyclovir. Due to the widespread use of ACV, the number of drug-resistant strains of ACV is increasing, so searching for new anti-HSV-1 drugs is urgent. The oleanolic-acid derivative AXX-18 showed a CC50 value of 44.69 μM for toxicity to HaCaT cells and an EC50 value of 1.47 μM for anti-HSV-1/F. In addition, AXX-18 showed significant inhibition of ACV-resistant strains 153, 106, and Blue, and the anti-HSV-1 activity of AXX-18 was higher than that of oleanolic acid. The mechanism of action of AXX-18 was found to be similar to that of oleanolic acid, except that AXX-18 could act on both the UL8 and UL52 proteins of the uncoupling helicase-primase enzyme, whereas oleanolic acid could only act on the UL8 protein. We have elucidated the antiviral mechanism of AXX-18 in detail and, finally, found that AXX-18 significantly inhibited the formation of skin herpes. In conclusion, we have explored the anti-HSV-1 activity of AXX-18 in vitro and in vivo as well as identification of its potential target proteins, which will provide a theoretical basis for the development of subsequent anti-HSV-1 drugs.
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Ming X, Bo Z, Miao Y, Chen H, Bao C, Sun L, Xi R, Zhong Q, Zhao P, Jung YS, Qian Y. Pseudorabies virus kinase UL13 phosphorylates H2AX to foster viral replication. FASEB J 2022; 36:e22221. [PMID: 35199383 DOI: 10.1096/fj.202101360rr] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2021] [Revised: 01/28/2022] [Accepted: 02/10/2022] [Indexed: 12/15/2022]
Abstract
The DNA damage response (DDR) pathway is critical for maintaining genomic integrity and sustaining organismal development. Viruses can either utilize or circumvent the DDR to facilitate their replication. Pseudorabies virus (PRV) infection was shown to induce apoptosis via stimulating DDR. However, the underlying mechanisms have not been fully explored to date. This study showed that PRV infection robustly activates the ATM and DNA-PK signaling pathways shortly after infection. However, inhibition of ATM, but not DNA-PK, could dampen PRV replication in cells. Importantly, we found that PRV-encoded serine/threonine kinase UL13 interacts with and subsequently phosphorylates H2AX. Furthermore, we found that UL13 deletion largely attenuates PRV neuroinvasiveness and virulence in vivo. In addtion, we showed that UL13 contributes to H2AX phosphorylation upon PRV infection both in vitro and in vivo, but does not affect ATM phosphorylation. Finally, we showed that knockdown of H2AX reduces PRV replication, while this reduction can be further enhanced by deletion of UL13. Taken together, we conclude that PRV-encoded kinase UL13 regulates DNA damage marker γH2AX and UL13-mediated H2AX phosphorylation plays a pivotal role in efficient PRV replication and progeny production.
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Affiliation(s)
- Xin Ming
- MOE Joint International Research Laboratory of Animal Health and Food Safety, MOA Key Laboratory of Animal Bacteriology, College of Veterinary Medicine, Nanjing Agricultural University, Nanjing, China
| | - Zongyi Bo
- MOE Joint International Research Laboratory of Animal Health and Food Safety, MOA Key Laboratory of Animal Bacteriology, College of Veterinary Medicine, Nanjing Agricultural University, Nanjing, China.,Joint International Research Laboratory of Agriculture and Agri-Product Safety, The Ministry of Education of China, Yangzhou University, Yangzhou, China
| | - Yurun Miao
- MOE Joint International Research Laboratory of Animal Health and Food Safety, MOA Key Laboratory of Animal Bacteriology, College of Veterinary Medicine, Nanjing Agricultural University, Nanjing, China
| | - Huan Chen
- MOE Joint International Research Laboratory of Animal Health and Food Safety, MOA Key Laboratory of Animal Bacteriology, College of Veterinary Medicine, Nanjing Agricultural University, Nanjing, China
| | - Chenyi Bao
- MOE Joint International Research Laboratory of Animal Health and Food Safety, MOA Key Laboratory of Animal Bacteriology, College of Veterinary Medicine, Nanjing Agricultural University, Nanjing, China
| | - Liumei Sun
- MOE Joint International Research Laboratory of Animal Health and Food Safety, MOA Key Laboratory of Animal Bacteriology, College of Veterinary Medicine, Nanjing Agricultural University, Nanjing, China
| | - Rui Xi
- MOE Joint International Research Laboratory of Animal Health and Food Safety, MOA Key Laboratory of Animal Bacteriology, College of Veterinary Medicine, Nanjing Agricultural University, Nanjing, China
| | - Qiuping Zhong
- MOE Joint International Research Laboratory of Animal Health and Food Safety, MOA Key Laboratory of Animal Bacteriology, College of Veterinary Medicine, Nanjing Agricultural University, Nanjing, China
| | - Pu Zhao
- MOE Joint International Research Laboratory of Animal Health and Food Safety, MOA Key Laboratory of Animal Bacteriology, College of Veterinary Medicine, Nanjing Agricultural University, Nanjing, China
| | - Yong-Sam Jung
- MOE Joint International Research Laboratory of Animal Health and Food Safety, MOA Key Laboratory of Animal Bacteriology, College of Veterinary Medicine, Nanjing Agricultural University, Nanjing, China
| | - Yingjuan Qian
- MOE Joint International Research Laboratory of Animal Health and Food Safety, MOA Key Laboratory of Animal Bacteriology, College of Veterinary Medicine, Nanjing Agricultural University, Nanjing, China.,Jiangsu Key Laboratory for High-Tech Research and Development of Veterinary Biopharmaceuticals, Jiangsu Agri-Animal Husbandry Vocational College, Taizhou, China
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Abstract
Human herpesviruses are large double-stranded DNA viruses belonging to the Herpesviridae family. The main characteristics of these viruses are their ability to establish a lifelong latency into the host with a potential to reactivate periodically. Primary infections and reactivations with herpesviruses are responsible for a large spectrum of diseases and may result in severe complications in immunocompromised patients. The viral DNA polymerase is a key enzyme in the replicative cycle of herpesviruses, and the target of most antiviral agents (i.e., nucleoside, nucleotide and pyrophosphate analogs). However, long-term prophylaxis and treatment with these antivirals may lead to the emergence of drug-resistant isolates harboring mutations in genes encoding viral enzymes that phosphorylate drugs (nucleoside analogs) and/or DNA polymerases, with potential cross-resistance between the different analogs. Drug resistance mutations mainly arise in conserved regions of the polymerase and exonuclease functional domains of these enzymes. In the polymerase domain, mutations associated with resistance to nucleoside/nucleotide analogs may directly or indirectly affect drug binding or incorporation into the primer strand, or increase the rate of extension of DNA to overcome chain termination. In the exonuclease domain, mutations conferring resistance to nucleoside/nucleotide analogs may reduce the rate of excision of incorporated drug, or continue DNA elongation after drug incorporation without excision. Mutations associated with resistance to pyrophosphate analogs may alter drug binding or the conformational changes of the polymerase domain required for an efficient activity of the enzyme. Novel herpesvirus inhibitors with a potent antiviral activity against drug-resistant isolates are thus needed urgently.
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Affiliation(s)
| | - Guy Boivin
- CHU de Québec-Université Laval, Quebec City, QC, Canada.
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Packard JE, Dembowski JA. HSV-1 DNA Replication-Coordinated Regulation by Viral and Cellular Factors. Viruses 2021; 13:v13102015. [PMID: 34696446 PMCID: PMC8539067 DOI: 10.3390/v13102015] [Citation(s) in RCA: 25] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2021] [Revised: 10/02/2021] [Accepted: 10/04/2021] [Indexed: 12/14/2022] Open
Abstract
DNA replication is an integral step in the herpes simplex virus type 1 (HSV-1) life cycle that is coordinated with the cellular DNA damage response, repair and recombination of the viral genome, and viral gene transcription. HSV-1 encodes its own DNA replication machinery, including an origin binding protein (UL9), single-stranded DNA binding protein (ICP8), DNA polymerase (UL30), processivity factor (UL42), and a helicase/primase complex (UL5/UL8/UL52). In addition, HSV-1 utilizes a combination of accessory viral and cellular factors to coordinate viral DNA replication with other viral and cellular processes. The purpose of this review is to outline the roles of viral and cellular proteins in HSV-1 DNA replication and replication-coupled processes, and to highlight how HSV-1 may modify and adapt cellular proteins to facilitate productive infection.
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12
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Botta L, Cesarini S, Zippilli C, Bizzarri BM, Fanelli A, Saladino R. Multicomponent reactions in the synthesis of antiviral compounds. Curr Med Chem 2021; 29:2013-2050. [PMID: 34620058 DOI: 10.2174/0929867328666211007121837] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2021] [Revised: 07/16/2021] [Accepted: 08/18/2021] [Indexed: 11/22/2022]
Abstract
BACKGROUND Multicomponent reactions are one-pot processes for the synthesis of highly functionalized hetero-cyclic and hetero-acyclic compounds, often endowed with biological activity. OBJECTIVE Multicomponent reactions are considered green processes with high atom economy. In addition, they present advantages compared to the classic synthetic methods such as high efficiency and low wastes production. METHOD In these reactions two or more reagents are combined together in the same flask to yield a product containing almost all the atoms of the starting materials. RESULTS The scope of this review is to present an overview of the application of multicomponent reactions in the synthesis of compounds endowed with antiviral activity. The syntheses are classified depending on the viral target. CONCLUSION Multicomponent reactions can be applied to all the stages of the drug discovery and development process making them very useful in the search for new agents active against emerging (viral) pathogens.
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Affiliation(s)
- Lorenzo Botta
- Department Biological and Ecological Sciences, University of Tuscia, Viterbo. Italy
| | - Silvia Cesarini
- Department Biological and Ecological Sciences, University of Tuscia, Viterbo. Italy
| | - Claudio Zippilli
- Department Biological and Ecological Sciences, University of Tuscia, Viterbo. Italy
| | | | - Angelica Fanelli
- Department Biological and Ecological Sciences, University of Tuscia, Viterbo. Italy
| | - Raffaele Saladino
- Department Biological and Ecological Sciences, University of Tuscia, Viterbo. Italy
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Piret J, Boivin G. Antiviral Drugs Against Herpesviruses. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2021; 1322:1-30. [PMID: 34258735 DOI: 10.1007/978-981-16-0267-2_1] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
The discovery of the nucleoside analogue, acyclovir, represented a milestone in the management of infections caused by herpes simplex virus and varicella-zoster virus. Ganciclovir, another nucleoside analogue, was then used for the management of systemic and organ-specific human cytomegalovirus diseases. The pyrophosphate analogue, foscarnet, and the nucleotide analogue, cidofovir, have been approved subsequently and constitute the second-line antiviral drugs. However, the viral DNA polymerase is the ultimate target of all these antiviral agents with a possible emergence of cross-resistance between these drugs. Recently, letermovir that targets the viral terminase complex was approved for the prophylaxis of human cytomegalovirus infections in hematopoietic stem cell transplant recipients. Other viral targets such as the protein kinase and the helicase-primase complex are also evaluated for the development of novel potent inhibitors against herpesviruses.
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Affiliation(s)
| | - Guy Boivin
- CHU de Québec-Laval University, Quebec City, QC, Canada.
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14
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Bailey C, Shoura MJ, Mischel PS, Swanton C. Extrachromosomal DNA-relieving heredity constraints, accelerating tumour evolution. Ann Oncol 2020; 31:884-893. [PMID: 32275948 DOI: 10.1016/j.annonc.2020.03.303] [Citation(s) in RCA: 51] [Impact Index Per Article: 12.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2020] [Accepted: 03/26/2020] [Indexed: 12/31/2022] Open
Abstract
Oncogene amplification on extrachromosomal DNA (ecDNA) provides a mechanism by which cancer cells can rapidly adapt to changes in the tumour microenvironment. These circular structures contain oncogenes and their regulatory elements, and, lacking centromeres, they are subject to unequal segregation during mitosis. This non-Mendelian mechanism of inheritance results in increased tumour heterogeneity with daughter cells that can contain increasingly amplified oncogene copy number. These structures also contain favourable epigenetic modifications including transcriptionally active chromatin, further fuelling positive selection. ecDNA drives aggressive tumour behaviour, is related to poorer survival outcomes and provides mechanisms of drug resistance. Recent evidence suggests one in four solid tumours contain cells with ecDNA structures. The concept of tumour evolution is one in which cancer cells compete to survive in a diverse tumour microenvironment under the Darwinian principles of variation and fitness heritability. Unconstrained by conventional segregation constraints, ecDNA can accelerate intratumoral heterogeneity and cellular fitness. In this review, we highlight some of the recent discoveries underpinning this process.
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Affiliation(s)
- C Bailey
- Cancer Evolution and Genome Instability Laboratory, The Francis Crick Institute, London, UK
| | - M J Shoura
- Department of Pathology, Stanford University School of Medicine, Stanford, USA
| | - P S Mischel
- Ludwig Institute for Cancer Research, University of California at San Diego, San Diego, USA; San Diego Moores Cancer Center, University of California, La Jolla, USA; Department of Pathology, University of California San Diego, La Jolla, USA
| | - C Swanton
- Cancer Evolution and Genome Instability Laboratory, The Francis Crick Institute, London, UK; Cancer Research UK Lung Cancer Centre of Excellence, University College London Cancer Institute, London, UK.
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15
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He D, Mao A, Li Y, Tam S, Zheng Y, Yao X, Birnbaumer L, Ambudkar IS, Ma X. TRPC1 participates in the HSV-1 infection process by facilitating viral entry. SCIENCE ADVANCES 2020; 6:eaaz3367. [PMID: 32206724 PMCID: PMC7080438 DOI: 10.1126/sciadv.aaz3367] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/31/2019] [Accepted: 12/20/2019] [Indexed: 06/10/2023]
Abstract
Mammalian transient receptor potential (TRP) channels are major components of Ca2+ signaling pathways and control a diversity of physiological functions. Here, we report a specific role for TRPC1 in the entry of herpes simplex virus type 1 (HSV-1) into cells. HSV-1-induced Ca2+ release and entry were dependent on Orai1, STIM1, and TRPC1. Inhibition of Ca2+ entry or knockdown of these proteins attenuated viral entry and infection. HSV-1 glycoprotein D interacted with the third ectodomain of TRPC1, and this interaction facilitated viral entry. Knockout of TRPC1 attenuated HSV-1-induced ocular abnormality and morbidity in vivo in TRPC1-/- mice. There was a strong correlation between HSV-1 infection and plasma membrane localization of TRPC1 in epithelial cells within oral lesions in buccal biopsies from HSV-1-infected patients. Together, our findings demonstrate a critical role for TRPC1 in HSV-1 infection and suggest the channel as a potential target for anti-HSV therapy.
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Affiliation(s)
- DongXu He
- Wuxi School of Medicine and School of Food Science and Technology, Jiangnan University, Jiangsu, China
| | - AiQin Mao
- Wuxi School of Medicine and School of Food Science and Technology, Jiangnan University, Jiangsu, China
| | - YouRan Li
- School of Biotechnology, Jiangnan University, Jiangsu, China
| | - SiuCheung Tam
- School of Biomedical Sciences, The Chinese University of Hong Kong, Hong Kong SAR, China
| | - YongTang Zheng
- Key Laboratory of Animal Models and Human Disease Mechanisms of the Chinese Academy of Sciences, Center for Biosafety Mega-Science, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, Yunnan 650223, China
| | - XiaoQiang Yao
- School of Biomedical Sciences, The Chinese University of Hong Kong, Hong Kong SAR, China
| | - Lutz Birnbaumer
- Laboratory of Signal Transduction, NIEHS, NIH, Research Triangle Park, NC, USA
- BIOMED, School of Medical Sciences, Catholic University of Argentina (UCA), Buenos Aires, Argentina
| | - Indu S. Ambudkar
- Secretory Physiology Section, MPTB, NIDCR, NIH, Bethesda, MD, USA
| | - Xin Ma
- Wuxi School of Medicine and School of Food Science and Technology, Jiangnan University, Jiangsu, China
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16
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Monteiro AFM, de Oliveira Viana J, Muratov E, Scotti MT, Scotti L. In Silico Studies against Viral Sexually Transmitted Diseases. Curr Protein Pept Sci 2020; 20:1135-1150. [PMID: 30854957 DOI: 10.2174/1389203720666190311142747] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2018] [Revised: 01/17/2019] [Accepted: 01/18/2019] [Indexed: 01/02/2023]
Abstract
Sexually Transmitted Diseases (STDs) refer to a variety of clinical syndromes and infections caused by pathogens that can be acquired and transmitted through sexual activity. Among STDs widely reported in the literature, viral sexual diseases have been increasing in a number of cases globally. This emphasizes the need for prevention and treatment. Among the methods widely used in drug planning are Computer-Aided Drug Design (CADD) studies and molecular docking which have the objective of investigating molecular interactions between two molecules to better understand the three -dimensional structural characteristics of the compounds. This review will discuss molecular docking studies applied to viral STDs, such as Ebola virus, Herpes virus and HIV, and reveal promising new drug candidates with high levels of specificity to their respective targets.
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Affiliation(s)
- Alex F M Monteiro
- Program of Natural and Synthetic Bioactive Products (PgPNSB), Health Sciences Center, Federal University of Paraíba, Joao Pessoa-PB, Brazil
| | - Jessika de Oliveira Viana
- Program of Natural and Synthetic Bioactive Products (PgPNSB), Health Sciences Center, Federal University of Paraíba, Joao Pessoa-PB, Brazil
| | - Engene Muratov
- Laboratory for Molecular Modeling, Division of Medicinal Chemistry and Natural Products, Eshelman School of Pharmacy, University of North Carolina, Beard Hall 301, CB#7568, Chapel Hill, NC, 27599, United States
| | - Marcus T Scotti
- Program of Natural and Synthetic Bioactive Products (PgPNSB), Health Sciences Center, Federal University of Paraíba, Joao Pessoa-PB, Brazil
| | - Luciana Scotti
- Program of Natural and Synthetic Bioactive Products (PgPNSB), Health Sciences Center, Federal University of Paraíba, Joao Pessoa-PB, Brazil.,Teaching and Research Management - University Hospital, Federal University of Paraíba, Campus I, 58051-900, João Pessoa-PB, Brazil
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17
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Pinto AMV, Leite JPG, Marinho RS, Forezi LDS, Batalha PN, Boechat FDC, Cunha AC, Silva DO, Gama IL, Faro LV, de Souza MC, Paixão ICP. Antiviral activity of 4-oxoquinoline-3-carboxamide derivatives against bovine herpesvirus type 5. Antivir Ther 2019; 25:13-20. [PMID: 31538962 DOI: 10.3851/imp3329] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 07/08/2019] [Indexed: 10/26/2022]
Abstract
BACKGROUND Bovine herpesvirus type 5 is an important agent of meningoencephalitis in cattle and has been identified in outbreaks of bovine neurological disease in several Brazilian states. In recent years, oxoquinoline derivatives have become an important focus in antiviral drug research. METHODS The cytotoxicity and anti BoHV-5RJ42/01 activity of a set of synthetic 4-oxoquinoline derivatives 4a-k were assayed on Madin-Darby Bovine Kidney cell and antiviral activity by plaque reduction assay. RESULTS The most promising substance (4h) exhibited CC50 and EC50 values of 1,239 µM ±5.5 and 6.0 µM ±1.5, respectively, with an SI =206. Two other compounds 4j (CC50 = 35 µM ±2 and EC50 = 24 µM ±7.0) and 4k (CC50= 55 µM ±2 and EC50 = 24 µM ±5.1) presented similar inhibitory profile and selectivity indexes of 1.4 and 2.9, respectively. The results of the time-of-addition studies revealed expressive reduction of virus production (≥80%) in different stages of virus replication cycle except for compound 4h that slightly inhibited virus yield in the first 2 h post infection, but it showed expressive virus inhibition after this time. CONCLUSIONS All three compounds slightly interact with the virus on the virucidal assay and they are not able to block virus attachment and penetration. Antiviral effect of oxoquinoline 4h was more prominent than acyclovir which leads us to suggest compound 4h as a promising molecule for further anti-BoHV-5 drug design.
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Affiliation(s)
- Ana Maria V Pinto
- Instituto Biomédico, Universidade Federal Fluminense, Rua Professor Hernani Melo, Niterói, Brazil.,Laboratório de Virologia Comparada e Ambiental, Fundação Oswaldo Cruz, Instituto Oswaldo Cruz, Rio de Janeiro, Brazil.,Instituto de Biologia, Universidade Federal Fluminense, Pós-graduação em Ciências e Biotecnologia e de Neurologia/Neurociências, Campus do Valonguinho, Niterói, Brazil
| | - José Paulo G Leite
- Laboratório de Virologia Comparada e Ambiental, Fundação Oswaldo Cruz, Instituto Oswaldo Cruz, Rio de Janeiro, Brazil
| | - Robson Ss Marinho
- Instituto Biomédico, Universidade Federal Fluminense, Rua Professor Hernani Melo, Niterói, Brazil
| | - Luana da Sm Forezi
- Instituto de Química, Universidade Federal Fluminense, Pós-graduação em Química, Campus do Valonguinho - Centro - Niterói, Brazil
| | - Pedro N Batalha
- Instituto de Química, Universidade Federal Fluminense, Pós-graduação em Química, Campus do Valonguinho - Centro - Niterói, Brazil
| | - Fernanda da Cs Boechat
- Instituto de Química, Universidade Federal Fluminense, Pós-graduação em Química, Campus do Valonguinho - Centro - Niterói, Brazil
| | - Anna C Cunha
- Instituto de Química, Universidade Federal Fluminense, Pós-graduação em Química, Campus do Valonguinho - Centro - Niterói, Brazil
| | - David O Silva
- Instituto de Química, Universidade Federal Fluminense, Pós-graduação em Química, Campus do Valonguinho - Centro - Niterói, Brazil
| | - Ivson L Gama
- Instituto de Química, Universidade Federal Fluminense, Pós-graduação em Química, Campus do Valonguinho - Centro - Niterói, Brazil
| | - Letícia V Faro
- Instituto de Química, Universidade Federal Fluminense, Pós-graduação em Química, Campus do Valonguinho - Centro - Niterói, Brazil
| | - Maria Cbv de Souza
- Instituto de Química, Universidade Federal Fluminense, Pós-graduação em Química, Campus do Valonguinho - Centro - Niterói, Brazil
| | - Izabel Christina P Paixão
- Instituto de Biologia, Universidade Federal Fluminense, Pós-graduação em Ciências e Biotecnologia e de Neurologia/Neurociências, Campus do Valonguinho, Niterói, Brazil
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18
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Frich CK, Krüger F, Walther R, Domar C, Andersen AHF, Tvilum A, Dagnæs-Hansen F, Denton PW, Tolstrup M, Paludan SR, Münch J, Zelikin AN. Non-covalent hitchhiking on endogenous carriers as a protraction mechanism for antiviral macromolecular prodrugs. J Control Release 2018; 294:298-310. [PMID: 30552954 DOI: 10.1016/j.jconrel.2018.12.016] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2018] [Revised: 11/26/2018] [Accepted: 12/11/2018] [Indexed: 12/23/2022]
Abstract
Albumin is a highly successful tool of drug delivery providing drastically extended body and blood residence time for the associated cargo, but it only traffics single drug copies at a time. In turn, macromolecular prodrugs (MP) are advantaged in carrying a high drug payload but offering only a modest extension of residence time to the conjugated drugs. In this work, we engineer MP to contain terminal groups that bind to albumin via non-covalent association and reveal that this facile measure affords a significant protraction for the associated polymers. This methodology is applied to MP of acyclovir, a successful drug against herpes simplex virus infection but with poor pharmacokinetics. Resulting albumin-affine MP were efficacious agents against herpes simplex virus type 2 (HSV-2) both in vitro and in vivo. In the latter case, sub-cutaneous administration of MP resulted in local (vaginal) antiviral effects and a systemic protection. Presented benefits of non-covalent association with albumin are readily transferrable to a wide variety of MP in development for drug delivery as anticancer, anti-inflammatory, and anti-viral measures.
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Affiliation(s)
| | - Franziska Krüger
- Institute of Molecular Virology, Ulm University Medical Center, 89081 Ulm, Germany
| | - Raoul Walther
- Department of Chemistry, Aarhus University, 8000 Aarhus C, Denmark
| | - Cecilie Domar
- Department of Chemistry, Aarhus University, 8000 Aarhus C, Denmark
| | - Anna H F Andersen
- Department of Infectious Diseases, Aarhus University Hospital, 8000 Aarhus C, Denmark; Department of Clinical Medicine, Aarhus University, 8000 Aarhus N, Denmark
| | - Anne Tvilum
- Department of Chemistry, Aarhus University, 8000 Aarhus C, Denmark
| | | | - Paul W Denton
- Department of Infectious Diseases, Aarhus University Hospital, 8000 Aarhus C, Denmark; Department of Clinical Medicine, Aarhus University, 8000 Aarhus N, Denmark
| | - Martin Tolstrup
- Department of Infectious Diseases, Aarhus University Hospital, 8000 Aarhus C, Denmark; Department of Clinical Medicine, Aarhus University, 8000 Aarhus N, Denmark
| | - Søren R Paludan
- Department of Biomedicine, Aarhus University, 8000 Aarhus C, Denmark
| | - Jan Münch
- Institute of Molecular Virology, Ulm University Medical Center, 89081 Ulm, Germany.
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19
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β-Carboline derivatives as novel antivirals for herpes simplex virus. Int J Antimicrob Agents 2018; 52:459-468. [DOI: 10.1016/j.ijantimicag.2018.06.019] [Citation(s) in RCA: 25] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2017] [Revised: 06/06/2018] [Accepted: 06/30/2018] [Indexed: 11/21/2022]
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20
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Britt WJ, Prichard MN. New therapies for human cytomegalovirus infections. Antiviral Res 2018; 159:153-174. [PMID: 30227153 DOI: 10.1016/j.antiviral.2018.09.003] [Citation(s) in RCA: 62] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2018] [Revised: 08/28/2018] [Accepted: 09/07/2018] [Indexed: 02/07/2023]
Abstract
The recent approval of letermovir marks a new era of therapy for human cytomegalovirus (HCMV) infections, particularly for the prevention of HCMV disease in hematopoietic stem cell transplant recipients. For almost 30 years ganciclovir has been the therapy of choice for these infections and by today's standards this drug exhibits only modest antiviral activity that is often insufficient to completely suppress viral replication, and drives the selection of drug-resistant variants that continue to replicate and contribute to disease. While ganciclovir remains the therapy of choice, additional drugs that inhibit novel molecular targets, such as letermovir, will be required as highly effective combination therapies are developed not only for the treatment of immunocompromised hosts, but also for congenitally infected infants. Sustained efforts, largely in the biotech industry and academia, have identified additional highly active lead compounds that have progressed into clinical studies with varying levels of success and at least two have the potential to be approved in the near future. Some of the new drugs in the pipeline inhibit new molecular targets, remain effective against isolates that have developed resistance to existing therapies, and promise to augment existing therapeutic regimens. Here, we will describe some of the unique features of HCMV biology and discuss their effect on therapeutic needs. Existing drugs will also be discussed and some of the more promising candidates will be reviewed with an emphasis on those progressing through clinical studies. The in vitro and in vivo antiviral activity, spectrum of antiviral activity, and mechanism of action of new compounds will be reviewed to provide an update on potential new therapies for HCMV infections that have progressed significantly in recent years.
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Affiliation(s)
- William J Britt
- Department of Pediatrics, University of Alabama School of Medicine, Birmingham AL 35233-1711, USA
| | - Mark N Prichard
- Department of Pediatrics, University of Alabama School of Medicine, Birmingham AL 35233-1711, USA.
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21
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Li Z, Bi Y, Xiao H, Sun L, Ren Y, Li Y, Chen C, Cun W. CRISPR-Cas9 system-driven site-specific selection pressure on Herpes simplex virus genomes. Virus Res 2018; 244:286-295. [PMID: 28279800 DOI: 10.1016/j.virusres.2017.03.010] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2016] [Revised: 02/03/2017] [Accepted: 03/05/2017] [Indexed: 01/05/2023]
Abstract
The CRISPR-Cas9 (clustered regularly interspaced short palindromic repeats and CRISPR-associated protein 9) system has been widely used for viral genome editing, transcription regulation and chromosomal localization in eukaryotic cells. In this study, a guide RNA (gRNA) that specifically recognizes HSV-1 viral genomes was used in the CRISPR-Cas9 system to inhibit viral replication. This inhibition could be achieved with both wild type Cas9 protein and Cas9 nickase (D10A). By targeting viral genomes containing sequences recognized by the gRNA, the CRISPR-Cas9 system distinguished between different viral genome sequences and provided single nucleotide-specific selection pressure to significantly change the proportions of viruses in a mixed viral pool. This finding indicates the utility of this tool for virus selection without the need for antibiotics or reporter genes, which could potentially save time compared to other methods used for screening and purifying mutant viruses.
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Affiliation(s)
- Zhihua Li
- Institute of Medical Biology, Chinese Academy of Medical Sciences & Peking Union Medical College, 935 Jiaoling Road, Wuhua District, Kunming, Yunnan, 650118 China; Yunnan Key Laboratory of Vaccine Research and Development of Severe Infectious Disease, Kunming, Yunnan, China; Centre for Tuberculosis Research, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China.
| | - Yanwei Bi
- Institute of Medical Biology, Chinese Academy of Medical Sciences & Peking Union Medical College, 935 Jiaoling Road, Wuhua District, Kunming, Yunnan, 650118 China; Yunnan Key Laboratory of Vaccine Research and Development of Severe Infectious Disease, Kunming, Yunnan, China; Centre for Tuberculosis Research, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China.
| | - Hongjian Xiao
- Institute of Medical Biology, Chinese Academy of Medical Sciences & Peking Union Medical College, 935 Jiaoling Road, Wuhua District, Kunming, Yunnan, 650118 China; Yunnan Key Laboratory of Vaccine Research and Development of Severe Infectious Disease, Kunming, Yunnan, China; Centre for Tuberculosis Research, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China.
| | - Le Sun
- Kunming Medical University, 1168 West Chunrong Road, Kunming, Yunnan, 650500, China.
| | - Yuan Ren
- Baoshan College of Traditional Chinese Medicine, No. 20, The sixth Community, Yaowan Village, Longyang District, Baoshan, Yunnan, 678000, China.
| | - Yadong Li
- Institute of Medical Biology, Chinese Academy of Medical Sciences & Peking Union Medical College, 935 Jiaoling Road, Wuhua District, Kunming, Yunnan, 650118 China; Yunnan Key Laboratory of Vaccine Research and Development of Severe Infectious Disease, Kunming, Yunnan, China.
| | - Chen Chen
- Institute of Medical Biology, Chinese Academy of Medical Sciences & Peking Union Medical College, 935 Jiaoling Road, Wuhua District, Kunming, Yunnan, 650118 China; Yunnan Key Laboratory of Vaccine Research and Development of Severe Infectious Disease, Kunming, Yunnan, China.
| | - Wei Cun
- Institute of Medical Biology, Chinese Academy of Medical Sciences & Peking Union Medical College, 935 Jiaoling Road, Wuhua District, Kunming, Yunnan, 650118 China; Yunnan Key Laboratory of Vaccine Research and Development of Severe Infectious Disease, Kunming, Yunnan, China; Centre for Tuberculosis Research, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China.
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22
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Wudiri GA, Nicola AV. Cellular Cholesterol Facilitates the Postentry Replication Cycle of Herpes Simplex Virus 1. J Virol 2017; 91:e00445-17. [PMID: 28446672 PMCID: PMC5487575 DOI: 10.1128/jvi.00445-17] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2017] [Accepted: 04/19/2017] [Indexed: 12/24/2022] Open
Abstract
Cholesterol is an essential component of cell membranes and is required for herpes simplex virus 1 (HSV-1) entry (1-3). Treatment of HSV-1-infected Vero cells with methyl beta-cyclodextrin from 2 to 9 h postentry reduced plaque numbers. Transport of incoming viral capsids to the nuclear periphery was unaffected by the cholesterol reduction, suggesting that cell cholesterol is important for the HSV-1 replicative cycle at a stage(s) beyond entry, after the arrival of capsids at the nucleus. The synthesis and release of infectious HSV-1 and cell-to-cell spread of infection were all impaired in cholesterol-reduced cells. Propagation of HSV-1 on DHCR24-/- fibroblasts, which lack the desmosterol-to-cholesterol conversion enzyme, resulted in the generation of infectious extracellular virions (HSVdes) that lack cholesterol and likely contain desmosterol. The specific infectivities (PFU per viral genome) of HSVchol and HSVdes were similar, suggesting cholesterol and desmosterol in the HSV envelope support similar levels of infectivity. However, infected DHCR24-/- fibroblasts released ∼1 log less infectious HSVdes and ∼1.5 log fewer particles than release of cholesterol-containing particles (HSVchol) from parental fibroblasts, suggesting that the hydrocarbon tail of cholesterol facilitates viral synthesis. Together, the results suggest multiple roles for cholesterol in the HSV-1 replicative cycle.IMPORTANCE HSV-1 infections are associated with a wide range of clinical manifestations that are of public health importance. Cholesterol is a key player in the complex interaction between viral and cellular factors that allows HSV-1 to enter host cells and establish infection. Previous reports have demonstrated a role for cellular cholesterol in the entry of HSV-1 into target cells. Here, we employed both chemical treatment and cells that were genetically defined to synthesize only desmosterol to demonstrate that cholesterol is important at stages following the initial entry and transport of viral capsids to the nucleus. Viral protein expression, encapsidation of the viral genome, and the release of mature virions were impacted by the reduction of cellular cholesterol. Cholesterol was also critical for cell-to-cell spread of infection. These findings provide new insights into the cholesterol dependence of HSV-1 replication.
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Affiliation(s)
- George A Wudiri
- Department of Veterinary Microbiology and Pathology and Paul G. Allen School for Global Animal Health, College of Veterinary Medicine, Washington State University, Pullman, Washington, USA
| | - Anthony V Nicola
- Department of Veterinary Microbiology and Pathology and Paul G. Allen School for Global Animal Health, College of Veterinary Medicine, Washington State University, Pullman, Washington, USA
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23
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Callegaro S, Perrone R, Scalabrin M, Doria F, Palù G, Richter SN. A core extended naphtalene diimide G-quadruplex ligand potently inhibits herpes simplex virus 1 replication. Sci Rep 2017; 7:2341. [PMID: 28539620 PMCID: PMC5443766 DOI: 10.1038/s41598-017-02667-3] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2017] [Accepted: 04/13/2017] [Indexed: 11/22/2022] Open
Abstract
G-quadruplexes (G4s) are nucleic acids secondary structures, epigenetic regulators in cells and viruses. In herpes simplex virus 1 (HSV-1)-infected cells, G4s are massively present during viral replication. We here aimed at investigating the possibility to target the HSV-1 G4s by a core extended naphtalene diimide (c-exNDI) G4 ligand. Biophysical and biomolecular analysis proved that c-exNDI stabilized the HSV-1 G4s in a concentration dependent manner. In MS competition assays, c-exNDI preferentially recognized HSV-1 G4s over cellular telomeric G4s, the most represented G4s within cells; other less abundant cellular G4s were also recognized. Treatment of HSV-1 infected cells with c-exNDI at low nanomolar concentrations induced significant virus inhibition with no cytotoxicity. The mechanism of action was ascribed to G4-mediated inhibition of viral DNA replication, with consequent impairment of viral genes transcription. Our data suggest that the observed potent antiviral activity and low cytotoxicity mainly depend on a combination of c-exNDI affinity for HSV-1 G4s and their massive presence during infection. HSV-1 G4s may thus represent new effective antiviral targets: the fact that no current antiherpetic drug exploits them and their presence at the viral genome, responsible for both active and latent HSV infections, makes them particularly attracting.
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Affiliation(s)
- Sara Callegaro
- Department of Molecular Medicine, University of Padua, via Gabelli 63, 35121, Padua, Italy
| | - Rosalba Perrone
- Department of Molecular Medicine, University of Padua, via Gabelli 63, 35121, Padua, Italy
| | - Matteo Scalabrin
- Department of Molecular Medicine, University of Padua, via Gabelli 63, 35121, Padua, Italy
| | - Filippo Doria
- Department of Chemistry, University of Pavia, V.le Taramelli 10, 27100, Pavia, Italy
| | - Giorgio Palù
- Department of Molecular Medicine, University of Padua, via Gabelli 63, 35121, Padua, Italy
| | - Sara N Richter
- Department of Molecular Medicine, University of Padua, via Gabelli 63, 35121, Padua, Italy.
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24
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Dickerson SM, Kuchta RD. Protein Displacement by Herpes Helicase-Primase and the Key Role of UL42 during Helicase-Coupled DNA Synthesis by the Herpes Polymerase. Biochemistry 2017; 56:2651-2662. [PMID: 28505413 DOI: 10.1021/acs.biochem.6b01128] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Abstract
The herpes helicase-primase (UL5-UL8-UL52) very inefficiently unwinds double-stranded DNA. To better understand the mechanistic consequences of this inefficiency, we investigated protein displacement activity by UL5-UL8-UL52, as well as the impact of coupling DNA synthesis by the herpes polymerase with helicase activity. While the helicase can displace proteins bound to the lagging strand template, bound proteins significantly impede helicase activity. Remarkably, UL5-UL8-UL52, an extremely inefficient helicase, disrupts the exceptionally tight interaction between streptavidin and biotin on the lagging strand template. It also unwinds DNA containing streptavidin bound to the leading strand template, although it does not displace the streptavidin. These data suggest that the helicase may largely or completely wrap around the lagging strand template, with minimal interactions with the leading strand template. We utilized synthetic DNA minicircles to study helicase activity coupled with the herpes polymerase-processivity factor (UL30-UL42). Coupling greatly enhances unwinding of DNA, although bound proteins still inhibit helicase activity. Surprisingly, while UL30-UL42 and two noncognate polymerases (Klenow Fragment and T4 DNA polymerase) all stimulate unwinding of DNA by the helicase, the isolated UL30 polymerase (i.e., no UL42 processivity factor) binds to the replication fork but in a manner that is incompetent in terms of coupled helicase-polymerase activity.
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Affiliation(s)
- Sarah Michelle Dickerson
- Department of Chemistry and Biochemistry, University of Colorado , Boulder, Colorado 80309, United States
| | - Robert D Kuchta
- Department of Chemistry and Biochemistry, University of Colorado , Boulder, Colorado 80309, United States
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25
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Zarrouk K, Piret J, Boivin G. Herpesvirus DNA polymerases: Structures, functions and inhibitors. Virus Res 2017; 234:177-192. [PMID: 28153606 DOI: 10.1016/j.virusres.2017.01.019] [Citation(s) in RCA: 56] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2016] [Revised: 01/10/2017] [Accepted: 01/22/2017] [Indexed: 11/25/2022]
Abstract
Human herpesviruses are large double-stranded DNA viruses belonging to the Herpesviridae family. These viruses have the ability to establish lifelong latency into the host and to periodically reactivate. Primary infections and reactivations of herpesviruses cause a large spectrum of diseases and may lead to severe complications in immunocompromised patients. The viral DNA polymerase is a key enzyme in the lytic phase of the infection by herpesviruses. This review focuses on the structures and functions of viral DNA polymerases of herpes simplex virus (HSV) and human cytomegalovirus (HCMV). DNA polymerases of HSV (UL30) and HCMV (UL54) belong to B family DNA polymerases with which they share seven regions of homology numbered I to VII as well as a δ-region C which is homologous to DNA polymerases δ. These DNA polymerases are multi-functional enzymes exhibiting polymerase, 3'-5' exonuclease proofreading and ribonuclease H activities. Furthermore, UL30 and UL54 DNA polymerases form a complex with UL42 and UL44 processivity factors, respectively. The mechanisms involved in their polymerisation activity have been elucidated based on structural analyses of the DNA polymerase of bacteriophage RB69 crystallized under different conformations, i.e. the enzyme alone or in complex with DNA and with both DNA and incoming nucleotide. All antiviral agents currently used for the prevention or treatment of HSV and HCMV infections target the viral DNA polymerases. However, long-term administration of these antivirals may lead to the emergence of drug-resistant isolates harboring mutations in genes encoding viral enzymes that phosphorylate drugs (i.e., nucleoside analogues) and/or DNA polymerases.
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Affiliation(s)
- Karima Zarrouk
- Research Center in Infectious Diseases, CHU de Québec and Laval University, Quebec City, Quebec, Canada
| | - Jocelyne Piret
- Research Center in Infectious Diseases, CHU de Québec and Laval University, Quebec City, Quebec, Canada
| | - Guy Boivin
- Research Center in Infectious Diseases, CHU de Québec and Laval University, Quebec City, Quebec, Canada.
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26
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Artusi S, Perrone R, Lago S, Raffa P, Di Iorio E, Palù G, Richter SN. Visualization of DNA G-quadruplexes in herpes simplex virus 1-infected cells. Nucleic Acids Res 2016; 44:10343-10353. [PMID: 27794039 PMCID: PMC5137459 DOI: 10.1093/nar/gkw968] [Citation(s) in RCA: 41] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2016] [Revised: 10/09/2016] [Accepted: 10/11/2016] [Indexed: 01/05/2023] Open
Abstract
We have previously shown that clusters of guanine quadruplex (G4) structures can form in the human herpes simplex-1 (HSV-1) genome. Here we used immunofluorescence and immune-electron microscopy with a G4-specific monoclonal antibody to visualize G4 structures in HSV-1 infected cells. We found that G4 formation and localization within the cells was virus cycle dependent: viral G4s peaked at the time of viral DNA replication in the cell nucleus, moved to the nuclear membrane at the time of virus nuclear egress and were later found in HSV-1 immature virions released from the cell nucleus. Colocalization of G4s with ICP8, a viral DNA processing protein, was observed in viral replication compartments. G4s were lost upon treatment with DNAse and inhibitors of HSV-1 DNA replication. The notable increase in G4s upon HSV-1 infection suggests a key role of these structures in the HSV-1 biology and indicates new targets to control both the lytic and latent infection.
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Affiliation(s)
- Sara Artusi
- Department of Molecular Medicine, University of Padua, Padua 35121, Italy
| | - Rosalba Perrone
- Department of Molecular Medicine, University of Padua, Padua 35121, Italy
| | - Sara Lago
- Department of Molecular Medicine, University of Padua, Padua 35121, Italy
| | - Paolo Raffa
- Department of Molecular Medicine, University of Padua, Padua 35121, Italy
| | - Enzo Di Iorio
- Department of Molecular Medicine, University of Padua, Padua 35121, Italy
| | - Giorgio Palù
- Department of Molecular Medicine, University of Padua, Padua 35121, Italy
| | - Sara N Richter
- Department of Molecular Medicine, University of Padua, Padua 35121, Italy
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27
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Blazier JC, Jansen RK, Mower JP, Govindu M, Zhang J, Weng ML, Ruhlman TA. Variable presence of the inverted repeat and plastome stability in Erodium. ANNALS OF BOTANY 2016; 117:1209-20. [PMID: 27192713 PMCID: PMC4904181 DOI: 10.1093/aob/mcw065] [Citation(s) in RCA: 70] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/16/2015] [Revised: 01/05/2016] [Accepted: 02/22/2016] [Indexed: 05/18/2023]
Abstract
BACKGROUND AND AIMS Several unrelated lineages such as plastids, viruses and plasmids, have converged on quadripartite genomes of similar size with large and small single copy regions and a large inverted repeat (IR). Except for Erodium (Geraniaceae), saguaro cactus and some legumes, the plastomes of all photosynthetic angiosperms display this structure. The functional significance of the IR is not understood and Erodium provides a system to examine the role of the IR in the long-term stability of these genomes. We compared the degree of genomic rearrangement in plastomes of Erodium that differ in the presence and absence of the IR. METHODS We sequenced 17 new Erodium plastomes. Using 454, Illumina, PacBio and Sanger sequences, 16 genomes were assembled and categorized along with one incomplete and two previously published Erodium plastomes. We conducted phylogenetic analyses among these species using a dataset of 19 protein-coding genes and determined if significantly higher evolutionary rates had caused the long branch seen previously in phylogenetic reconstructions within the genus. Bioinformatic comparisons were also performed to evaluate plastome evolution across the genus. KEY RESULTS Erodium plastomes fell into four types (Type 1-4) that differ in their substitution rates, short dispersed repeat content and degree of genomic rearrangement, gene and intron content and GC content. Type 4 plastomes had significantly higher rates of synonymous substitutions (dS) for all genes and for 14 of the 19 genes non-synonymous substitutions (dN) were significantly accelerated. We evaluated the evidence for a single IR loss in Erodium and in doing so discovered that Type 4 plastomes contain a novel IR. CONCLUSIONS The presence or absence of the IR does not affect plastome stability in Erodium. Rather, the overall repeat content shows a negative correlation with genome stability, a pattern in agreement with other angiosperm groups and recent findings on genome stability in bacterial endosymbionts.
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Affiliation(s)
- John C Blazier
- Department of Integrative Biology, University of Texas at Austin, Austin, TX, USA
| | - Robert K Jansen
- Department of Integrative Biology, University of Texas at Austin, Austin, TX, USA Department of Biological Science, Faculty of Science, King Abdulaziz University, Jeddah 21589, Saudi Arabia
| | - Jeffrey P Mower
- Center for Plant Science Innovation, University of Nebraska-Lincoln, Lincoln, NE, USA
| | - Madhu Govindu
- Department of Integrative Biology, University of Texas at Austin, Austin, TX, USA
| | - Jin Zhang
- Department of Integrative Biology, University of Texas at Austin, Austin, TX, USA
| | - Mao-Lun Weng
- Department of Integrative Biology, University of Texas at Austin, Austin, TX, USA
| | - Tracey A Ruhlman
- Department of Integrative Biology, University of Texas at Austin, Austin, TX, USA
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28
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Wang YP, Du WJ, Huang LP, Wei YW, Wu HL, Feng L, Liu CM. The Pseudorabies Virus DNA Polymerase Accessory Subunit UL42 Directs Nuclear Transport of the Holoenzyme. Front Microbiol 2016; 7:124. [PMID: 26913023 PMCID: PMC4753316 DOI: 10.3389/fmicb.2016.00124] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2015] [Accepted: 01/25/2016] [Indexed: 01/13/2023] Open
Abstract
Pseudorabies virus (PRV) DNA replication occurs in the nuclei of infected cells and requires the viral DNA polymerase. The PRV DNA polymerase comprises a catalytic subunit, UL30, and an accessory subunit, UL42, that confers processivity to the enzyme. Its nuclear localization is a prerequisite for its enzymatic function in the initiation of viral DNA replication. However, the mechanisms by which the PRV DNA polymerase holoenzyme enters the nucleus have not been determined. In this study, we characterized the nuclear import pathways of the PRV DNA polymerase catalytic and accessory subunits. Immunofluorescence analysis showed that UL42 localizes independently in the nucleus, whereas UL30 alone predominantly localizes in the cytoplasm. Intriguingly, the localization of UL30 was completely shifted to the nucleus when it was coexpressed with UL42, demonstrating that nuclear transport of UL30 occurs in an UL42-dependent manner. Deletion analysis and site-directed mutagenesis of the two proteins showed that UL42 contains a functional and transferable bipartite nuclear localization signal (NLS) at amino acids 354–370 and that K354, R355, and K367 are important for the NLS function, whereas UL30 has no NLS. Coimmunoprecipitation assays verified that UL42 interacts with importins α3 and α4 through its NLS. In vitro nuclear import assays demonstrated that nuclear accumulation of UL42 is a temperature- and energy-dependent process and requires both importins α and β, confirming that UL42 utilizes the importin α/β-mediated pathway for nuclear entry. In an UL42 NLS-null mutant, the UL42/UL30 heterodimer was completely confined to the cytoplasm when UL42 was coexpressed with UL30, indicating that UL30 utilizes the NLS function of UL42 for its translocation into the nucleus. Collectively, these findings suggest that UL42 contains an importin α/β-mediated bipartite NLS that transports the viral DNA polymerase holoenzyme into the nucleus in an in vitro expression system.
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Affiliation(s)
- Yi-Ping Wang
- Division of Swine Infectious Diseases, State Key Laboratory of Veterinary Biotechnology, Harbin Veterinary Research Institute, Chinese Academy of Agricultural Sciences Harbin, China
| | - Wen-Juan Du
- Division of Swine Infectious Diseases, State Key Laboratory of Veterinary Biotechnology, Harbin Veterinary Research Institute, Chinese Academy of Agricultural Sciences Harbin, China
| | - Li-Ping Huang
- Division of Swine Infectious Diseases, State Key Laboratory of Veterinary Biotechnology, Harbin Veterinary Research Institute, Chinese Academy of Agricultural Sciences Harbin, China
| | - Yan-Wu Wei
- Division of Swine Infectious Diseases, State Key Laboratory of Veterinary Biotechnology, Harbin Veterinary Research Institute, Chinese Academy of Agricultural Sciences Harbin, China
| | - Hong-Li Wu
- Division of Swine Infectious Diseases, State Key Laboratory of Veterinary Biotechnology, Harbin Veterinary Research Institute, Chinese Academy of Agricultural Sciences Harbin, China
| | - Li Feng
- Division of Swine Infectious Diseases, State Key Laboratory of Veterinary Biotechnology, Harbin Veterinary Research Institute, Chinese Academy of Agricultural Sciences Harbin, China
| | - Chang-Ming Liu
- Division of Swine Infectious Diseases, State Key Laboratory of Veterinary Biotechnology, Harbin Veterinary Research Institute, Chinese Academy of Agricultural Sciences Harbin, China
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29
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Vashishtha AK, Kuchta RD. Effects of Acyclovir, Foscarnet, and Ribonucleotides on Herpes Simplex Virus-1 DNA Polymerase: Mechanistic Insights and a Novel Mechanism for Preventing Stable Incorporation of Ribonucleotides into DNA. Biochemistry 2016; 55:1168-77. [PMID: 26836009 DOI: 10.1021/acs.biochem.6b00065] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
We examined the impact of two clinically approved anti-herpes drugs, acyclovir and Forscarnet (phosphonoformate), on the exonuclease activity of the herpes simplex virus-1 DNA polymerase, UL30. Acyclovir triphosphate and Foscarnet, along with the closely related phosphonoacetic acid, did not affect exonuclease activity on single-stranded DNA. Furthermore, blocking the polymerase active site due to either binding of Foscarnet or phosphonoacetic acid to the E-DNA complex or polymerization of acyclovir onto the DNA also had a minimal effect on exonuclease activity. The inability of the exonuclease to excise acyclovir from the primer 3'-terminus results from the altered sugar structure directly impeding phosphodiester bond hydrolysis as opposed to inhibiting binding, unwinding of the DNA by the exonuclease, or transfer of the DNA from the polymerase to the exonuclease. Removing the 3'-hydroxyl or the 2'-carbon from the nucleotide at the 3'-terminus of the primer strongly inhibited exonuclease activity, although addition of a 2'-hydroxyl did not affect exonuclease activity. The biological consequences of these results are twofold. First, the ability of acyclovir and Foscarnet to block dNTP polymerization without impacting exonuclease activity raises the possibility that their effects on herpes replication may involve both direct inhibition of dNTP polymerization and exonuclease-mediated destruction of herpes DNA. Second, the ability of the exonuclease to rapidly remove a ribonucleotide at the primer 3'-terminus in combination with the polymerase not efficiently adding dNTPs onto this primer provides a novel mechanism by which the herpes replication machinery can prevent incorporation of ribonucleotides into newly synthesized DNA.
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Affiliation(s)
- Ashwani Kumar Vashishtha
- Department of Chemistry and Biochemistry, University of Colorado , Boulder, Colorado 80309-0215, United States
| | - Robert D Kuchta
- Department of Chemistry and Biochemistry, University of Colorado , Boulder, Colorado 80309-0215, United States
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30
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Wang YP, Huang LP, Du WJ, Wei YW, Xia DL, Wu HL, Feng L, Liu CM. The pseudorabies virus DNA polymerase processivity factor UL42 exists as a monomer in vitro and in vivo. Arch Virol 2016; 161:1027-31. [PMID: 26733297 DOI: 10.1007/s00705-015-2735-1] [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: 11/09/2015] [Accepted: 12/20/2015] [Indexed: 10/22/2022]
Abstract
The processivity factors (PFs) of herpesviruses confer processivity to the DNA polymerase. Understanding whether the herpesvirus PFs function as monomers or multimers is important for clarifying the mechanism by which they provide the DNA polymerase with processivity. Herpes simplex virus type 1 UL42 is a monomer, whereas human cytomegalovirus UL44, Epstein-Barr virus BMRF1, and Kaposi's sarcoma-associated herpesvirus PF-8 exist as dimers. However, the oligomeric status of the pseudorabies virus (PRV) DNA polymerase PF UL42 has not been determined. Using fluorescence confocal microscopy and chemical crosslinking, we confirmed that UL42 is a monomer when expressed in vitro. Crosslinking of nuclear extracts from PRV-infected or uninfected PK-15 cells verified that UL42 exists as a monomer in vivo. Our demonstration that UL42 exists as a monomer in vitro and in vivo contributes to the further investigation of the mechanism used by UL42 to achieve processivity.
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Affiliation(s)
- Yi-Ping Wang
- Division of Swine Infectious Diseases, State Key Laboratory of Veterinary Biotechnology, Harbin Veterinary Research Institute, Chinese Academy of Agricultural Sciences, 427 Maduan Street, Nangang District, Harbin, 150001, People's Republic of China
| | - Li-Ping Huang
- Division of Swine Infectious Diseases, State Key Laboratory of Veterinary Biotechnology, Harbin Veterinary Research Institute, Chinese Academy of Agricultural Sciences, 427 Maduan Street, Nangang District, Harbin, 150001, People's Republic of China
| | - Wen-Juan Du
- Division of Swine Infectious Diseases, State Key Laboratory of Veterinary Biotechnology, Harbin Veterinary Research Institute, Chinese Academy of Agricultural Sciences, 427 Maduan Street, Nangang District, Harbin, 150001, People's Republic of China
| | - Yan-Wu Wei
- Division of Swine Infectious Diseases, State Key Laboratory of Veterinary Biotechnology, Harbin Veterinary Research Institute, Chinese Academy of Agricultural Sciences, 427 Maduan Street, Nangang District, Harbin, 150001, People's Republic of China
| | - De-Li Xia
- Division of Swine Infectious Diseases, State Key Laboratory of Veterinary Biotechnology, Harbin Veterinary Research Institute, Chinese Academy of Agricultural Sciences, 427 Maduan Street, Nangang District, Harbin, 150001, People's Republic of China
| | - Hong-Li Wu
- Division of Swine Infectious Diseases, State Key Laboratory of Veterinary Biotechnology, Harbin Veterinary Research Institute, Chinese Academy of Agricultural Sciences, 427 Maduan Street, Nangang District, Harbin, 150001, People's Republic of China
| | - Li Feng
- Division of Swine Infectious Diseases, State Key Laboratory of Veterinary Biotechnology, Harbin Veterinary Research Institute, Chinese Academy of Agricultural Sciences, 427 Maduan Street, Nangang District, Harbin, 150001, People's Republic of China
| | - Chang-Ming Liu
- Division of Swine Infectious Diseases, State Key Laboratory of Veterinary Biotechnology, Harbin Veterinary Research Institute, Chinese Academy of Agricultural Sciences, 427 Maduan Street, Nangang District, Harbin, 150001, People's Republic of China.
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31
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Greive SJ, Fung HKH, Chechik M, Jenkins HT, Weitzel SE, Aguiar PM, Brentnall AS, Glousieau M, Gladyshev GV, Potts JR, Antson AA. DNA recognition for virus assembly through multiple sequence-independent interactions with a helix-turn-helix motif. Nucleic Acids Res 2015; 44:776-89. [PMID: 26673721 PMCID: PMC4737164 DOI: 10.1093/nar/gkv1467] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2015] [Accepted: 11/30/2015] [Indexed: 11/14/2022] Open
Abstract
The helix-turn-helix (HTH) motif features frequently in protein DNA-binding assemblies. Viral pac site-targeting small terminase proteins possess an unusual architecture in which the HTH motifs are displayed in a ring, distinct from the classical HTH dimer. Here we investigate how such a circular array of HTH motifs enables specific recognition of the viral genome for initiation of DNA packaging during virus assembly. We found, by surface plasmon resonance and analytical ultracentrifugation, that individual HTH motifs of the Bacillus phage SF6 small terminase bind the packaging regions of SF6 and related SPP1 genome weakly, with little local sequence specificity. Nuclear magnetic resonance chemical shift perturbation studies with an arbitrary single-site substrate suggest that the HTH motif contacts DNA similarly to how certain HTH proteins contact DNA non-specifically. Our observations support a model where specificity is generated through conformational selection of an intrinsically bent DNA segment by a ring of HTHs which bind weakly but cooperatively. Such a system would enable viral gene regulation and control of the viral life cycle, with a minimal genome, conferring a major evolutionary advantage for SPP1-like viruses.
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Affiliation(s)
- Sandra J Greive
- York Structural Biology Laboratory, Department of Chemistry, University of York, York YO10 5DD, UK
| | - Herman K H Fung
- York Structural Biology Laboratory, Department of Chemistry, University of York, York YO10 5DD, UK Department of Biology, University of York, York YO10 5DD, UK
| | - Maria Chechik
- York Structural Biology Laboratory, Department of Chemistry, University of York, York YO10 5DD, UK
| | - Huw T Jenkins
- York Structural Biology Laboratory, Department of Chemistry, University of York, York YO10 5DD, UK
| | - Stephen E Weitzel
- Institute of Molecular Biology, University of Oregon, Eugene, Oregon 97403, USA
| | - Pedro M Aguiar
- Department of Chemistry, University of York, York YO10 5DD, UK
| | | | - Matthieu Glousieau
- York Structural Biology Laboratory, Department of Chemistry, University of York, York YO10 5DD, UK
| | - Grigory V Gladyshev
- Department of Biochemistry, School of Biology, Moscow State University, Moscow 119234, Russian Federation
| | | | - Alfred A Antson
- York Structural Biology Laboratory, Department of Chemistry, University of York, York YO10 5DD, UK
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32
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Berard AR, Coombs KM, Severini A. Quantification of the host response proteome after herpes simplex virus type 1 infection. J Proteome Res 2015; 14:2121-42. [PMID: 25815715 DOI: 10.1021/pr5012284] [Citation(s) in RCA: 29] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
Viruses employ numerous host cell metabolic functions to propagate and manage to evade the host immune system. For herpes simplex virus type 1 (HSV1), a virus that has evolved to efficiently infect humans without seriously harming the host in most cases, the virus-host interaction is specifically interesting. This interaction can be best characterized by studying the proteomic changes that occur in the host during infection. Previous studies have been successful at identifying numerous host proteins that play important roles in HSV infection; however, there is still much that we do not know. This study identifies host metabolic functions and proteins that play roles in HSV infection, using global quantitative stable isotope labeling by amino acids in cell culture (SILAC) proteomic profiling of the host cell combined with LC-MS/MS. We showed differential proteins during early, mid and late infection, using both cytosolic and nuclear fractions. We identified hundreds of differentially regulated proteins involved in fundamental cellular functions, including gene expression, DNA replication, inflammatory response, cell movement, cell death, and RNA post-transcriptional modification. Novel differentially regulated proteins in HSV infections include some previously identified in other virus systems, as well as fusion protein, involved in malignant liposarcoma (FUS) and hypoxia up-regulated 1 protein precursor (HYOU1), which have not been identified previously in any virus infection.
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Affiliation(s)
- Alicia R Berard
- †Department of Medical Microbiology, Faculty of Medicine, University of Manitoba, Winnipeg, Manitoba, Canada R3E 0J9.,‡Manitoba Center for Proteomics and Systems Biology, University of Manitoba, Room 799 John Buhler Research Centre, Winnipeg, Manitoba, Canada R3E 3P4
| | - Kevin M Coombs
- †Department of Medical Microbiology, Faculty of Medicine, University of Manitoba, Winnipeg, Manitoba, Canada R3E 0J9.,‡Manitoba Center for Proteomics and Systems Biology, University of Manitoba, Room 799 John Buhler Research Centre, Winnipeg, Manitoba, Canada R3E 3P4.,§Manitoba Institute of Child Health, University of Manitoba, Room 641 John Buhler Research Centre, Winnipeg, Manitoba, Canada R3E 3P4
| | - Alberto Severini
- †Department of Medical Microbiology, Faculty of Medicine, University of Manitoba, Winnipeg, Manitoba, Canada R3E 0J9.,∥National Microbiology Laboratory, Public Health Agency of Canada, 1015 Arlington Street, Winnipeg, Manitoba, Canada R3E 3P6
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Vashishtha AK, Kuchta RD. Polymerase and exonuclease activities in herpes simplex virus type 1 DNA polymerase are not highly coordinated. Biochemistry 2015; 54:240-9. [PMID: 25517265 PMCID: PMC4303300 DOI: 10.1021/bi500840v] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
![]()
The
herpes polymerase–processivity factor complex consists
of the catalytic UL30 subunit containing both polymerase and proofreading
exonuclease activities and the UL42 subunit that acts as a processivity
factor. Curiously, the highly active exonuclease has minimal impact
on the accumulation of mismatches generated by the polymerase activity.
We utilized a series of oligonucleotides of defined sequence to define
the interactions between the polymerase and exonuclease active sites.
Exonuclease activity requires unwinding of two nucleotides of the
duplex primer–template. Surprisingly, even though the exonuclease
rate is much higher than the rate of DNA dissociation, the exonuclease
degrades both single- and double-stranded DNA in a nonprocessive manner.
Efficient proofreading of incorrect nucleotides incorporated by the
polymerase would seem to require efficient translocation of DNA between
the exonuclease and polymerase active sites. However, we found that translocation of
DNA from the exonuclease to polymerase active site is remarkably inefficient.
Consistent with inefficient translocation, the DNA binding sites for
the exonuclease and polymerase active sites appear to be largely independent,
such that the two activities appear noncoordinated. Finally, the presence
or absence of UL42 did not impact the coordination of the polymerase
and exonuclease activities. In addition to providing fundamental insights
into how the polymerase and exonuclease function together, these activities
provide a rationale for understanding why the exonuclease minimally
impacts accumulation of mismatches by the purified polymerase and
raise the question of how these two activities function together in
vivo.
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Affiliation(s)
- Ashwani Kumar Vashishtha
- Department of Chemistry and Biochemistry, University of Colorado , Boulder, Colorado 80309-0215, United States
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James SH, Larson KB, Acosta EP, Prichard MN. Helicase-primase as a target of new therapies for herpes simplex virus infections. Clin Pharmacol Ther 2014; 97:66-78. [PMID: 25670384 DOI: 10.1002/cpt.3] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2014] [Accepted: 09/16/2014] [Indexed: 01/13/2023]
Abstract
The seminal discovery of acyclovir 40 years ago heralded the modern era of truly selective antiviral therapies and this drug remains the therapy of choice for herpes simplex virus infections. Yet by modern standards, its antiviral activity is modest and new drugs against novel molecular targets such as the helicase-primase have the potential to improve clinical outcome, particularly in high-risk patients. A brief synopsis of current therapies for these infections and clinical need is provided to help provide an initial perspective. The function of the helicase-primase complex is then summarized and the development of new inhibitors of the helicase-primase complex, such as pritelivir and amenamevir, is discussed. We review their mechanism of action, propensity for drug resistance, and pharmacokinetic characteristics and discuss their potential to advance current therapeutic options. Strategies that include combinations of these inhibitors with acyclovir are also considered, as they will likely maximize clinical efficacy.
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Affiliation(s)
- S H James
- Division of Infectious Diseases, Department of Pediatrics, University of Alabama at Birmingham, Birmingham, Alabama, USA
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Kawato Y, Yuasa K, Shimahara Y, Oseko N. Detection and application of circular (concatemeric) DNA as an indicator of koi herpesvirus infection. DISEASES OF AQUATIC ORGANISMS 2014; 112:37-44. [PMID: 25392041 DOI: 10.3354/dao02785] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/04/2023]
Abstract
Herpesviruses form a long continuous DNA molecule, or head-to-tail concatemer, as a replicating intermediate in the host. In this study, we developed a DNA-specific PCR assay for detecting the infection stage of koi herpesvirus (KHV) based on the presence of this 'endless' DNA. The 295 kbp double-stranded DNA KHV genome consists of a 251 kbp unique long region and two 22 kbp direct repeats (DRL and DRR) at each genome terminus. We designed a new primer set (DR primer set) based on the DR region spanning the presumed circular or concatemeric junction. Using the DR primer set, a PCR product was obtained from KHV-infected common carp brain (CCB) cells, but not from the virus-infected cell culture supernatant, implying that the PCR assay could detect intracellular virus in the host. The synthesis of a presumptive circular or concatemeric genome in virus-infected CCB cells was examined in a time-course experiment together with viral mRNA of the terminase gene, copy numbers of the viral genome, and infectious viral titer. The mRNA was first detected in the cells at 6 h post-inoculation (hpi), and the copy number of viral genome in the cells started to increase at 12 hpi. Subsequently, circular or concatemeric DNA was detected in the cells at 18 hpi, and progeny virus was detected in the cell culture supernatant at 24 hpi. These findings suggest that detection of the circular or concatemeric KHV genome with the developed PCR method can be used to determine the stage of KHV infection.
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Affiliation(s)
- Yasuhiko Kawato
- National Research Institute of Aquaculture, Fisheries Research Agency, Minamiise, Mie 516-0193, Japan
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36
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Rupesh KR, Smith A, Boehmer PE. Ligand induced stabilization of the melting temperature of the HSV-1 single-strand DNA binding protein using the thermal shift assay. Biochem Biophys Res Commun 2014; 454:604-8. [PMID: 25449284 DOI: 10.1016/j.bbrc.2014.10.145] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2014] [Accepted: 10/29/2014] [Indexed: 11/16/2022]
Abstract
We have adapted the thermal shift assay to measure the ligand binding properties of the herpes simplex virus-1 single-strand DNA binding protein, ICP8. By measuring SYPRO Orange fluorescence in microtiter plates using a fluorescence-enabled thermal cycler, we have quantified the effects of oligonucleotide ligands on the melting temperature of ICP8. We found that single-stranded oligomers raise the melting temperature of ICP8 in a length- and concentration-dependent manner, ranging from 1°C for (dT)5 to a maximum of 9°C with oligomers ⩾10 nucleotides, with an apparent Kd of <1μM for (dT)20. Specifically, the results indicate that ICP8 is capable of interacting with oligomers as short as 5 nucleotides. Moreover, the observed increases in melting temperature of up to 9°C, indicates that single-strand DNA binding significantly stabilizes the structure of ICP8. This assay may be applied to investigate the ligand binding proteins of other single-strand DNA binding proteins and used as a high-throughput screen to identify compounds with therapeutic potential that inhibit single-strand DNA binding. As proof of concept, the single-strand DNA binding agent ciprofloxacin reduces the ligand induced stabilization of the melting temperature of ICP8 in a dose-dependent manner.
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Affiliation(s)
- Kanchi Ravi Rupesh
- Department of Basic Medical Sciences, The University of Arizona College of Medicine-Phoenix, Phoenix, AZ 85004-2157, USA
| | - Aaron Smith
- Department of Basic Medical Sciences, The University of Arizona College of Medicine-Phoenix, Phoenix, AZ 85004-2157, USA
| | - Paul E Boehmer
- Department of Basic Medical Sciences, The University of Arizona College of Medicine-Phoenix, Phoenix, AZ 85004-2157, USA.
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Rizvi AZ, Bhattacharya C. Detection of Replication Origin Sites in Herpesvirus Genomes by Clustering and Scoring of Palindromes with Quadratic Entropy Measures. IEEE/ACM TRANSACTIONS ON COMPUTATIONAL BIOLOGY AND BIOINFORMATICS 2014; 11:1108-1118. [PMID: 26357048 DOI: 10.1109/tcbb.2014.2330622] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/05/2023]
Abstract
Replication in herpesvirus genomes is a major concern of public health as they multiply rapidly during the lytic phase of infection that cause maximum damage to the host cells. Earlier research has established that sites of replication origin are dominated by high concentration of rare palindrome sequences of DNA. Computational methods are devised based on scoring to determine the concentration of palindromes. In this paper, we propose both extraction and localization of rare palindromes in an automated manner. Discrete Cosine Transform (DCT-II), a widely recognized image compression algorithm is utilized here to extract palindromic sequences based on their reverse complimentary symmetry property of existence. We formulate a novel approach to localize the rare palindrome clusters by devising a Minimum Quadratic Entropy (MQE) measure based on the Renyi's Quadratic Entropy (RQE) function. Experimental results over a large number of herpesvirus genomes show that the RQE based scoring of rare palindromes have higher order of sensitivity, and lesser false alarm in detecting concentration of rare palindromes and thereby sites of replication origin.
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An image-based genetic assay identifies genes in T1D susceptibility loci controlling cellular antiviral immunity in mouse. PLoS One 2014; 9:e108777. [PMID: 25268627 PMCID: PMC4182575 DOI: 10.1371/journal.pone.0108777] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2014] [Accepted: 08/25/2014] [Indexed: 11/19/2022] Open
Abstract
The pathogenesis of complex diseases, such as type 1 diabetes (T1D), derives from interactions between host genetics and environmental factors. Previous studies have suggested that viral infection plays a significant role in initiation of T1D in genetically predisposed individuals. T1D susceptibility loci may therefore be enriched in previously uncharacterized genes functioning in antiviral defense pathways. To identify genes involved in antiviral immunity, we performed an image-based high-throughput genetic screen using short hairpin RNAs (shRNAs) against 161 genes within T1D susceptibility loci. RAW 264.7 cells transduced with shRNAs were infected with GFP-expressing herpes simplex virus type 1 (HSV-1) and fluorescent microscopy was performed to assess the viral infectivity by fluorescence reporter activity. Of the 14 candidates identified with high confidence, two candidates were selected for further investigation, Il27 and Tagap. Administration of recombinant IL-27 during viral infection was found to act synergistically with interferon gamma (IFN-γ) to activate expression of type I IFNs and proinflammatory cytokines, and to enhance the activities of interferon regulatory factor 3 (IRF3). Consistent with a role in antiviral immunity, Tagap-deficient macrophages demonstrated increased viral replication, reduced expression of proinflammatory chemokines and cytokines, and decreased production of IFN-β. Taken together, our unbiased loss-of-function genetic screen identifies genes that play a role in host antiviral immunity and delineates roles for IL-27 and Tagap in the production of antiviral cytokines.
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Inhibitors of nucleotidyltransferase superfamily enzymes suppress herpes simplex virus replication. Antimicrob Agents Chemother 2014; 58:7451-61. [PMID: 25267681 DOI: 10.1128/aac.03875-14] [Citation(s) in RCA: 37] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023] Open
Abstract
Herpesviruses are large double-stranded DNA viruses that cause serious human diseases. Herpesvirus DNA replication depends on multiple processes typically catalyzed by nucleotidyltransferase superfamily (NTS) enzymes. Therefore, we investigated whether inhibitors of NTS enzymes would suppress replication of herpes simplex virus 1 (HSV-1) and HSV-2. Eight of 42 NTS inhibitors suppressed HSV-1 and/or HSV-2 replication by >10-fold at 5 μM, with suppression at 50 μM reaching ∼1 million-fold. Five compounds in two chemical families inhibited HSV replication in Vero and human foreskin fibroblast cells as well as the approved drug acyclovir did. The compounds had 50% effective concentration values as low as 0.22 μM with negligible cytotoxicity in the assays employed. The inhibitors suppressed accumulation of viral genomes and infectious particles and blocked events in the viral replication cycle before and during viral DNA replication. Acyclovir-resistant mutants of HSV-1 and HSV-2 remained highly sensitive to the NTS inhibitors. Five of six NTS inhibitors of the HSVs also blocked replication of another herpesvirus pathogen, human cytomegalovirus. Therefore, NTS enzyme inhibitors are promising candidates for new herpesvirus treatments that may have broad efficacy against members of the herpesvirus family.
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Jin F, Li S, Zheng K, Zhuo C, Ma K, Chen M, Wang Q, Zhang P, Fan J, Ren Z, Wang Y. Silencing herpes simplex virus type 1 capsid protein encoding genes by siRNA: a promising antiviral therapeutic approach. PLoS One 2014; 9:e96623. [PMID: 24794394 PMCID: PMC4008601 DOI: 10.1371/journal.pone.0096623] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/26/2013] [Accepted: 04/09/2014] [Indexed: 11/25/2022] Open
Abstract
Herpes simplex virus type 1 (HSV-1), a member of the herpesviridae, causes a variety of human viral diseases globally. Although a series of antiviral drugs are available for the treatment of infection and suppression of dissemination, HSV-1 remains highly prevalent worldwide. Therefore, the development of novel antiviral agents with different mechanisms of action is a matter of extreme urgency. During the proliferation of HSV-1, capsid assembly is essential for viral growth, and it is highly conserved in all HSV-1 strains. In this study, small interfering RNAs (siRNAs) against the HSV-1 capsid protein were screened to explore the influence of silencing capsid expression on the replication of HSV-1. We designed and chemically synthesized siRNAs for the capsid gene and assessed their inhibitory effects on the expression of target mRNA and the total intracellular viral genome loads by quantitative real-time PCR, as well as on the replication of HSV-1 via plaque reduction assays and electron microscopy. Our results showed that siRNA was an effective approach to inhibit the expression of capsid protein encoding genes including UL18, UL19, UL26, UL26.5, UL35 and UL38 in vitro. Interference of capsid proteins VP23 (UL18) and VP5 (UL19) individually or jointly greatly affected the replication of clinically isolated acyclovir-resistant HSV-1 as well as HSV-1/F and HSV-2/333. Plaque numbers and intracellular virions were significantly reduced by simultaneous knockdown of UL18 and UL19. The total intracellular viral genome loads were also significantly decreased in the UL18 and UL19 knockdown groups compared with the viral control. In conclusion, interfering with UL18 and UL19 gene expression could inhibit HSV-1 replication efficiently in vitro. Our research offers new targets for an RNA interference-based therapeutic strategy against HSV-1.
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Affiliation(s)
- Fujun Jin
- Guangzhou Jinan Biomedicine Research and Development Center, National Engineering Research Center of Genetic Medicine, Jinan University, Guangzhou, Guangdong, China
- College of Pharmacy, Jinan University, Guangzhou, Guangdong, China
| | - Shen Li
- Department of Molecular Pathology, Interdisciplinary Graduate School of Medicine and Engineering, University of Yamanashi, Yamanashi, Japan
| | - Kai Zheng
- Guangzhou Jinan Biomedicine Research and Development Center, National Engineering Research Center of Genetic Medicine, Jinan University, Guangzhou, Guangdong, China
| | - Cuiqin Zhuo
- Guangzhou Jinan Biomedicine Research and Development Center, National Engineering Research Center of Genetic Medicine, Jinan University, Guangzhou, Guangdong, China
- College of Pharmacy, Jinan University, Guangzhou, Guangdong, China
| | - Kaiqi Ma
- Guangzhou Jinan Biomedicine Research and Development Center, National Engineering Research Center of Genetic Medicine, Jinan University, Guangzhou, Guangdong, China
| | - Maoyun Chen
- Guangzhou Jinan Biomedicine Research and Development Center, National Engineering Research Center of Genetic Medicine, Jinan University, Guangzhou, Guangdong, China
- College of Pharmacy, Jinan University, Guangzhou, Guangdong, China
| | - Qiaoli Wang
- Guangzhou Jinan Biomedicine Research and Development Center, National Engineering Research Center of Genetic Medicine, Jinan University, Guangzhou, Guangdong, China
| | | | - Jianglin Fan
- Department of Molecular Pathology, Interdisciplinary Graduate School of Medicine and Engineering, University of Yamanashi, Yamanashi, Japan
| | - Zhe Ren
- Guangzhou Jinan Biomedicine Research and Development Center, National Engineering Research Center of Genetic Medicine, Jinan University, Guangzhou, Guangdong, China
- * E-mail: (ZR); (YFW)
| | - Yifei Wang
- Guangzhou Jinan Biomedicine Research and Development Center, National Engineering Research Center of Genetic Medicine, Jinan University, Guangzhou, Guangdong, China
- * E-mail: (ZR); (YFW)
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41
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A dihydro-pyrido-indole potently inhibits HSV-1 infection by interfering the viral immediate early transcriptional events. Antiviral Res 2014; 105:126-34. [PMID: 24576908 DOI: 10.1016/j.antiviral.2014.02.007] [Citation(s) in RCA: 42] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2013] [Revised: 02/10/2014] [Accepted: 02/11/2014] [Indexed: 11/23/2022]
Abstract
In our continued quest for identifying novel molecules from ethnomedicinal source we have isolated an alkaloid 7-methoxy-1-methyl-4,9-dihydro-3H-pyrido[3,4-b]indole, also known as Harmaline (HM), from an ethnomedicinal herb Ophiorrhiza nicobarica. The compound exhibited a potent anti-HSV-1 activity against both wild type and clinical isolates of HSV-1. Further we demonstrated that HM did not interfere in viral entry but the recruitment of lysine-specific demethylase-1 (LSD1) and the binding of immediate-early (IE) complex on ICP0 promoter. This leads to the suppression of viral IE gene synthesis and thereby the reduced expression of ICP4 and ICP27. Moreover, HM at its virucidal concentration is nontoxic and reduced virus yields in cutaneously infected Balb/C mice. Thus, the interference in the binding of IE complex, a decisive factor for HSV lytic cycle or latency by HM reveals an interesting target for developing non-nucleotide antiherpetic agent with different mode of action than Acyclovir.
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42
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Karampuri S, Ojha D, Bag P, Chakravarty H, Bal C, Chattopadhyay D, Sharon A. Anti-HSV activity and mode of action study of α-pyrone carboxamides. RSC Adv 2014. [DOI: 10.1039/c4ra01303d] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
Abstract
Potential anti-HSV lead candidate3d(EC50= 9.8 μg ml−1) and its possible binding mode to utilize cavity-A and cavity-B of viral enzyme HSV polymerase.
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Affiliation(s)
- Srinivas Karampuri
- Department of Applied Chemistry
- Birla Institute of Technology
- Ranchi 835215, India
| | - Durbadal Ojha
- ICMR Virus Unit
- ID & BG Hospital
- Kolkata 700010, India
| | - Paromita Bag
- ICMR Virus Unit
- ID & BG Hospital
- Kolkata 700010, India
| | | | - Chandralata Bal
- Department of Applied Chemistry
- Birla Institute of Technology
- Ranchi 835215, India
| | | | - Ashoke Sharon
- Department of Applied Chemistry
- Birla Institute of Technology
- Ranchi 835215, India
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43
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PNKP knockdown by RNA interference inhibits herpes simplex virus-1 replication in astrocytes. Virol Sin 2013; 28:345-51. [PMID: 24213989 DOI: 10.1007/s12250-013-3350-5] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2013] [Accepted: 10/24/2013] [Indexed: 10/26/2022] Open
Abstract
Herpes simplex virus-1 (HSV-1) is a major pathogen that causes various central nervous system (CNS) diseases, including herpes simplex encephalitis and meningitis. According to recent studies, PNKP significantly affects the proliferation of HSV-1 in astrocytes. Here, we used viral proliferation curves to confirm the significant inhibitory effects of PNKP on HSV-1 proliferation. PNKP downregulation was also confirmed by analyzing the transcription of viral genes. We found that PNKP downregulation affects the viral DNA copy number. This study preliminarily confirms that PNKP affects viral proliferation by affecting HSV-1 genome cyclization. These results also suggest that astrocytes play a specific role in preventing HSV-1 infection.
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Weller SK, Kuchta RD. The DNA helicase-primase complex as a target for herpes viral infection. Expert Opin Ther Targets 2013; 17:1119-32. [PMID: 23930666 DOI: 10.1517/14728222.2013.827663] [Citation(s) in RCA: 31] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/23/2023]
Abstract
INTRODUCTION The Herpesviridae are responsible for debilitating acute and chronic infections, and some members of this family are associated with human cancers. Conventional anti-herpesviral therapy targets the viral DNA polymerase and has been extremely successful; however, the emergence of drug-resistant virus strains, especially in neonates and immunocompromised patients, underscores the need for continued development of anti-herpes drugs. In this article, we explore an alternative target for antiviral therapy, the HSV helicase/primase complex. AREAS COVERED This review addresses the current state of knowledge of HSV DNA replication and the important roles played by the herpesvirus helicase- primase complex. In the last 10 years several helicase/primase inhibitors (HPIs) have been described, and in this article, we discuss and contrast these new agents with established inhibitors. EXPERT OPINION The outstanding safety profile of existing nucleoside analogues for α-herpesvirus infection make the development of new therapeutic agents a challenge. Currently used nucleoside analogues exhibit few side effects and have low occurrence of clinically relevant resistance. For HCMV, however, existing drugs have significant toxicity issues and the frequency of drug resistance is high, and no antiviral therapies are available for EBV and KSHV. The development of new anti-herpesvirus drugs is thus well worth pursuing especially for immunocompromised patients and those who develop drug-resistant infections. Although the HPIs are promising, limitations to their development into a successful drug strategy remain.
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Affiliation(s)
- Sandra K Weller
- University of Connecticut Health Center, Department of Molecular Microbial and Structural Biology , Farmington CT 06030 , USA +1 860 679 2310 ;
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Prusty BK, Siegl C, Hauck P, Hain J, Korhonen SJ, Hiltunen-Back E, Puolakkainen M, Rudel T. Chlamydia trachomatis infection induces replication of latent HHV-6. PLoS One 2013; 8:e61400. [PMID: 23620749 PMCID: PMC3631192 DOI: 10.1371/journal.pone.0061400] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2013] [Accepted: 03/08/2013] [Indexed: 11/19/2022] Open
Abstract
Human herpesvirus-6 (HHV-6) exists in latent form either as a nuclear episome or integrated into human chromosomes in more than 90% of healthy individuals without causing clinical symptoms. Immunosuppression and stress conditions can reactivate HHV-6 replication, associated with clinical complications and even death. We have previously shown that co-infection of Chlamydia trachomatis and HHV-6 promotes chlamydial persistence and increases viral uptake in an in vitro cell culture model. Here we investigated C. trachomatis-induced HHV-6 activation in cell lines and fresh blood samples from patients having Chromosomally integrated HHV-6 (CiHHV-6). We observed activation of latent HHV-6 DNA replication in CiHHV-6 cell lines and fresh blood cells without formation of viral particles. Interestingly, we detected HHV-6 DNA in blood as well as cervical swabs from C. trachomatis-infected women. Low virus titers correlated with high C. trachomatis load and vice versa, demonstrating a potentially significant interaction of these pathogens in blood cells and in the cervix of infected patients. Our data suggest a thus far underestimated interference of HHV-6 and C. trachomatis with a likely impact on the disease outcome as consequence of co-infection.
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Affiliation(s)
- Bhupesh K. Prusty
- Biocenter, Chair of Microbiology, University of Würzburg, Würzburg, Germany
| | - Christine Siegl
- Biocenter, Chair of Microbiology, University of Würzburg, Würzburg, Germany
| | - Petra Hauck
- Biocenter, Chair of Microbiology, University of Würzburg, Würzburg, Germany
| | - Johannes Hain
- Institute of Mathematics, Chair of Mathematics VIII (Statistics), University of Würzburg, Würzburg, Germany
| | - Suvi J. Korhonen
- Haartman Institute, Department of Virology, University of Helsinki, Helsinki, Finland
| | - Eija Hiltunen-Back
- Clinic of Venereal Diseases, Skin and Allergy Hospital, Helsinki University Central Hospital, Helsinki, Finland
- Department of Infectious Disease Surveillance and Control, National Institute of Health and Welfare, Helsinki, Finland
| | - Mirja Puolakkainen
- Haartman Institute, Department of Virology, University of Helsinki, Helsinki, Finland
- Helsinki University Central Hospital, Laboratory Division (HUSLAB), Department of Virology and Immunology, Helsinki, Finland
| | - Thomas Rudel
- Biocenter, Chair of Microbiology, University of Würzburg, Würzburg, Germany
- * E-mail:
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Structure and Mechanisms of SF1 DNA Helicases. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2013; 767:17-46. [PMID: 23161005 DOI: 10.1007/978-1-4614-5037-5_2] [Citation(s) in RCA: 46] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/03/2022]
Abstract
Superfamily I is a large and diverse group of monomeric and dimeric helicases defined by a set of conserved sequence motifs. Members of this class are involved in essential processes in both DNA and RNA metabolism in all organisms. In addition to conserved amino acid sequences, they also share a common structure containing two RecA-like motifs involved in ATP binding and hydrolysis and nucleic acid binding and unwinding. Unwinding is facilitated by a "pin" structure which serves to split the incoming duplex. This activity has been measured using both ensemble and single-molecule conditions. SF1 helicase activity is modulated through interactions with other proteins.
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Ackermann M, Koriabine M, Hartmann-Fritsch F, de Jong PJ, Lewis TD, Schetle N, Work TM, Dagenais J, Balazs GH, Leong JAC. The genome of Chelonid herpesvirus 5 harbors atypical genes. PLoS One 2012; 7:e46623. [PMID: 23056373 PMCID: PMC3462797 DOI: 10.1371/journal.pone.0046623] [Citation(s) in RCA: 43] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2011] [Accepted: 09/06/2012] [Indexed: 11/18/2022] Open
Abstract
The Chelonid fibropapilloma-associated herpesvirus (CFPHV; ChHV5) is believed to be the causative agent of fibropapillomatosis (FP), a neoplastic disease of marine turtles. While clinical signs and pathology of FP are well known, research on ChHV5 has been impeded because no cell culture system for its propagation exists. We have cloned a BAC containing ChHV5 in pTARBAC2.1 and determined its nucleotide sequence. Accordingly, ChHV5 has a type D genome and its predominant gene order is typical for the varicellovirus genus within the alphaherpesvirinae. However, at least four genes that are atypical for an alphaherpesvirus genome were also detected, i.e. two members of the C-type lectin-like domain superfamily (F-lec1, F-lec2), an orthologue to the mouse cytomegalovirus M04 (F-M04) and a viral sialyltransferase (F-sial). Four lines of evidence suggest that these atypical genes are truly part of the ChHV5 genome: (1) the pTARBAC insertion interrupted the UL52 ORF, leaving parts of the gene to either side of the insertion and suggesting that an intact molecule had been cloned. (2) Using FP-associated UL52 (F-UL52) as an anchor and the BAC-derived sequences as a means to generate primers, overlapping PCR was performed with tumor-derived DNA as template, which confirmed the presence of the same stretch of “atypical” DNA in independent FP cases. (3) Pyrosequencing of DNA from independent tumors did not reveal previously undetected viral sequences, suggesting that no apparent loss of viral sequence had happened due to the cloning strategy. (4) The simultaneous presence of previously known ChHV5 sequences and F-sial as well as F-M04 sequences was also confirmed in geographically distinct Australian cases of FP. Finally, transcripts of F-sial and F-M04 but not transcripts of lytic viral genes were detected in tumors from Hawaiian FP-cases. Therefore, we suggest that F-sial and F-M04 may play a role in FP pathogenesis.
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48
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Mohr H, Mohr CA, Schneider MR, Scrivano L, Adler B, Kraner-Schreiber S, Schnieke A, Dahlhoff M, Wolf E, Koszinowski UH, Ruzsics Z. Cytomegalovirus replicon-based regulation of gene expression in vitro and in vivo. PLoS Pathog 2012; 8:e1002728. [PMID: 22685399 PMCID: PMC3369935 DOI: 10.1371/journal.ppat.1002728] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2011] [Accepted: 04/18/2012] [Indexed: 12/14/2022] Open
Abstract
There is increasing evidence for a connection between DNA replication and the expression of adjacent genes. Therefore, this study addressed the question of whether a herpesvirus origin of replication can be used to activate or increase the expression of adjacent genes. Cell lines carrying an episomal vector, in which reporter genes are linked to the murine cytomegalovirus (MCMV) origin of lytic replication (oriLyt), were constructed. Reporter gene expression was silenced by a histone-deacetylase-dependent mechanism, but was resolved upon lytic infection with MCMV. Replication of the episome was observed subsequent to infection, leading to the induction of gene expression by more than 1000-fold. oriLyt-based regulation thus provided a unique opportunity for virus-induced conditional gene expression without the need for an additional induction mechanism. This principle was exploited to show effective late trans-complementation of the toxic viral protein M50 and the glycoprotein gO of MCMV. Moreover, the application of this principle for intracellular immunization against herpesvirus infection was demonstrated. The results of the present study show that viral infection specifically activated the expression of a dominant-negative transgene, which inhibited viral growth. This conditional system was operative in explant cultures of transgenic mice, but not in vivo. Several applications are discussed. All herpesviruses show a precisely regulated gene expression profile, including true-late genes, which are turned on only after the onset of DNA replication. We used this intrinsic viral mechanism to generate a versatile conditional gene expression system that exploits the activity of the murine cytomegalovirus (MCMV) viral origin of lytic replication (oriLyt). Upon virus infection, replication of the viral genome also led to the replication and activation of the oriLyt-coupled episomal transgene. The oriLyt-based replicons were silenced in all stable cell lines and transgenic mice; however, virus infection liberated the plasmids from histone-deacetylase-induced inactivation. As maximum gene expression relied on relief from silencing via replication of the episomal constructs, very strong induction of the reporter gene was achieved. We showed that this system can be used for trans-complementation of late, toxic viral genes, to block virus production by activating dominant-negative (DN) transgenes, and to provide a new tool to study the principles of viral replication.
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Affiliation(s)
- Hermine Mohr
- Max von Pettenkofer-Institute, Ludwig-Maximilians-Universität München, Munich, Germany
| | - Christian A. Mohr
- Max von Pettenkofer-Institute, Ludwig-Maximilians-Universität München, Munich, Germany
| | - Marlon R. Schneider
- Institute of Molecular Animal Breeding and Biotechnology, Ludwig-Maximilians-Universität München, Munich, Germany
| | - Laura Scrivano
- Institute of Molecular Animal Breeding and Biotechnology, Ludwig-Maximilians-Universität München, Munich, Germany
| | - Barbara Adler
- Max von Pettenkofer-Institute, Ludwig-Maximilians-Universität München, Munich, Germany
| | | | - Angelika Schnieke
- Chair of Livestock Biotechnology, Technische Universität München, Freising, Germany
| | - Maik Dahlhoff
- Chair of Livestock Biotechnology, Technische Universität München, Freising, Germany
| | - Eckhard Wolf
- Institute of Molecular Animal Breeding and Biotechnology, Ludwig-Maximilians-Universität München, Munich, Germany
| | - Ulrich H. Koszinowski
- Max von Pettenkofer-Institute, Ludwig-Maximilians-Universität München, Munich, Germany
- * E-mail:
| | - Zsolt Ruzsics
- Max von Pettenkofer-Institute, Ludwig-Maximilians-Universität München, Munich, Germany
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The potential link between PML NBs and ICP0 in regulating lytic and latent infection of HSV-1. Protein Cell 2012; 3:372-82. [PMID: 22544561 DOI: 10.1007/s13238-012-2021-x] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2011] [Accepted: 01/19/2012] [Indexed: 01/28/2023] Open
Abstract
Herpes simplex virus type 1 (HSV-1) is a common human pathogen causing cold sores and even more serious diseases. It can establish a latent stage in sensory ganglia after primary epithelial infections, and reactivate in response to stress or sunlight. Previous studies have demonstrated that viral immediate-early protein ICP0 plays a key role in regulating the balance between lytic and latent infection. Recently, It has been determined that promyelocytic leukemia (PML) nuclear bodies (NBs), small nuclear sub-structures, contribute to the repression of HSV-1 infection in the absence of functional ICP0. In this review, we discuss the fundamentals of the interaction between ICP0 and PML NBs, suggesting a potential link between PML NBs and ICP0 in regulating lytic and latent infection of HSV-1.
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50
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Stimulation of homology-directed repair at I-SceI-induced DNA breaks during the permissive life cycle of human cytomegalovirus. J Virol 2011; 85:6049-54. [PMID: 21490102 DOI: 10.1128/jvi.02514-10] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Human cytomegalovirus (HCMV) selectively relocalizes many DNA repair proteins, thereby avoiding a potentially detrimental damage response. In the present study, we evaluated interactions between HCMV and the homology-directed repair (HDR) pathway. In permissive human foreskin fibroblasts, a fluorescence-based double-stranded break repair assay was used to determine that HCMV stimulated HDR. Repair of both stably integrated and extrachromosomal reporter substrates was observed to increase. HDR was also stimulated through individual expression of the viral immediate-early protein IE1-72, mimicking full virus infection. These experiments further demonstrate HCMV's role in modulating critical cellular processes during a permissive infection.
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