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Holmes AC, Zagnoli-Vieira G, Caldecott KW, Semler BL. Effects of TDP2/VPg Unlinkase Activity on Picornavirus Infections Downstream of Virus Translation. Viruses 2020; 12:E166. [PMID: 32023921 PMCID: PMC7077319 DOI: 10.3390/v12020166] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/28/2019] [Revised: 01/20/2020] [Accepted: 01/22/2020] [Indexed: 12/12/2022] Open
Abstract
In this study, we characterized the role of host cell protein tyrosyl-DNA phosphodiesterase 2 (TDP2) activity, also known as VPg unlinkase, in picornavirus infections in a human cell model of infection. TDP2/VPg unlinkase is used by picornaviruses to remove the small polypeptide, VPg (Virus Protein genome-linked, the primer for viral RNA synthesis), from virus genomic RNA. We utilized a CRISPR/Cas-9-generated TDP2 knock out (KO) human retinal pigment epithelial-1 (hRPE-1) cell line, in addition to the wild type (WT) counterpart for our studies. We determined that in the absence of TDP2, virus growth kinetics for two enteroviruses (poliovirus and coxsackievirus B3) were delayed by about 2 h. Virus titers were reduced by ~2 log10 units for poliovirus and 0.5 log10 units for coxsackievirus at 4 hours post-infection (hpi), and by ~1 log10 unit at 6 hpi for poliovirus. However, virus titers were nearly indistinguishable from those of control cells by the end of the infectious cycle. We determined that this was not the result of an alternative source of VPg unlinkase activity being activated in the absence of TPD2 at late times of infection. Viral protein production in TDP2 KO cells was also substantially reduced at 4 hpi for poliovirus infection, consistent with the observed growth kinetics delay, but reached normal levels by 6 hpi. Interestingly, this result differs somewhat from what has been reported previously for the TDP2 KO mouse cell model, suggesting that either cell type or species-specific differences might be playing a role in the observed phenotype. We also determined that catalytically inactive TDP2 does not rescue the growth defect, confirming that TDP2 5' phosphodiesterase activity is required for efficient virus replication. Importantly, we show for the first time that polysomes can assemble efficiently on VPg-linked RNA after the initial round of translation in a cell culture model, but both positive and negative strand RNA production is impaired in the absence of TDP2 at mid-times of infection, indicating that the presence of VPg on the viral RNA affects a step in the replication cycle downstream of translation (e.g., RNA synthesis). In agreement with this conclusion, we found that double-stranded RNA production (a marker of viral RNA synthesis) is delayed in TDP2 KO RPE-1 cells. Moreover, we show that premature encapsidation of nascent, VPg-linked RNA is not responsible for the observed virus growth defect. Our studies provide the first lines of evidence to suggest that either negative- or positive-strand RNA synthesis (or both) is a likely candidate for the step that requires the removal of VPg from the RNA for an enterovirus infection to proceed efficiently.
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Affiliation(s)
- Autumn C. Holmes
- Department of Microbiology & Molecular Genetics and Center for Virus Research, University of California, Irvine, CA 92697, USA;
| | - Guido Zagnoli-Vieira
- Genome Damage and Stability Centre, University of Sussex, Falmer, Brighton BN1 9RQ, UK; (G.Z.-V.); (K.W.C.)
| | - Keith W. Caldecott
- Genome Damage and Stability Centre, University of Sussex, Falmer, Brighton BN1 9RQ, UK; (G.Z.-V.); (K.W.C.)
| | - Bert L. Semler
- Department of Microbiology & Molecular Genetics and Center for Virus Research, University of California, Irvine, CA 92697, USA;
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Chu CC, Silverman SK. Assessing histidine tags for recruiting deoxyribozymes to catalyze peptide and protein modification reactions. Org Biomol Chem 2018; 14:4697-703. [PMID: 27138704 DOI: 10.1039/c6ob00716c] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
We evaluate the ability of hexahistidine (His6) tags on peptide and protein substrates to recruit deoxyribozymes for modifying those substrates. For two different deoxyribozymes, one that creates tyrosine-RNA nucleopeptides and another that phosphorylates tyrosine side chains, we find substantial improvements in yield, kobs, and Km for peptide substrates due to recruiting by His6/Cu(2+). However, the recruiting benefits of the histidine tag are not observed for larger protein substrates, likely because the tested deoxyribozymes either cannot access the target peptide segments or cannot function when these segments are presented in a structured protein context.
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Affiliation(s)
- Chih-Chi Chu
- Department of Chemistry, University of Illinois at Urbana-Champaign, 600 South Mathews Avenue, Urbana, Illinois 61801, USA.
| | - Scott K Silverman
- Department of Chemistry, University of Illinois at Urbana-Champaign, 600 South Mathews Avenue, Urbana, Illinois 61801, USA.
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Li ZH, Yue YY, Li P, Song NN, Li B, Zhang Y, Meng H, Jiang GS, Qin L. MA104 Cell line presents characteristics suitable for enterovirus A71 isolation and proliferation. Microbiol Immunol 2016; 59:477-82. [PMID: 26138857 DOI: 10.1111/1348-0421.12281] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2015] [Revised: 06/09/2015] [Accepted: 06/28/2015] [Indexed: 11/27/2022]
Abstract
Enterovirus A71 (EV-A71), one of the most important causative agents of hand, foot and mouth disease (HFMD) in children, can lead to severe clinical outcomes, even death. However, the infection spectrum of EV-A71 in different cell lines remains unknown. Therefore, in this study, the biological characteristics of EV-A71 Subgroup C4 in different cell lines were investigated. To this end, the infectivity of EV-A71Jinan1002 isolated from children with severe HFMD was assessed in 18 different host cell lines. It was found that the MA104 cell line displayed biological characteristics suitable for EV-A71 Subgroup C4 strain isolation and proliferation; indeed, it was found that a broad spectrum of cell lines can be infected by EV-A71Jinan1002. Among the screened cells, four cell lines (HEK293, RD, MA104 and Marc145) produced high 50% tissue culture infective dose (TCID50 ) values calculated in viral proliferations (ranged from 10(7.6) to 10(7.8) ); the TCID50 being negatively associated with the time to appearance of CPE. Proliferation curves demonstrated that EV-A71Jinan1002 amplifies more efficiently in MA104, Hep-2 and RD cells. Remarkably, the virus isolation rate was much higher in MA104 cells than in RD cells. Thus this study, to our knowledge, is for the first to explore the infection spectrum of EV-A71 subgroup C4 in such a large number of different cell lines. Our data provide useful reference data for facilitating further study of EV-A71.
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Affiliation(s)
- Zhi-Hui Li
- Department of Microbiology, Institute of Basic Medicine, Shandong Academy of Medical Sciences, Key Laboratory of Rare and Uncommon Diseases, 18877 Jingshi Road, Jinan 250062
| | - Ying-Ying Yue
- Department of Microbiology, Institute of Basic Medicine, Shandong Academy of Medical Sciences, Key Laboratory of Rare and Uncommon Diseases, 18877 Jingshi Road, Jinan 250062
| | - Peng Li
- Department of Microbiology, Institute of Basic Medicine, Shandong Academy of Medical Sciences, Key Laboratory of Rare and Uncommon Diseases, 18877 Jingshi Road, Jinan 250062
| | - Nan-Nan Song
- Department of Microbiology, Institute of Basic Medicine, Shandong Academy of Medical Sciences, Key Laboratory of Rare and Uncommon Diseases, 18877 Jingshi Road, Jinan 250062
| | - Bingqing Li
- Department of Microbiology, Institute of Basic Medicine, Shandong Academy of Medical Sciences, Key Laboratory of Rare and Uncommon Diseases, 18877 Jingshi Road, Jinan 250062
| | - Ying Zhang
- Jinan Infectious Disease Hospital, 22029 Jingshi Road, Jinan 250021, China
| | - Hong Meng
- Department of Microbiology, Institute of Basic Medicine, Shandong Academy of Medical Sciences, Key Laboratory of Rare and Uncommon Diseases, 18877 Jingshi Road, Jinan 250062
| | - Guo-Sheng Jiang
- Department of Microbiology, Institute of Basic Medicine, Shandong Academy of Medical Sciences, Key Laboratory of Rare and Uncommon Diseases, 18877 Jingshi Road, Jinan 250062
| | - Lizeng Qin
- Department of Microbiology, Institute of Basic Medicine, Shandong Academy of Medical Sciences, Key Laboratory of Rare and Uncommon Diseases, 18877 Jingshi Road, Jinan 250062
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Maciejewski S, Nguyen JHC, Gómez-Herreros F, Cortés-Ledesma F, Caldecott KW, Semler BL. Divergent Requirement for a DNA Repair Enzyme during Enterovirus Infections. mBio 2015; 7:e01931-15. [PMID: 26715620 PMCID: PMC4725011 DOI: 10.1128/mbio.01931-15] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2015] [Accepted: 11/09/2015] [Indexed: 01/13/2023] Open
Abstract
UNLABELLED Viruses of the Enterovirus genus of picornaviruses, including poliovirus, coxsackievirus B3 (CVB3), and human rhinovirus, commandeer the functions of host cell proteins to aid in the replication of their small viral genomic RNAs during infection. One of these host proteins is a cellular DNA repair enzyme known as 5' tyrosyl-DNA phosphodiesterase 2 (TDP2). TDP2 was previously demonstrated to mediate the cleavage of a unique covalent linkage between a viral protein (VPg) and the 5' end of picornavirus RNAs. Although VPg is absent from actively translating poliovirus mRNAs, the removal of VPg is not required for the in vitro translation and replication of the RNA. However, TDP2 appears to be excluded from replication and encapsidation sites during peak times of poliovirus infection of HeLa cells, suggesting a role for TDP2 during the viral replication cycle. Using a mouse embryonic fibroblast cell line lacking TDP2, we found that TDP2 is differentially required among enteroviruses. Our single-cycle viral growth analysis shows that CVB3 replication has a greater dependency on TDP2 than does poliovirus or human rhinovirus replication. During infection, CVB3 protein accumulation is undetectable (by Western blot analysis) in the absence of TDP2, whereas poliovirus protein accumulation is reduced but still detectable. Using an infectious CVB3 RNA with a reporter, CVB3 RNA could still be replicated in the absence of TDP2 following transfection, albeit at reduced levels. Overall, these results indicate that TDP2 potentiates viral replication during enterovirus infections of cultured cells, making TDP2 a potential target for antiviral development for picornavirus infections. IMPORTANCE Picornaviruses are one of the most prevalent groups of viruses that infect humans and livestock worldwide. These viruses include the human pathogens belonging to the Enterovirus genus, such as poliovirus, coxsackievirus B3 (CVB3), and human rhinovirus. Diseases caused by enteroviruses pose a major problem for public health and have significant economic impact. Poliovirus can cause paralytic poliomyelitis. CVB3 can cause hand, foot, and mouth disease and myocarditis. Human rhinovirus is the causative agent of the common cold, which has a severe economic impact due to lost productivity and severe health consequences in individuals with respiratory dysfunction, such as asthma. By gaining a better understanding of the enterovirus replication cycle, antiviral drugs against enteroviruses may be developed. Here, we report that the absence of the cellular enzyme TDP2 can significantly decrease viral yields of poliovirus, CVB3, and human rhinovirus, making TDP2 a potential target for an antiviral against enterovirus infections.
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Affiliation(s)
- Sonia Maciejewski
- Department of Microbiology and Molecular Genetics, School of Medicine, University of California, Irvine, California, USA
| | - Joseph H C Nguyen
- Department of Microbiology and Molecular Genetics, School of Medicine, University of California, Irvine, California, USA
| | - Fernando Gómez-Herreros
- School of Life Sciences, Genome Damage and Stability Centre, University of Sussex, Brighton, United Kingdom
| | - Felipe Cortés-Ledesma
- School of Life Sciences, Genome Damage and Stability Centre, University of Sussex, Brighton, United Kingdom
| | - Keith W Caldecott
- School of Life Sciences, Genome Damage and Stability Centre, University of Sussex, Brighton, United Kingdom
| | - Bert L Semler
- Department of Microbiology and Molecular Genetics, School of Medicine, University of California, Irvine, California, USA
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Pankovics P, Boros Á, Reuter G. Novel 5′/3′RACE Method for Amplification and Determination of Single-Stranded RNAs Through Double-Stranded RNA (dsRNA) Intermediates. Mol Biotechnol 2015; 57:974-81. [DOI: 10.1007/s12033-015-9889-7] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
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Chu CC, Wong OY, Silverman SK. A generalizable DNA-catalyzed approach to peptide-nucleic acid conjugation. Chembiochem 2014; 15:1905-10. [PMID: 25056930 DOI: 10.1002/cbic.201402255] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/21/2014] [Indexed: 01/11/2023]
Abstract
We report DNA catalysts (deoxyribozymes) that join tyrosine-containing peptides to RNA and DNA in one step and without requiring protecting groups on either the peptide or the nucleic acid. Our previous efforts towards this goal required tethering the peptide to a DNA anchor oligonucleotide. Here, we established direct in vitro selection for deoxyribozymes that use untethered, free peptide substrates. This approach enables imposition of selection pressure via reduced peptide concentration and leads to preparatively useful lower apparent Km values of ∼100 μM peptide. Use of phosphorimidazolide (Imp) rather than triphosphate as the electrophile enables reactivity of either terminus (5' or 3') of both RNA and DNA. Our findings establish a generalizable means of joining unprotected peptide to nucleic acid in one step by using DNA catalysts identified by in vitro selection.
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Affiliation(s)
- Chih-Chi Chu
- Department of Chemistry, University of Illinois at Urbana-Champaign, 600 South Mathews Avenue, Urbana, IL 61801 (USA)
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Langereis MA, Feng Q, Nelissen FHT, Virgen-Slane R, van der Heden van Noort GJ, Maciejewski S, Filippov DV, Semler BL, van Delft FL, van Kuppeveld FJM. Modification of picornavirus genomic RNA using 'click' chemistry shows that unlinking of the VPg peptide is dispensable for translation and replication of the incoming viral RNA. Nucleic Acids Res 2013; 42:2473-82. [PMID: 24243841 PMCID: PMC3936719 DOI: 10.1093/nar/gkt1162] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022] Open
Abstract
Picornaviruses constitute a large group of viruses comprising medically and economically
important pathogens such as poliovirus, coxsackievirus, rhinovirus, enterovirus 71 and
foot-and-mouth disease virus. A unique characteristic of these viruses is the use of a
viral peptide (VPg) as primer for viral RNA synthesis. As a consequence, all newly formed
viral RNA molecules possess a covalently linked VPg peptide. It is known that VPg is
enzymatically released from the incoming viral RNA by a host protein, called TDP2, but it
is still unclear whether the release of VPg is necessary to initiate RNA translation. To
study the possible requirement of VPg release for RNA translation, we developed a novel
method to modify the genomic viral RNA with VPg linked via a ‘non-cleavable’
bond. We coupled an azide-modified VPg peptide to an RNA primer harboring a cyclooctyne
[bicyclo[6.1.0]nonyne (BCN)] by a copper-free ‘click’ reaction, leading to a
VPg-triazole-RNA construct that was ‘non-cleavable’ by TDP2. We successfully
ligated the VPg-RNA complex to the viral genomic RNA, directed by base pairing. We show
that the lack of VPg unlinkase does not influence RNA translation or replication. Thus,
the release of the VPg from the incoming viral RNA is not a prerequisite for RNA
translation or replication.
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Affiliation(s)
- Martijn A Langereis
- Virology Division, Department of Infectious Diseases and Immunology, Faculty of Veterinary Medicine, Utrecht University, Utrecht, 3584 CL, The Netherlands, Institute for Molecules and Materials, Radboud University Nijmegen, Nijmegen, 6500 HB, The Netherlands, Department of Microbiology and Molecular Genetics, School of Medicine, University of California, Irvine, CA 92697, USA and Leiden Institute of Chemistry, Leiden University, Bioorganic Synthesis Leiden, 2300 RA, The Netherlands
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Feng Q, Hato SV, Langereis MA, Zoll J, Virgen-Slane R, Peisley A, Hur S, Semler BL, van Rij RP, van Kuppeveld FJM. MDA5 detects the double-stranded RNA replicative form in picornavirus-infected cells. Cell Rep 2012; 2:1187-96. [PMID: 23142662 PMCID: PMC7103987 DOI: 10.1016/j.celrep.2012.10.005] [Citation(s) in RCA: 185] [Impact Index Per Article: 15.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2012] [Revised: 06/26/2012] [Accepted: 10/08/2012] [Indexed: 12/24/2022] Open
Abstract
RIG-I and MDA5 are cytosolic RNA sensors that play a critical role in innate antiviral responses. Major advances have been made in identifying RIG-I ligands, but our knowledge of the ligands for MDA5 remains restricted to data from transfection experiments mostly using poly(I:C), a synthetic dsRNA mimic. Here, we dissected the IFN-α/β-stimulatory activity of different viral RNA species produced during picornavirus infection, both by RNA transfection and in infected cells in which specific steps of viral RNA replication were inhibited. Our results show that the incoming genomic plus-strand RNA does not activate MDA5, but minus-strand RNA synthesis and production of the 7.5 kbp replicative form trigger a strong IFN-α/β response. IFN-α/β production does not rely on plus-strand RNA synthesis and thus generation of the partially double-stranded replicative intermediate. This study reports MDA5 activation by a natural RNA ligand under physiological conditions.
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Affiliation(s)
- Qian Feng
- Department of Medical Microbiology, Radboud University Nijmegen Medical Centre, Nijmegen, PO Box 9101, 6500 HB, The Netherlands
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An RNA virus hijacks an incognito function of a DNA repair enzyme. Proc Natl Acad Sci U S A 2012; 109:14634-9. [PMID: 22908287 DOI: 10.1073/pnas.1208096109] [Citation(s) in RCA: 69] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
A previously described mammalian cell activity, called VPg unlinkase, specifically cleaves a unique protein-RNA covalent linkage generated during the viral genomic RNA replication steps of a picornavirus infection. For over three decades, the identity of this cellular activity and its normal role in the uninfected cell had remained elusive. Here we report the purification and identification of VPg unlinkase as the DNA repair enzyme, 5'-tyrosyl-DNA phosphodiesterase-2 (TDP2). Our data show that VPg unlinkase activity in different mammalian cell lines correlates with their differential expression of TDP2. Furthermore, we show that recombinant TDP2 can cleave the protein-RNA linkage generated by different picornaviruses without impairing the integrity of viral RNA. Our results reveal a unique RNA repair-like function for TDP2 and suggest an unusual role in host-pathogen interactions for this cellular enzyme. On the basis of the identification of TDP2 as a potential antiviral target, our findings may lead to the development of universal therapeutics to treat the millions of individuals afflicted annually with diseases caused by picornaviruses, including myocarditis, aseptic meningitis, encephalitis, hepatitis, and the common cold.
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Goodfellow I. The genome-linked protein VPg of vertebrate viruses - a multifaceted protein. Curr Opin Virol 2011; 1:355-62. [PMID: 22440837 DOI: 10.1016/j.coviro.2011.09.003] [Citation(s) in RCA: 81] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2011] [Accepted: 09/20/2011] [Indexed: 12/24/2022]
Abstract
Several vertebrate positive-sense RNA viruses, namely the Picornaviridae and Caliciviridae have evolved to use a protein-primed mechanism of genome replication. This results in the covalent linkage of a virus encoded protein, VPg (viral protein genome-linked), to the 5' end of viral RNA. Recent studies have highlighted the pivotal role VPg plays in the life cycle of these viruses, which in the case of the Caliciviridae, includes a role in viral protein synthesis. This article provides an overview of the current knowledge of the functions of vertebrate RNA virus VPg proteins, illustrating their diverse function and the parallels they share with plant virus VPg proteins.
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Affiliation(s)
- Ian Goodfellow
- Section of Virology, Department of Medicine, Imperial College London, London, United Kingdom
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