1
|
Chu H, Wang L, Wang J, Zhang Y, Jin N, Liu F, Li Y. Genomic profile of eGFP-tagged senecavirus A subjected to serial plaque-to-plaque transfers. Microb Pathog 2024; 191:106661. [PMID: 38657711 DOI: 10.1016/j.micpath.2024.106661] [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: 03/26/2024] [Revised: 04/14/2024] [Accepted: 04/19/2024] [Indexed: 04/26/2024]
Abstract
Senecavirus A (SVA) belongs to the genus Senecavirus in the family Picornaviridae. This virus possesses a positive-sense, single-stranded RNA genome, approximately 7200 nt in length, composed of a single 5' untranslated region, encoding region and 3' untranslated region. In this study, a recombinant SVA tagged with enhanced green fluorescent protein (eGFP) sequence, rSVA-eGFP, was rescued from its cDNA clone using reverse genetics. The passage-5 (P5) rSVA-eGFP was totally subjected to 55 rounds of consecutive fluorescent plaque-to-fluorescent plaque (FP-FP) transfers, and one extra common passaging in vitro. The P61 viral stock was analyzed by next-generation sequencing. The result showed ten single-nucleotide mutations (SNMs) in the rSVA-eGFP genome, including nine transitions and only one transversion. The P61 progeny still showed a complete eGFP sequence, indicating no occurrence of copy-choice recombination within the eGFP region during serial FP-FP transfers. In other words, this progeny was genetically deficient in the recombination of eGFP sequence (RES), namely, an RES-deficient strain. Out of ten SNMs, three were missense mutations, leading to single-amino acid mutations (SAAMs): F15V in L protein, A74T in VP2, and E53R in 3D protein. The E53R was predicted to be spatially adjacent to the RNA channel of 3D protein, perhaps involved in the emergence of RES-deficient strain. In conclusion, this study uncovered a global landscape of rSVA-eGFP genome after serial FP-FP transfers, and moreover shed light on a putative SAAM possibly related to the RES-deficient mechanism.
Collapse
Affiliation(s)
- Huanhuan Chu
- College of Veterinary Medicine, Northwest A&F University, Yangling, 712100, China; College of Veterinary Medicine, Qingdao Agricultural University, Qingdao, 266109, China
| | - Ling Wang
- University Hospital, Qingdao Agricultural University, Qingdao, 266109, China
| | - Jie Wang
- College of Veterinary Medicine, Qingdao Agricultural University, Qingdao, 266109, China
| | - Youming Zhang
- State Key Laboratory of Microbial Technology, Shandong University, Qingdao, 266237, China
| | - Ningyi Jin
- College of Veterinary Medicine, Northwest A&F University, Yangling, 712100, China; Changchun Institute of Veterinary Medicine, Chinese Academy of Agricultural Sciences, Changchun, 130122, China.
| | - Fuxiao Liu
- College of Veterinary Medicine, Qingdao Agricultural University, Qingdao, 266109, China.
| | - Yan Li
- Qingdao Center for Animal Disease Control & Prevention, Qingdao, 266199, China.
| |
Collapse
|
2
|
Wang Q, Meng H, Ge D, Shan H, Geri L, Liu F. Structural and nonstructural proteins of Senecavirus A: Recent research advances, and lessons learned from those of other picornaviruses. Virology 2023; 585:155-163. [PMID: 37348144 DOI: 10.1016/j.virol.2023.06.004] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2023] [Revised: 06/04/2023] [Accepted: 06/06/2023] [Indexed: 06/24/2023]
Abstract
Senecavirus A (SVA) is an emerging virus, causing vesicular disease in swine. SVA is a single-stranded, positive-sense RNA virus, which is the only member of the genus Senecavirus in the family Picornaviridae. SVA genome encodes 12 proteins: L, VP4, VP2, VP3, VP1, 2A, 2B, 2C, 3A, 3B, 3C and 3D. The VP1 to VP4 are structural proteins, and the others are nonstructural proteins. The replication of SVA in host cells is a complex process coordinated by an elaborate interplay between the structural and nonstructural proteins. Structural proteins are primarily involved in the invasion and assembly of virions. Nonstructural proteins modulate viral RNA translation and replication, and also take part in antagonizing the antiviral host response and in disrupting some cellular processes to allow virus replication. Here, we systematically reviewed the molecular functions of SVA structural and nonstructural proteins by reference to literatures of SVA itself and other picornaviruses.
Collapse
Affiliation(s)
- Qianqian Wang
- College of Veterinary Medicine, Qingdao Agricultural University, Qingdao, 266109, China; College of Veterinary Medicine, Inner Mongolia Agricultural University, Hohhot, 010011, China
| | - Hailan Meng
- College of Veterinary Medicine, Qingdao Agricultural University, Qingdao, 266109, China
| | - Dong Ge
- Qingdao Lijian Bio-tech Co., Ltd., Qingdao, 266114, China
| | - Hu Shan
- College of Veterinary Medicine, Qingdao Agricultural University, Qingdao, 266109, China
| | - Letu Geri
- College of Veterinary Medicine, Inner Mongolia Agricultural University, Hohhot, 010011, China.
| | - Fuxiao Liu
- College of Veterinary Medicine, Qingdao Agricultural University, Qingdao, 266109, China.
| |
Collapse
|
3
|
Fidelity of Ribonucleotide Incorporation by the SARS-CoV-2 Replication Complex. J Mol Biol 2023; 435:167973. [PMID: 36690070 PMCID: PMC9854147 DOI: 10.1016/j.jmb.2023.167973] [Citation(s) in RCA: 9] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/22/2022] [Revised: 01/16/2023] [Accepted: 01/17/2023] [Indexed: 01/21/2023]
Abstract
The SARS-CoV-2 coronavirus has caused a global pandemic. Despite the initial success of vaccines at preventing infection, genomic variation has led to the proliferation of variants capable of higher infectivity. Mutations in the SARS-CoV-2 genome are the consequence of replication errors, highlighting the importance of understanding the determinants of SARS-CoV-2 replication fidelity. The RNA-dependent RNA polymerase (RdRp) is the central catalytic subunit for SARS-CoV-2 RNA replication and genome transcription. Here, we report the fidelity of ribonucleotide incorporation by SARS-CoV-2 RdRp (nsp12), along with its co-factors nsp7/nsp8, using steady-state kinetic analysis. Our analysis suggests that in the absence of the proofreading subunit (nsp14), the nsp12/7/8 complex has a surprisingly low base substitution fidelity (10-1-10-3). This is orders of magnitude lower than the fidelity reported for other coronaviruses (10-6-10-7), highlighting the importance of proofreading for faithful SARS-CoV-2 replication. We performed a mutational analysis of all reported SARS-CoV-2 genomes and identified mutations in both nsp12 and nsp14 that appear likely to lower viral replication fidelity through mechanisms that include impairing the nsp14 exonuclease activity or its association with the RdRp. Our observations provide novel insight into the mechanistic basis of replication fidelity in SARS-CoV-2 and the potential effect of nsp12 and nsp14 mutations on replication fidelity, informing the development of future antiviral agents and SARS-CoV-2 vaccines.
Collapse
|
4
|
Yeager C, Carter G, Gohara DW, Yennawar NH, Enemark E, Arnold J, Cameron CE. Enteroviral 2C protein is an RNA-stimulated ATPase and uses a two-step mechanism for binding to RNA and ATP. Nucleic Acids Res 2022; 50:11775-11798. [PMID: 36399514 PMCID: PMC9723501 DOI: 10.1093/nar/gkac1054] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2022] [Revised: 10/16/2022] [Accepted: 10/26/2022] [Indexed: 11/19/2022] Open
Abstract
The enteroviral 2C protein is a therapeutic target, but the absence of a mechanistic framework for this enzyme limits our understanding of inhibitor mechanisms. Here, we use poliovirus 2C and a derivative thereof to elucidate the first biochemical mechanism for this enzyme and confirm the applicability of this mechanism to other members of the enterovirus genus. Our biochemical data are consistent with a dimer forming in solution, binding to RNA, which stimulates ATPase activity by increasing the rate of hydrolysis without impacting affinity for ATP substantially. Both RNA and DNA bind to the same or overlapping site on 2C, driven by the phosphodiester backbone, but only RNA stimulates ATP hydrolysis. We propose that RNA binds to 2C driven by the backbone, with reorientation of the ribose hydroxyls occurring in a second step to form the catalytically competent state. 2C also uses a two-step mechanism for binding to ATP. Initial binding is driven by the α and β phosphates of ATP. In the second step, the adenine base and other substituents of ATP are used to organize the active site for catalysis. These studies provide the first biochemical description of determinants driving specificity and catalytic efficiency of a picornaviral 2C ATPase.
Collapse
Affiliation(s)
- Calvin Yeager
- Department of Microbiology & Immunology, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
| | - Griffin Carter
- Department of Microbiology & Immunology, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
| | - David W Gohara
- Department of Biochemistry and Molecular Biology, St. Louis University, St. Louis, MO 63104, USA
| | - Neela H Yennawar
- The Huck Institutes of the Life Sciences, The Pennsylvania State University, University Park, PA 16802, USA
| | - Eric J Enemark
- Department of Biochemistry and Molecular Biology, University of Arkansas for Medical Sciences, Little Rock, AR 72205, USA
| | - Jamie J Arnold
- Department of Microbiology & Immunology, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
| | - Craig E Cameron
- To whom correspondence should be addressed. Tel: +1 919 966 9699; Fax: +1 919 962 8103;
| |
Collapse
|
5
|
Takahashi S, Matsumoto S, Chilka P, Ghosh S, Okura H, Sugimoto N. Dielectricity of a molecularly crowded solution accelerates NTP misincorporation during RNA-dependent RNA polymerization by T7 RNA polymerase. Sci Rep 2022; 12:1149. [PMID: 35064200 PMCID: PMC8782835 DOI: 10.1038/s41598-022-05136-8] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2021] [Accepted: 01/06/2022] [Indexed: 11/09/2022] Open
Abstract
In biological systems, the synthesis of nucleic acids, such as DNA and RNA, is catalyzed by enzymes in various aqueous solutions. However, substrate specificity is derived from the chemical properties of the residues, which implies that perturbations of the solution environment may cause changes in the fidelity of the reaction. Here, we investigated non-promoter-based synthesis of RNA using T7 RNA polymerase (T7 RNAP) directed by an RNA template in the presence of polyethylene glycol (PEG) of various molecular weights, which can affect polymerization fidelity by altering the solution properties. We found that the mismatch extensions of RNA propagated downstream polymerization. Furthermore, PEG promoted the polymerization of non-complementary ribonucleoside triphosphates, mainly due to the decrease in the dielectric constant of the solution. These results indicate that the mismatch extension of RNA-dependent RNA polymerization by T7 RNAP is driven by the stacking interaction of bases of the primer end and the incorporated nucleotide triphosphates (NTP) rather than base pairing between them. Thus, proteinaceous RNA polymerase may display different substrate specificity with changes in dielectricity caused by molecular crowding conditions, which can result in increased genetic diversity without proteinaceous modification.
Collapse
Affiliation(s)
- Shuntaro Takahashi
- Frontier Institute for Biomolecular Engineering Research (FIBER), Konan University, 7-1-20 Minatojima-Minamimachi, Kobe, 650-0047, Japan
| | - Saki Matsumoto
- Frontier Institute for Biomolecular Engineering Research (FIBER), Konan University, 7-1-20 Minatojima-Minamimachi, Kobe, 650-0047, Japan
| | - Pallavi Chilka
- Frontier Institute for Biomolecular Engineering Research (FIBER), Konan University, 7-1-20 Minatojima-Minamimachi, Kobe, 650-0047, Japan
| | - Saptarshi Ghosh
- Frontier Institute for Biomolecular Engineering Research (FIBER), Konan University, 7-1-20 Minatojima-Minamimachi, Kobe, 650-0047, Japan
| | - Hiromichi Okura
- Frontier Institute for Biomolecular Engineering Research (FIBER), Konan University, 7-1-20 Minatojima-Minamimachi, Kobe, 650-0047, Japan
| | - Naoki Sugimoto
- Frontier Institute for Biomolecular Engineering Research (FIBER), Konan University, 7-1-20 Minatojima-Minamimachi, Kobe, 650-0047, Japan.
- Graduate School of Frontiers of Innovative Research in Science and Technology (FIRST), Konan University, 7-1-20 Minatojima-Minamimachi, Kobe, 650-0047, Japan.
| |
Collapse
|
6
|
Janissen R, Woodman A, Shengjuler D, Vallet T, Lee KM, Kuijpers L, Moustafa IM, Fitzgerald F, Huang PN, Perkins AL, Harki DA, Arnold JJ, Solano B, Shih SR, Vignuzzi M, Cameron CE, Dekker NH. Induced intra- and intermolecular template switching as a therapeutic mechanism against RNA viruses. Mol Cell 2021; 81:4467-4480.e7. [PMID: 34687604 PMCID: PMC8628313 DOI: 10.1016/j.molcel.2021.10.003] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2020] [Revised: 05/25/2021] [Accepted: 10/02/2021] [Indexed: 12/12/2022]
Abstract
Viral RNA-dependent RNA polymerases (RdRps) are a target for broad-spectrum antiviral therapeutic agents. Recently, we demonstrated that incorporation of the T-1106 triphosphate, a pyrazine-carboxamide ribonucleotide, into nascent RNA increases pausing and backtracking by the poliovirus RdRp. Here, by monitoring enterovirus A-71 RdRp dynamics during RNA synthesis using magnetic tweezers, we identify the "backtracked" state as an intermediate used by the RdRp for copy-back RNA synthesis and homologous recombination. Cell-based assays and RNA sequencing (RNA-seq) experiments further demonstrate that the pyrazine-carboxamide ribonucleotide stimulates these processes during infection. These results suggest that pyrazine-carboxamide ribonucleotides do not induce lethal mutagenesis or chain termination but function by promoting template switching and formation of defective viral genomes. We conclude that RdRp-catalyzed intra- and intermolecular template switching can be induced by pyrazine-carboxamide ribonucleotides, defining an additional mechanistic class of antiviral ribonucleotides with potential for broad-spectrum activity.
Collapse
Affiliation(s)
- Richard Janissen
- Department of Bionanoscience, Kavli Institute of Nanoscience, 2629 HZ Delft, the Netherlands
| | - Andrew Woodman
- Department of Biochemistry and Molecular Biology, Pennsylvania State University, State College, PA 16801, USA
| | - Djoshkun Shengjuler
- Viral Populations and Pathogenesis Unit, CNRS UMR 3569, Institut Pasteur, Paris, France
| | - Thomas Vallet
- Viral Populations and Pathogenesis Unit, CNRS UMR 3569, Institut Pasteur, Paris, France
| | - Kuo-Ming Lee
- Research Center for Emerging Viral Infections, College of Medicine, Chang Gung University, 33302 Taoyuan, Taiwan
| | - Louis Kuijpers
- Department of Bionanoscience, Kavli Institute of Nanoscience, 2629 HZ Delft, the Netherlands
| | - Ibrahim M Moustafa
- Department of Biochemistry and Molecular Biology, Pennsylvania State University, State College, PA 16801, USA
| | - Fiona Fitzgerald
- Department of Biochemistry and Molecular Biology, Pennsylvania State University, State College, PA 16801, USA
| | - Peng-Nien Huang
- Research Center for Emerging Viral Infections, College of Medicine, Chang Gung University, 33302 Taoyuan, Taiwan
| | - Angela L Perkins
- Department of Chemistry, University of Minnesota, Minneapolis, MN 55455, USA
| | - Daniel A Harki
- Department of Chemistry, University of Minnesota, Minneapolis, MN 55455, USA; Department of Medicinal Chemistry, University of Minnesota, Minneapolis, MN 55455, USA
| | - Jamie J Arnold
- Department of Biochemistry and Molecular Biology, Pennsylvania State University, State College, PA 16801, USA
| | - Belén Solano
- Department of Bionanoscience, Kavli Institute of Nanoscience, 2629 HZ Delft, the Netherlands
| | - Shin-Ru Shih
- Research Center for Emerging Viral Infections, College of Medicine, Chang Gung University, 33302 Taoyuan, Taiwan
| | - Marco Vignuzzi
- Viral Populations and Pathogenesis Unit, CNRS UMR 3569, Institut Pasteur, Paris, France
| | - Craig E Cameron
- Department of Biochemistry and Molecular Biology, Pennsylvania State University, State College, PA 16801, USA.
| | - Nynke H Dekker
- Department of Bionanoscience, Kavli Institute of Nanoscience, 2629 HZ Delft, the Netherlands.
| |
Collapse
|
7
|
Domingo E, García-Crespo C, Lobo-Vega R, Perales C. Mutation Rates, Mutation Frequencies, and Proofreading-Repair Activities in RNA Virus Genetics. Viruses 2021; 13:1882. [PMID: 34578463 PMCID: PMC8473064 DOI: 10.3390/v13091882] [Citation(s) in RCA: 49] [Impact Index Per Article: 16.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2021] [Revised: 09/06/2021] [Accepted: 09/17/2021] [Indexed: 12/29/2022] Open
Abstract
The error rate displayed during template copying to produce viral RNA progeny is a biologically relevant parameter of the replication complexes of viruses. It has consequences for virus-host interactions, and it represents the first step in the diversification of viruses in nature. Measurements during infections and with purified viral polymerases indicate that mutation rates for RNA viruses are in the range of 10-3 to 10-6 copying errors per nucleotide incorporated into the nascent RNA product. Although viruses are thought to exploit high error rates for adaptation to changing environments, some of them possess misincorporation correcting activities. One of them is a proofreading-repair 3' to 5' exonuclease present in coronaviruses that may decrease the error rate during replication. Here we review experimental evidence and models of information maintenance that explain why elevated mutation rates have been preserved during the evolution of RNA (and some DNA) viruses. The models also offer an interpretation of why error correction mechanisms have evolved to maintain the stability of genetic information carried out by large viral RNA genomes such as the coronaviruses.
Collapse
Affiliation(s)
- Esteban Domingo
- Centro de Biología Molecular “Severo Ochoa” (CSIC-UAM), Consejo Superior de Investigaciones Científicas (CSIC), Campus de Cantoblanco, 28049 Madrid, Spain;
- Centro de Investigación Biomédica en Red de Enfermedades Hepáticas y Digestivas (CIBERehd), Instituto de Salud Carlos III, 28029 Madrid, Spain
| | - Carlos García-Crespo
- Centro de Biología Molecular “Severo Ochoa” (CSIC-UAM), Consejo Superior de Investigaciones Científicas (CSIC), Campus de Cantoblanco, 28049 Madrid, Spain;
| | - Rebeca Lobo-Vega
- Department of Clinical Microbiology, Instituto de Investigación Sanitaria-Fundación Jiménez Díaz University Hospital, Universidad Autónoma de Madrid (IIS-FJD, UAM), Av. Reyes Católicos 2, 28040 Madrid, Spain;
| | - Celia Perales
- Centro de Biología Molecular “Severo Ochoa” (CSIC-UAM), Consejo Superior de Investigaciones Científicas (CSIC), Campus de Cantoblanco, 28049 Madrid, Spain;
- Centro de Investigación Biomédica en Red de Enfermedades Hepáticas y Digestivas (CIBERehd), Instituto de Salud Carlos III, 28029 Madrid, Spain
- Department of Clinical Microbiology, Instituto de Investigación Sanitaria-Fundación Jiménez Díaz University Hospital, Universidad Autónoma de Madrid (IIS-FJD, UAM), Av. Reyes Católicos 2, 28040 Madrid, Spain;
| |
Collapse
|
8
|
Rescue of Senecavirus A to uncover mutation profiles of its progenies during 80 serial passages in vitro. Vet Microbiol 2020; 253:108969. [PMID: 33450657 DOI: 10.1016/j.vetmic.2020.108969] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2020] [Accepted: 12/20/2020] [Indexed: 02/07/2023]
Abstract
Senecavirus A (SVA), also known as Seneca Valley virus, belongs to the genus Senecavirus in the family Picornaviridae. In this study, a China SVA isolate (CH-LX-01-2016) was rescued from its cDNA clone, and then identified by RT-PCR, indirect immunofluorescence assay and mass spectrometry. The rescued SVA could separately induce typical plaque formations and cytopathic effects in cell monolayers. In order to uncover its evolutionary dynamics, the SVA was subjected to eighty serial passages in vitro. Its progenies per ten passages were analyzed by next-generation sequencing (NGS). The NGS analyses showed that neither sequence-deleting nor -inserting phenotype was detectable in eight progenies, within which a total of forty-one intra-host single-nucleotide variations (SNVs) arose with passaging. Almost all SNVs were identified as the single-nucleotide polymorphism with mixture of two nucleotides. SNVs led to eighteen nonsynonymous mutations, out of which sixteen could directly reflect their own frequencies of amino acid mutation, due to only one SNV occurring in their individual codons. Compared with its parental virus without passaging, the passage-80 SVA progeny had formed a viral quasispecies, as evidenced by a total of twenty-eight SNVs identified in it.
Collapse
|
9
|
Seifert M, van Nies P, Papini FS, Arnold JJ, Poranen MM, Cameron CE, Depken M, Dulin D. Temperature controlled high-throughput magnetic tweezers show striking difference in activation energies of replicating viral RNA-dependent RNA polymerases. Nucleic Acids Res 2020; 48:5591-5602. [PMID: 32286652 PMCID: PMC7261197 DOI: 10.1093/nar/gkaa233] [Citation(s) in RCA: 23] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2020] [Revised: 03/10/2020] [Accepted: 03/30/2020] [Indexed: 01/05/2023] Open
Abstract
RNA virus survival depends on efficient viral genome replication, which is performed by the viral RNA dependent RNA polymerase (RdRp). The recent development of high throughput magnetic tweezers has enabled the simultaneous observation of dozens of viral RdRp elongation traces on kilobases long templates, and this has shown that RdRp nucleotide addition kinetics is stochastically interrupted by rare pauses of 1-1000 s duration, of which the short-lived ones (1-10 s) are the temporal signature of a low fidelity catalytic pathway. We present a simple and precise temperature controlled system for magnetic tweezers to characterize the replication kinetics temperature dependence between 25°C and 45°C of RdRps from three RNA viruses, i.e. the double-stranded RNA bacteriophage Φ6, and the positive-sense single-stranded RNA poliovirus (PV) and human rhinovirus C (HRV-C). We found that Φ6 RdRp is largely temperature insensitive, while PV and HRV-C RdRps replication kinetics are activated by temperature. Furthermore, the activation energies we measured for PV RdRp catalytic state corroborate previous estimations from ensemble pre-steady state kinetic studies, further confirming the catalytic origin of the short pauses and their link to temperature independent RdRp fidelity. This work will enable future temperature controlled study of biomolecular complex at the single molecule level.
Collapse
Affiliation(s)
- Mona Seifert
- Junior Research Group 2, Interdisciplinary Center for Clinical Research, Friedrich-Alexander-University Erlangen-Nürnberg (FAU), Cauerstr. 3, 91058 Erlangen, Germany
| | - Pauline van Nies
- Junior Research Group 2, Interdisciplinary Center for Clinical Research, Friedrich-Alexander-University Erlangen-Nürnberg (FAU), Cauerstr. 3, 91058 Erlangen, Germany
| | - Flávia S Papini
- Junior Research Group 2, Interdisciplinary Center for Clinical Research, Friedrich-Alexander-University Erlangen-Nürnberg (FAU), Cauerstr. 3, 91058 Erlangen, Germany
| | - Jamie J Arnold
- Department of Microbiology and Immunology, School of Medicine, The University of North Carolina Chapel Hill, 6012 Marsico Hall, CB 7290 Mason Farm Road, NC 27599, USA
| | - Minna M Poranen
- Molecular and Integrative Biosciences Research Program, Faculty of Biological and Environmental Sciences, University of Helsinki, Viikki Biocenter 1, P.O. Box 56 (Viikinkaari 9), 00014 Helsinki, Finland
| | - Craig E Cameron
- Department of Microbiology and Immunology, School of Medicine, The University of North Carolina Chapel Hill, 6012 Marsico Hall, CB 7290 Mason Farm Road, NC 27599, USA
| | - Martin Depken
- Department of Bionanoscience, Kavli Institute of Nanoscience, Delft University of Technology, Van der Maasweg 9, 2629 HZ Delft, The Netherlands,Correspondence may also be addressed to Martin Depken. Tel: +31 15 27 81305;
| | - David Dulin
- Junior Research Group 2, Interdisciplinary Center for Clinical Research, Friedrich-Alexander-University Erlangen-Nürnberg (FAU), Cauerstr. 3, 91058 Erlangen, Germany,To whom correspondence should be addressed. Tel: +49 9131 85 70347; Fax: +49 9131 85 35903;
| |
Collapse
|
10
|
RNA-Dependent RNA Polymerase Speed and Fidelity are not the Only Determinants of the Mechanism or Efficiency of Recombination. Genes (Basel) 2019; 10:genes10120968. [PMID: 31775299 PMCID: PMC6947342 DOI: 10.3390/genes10120968] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2019] [Revised: 11/14/2019] [Accepted: 11/21/2019] [Indexed: 01/05/2023] Open
Abstract
Using the RNA-dependent RNA polymerase (RdRp) from poliovirus (PV) as our model system, we have shown that Lys-359 in motif-D functions as a general acid in the mechanism of nucleotidyl transfer. A K359H (KH) RdRp derivative is slow and faithful relative to wild-type enzyme. In the context of the KH virus, RdRp-coding sequence evolves, selecting for the following substitutions: I331F (IF, motif-C) and P356S (PS, motif-D). We have evaluated IF-KH, PS-KH, and IF-PS-KH viruses and enzymes. The speed and fidelity of each double mutant are equivalent. Each exhibits a unique recombination phenotype, with IF-KH being competent for copy-choice recombination and PS-KH being competent for forced-copy-choice recombination. Although the IF-PS-KH RdRp exhibits biochemical properties within twofold of wild type, the virus is impaired substantially for recombination in cells. We conclude that there are biochemical properties of the RdRp in addition to speed and fidelity that determine the mechanism and efficiency of recombination. The interwoven nature of speed, fidelity, the undefined property suggested here, and recombination makes it impossible to attribute a single property of the RdRp to fitness. However, the derivatives described here may permit elucidation of the importance of recombination on the fitness of the viral population in a background of constant polymerase speed and fidelity.
Collapse
|
11
|
Prostova MA, Smertina E, Bakhmutov DV, Gasparyan AA, Khitrina EV, Kolesnikova MS, Shishova AA, Gmyl AP, Agol VI. Characterization of Mutational Tolerance of a Viral RNA-Protein Interaction. Viruses 2019; 11:v11050479. [PMID: 31130655 PMCID: PMC6563195 DOI: 10.3390/v11050479] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2019] [Revised: 05/20/2019] [Accepted: 05/22/2019] [Indexed: 01/01/2023] Open
Abstract
Replication of RNA viruses is generally markedly error-prone. Nevertheless, these viruses usually retain their identity under more or less constant conditions due to different mechanisms of mutation tolerance. However, there exists only limited information on quantitative aspects of the mutational tolerance of distinct viral functions. To address this problem, we used here as a model the interaction between a replicative cis-acting RNA element (oriL) of poliovirus and its ligand (viral protein 3CD). The mutational tolerance of a conserved tripeptide of 3CD, directly involved in this interaction, was investigated. Randomization of the relevant codons and reverse genetics were used to define the space of viability-compatible sequences. Surprisingly, at least 11 different amino acid substitutions in this tripeptide were not lethal. Several altered viruses exhibited wild-type-like phenotypes, whereas debilitated (but viable) genomes could increase their fitness by the acquisition of reversions or compensatory mutations. Together with our study on the tolerance of oriL (Prostova et al., 2015), the results demonstrate that at least 42 out of 51 possible nucleotide replacements within the two relevant genomic regions are viability-compatible. These results provide new insights into structural aspects of an important viral function as well as into the general problems of viral mutational robustness and evolution.
Collapse
Affiliation(s)
- Maria A Prostova
- Institute of Poliomyelitis, M. P. Chumakov Center for Research and Development of Immunobiological Products, Russian Academy of Sciences, 108819 Moscow, Russia.
- Institute of Molecular Genetics, Russian Academy of Sciences, 123182 Moscow, Russia.
| | - Elena Smertina
- Institute of Poliomyelitis, M. P. Chumakov Center for Research and Development of Immunobiological Products, Russian Academy of Sciences, 108819 Moscow, Russia.
- Faculty of Fundamental Medicine, M. V. Lomonosov Moscow State University, 117192 Moscow, Russia.
| | - Denis V Bakhmutov
- Institute of Poliomyelitis, M. P. Chumakov Center for Research and Development of Immunobiological Products, Russian Academy of Sciences, 108819 Moscow, Russia.
| | - Anna A Gasparyan
- Institute of Poliomyelitis, M. P. Chumakov Center for Research and Development of Immunobiological Products, Russian Academy of Sciences, 108819 Moscow, Russia.
- Faculty of Biology, M. V. Lomonosov Moscow State University, 119991 Moscow, Russia.
| | - Elena V Khitrina
- Institute of Poliomyelitis, M. P. Chumakov Center for Research and Development of Immunobiological Products, Russian Academy of Sciences, 108819 Moscow, Russia.
- A. N. Belozersky Institute of Physical-Chemical Biology, M. V. Lomonosov Moscow State University, 119899 Moscow, Russia.
| | - Marina S Kolesnikova
- Institute of Poliomyelitis, M. P. Chumakov Center for Research and Development of Immunobiological Products, Russian Academy of Sciences, 108819 Moscow, Russia.
| | - Anna A Shishova
- Institute of Poliomyelitis, M. P. Chumakov Center for Research and Development of Immunobiological Products, Russian Academy of Sciences, 108819 Moscow, Russia.
| | - Anatoly P Gmyl
- Institute of Poliomyelitis, M. P. Chumakov Center for Research and Development of Immunobiological Products, Russian Academy of Sciences, 108819 Moscow, Russia.
- Faculty of Biology, M. V. Lomonosov Moscow State University, 119991 Moscow, Russia.
- Sechenov First Moscow State Medical University, 119991 Moscow, Russia.
| | - Vadim I Agol
- Institute of Poliomyelitis, M. P. Chumakov Center for Research and Development of Immunobiological Products, Russian Academy of Sciences, 108819 Moscow, Russia.
- A. N. Belozersky Institute of Physical-Chemical Biology, M. V. Lomonosov Moscow State University, 119899 Moscow, Russia.
| |
Collapse
|
12
|
RNA Virus Fidelity Mutants: A Useful Tool for Evolutionary Biology or a Complex Challenge? Viruses 2018; 10:v10110600. [PMID: 30388745 PMCID: PMC6267201 DOI: 10.3390/v10110600] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2018] [Revised: 10/29/2018] [Accepted: 10/31/2018] [Indexed: 12/30/2022] Open
Abstract
RNA viruses replicate with low fidelity due to the error-prone nature of the RNA-dependent RNA polymerase, which generates approximately one mutation per round of genome replication. Due to the large population sizes produced by RNA viruses during replication, this results in a cloud of closely related virus variants during host infection, of which small increases or decreases in replication fidelity have been shown to result in virus attenuation in vivo, but not typically in vitro. Since the discovery of the first RNA virus fidelity mutants during the mid-aughts, the field has exploded with the identification of over 50 virus fidelity mutants distributed amongst 7 RNA virus families. This review summarizes the current RNA virus fidelity mutant literature, with a focus upon the definition of a fidelity mutant as well as methods to confirm any mutational changes associated with the fidelity mutant. Due to the complexity of such a definition, in addition to reports of unstable virus fidelity phenotypes, the future translational utility of these mutants and applications for basic science are examined.
Collapse
|
13
|
Dulin D, Arnold JJ, van Laar T, Oh HS, Lee C, Perkins AL, Harki DA, Depken M, Cameron CE, Dekker NH. Signatures of Nucleotide Analog Incorporation by an RNA-Dependent RNA Polymerase Revealed Using High-Throughput Magnetic Tweezers. Cell Rep 2018; 21:1063-1076. [PMID: 29069588 PMCID: PMC5670035 DOI: 10.1016/j.celrep.2017.10.005] [Citation(s) in RCA: 36] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2017] [Revised: 09/20/2017] [Accepted: 10/02/2017] [Indexed: 11/04/2022] Open
Abstract
RNA viruses pose a threat to public health that is exacerbated by the dearth of antiviral therapeutics. The RNA-dependent RNA polymerase (RdRp) holds promise as a broad-spectrum, therapeutic target because of the conserved nature of the nucleotide-substrate-binding and catalytic sites. Conventional, quantitative, kinetic analysis of antiviral ribonucleotides monitors one or a few incorporation events. Here, we use a high-throughput magnetic tweezers platform to monitor the elongation dynamics of a prototypical RdRp over thousands of nucleotide-addition cycles in the absence and presence of a suite of nucleotide analog inhibitors. We observe multiple RdRp-RNA elongation complexes; only a subset of which are competent for analog utilization. Incorporation of a pyrazine-carboxamide nucleotide analog, T-1106, leads to RdRp backtracking. This analysis reveals a mechanism of action for this antiviral ribonucleotide that is corroborated by cellular studies. We propose that induced backtracking represents a distinct mechanistic class of antiviral ribonucleotides. Several unique conformational states of an elongating RdRp exist Only one conformation incorporates nucleotide analogs with therapeutic potential An analog thought to be a chain terminator actually promotes RdRp backtracking Distinctive behavior of backtrack-inducing analog on virus variants in cell culture
Collapse
Affiliation(s)
- David Dulin
- Department of Bionanoscience, Kavli Institute of Nanoscience, Delft University of Technology, Van der Maasweg 9, 2629 HZ Delft, the Netherlands; Junior Research Group 2, Interdisciplinary Center for Clinical Research, Friedrich Alexander University Erlangen-Nürnberg (FAU), Hartmannstr. 14, 91052 Erlangen, Germany
| | - Jamie J Arnold
- Department of Biochemistry and Molecular Biology, The Pennsylvania State University, University Park, PA 16802, USA
| | - Theo van Laar
- Department of Bionanoscience, Kavli Institute of Nanoscience, Delft University of Technology, Van der Maasweg 9, 2629 HZ Delft, the Netherlands
| | - Hyung-Suk Oh
- Department of Biochemistry and Molecular Biology, The Pennsylvania State University, University Park, PA 16802, USA
| | - Cheri Lee
- Department of Biochemistry and Molecular Biology, The Pennsylvania State University, University Park, PA 16802, USA
| | - Angela L Perkins
- Department of Medicinal Chemistry, University of Minnesota, Minneapolis, MN 55455, USA
| | - Daniel A Harki
- Department of Medicinal Chemistry, University of Minnesota, Minneapolis, MN 55455, USA
| | - Martin Depken
- Department of Bionanoscience, Kavli Institute of Nanoscience, Delft University of Technology, Van der Maasweg 9, 2629 HZ Delft, the Netherlands.
| | - Craig E Cameron
- Department of Biochemistry and Molecular Biology, The Pennsylvania State University, University Park, PA 16802, USA.
| | - Nynke H Dekker
- Department of Bionanoscience, Kavli Institute of Nanoscience, Delft University of Technology, Van der Maasweg 9, 2629 HZ Delft, the Netherlands.
| |
Collapse
|
14
|
Abstract
Reproduction of RNA viruses is typically error-prone due to the infidelity of their replicative machinery and the usual lack of proofreading mechanisms. The error rates may be close to those that kill the virus. Consequently, populations of RNA viruses are represented by heterogeneous sets of genomes with various levels of fitness. This is especially consequential when viruses encounter various bottlenecks and new infections are initiated by a single or few deviating genomes. Nevertheless, RNA viruses are able to maintain their identity by conservation of major functional elements. This conservatism stems from genetic robustness or mutational tolerance, which is largely due to the functional degeneracy of many protein and RNA elements as well as to negative selection. Another relevant mechanism is the capacity to restore fitness after genetic damages, also based on replicative infidelity. Conversely, error-prone replication is a major tool that ensures viral evolvability. The potential for changes in debilitated genomes is much higher in small populations, because in the absence of stronger competitors low-fit genomes have a choice of various trajectories to wander along fitness landscapes. Thus, low-fit populations are inherently unstable, and it may be said that to run ahead it is useful to stumble. In this report, focusing on picornaviruses and also considering data from other RNA viruses, we review the biological relevance and mechanisms of various alterations of viral RNA genomes as well as pathways and mechanisms of rehabilitation after loss of fitness. The relationships among mutational robustness, resilience, and evolvability of viral RNA genomes are discussed.
Collapse
|
15
|
Korotkova E, Laassri M, Zagorodnyaya T, Petrovskaya S, Rodionova E, Cherkasova E, Gmyl A, Ivanova OE, Eremeeva TP, Lipskaya GY, Agol VI, Chumakov K. Pressure for Pattern-Specific Intertypic Recombination between Sabin Polioviruses: Evolutionary Implications. Viruses 2017; 9:v9110353. [PMID: 29165333 PMCID: PMC5707560 DOI: 10.3390/v9110353] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/23/2017] [Revised: 11/15/2017] [Accepted: 11/20/2017] [Indexed: 11/29/2022] Open
Abstract
Complete genomic sequences of a non-redundant set of 70 recombinants between three serotypes of attenuated Sabin polioviruses as well as location (based on partial sequencing) of crossover sites of 28 additional recombinants were determined and compared with the previously published data. It is demonstrated that the genomes of Sabin viruses contain distinct strain-specific segments that are eliminated by recombination. The presumed low fitness of these segments could be linked to mutations acquired upon derivation of the vaccine strains and/or may have been present in wild-type parents of Sabin viruses. These “weak” segments contribute to the propensity of these viruses to recombine with each other and with other enteroviruses as well as determine the choice of crossover sites. The knowledge of location of such segments opens additional possibilities for the design of more genetically stable and/or more attenuated variants, i.e., candidates for new oral polio vaccines. The results also suggest that the genome of wild polioviruses, and, by generalization, of other RNA viruses, may harbor hidden low-fitness segments that can be readily eliminated only by recombination.
Collapse
Affiliation(s)
- Ekaterina Korotkova
- AN Belozersky Institute of Physical-Chemical Biology, MV Lomonosov Moscow State University, Moscow 119899, Russia.
- Institute of Poliomyelitis and Viral Encephalitides of MP Chumakov Federal Scientific Center for Research and Development of Immune-and-Biological Products of Russian Academy of Sciences, Moscow 108819, Russia.
| | - Majid Laassri
- US Food and Drug Administration, Silver Spring, MD 20993, USA.
| | | | | | | | - Elena Cherkasova
- National Heart, Lung, and Blood Institute, National Institutes of Health, Bethesda, MD 20895, USA.
| | - Anatoly Gmyl
- Institute of Poliomyelitis and Viral Encephalitides of MP Chumakov Federal Scientific Center for Research and Development of Immune-and-Biological Products of Russian Academy of Sciences, Moscow 108819, Russia.
- IM Sechenov First Moscow State Medical University, Moscow 119991, Russia.
| | - Olga E Ivanova
- Institute of Poliomyelitis and Viral Encephalitides of MP Chumakov Federal Scientific Center for Research and Development of Immune-and-Biological Products of Russian Academy of Sciences, Moscow 108819, Russia.
- IM Sechenov First Moscow State Medical University, Moscow 119991, Russia.
| | - Tatyana P Eremeeva
- Institute of Poliomyelitis and Viral Encephalitides of MP Chumakov Federal Scientific Center for Research and Development of Immune-and-Biological Products of Russian Academy of Sciences, Moscow 108819, Russia.
| | - Galina Y Lipskaya
- AN Belozersky Institute of Physical-Chemical Biology, MV Lomonosov Moscow State University, Moscow 119899, Russia.
| | - Vadim I Agol
- AN Belozersky Institute of Physical-Chemical Biology, MV Lomonosov Moscow State University, Moscow 119899, Russia.
- Institute of Poliomyelitis and Viral Encephalitides of MP Chumakov Federal Scientific Center for Research and Development of Immune-and-Biological Products of Russian Academy of Sciences, Moscow 108819, Russia.
| | | |
Collapse
|