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Kleiner VA, Fearns R. How does the polymerase of non-segmented negative strand RNA viruses commit to transcription or genome replication? J Virol 2024; 98:e0033224. [PMID: 39078194 PMCID: PMC11334523 DOI: 10.1128/jvi.00332-24] [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] [Indexed: 07/31/2024] Open
Abstract
The Mononegavirales, or non-segmented negative-sense RNA viruses (nsNSVs), includes significant human pathogens, such as respiratory syncytial virus, parainfluenza virus, measles virus, Ebola virus, and rabies virus. Although these viruses differ widely in their pathogenic properties, they are united by each having a genome consisting of a single strand of negative-sense RNA. Consistent with their shared genome structure, the nsNSVs have evolved similar ways to transcribe their genome into mRNAs and replicate it to produce new genomes. Importantly, both mRNA transcription and genome replication are performed by a single virus-encoded polymerase. A fundamental and intriguing question is: how does the nsNSV polymerase commit to being either an mRNA transcriptase or a replicase? The polymerase must become committed to one process or the other either before it interacts with the genome template or in its initial interactions with the promoter sequence at the 3´ end of the genomic RNA. This review examines the biochemical, molecular biology, and structural biology data regarding the first steps of transcription and RNA replication that have been gathered over several decades for different families of nsNSVs. These findings are discussed in relation to possible models that could explain how an nsNSV polymerase initiates and commits to either transcription or genome replication.
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Affiliation(s)
- Victoria A. Kleiner
- Department of Virology, Immunology & Microbiology, Boston University Chobanian & Avedisian School of Medicine, Boston, Massachusetts, USA
| | - Rachel Fearns
- Department of Virology, Immunology & Microbiology, Boston University Chobanian & Avedisian School of Medicine, Boston, Massachusetts, USA
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2
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Brennan JW, Sun Y. Defective viral genomes: advances in understanding their generation, function, and impact on infection outcomes. mBio 2024; 15:e0069224. [PMID: 38567955 PMCID: PMC11077978 DOI: 10.1128/mbio.00692-24] [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] [Indexed: 05/09/2024] Open
Abstract
Defective viral genomes (DVGs) are truncated derivatives of their parental viral genomes generated during an aberrant round of viral genomic replication. Distinct classes of DVGs have been identified in most families of both positive- and negative-sense RNA viruses. Importantly, DVGs have been detected in clinical samples from virally infected individuals and an emerging body of association studies implicates DVGs in shaping the severity of disease caused by viral infections in humans. Consequently, there is growing interest in understanding the molecular mechanisms of de novo DVG generation, how DVGs interact with the innate immune system, and harnessing DVGs as novel therapeutics and vaccine adjuvants to attenuate viral pathogenesis. This minireview focuses on single-stranded RNA viruses (excluding retroviridae), and summarizes the current knowledge of DVG generation, the functions and diversity of DVG species, the roles DVGs play in influencing disease progression, and their application as antivirals and vaccine adjuvants.
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Affiliation(s)
- Justin W. Brennan
- Department of Microbiology and Immunology, University of Rochester Medical Center, Rochester, New York, USA
| | - Yan Sun
- Department of Microbiology and Immunology, University of Rochester Medical Center, Rochester, New York, USA
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3
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Cox RM, Plemper RK. Design and Execution of In Vitro Polymerase Assays for Measles Virus and Related Mononegaviruses. Methods Mol Biol 2024; 2808:19-33. [PMID: 38743360 DOI: 10.1007/978-1-0716-3870-5_3] [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] [Indexed: 05/16/2024]
Abstract
Morbilliviruses such as measles virus (MeV) are responsible for major morbidity and mortality worldwide, despite the availability of an effective vaccine and global vaccination campaigns. MeV belongs to the mononegavirus order of viral pathogens that store their genetic information in non-segmented negative polarity RNA genomes. Genome replication and viral gene expression are carried out by a virus-encoded RNA-dependent RNA polymerase (RdRP) complex that has no immediate host cell analog. To better understand the organization and regulation of the viral RdRP and mechanistically characterize antiviral candidates, biochemical RdRP assays have been developed that employ purified recombinant polymerase complexes and synthetic RNA templates to monitor the initiation of RNA synthesis and RNA elongation in vitro. In this article, we will discuss strategies for the efficient expression and preparation of mononegavirus polymerase complexes, provide detailed protocols for the execution and optimization of RdRP assays, evaluate alternative options for the choice of template and detection system, and describe the application of the assay for the characterization of inhibitor candidates. Although MeV RdRP assays are the focus of this article, the general strategies and experimental approaches are readily transferable to related viruses in the mononegavirus order.
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Affiliation(s)
- Robert M Cox
- Center for Translational Antiviral Research, Institute for Biomedical Sciences, Georgia State University, Atlanta, GA, USA
| | - Richard K Plemper
- Center for Translational Antiviral Research, Institute for Biomedical Sciences, Georgia State University, Atlanta, GA, USA.
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Abstract
The nonsegmented, negative-strand RNA viruses (nsNSVs), also known as the order Mononegavirales, have a genome consisting of a single strand of negative-sense RNA. Integral to the nsNSV replication cycle is the viral polymerase, which is responsible for transcribing the viral genome, to produce an array of capped and polyadenylated messenger RNAs, and replicating it to produce new genomes. To perform the different steps that are necessary for these processes, the nsNSV polymerases undergo a series of coordinated conformational transitions. While much is still to be learned regarding the intersection of nsNSV polymerase dynamics, structure, and function, recently published polymerase structures, combined with a history of biochemical and molecular biology studies, have provided new insights into how nsNSV polymerases function as dynamic machines. In this review, we consider each of the steps involved in nsNSV transcription and replication and suggest how these relate to solved polymerase structures.
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Affiliation(s)
- Mohamed Ouizougun-Oubari
- Department of Virology, Immunology & Microbiology, National Emerging Infectious Diseases Laboratories, Boston University Chobanian & Avedisian School of Medicine, Boston, Massachusetts, USA;
| | - Rachel Fearns
- Department of Virology, Immunology & Microbiology, National Emerging Infectious Diseases Laboratories, Boston University Chobanian & Avedisian School of Medicine, Boston, Massachusetts, USA;
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5
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The P323L substitution in the SARS-CoV-2 polymerase (NSP12) confers a selective advantage during infection. Genome Biol 2023. [PMID: 36915185 PMCID: PMC10009825 DOI: 10.1186/s13059-023-02881-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/16/2023] Open
Abstract
BACKGROUND The mutational landscape of SARS-CoV-2 varies at the dominant viral genome sequence and minor genomic variant population. During the COVID-19 pandemic, an early substitution in the genome was the D614G change in the spike protein, associated with an increase in transmissibility. Genomes with D614G are accompanied by a P323L substitution in the viral polymerase (NSP12). However, P323L is not thought to be under strong selective pressure. RESULTS Investigation of P323L/D614G substitutions in the population shows rapid emergence during the containment phase and early surge phase during the first wave. These substitutions emerge from minor genomic variants which become dominant viral genome sequence. This is investigated in vivo and in vitro using SARS-CoV-2 with P323 and D614 in the dominant genome sequence and L323 and G614 in the minor variant population. During infection, there is rapid selection of L323 into the dominant viral genome sequence but not G614. Reverse genetics is used to create two viruses (either P323 or L323) with the same genetic background. L323 shows greater abundance of viral RNA and proteins and a smaller plaque morphology than P323. CONCLUSIONS These data suggest that P323L is an important contribution in the emergence of variants with transmission advantages. Sequence analysis of viral populations suggests it may be possible to predict the emergence of a new variant based on tracking the frequency of minor variant genomes. The ability to predict an emerging variant of SARS-CoV-2 in the global landscape may aid in the evaluation of medical countermeasures and non-pharmaceutical interventions.
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6
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Sutto-Ortiz P, Eléouët JF, Ferron F, Decroly E. Biochemistry of the Respiratory Syncytial Virus L Protein Embedding RNA Polymerase and Capping Activities. Viruses 2023; 15:v15020341. [PMID: 36851554 PMCID: PMC9960070 DOI: 10.3390/v15020341] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2022] [Revised: 01/12/2023] [Accepted: 01/21/2023] [Indexed: 01/27/2023] Open
Abstract
The human respiratory syncytial virus (RSV) is a negative-sense, single-stranded RNA virus. It is the major cause of severe acute lower respiratory tract infection in infants, the elderly population, and immunocompromised individuals. There is still no approved vaccine or antiviral treatment against RSV disease, but new monoclonal prophylactic antibodies are yet to be commercialized, and clinical trials are in progress. Hence, urgent efforts are needed to develop efficient therapeutic treatments. RSV RNA synthesis comprises viral transcription and replication that are catalyzed by the large protein (L) in coordination with the phosphoprotein polymerase cofactor (P), the nucleoprotein (N), and the M2-1 transcription factor. The replication/transcription is orchestrated by the L protein, which contains three conserved enzymatic domains: the RNA-dependent RNA polymerase (RdRp), the polyribonucleotidyl transferase (PRNTase or capping), and the methyltransferase (MTase) domain. These activities are essential for the RSV replicative cycle and are thus considered as attractive targets for the development of therapeutic agents. In this review, we summarize recent findings about RSV L domains structure that highlight how the enzymatic activities of RSV L domains are interconnected, discuss the most relevant and recent antivirals developments that target the replication/transcription complex, and conclude with a perspective on identified knowledge gaps that enable new research directions.
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Affiliation(s)
| | - Jean-François Eléouët
- Unité de Virologie et Immunologie Moléculaires, INRAE, Université Paris Saclay, F78350 Jouy en Josas, France
| | - François Ferron
- Aix Marseille Université, CNRS, AFMB, UMR, 7257 Marseille, France
- European Virus Bioinformatics Center, Leutragraben 1, 07743 Jena, Germany
| | - Etienne Decroly
- Aix Marseille Université, CNRS, AFMB, UMR, 7257 Marseille, France
- Correspondence:
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Cao D, Gooneratne I, Mera C, Vy J, Royal M, Huang B, Park Y, Manjunath A, Liang B. Analysis of Template Variations on RNA Synthesis by Respiratory Syncytial Virus Polymerase. Viruses 2022; 15:47. [PMID: 36680087 PMCID: PMC9863079 DOI: 10.3390/v15010047] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2022] [Revised: 12/18/2022] [Accepted: 12/21/2022] [Indexed: 12/28/2022] Open
Abstract
Respiratory syncytial virus (RSV) is a significant threat to infants and elderly individuals globally. Currently, there are no effective therapies or treatments for RSV infection because of an insufficient understanding of the RSV viral machinery. In this study, we investigated the effects of the template variations on RNA synthesis by the RSV polymerase through in vitro RNA synthesis assays. We confirmed the previously reported back-priming activity of the RSV polymerase, which is likely due to the secondary structure of the RNA template. We found that the expansion of the hairpin loop size of the RNA template abolishes the RSV polymerase back-priming activity. At the same time, it seemingly does not affect the de novo RNA synthesis activities of the RSV polymerase. Interestingly, our results show that the RSV polymerase also has a new primer-based terminal extension activity that adds nucleotides to the template and primer in a nonspecific manner. We also mapped the impact of the RNA 5' chemical group on its mobility in a urea-denaturing RNA gel shift assay. Overall, these results enhance our knowledge about the RNA synthesis processes of the RSV polymerase and may guide future therapeutic efforts to develop effective antiviral drugs for RSV treatment.
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Affiliation(s)
| | | | | | | | | | | | | | | | - Bo Liang
- Department of Biochemistry, Emory University School of Medicine, Atlanta, GA 30322, USA
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8
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Pareek A, Kumar R, Mudgal R, Neetu N, Sharma M, Kumar P, Tomar S. Alphavirus antivirals targeting RNA‐dependent RNA polymerase domain of nsP4 divulged using surface plasmon resonance. FEBS J 2022; 289:4901-4924. [DOI: 10.1111/febs.16397] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2021] [Revised: 01/13/2022] [Accepted: 02/11/2022] [Indexed: 01/01/2023]
Affiliation(s)
- Akshay Pareek
- Department of Biosciences and Bioengineering Indian Institute of Technology Roorkee Roorkee India
| | - Ravi Kumar
- Department of Biosciences and Bioengineering Indian Institute of Technology Roorkee Roorkee India
| | - Rajat Mudgal
- Department of Biosciences and Bioengineering Indian Institute of Technology Roorkee Roorkee India
| | - Neetu Neetu
- Department of Biosciences and Bioengineering Indian Institute of Technology Roorkee Roorkee India
| | - Monica Sharma
- Department of Biosciences and Bioengineering Indian Institute of Technology Roorkee Roorkee India
| | - Pravindra Kumar
- Department of Biosciences and Bioengineering Indian Institute of Technology Roorkee Roorkee India
| | - Shailly Tomar
- Department of Biosciences and Bioengineering Indian Institute of Technology Roorkee Roorkee India
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9
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Cressey TN, Shareef AM, Kleiner VA, Noton SL, Byrne PO, McLellan JS, Mühlberger E, Fearns R. Distinctive features of the respiratory syncytial virus priming loop compared to other non-segmented negative strand RNA viruses. PLoS Pathog 2022; 18:e1010451. [PMID: 35731802 PMCID: PMC9255747 DOI: 10.1371/journal.ppat.1010451] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2022] [Revised: 07/05/2022] [Accepted: 05/20/2022] [Indexed: 11/23/2022] Open
Abstract
De novo initiation by viral RNA-dependent RNA polymerases often requires a polymerase priming residue, located within a priming loop, to stabilize the initiating NTPs. Polymerase structures from three different non-segmented negative strand RNA virus (nsNSV) families revealed putative priming loops in different conformations, and an aromatic priming residue has been identified in the rhabdovirus polymerase. In a previous study of the respiratory syncytial virus (RSV) polymerase, we found that Tyr1276, the L protein aromatic amino acid residue that most closely aligns with the rhabdovirus priming residue, is not required for RNA synthesis but two nearby residues, Pro1261 and Trp1262, were required. In this study, we examined the roles of Pro1261 and Trp1262 in RNA synthesis initiation. Biochemical studies showed that substitution of Pro1261 inhibited RNA synthesis initiation without inhibiting back-priming, indicating a defect in initiation. Biochemical and minigenome experiments showed that the initiation defect incurred by a P1261A substitution could be rescued by factors that would be expected to increase the stability of the initiation complex, specifically increased NTP concentration, manganese, and a more efficient promoter sequence. These findings indicate that Pro1261 of the RSV L protein plays a role in initiation, most likely in stabilizing the initiation complex. However, we found that substitution of the corresponding proline residue in a filovirus polymerase had no effect on RNA synthesis initiation or elongation. These results indicate that despite similarities between the nsNSV polymerases, there are differences in the features required for RNA synthesis initiation. RSV has a significant impact on human health. It is the major cause of respiratory disease in infants and exerts a significant toll on the elderly and immunocompromised. RSV is a member of the Mononegavirales, the non-segmented, negative strand RNA viruses (nsNSVs). Like other viruses in this order, RSV encodes an RNA dependent RNA polymerase, which is responsible for transcribing and replicating the viral genome. Due to its essential role during the viral replication cycle, the polymerase is a promising candidate target for antiviral inhibitors and so a greater understanding of the mechanistic basis of its activities could aid antiviral drug development. In this study, we identified an amino acid residue within the RSV polymerase that appears to stabilize the RNA synthesis initiation complex and showed that it plays a role in both transcription and RNA replication. However, the corresponding residue in a different nsNSV polymerase does not appear to play a similar role. This work reveals a key feature of the RSV polymerase but identifies differences with the polymerases of other related viruses.
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Affiliation(s)
- Tessa N. Cressey
- Department of Microbiology, Boston University School of Medicine, Boston, Massachusetts, United States of America
- National Emerging Infectious Diseases Laboratories (NEIDL), Boston University, Boston, Massachusetts, United States of America
| | - Afzaal M. Shareef
- Department of Microbiology, Boston University School of Medicine, Boston, Massachusetts, United States of America
- National Emerging Infectious Diseases Laboratories (NEIDL), Boston University, Boston, Massachusetts, United States of America
| | - Victoria A. Kleiner
- Department of Microbiology, Boston University School of Medicine, Boston, Massachusetts, United States of America
- National Emerging Infectious Diseases Laboratories (NEIDL), Boston University, Boston, Massachusetts, United States of America
| | - Sarah L. Noton
- Department of Microbiology, Boston University School of Medicine, Boston, Massachusetts, United States of America
- National Emerging Infectious Diseases Laboratories (NEIDL), Boston University, Boston, Massachusetts, United States of America
| | - Patrick O. Byrne
- Department of Molecular Biosciences, The University of Texas at Austin, Austin, Texas, United States of America
| | - Jason S. McLellan
- Department of Molecular Biosciences, The University of Texas at Austin, Austin, Texas, United States of America
| | - Elke Mühlberger
- Department of Microbiology, Boston University School of Medicine, Boston, Massachusetts, United States of America
- National Emerging Infectious Diseases Laboratories (NEIDL), Boston University, Boston, Massachusetts, United States of America
| | - Rachel Fearns
- Department of Microbiology, Boston University School of Medicine, Boston, Massachusetts, United States of America
- National Emerging Infectious Diseases Laboratories (NEIDL), Boston University, Boston, Massachusetts, United States of America
- * E-mail:
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10
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Comparison of RNA synthesis initiation properties of non-segmented negative strand RNA virus polymerases. PLoS Pathog 2021; 17:e1010151. [PMID: 34914795 PMCID: PMC8717993 DOI: 10.1371/journal.ppat.1010151] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2021] [Revised: 12/30/2021] [Accepted: 11/26/2021] [Indexed: 11/19/2022] Open
Abstract
It is generally thought that the promoters of non-segmented, negative strand RNA viruses (nsNSVs) direct the polymerase to initiate RNA synthesis exclusively opposite the 3´ terminal nucleotide of the genome RNA by a de novo (primer independent) initiation mechanism. However, recent studies have revealed that there is diversity between different nsNSVs with pneumovirus promoters directing the polymerase to initiate at positions 1 and 3 of the genome, and ebolavirus polymerases being able to initiate at position 2 on the template. Studies with other RNA viruses have shown that polymerases that engage in de novo initiation opposite position 1 typically have structural features to stabilize the initiation complex and ensure efficient and accurate initiation. This raised the question of whether different nsNSV polymerases have evolved fundamentally different structural properties to facilitate initiation at different sites on their promoters. Here we examined the functional properties of polymerases of respiratory syncytial virus (RSV), a pneumovirus, human parainfluenza virus type 3 (PIV-3), a paramyxovirus, and Marburg virus (MARV), a filovirus, both on their cognate promoters and on promoters of other viruses. We found that in contrast to the RSV polymerase, which initiated at positions 1 and 3 of its promoter, the PIV-3 and MARV polymerases initiated exclusively at position 1 on their cognate promoters. However, all three polymerases could recognize and initiate from heterologous promoters, with the promoter sequence playing a key role in determining initiation site selection. In addition to examining de novo initiation, we also compared the ability of the RSV and PIV-3 polymerases to engage in back-priming, an activity in which the promoter template is folded into a secondary structure and nucleotides are added to the template 3´ end. This analysis showed that whereas the RSV polymerase was promiscuous in back-priming activity, the PIV-3 polymerase generated barely detectable levels of back-primed product, irrespective of promoter template sequence. Overall, this study shows that the polymerases from these three nsNSV families are fundamentally similar in their initiation properties, but have differences in their abilities to engage in back-priming.
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11
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In Vitro Primer-Based RNA Elongation and Promoter Fine Mapping of the Respiratory Syncytial Virus. J Virol 2020; 95:JVI.01897-20. [PMID: 33028717 PMCID: PMC7737744 DOI: 10.1128/jvi.01897-20] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2020] [Accepted: 09/29/2020] [Indexed: 11/20/2022] Open
Abstract
Respiratory syncytial virus (RSV) is a nonsegmented negative-sense (NNS) RNA virus and shares a similar RNA synthesis strategy with other members of NNS RNA viruses, such as measles, rabies virus, and Ebola virus. RSV RNA synthesis is catalyzed by a multifunctional RNA-dependent RNA polymerase (RdRP), which is composed of a large (L) protein that catalyzes three distinct enzymatic functions and an essential coenzyme phosphoprotein (P). Here, we successfully prepared highly pure, full-length, wild-type and mutant RSV polymerase (L-P) complexes. We demonstrated that the RSV polymerase could carry out both de novo and primer-based RNA synthesis. We defined the minimal length of the RNA template for in vitro de novo RNA synthesis using the purified RSV polymerase as 8 nucleotides (nt), shorter than previously reported. We showed that the RSV polymerase catalyzed primer-dependent RNA elongation with different lengths of primers on both short (10-nt) and long (25-nt) RNA templates. We compared the sequence specificity of different viral promoters and identified positions 3, 5, and 8 of the promoter sequence as essential to the in vitro RSV polymerase activity, consistent with the results previously mapped with the in vivo minigenome assay. Overall, these findings agree well with those of previous biochemical studies and extend our understanding of the promoter sequence and the mechanism of RSV RNA synthesis.IMPORTANCE As a major human pathogen, RSV affects 3.4 million children worldwide annually. However, no effective antivirals or vaccines are available. An in-depth mechanistic understanding of the RSV RNA synthesis machinery remains a high priority among the NNS RNA viruses. There is a strong public health need for research on this virus, due to major fundamental gaps in our understanding of NNS RNA virus replication. As the key enzyme executing transcription and replication of the virus, the RSV RdRP is a logical target for novel antiviral drugs. Therefore, exploring the primer-dependent RNA elongation extends our mechanistic understanding of the RSV RNA synthesis. Further fine mapping of the promoter sequence paves the way to better understand the function and structure of the RSV polymerase.
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12
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Gao Y, Cao D, Ahn HM, Swain A, Hill S, Ogilvie C, Kurien M, Rahmatullah T, Liang B. In vitro trackable assembly of RNA-specific nucleocapsids of the respiratory syncytial virus. J Biol Chem 2020. [DOI: 10.1016/s0021-9258(17)49942-x] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/22/2022] Open
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13
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Gao Y, Cao D, Ahn HM, Swain A, Hill S, Ogilvie C, Kurien M, Rahmatullah T, Liang B. In vitro trackable assembly of RNA-specific nucleocapsids of the respiratory syncytial virus. J Biol Chem 2019; 295:883-895. [PMID: 31822560 PMCID: PMC6970927 DOI: 10.1074/jbc.ra119.011602] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/23/2019] [Revised: 11/26/2019] [Indexed: 12/25/2022] Open
Abstract
The templates for transcription and replication by respiratory syncytial virus (RSV) polymerase are helical nucleocapsids (NCs), formed by viral RNAs that are encapsidated by the nucleoprotein (N). Proper NC assembly is vital for RSV polymerase to engage the RNA template for RNA synthesis. Previous studies of NCs or nucleocapsid-like particles (NCLPs) from RSV and other nonsegmented negative-sense RNA viruses have provided insights into the overall NC architecture. However, in these studies, the RNAs were either random cellular RNAs or average viral genomic RNAs. An in-depth mechanistic understanding of NCs has been hampered by lack of an in vitro assay that can track NC or NCLP assembly. Here we established a protocol to obtain RNA-free N protein (N0) and successfully demonstrated the utility of a new assay for tracking assembly of N with RNA oligonucleotides into NCLPs. We discovered that the efficiency of the NCLP (N–RNA) assembly depends on the length and sequence of the RNA incorporated into NCLPs. This work provides a framework to generate purified N0 and incorporate it with RNA into NCLPs in a controllable manner. We anticipate that our assay for in vitro trackable assembly of RSV-specific nucleocapsids may enable in-depth mechanistic analyses of this process.
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Affiliation(s)
- Yunrong Gao
- Department of Biochemistry, Emory University School of Medicine, Atlanta, Georgia 30322
| | - Dongdong Cao
- Department of Biochemistry, Emory University School of Medicine, Atlanta, Georgia 30322
| | - Hyunjun Max Ahn
- Department of Biochemistry, Emory University School of Medicine, Atlanta, Georgia 30322
| | - Anshuman Swain
- Department of Biochemistry, Emory University School of Medicine, Atlanta, Georgia 30322
| | - Shaylan Hill
- Department of Biochemistry, Emory University School of Medicine, Atlanta, Georgia 30322
| | - Claire Ogilvie
- Department of Biochemistry, Emory University School of Medicine, Atlanta, Georgia 30322
| | - Matthew Kurien
- Department of Biochemistry, Emory University School of Medicine, Atlanta, Georgia 30322
| | - Taha Rahmatullah
- Department of Biochemistry, Emory University School of Medicine, Atlanta, Georgia 30322
| | - Bo Liang
- Department of Biochemistry, Emory University School of Medicine, Atlanta, Georgia 30322
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14
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Ludeke B, Fearns R. The respiratory syncytial virus polymerase can perform RNA synthesis with modified primers and nucleotide analogs. Virology 2019; 540:66-74. [PMID: 31739186 DOI: 10.1016/j.virol.2019.11.002] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2019] [Revised: 11/03/2019] [Accepted: 11/03/2019] [Indexed: 12/29/2022]
Abstract
Respiratory syncytial virus (RSV) is significant for public health, capable of causing respiratory tract disease in infants, the elderly and the immunocompromised. The RSV polymerase is an attractive target for antiviral drug development, but as yet, there is no high throughput assay for analyzing RSV polymerase activity, specifically. In this study, using a primer elongation assay as a basis, we analyzed the tolerance of the RSV polymerase for modifications at the 5' end of the primer, and nucleotide analogs. The RSV polymerase was found to accept primers containing 5' biotin or digoxygenin modifications, and nucleotide analogs that are reactive or fluorescent, including 5-ethynyl UTP, 8-azido ATP, 2-amino PTP, and thieno-GTP. These findings provide a menu of options for developing non-isotopic high throughput assays for RSV polymerase RNA synthesis activity, and yield insight regarding the molecular biology of the polymerase complex.
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Affiliation(s)
- Barbara Ludeke
- Department of Microbiology, Boston University School of Medicine, Boston, MA, USA; National Emerging Infectious Diseases Laboratories, Boston University, Boston, MA, USA
| | - Rachel Fearns
- Department of Microbiology, Boston University School of Medicine, Boston, MA, USA; National Emerging Infectious Diseases Laboratories, Boston University, Boston, MA, USA.
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15
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Gilman MSA, Liu C, Fung A, Behera I, Jordan P, Rigaux P, Ysebaert N, Tcherniuk S, Sourimant J, Eléouët JF, Sutto-Ortiz P, Decroly E, Roymans D, Jin Z, McLellan JS. Structure of the Respiratory Syncytial Virus Polymerase Complex. Cell 2019; 179:193-204.e14. [PMID: 31495574 PMCID: PMC7111336 DOI: 10.1016/j.cell.2019.08.014] [Citation(s) in RCA: 87] [Impact Index Per Article: 17.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2019] [Revised: 08/03/2019] [Accepted: 08/06/2019] [Indexed: 01/29/2023]
Abstract
Numerous interventions are in clinical development for respiratory syncytial virus (RSV) infection, including small molecules that target viral transcription and replication. These processes are catalyzed by a complex comprising the RNA-dependent RNA polymerase (L) and the tetrameric phosphoprotein (P). RSV P recruits multiple proteins to the polymerase complex and, with the exception of its oligomerization domain, is thought to be intrinsically disordered. Despite their critical roles in RSV transcription and replication, structures of L and P have remained elusive. Here, we describe the 3.2-Å cryo-EM structure of RSV L bound to tetrameric P. The structure reveals a striking tentacular arrangement of P, with each of the four monomers adopting a distinct conformation. The structure also rationalizes inhibitor escape mutants and mutations observed in live-attenuated vaccine candidates. These results provide a framework for determining the molecular underpinnings of RSV replication and transcription and should facilitate the design of effective RSV inhibitors.
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Affiliation(s)
- Morgan S A Gilman
- Department of Molecular Biosciences, University of Texas at Austin, Austin, TX 78712, USA
| | - Cheng Liu
- Janssen BioPharma, Inc., Janssen Pharmaceutical Companies, South San Francisco, CA 94080, USA
| | - Amy Fung
- Janssen BioPharma, Inc., Janssen Pharmaceutical Companies, South San Francisco, CA 94080, USA
| | - Ishani Behera
- Janssen BioPharma, Inc., Janssen Pharmaceutical Companies, South San Francisco, CA 94080, USA
| | - Paul Jordan
- Janssen BioPharma, Inc., Janssen Pharmaceutical Companies, South San Francisco, CA 94080, USA
| | - Peter Rigaux
- Janssen Infectious Diseases and Vaccines, 2340 Beerse, Belgium
| | - Nina Ysebaert
- Janssen Infectious Diseases and Vaccines, 2340 Beerse, Belgium
| | - Sergey Tcherniuk
- Unité de Virologie et Immunologie Moléculaires, INRA, Université Paris Saclay, 78350 Jouy en Josas, France
| | - Julien Sourimant
- Unité de Virologie et Immunologie Moléculaires, INRA, Université Paris Saclay, 78350 Jouy en Josas, France
| | - Jean-François Eléouët
- Unité de Virologie et Immunologie Moléculaires, INRA, Université Paris Saclay, 78350 Jouy en Josas, France
| | | | - Etienne Decroly
- Aix Marseille Université, CNRS, AFMB UMR 7257, Marseille, France
| | - Dirk Roymans
- Janssen Infectious Diseases and Vaccines, 2340 Beerse, Belgium
| | - Zhinan Jin
- Janssen BioPharma, Inc., Janssen Pharmaceutical Companies, South San Francisco, CA 94080, USA
| | - Jason S McLellan
- Department of Molecular Biosciences, University of Texas at Austin, Austin, TX 78712, USA.
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16
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Cressey TN, Noton SL, Nagendra K, Braun MR, Fearns R. Mechanism for de novo initiation at two sites in the respiratory syncytial virus promoter. Nucleic Acids Res 2019; 46:6785-6796. [PMID: 29873775 PMCID: PMC6061868 DOI: 10.1093/nar/gky480] [Citation(s) in RCA: 21] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2018] [Accepted: 05/17/2018] [Indexed: 12/18/2022] Open
Abstract
The respiratory syncytial virus (RSV) RNA dependent RNA polymerase (RdRp) initiates two RNA synthesis processes from the viral promoter: genome replication from position 1U and mRNA transcription from position 3C. Here, we examined the mechanism by which a single promoter can direct initiation from two sites. We show that initiation at 1U and 3C occurred independently of each other, and that the same RdRp was capable of precisely selecting the two sites. The RdRp preferred to initiate at 3C, but initiation site selection could be modulated by the relative concentrations of ATP versus GTP. Analysis of template mutations indicated that the RdRp could bind ATP and CTP, or GTP, independently of template nucleotides. The data suggest a model in which innate affinity of the RdRp for particular NTPs, coupled with a repeating element within the promoter, allows precise initiation of replication at 1U or transcription at 3C.
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Affiliation(s)
- Tessa N Cressey
- Department of Microbiology, Boston University School of Medicine, Boston, MA 02118, USA
| | - Sarah L Noton
- Department of Microbiology, Boston University School of Medicine, Boston, MA 02118, USA
| | - Kartikeya Nagendra
- Department of Microbiology, Boston University School of Medicine, Boston, MA 02118, USA
| | - Molly R Braun
- Department of Microbiology, Boston University School of Medicine, Boston, MA 02118, USA
| | - Rachel Fearns
- Department of Microbiology, Boston University School of Medicine, Boston, MA 02118, USA
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17
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Noton SL, Tremaglio CZ, Fearns R. Killing two birds with one stone: How the respiratory syncytial virus polymerase initiates transcription and replication. PLoS Pathog 2019; 15:e1007548. [PMID: 30817806 PMCID: PMC6394897 DOI: 10.1371/journal.ppat.1007548] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/16/2023] Open
Affiliation(s)
- Sarah L. Noton
- Department of Microbiology, Boston University School of Medicine, Boston, Massachusetts, United States of America
| | - Chadene Z. Tremaglio
- Department of Biology, University of Saint Joseph, West Hartford, Connecticut, United States of America
| | - Rachel Fearns
- Department of Microbiology, Boston University School of Medicine, Boston, Massachusetts, United States of America
- * E-mail:
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18
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Jordan PC, Liu C, Raynaud P, Lo MK, Spiropoulou CF, Symons JA, Beigelman L, Deval J. Initiation, extension, and termination of RNA synthesis by a paramyxovirus polymerase. PLoS Pathog 2018; 14:e1006889. [PMID: 29425244 PMCID: PMC5823471 DOI: 10.1371/journal.ppat.1006889] [Citation(s) in RCA: 88] [Impact Index Per Article: 14.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2017] [Revised: 02/22/2018] [Accepted: 01/21/2018] [Indexed: 01/27/2023] Open
Abstract
Paramyxoviruses represent a family of RNA viruses causing significant human diseases. These include measles virus, the most infectious virus ever reported, in addition to parainfluenza virus, and other emerging viruses. Paramyxoviruses likely share common replication machinery but their mechanisms of RNA biosynthesis activities and details of their complex polymerase structures are unknown. Mechanistic and functional details of a paramyxovirus polymerase would have sweeping implications for understanding RNA virus replication and for the development of new antiviral medicines. To study paramyxovirus polymerase structure and function, we expressed an active recombinant Nipah virus (NiV) polymerase complex assembled from the multifunctional NiV L protein bound to its phosphoprotein cofactor. NiV is an emerging highly pathogenic virus that causes severe encephalitis and has been declared a global public health concern due to its high mortality rate. Using negative-stain electron microscopy, we demonstrated NiV polymerase forms ring-like particles resembling related RNA polymerases. We identified conserved sequence elements driving recognition of the 3′-terminal genomic promoter by NiV polymerase, and leading to initiation of RNA synthesis, primer extension, and transition to elongation mode. Polyadenylation resulting from NiV polymerase stuttering provides a mechanistic basis for transcription termination. It also suggests a divergent adaptation in promoter recognition between pneumo- and paramyxoviruses. The lack of available antiviral therapy for NiV prompted us to identify the triphosphate forms of R1479 and GS-5734, two clinically relevant nucleotide analogs, as substrates and inhibitors of NiV polymerase activity by delayed chain termination. Overall, these findings provide low-resolution structural details and the mechanism of an RNA polymerase from a previously uncharacterized virus family. This work illustrates important functional differences yet remarkable similarities between the polymerases of nonsegmented negative-strand RNA viruses. RNA viruses replicate and transcribe their genomes using complex enzymatic machines known as RNA-dependent RNA polymerases. The chemical reactions driving nucleotide addition are shared among nucleic acid polymerases but the underlying mechanisms of RNA biosynthesis and the complex polymerase structures are diverse. Of these RNA viruses is the paramyxovirus family, which includes major human pathogens. Paramyxoviruses have common biological and genetic properties but little is known about their replication machinery. Insights into the structure, function, and mechanisms of RNA synthesis of one paramyxovirus polymerase will likely extend to the entire virus family. An emerging, highly pathogenic paramyxovirus is Nipah virus (NiV), which causes encephalitis in humans. We have purified NiV polymerase, probed its enzymatic and biophysical properties and developed it as a model paramyxovirus polymerase. We investigated template strand sequence elements driving RNA biosynthesis for NiV polymerase and obtained a snapshot of NiV polymerase molecular organization using electron microscopy to provide the first structural information on a paramyxovirus polymerase. This work extends previous knowledge by producing the first recombinant paramyxovirus polymerase and using this protein in enzymatic assays to highlight key functional and structural characteristics for the design of new medicines.
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Affiliation(s)
- Paul C. Jordan
- Alios BioPharma, Inc. a Janssen Pharmaceutical Company of Johnson & Johnson, South San Francisco, California, United States of America
| | - Cheng Liu
- Alios BioPharma, Inc. a Janssen Pharmaceutical Company of Johnson & Johnson, South San Francisco, California, United States of America
| | - Pauline Raynaud
- Alios BioPharma, Inc. a Janssen Pharmaceutical Company of Johnson & Johnson, South San Francisco, California, United States of America
| | - Michael K. Lo
- Centers for Disease Control and Prevention, Atlanta, Georgia, United States of America
| | | | - Julian A. Symons
- Alios BioPharma, Inc. a Janssen Pharmaceutical Company of Johnson & Johnson, South San Francisco, California, United States of America
| | - Leo Beigelman
- Alios BioPharma, Inc. a Janssen Pharmaceutical Company of Johnson & Johnson, South San Francisco, California, United States of America
| | - Jerome Deval
- Alios BioPharma, Inc. a Janssen Pharmaceutical Company of Johnson & Johnson, South San Francisco, California, United States of America
- * E-mail:
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19
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Braun MR, Deflubé LR, Noton SL, Mawhorter ME, Tremaglio CZ, Fearns R. RNA elongation by respiratory syncytial virus polymerase is calibrated by conserved region V. PLoS Pathog 2017; 13:e1006803. [PMID: 29281742 PMCID: PMC5760109 DOI: 10.1371/journal.ppat.1006803] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2017] [Revised: 01/09/2018] [Accepted: 12/11/2017] [Indexed: 02/06/2023] Open
Abstract
The large polymerase subunit (L) of non-segmented negative strand RNA viruses transcribes viral mRNAs and replicates the viral genome. Studies with VSV have shown that conserved region V (CRV) of the L protein is part of the capping domain. However, CRV folds over and protrudes into the polymerization domain, suggesting that it might also have a role in RNA synthesis. In this study, the role of respiratory syncytial virus (RSV) CRV was evaluated using single amino acid substitutions and a small molecule inhibitor called BI-D. Effects were analyzed using cell-based minigenome and in vitro biochemical assays. Several amino acid substitutions inhibited production of capped, full-length mRNA and instead resulted in accumulation of short transcripts of approximately 40 nucleotides in length, confirming that RSV CRV has a role in capping. In addition, all six variants tested were either partially or completely defective in RNA replication. This was due to an inability of the polymerase to efficiently elongate the RNA within the promoter region. BI-D also inhibited transcription and replication. In this case, polymerase elongation activity within the promoter region was enhanced, such that the small RNA transcribed from the promoter was not released and instead was elongated past the first gene start signal. This was accompanied by a decrease in mRNA initiation at the first gene start signal and accumulation of aberrant RNAs of varying length. Thus, in addition to its function in mRNA capping, conserved region V modulates the elongation properties of the polymerase to enable productive transcription and replication to occur.
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MESH Headings
- Amino Acid Sequence
- Amino Acid Substitution
- Antiviral Agents/pharmacology
- Cell Line
- Conserved Sequence
- Drug Discovery
- Genes, Viral
- Humans
- Models, Molecular
- Promoter Regions, Genetic
- RNA Caps/genetics
- RNA Caps/metabolism
- RNA, Messenger/genetics
- RNA, Messenger/metabolism
- RNA, Viral/genetics
- RNA, Viral/metabolism
- RNA-Dependent RNA Polymerase/chemistry
- RNA-Dependent RNA Polymerase/genetics
- RNA-Dependent RNA Polymerase/metabolism
- Respiratory Syncytial Virus Infections/drug therapy
- Respiratory Syncytial Virus Infections/virology
- Respiratory Syncytial Virus, Human/genetics
- Respiratory Syncytial Virus, Human/metabolism
- Respiratory Syncytial Virus, Human/pathogenicity
- Transcription Elongation, Genetic
- Viral Proteins/chemistry
- Viral Proteins/genetics
- Viral Proteins/metabolism
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Affiliation(s)
- Molly R. Braun
- Department of Microbiology, Boston University School of Medicine, Boston, MA, United States of America
| | - Laure R. Deflubé
- Department of Microbiology, Boston University School of Medicine, Boston, MA, United States of America
| | - Sarah L. Noton
- Department of Microbiology, Boston University School of Medicine, Boston, MA, United States of America
| | - Michael E. Mawhorter
- Department of Microbiology, Boston University School of Medicine, Boston, MA, United States of America
| | - Chadene Z. Tremaglio
- Department of Microbiology, Boston University School of Medicine, Boston, MA, United States of America
| | - Rachel Fearns
- Department of Microbiology, Boston University School of Medicine, Boston, MA, United States of America
- * E-mail:
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20
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Respiratory Syncytial Virus: Infection, Detection, and New Options for Prevention and Treatment. Clin Microbiol Rev 2017; 30:277-319. [PMID: 27903593 DOI: 10.1128/cmr.00010-16] [Citation(s) in RCA: 342] [Impact Index Per Article: 48.9] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022] Open
Abstract
Respiratory syncytial virus (RSV) infection is a significant cause of hospitalization of children in North America and one of the leading causes of death of infants less than 1 year of age worldwide, second only to malaria. Despite its global impact on human health, there are relatively few therapeutic options available to prevent or treat RSV infection. Paradoxically, there is a very large volume of information that is constantly being refined on RSV replication, the mechanisms of RSV-induced pathology, and community transmission. Compounding the burden of acute RSV infections is the exacerbation of preexisting chronic airway diseases and the chronic sequelae of RSV infection. A mechanistic link is even starting to emerge between asthma and those who suffer severe RSV infection early in childhood. In this article, we discuss developments in the understanding of RSV replication, pathogenesis, diagnostics, and therapeutics. We attempt to reconcile the large body of information on RSV and why after many clinical trials there is still no efficacious RSV vaccine and few therapeutics.
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21
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Duvall JR, VerPlank L, Ludeke B, McLeod SM, Lee MD, Vishwanathan K, Mulrooney CA, Le Quement S, Yu Q, Palmer MA, Fleming P, Fearns R, Foley MA, Scherer CA. Novel diversity-oriented synthesis-derived respiratory syncytial virus inhibitors identified via a high throughput replicon-based screen. Antiviral Res 2016; 131:19-25. [PMID: 27059228 DOI: 10.1016/j.antiviral.2016.03.015] [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: 07/17/2015] [Revised: 03/27/2016] [Accepted: 03/29/2016] [Indexed: 01/23/2023]
Abstract
Respiratory syncytial virus (RSV) infections affect millions of children and adults every year. Despite the significant disease burden, there are currently no safe and effective vaccines or therapeutics. We employed a replicon-based high throughput screen combined with live-virus triaging assays to identify three novel diversity-oriented synthesis-derived scaffolds with activity against RSV. One of these small molecules is shown to target the RSV polymerase (L protein) to inhibit viral replication and transcription; the mechanisms of action of the other small molecules are currently unknown. The compounds described herein may provide attractive inhibitors for lead optimization campaigns.
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Affiliation(s)
- Jeremy R Duvall
- Broad Institute of MIT and Harvard, 415 Main St., Cambridge, MA 02142, United States
| | - Lynn VerPlank
- Broad Institute of MIT and Harvard, 415 Main St., Cambridge, MA 02142, United States
| | - Barbara Ludeke
- Boston University School of Medicine, 72 East Concord Street, Boston, MA 02118, United States
| | - Sarah M McLeod
- AstraZeneca R&D Boston, Infection Innovative Medicines Unit, 35 Gatehouse Drive, Waltham, MA 02451, United States
| | - Maurice D Lee
- Broad Institute of MIT and Harvard, 415 Main St., Cambridge, MA 02142, United States
| | - Karthick Vishwanathan
- AstraZeneca R&D Boston, Early Clinical Development, 35 Gatehouse Drive, Waltham, MA 02451, United States
| | - Carol A Mulrooney
- Broad Institute of MIT and Harvard, 415 Main St., Cambridge, MA 02142, United States
| | - Sebastian Le Quement
- Broad Institute of MIT and Harvard, 415 Main St., Cambridge, MA 02142, United States
| | - Qin Yu
- AstraZeneca R&D Boston, Infection Innovative Medicines Unit, 35 Gatehouse Drive, Waltham, MA 02451, United States
| | - Michelle A Palmer
- Broad Institute of MIT and Harvard, 415 Main St., Cambridge, MA 02142, United States
| | - Paul Fleming
- AstraZeneca R&D Boston, Infection Innovative Medicines Unit, 35 Gatehouse Drive, Waltham, MA 02451, United States
| | - Rachel Fearns
- Boston University School of Medicine, 72 East Concord Street, Boston, MA 02118, United States
| | - Michael A Foley
- Broad Institute of MIT and Harvard, 415 Main St., Cambridge, MA 02142, United States
| | - Christina A Scherer
- Broad Institute of MIT and Harvard, 415 Main St., Cambridge, MA 02142, United States.
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22
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Respiratory Syncytial Virus Inhibitor AZ-27 Differentially Inhibits Different Polymerase Activities at the Promoter. J Virol 2015; 89:7786-98. [PMID: 25995255 DOI: 10.1128/jvi.00530-15] [Citation(s) in RCA: 41] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2015] [Accepted: 05/11/2015] [Indexed: 11/20/2022] Open
Abstract
UNLABELLED Respiratory syncytial virus (RSV) is the leading cause of pediatric respiratory disease. RSV has an RNA-dependent RNA polymerase that transcribes and replicates the viral negative-sense RNA genome. The large polymerase subunit (L) has multiple enzymatic activities, having the capability to synthesize RNA and add and methylate a cap on each of the viral mRNAs. Previous studies (H. Xiong et al., Bioorg Med Chem Lett, 23:6789-6793, 2013, http://dx.doi.org/10.1016/j.bmcl.2013.10.018; C. L. Tiong-Yip et al., Antimicrob Agents Chemother, 58:3867-3873, 2014, http://dx.doi.org/10.1128/AAC.02540-14) had identified a small-molecule inhibitor, AZ-27, that targets the L protein. In this study, we examined the effect of AZ-27 on different aspects of RSV polymerase activity. AZ-27 was found to inhibit equally both mRNA transcription and genome replication in cell-based minigenome assays, indicating that it inhibits a step common to both of these RNA synthesis processes. Analysis in an in vitro transcription run-on assay, containing RSV nucleocapsids, showed that AZ-27 inhibits synthesis of transcripts from the 3' end of the genome to a greater extent than those from the 5' end, indicating that it inhibits transcription initiation. Consistent with this finding, experiments that assayed polymerase activity on the promoter showed that AZ-27 inhibited transcription and replication initiation. The RSV polymerase also can utilize the promoter sequence to perform a back-priming reaction. Interestingly, addition of AZ-27 had no effect on the addition of up to three nucleotides by back-priming but inhibited further extension of the back-primed RNA. These data provide new information regarding the mechanism of inhibition by AZ-27. They also suggest that the RSV polymerase adopts different conformations to perform its different activities at the promoter. IMPORTANCE Currently, there are no effective antiviral drugs to treat RSV infection. The RSV polymerase is an attractive target for drug development, but this large enzymatic complex is poorly characterized, hampering drug development efforts. AZ-27 is a small-molecule inhibitor previously shown to target the RSV large polymerase subunit (C. L. Tiong-Yip et al., Antimicrob Agents Chemother, 58:3867-3873, 2014, http://dx.doi.org/10.1128/AAC.02540-14), but its inhibitory mechanism was unknown. Understanding this would be valuable both for characterizing the polymerase and for further development of inhibitors. Here, we show that AZ-27 inhibits an early stage in mRNA transcription, as well as genome replication, by inhibiting initiation of RNA synthesis from the promoter. However, the compound does not inhibit back priming, another RNA synthesis activity of the RSV polymerase. These findings provide insight into the different activities of the RSV polymerase and will aid further development of antiviral agents against RSV.
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23
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Cox R, Plemper RK. The paramyxovirus polymerase complex as a target for next-generation anti-paramyxovirus therapeutics. Front Microbiol 2015; 6:459. [PMID: 26029193 PMCID: PMC4428208 DOI: 10.3389/fmicb.2015.00459] [Citation(s) in RCA: 38] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2015] [Accepted: 04/27/2015] [Indexed: 12/04/2022] Open
Abstract
The paramyxovirus family includes major human and animal pathogens, including measles virus, mumps virus, and human respiratory syncytial virus (RSV), as well as the emerging zoonotic Hendra and Nipah viruses. In the U.S., RSV is the leading cause of infant hospitalizations due to viral infectious disease. Despite their clinical significance, effective drugs for the improved management of paramyxovirus disease are lacking. The development of novel anti-paramyxovirus therapeutics is therefore urgently needed. Paramyxoviruses contain RNA genomes of negative polarity, necessitating a virus-encoded RNA-dependent RNA polymerase (RdRp) complex for replication and transcription. Since an equivalent enzymatic activity is absent in host cells, the RdRp complex represents an attractive druggable target, although structure-guided drug development campaigns are hampered by the lack of high-resolution RdRp crystal structures. Here, we review the current structural and functional insight into the paramyxovirus polymerase complex in conjunction with an evaluation of the mechanism of activity and developmental status of available experimental RdRp inhibitors. Our assessment spotlights the importance of the RdRp complex as a premier target for therapeutic intervention and examines how high-resolution insight into the organization of the complex will pave the path toward the structure-guided design and optimization of much-needed next-generation paramyxovirus RdRp blockers.
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Affiliation(s)
- Robert Cox
- Institute for Biomedical Sciences, Petit Science Center, Georgia State University, Atlanta, GA USA
| | - Richard K Plemper
- Institute for Biomedical Sciences, Petit Science Center, Georgia State University, Atlanta, GA USA
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24
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Niyomrattanakit P, Wan KF, Chung KY, Abas SN, Seh CC, Dong H, Lim CC, Chao AT, Lee CB, Nilar S, Lescar J, Shi PY, Beer D, Lim SP. Stabilization of dengue virus polymerase in de novo initiation assay provides advantages for compound screening. Antiviral Res 2015; 119:36-46. [PMID: 25896272 DOI: 10.1016/j.antiviral.2015.04.007] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2015] [Revised: 04/08/2015] [Accepted: 04/12/2015] [Indexed: 02/06/2023]
Abstract
Dengue virus (DENV) NS5 protein comprises an N-terminal methyltransferase domain and a C-terminal RNA-dependent RNA polymerase domain (RdRp). DENV RdRp is responsible for viral RNA synthesis via a de novo initiation mechanism and represents an attractive target for anti-viral therapy. Herein we describe the characterization of its de novo initiation activities by PAGE analyses and the knowledge gained was used to develop a fluorescent-based assay. A highly processive and robust assay was achieved by addition of cysteine in the assay buffer. This stabilized the apo-enzyme, and rendered optimal de novo initiation activity while balancing its intrinsic terminal transferase activity. Steady-state kinetic parameters of the NTP and RNA substrates under these optimal conditions were determined for DENV1-4 FL NS5. Heavy metal ions such as Zn(++) and Co(++) as well as high levels of monovalent salts, suppressed DENV polymerase de novo initiation activities. This assay was validated with nucleotide chain terminators and used to screen two diverse small library sets. The screen data obtained was further compared with concurrent screens performed with a DENV polymerase elongation fluorescent assay utilizing pre-complexed enzyme-RNA. A higher hit-rate was obtained for the de novo initiation assay compared to the elongation assay (∼2% versus ∼0.1%). All the hits from the latter assay are also identified in the de novo initiation assay, indicating that the de novo initiation assay performed with the stabilized apo-enzyme has the advantage of providing additional chemical starting entities for inhibiting this enzyme.
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Affiliation(s)
- Pornwaratt Niyomrattanakit
- Novartis Institute for Tropical Diseases, Singapore; Maveta Company Limited, 26/522 Paholyothin 62/1 S, Saimai, Bangkok 10220, Thailand(1)
| | - Kah Fei Wan
- Novartis Institute for Tropical Diseases, Singapore.
| | - Ka Yan Chung
- Novartis Institute for Tropical Diseases, Singapore; Division of Structural Biology and Biochemistry, School of Biological Sciences, Nanyang Technological University, Singapore
| | | | | | | | | | | | | | - Shahul Nilar
- Novartis Institute for Tropical Diseases, Singapore
| | - Julien Lescar
- Division of Structural Biology and Biochemistry, School of Biological Sciences, Nanyang Technological University, Singapore; INSERM UMRS 945 "Immunité et Infection", Centre Hospitalier Universitaire Pitié-Salpêtrière, Faculté de Médecine et Université Pierre et Marie Curie, 91 Bd de l'Hôpital, 75013 Paris, France
| | - Pei-Yong Shi
- Novartis Institute for Tropical Diseases, Singapore
| | - David Beer
- Novartis Institute for Tropical Diseases, Singapore
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25
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Initiation and regulation of paramyxovirus transcription and replication. Virology 2015; 479-480:545-54. [PMID: 25683441 DOI: 10.1016/j.virol.2015.01.014] [Citation(s) in RCA: 91] [Impact Index Per Article: 10.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2014] [Accepted: 01/04/2015] [Indexed: 12/18/2022]
Abstract
The paramyxovirus family has a genome consisting of a single strand of negative sense RNA. This genome acts as a template for two distinct processes: transcription to generate subgenomic, capped and polyadenylated mRNAs, and genome replication. These viruses only encode one polymerase. Thus, an intriguing question is, how does the viral polymerase initiate and become committed to either transcription or replication? By answering this we can begin to understand how these two processes are regulated. In this review article, we present recent findings from studies on the paramyxovirus, respiratory syncytial virus, which show how its polymerase is able to initiate transcription and replication from a single promoter. We discuss how these findings apply to other paramyxoviruses. Then, we examine how trans-acting proteins and promoter secondary structure might serve to regulate transcription and replication during different phases of the paramyxovirus replication cycle.
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