1
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Wang Y, Fan L, Ye P, Wang Z, Liang C, Liu Q, Yang X, Long Z, Shi W, Zhou Y, Lin J, Yan H, Huang H, Liu L, Qian J. Novel transcription and replication-competent virus-like particles system modelling the Nipah virus life cycle. Emerg Microbes Infect 2024; 13:2368217. [PMID: 38865205 PMCID: PMC11229746 DOI: 10.1080/22221751.2024.2368217] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2024] [Accepted: 06/10/2024] [Indexed: 06/14/2024]
Abstract
Nipah virus (NiV), a highly pathogenic Henipavirus in humans, has been responsible for annual outbreaks in recent years. Experiments involving live NiV are highly restricted to biosafety level 4 (BSL-4) laboratories, which impedes NiV research. In this study, we developed transcription and replication-competent NiV-like particles (trVLP-NiV) lacking N, P, and L genes. This trVLP-NiV exhibited the ability to infect and continuously passage in cells ectopically expressing N, P, and L proteins while maintaining stable genetic characteristics. Moreover, the trVLP-NiV displayed a favourable safety profile in hamsters. Using the system, we found the NiV nucleoprotein residues interacting with viral RNA backbone affected viral replication in opposite patterns. This engineered system was sensitive to well-established antiviral drugs, innate host antiviral factors, and neutralizing antibodies. We then established a high-throughput screening platform utilizing the trVLP-NiV, leading to the identification of tunicamycin as a potential anti-NiV compound. Evidence showed that tunicamycin inhibited NiV replication by decreasing the infectivity of progeny virions. In conclusion, this trVLP-NiV system provided a convenient and versatile molecular tool for investigating NiV molecular biology and conducting antiviral drug screening under BSL-2 conditions. Its application will contribute to the development of medical countermeasures against NiV infections.
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Affiliation(s)
- Yulong Wang
- Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou, People’s Republic of China
- Institute of Infectious Diseases, Guangzhou Eighth people’s Hospital, Guangzhou Medical University, Guangzhou, People’s Republic of China
| | - Linjin Fan
- Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou, People’s Republic of China
- School of Public Health (Shenzhen), Shenzhen Campus of Sun Yat-sen University, Shenzhen, People’s Republic of China
| | - Pengfei Ye
- Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou, People’s Republic of China
| | - Zequn Wang
- Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou, People’s Republic of China
| | - Chudan Liang
- Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou, People’s Republic of China
| | - Quan Liu
- Guangdong Key Laboratory of Animal Conservation and Resource Utilization, Guangdong Public Laboratory of Wild Animal Conservation and Utilization, Institute of Zoology, Guangdong Academy of Sciences, Guangzhou, People’s Republic of China
| | - Xiaofeng Yang
- Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou, People’s Republic of China
| | - Zhenyu Long
- Institute of Infectious Diseases, Guangzhou Eighth people’s Hospital, Guangzhou Medical University, Guangzhou, People’s Republic of China
| | - Wendi Shi
- Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou, People’s Republic of China
| | - Yuandong Zhou
- Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou, People’s Republic of China
| | - Jingyan Lin
- Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou, People’s Republic of China
| | - Huijun Yan
- Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou, People’s Republic of China
| | - Hongxin Huang
- Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou, People’s Republic of China
| | - Linna Liu
- Institute of Infectious Diseases, Guangzhou Eighth people’s Hospital, Guangzhou Medical University, Guangzhou, People’s Republic of China
| | - Jun Qian
- Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou, People’s Republic of China
- School of Public Health (Shenzhen), Shenzhen Campus of Sun Yat-sen University, Shenzhen, People’s Republic of China
- Shenzhen Key Laboratory of Pathogenic Microbes and Biosafety, Shenzhen, People’s Republic of China
- Guangdong Provincial Highly Pathogenic Microorganism Science Data Centre, Guangzhou, People’s Republic of China
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2
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Steiner S, Kratzel A, Barut GT, Lang RM, Aguiar Moreira E, Thomann L, Kelly JN, Thiel V. SARS-CoV-2 biology and host interactions. Nat Rev Microbiol 2024; 22:206-225. [PMID: 38225365 DOI: 10.1038/s41579-023-01003-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 12/01/2023] [Indexed: 01/17/2024]
Abstract
The zoonotic emergence of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) and the ensuing coronavirus disease 2019 (COVID-19) pandemic have profoundly affected our society. The rapid spread and continuous evolution of new SARS-CoV-2 variants continue to threaten global public health. Recent scientific advances have dissected many of the molecular and cellular mechanisms involved in coronavirus infections, and large-scale screens have uncovered novel host-cell factors that are vitally important for the virus life cycle. In this Review, we provide an updated summary of the SARS-CoV-2 life cycle, gene function and virus-host interactions, including recent landmark findings on general aspects of coronavirus biology and newly discovered host factors necessary for virus replication.
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Affiliation(s)
- Silvio Steiner
- Institute of Virology and Immunology, Bern and Mittelhäusern, Bern, Switzerland
- Department of Infectious Diseases and Pathobiology, Vetsuisse Faculty, University of Bern, Bern, Switzerland
| | - Annika Kratzel
- Institute of Virology and Immunology, Bern and Mittelhäusern, Bern, Switzerland
- Department of Infectious Diseases and Pathobiology, Vetsuisse Faculty, University of Bern, Bern, Switzerland
| | - G Tuba Barut
- Institute of Virology and Immunology, Bern and Mittelhäusern, Bern, Switzerland
- Department of Infectious Diseases and Pathobiology, Vetsuisse Faculty, University of Bern, Bern, Switzerland
| | - Reto M Lang
- Institute of Virology and Immunology, Bern and Mittelhäusern, Bern, Switzerland
- Department of Infectious Diseases and Pathobiology, Vetsuisse Faculty, University of Bern, Bern, Switzerland
- Graduate School for Cellular and Biomedical Sciences, University of Bern, Bern, Switzerland
| | - Etori Aguiar Moreira
- Institute of Virology and Immunology, Bern and Mittelhäusern, Bern, Switzerland
- Department of Infectious Diseases and Pathobiology, Vetsuisse Faculty, University of Bern, Bern, Switzerland
| | - Lisa Thomann
- Institute of Virology and Immunology, Bern and Mittelhäusern, Bern, Switzerland
- Department of Infectious Diseases and Pathobiology, Vetsuisse Faculty, University of Bern, Bern, Switzerland
| | - Jenna N Kelly
- Institute of Virology and Immunology, Bern and Mittelhäusern, Bern, Switzerland
- Department of Infectious Diseases and Pathobiology, Vetsuisse Faculty, University of Bern, Bern, Switzerland
- Multidisciplinary Center for Infectious Diseases, University of Bern, Bern, Switzerland
- European Virus Bioinformatics Center, Jena, Germany
| | - Volker Thiel
- Institute of Virology and Immunology, Bern and Mittelhäusern, Bern, Switzerland.
- Department of Infectious Diseases and Pathobiology, Vetsuisse Faculty, University of Bern, Bern, Switzerland.
- Multidisciplinary Center for Infectious Diseases, University of Bern, Bern, Switzerland.
- European Virus Bioinformatics Center, Jena, Germany.
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3
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Tsukamoto Y, Igarashi M, Kato H. Targeting cap1 RNA methyltransferases as an antiviral strategy. Cell Chem Biol 2024; 31:86-99. [PMID: 38091983 DOI: 10.1016/j.chembiol.2023.11.011] [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: 07/24/2023] [Revised: 10/30/2023] [Accepted: 11/20/2023] [Indexed: 01/21/2024]
Abstract
Methylation is one of the critical modifications that regulates numerous biological processes. Guanine capping and methylation at the 7th position (m7G) have been shown to mature mRNA for increased RNA stability and translational efficiency. The m7G capped cap0 RNA remains immature and requires additional methylation at the first nucleotide (N1-2'-O-Me), designated as cap1, to achieve full maturation. This cap1 RNA with N1-2'-O-Me prevents its recognition by innate immune sensors as non-self. Viruses have also evolved various strategies to produce self-like capped RNAs with the N1-2'-O-Me that potentially evades the antiviral response and establishes an efficient replication. In this review, we focus on the importance of the presence of N1-2'-O-Me in viral RNAs and discuss the potential for drug development by targeting host and viral N1-2'-O-methyltransferases.
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Affiliation(s)
- Yuta Tsukamoto
- Institute of Cardiovascular Immunology, Medical Faculty, University Hospital Bonn, University of Bonn, Bonn, Germany
| | - Manabu Igarashi
- Division of Global Epidemiology, International Institute for Zoonosis Control, Hokkaido University, Sapporo, Japan; International Collaboration Unit, International Institute for Zoonosis Control, Hokkaido University, Sapporo, Hokkaido, Japan
| | - Hiroki Kato
- Institute of Cardiovascular Immunology, Medical Faculty, University Hospital Bonn, University of Bonn, Bonn, Germany.
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4
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Tahara M, Okura T, Sato M, Takeda M. Optical Control of Mononegavirus Gene Expression and Replication. Methods Mol Biol 2024; 2808:35-56. [PMID: 38743361 DOI: 10.1007/978-1-0716-3870-5_4] [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
Mononegaviruses are promising tools as oncolytic and transgene vectors for gene therapy and regenerative medicine. However, when mononegaviruses are used for therapeutic applications, the viral activity must be strictly controlled due to concerns about toxicity and severe side effects. With this technology, mononegavirus vectors can be grown where they are intended and can be easily removed when they are no longer needed. In particular, a photoswitch protein called Magnet (consisting of two magnet domains) is incorporated into the hinge region between the connector and methyltransferase domains of the mononegavirus polymerase protein (L protein) to disrupt the L protein functions. Blue light (470 ± 20 nm) irradiation causes the dimerization of the two magnet domains, and the L protein is restored to activity, allowing viral gene expression and virus replication. Since the magnet domains' dimerization is reversible, viral gene expression and replication cease when blue light irradiation is stopped.
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Affiliation(s)
- Maino Tahara
- Department of Virology 3, National Institute of Infectious Diseases, Tokyo, Japan
| | - Takashi Okura
- Department of Virology 3, National Institute of Infectious Diseases, Tokyo, Japan
| | - Moritoshi Sato
- Graduate School of Arts and Sciences, The University of Tokyo, Tokyo, Japan
| | - Makoto Takeda
- Department of Microbiology, Graduate School of Medicine and Faculty of Medicine, The University of Tokyo, Tokyo, Japan.
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5
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Abduljalil JM, Elfiky AA, Sayed ESTA, AlKhazindar MM. In silico structural elucidation of Nipah virus L protein and targeting RNA-dependent RNA polymerase domain by nucleoside analogs. J Biomol Struct Dyn 2023; 41:8215-8229. [PMID: 36205638 DOI: 10.1080/07391102.2022.2130987] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2022] [Accepted: 09/25/2022] [Indexed: 10/10/2022]
Abstract
The large (L) protein of Mononegavirales is a multi-domain protein that performs transcription and genome replication. One of the important domains in L is the RNA-dependent RNA polymerase (RdRp), a promising target for antiviral drugs. In this work, we employed rigorous computational comparative modeling to predict the structure of L protein of Nipah virus (NiV). The RdRp domain was targeted by a panel of nucleotide analogs, previously reported to inhibit different viral RNA polymerases, using molecular docking. Best binder compounds were subjected to molecular dynamics simulation to validate their binding. Molecular mechanics/generalized-born surface area (MM/GBSA) calculations estimated the binding free energy. The predicted model of NiV L has an excellent quality as judged by physics- and knowledge-based validation tests. Galidesivir, AT-9010 and Norov-29 scored the top nucleotide analogs to bind to the RdRp. Their binding free energies obtained by MM/GBSA (-31.01 ± 3.9 to -38.37 ± 4.8 kcal/mol) ranked Norov-29 as the best potential inhibitor. Purine nucleotide analogs are expected to harbor the scaffold for an effective drug against NiV. Finally, this study is expected to provide a start point for medicinal chemistry and drug discovery campaigns toward identification of effective chemotherapeutic agent(s) against NiV.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Jameel M Abduljalil
- Department of Botany and Microbiology, Faculty of Science, Cairo University, Giza, Egypt
- Department of Biological Sciences, Faculty of Applied Sciences, Thamar University, Dhamar, Yemen
| | - Abdo A Elfiky
- Department of Biophysics, Faculty of Science, Cairo University, Giza, Egypt
| | - El-Sayed T A Sayed
- Department of Botany and Microbiology, Faculty of Science, Cairo University, Giza, Egypt
| | - Maha M AlKhazindar
- Department of Botany and Microbiology, Faculty of Science, Cairo University, Giza, Egypt
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6
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Peng Q, Yuan B, Cheng J, Wang M, Gao S, Bai S, Zhao X, Qi J, Gao GF, Shi Y. Molecular mechanism of de novo replication by the Ebola virus polymerase. Nature 2023; 622:603-610. [PMID: 37699521 DOI: 10.1038/s41586-023-06608-1] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2023] [Accepted: 09/05/2023] [Indexed: 09/14/2023]
Abstract
Non-segmented negative-strand RNA viruses, including Ebola virus (EBOV), rabies virus, human respiratory syncytial virus and pneumoviruses, can cause respiratory infections, haemorrhagic fever and encephalitis in humans and animals, and are considered a substantial health and economic burden worldwide1. Replication and transcription of the viral genome are executed by the large (L) polymerase, which is a promising target for the development of antiviral drugs. Here, using the L polymerase of EBOV as a representative, we show that de novo replication of L polymerase is controlled by the specific 3' leader sequence of the EBOV genome in an enzymatic assay, and that formation of at least three base pairs can effectively drive the elongation process of RNA synthesis independent of the specific RNA sequence. We present the high-resolution structures of the EBOV L-VP35-RNA complex and show that the 3' leader RNA binds in the template entry channel with a distinctive stable bend conformation. Using mutagenesis assays, we confirm that the bend conformation of the RNA is required for the de novo replication activity and reveal the key residues of the L protein that stabilize the RNA conformation. These findings provide a new mechanistic understanding of RNA synthesis for polymerases of non-segmented negative-strand RNA viruses, and reveal important targets for the development of antiviral drugs.
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Affiliation(s)
- Qi Peng
- International Institute of Vaccine Research and Innovation (iVac), Savaid Medical School, University of Chinese Academy of Sciences, Beijing, China
- CAS Key Laboratory of Pathogen Microbiology and Immunology, Institute of Microbiology, Chinese Academy of Sciences, Beijing, China
| | - Bin Yuan
- International Institute of Vaccine Research and Innovation (iVac), Savaid Medical School, University of Chinese Academy of Sciences, Beijing, China
- CAS Key Laboratory of Pathogen Microbiology and Immunology, Institute of Microbiology, Chinese Academy of Sciences, Beijing, China
| | - Jinlong Cheng
- International Institute of Vaccine Research and Innovation (iVac), Savaid Medical School, University of Chinese Academy of Sciences, Beijing, China
- CAS Key Laboratory of Pathogen Microbiology and Immunology, Institute of Microbiology, Chinese Academy of Sciences, Beijing, China
| | - Min Wang
- International Institute of Vaccine Research and Innovation (iVac), Savaid Medical School, University of Chinese Academy of Sciences, Beijing, China
- CAS Key Laboratory of Pathogen Microbiology and Immunology, Institute of Microbiology, Chinese Academy of Sciences, Beijing, China
| | - Siwei Gao
- International Institute of Vaccine Research and Innovation (iVac), Savaid Medical School, University of Chinese Academy of Sciences, Beijing, China
- CAS Key Laboratory of Pathogen Microbiology and Immunology, Institute of Microbiology, Chinese Academy of Sciences, Beijing, China
| | - Suran Bai
- International Institute of Vaccine Research and Innovation (iVac), Savaid Medical School, University of Chinese Academy of Sciences, Beijing, China
- CAS Key Laboratory of Pathogen Microbiology and Immunology, Institute of Microbiology, Chinese Academy of Sciences, Beijing, China
| | - Xuejin Zhao
- International Institute of Vaccine Research and Innovation (iVac), Savaid Medical School, University of Chinese Academy of Sciences, Beijing, China
- CAS Key Laboratory of Pathogen Microbiology and Immunology, Institute of Microbiology, Chinese Academy of Sciences, Beijing, China
| | - Jianxun Qi
- International Institute of Vaccine Research and Innovation (iVac), Savaid Medical School, University of Chinese Academy of Sciences, Beijing, China.
- CAS Key Laboratory of Pathogen Microbiology and Immunology, Institute of Microbiology, Chinese Academy of Sciences, Beijing, China.
- Beijing Life Science Academy, Beijing, China.
| | - George F Gao
- International Institute of Vaccine Research and Innovation (iVac), Savaid Medical School, University of Chinese Academy of Sciences, Beijing, China.
- CAS Key Laboratory of Pathogen Microbiology and Immunology, Institute of Microbiology, Chinese Academy of Sciences, Beijing, China.
- Beijing Life Science Academy, Beijing, China.
- Center for Influenza Research and Early-warning (CASCIRE), CAS-TWAS Center of Excellence for Emerging Infectious Disease (CEEID), Chinese Academy of Sciences, Beijing, China.
- Research Unit of Adaptive Evolution and Control of Emerging Viruses, Chinese Academy of Medical Sciences, Beijing, China.
| | - Yi Shi
- International Institute of Vaccine Research and Innovation (iVac), Savaid Medical School, University of Chinese Academy of Sciences, Beijing, China.
- CAS Key Laboratory of Pathogen Microbiology and Immunology, Institute of Microbiology, Chinese Academy of Sciences, Beijing, China.
- Beijing Life Science Academy, Beijing, China.
- Center for Influenza Research and Early-warning (CASCIRE), CAS-TWAS Center of Excellence for Emerging Infectious Disease (CEEID), Chinese Academy of Sciences, Beijing, China.
- Research Unit of Adaptive Evolution and Control of Emerging Viruses, Chinese Academy of Medical Sciences, Beijing, China.
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7
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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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8
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Sinnott JT, Kim K, Somboonwit C, Cosnett C, Segal D, Shapshak P. Emergent Risk Group-4 (RG-4) Filoviruses: A paradox in progress. Bioinformation 2023; 19:829-832. [PMID: 37908613 PMCID: PMC10613816 DOI: 10.6026/97320630019829] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2023] [Revised: 08/31/2023] [Accepted: 08/31/2023] [Indexed: 11/02/2023] Open
Abstract
Filoviruses, categorized as World Health Organization (WHO) Risk Group 4 (RG-4) pathogens, represent significant global health risks due to their extraordinary virulence. The Filoviridae family encompasses Ebola strains such as Sudan, Zaire, Bundibugyo, Tai Forest (formerly known as Ivory Coast), Reston, and Bombali, in addition to the closely related Marburg and Ravn virus strains. Filoviruses originated from a common ancestor about 10,000 years ago and displayed remarkable consistency in genetic heterogeneity until the 20th century. However, they overcame a genetic bottleneck by mid-century. Paradoxically, this resulted in the emergence of boosted virulent strains from the 1970's onward. Filovirus research is included in the NIAID Biodefense Program and utilizes the highest level specialized protective laboratories, Biosafety Laboratory (BSL)-4. The spread of Filoviruses as well as other RG-4 pathogens within Africa poses a significant health threat increasingly both in Africa and out of Africa.
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Affiliation(s)
- John T Sinnott
- />Division of Infectious Diseases and International Health, Department of Internal Medicine, Morsani College of Medicine, Tampa, Florida 33606. USA
| | - Kami Kim
- />Division of Infectious Diseases and International Health, Department of Internal Medicine, Morsani College of Medicine, Tampa, Florida 33606. USA
| | - Charurut Somboonwit
- />Division of Infectious Diseases and International Health, Department of Internal Medicine, Morsani College of Medicine, Tampa, Florida 33606. USA
| | - Conor Cosnett
- />Wolfram Research Inc., Champaigne, Illinois 61820 USA
| | - David Segal
- />College of Health Sciences and Public Policy, Walden University, Minneapolis, Minnesota 55401 USA
| | - Paul Shapshak
- />Division of Infectious Diseases and International Health, Department of Internal Medicine, Morsani College of Medicine, Tampa, Florida 33606. USA
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9
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Gupta N, Ogino M, Watkins DE, Yu T, Green TJ, Ogino T. Discontinuous L-binding motifs in the transactivation domain of the vesicular stomatitis virus P protein are required for terminal de novo transcription initiation by the L protein. J Virol 2023; 97:e0024623. [PMID: 37578231 PMCID: PMC10506490 DOI: 10.1128/jvi.00246-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2023] [Accepted: 06/18/2023] [Indexed: 08/15/2023] Open
Abstract
The phospho- (P) protein, the co-factor of the RNA polymerase large (L) protein, of vesicular stomatitis virus (VSV, a prototype of nonsegmented negative-strand RNA viruses) plays pivotal roles in transcription and replication. However, the precise mechanism underlying the transcriptional transactivation by the P protein has remained elusive. Here, using an in vitro transcription system and a series of deletion mutants of the P protein, we mapped a region encompassing residues 51-104 as a transactivation domain (TAD) that is critical for terminal de novo initiation, the initial step of synthesis of the leader RNA and anti-genome/genome, with the L protein. Site-directed mutagenesis revealed that conserved amino acid residues in three discontinuous L-binding sites within the TAD are essential for the transactivation activity of the P protein or important for maintaining its full activity. Importantly, relative inhibitory effects of TAD point mutations on synthesis of the full-length leader RNA and mRNAs from the 3'-terminal leader region and internal genes, respectively, of the genome were similar to those on terminal de novo initiation. Furthermore, any of the examined TAD mutations did not alter the gradient pattern of mRNAs synthesized from internal genes, nor did they induce the production of readthrough transcripts. These results suggest that these TAD mutations impact mainly terminal de novo initiation but rarely other steps (e.g., elongation, termination, internal initiation) of single-entry stop-start transcription. Consistently, the mutations of the essential or important amino acid residues within the P TAD were lethal or deleterious to VSV replication in host cells. IMPORTANCE RNA-dependent RNA polymerase L proteins of nonsegmented negative-strand RNA viruses belonging to the Mononegavirales order require their cognate co-factor P proteins or their counterparts for genome transcription and replication. However, exact roles of these co-factor proteins in modulating functions of L proteins during transcription and replication remain unknown. In this study, we revealed that three discrete L-binding motifs within a transactivation domain of the P protein of vesicular stomatitis virus, a prototypic nonsegmented negative-strand RNA virus, are required for terminal de novo initiation mediated by the L protein, which is the first step of synthesis of the leader RNA as well as genome/anti-genome.
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Affiliation(s)
- Nirmala Gupta
- Department of Molecular Biology and Microbiology, Case Western Reserve University School of Medicine, Cleveland, Ohio, USA
| | - Minako Ogino
- Department of Molecular Biology and Microbiology, Case Western Reserve University School of Medicine, Cleveland, Ohio, USA
- Department of Medical Microbiology and Immunology, College of Medicine and Life Sciences, University of Toledo, Toledo, Ohio, USA
| | - Dean E. Watkins
- Department of Medical Microbiology and Immunology, College of Medicine and Life Sciences, University of Toledo, Toledo, Ohio, USA
| | - Tiffany Yu
- Department of Medical Microbiology and Immunology, College of Medicine and Life Sciences, University of Toledo, Toledo, Ohio, USA
| | - Todd J. Green
- Department of Microbiology, School of Medicine, University of Alabama at Birmingham, Birmingham, Alabama, USA
| | - Tomoaki Ogino
- Department of Molecular Biology and Microbiology, Case Western Reserve University School of Medicine, Cleveland, Ohio, USA
- Department of Medical Microbiology and Immunology, College of Medicine and Life Sciences, University of Toledo, Toledo, Ohio, USA
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10
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Kleiner VA, O Fischmann T, Howe JA, Beshore DC, Eddins MJ, Hou Y, Mayhood T, Klein D, Nahas DD, Lucas BJ, Xi H, Murray E, Ma DY, Getty K, Fearns R. Conserved allosteric inhibitory site on the respiratory syncytial virus and human metapneumovirus RNA-dependent RNA polymerases. Commun Biol 2023; 6:649. [PMID: 37337079 DOI: 10.1038/s42003-023-04990-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2023] [Accepted: 05/26/2023] [Indexed: 06/21/2023] Open
Abstract
Respiratory syncytial virus (RSV) and human metapneumovirus (HMPV) are related RNA viruses responsible for severe respiratory infections and resulting disease in infants, elderly, and immunocompromised adults1-3. Therapeutic small molecule inhibitors that bind to the RSV polymerase and inhibit viral replication are being developed, but their binding sites and molecular mechanisms of action remain largely unknown4. Here we report a conserved allosteric inhibitory site identified on the L polymerase proteins of RSV and HMPV that can be targeted by a dual-specificity, non-nucleoside inhibitor, termed MRK-1. Cryo-EM structures of the inhibitor in complexes with truncated RSV and full-length HMPV polymerase proteins provide a structural understanding of how MRK-1 is active against both viruses. Functional analyses indicate that MRK-1 inhibits conformational changes necessary for the polymerase to engage in RNA synthesis initiation and to transition into an elongation mode. Competition studies reveal that the MRK-1 binding pocket is distinct from that of a capping inhibitor with an overlapping resistance profile, suggesting that the polymerase conformation bound by MRK-1 may be distinct from that involved in mRNA capping. These findings should facilitate optimization of dual RSV and HMPV replication inhibitors and provide insights into the molecular mechanisms underlying their polymerase activities.
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Affiliation(s)
- Victoria A Kleiner
- Department of Virology, Immunology & Microbiology, National Emerging Infectious Diseases Laboratories, Boston University Chobanian and Avedisian School of Medicine, Boston, MA, USA
| | | | | | | | | | - Yan Hou
- MRL, Merck & Co., Inc., Rahway, NJ, USA
| | | | | | | | | | - He Xi
- MRL, Merck & Co., Inc., Rahway, NJ, USA
| | | | | | | | - Rachel Fearns
- Department of Virology, Immunology & Microbiology, National Emerging Infectious Diseases Laboratories, Boston University Chobanian and Avedisian School of Medicine, Boston, MA, USA.
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11
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Olendraite I, Brown K, Firth AE. Identification of RNA Virus-Derived RdRp Sequences in Publicly Available Transcriptomic Data Sets. Mol Biol Evol 2023; 40:msad060. [PMID: 37014783 PMCID: PMC10101049 DOI: 10.1093/molbev/msad060] [Citation(s) in RCA: 9] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2022] [Revised: 01/15/2023] [Accepted: 03/08/2023] [Indexed: 04/05/2023] Open
Abstract
RNA viruses are abundant and highly diverse and infect all or most eukaryotic organisms. However, only a tiny fraction of the number and diversity of RNA virus species have been catalogued. To cost-effectively expand the diversity of known RNA virus sequences, we mined publicly available transcriptomic data sets. We developed 77 family-level Hidden Markov Model profiles for the viral RNA-dependent RNA polymerase (RdRp)-the only universal "hallmark" gene of RNA viruses. By using these to search the National Center for Biotechnology Information Transcriptome Shotgun Assembly database, we identified 5,867 contigs encoding RNA virus RdRps or fragments thereof and analyzed their diversity, taxonomic classification, phylogeny, and host associations. Our study expands the known diversity of RNA viruses, and the 77 curated RdRp Profile Hidden Markov Models provide a useful resource for the virus discovery community.
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Affiliation(s)
- Ingrida Olendraite
- Division of Virology, Department of Pathology, Addenbrookes Hospital, University of Cambridge, Cambridge, United Kingdom
| | - Katherine Brown
- Division of Virology, Department of Pathology, Addenbrookes Hospital, University of Cambridge, Cambridge, United Kingdom
| | - Andrew E Firth
- Division of Virology, Department of Pathology, Addenbrookes Hospital, University of Cambridge, Cambridge, United Kingdom
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12
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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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13
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Nonclinical pharmacokinetics and biodistribution of VSV-GP using methods to decouple input drug disposition and viral replication. Mol Ther Methods Clin Dev 2022; 28:190-207. [PMID: 36700123 PMCID: PMC9843450 DOI: 10.1016/j.omtm.2022.12.013] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2022] [Accepted: 12/22/2022] [Indexed: 12/29/2022]
Abstract
Viral replication places oncolytic viruses (OVs) in a unique niche in the field of drug pharmacokinetics (PK) as their self-amplification obscures exposure-response relationships. Moreover, standard bioanalytical techniques are unable to distinguish the input from replicated drug products. Here, we combine two novel approaches to characterize PK and biodistribution (BD) after systemic administration of vesicular stomatitis virus pseudotyped with lymphocytic choriomeningitis virus glycoprotein (VSV-GP) in healthy mice. First: to decouple input drug PK/BD versus replication PK/BD, we developed and fully characterized a replication-incompetent tool virus that retained all other critical attributes of the drug. We used this approach to quantify replication in blood and tissues and to determine its impact on PK and BD. Second: to discriminate the genomic and antigenomic viral RNA strands contributing to replication dynamics in tissues, we developed an in situ hybridization method using strand-specific probes and assessed their spatiotemporal distribution in tissues. This latter approach demonstrated that distribution, transcription, and replication localized to tissue-resident macrophages, indicating their role in PK and BD. Ultimately, our study results in a refined PK/BD profile for a replicating OV, new proposed PK parameters, and deeper understanding of OV PK/BD using unique approaches that could be applied to other replicating vectors.
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14
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Abstract
Arctic permafrost is thawing due to global warming, with unknown consequences on the microbial inhabitants or associated viruses. DNA viruses have previously been shown to be abundant and active in thawing permafrost, but little is known about RNA viruses in these systems. To address this knowledge gap, we assessed the composition of RNA viruses in thawed permafrost samples that were incubated for 97 days at 4°C to simulate thaw conditions. A diverse RNA viral community was assembled from metatranscriptome data including double-stranded RNA viruses, dominated by Reoviridae and Hypoviridae, and negative and positive single-stranded RNA viruses, with relatively high representations of Rhabdoviridae and Leviviridae, respectively. Sequences corresponding to potential plant and human pathogens were also detected. The detected RNA viruses primarily targeted dominant eukaryotic taxa in the samples (e.g., fungi, Metazoa and Viridiplantae) and the viral community structures were significantly associated with predicted host populations. These results indicate that RNA viruses are linked to eukaryotic host dynamics. Several of the RNA viral sequences contained auxiliary metabolic genes encoding proteins involved in carbon utilization (e.g., polygalacturosase), implying their potential roles in carbon cycling in thawed permafrost. IMPORTANCE Permafrost is thawing at a rapid pace in the Arctic with largely unknown consequences on ecological processes that are fundamental to Arctic ecosystems. This is the first study to determine the composition of RNA viruses in thawed permafrost. Other recent studies have characterized DNA viruses in thawing permafrost, but the majority of DNA viruses are bacteriophages that target bacterial hosts. By contrast RNA viruses primarily target eukaryotic hosts and thus represent potential pathogenic threats to humans, animals, and plants. Here, we find that RNA viruses in permafrost are novel and distinct from those in other habitats studied to date. The COVID-19 pandemic has heightened awareness of the importance of potential environmental reservoirs of emerging RNA viral pathogens. We demonstrate that some potential pathogens were detected after an experimental thawing regime. These results are important for understanding critical viral-host interactions and provide a better understanding of the ecological roles that RNA viruses play as permafrost thaws.
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15
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Free ISG15 Inhibits the Replication of Peste des Petits Ruminants Virus by Breaking the Interaction of Nucleoprotein and Phosphoprotein. Microbiol Spectr 2022; 10:e0103122. [PMID: 36036587 PMCID: PMC9603952 DOI: 10.1128/spectrum.01031-22] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022] Open
Abstract
Peste des petits ruminants virus (PPRV) causes a highly contagious disease in small ruminants and severe economic losses in developing countries. PPRV infection can stimulate high levels of interferon (IFN) and many IFN-stimulated genes (ISGs), such as ISG15, which may play a key role in the process of viral infection. However, the role of ISG15 in PPRV infection and replication has not yet been reported. In this study, we found ISG15 expression to be significantly upregulated after PPRV infection of caprine endometrial epithelial cells (EECs), and ISG15 inhibits the proliferation of PPRV. Further analysis showed that free ISG15 could inhibit PPRV proliferation. Moreover, ISG15 does not affect the binding, entry, and transcription but does suppress the replication of PPRV. A detailed analysis revealed that ISG15 interacts and colocalizes with both viral N and P proteins and that its interactive regions are all located in the N-terminal domain. Further studies showed that ISG15 can competitively interact with N and P proteins and significantly interfere with their binding. Finally, through the construction of the C-terminal mutants of ISG15 with different lengths, it was found that amino acids (aa) 77 to 101 play a key role in inhibiting the binding of N and P proteins and that interaction with the P protein disappears after the deletion of 77 to 101 aa. The present study revealed a novel mechanism of ISG15 in disrupting the activity of the N0-P complex to inhibit viral replication. IMPORTANCE PPRV, a widespread and fatal disease of small ruminants, is one of the most devastating animal diseases in Africa, the Middle East, and Asia, causing severe economic losses. IFNs play an important role as a component of natural immunity against pathogens, yet the role of ISG15, an IFN-stimulated gene, in protecting against PPRV infection is currently unknown. We demonstrated, for the first time, that free ISG15 inhibits PPRV proliferation by disrupting the activity of the N0-P complex, a finding that has not been reported in other viruses. Our results provide important insights that can further understand the pathogenesis and innate immune mechanisms of PPRV.
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16
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Park GJ, Osinski A, Hernandez G, Eitson JL, Majumdar A, Tonelli M, Henzler-Wildman K, Pawłowski K, Chen Z, Li Y, Schoggins JW, Tagliabracci VS. The mechanism of RNA capping by SARS-CoV-2. Nature 2022; 609:793-800. [PMID: 35944563 PMCID: PMC9492545 DOI: 10.1038/s41586-022-05185-z] [Citation(s) in RCA: 27] [Impact Index Per Article: 13.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2022] [Accepted: 08/03/2022] [Indexed: 11/29/2022]
Abstract
The RNA genome of SARS-CoV-2 contains a 5′ cap that facilitates the translation of viral proteins, protection from exonucleases and evasion of the host immune response1–4. How this cap is made in SARS-CoV-2 is not completely understood. Here we reconstitute the N7- and 2′-O-methylated SARS-CoV-2 RNA cap (7MeGpppA2′-O-Me) using virally encoded non-structural proteins (nsps). We show that the kinase-like nidovirus RdRp-associated nucleotidyltransferase (NiRAN) domain5 of nsp12 transfers the RNA to the amino terminus of nsp9, forming a covalent RNA–protein intermediate (a process termed RNAylation). Subsequently, the NiRAN domain transfers the RNA to GDP, forming the core cap structure GpppA-RNA. The nsp146 and nsp167 methyltransferases then add methyl groups to form functional cap structures. Structural analyses of the replication–transcription complex bound to nsp9 identified key interactions that mediate the capping reaction. Furthermore, we demonstrate in a reverse genetics system8 that the N terminus of nsp9 and the kinase-like active-site residues in the NiRAN domain are required for successful SARS-CoV-2 replication. Collectively, our results reveal an unconventional mechanism by which SARS-CoV-2 caps its RNA genome, thus exposing a new target in the development of antivirals to treat COVID-19. Reconstitution of the SARS-CoV-2 RNA 5′ cap reveals the unconventional mechanism by which SARS-CoV-2 caps its RNA genome, providing a new target in the development of antiviral agents to treat COVID-19.
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Affiliation(s)
- Gina J Park
- Department of Molecular Biology, University of Texas Southwestern Medical Center, Dallas, TX, USA
| | - Adam Osinski
- Department of Molecular Biology, University of Texas Southwestern Medical Center, Dallas, TX, USA
| | - Genaro Hernandez
- Department of Molecular Biology, University of Texas Southwestern Medical Center, Dallas, TX, USA
| | - Jennifer L Eitson
- Department of Microbiology, University of Texas Southwestern Medical Center, Dallas, TX, USA
| | - Abir Majumdar
- Department of Molecular Biology, University of Texas Southwestern Medical Center, Dallas, TX, USA
| | - Marco Tonelli
- Department of Biochemistry, University of Wisconsin-Madison, Madison, WI, USA
| | | | - Krzysztof Pawłowski
- Department of Molecular Biology, University of Texas Southwestern Medical Center, Dallas, TX, USA.,Department of Biochemistry and Microbiology, Institute of Biology, Warsaw University of Life Sciences, Warsaw, Poland
| | - Zhe Chen
- Department of Biophysics, University of Texas Southwestern Medical Center, Dallas, TX, USA
| | - Yang Li
- Department of Biophysics, University of Texas Southwestern Medical Center, Dallas, TX, USA
| | - John W Schoggins
- Department of Microbiology, University of Texas Southwestern Medical Center, Dallas, TX, USA
| | - Vincent S Tagliabracci
- Department of Molecular Biology, University of Texas Southwestern Medical Center, Dallas, TX, USA. .,Harold C. Simmons Comprehensive Cancer Center, University of Texas Southwestern Medical Center, Dallas, Texas, USA. .,Hamon Center for Regenerative Science and Medicine, University of Texas Southwestern Medical Center, Dallas, Texas, USA. .,Howard Hughes Medical Institute, University of Texas Southwestern Medical Center, Dallas, Texas, USA.
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17
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Mahfuz A, Khan MA, Sajib EH, Deb A, Mahmud S, Hasan M, Saha O, Islam A, Rahaman MM. Designing potential siRNA molecules for silencing the gene of the nucleocapsid protein of Nipah virus: A computational investigation. INFECTION, GENETICS AND EVOLUTION : JOURNAL OF MOLECULAR EPIDEMIOLOGY AND EVOLUTIONARY GENETICS IN INFECTIOUS DISEASES 2022; 102:105310. [PMID: 35636695 DOI: 10.1016/j.meegid.2022.105310] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/18/2021] [Revised: 05/20/2022] [Accepted: 05/24/2022] [Indexed: 06/15/2023]
Abstract
Nipah virus (NiV), a zoonotic virus, engenders severe infections with noticeable complications and deaths in humans and animals. Since its emergence, it is frightening, this virus has been causing regular outbreaks in various countries, particularly in Bangladesh, India, and Malaysia. Unfortunately, no efficient vaccine or drug is available now to combat this baneful virus. NiV employs its nucleocapsid protein for genetic material packaging, which is crucial for viral replication inside the host cells. The small interfering RNAs (siRNAs) can play a central role in inhibiting the expression of disease-causing viral genes by hybridization and subsequent inactivation of the complementary target viral mRNAs through the RNA interference (RNAi) pathway. Therefore, potential siRNAs as molecular therapeutics against the nucleocapsid protein gene of NiV were designed in this study. First, ten prospective siRNAs were identified using the conserved nucleocapsid gene sequences among all available NiV strains collected from various countries. After that, off-target binding, GC (guanine-cytosine) content, secondary structure, binding affinity with the target, melting temperature, efficacy analysis, and binding capacity with the human argonaute protein 2 (AGO2) of these siRNAs were evaluated to predict their suitability. These designed siRNA molecules bear promise in silencing the NiV gene encoding the nucleocapsid protein and thus can alleviate the severity of this dangerous virus. Further in vivo experiments are recommended before using these designed siRNAs as alternative and effective molecular therapeutic agents against NiV.
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Affiliation(s)
- Amub Mahfuz
- Department of Biotechnology and Genetic Engineering, University of Development Alternative, Dhaka 1209, Bangladesh
| | - Md Arif Khan
- Department of Biotechnology and Genetic Engineering, University of Development Alternative, Dhaka 1209, Bangladesh; Institute of Epidemiology, Disease Control and Research (IEDCR), Dhaka 1212, Bangladesh.
| | - Emran Hossain Sajib
- Faculty of Biotechnology and Genetic Engineering, Sylhet Agricultural University, Sylhet 3100, Bangladesh
| | - Anamika Deb
- Department of Pharmaceuticals and Industrial Biotechnology, Faculty of Biotechnology and Genetic Engineering, Sylhet Agricultural University, Sylhet 3100, Bangladesh
| | - Shafi Mahmud
- Microbiology Laboratory, Bioinformatics Division, Department of Genetic Engineering and Biotechnology, University of Rajshahi, Rajshahi 6205, Bangladesh
| | - Mahmudul Hasan
- Faculty of Biotechnology and Genetic Engineering, Sylhet Agricultural University, Sylhet 3100, Bangladesh; Department of Pharmaceuticals and Industrial Biotechnology, Faculty of Biotechnology and Genetic Engineering, Sylhet Agricultural University, Sylhet 3100, Bangladesh
| | - Otun Saha
- Department of Microbiology, Noakhali Science and Technology University, Noakhali 3814, Bangladesh
| | - Ariful Islam
- Institute of Epidemiology, Disease Control and Research (IEDCR), Dhaka 1212, Bangladesh; EcoHealth Alliance, New York, NY 10018, USA
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18
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Mersinoglu B, Cristinelli S, Ciuffi A. The Impact of Epitranscriptomics on Antiviral Innate Immunity. Viruses 2022; 14:v14081666. [PMID: 36016289 PMCID: PMC9412694 DOI: 10.3390/v14081666] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2022] [Revised: 07/21/2022] [Accepted: 07/25/2022] [Indexed: 11/18/2022] Open
Abstract
Epitranscriptomics, i.e., chemical modifications of RNA molecules, has proven to be a new layer of modulation and regulation of protein expression, asking for the revisiting of some aspects of cellular biology. At the virological level, epitranscriptomics can thus directly impact the viral life cycle itself, acting on viral or cellular proteins promoting replication, or impacting the innate antiviral response of the host cell, the latter being the focus of the present review.
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19
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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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20
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Wang F, Sheppard CM, Mistry B, Staller E, Barclay WS, Grimes JM, Fodor E, Fan H. The C-terminal LCAR of host ANP32 proteins interacts with the influenza A virus nucleoprotein to promote the replication of the viral RNA genome. Nucleic Acids Res 2022; 50:5713-5725. [PMID: 35639917 PMCID: PMC9177957 DOI: 10.1093/nar/gkac410] [Citation(s) in RCA: 13] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/26/2021] [Revised: 04/11/2022] [Accepted: 05/09/2022] [Indexed: 12/12/2022] Open
Abstract
The segmented negative-sense RNA genome of influenza A virus is assembled into ribonucleoprotein complexes (RNP) with viral RNA-dependent RNA polymerase and nucleoprotein (NP). It is in the context of these RNPs that the polymerase transcribes and replicates viral RNA (vRNA). Host acidic nuclear phosphoprotein 32 (ANP32) family proteins play an essential role in vRNA replication by mediating the dimerization of the viral polymerase via their N-terminal leucine-rich repeat (LRR) domain. However, whether the C-terminal low-complexity acidic region (LCAR) plays a role in RNA synthesis remains unknown. Here, we report that the LCAR is required for viral genome replication during infection. Specifically, we show that the LCAR directly interacts with NP and this interaction is mutually exclusive with RNA. Furthermore, we show that the replication of a short vRNA-like template that can be replicated in the absence of NP is less sensitive to LCAR truncations compared with the replication of full-length vRNA segments which is NP-dependent. We propose a model in which the LCAR interacts with NP to promote NP recruitment to nascent RNA during influenza virus replication, ensuring the co-replicative assembly of RNA into RNPs.
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Affiliation(s)
- Fangzheng Wang
- Sir William Dunn School of Pathology, University of Oxford, Oxford, UK
| | - Carol M Sheppard
- Department of Infectious Disease, Faculty of Medicine, Imperial College, London, UK
| | - Bhakti Mistry
- Department of Infectious Disease, Faculty of Medicine, Imperial College, London, UK
| | - Ecco Staller
- Sir William Dunn School of Pathology, University of Oxford, Oxford, UK.,Department of Infectious Disease, Faculty of Medicine, Imperial College, London, UK
| | - Wendy S Barclay
- Department of Infectious Disease, Faculty of Medicine, Imperial College, London, UK
| | - Jonathan M Grimes
- Division of Structural Biology, Henry Wellcome Building for Genomic Medicine, University of Oxford, Oxford, UK.,Diamond Light Source Ltd, Diamond House, Harwell Science and Innovation Campus, Didcot, UK
| | - Ervin Fodor
- Sir William Dunn School of Pathology, University of Oxford, Oxford, UK
| | - Haitian Fan
- Sir William Dunn School of Pathology, University of Oxford, Oxford, UK
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21
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Sakamoto K, Satoh Y, Takahashi KI, Wakimoto H, Kitagawa Y, Gotoh B, Ayata M, Itoh M. Upregulation of viral RNA polymerase activity promotes adaptation of SSPE virus to neuronal cells. Virology 2022; 573:1-11. [DOI: 10.1016/j.virol.2022.05.006] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2022] [Revised: 05/13/2022] [Accepted: 05/24/2022] [Indexed: 11/26/2022]
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22
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Bourhis JM, Yabukarski F, Communie G, Schneider R, Volchkova VA, Frénéat M, Gérard F, Ducournau C, Mas C, Tarbouriech N, Ringkjøbing Jensen M, Volchkov VE, Blackledge M, Jamin M. Structural dynamics of the C-terminal X domain of Nipah and Hendra viruses controls the attachment to the C-terminal tail of the nucleocapsid protein. J Mol Biol 2022; 434:167551. [DOI: 10.1016/j.jmb.2022.167551] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2021] [Revised: 03/01/2022] [Accepted: 03/14/2022] [Indexed: 10/18/2022]
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23
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Park GJ, Osinski A, Hernandez G, Eitson JL, Majumdar A, Tonelli M, Henzler-Wildman K, Pawłowski K, Chen Z, Li Y, Schoggins JW, Tagliabracci VS. The mechanism of RNA capping by SARS-CoV-2. RESEARCH SQUARE 2022:rs.3.rs-1336910. [PMID: 35194601 PMCID: PMC8863163 DOI: 10.21203/rs.3.rs-1336910/v1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
Abstract
The SARS-CoV-2 RNA genome contains a 5'-cap that facilitates translation of viral proteins, protection from exonucleases and evasion of the host immune response1-4. How this cap is made is not completely understood. Here, we reconstitute the SARS-CoV-2 7MeGpppA2'-O-Me-RNA cap using virally encoded non-structural proteins (nsps). We show that the kinase-like NiRAN domain5 of nsp12 transfers RNA to the amino terminus of nsp9, forming a covalent RNA-protein intermediate (a process termed RNAylation). Subsequently, the NiRAN domain transfers RNA to GDP, forming the cap core structure GpppA-RNA. The nsp146 and nsp167 methyltransferases then add methyl groups to form functional cap structures. Structural analyses of the replication-transcription complex bound to nsp9 identified key interactions that mediate the capping reaction. Furthermore, we demonstrate in a reverse genetics system8 that the N-terminus of nsp9 and the kinase-like active site residues in the NiRAN domain are required for successful SARS-CoV-2 replication. Collectively, our results reveal an unconventional mechanism by which SARS-CoV-2 caps its RNA genome, thus exposing a new target in the development of antivirals to treat COVID-19.
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Affiliation(s)
- Gina J. Park
- Department of Molecular Biology, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
| | - Adam Osinski
- Department of Molecular Biology, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
| | - Genaro Hernandez
- Department of Molecular Biology, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
| | - Jennifer L. Eitson
- Department of Microbiology, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
| | - Abir Majumdar
- Department of Molecular Biology, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
| | - Marco Tonelli
- Department of Biochemistry, University of Wisconsin-Madison, Madison, WI 53706, USA
| | | | - Krzysztof Pawłowski
- Department of Molecular Biology, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
- Department of Biochemistry and Microbiology, Institute of Biology, Warsaw University of Life Sciences, Warsaw 02-776, Poland
| | - Zhe Chen
- Department of Biophysics, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
| | - Yang Li
- Department of Biophysics, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
| | - John W. Schoggins
- Department of Microbiology, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
| | - Vincent S. Tagliabracci
- Department of Molecular Biology, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
- Harold C. Simmons Comprehensive Cancer Center, University of Texas Southwestern Medical Center, Dallas, Texas 75390, USA
- Hamon Center for Regenerative Science and Medicine, University of Texas Southwestern Medical Center, Dallas, Texas 75390, USA
- Howard Hughes Medical Institute, University of Texas Southwestern Medical Center, Dallas, Texas 75390, USA
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24
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Detailed Analyses of Molecular Interactions between Favipiravir and RNA Viruses In Silico. Viruses 2022; 14:v14020338. [PMID: 35215932 PMCID: PMC8879546 DOI: 10.3390/v14020338] [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: 12/24/2021] [Revised: 02/01/2022] [Accepted: 02/05/2022] [Indexed: 02/05/2023] Open
Abstract
There are currently no antiviral agents for human metapneumovirus (HMPV), respiratory syncytial virus (RSV), mumps virus (MuV), or measles virus (MeV). Favipiravir has been developed as an anti-influenza agent, and this agent may be effective against these viruses in vitro. However, the molecular mechanisms through which the agent affects virus replication remain to be fully elucidated. Thus, to clarify the detailed molecular interactions between favipiravir and the RNA-dependent RNA polymerase (RdRp) of HMPV, RSV, MuV, MeV, and influenza virus, we performed in silico studies using authentic bioinformatics technologies. As a result, we found that the active form of favipiravir (favipiravir ribofuranosyl-5′-triphosphate [F-RTP]) can bind to the RdRp active sites of HMPV, RSV, MuV, and MeV. The aspartic acid residue of RdRp active sites was involved in the interaction. Moreover, F-RTP was incorporated into the growing viral RNA chain in the presence of nucleotide triphosphate and magnesium ions. The results suggested that favipiravir shows two distinct mechanisms in various viruses: RdRp active site inhibition and/or genome replication inhibition.
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Ogino M, Green TJ, Ogino T. GDP polyribonucleotidyltransferase domain of vesicular stomatitis virus polymerase regulates leader-promoter escape and polyadenylation-coupled termination during stop-start transcription. PLoS Pathog 2022; 18:e1010287. [PMID: 35108335 PMCID: PMC8843114 DOI: 10.1371/journal.ppat.1010287] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2021] [Revised: 02/14/2022] [Accepted: 01/19/2022] [Indexed: 11/23/2022] Open
Abstract
The unconventional mRNA capping enzyme (GDP polyribonucleotidyltransferase, PRNTase) domain of the vesicular stomatitis virus (VSV) L protein possesses a dual-functional "priming-capping loop" that governs terminal de novo initiation for leader RNA synthesis and capping of monocistronic mRNAs during the unique stop-start transcription cycle. Here, we investigated the roles of basic amino acid residues on a helix structure directly connected to the priming-capping loop in viral RNA synthesis and identified single point mutations that cause previously unreported defective phenotypes at different steps of stop-start transcription. Mutations of residue R1183 (R1183A and R1183K) dramatically reduced the leader RNA synthesis activity by hampering early elongation, but not terminal de novo initiation or productive elongation, suggesting that the mutations negatively affect escape from the leader promoter. On the other hand, mutations of residue R1178 (R1178A and R1178K) decreased the efficiency of polyadenylation-coupled termination of mRNA synthesis at the gene junctions, but not termination of leader RNA synthesis at the leader-to-N-gene junction, resulting in the generation of larger amounts of aberrant polycistronic mRNAs. In contrast, both the R1183 and R1178 residues are not essential for cap-forming activities. The R1183K mutation was lethal to VSV, whereas the R1178K mutation attenuated VSV and triggered the production of the polycistronic mRNAs in infected cells. These observations suggest that the PRNTase domain plays multiple roles in conducting accurate stop-start transcription beyond its known role in pre-mRNA capping. Vesicular stomatitis virus (VSV), an animal rhabdovirus closely related to rabies virus, has served as a paradigm for understanding the basic molecular mechanisms of transcription and replication by rhabdoviruses (e.g., rabies) and other non-segmented negative strand (NNS) RNA viruses, such as measles and Ebola. NNS RNA viral polymerases sequentially synthesize the non-coding leader RNA and monocistronic mRNAs from the 3′-terminal leader region and internal genes, respectively, on their genomes by the stop-start transcription mechanism. A hallmark of NNS RNA viral polymerases is the presence of a unique enzymatic domain, called GDP polyribonucleotidyltransferase (PRNTase), which catalyzes pre-mRNA 5′-capping, one of the essential mRNA modifications. Our recent study revealed that the VSV PRNTase domain directs transcription initiation at the 3′-end of the genome as well as pre-mRNA capping with the dual functional priming-capping loop during stop-start transcription. Here, we further show that a helix structure flanked by the priming-capping loop regulates not only transcription elongation at an early phase of leader RNA synthesis but also polyadenylation-coupled transcription termination at gene junctions. These findings indicate that the PRNTase domain acts as a key regulatory domain for stop-start transcription as well as a catalytic domain for pre-mRNA capping.
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Affiliation(s)
- Minako Ogino
- Department of Medical Microbiology and Immunology, College of Medicine and Life Sciences, University of Toledo, Toledo, Ohio, United States of America
| | - Todd J. Green
- Department of Microbiology, School of Medicine, University of Alabama at Birmingham, Birmingham, Alabama, United States of America
| | - Tomoaki Ogino
- Department of Medical Microbiology and Immunology, College of Medicine and Life Sciences, University of Toledo, Toledo, Ohio, United States of America
- * E-mail:
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Camero M, Lanave G, Catella C, Lucente MS, Sposato A, Mari V, Tempesta M, Martella V, Buonavoglia A. ERDRP-0519 inhibits feline coronavirus in vitro. BMC Vet Res 2022; 18:55. [PMID: 35078478 PMCID: PMC8787031 DOI: 10.1186/s12917-022-03153-3] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2020] [Accepted: 01/07/2022] [Indexed: 11/15/2022] Open
Abstract
Background Coronaviruses (CoVs) are major human and animal pathogens and antiviral drugs are pursued as a complementary strategy, chiefly if vaccines are not available. Feline infectious peritonitis (FIP) is a fatal systemic disease of felids caused by FIP virus (FIPV), a virulent pathotype of feline enteric coronavirus (FeCoV). Some antiviral drugs active on FIPV have been identified, but they are not available in veterinary medicine. ERDRP-0519 (ERDRP) is a non-nucleoside inhibitor, targeting viral RNA polymerase, effective against morbilliviruses in vitro and in vivo. Results The antiviral efficacy of ERDRP against a type II FIPV was evaluated in vitro in Crandell Reese Feline Kidney (CRFK) cells. ERDRP significantly inhibited replication of FIPV in a dose-dependent manner. Viral infectivity was decreased by up to 3.00 logarithms in cell cultures whilst viral load, estimated by quantification of nucleic acids, was reduced by nearly 3.11 logaritms. Conclusions These findings confirm that ERDRP is highly effective against a CoV. Experiments will be necessary to assess whether ERDRP is suitable for treatment of FIPV in vivo. Supplementary Information The online version contains supplementary material available at 10.1186/s12917-022-03153-3.
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Affiliation(s)
- Michele Camero
- Department of Veterinary Medicine, University of Bari, Valenzano, Italy
| | - Gianvito Lanave
- Department of Veterinary Medicine, University of Bari, Valenzano, Italy.
| | - Cristiana Catella
- Department of Veterinary Medicine, University of Bari, Valenzano, Italy
| | | | - Alessio Sposato
- Department of Veterinary Medicine, University of Bari, Valenzano, Italy
| | - Viviana Mari
- Department of Veterinary Medicine, University of Bari, Valenzano, Italy
| | - Maria Tempesta
- Department of Veterinary Medicine, University of Bari, Valenzano, Italy
| | - Vito Martella
- Department of Veterinary Medicine, University of Bari, Valenzano, Italy
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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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The Nucleocapsid of Paramyxoviruses: Structure and Function of an Encapsidated Template. Viruses 2021; 13:v13122465. [PMID: 34960734 PMCID: PMC8708338 DOI: 10.3390/v13122465] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2021] [Revised: 12/07/2021] [Accepted: 12/07/2021] [Indexed: 01/28/2023] Open
Abstract
Viruses of the Paramyxoviridae family share a common and complex molecular machinery for transcribing and replicating their genomes. Their non-segmented, negative-strand RNA genome is encased in a tight homopolymer of viral nucleoproteins (N). This ribonucleoprotein complex, termed a nucleocapsid, is the template of the viral polymerase complex made of the large protein (L) and its co-factor, the phosphoprotein (P). This review summarizes the current knowledge on several aspects of paramyxovirus transcription and replication, including structural and functional data on (1) the architecture of the nucleocapsid (structure of the nucleoprotein, interprotomer contacts, interaction with RNA, and organization of the disordered C-terminal tail of N), (2) the encapsidation of the genomic RNAs (structure of the nucleoprotein in complex with its chaperon P and kinetics of RNA encapsidation in vitro), and (3) the use of the nucleocapsid as a template for the polymerase complex (release of the encased RNA and interaction network allowing the progress of the polymerase complex). Finally, this review presents models of paramyxovirus transcription and replication.
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Bach S, Demper JC, Klemm P, Schlereth J, Lechner M, Schoen A, Kämper L, Weber F, Becker S, Biedenkopf N, Hartmann RK. Identification and characterization of short leader and trailer RNAs synthesized by the Ebola virus RNA polymerase. PLoS Pathog 2021; 17:e1010002. [PMID: 34699554 PMCID: PMC8547711 DOI: 10.1371/journal.ppat.1010002] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2021] [Accepted: 10/04/2021] [Indexed: 11/21/2022] Open
Abstract
Transcription of non-segmented negative sense (NNS) RNA viruses follows a stop-start mechanism and is thought to be initiated at the genome’s very 3’-end. The synthesis of short abortive leader transcripts (leaderRNAs) has been linked to transcription initiation for some NNS viruses. Here, we identified the synthesis of abortive leaderRNAs (as well as trailer RNAs) that are specifically initiated opposite to (anti)genome nt 2; leaderRNAs are predominantly terminated in the region of nt ~ 60–80. LeaderRNA synthesis requires hexamer phasing in the 3’-leader promoter. We determined a steady-state NP mRNA:leaderRNA ratio of ~10 to 30-fold at 48 h after Ebola virus (EBOV) infection, and this ratio was higher (70 to 190-fold) for minigenome-transfected cells. LeaderRNA initiation at nt 2 and the range of termination sites were not affected by structure and length variation between promoter elements 1 and 2, nor the presence or absence of VP30. Synthesis of leaderRNA is suppressed in the presence of VP30 and termination of leaderRNA is not mediated by cryptic gene end (GE) signals in the 3’-leader promoter. We further found different genomic 3’-end nucleotide requirements for transcription versus replication, suggesting that promoter recognition is different in the replication and transcription mode of the EBOV polymerase. We further provide evidence arguing against a potential role of EBOV leaderRNAs as effector molecules in innate immunity. Taken together, our findings are consistent with a model according to which leaderRNAs are abortive replicative RNAs whose synthesis is not linked to transcription initiation. Rather, replication and transcription complexes are proposed to independently initiate RNA synthesis at separate sites in the 3’-leader promoter, i.e., at the second nucleotide of the genome 3’-end and at the more internally positioned transcription start site preceding the first gene, respectively, as reported for Vesicular stomatitis virus. The RNA polymerase (RdRp) of Ebola virus (EBOV) initiates RNA synthesis at the 3’-leader promoter of its encapsidated, non-segmented negative sense (NNS) RNA genome, either at the penultimate 3’-end position of the genome in the replicative mode or more internally (position 56) at the transcription start site (TSS) in its transcription mode. Here we identified the synthesis of abortive replicative RNAs that are specifically initiated opposite to genome nt 2 (termed leaderRNAs) and predominantly terminated in the region of nt ~ 60–80 near the TSS. The functional role of abortive leaderRNA synthesis is still enigmatic; a role in interferon induction could be excluded. Our findings indirectly link leaderRNA termination to nucleoprotein (NP) availability for encapsidation of nascent replicative RNA or to NP removal from the template RNA. Our findings further argue against the model that leaderRNA synthesis is a prerequisite for each transcription initiation event at the TSS. Rather, our findings are in line with the existence of distinct replicase and transcriptase complexes of RdRp that interact differently with the 3’-leader promoter and intiate RNA synthesis independently at different sites (position 2 or 56 of the genome), mechanistically similar to another NNS virus, Vesicular stomatitis virus.
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Affiliation(s)
- Simone Bach
- Institut für Pharmazeutische Chemie, Philipps-Universität Marburg, Marburg, Germany
| | - Jana-Christin Demper
- Institut für Pharmazeutische Chemie, Philipps-Universität Marburg, Marburg, Germany
| | - Paul Klemm
- Zentrum für Synthetische Mikrobiologie, Philipps-Universität Marburg, Marburg, Germany
| | - Julia Schlereth
- Institut für Pharmazeutische Chemie, Philipps-Universität Marburg, Marburg, Germany
| | - Marcus Lechner
- Zentrum für Synthetische Mikrobiologie, Philipps-Universität Marburg, Marburg, Germany
| | - Andreas Schoen
- Institut für Virologie, Justus-Liebig-Universität Gießen, Gießen, Germany
| | - Lennart Kämper
- Institut für Virologie, Philipps-Universität Marburg, Marburg, Germany
| | - Friedemann Weber
- Institut für Virologie, Justus-Liebig-Universität Gießen, Gießen, Germany
| | - Stephan Becker
- Institut für Virologie, Philipps-Universität Marburg, Marburg, Germany
| | - Nadine Biedenkopf
- Institut für Virologie, Philipps-Universität Marburg, Marburg, Germany
- * E-mail: (NB); (RKH)
| | - Roland K. Hartmann
- Institut für Pharmazeutische Chemie, Philipps-Universität Marburg, Marburg, Germany
- * E-mail: (NB); (RKH)
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Structural and Functional Aspects of Ebola Virus Proteins. Pathogens 2021; 10:pathogens10101330. [PMID: 34684279 PMCID: PMC8538763 DOI: 10.3390/pathogens10101330] [Citation(s) in RCA: 21] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2021] [Revised: 10/11/2021] [Accepted: 10/14/2021] [Indexed: 01/14/2023] Open
Abstract
Ebola virus (EBOV), member of genus Ebolavirus, family Filoviridae, have a non-segmented, single-stranded RNA that contains seven genes: (a) nucleoprotein (NP), (b) viral protein 35 (VP35), (c) VP40, (d) glycoprotein (GP), (e) VP30, (f) VP24, and (g) RNA polymerase (L). All genes encode for one protein each except GP, producing three pre-proteins due to the transcriptional editing. These pre-proteins are translated into four products, namely: (a) soluble secreted glycoprotein (sGP), (b) Δ-peptide, (c) full-length transmembrane spike glycoprotein (GP), and (d) soluble small secreted glycoprotein (ssGP). Further, shed GP is released from infected cells due to cleavage of GP by tumor necrosis factor α-converting enzyme (TACE). This review presents a detailed discussion on various functional aspects of all EBOV proteins and their residues. An introduction to ebolaviruses and their life cycle is also provided for clarity of the available analysis. We believe that this review will help understand the roles played by different EBOV proteins in the pathogenesis of the disease. It will help in targeting significant protein residues for therapeutic and multi-protein/peptide vaccine development.
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Wang B, Svetlov D, Artsimovitch I. NMPylation and de-NMPylation of SARS-CoV-2 nsp9 by the NiRAN domain. Nucleic Acids Res 2021; 49:8822-8835. [PMID: 34352100 PMCID: PMC8385902 DOI: 10.1093/nar/gkab677] [Citation(s) in RCA: 29] [Impact Index Per Article: 9.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2021] [Revised: 07/15/2021] [Accepted: 07/26/2021] [Indexed: 12/11/2022] Open
Abstract
The catalytic subunit of SARS-CoV-2 RNA-dependent RNA polymerase (RdRp) contains two active sites that catalyze nucleotidyl-monophosphate transfer (NMPylation). Mechanistic studies and drug discovery have focused on RNA synthesis by the highly conserved RdRp. The second active site, which resides in a Nidovirus RdRp-Associated Nucleotidyl transferase (NiRAN) domain, is poorly characterized, but both catalytic reactions are essential for viral replication. One study showed that NiRAN transfers NMP to the first residue of RNA-binding protein nsp9; another reported a structure of nsp9 containing two additional N-terminal residues bound to the NiRAN active site but observed NMP transfer to RNA instead. We show that SARS-CoV-2 RdRp NMPylates the native but not the extended nsp9. Substitutions of the invariant NiRAN residues abolish NMPylation, whereas substitution of a catalytic RdRp Asp residue does not. NMPylation can utilize diverse nucleotide triphosphates, including remdesivir triphosphate, is reversible in the presence of pyrophosphate, and is inhibited by nucleotide analogs and bisphosphonates, suggesting a path for rational design of NiRAN inhibitors. We reconcile these and existing findings using a new model in which nsp9 remodels both active sites to alternately support initiation of RNA synthesis by RdRp or subsequent capping of the product RNA by the NiRAN domain.
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Affiliation(s)
- Bing Wang
- Department of Microbiology, The Ohio State University, Columbus, OH 43210, USA
- The Center for RNA Biology, The Ohio State University, Columbus, OH 43210, USA
| | | | - Irina Artsimovitch
- Department of Microbiology, The Ohio State University, Columbus, OH 43210, USA
- The Center for RNA Biology, The Ohio State University, Columbus, OH 43210, USA
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Cardone C, Caseau CM, Bardiaux B, Thureaux A, Galloux M, Bajorek M, Eléouët JF, Litaudon M, Bontems F, Sizun C. A Structural and Dynamic Analysis of the Partially Disordered Polymerase-Binding Domain in RSV Phosphoprotein. Biomolecules 2021; 11:biom11081225. [PMID: 34439894 PMCID: PMC8392014 DOI: 10.3390/biom11081225] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2021] [Revised: 08/10/2021] [Accepted: 08/13/2021] [Indexed: 12/11/2022] Open
Abstract
The phosphoprotein P of Mononegavirales (MNV) is an essential co-factor of the viral RNA polymerase L. Its prime function is to recruit L to the ribonucleocapsid composed of the viral genome encapsidated by the nucleoprotein N. MNV phosphoproteins often contain a high degree of disorder. In Pneumoviridae phosphoproteins, the only domain with well-defined structure is a small oligomerization domain (POD). We previously characterized the differential disorder in respiratory syncytial virus (RSV) phosphoprotein by NMR. We showed that outside of RSV POD, the intrinsically disordered N-and C-terminal regions displayed a structural and dynamic diversity ranging from random coil to high helical propensity. Here we provide additional insight into the dynamic behavior of PCα, a domain that is C-terminal to POD and constitutes the RSV L-binding region together with POD. By using small phosphoprotein fragments centered on or adjacent to POD, we obtained a structural picture of the POD–PCα region in solution, at the single residue level by NMR and at lower resolution by complementary biophysical methods. We probed POD–PCα inter-domain contacts and showed that small molecules were able to modify the dynamics of PCα. These structural properties are fundamental to the peculiar binding mode of RSV phosphoprotein to L, where each of the four protomers binds to L in a different way.
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Affiliation(s)
- Christophe Cardone
- Institut de Chimie des Substances Naturelles, CNRS, Université Paris Saclay, 91190 Gif-sur-Yvette, France; (C.C.); (C.-M.C.); (M.L.); (F.B.)
| | - Claire-Marie Caseau
- Institut de Chimie des Substances Naturelles, CNRS, Université Paris Saclay, 91190 Gif-sur-Yvette, France; (C.C.); (C.-M.C.); (M.L.); (F.B.)
| | - Benjamin Bardiaux
- Structural Bioinformatics Unit, Department of Structural Biology and Chemistry, Institut Pasteur, CNRS UMR3528, 78015 Paris, France;
| | | | - Marie Galloux
- Unité de Virologie et Immunologie Moléculaires, INRAE, Université Paris Saclay, 78352 Jouy-en-Josas, France; (M.G.); (M.B.); (J.-F.E.)
| | - Monika Bajorek
- Unité de Virologie et Immunologie Moléculaires, INRAE, Université Paris Saclay, 78352 Jouy-en-Josas, France; (M.G.); (M.B.); (J.-F.E.)
| | - Jean-François Eléouët
- Unité de Virologie et Immunologie Moléculaires, INRAE, Université Paris Saclay, 78352 Jouy-en-Josas, France; (M.G.); (M.B.); (J.-F.E.)
| | - Marc Litaudon
- Institut de Chimie des Substances Naturelles, CNRS, Université Paris Saclay, 91190 Gif-sur-Yvette, France; (C.C.); (C.-M.C.); (M.L.); (F.B.)
| | - François Bontems
- Institut de Chimie des Substances Naturelles, CNRS, Université Paris Saclay, 91190 Gif-sur-Yvette, France; (C.C.); (C.-M.C.); (M.L.); (F.B.)
| | - Christina Sizun
- Institut de Chimie des Substances Naturelles, CNRS, Université Paris Saclay, 91190 Gif-sur-Yvette, France; (C.C.); (C.-M.C.); (M.L.); (F.B.)
- Correspondence:
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Ker DS, Jenkins HT, Greive SJ, Antson AA. CryoEM structure of the Nipah virus nucleocapsid assembly. PLoS Pathog 2021; 17:e1009740. [PMID: 34270629 PMCID: PMC8318291 DOI: 10.1371/journal.ppat.1009740] [Citation(s) in RCA: 21] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2021] [Revised: 07/28/2021] [Accepted: 06/22/2021] [Indexed: 11/18/2022] Open
Abstract
Nipah and its close relative Hendra are highly pathogenic zoonotic viruses, storing their ssRNA genome in a helical nucleocapsid assembly formed by the N protein, a major viral immunogen. Here, we report the first cryoEM structure for a Henipavirus RNA-bound nucleocapsid assembly, at 3.5 Å resolution. The helical assembly is stabilised by previously undefined N- and C-terminal segments, contributing to subunit-subunit interactions. RNA is wrapped around the nucleocapsid protein assembly with a periodicity of six nucleotides per protomer, in the “3-bases-in, 3-bases-out” conformation, with protein plasticity enabling non-sequence specific interactions. The structure reveals commonalities in RNA binding pockets and in the conformation of bound RNA, not only with members of the Paramyxoviridae family, but also with the evolutionarily distant Filoviridae Ebola virus. Significant structural differences with other Paramyxoviridae members are also observed, particularly in the position and length of the exposed α-helix, residues 123–139, which may serve as a valuable epitope for surveillance and diagnostics. Nipah virus is a highly pathogenic RNA virus which, along with the closely related Hendra virus, emerged relatively recently. Due to ~40% mortality rate and evidence of animal-to-human as well as human-to-human transmission, development of antivirals against the Nipah and henipaviral disease is particularly urgent. In common with other single-stranded RNA viruses, including Ebola and coronaviruses, the nucleocapsid assembly of the Nipah virus safeguards the viral genome, protecting it from degradation and facilitating its encapsidation and storage inside the virion. Here, we used cryo-electron microscopy to determine accurate three-dimensional structure for several different assemblies of the Nipah virus nucleocapsid protein, in particular a detailed structure for the complex of this protein with RNA. This structural information is important for understanding detailed molecular interactions driving and stabilizing the nucleocapsid assembly formation that are of fundamental importance for understanding similar processes in a large group of ssRNA viruses. Apart from highlighting structural similarities and differences with nucleocapsid proteins of other viruses of the Paramyxoviridae family, these data will inform the development of new antiviral approaches for the henipaviruses.
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Affiliation(s)
- De-Sheng Ker
- York Structural Biology Laboratory, Department of Chemistry, University of York, York, United Kingdom
| | - Huw T. Jenkins
- York Structural Biology Laboratory, Department of Chemistry, University of York, York, United Kingdom
| | - Sandra J. Greive
- York Structural Biology Laboratory, Department of Chemistry, University of York, York, United Kingdom
| | - Alfred A. Antson
- York Structural Biology Laboratory, Department of Chemistry, University of York, York, United Kingdom
- * E-mail:
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Dolnik O, Gerresheim GK, Biedenkopf N. New Perspectives on the Biogenesis of Viral Inclusion Bodies in Negative-Sense RNA Virus Infections. Cells 2021; 10:cells10061460. [PMID: 34200781 PMCID: PMC8230417 DOI: 10.3390/cells10061460] [Citation(s) in RCA: 24] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2021] [Revised: 06/06/2021] [Accepted: 06/08/2021] [Indexed: 12/13/2022] Open
Abstract
Infections by negative strand RNA viruses (NSVs) induce the formation of viral inclusion bodies (IBs) in the host cell that segregate viral as well as cellular proteins to enable efficient viral replication. The induction of those membrane-less viral compartments leads inevitably to structural remodeling of the cellular architecture. Recent studies suggested that viral IBs have properties of biomolecular condensates (or liquid organelles), as have previously been shown for other membrane-less cellular compartments like stress granules or P-bodies. Biomolecular condensates are highly dynamic structures formed by liquid-liquid phase separation (LLPS). Key drivers for LLPS in cells are multivalent protein:protein and protein:RNA interactions leading to specialized areas in the cell that recruit molecules with similar properties, while other non-similar molecules are excluded. These typical features of cellular biomolecular condensates are also a common characteristic in the biogenesis of viral inclusion bodies. Viral IBs are predominantly induced by the expression of the viral nucleoprotein (N, NP) and phosphoprotein (P); both are characterized by a special protein architecture containing multiple disordered regions and RNA-binding domains that contribute to different protein functions. P keeps N soluble after expression to allow a concerted binding of N to the viral RNA. This results in the encapsidation of the viral genome by N, while P acts additionally as a cofactor for the viral polymerase, enabling viral transcription and replication. Here, we will review the formation and function of those viral inclusion bodies upon infection with NSVs with respect to their nature as biomolecular condensates.
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Bishnoi S, Kumari A, Rehman S, Minz A, Senapati S, Nayak D, Gupta S. Fusogenic Viral Protein-Based Near-Infrared Active Nanocarriers for Biomedical Imaging. ACS Biomater Sci Eng 2021; 7:3351-3360. [PMID: 34111927 DOI: 10.1021/acsbiomaterials.1c00267] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
An effective drug delivery system (DDS) relies on an efficient cellular uptake and faster intracellular delivery of theranostic agents, bypassing the endosomal mediated degradation of the payload. The use of viral nanoparticles (VNPs) permits such advancement, as the viruses are naturally evolved to infiltrate the host cells to deliver their genetic material. As a proof of concept, we bioengineered the vesicular stomatitis virus glycoprotein (VSV-G)-based near-infrared (NIR) active viral nanoconstructs (NAVNs) encapsulating indocyanine green dye (ICG) for NIR bioimaging. NAVNs are spherical in size and have the intrinsic cellular-fusogenic properties of VSV-G. Further, the NIR imaging displaying higher fluorescence intensity in NAVNs treated cells suggests enhanced cellular uptake and delivery of ICG by NAVNs compared to the free form of ICG. The overall study highlights the effectiveness of VSV-G-based VNPs as an efficient delivery system for NIR fluorescence imaging.
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Affiliation(s)
- Suman Bishnoi
- Department of Biosciences and Biomedical Engineering, Indian Institute of Technology Indore, Indore 453552, India
| | - Anshu Kumari
- Department of Biosciences and Biomedical Engineering, Indian Institute of Technology Indore, Indore 453552, India.,School of Medicine, University of Maryland Baltimore, Maryland 21201, United States
| | - Sheeba Rehman
- Department of Biosciences and Biomedical Engineering, Indian Institute of Technology Indore, Indore 453552, India
| | - Aliva Minz
- Institute of Life Sciences, Nalco Square, Bhubaneswar, Odisha 751023, India
| | | | - Debasis Nayak
- Department of Biosciences and Biomedical Engineering, Indian Institute of Technology Indore, Indore 453552, India
| | - Sharad Gupta
- Department of Biosciences and Biomedical Engineering, Indian Institute of Technology Indore, Indore 453552, India.,School of Biotechnology, Jawaharlal Nehru University, New Delhi 110067, India
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Structural Insights into the Respiratory Syncytial Virus RNA Synthesis Complexes. Viruses 2021; 13:v13050834. [PMID: 34063087 PMCID: PMC8147935 DOI: 10.3390/v13050834] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2021] [Revised: 04/30/2021] [Accepted: 05/02/2021] [Indexed: 12/13/2022] Open
Abstract
RNA synthesis in respiratory syncytial virus (RSV), a negative-sense (-) nonsegmented RNA virus, consists of viral gene transcription and genome replication. Gene transcription includes the positive-sense (+) viral mRNA synthesis, 5'-RNA capping and methylation, and 3' end polyadenylation. Genome replication includes (+) RNA antigenome and (-) RNA genome synthesis. RSV executes the viral RNA synthesis using an RNA synthesis ribonucleoprotein (RNP) complex, comprising four proteins, the nucleoprotein (N), the large protein (L), the phosphoprotein (P), and the M2-1 protein. We provide an overview of the RSV RNA synthesis and the structural insights into the RSV gene transcription and genome replication process. We propose a model of how the essential four proteins coordinate their activities in different RNA synthesis processes.
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Fearns R. Negative‐strand RNA Viruses. Virology 2021. [DOI: 10.1002/9781119818526.ch3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/21/2022]
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Cox RM, Sourimant J, Govindarajan M, Natchus MG, Plemper RK. Therapeutic targeting of measles virus polymerase with ERDRP-0519 suppresses all RNA synthesis activity. PLoS Pathog 2021; 17:e1009371. [PMID: 33621266 PMCID: PMC7935272 DOI: 10.1371/journal.ppat.1009371] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2020] [Revised: 03/05/2021] [Accepted: 02/10/2021] [Indexed: 12/20/2022] Open
Abstract
Morbilliviruses, such as measles virus (MeV) and canine distemper virus (CDV), are highly infectious members of the paramyxovirus family. MeV is responsible for major morbidity and mortality in non-vaccinated populations. ERDRP-0519, a pan-morbillivirus small molecule inhibitor for the treatment of measles, targets the morbillivirus RNA-dependent RNA-polymerase (RdRP) complex and displayed unparalleled oral efficacy against lethal infection of ferrets with CDV, an established surrogate model for human measles. Resistance profiling identified the L subunit of the RdRP, which harbors all enzymatic activity of the polymerase complex, as the molecular target of inhibition. Here, we examined binding characteristics, physical docking site, and the molecular mechanism of action of ERDRP-0519 through label-free biolayer interferometry, photoaffinity cross-linking, and in vitro RdRP assays using purified MeV RdRP complexes and synthetic templates. Results demonstrate that unlike all other mononegavirus small molecule inhibitors identified to date, ERDRP-0519 inhibits all phosphodiester bond formation in both de novo initiation of RNA synthesis at the promoter and RNA elongation by a committed polymerase complex. Photocrosslinking and resistance profiling-informed ligand docking revealed that this unprecedented mechanism of action of ERDRP-0519 is due to simultaneous engagement of the L protein polyribonucleotidyl transferase (PRNTase)-like domain and the flexible intrusion loop by the compound, pharmacologically locking the polymerase in pre-initiation conformation. This study informs selection of ERDRP-0519 as clinical candidate for measles therapy and identifies a previously unrecognized druggable site in mononegavirus L polymerase proteins that can silence all synthesis of viral RNA. The mononegavirus order contains major established and recently emerged human pathogens. Despite the threat to human health, antiviral therapeutics directed against this order remain understudied. The mononegavirus polymerase complex represents a promising drug target due to its central importance for both virus replication and viral mitigation of the innate host antiviral response. In this study, we have mechanistically characterized a clinical candidate small-molecule MeV polymerase inhibitor. The compound blocked all phosphodiester bond formation activity, a unique mechanism of action unlike all other known mononegavirus polymerase inhibitors. Photocrosslinking-based target site mapping demonstrated that this class-defining prototype inhibitor stabilizes a pre-initiation conformation of the viral polymerase complex that sterically cannot accommodate template RNA. Function-equivalent druggable sites exist in all mononegavirus polymerases. In addition to its direct anti-MeV impact, the insight gained in this study can therefore serve as a blueprint for indication spectrum expansion through structure-informed scaffold engineering or targeted drug discovery.
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Affiliation(s)
- Robert M. Cox
- Institute for Biomedical Sciences, Georgia State University, Atlanta, Georgia, United States of America
| | - Julien Sourimant
- Institute for Biomedical Sciences, Georgia State University, Atlanta, Georgia, United States of America
| | - Mugunthan Govindarajan
- Emory Institute for Drug Development, Emory University, Atlanta, Georgia, United States of America
| | - Michael G. Natchus
- Emory Institute for Drug Development, Emory University, Atlanta, Georgia, United States of America
| | - Richard K. Plemper
- Institute for Biomedical Sciences, Georgia State University, Atlanta, Georgia, United States of America
- * E-mail:
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Abstract
RNA viruses include many important human and animal pathogens, such as the influenza viruses, respiratory syncytial virus, Ebola virus, measles virus and rabies virus. The genomes of these viruses consist of single or multiple RNA segments that assemble with oligomeric viral nucleoprotein into ribonucleoprotein complexes. Replication and transcription of the viral genome is performed by ~250-450 kDa viral RNA-dependent RNA polymerases that also contain capping or cap-snatching activity. In this Review, we compare recent high-resolution X-ray and cryoelectron microscopy structures of RNA polymerases of negative-sense RNA viruses with segmented and non-segmented genomes, including orthomyxoviruses, peribunyaviruses, phenuiviruses, arenaviruses, rhabdoviruses, pneumoviruses and paramyxoviruses. In addition, we discuss how structural insights into these enzymes contribute to our understanding of the molecular mechanisms of viral transcription and replication, and how we can use these insights to identify targets for antiviral drug design.
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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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Abstract
Mononegavirales, known as nonsegmented negative-sense (NNS) RNA viruses, are a class of pathogenic and sometimes deadly viruses that include rabies virus (RABV), human respiratory syncytial virus (HRSV), and Ebola virus (EBOV). Unfortunately, no effective vaccines and antiviral therapeutics against many Mononegavirales are currently available. Viral polymerases have been attractive and major antiviral therapeutic targets. Therefore, Mononegavirales polymerases have been extensively investigated for their structures and functions. Mononegavirales, known as nonsegmented negative-sense (NNS) RNA viruses, are a class of pathogenic and sometimes deadly viruses that include rabies virus (RABV), human respiratory syncytial virus (HRSV), and Ebola virus (EBOV). Unfortunately, no effective vaccines and antiviral therapeutics against many Mononegavirales are currently available. Viral polymerases have been attractive and major antiviral therapeutic targets. Therefore, Mononegavirales polymerases have been extensively investigated for their structures and functions. Mononegavirales mimic RNA synthesis of their eukaryotic counterparts by utilizing multifunctional RNA polymerases to replicate entire viral genomes and transcribe viral mRNAs from individual viral genes as well as synthesize 5′ methylated cap and 3′ poly(A) tail of the transcribed viral mRNAs. The catalytic subunit large protein (L) and cofactor phosphoprotein (P) constitute the Mononegavirales polymerases. In this review, we discuss the shared and unique features of RNA synthesis, the monomeric multifunctional enzyme L, and the oligomeric multimodular adapter P of Mononegavirales. We outline the structural analyses of the Mononegavirales polymerases since the first structure of the vesicular stomatitis virus (VSV) L protein determined in 2015 and highlight multiple high-resolution cryo-electron microscopy (cryo-EM) structures of the polymerases of Mononegavirales, namely, VSV, RABV, HRSV, human metapneumovirus (HMPV), and human parainfluenza virus (HPIV), that have been reported in recent months (2019 to 2020). We compare the structures of those polymerases grouped by virus family, illustrate the similarities and differences among those polymerases, and reveal the potential RNA synthesis mechanisms and models of highly conserved Mononegavirales. We conclude by the discussion of remaining questions, evolutionary perspectives, and future directions.
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Luo M, Terrell JR, Mcmanus SA. Nucleocapsid Structure of Negative Strand RNA Virus. Viruses 2020; 12:E835. [PMID: 32751700 PMCID: PMC7472042 DOI: 10.3390/v12080835] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2020] [Revised: 07/23/2020] [Accepted: 07/27/2020] [Indexed: 12/14/2022] Open
Abstract
Negative strand RNA viruses (NSVs) include many important human pathogens, such as influenza virus, Ebola virus, and rabies virus. One of the unique characteristics that NSVs share is the assembly of the nucleocapsid and its role in viral RNA synthesis. In NSVs, the single strand RNA genome is encapsidated in the linear nucleocapsid throughout the viral replication cycle. Subunits of the nucleocapsid protein are parallelly aligned along the RNA genome that is sandwiched between two domains composed of conserved helix motifs. The viral RNA-dependent-RNA polymerase (vRdRp) must recognize the protein-RNA complex of the nucleocapsid and unveil the protected genomic RNA in order to initiate viral RNA synthesis. In addition, vRdRp must continuously translocate along the protein-RNA complex during elongation in viral RNA synthesis. This unique mechanism of viral RNA synthesis suggests that the nucleocapsid may play a regulatory role during NSV replication.
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Affiliation(s)
- Ming Luo
- Department of Chemistry, Georgia State University, Atlanta, GA 30302, USA; (J.R.T.); (S.A.M.)
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Jensen MR, Yabukarski F, Communie G, Condamine E, Mas C, Volchkova V, Tarbouriech N, Bourhis JM, Volchkov V, Blackledge M, Jamin M. Structural Description of the Nipah Virus Phosphoprotein and Its Interaction with STAT1. Biophys J 2020; 118:2470-2488. [PMID: 32348724 PMCID: PMC7231922 DOI: 10.1016/j.bpj.2020.04.010] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2019] [Revised: 03/31/2020] [Accepted: 04/06/2020] [Indexed: 12/25/2022] Open
Abstract
The structural characterization of modular proteins containing long intrinsically disordered regions intercalated with folded domains is complicated by their conformational diversity and flexibility and requires the integration of multiple experimental approaches. Nipah virus (NiV) phosphoprotein, an essential component of the viral RNA transcription/replication machine and a component of the viral arsenal that hijacks cellular components and counteracts host immune responses, is a prototypical model for such modular proteins. Curiously, the phosphoprotein of NiV is significantly longer than the corresponding protein of other paramyxoviruses. Here, we combine multiple biophysical methods, including x-ray crystallography, NMR spectroscopy, and small angle x-ray scattering, to characterize the structure of this protein and provide an atomistic representation of the full-length protein in the form of a conformational ensemble. We show that full-length NiV phosphoprotein is tetrameric, and we solve the crystal structure of its tetramerization domain. Using NMR spectroscopy and small angle x-ray scattering, we show that the long N-terminal intrinsically disordered region and the linker connecting the tetramerization domain to the C-terminal X domain exchange between multiple conformations while containing short regions of residual secondary structure. Some of these transient helices are known to interact with partners, whereas others represent putative binding sites for yet unidentified proteins. Finally, using NMR spectroscopy and isothermal titration calorimetry, we map a region of the phosphoprotein, comprising residues between 110 and 140 and common to the V and W proteins, that binds with weak affinity to STAT1 and confirm the involvement of key amino acids of the viral protein in this interaction. This provides new, to our knowledge, insights into how the phosphoprotein and the nonstructural V and W proteins of NiV perform their multiple functions.
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Affiliation(s)
| | - Filip Yabukarski
- Institut de Biologie Structurale, University Grenoble Alpes, CEA, CNRS, Grenoble, France
| | - Guillaume Communie
- Institut de Biologie Structurale, University Grenoble Alpes, CEA, CNRS, Grenoble, France
| | - Eric Condamine
- Institut de Biologie Structurale, University Grenoble Alpes, CEA, CNRS, Grenoble, France
| | - Caroline Mas
- Integrated Structural Biology Grenoble CNRS, CEA, University Grenoble Alpes, EMBL, Grenoble, France
| | - Valentina Volchkova
- Molecular Basis of Viral Pathogenicity, Centre International de Recherche en Infectiologie, INSERMU1111-CNRS UMR5308, Université Claude Bernard Lyon 1, ENS de Lyon, Lyon, France
| | - Nicolas Tarbouriech
- Institut de Biologie Structurale, University Grenoble Alpes, CEA, CNRS, Grenoble, France
| | - Jean-Marie Bourhis
- Institut de Biologie Structurale, University Grenoble Alpes, CEA, CNRS, Grenoble, France
| | - Viktor Volchkov
- Molecular Basis of Viral Pathogenicity, Centre International de Recherche en Infectiologie, INSERMU1111-CNRS UMR5308, Université Claude Bernard Lyon 1, ENS de Lyon, Lyon, France
| | - Martin Blackledge
- Institut de Biologie Structurale, University Grenoble Alpes, CEA, CNRS, Grenoble, France
| | - Marc Jamin
- Institut de Biologie Structurale, University Grenoble Alpes, CEA, CNRS, Grenoble, France.
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Cao D, Liang B. Cryo-Electron Microscopy Structures of the Pneumoviridae Polymerases. Viral Immunol 2020; 34:18-26. [PMID: 32429800 DOI: 10.1089/vim.2020.0018] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
The resolution revolution of cryo-electron microscopy (cryo-EM) has made a significant impact on the structural analysis of the Pneumoviridae multifunctional RNA polymerases. In recent months, several high-resolution structures of apo RNA polymerases of Pneumoviridae, which includes the human respiratory syncytial virus (HRSV) and human metapneumovirus (HMPV), have been determined by single-particle cryo-EM. These structures illustrated high similarities and minor differences between the Pneumoviridae polymerases and revealed the potential mechanisms of the Pneumoviridae RNA synthesis.
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Affiliation(s)
- Dongdong Cao
- Department of Biochemistry, Emory University School of Medicine, Atlanta, Georgia, USA
| | - Bo Liang
- Department of Biochemistry, Emory University School of Medicine, Atlanta, Georgia, USA
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Bach S, Biedenkopf N, Grünweller A, Becker S, Hartmann RK. Hexamer phasing governs transcription initiation in the 3'-leader of Ebola virus. RNA (NEW YORK, N.Y.) 2020; 26:439-453. [PMID: 31924730 PMCID: PMC7075260 DOI: 10.1261/rna.073718.119] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/22/2019] [Accepted: 01/08/2020] [Indexed: 05/05/2023]
Abstract
The genomic, bipartite replication promoter of Ebola virus (EBOV) consists of elements 1 (PE1) and 2 (PE2). PE1 (55 nt at the 3'-terminus) is separated from PE2 (harboring eight 3'-UN5 hexamers) by the transcription start sequence (TSS) of the first nucleoprotein (NP) gene plus a spacer sequence. Insertions or deletions in the spacer were reported to support genome replication if comprising 6 or 12, but not 1/2/3/5/9 nt. This gave rise to the formulation of the "rule of 6" for the EBOV replication promoter. Here, we studied the impact of such hexamer phasing on viral transcription using a series of replication-competent and -deficient monocistronic minigenomes, in which the spacer of the NP gene was mutated or replaced with that of internal EBOV genes and mutated variants thereof. Beyond reporter gene assays, we conducted qRT-PCR to determine the levels of mRNA, genomic and antigenomic RNA. We demonstrate that hexamer phasing is also essential for viral transcription, that UN5 hexamer periodicity extends into PE1 and that the spacer region can be expanded by 48 nt without losses of transcriptional activity. Making the UN5 hexamer phasing continuous between PE1 and PE2 enhanced the efficiency of transcription and replication. We show that the 2 nt preceding the TSS are essential for transcription. We further propose a role for UN5 hexamer phasing in positioning NP during initiation of RNA synthesis, or in dissociation/reassociation of NP from the template RNA strand while threading the RNA through the active site of the elongating polymerase during replication and transcription.
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Affiliation(s)
- Simone Bach
- Institut für Pharmazeutische Chemie, Philipps-Universität Marburg, 35037 Marburg, Germany
| | - Nadine Biedenkopf
- Institut für Virologie, Philipps-Universität Marburg, 35043 Marburg, Germany
| | - Arnold Grünweller
- Institut für Pharmazeutische Chemie, Philipps-Universität Marburg, 35037 Marburg, Germany
| | - Stephan Becker
- Institut für Virologie, Philipps-Universität Marburg, 35043 Marburg, Germany
| | - Roland K Hartmann
- Institut für Pharmazeutische Chemie, Philipps-Universität Marburg, 35037 Marburg, Germany
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Structure of a paramyxovirus polymerase complex reveals a unique methyltransferase-CTD conformation. Proc Natl Acad Sci U S A 2020; 117:4931-4941. [PMID: 32075920 PMCID: PMC7060699 DOI: 10.1073/pnas.1919837117] [Citation(s) in RCA: 57] [Impact Index Per Article: 14.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022] Open
Abstract
Paramyxoviruses are enveloped, nonsegmented, negative-strand RNA viruses that cause a wide spectrum of human and animal diseases. The viral genome, packaged by the nucleoprotein (N), serves as a template for the polymerase complex, composed of the large protein (L) and the homo-tetrameric phosphoprotein (P). The ∼250-kDa L possesses all enzymatic activities necessary for its function but requires P in vivo. Structural information is available for individual P domains from different paramyxoviruses, but how P interacts with L and how that affects the activity of L is largely unknown due to the lack of high-resolution structures of this complex in this viral family. In this study we determined the structure of the L-P complex from parainfluenza virus 5 (PIV5) at 4.3-Å resolution using cryoelectron microscopy, as well as the oligomerization domain (OD) of P at 1.4-Å resolution using X-ray crystallography. P-OD associates with the RNA-dependent RNA polymerase domain of L and protrudes away from it, while the X domain of one chain of P is bound near the L nucleotide entry site. The methyltransferase (MTase) domain and the C-terminal domain (CTD) of L adopt a unique conformation, positioning the MTase active site immediately above the poly-ribonucleotidyltransferase domain and near the likely exit site for the product RNA 5' end. Our study reveals a potential mechanism that mononegavirus polymerases may employ to switch between transcription and genome replication. This knowledge will assist in the design and development of antivirals against paramyxoviruses.
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Insight into the multifunctional RNA synthesis machine of rabies virus. Proc Natl Acad Sci U S A 2020; 117:3895-3897. [PMID: 31992635 DOI: 10.1073/pnas.2000120117] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
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48
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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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49
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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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50
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Ogino M, Fedorov Y, Adams DJ, Okada K, Ito N, Sugiyama M, Ogino T. Vesiculopolins, a New Class of Anti-Vesiculoviral Compounds, Inhibit Transcription Initiation of Vesiculoviruses. Viruses 2019; 11:v11090856. [PMID: 31540123 PMCID: PMC6783830 DOI: 10.3390/v11090856] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/19/2019] [Revised: 09/11/2019] [Accepted: 09/11/2019] [Indexed: 01/09/2023] Open
Abstract
Vesicular stomatitis virus (VSV) represents a promising platform for developing oncolytic viruses, as well as vaccines against significant human pathogens. To safely control VSV infection in humans, small-molecule drugs that selectively inhibit VSV infection may be needed. Here, using a cell-based high-throughput screening assay followed by an in vitro transcription assay, compounds with a 7-hydroxy-6-methyl-3,4-dihydroquinolin-2(1H)-one structure and an aromatic group at position 4 (named vesiculopolins, VPIs) were identified as VSV RNA polymerase inhibitors. The most effective compound, VPI A, inhibited VSV-induced cytopathic effects and in vitro mRNA synthesis with micromolar to submicromolar 50% inhibitory concentrations. VPI A was found to inhibit terminal de novo initiation rather than elongation for leader RNA synthesis, but not mRNA capping, with the VSV L protein, suggesting that VPI A is targeted to the polymerase domain in the L protein. VPI A inhibited transcription of Chandipura virus, but not of human parainfluenza virus 3, suggesting that it specifically acts on vesiculoviral L proteins. These results suggest that VPIs may serve not only as molecular probes to elucidate the mechanisms of transcription of vesiculoviruses, but also as lead compounds to develop antiviral drugs against vesiculoviruses and other related rhabdoviruses.
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Affiliation(s)
- Minako Ogino
- Department of Molecular Biology and Microbiology, Case Western Reserve University School of Medicine, Cleveland, OH 44106, USA.
| | - Yuriy Fedorov
- Small Molecule Drug Development Core, Case Western Reserve University School of Medicine, Cleveland, OH 44106, USA.
| | - Drew J Adams
- Department of Genetics and Genome Sciences, Case Western Reserve University School of Medicine, Cleveland, OH 44106, USA.
| | - Kazuma Okada
- Laboratory of Zoonotic Diseases, Faculty of Applied Biological Sciences, Gifu University, 1-1 Yanagido, Gifu 501-1193, Japan.
| | - Naoto Ito
- Laboratory of Zoonotic Diseases, Faculty of Applied Biological Sciences, Gifu University, 1-1 Yanagido, Gifu 501-1193, Japan.
- Gifu Center for Highly Advanced Integration of Nanosciences and Life Sciences (G-CHAIN), Gifu University, 1-1 Yanagido, Gifu 501-1193, Japan.
| | - Makoto Sugiyama
- Laboratory of Zoonotic Diseases, Faculty of Applied Biological Sciences, Gifu University, 1-1 Yanagido, Gifu 501-1193, Japan.
| | - Tomoaki Ogino
- Department of Molecular Biology and Microbiology, Case Western Reserve University School of Medicine, Cleveland, OH 44106, USA.
- Department of Inflammation and Immunity, Lerner Research Institute, Cleveland Clinic, Cleveland, OH 44195, USA.
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