1
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Beniston E, Skittrall JP. Locations and structures of influenza A virus packaging-associated signals and other functional elements via an in silico pipeline for predicting constrained features in RNA viruses. PLoS Comput Biol 2024; 20:e1012009. [PMID: 38648223 PMCID: PMC11034665 DOI: 10.1371/journal.pcbi.1012009] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2023] [Accepted: 03/18/2024] [Indexed: 04/25/2024] Open
Abstract
Influenza A virus contains regions of its segmented genome associated with ability to package the segments into virions, but many such regions are poorly characterised. We provide detailed predictions of the key locations within these packaging-associated regions, and their structures, by applying a recently-improved pipeline for delineating constrained regions in RNA viruses and applying structural prediction algorithms. We find and characterise other known constrained regions within influenza A genomes, including the region associated with the PA-X frameshift, regions associated with alternative splicing, and constraint around the initiation motif for a truncated PB1 protein, PB1-N92, associated with avian viruses. We further predict the presence of constrained regions that have not previously been described. The extra characterisation our work provides allows investigation of these key regions for drug target potential, and points towards determinants of packaging compatibility between segments.
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Affiliation(s)
- Emma Beniston
- Department of Pathology, University of Cambridge, Cambridge, United Kingdom
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2
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Yang R, Pan M, Guo J, Huang Y, Zhang QC, Deng T, Wang J. Mapping of the influenza A virus genome RNA structure and interactions reveals essential elements of viral replication. Cell Rep 2024; 43:113833. [PMID: 38416642 DOI: 10.1016/j.celrep.2024.113833] [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: 05/31/2023] [Revised: 12/04/2023] [Accepted: 02/02/2024] [Indexed: 03/01/2024] Open
Abstract
Influenza A virus (IAV) represents a constant public health threat. The single-stranded, segmented RNA genome of IAV is replicated in host cell nuclei as a series of 8 ribonucleoprotein complexes (vRNPs) with RNA structures known to exert essential function to support viral replication. Here, we investigate RNA secondary structures and RNA interactions networks of the IAV genome and construct an in vivo structure model for each of the 8 IAV genome segments. Our analyses reveal an overall in vivo and in virio resemblance of the IAV genome conformation but also wide disparities among long-range and intersegment interactions. Moreover, we identify a long-range RNA interaction that exerts an essential role in genome packaging. Disrupting this structure displays reduced infectivity, attenuating virus pathogenicity in mice. Our findings characterize the in vivo RNA structural landscape of the IAV genome and reveal viral RNA structures that can be targeted to develop antiviral interventions.
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Affiliation(s)
- Rui Yang
- The State Key Laboratory of Membrane Biology, Beijing Frontier Research Center for Biological Structure, Tsinghua University-Peking University Joint Center for Life Sciences, School of Life Sciences, Tsinghua University, Beijing 100084, China
| | - Minglei Pan
- NHC Key Laboratory of Systems Biology of Pathogens, Institute of Pathogen Biology, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing 100730, China
| | - Jiamei Guo
- CAS Key Laboratory of Pathogen Microbiology and Immunology, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, China
| | - Yong Huang
- The State Key Laboratory of Membrane Biology, Beijing Frontier Research Center for Biological Structure, Tsinghua University-Peking University Joint Center for Life Sciences, School of Life Sciences, Tsinghua University, Beijing 100084, China
| | - Qiangfeng Cliff Zhang
- The State Key Laboratory of Membrane Biology, Beijing Frontier Research Center for Biological Structure, Tsinghua University-Peking University Joint Center for Life Sciences, School of Life Sciences, Tsinghua University, Beijing 100084, China.
| | - Tao Deng
- NHC Key Laboratory of Systems Biology of Pathogens, Institute of Pathogen Biology, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing 100730, China; CAS Key Laboratory of Pathogen Microbiology and Immunology, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, China.
| | - Jianwei Wang
- NHC Key Laboratory of Systems Biology of Pathogens and Christophe Mérieux Laboratory, Institute of Pathogen Biology, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing 100730, China; Key Laboratory of Respiratory Disease Pathogenomics, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing 100730, China.
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3
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Quignon E, Ferhadian D, Hache A, Vivet-Boudou V, Isel C, Printz-Schweigert A, Donchet A, Crépin T, Marquet R. Structural Impact of the Interaction of the Influenza A Virus Nucleoprotein with Genomic RNA Segments. Viruses 2024; 16:421. [PMID: 38543786 PMCID: PMC10974462 DOI: 10.3390/v16030421] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2024] [Revised: 03/01/2024] [Accepted: 03/06/2024] [Indexed: 05/23/2024] Open
Abstract
Influenza A viruses (IAVs) possess a segmented genome consisting of eight viral RNAs (vRNAs) associated with multiple copies of viral nucleoprotein (NP) and a viral polymerase complex. Despite the crucial role of RNA structure in IAV replication, the impact of NP binding on vRNA structure is not well understood. In this study, we employed SHAPE chemical probing to compare the structure of NS and M vRNAs of WSN IAV in various states: before the addition of NP, in complex with NP, and after the removal of NP. Comparison of the RNA structures before the addition of NP and after its removal reveals that NP, while introducing limited changes, remodels local structures in both vRNAs and long-range interactions in the NS vRNA, suggesting a potentially biologically relevant RNA chaperone activity. In contrast, NP significantly alters the structure of vRNAs in vRNA/NP complexes, though incorporating experimental data into RNA secondary structure prediction proved challenging. Finally, our results suggest that NP not only binds single-stranded RNA but also helices with interruptions, such as bulges or small internal loops, with a preference for G-poor and C/U-rich regions.
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Affiliation(s)
- Erwan Quignon
- Université de Strasbourg, CNRS, Architecture et Réactivité de l’ARN, UPR9002, 67000 Strasbourg, France; (E.Q.); (A.H.); (V.V.-B.); (C.I.)
| | - Damien Ferhadian
- Université de Strasbourg, CNRS, Architecture et Réactivité de l’ARN, UPR9002, 67000 Strasbourg, France; (E.Q.); (A.H.); (V.V.-B.); (C.I.)
| | - Antoine Hache
- Université de Strasbourg, CNRS, Architecture et Réactivité de l’ARN, UPR9002, 67000 Strasbourg, France; (E.Q.); (A.H.); (V.V.-B.); (C.I.)
| | - Valérie Vivet-Boudou
- Université de Strasbourg, CNRS, Architecture et Réactivité de l’ARN, UPR9002, 67000 Strasbourg, France; (E.Q.); (A.H.); (V.V.-B.); (C.I.)
| | - Catherine Isel
- Université de Strasbourg, CNRS, Architecture et Réactivité de l’ARN, UPR9002, 67000 Strasbourg, France; (E.Q.); (A.H.); (V.V.-B.); (C.I.)
| | - Anne Printz-Schweigert
- Université de Strasbourg, CNRS, Architecture et Réactivité de l’ARN, UPR9002, 67000 Strasbourg, France; (E.Q.); (A.H.); (V.V.-B.); (C.I.)
| | - Amélie Donchet
- Université Grenoble Alpes, CNRS, CEA, Institut de Biologie Structurale, 38000 Grenoble, France (T.C.)
| | - Thibaut Crépin
- Université Grenoble Alpes, CNRS, CEA, Institut de Biologie Structurale, 38000 Grenoble, France (T.C.)
| | - Roland Marquet
- Université de Strasbourg, CNRS, Architecture et Réactivité de l’ARN, UPR9002, 67000 Strasbourg, France; (E.Q.); (A.H.); (V.V.-B.); (C.I.)
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4
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Kretsch RC, Xu L, Zheludev IN, Zhou X, Huang R, Nye G, Li S, Zhang K, Chiu W, Das R. Tertiary folds of the SL5 RNA from the 5' proximal region of SARS-CoV-2 and related coronaviruses. Proc Natl Acad Sci U S A 2024; 121:e2320493121. [PMID: 38427602 DOI: 10.1073/pnas.2320493121] [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: 11/26/2023] [Accepted: 01/05/2024] [Indexed: 03/03/2024] Open
Abstract
Coronavirus genomes sequester their start codons within stem-loop 5 (SL5), a structured, 5' genomic RNA element. In most alpha- and betacoronaviruses, the secondary structure of SL5 is predicted to contain a four-way junction of helical stems, some of which are capped with UUYYGU hexaloops. Here, using cryogenic electron microscopy (cryo-EM) and computational modeling with biochemically determined secondary structures, we present three-dimensional structures of SL5 from six coronaviruses. The SL5 domain of betacoronavirus severe-acute-respiratory-syndrome-related coronavirus 2 (SARS-CoV-2), resolved at 4.7 Å resolution, exhibits a T-shaped structure, with its UUYYGU hexaloops at opposing ends of a coaxial stack, the T's "arms." Further analysis of SL5 domains from SARS-CoV-1 and MERS (7.1 and 6.4 to 6.9 Å resolution, respectively) indicate that the junction geometry and inter-hexaloop distances are conserved features across these human-infecting betacoronaviruses. The MERS SL5 domain displays an additional tertiary interaction, which is also observed in the non-human-infecting betacoronavirus BtCoV-HKU5 (5.9 to 8.0 Å resolution). SL5s from human-infecting alphacoronaviruses, HCoV-229E and HCoV-NL63 (6.5 and 8.4 to 9.0 Å resolution, respectively), exhibit the same coaxial stacks, including the UUYYGU-capped arms, but with a phylogenetically distinct crossing angle, an X-shape. As such, all SL5 domains studied herein fold into stable tertiary structures with cross-genus similarities and notable differences, with implications for potential protein-binding modes and therapeutic targets.
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Affiliation(s)
| | - Lily Xu
- Department of Microbiology and Immunology, Stanford University, Stanford, CA 94305
| | - Ivan N Zheludev
- Department of Biochemistry, Stanford University, Stanford, CA 94305
| | - Xueting Zhou
- Department of Bioengineering, James H. Clark Center, Stanford University, Stanford, CA 94305
| | - Rui Huang
- Department of Biochemistry, Stanford University, Stanford, CA 94305
| | - Grace Nye
- Department of Biochemistry, Stanford University, Stanford, CA 94305
| | - Shanshan Li
- Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei 230027, China
| | - Kaiming Zhang
- Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei 230027, China
| | - Wah Chiu
- Biophysics Program, Stanford University, Stanford, CA 94305
- Department of Bioengineering, James H. Clark Center, Stanford University, Stanford, CA 94305
- CryoEM and Bioimaging Division, Stanford Synchrotron Radiation Lightsource, SLAC National Accelerator Laboratory, Stanford University, Menlo Park, CA 94025
| | - Rhiju Das
- Biophysics Program, Stanford University, Stanford, CA 94305
- Department of Biochemistry, Stanford University, Stanford, CA 94305
- HHMI, Stanford University, Stanford, CA 94305
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5
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Kretsch RC, Xu L, Zheludev IN, Zhou X, Huang R, Nye G, Li S, Zhang K, Chiu W, Das R. Tertiary folds of the SL5 RNA from the 5' proximal region of SARS-CoV-2 and related coronaviruses. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.11.22.567964. [PMID: 38076883 PMCID: PMC10705266 DOI: 10.1101/2023.11.22.567964] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Indexed: 12/23/2023]
Abstract
Coronavirus genomes sequester their start codons within stem-loop 5 (SL5), a structured, 5' genomic RNA element. In most alpha- and betacoronaviruses, the secondary structure of SL5 is predicted to contain a four-way junction of helical stems, some of which are capped with UUYYGU hexaloops. Here, using cryogenic electron microscopy (cryo-EM) and computational modeling with biochemically-determined secondary structures, we present three-dimensional structures of SL5 from six coronaviruses. The SL5 domain of betacoronavirus SARS-CoV-2, resolved at 4.7 Å resolution, exhibits a T-shaped structure, with its UUYYGU hexaloops at opposing ends of a coaxial stack, the T's "arms." Further analysis of SL5 domains from SARS-CoV-1 and MERS (7.1 and 6.4-6.9 Å resolution, respectively) indicate that the junction geometry and inter-hexaloop distances are conserved features across the studied human-infecting betacoronaviruses. The MERS SL5 domain displays an additional tertiary interaction, which is also observed in the non-human-infecting betacoronavirus BtCoV-HKU5 (5.9-8.0 Å resolution). SL5s from human-infecting alphacoronaviruses, HCoV-229E and HCoV-NL63 (6.5 and 8.4-9.0 Å resolution, respectively), exhibit the same coaxial stacks, including the UUYYGU-capped arms, but with a phylogenetically distinct crossing angle, an X-shape. As such, all SL5 domains studied herein fold into stable tertiary structures with cross-genus similarities, with implications for potential protein-binding modes and therapeutic targets.
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Affiliation(s)
| | - Lily Xu
- Department of Microbiology and Immunology, Stanford University, Stanford, CA, USA
| | - Ivan N. Zheludev
- Department of Biochemistry, Stanford University, Stanford, CA, USA
| | - Xueting Zhou
- Department of Bioengineering, James H. Clark Center, Stanford University, Stanford, CA, USA
| | - Rui Huang
- Department of Biochemistry, Stanford University, Stanford, CA, USA
| | - Grace Nye
- Department of Biochemistry, Stanford University, Stanford, CA, USA
| | - Shanshan Li
- Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei 230027, China
| | - Kaiming Zhang
- Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei 230027, China
| | - Wah Chiu
- Biophysics Program, Stanford University, Stanford, CA, USA
- Department of Bioengineering, James H. Clark Center, Stanford University, Stanford, CA, USA
- CryoEM and Bioimaging Division, Stanford Synchrotron Radiation Lightsource, SLAC National Accelerator Laboratory, Stanford University, Menlo Park, CA, USA
| | - Rhiju Das
- Biophysics Program, Stanford University, Stanford, CA, USA
- Department of Biochemistry, Stanford University, Stanford, CA, USA
- Howard Hughes Medical Institute, Stanford, CA, USA
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6
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Takizawa N, Kawaguchi RK. Comprehensive in virio structure probing analysis of the influenza A virus identifies functional RNA structures involved in viral genome replication. Comput Struct Biotechnol J 2023; 21:5259-5272. [PMID: 37954152 PMCID: PMC10632597 DOI: 10.1016/j.csbj.2023.10.036] [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: 08/03/2023] [Revised: 10/17/2023] [Accepted: 10/17/2023] [Indexed: 11/14/2023] Open
Abstract
The influenza A virus genome is segmented into eight viral RNAs (vRNA). Secondary structures of vRNA are known to be involved in the viral proliferation process. Comprehensive vRNA structures in vitro, in virio, and in cellulo have been analyzed. However, the resolution of the structure map can be improved by comparative analysis and statistical modeling. Construction of a more high-resolution and reliable RNA structure map can identify uncharacterized functional structure motifs on vRNA in virion. Here, we establish the global map of the vRNA secondary structure in virion using the combination of dimethyl sulfate (DMS)-seq and selective 2'-hydroxyl acylation analyzed by primer extension (SHAPE)-seq with a robust statistical analysis. Our high-resolution analysis identified a stem-loop structure at nucleotide positions 39 - 60 of segment 6 and further validated the structure at nucleotide positions 87 - 130 of segment 5 that was previously predicted to form a pseudoknot structure in silico. Notably, when the cells were infected with recombinant viruses which possess the mutations to disrupt the structure, the replication and packaging of the viral genome were drastically decreased. Our results provide comprehensive and high-resolution information on the influenza A virus genome structures in virion and evidence that the functional RNA structure motifs on the influenza A virus genome are associated with appropriate replication and packaging of the viral genome.
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Affiliation(s)
- Naoki Takizawa
- Laboratory of Virology, Institute of Microbial Chemistry (BIKAKEN), Tokyo, Japan
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7
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Okamoto S, Echigoya Y, Tago A, Segawa T, Sato Y, Itou T. Antiviral Efficacy of RNase H-Dependent Gapmer Antisense Oligonucleotides against Japanese Encephalitis Virus. Int J Mol Sci 2023; 24:14846. [PMID: 37834294 PMCID: PMC10573891 DOI: 10.3390/ijms241914846] [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: 08/11/2023] [Revised: 09/23/2023] [Accepted: 09/28/2023] [Indexed: 10/15/2023] Open
Abstract
RNase H-dependent gapmer antisense oligonucleotides (ASOs) are a promising therapeutic approach via sequence-specific binding to and degrading target RNAs. However, the efficacy and mechanism of antiviral gapmer ASOs have remained unclear. Here, we investigated the inhibitory effects of gapmer ASOs containing locked nucleic acids (LNA gapmers) on proliferating a mosquito-borne flavivirus, Japanese encephalitis virus (JEV), with high mortality. We designed several LNA gapmers targeting the 3' untranslated region of JEV genomic RNAs. In vitro screening by plaque assay using Vero cells revealed that LNA gapmers targeting a stem-loop region effectively inhibit JEV proliferation. Cell-based and RNA cleavage assays using mismatched LNA gapmers exhibited an underlying mechanism where the inhibition of viral production results from JEV RNA degradation by LNA gapmers in a sequence- and modification-dependent manner. Encouragingly, LNA gapmers potently inhibited the proliferation of five JEV strains of predominant genotypes I and III in human neuroblastoma cells without apparent cytotoxicity. Database searching showed a low possibility of off-target binding of our LNA gapmers to human RNAs. The target viral RNA sequence conservation observed here highlighted their broad-spectrum antiviral potential against different JEV genotypes/strains. This work will facilitate the development of an antiviral LNA gapmer therapy for JEV and other flavivirus infections.
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Affiliation(s)
- Shunsuke Okamoto
- Laboratory of Preventive Veterinary Medicine and Animal Health, Department of Veterinary Medicine, College of Bioresource Sciences, Nihon University, Fujisawa, Kanagawa 252-0880, Japan; (S.O.); (T.S.); (T.I.)
- Nihon University Veterinary Research Center, Fujisawa, Kanagawa 252-0880, Japan; (A.T.); (Y.S.)
| | - Yusuke Echigoya
- Nihon University Veterinary Research Center, Fujisawa, Kanagawa 252-0880, Japan; (A.T.); (Y.S.)
- Laboratory of Biomedical Science, Department of Veterinary Medicine, College of Bioresource Sciences, Nihon University, Fujisawa, Kanagawa 252-0880, Japan
| | - Ayaka Tago
- Nihon University Veterinary Research Center, Fujisawa, Kanagawa 252-0880, Japan; (A.T.); (Y.S.)
- Laboratory of Biomedical Science, Department of Veterinary Medicine, College of Bioresource Sciences, Nihon University, Fujisawa, Kanagawa 252-0880, Japan
| | - Takao Segawa
- Laboratory of Preventive Veterinary Medicine and Animal Health, Department of Veterinary Medicine, College of Bioresource Sciences, Nihon University, Fujisawa, Kanagawa 252-0880, Japan; (S.O.); (T.S.); (T.I.)
- Nihon University Veterinary Research Center, Fujisawa, Kanagawa 252-0880, Japan; (A.T.); (Y.S.)
| | - Yukita Sato
- Nihon University Veterinary Research Center, Fujisawa, Kanagawa 252-0880, Japan; (A.T.); (Y.S.)
- Laboratory of Biomedical Science, Department of Veterinary Medicine, College of Bioresource Sciences, Nihon University, Fujisawa, Kanagawa 252-0880, Japan
| | - Takuya Itou
- Laboratory of Preventive Veterinary Medicine and Animal Health, Department of Veterinary Medicine, College of Bioresource Sciences, Nihon University, Fujisawa, Kanagawa 252-0880, Japan; (S.O.); (T.S.); (T.I.)
- Nihon University Veterinary Research Center, Fujisawa, Kanagawa 252-0880, Japan; (A.T.); (Y.S.)
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8
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Karim M, Lo CW, Einav S. Preparing for the next viral threat with broad-spectrum antivirals. J Clin Invest 2023; 133:e170236. [PMID: 37259914 PMCID: PMC10232003 DOI: 10.1172/jci170236] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/02/2023] Open
Abstract
There is a large global unmet need for the development of countermeasures to combat hundreds of viruses known to cause human disease and for the establishment of a therapeutic portfolio for future pandemic preparedness. Most approved antiviral therapeutics target proteins encoded by a single virus, providing a narrow spectrum of coverage. This, combined with the slow pace and high cost of drug development, limits the scalability of this direct-acting antiviral (DAA) approach. Here, we summarize progress and challenges in the development of broad-spectrum antivirals that target either viral elements (proteins, genome structures, and lipid envelopes) or cellular proviral factors co-opted by multiple viruses via newly discovered compounds or repurposing of approved drugs. These strategies offer new means for developing therapeutics against both existing and emerging viral threats that complement DAAs.
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Affiliation(s)
- Marwah Karim
- Division of Infectious Diseases and Geographic Medicine, Department of Medicine, and
| | - Chieh-Wen Lo
- Division of Infectious Diseases and Geographic Medicine, Department of Medicine, and
| | - Shirit Einav
- Division of Infectious Diseases and Geographic Medicine, Department of Medicine, and
- Department of Microbiology and Immunology, Stanford University School of Medicine, Stanford, California, USA
- Chan Zuckerberg Biohub San Francisco, San Francisco, California, USA
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9
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Mirska B, Woźniak T, Lorent D, Ruszkowska A, Peterson JM, Moss WN, Mathews DH, Kierzek R, Kierzek E. In vivo secondary structural analysis of Influenza A virus genomic RNA. Cell Mol Life Sci 2023; 80:136. [PMID: 37131079 PMCID: PMC10153785 DOI: 10.1007/s00018-023-04764-1] [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: 10/28/2022] [Revised: 03/19/2023] [Accepted: 03/19/2023] [Indexed: 05/04/2023]
Abstract
Influenza A virus (IAV) is a respiratory virus that causes epidemics and pandemics. Knowledge of IAV RNA secondary structure in vivo is crucial for a better understanding of virus biology. Moreover, it is a fundament for the development of new RNA-targeting antivirals. Chemical RNA mapping using selective 2'-hydroxyl acylation analyzed by primer extension (SHAPE) coupled with Mutational Profiling (MaP) allows for the thorough examination of secondary structures in low-abundance RNAs in their biological context. So far, the method has been used for analyzing the RNA secondary structures of several viruses including SARS-CoV-2 in virio and in cellulo. Here, we used SHAPE-MaP and dimethyl sulfate mutational profiling with sequencing (DMS-MaPseq) for genome-wide secondary structure analysis of viral RNA (vRNA) of the pandemic influenza A/California/04/2009 (H1N1) strain in both in virio and in cellulo environments. Experimental data allowed the prediction of the secondary structures of all eight vRNA segments in virio and, for the first time, the structures of vRNA5, 7, and 8 in cellulo. We conducted a comprehensive structural analysis of the proposed vRNA structures to reveal the motifs predicted with the highest accuracy. We also performed a base-pairs conservation analysis of the predicted vRNA structures and revealed many highly conserved vRNA motifs among the IAVs. The structural motifs presented herein are potential candidates for new IAV antiviral strategies.
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Affiliation(s)
- Barbara Mirska
- Institute of Bioorganic Chemistry, Polish Academy of Sciences, Noskowskiego 12/14, 61-704, Poznan, Poland
| | - Tomasz Woźniak
- Institute of Human Genetics, Polish Academy of Sciences, Strzeszynska 32, 60-479, Poznan, Poland
| | - Dagny Lorent
- Institute of Bioorganic Chemistry, Polish Academy of Sciences, Noskowskiego 12/14, 61-704, Poznan, Poland
| | - Agnieszka Ruszkowska
- Institute of Bioorganic Chemistry, Polish Academy of Sciences, Noskowskiego 12/14, 61-704, Poznan, Poland
| | - Jake M Peterson
- Roy J. Carver Department of Biophysics, Biochemistry and Molecular Biology, Iowa State University, Ames, IA, 50011, USA
| | - Walter N Moss
- Roy J. Carver Department of Biophysics, Biochemistry and Molecular Biology, Iowa State University, Ames, IA, 50011, USA
| | - David H Mathews
- Department of Biochemistry & Biophysics and Center for RNA Biology, School of Medicine and Dentistry, University of Rochester, 601 Elmwood Avenue, Box 712, Rochester, NY, 14642, USA
| | - Ryszard Kierzek
- Institute of Bioorganic Chemistry, Polish Academy of Sciences, Noskowskiego 12/14, 61-704, Poznan, Poland
| | - Elzbieta Kierzek
- Institute of Bioorganic Chemistry, Polish Academy of Sciences, Noskowskiego 12/14, 61-704, Poznan, Poland.
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10
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Allan MF, Brivanlou A, Rouskin S. RNA levers and switches controlling viral gene expression. Trends Biochem Sci 2023; 48:391-406. [PMID: 36710231 DOI: 10.1016/j.tibs.2022.12.002] [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: 09/12/2022] [Revised: 11/27/2022] [Accepted: 12/15/2022] [Indexed: 01/29/2023]
Abstract
RNA viruses are diverse and abundant pathogens that are responsible for numerous human diseases. RNA viruses possess relatively compact genomes and have therefore evolved multiple mechanisms to maximize their coding capacities, often by encoding overlapping reading frames. These reading frames are then decoded by mechanisms such as alternative splicing and ribosomal frameshifting to produce multiple distinct proteins. These solutions are enabled by the ability of the RNA genome to fold into 3D structures that can mimic cellular RNAs, hijack host proteins, and expose or occlude regulatory protein-binding motifs to ultimately control key process in the viral life cycle. We highlight recent findings focusing on less conventional mechanisms of gene expression and new discoveries on the role of RNA structures.
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Affiliation(s)
- Matthew F Allan
- Department of Microbiology, Harvard Medical School, Boston, MA 02115, USA; Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA 02139, USA; Computational and Systems Biology, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
| | - Amir Brivanlou
- Department of Microbiology, Harvard Medical School, Boston, MA 02115, USA
| | - Silvi Rouskin
- Department of Microbiology, Harvard Medical School, Boston, MA 02115, USA.
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11
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Morens DM, Taubenberger JK, Fauci AS. Rethinking next-generation vaccines for coronaviruses, influenzaviruses, and other respiratory viruses. Cell Host Microbe 2023; 31:146-157. [PMID: 36634620 PMCID: PMC9832587 DOI: 10.1016/j.chom.2022.11.016] [Citation(s) in RCA: 52] [Impact Index Per Article: 52.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2022] [Revised: 10/26/2022] [Accepted: 11/29/2022] [Indexed: 01/13/2023]
Abstract
Viruses that replicate in the human respiratory mucosa without infecting systemically, including influenza A, SARS-CoV-2, endemic coronaviruses, RSV, and many other "common cold" viruses, cause significant mortality and morbidity and are important public health concerns. Because these viruses generally do not elicit complete and durable protective immunity by themselves, they have not to date been effectively controlled by licensed or experimental vaccines. In this review, we examine challenges that have impeded development of effective mucosal respiratory vaccines, emphasizing that all of these viruses replicate extremely rapidly in the surface epithelium and are quickly transmitted to other hosts, within a narrow window of time before adaptive immune responses are fully marshaled. We discuss possible approaches to developing next-generation vaccines against these viruses, in consideration of several variables such as vaccine antigen configuration, dose and adjuventation, route and timing of vaccination, vaccine boosting, adjunctive therapies, and options for public health vaccination polices.
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Affiliation(s)
- David M. Morens
- Office of the Director, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892, USA
| | - Jeffery K. Taubenberger
- Viral Pathogenesis and Evolution Section, Laboratory of Infectious Diseases, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892, USA,Corresponding author
| | - Anthony S. Fauci
- Office of the Director, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892, USA
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Szczesniak I, Baliga-Gil A, Jarmolowicz A, Soszynska-Jozwiak M, Kierzek E. Structural and Functional RNA Motifs of SARS-CoV-2 and Influenza A Virus as a Target of Viral Inhibitors. Int J Mol Sci 2023; 24:ijms24021232. [PMID: 36674746 PMCID: PMC9860923 DOI: 10.3390/ijms24021232] [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: 12/02/2022] [Revised: 12/28/2022] [Accepted: 12/29/2022] [Indexed: 01/11/2023] Open
Abstract
Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is responsible for the COVID-19 pandemic, whereas the influenza A virus (IAV) causes seasonal epidemics and occasional pandemics. Both viruses lead to widespread infection and death. SARS-CoV-2 and the influenza virus are RNA viruses. The SARS-CoV-2 genome is an approximately 30 kb, positive sense, 5' capped single-stranded RNA molecule. The influenza A virus genome possesses eight single-stranded negative-sense segments. The RNA secondary structure in the untranslated and coding regions is crucial in the viral replication cycle. The secondary structure within the RNA of SARS-CoV-2 and the influenza virus has been intensively studied. Because the whole of the SARS-CoV-2 and influenza virus replication cycles are dependent on RNA with no DNA intermediate, the RNA is a natural and promising target for the development of inhibitors. There are a lot of RNA-targeting strategies for regulating pathogenic RNA, such as small interfering RNA for RNA interference, antisense oligonucleotides, catalytic nucleic acids, and small molecules. In this review, we summarized the knowledge about the inhibition of SARS-CoV-2 and influenza A virus propagation by targeting their RNA secondary structure.
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Pannu J, Glenn JS. Programmable Antivirals and Just-in-Time Vaccines: Biosecurity Implications of Viral RNA Secondary Structure Targeting. Health Secur 2023; 21:81-84. [PMID: 36576394 DOI: 10.1089/hs.2022.0098] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022] Open
Affiliation(s)
- Jaspreet Pannu
- Jaspreet Pannu, MD, is a Resident Physician, Department of Medicine, Stanford University School of Medicine, Stanford, CA; and a Fellow, Center for Health Security, Johns Hopkins School of Public Health, Baltimore, MD
| | - Jeffrey S Glenn
- Jeffrey S. Glenn, MD, PhD, is the Joseph D. Grant Professor, Department of Medicine, and Professor, Department of Microbiology and Immunology, Stanford University School of Medicine, Stanford, CA; and Director, ViRx@Stanford, Stanford Medicine, Stanford, CA. He is also a Physician, Veterans Administration Medical Center, Palo Alto, CA
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Pekarek L, Zimmer MM, Gribling-Burrer AS, Buck S, Smyth R, Caliskan N. Cis-mediated interactions of the SARS-CoV-2 frameshift RNA alter its conformations and affect function. Nucleic Acids Res 2022; 51:728-743. [PMID: 36537211 PMCID: PMC9881162 DOI: 10.1093/nar/gkac1184] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2022] [Revised: 11/11/2022] [Accepted: 12/13/2022] [Indexed: 12/24/2022] Open
Abstract
The RNA genome of SARS-CoV-2 contains a frameshift stimulatory element (FSE) that allows access to an alternative reading frame through -1 programmed ribosomal frameshifting (PRF). -1PRF in the 1a/1b gene is essential for efficient viral replication and transcription of the viral genome. -1PRF efficiency relies on the presence of conserved RNA elements within the FSE. One of these elements is a three-stemmed pseudoknot, although alternative folds of the frameshift site might have functional roles as well. Here, by complementing ensemble and single-molecule structural analysis of SARS-CoV-2 frameshift RNA variants with functional data, we reveal a conformational interplay of the 5' and 3' immediate regions with the FSE and show that the extended FSE exists in multiple conformations. Furthermore, limiting the base pairing of the FSE with neighboring nucleotides can favor or impair the formation of the alternative folds, including the pseudoknot. Our results demonstrate that co-existing RNA structures can function together to fine-tune SARS-CoV-2 gene expression, which will aid efforts to design specific inhibitors of viral frameshifting.
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Affiliation(s)
- Lukas Pekarek
- Helmholtz Institute for RNA-based Infection Research (HIRI-HZI), Würzburg, Germany
| | | | | | | | - Redmond Smyth
- Correspondence may also be addressed to Redmond Smyth.
| | - Neva Caliskan
- To whom correspondence should be addressed. Tel: +49 931 318 5298;
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Nalewaj M, Szabat M. Examples of Structural Motifs in Viral Genomes and Approaches for RNA Structure Characterization. Int J Mol Sci 2022; 23:ijms232415917. [PMID: 36555559 PMCID: PMC9784701 DOI: 10.3390/ijms232415917] [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: 10/19/2022] [Revised: 12/04/2022] [Accepted: 12/13/2022] [Indexed: 12/23/2022] Open
Abstract
The relationship between conserved structural motifs and their biological function in the virus replication cycle is the interest of many researchers around the world. RNA structure is closely related to RNA function. Therefore, technological progress in high-throughput approaches for RNA structure analysis and the development of new ones are very important. In this mini review, we discuss a few perspectives on the structural elements of viral genomes and some methods used for RNA structure prediction and characterization. Based on the recent literature, we describe several examples of studies concerning the viral genomes, especially severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) and influenza A virus (IAV). Herein, we emphasize that a better understanding of viral genome architecture allows for the discovery of the structure-function relationship, and as a result, the discovery of new potential antiviral therapeutics.
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Oriola AO, Oyedeji AO. Essential Oils and Their Compounds as Potential Anti-Influenza Agents. MOLECULES (BASEL, SWITZERLAND) 2022; 27:molecules27227797. [PMID: 36431899 PMCID: PMC9693178 DOI: 10.3390/molecules27227797] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 10/19/2022] [Revised: 11/07/2022] [Accepted: 11/08/2022] [Indexed: 11/16/2022]
Abstract
Essential oils (EOs) are chemical substances, mostly produced by aromatic plants in response to stress, that have a history of medicinal use for many diseases. In the last few decades, EOs have continued to gain more attention because of their proven therapeutic applications against the flu and other infectious diseases. Influenza (flu) is an infectious zoonotic disease that affects the lungs and their associated organs. It is a public health problem with a huge health burden, causing a seasonal outbreak every year. Occasionally, it comes as a disease pandemic with unprecedentedly high hospitalization and mortality. Currently, influenza is managed by vaccination and antiviral drugs such as Amantadine, Rimantadine, Oseltamivir, Peramivir, Zanamivir, and Baloxavir. However, the adverse side effects of these drugs, the rapid and unlimited variabilities of influenza viruses, and the emerging resistance of new virus strains to the currently used vaccines and drugs have necessitated the need to obtain more effective anti-influenza agents. In this review, essential oils are discussed in terms of their chemistry, ethnomedicinal values against flu-related illnesses, biological potential as anti-influenza agents, and mechanisms of action. In addition, the structure-activity relationships of lead anti-influenza EO compounds are also examined. This is all to identify leading agents that can be optimized as drug candidates for the management of influenza. Eucalyptol, germacrone, caryophyllene derivatives, eugenol, terpin-4-ol, bisabolene derivatives, and camphecene are among the promising EO compounds identified, based on their reported anti-influenza activities and plausible molecular actions, while nanotechnology may be a new strategy to achieve the efficient delivery of these therapeutically active EOs to the active virus site.
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Stincarelli MA, Rocca A, Antonelli A, Rossolini GM, Giannecchini S. Antiviral Activity of Oligonucleotides Targeting the SARS-CoV-2 Genomic RNA Stem-Loop Sequences within the 3'-End of the ORF1b. Pathogens 2022; 11:1286. [PMID: 36365037 PMCID: PMC9696570 DOI: 10.3390/pathogens11111286] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2022] [Revised: 10/27/2022] [Accepted: 10/29/2022] [Indexed: 08/30/2023] Open
Abstract
Increased evidence shows vaccines against severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) exhibited no long-term efficacy and limited worldwide availability, while existing antivirals and treatment options have only limited efficacy. In this study, the main objective was the development of antiviral strategies using nucleic acid-based molecules. To this purpose, partially overlapped 6-19-mer phosphorothioate deoxyoligonucleotides (S-ONs) designed on the SARS-CoV-2 genomic RNA stem-loop packaging sequences within the 3' end of the ORF1b were synthetized using the direct and complementary sequence. Among the S-ONs tested, several oligonucleotides exhibited a fifty percent inhibitory concentration antiviral activity ranging from 0.27 to 34 μM, in the absence of cytotoxicity. The S-ON with a scrambled sequence used in the same conditions was not active. Moreover, selected 10-mer S-ONs were tested using different infectious doses and against different SARS-CoV-2 variants, showing comparable antiviral activity that was abrogated when the central sequence was mutated. Experiments to evaluate the intracellular functional target localization of the S-ON inhibitory activity were also performed. Collectively the data indicate that the SARS-CoV-2 packaging region in the 3' end of the ORF1b may be a promising target candidate for further investigation to develop innovative nucleic-acid-based antiviral therapy.
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Affiliation(s)
| | - Arianna Rocca
- Department of Experimental and Clinical Medicine, University of Florence, I-50134 Florence, Italy
| | - Alberto Antonelli
- Department of Experimental and Clinical Medicine, University of Florence, I-50134 Florence, Italy
| | - Gian Maria Rossolini
- Department of Experimental and Clinical Medicine, University of Florence, I-50134 Florence, Italy
- Microbiology and Virology Unit, Florence Careggi University Hospital, I-50134 Florence, Italy
| | - Simone Giannecchini
- Department of Experimental and Clinical Medicine, University of Florence, I-50134 Florence, Italy
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Moderate to severe SARS-CoV-2 infection primes vaccine-induced immunity more effectively than asymptomatic or mild infection. NPJ Vaccines 2022; 7:122. [PMID: 36271095 DOI: 10.1038/s41541-022-00546-1] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2022] [Accepted: 10/06/2022] [Indexed: 11/08/2022] Open
Abstract
Hybrid immunity induced by vaccination following recovery from SARS-CoV-2 infection is more robust than immunity induced by either infection or vaccination alone. To investigate how infection severity influenced the strength and character of subsequent vaccine-induced humoral or cellular immune responses against SARS-CoV-2, we assessed humoral and cellular immune responses against SARS-CoV-2 following recovery from infection, vaccine dose 1 and vaccine dose 2 in 35 persons recovered from COVID-19. Persons with polymerase chain reaction or serologically confirmed SARS-CoV-2 infection were recruited into a study of immunity against SARS-CoV-2. Self-reported symptoms categorized them as experiencing asymptomatic, mild, moderate or severe infection based on duration, intensity and need for hospitalization. Whole blood was obtained before vaccination and after first and second doses. Humoral immunity was assessed by ELISA and cellular immunity by ELISpot and intracellular flow cytometry. Responses were compared between groups recovered from either asymptomatic/mild (n = 14) or moderate/severe (n = 21) infection. Most subjects experienced robust increases in humoral and cellular immunity against SARS-CoV-2 spike (S) protein following 1 vaccination. Quantitative responses to second vaccination were marginal when measured 2.5 months afterwards and moderate or severe infection maintained stronger responses. Polyfunctional CD8+ T cell responses were largely restricted to subjects recovered from moderate or severe infection. One vaccine dose triggered stronger immune responses than in a comparable group never infected with SARS-CoV-2, while the second dose produced only minor lasting increases in humoral or cellular responses. Infection history should be considered in planning COVID-19 vaccine administration.
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Designer antiviral takes aim at one of influenza's soft spots. Nature 2022. [PMID: 35999368 DOI: 10.1038/d41586-022-02282-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
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RNA structure guides antiviral ASO design. Nat Rev Drug Discov 2022; 21:714. [PMID: 36008548 DOI: 10.1038/d41573-022-00142-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
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