1
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Ciminski K, Flore V, Jakob C, Mues H, Smedegaard Frederiksen A, Schwemmle M, Bolte H, Giese S. Functionality of IAV packaging signals depends on site-specific charges within the viral nucleoprotein. J Virol 2024; 98:e0197223. [PMID: 38470155 PMCID: PMC11019843 DOI: 10.1128/jvi.01972-23] [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: 12/15/2023] [Accepted: 02/20/2024] [Indexed: 03/13/2024] Open
Abstract
The coordinated packaging of the segmented genome of the influenza A virus (IAV) into virions is an essential step of the viral life cycle. This process is controlled by the interaction of packaging signals present in all eight viral RNA (vRNA) segments and the viral nucleoprotein (NP), which binds vRNA via a positively charged binding groove. However, mechanistic models of how the packaging signals and NP work together to coordinate genome packaging are missing. Here, we studied genome packaging in influenza A/SC35M virus mutants that carry mutated packaging signals as well as specific amino acid substitutions at the highly conserved lysine (K) residues 184 and 229 in the RNA-binding groove of NP. Because these lysines are acetylated and thus neutrally charged in infected host cells, we replaced them with glutamine to mimic the acetylated, neutrally charged state or arginine to mimic the non-acetylated, positively charged state. Our analysis shows that the coordinated packaging of eight vRNAs is influenced by (i) the charge state of the replacing amino acid and (ii) its location within the RNA-binding groove. Accordingly, we propose that lysine acetylation induces different charge states within the RNA-binding groove of NP, thereby supporting the activity of specific packaging signals during coordinated genome packaging. IMPORTANCE Influenza A viruses (IAVs) have a segmented viral RNA (vRNA) genome encapsidated by multiple copies of the viral nucleoprotein (NP) and organized into eight distinct viral ribonucleoprotein complexes. Although genome segmentation contributes significantly to viral evolution and adaptation, it requires a highly sophisticated genome-packaging mechanism. How eight distinct genome complexes are incorporated into the virion is poorly understood, but previous research suggests an essential role for both vRNA packaging signals and highly conserved NP amino acids. By demonstrating that the packaging process is controlled by charge-dependent interactions of highly conserved lysine residues in NP and vRNA packaging signals, our study provides new insights into the sophisticated packaging mechanism of IAVs.
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Affiliation(s)
- Kevin Ciminski
- Institute of Virology, Freiburg University Medical Center, Faculty of Medicine, University of Freiburg, Freiburg, Germany
| | - Viktoria Flore
- Institute of Virology, Freiburg University Medical Center, Faculty of Medicine, University of Freiburg, Freiburg, Germany
| | - Celia Jakob
- Institute of Virology, Freiburg University Medical Center, Faculty of Medicine, University of Freiburg, Freiburg, Germany
| | - Helen Mues
- Institute of Virology, Freiburg University Medical Center, Faculty of Medicine, University of Freiburg, Freiburg, Germany
| | - Anne Smedegaard Frederiksen
- Institute of Virology, Freiburg University Medical Center, Faculty of Medicine, University of Freiburg, Freiburg, Germany
| | - Martin Schwemmle
- Institute of Virology, Freiburg University Medical Center, Faculty of Medicine, University of Freiburg, Freiburg, Germany
| | - Hardin Bolte
- Institute of Virology, Freiburg University Medical Center, Faculty of Medicine, University of Freiburg, Freiburg, Germany
| | - Sebastian Giese
- Institute of Virology, Freiburg University Medical Center, Faculty of Medicine, University of Freiburg, Freiburg, Germany
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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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Saka N, Ohta K, Kolakofsky D, Nishio M. The bipartite promoter of Orthonairovirus hazaraense large segment. J Virol 2023; 97:e0091823. [PMID: 37916836 PMCID: PMC10688357 DOI: 10.1128/jvi.00918-23] [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: 06/21/2023] [Accepted: 10/03/2023] [Indexed: 11/03/2023] Open
Abstract
IMPORTANCE The realization that segmented negative-strand RNA virus genome ribonucleoproteins are never free as their RNA ends are always bound to the viral polymerase has highlighted the problem of how these genome segments are replicated and express their mRNAs while their RNA ends remain associated with the polymerase throughout the cycles of RNA synthesis. This study of the length and nucleotide composition of the Orthonairovirus hazaraense L segment-specific double-stranded RNA (dsRNA) promoter element (the promoter duplex) provides insight into how its mRNA might be initiated and suggests that this promoter element acts via its separated single strands as well as via dsRNA.
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Affiliation(s)
- Naoki Saka
- Department of Microbiology, School of Medicine, Wakayama Medical University, Wakayama, Japan
| | - Keisuke Ohta
- Department of Microbiology, School of Medicine, Wakayama Medical University, Wakayama, Japan
| | - Daniel Kolakofsky
- Department of Microbiology and Molecular Medicine, University of Geneva School of Medicine, Geneva, Switzerland
| | - Machiko Nishio
- Department of Microbiology, School of Medicine, Wakayama Medical University, Wakayama, Japan
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5
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Rigby CV, Sabsay KR, Bisht K, Eggink D, Jalal H, te Velthuis AJW. Evolution of transient RNA structure-RNA polymerase interactions in respiratory RNA virus genomes. Virus Evol 2023; 9:vead056. [PMID: 37692892 PMCID: PMC10492445 DOI: 10.1093/ve/vead056] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2023] [Revised: 08/02/2023] [Accepted: 08/24/2023] [Indexed: 09/12/2023] Open
Abstract
RNA viruses are important human pathogens that cause seasonal epidemics and occasional pandemics. Examples are influenza A viruses (IAV) and coronaviruses (CoV). When emerging IAV and CoV spill over to humans, they adapt to evade immune responses and optimize their replication and spread in human cells. In IAV, adaptation occurs in all viral proteins, including the viral ribonucleoprotein (RNP) complex. RNPs consist of a copy of the viral RNA polymerase, a double-helical coil of nucleoprotein, and one of the eight segments of the IAV RNA genome. The RNA segments and their transcripts are partially structured to coordinate the packaging of the viral genome and modulate viral mRNA translation. In addition, RNA structures can affect the efficiency of viral RNA synthesis and the activation of host innate immune response. Here, we investigated if RNA structures that modulate IAV replication processivity, so-called template loops (t-loops), vary during the adaptation of pandemic and emerging IAV to humans. Using cell culture-based replication assays and in silico sequence analyses, we find that the sensitivity of the IAV H3N2 RNA polymerase to t-loops increased between isolates from 1968 and 2017, whereas the total free energy of t-loops in the IAV H3N2 genome was reduced. This reduction is particularly prominent in the PB1 gene. In H1N1 IAV, we find two separate reductions in t-loop free energy, one following the 1918 pandemic and one following the 2009 pandemic. No destabilization of t-loops is observed in the influenza B virus genome, whereas analysis of SARS-CoV-2 isolates reveals destabilization of viral RNA structures. Overall, we propose that a loss of free energy in the RNA genome of emerging respiratory RNA viruses may contribute to the adaption of these viruses to the human population.
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Affiliation(s)
- Charlotte V Rigby
- Lewis Thomas Laboratory, Department of Molecular Biology, Princeton University, Washington Road, Princeton, NJ 08544, USA
- Department of Pathology, Addenbrooke’s Hospital, University of Cambridge, Hills Road, Cambridge CB2 2QQ, UK
- Addenbrooke’s Hospital, Public Health England, Hills Road, Cambridge CB2 2QQ, UK
| | - Kimberly R Sabsay
- Lewis Thomas Laboratory, Department of Molecular Biology, Princeton University, Washington Road, Princeton, NJ 08544, USA
- Carl Icahn Laboratory, Lewis-Sigler Institute, Princeton University, South Drive, Princeton, NJ 08544, USA
| | - Karishma Bisht
- Lewis Thomas Laboratory, Department of Molecular Biology, Princeton University, Washington Road, Princeton, NJ 08544, USA
| | - Dirk Eggink
- Department of Medical Microbiology, Amsterdam UMC, Meibergdreef 9, Amsterdam 1105 AZ, The Netherlands
| | - Hamid Jalal
- Addenbrooke’s Hospital, Public Health England, Hills Road, Cambridge CB2 2QQ, UK
| | - Aartjan J W te Velthuis
- Lewis Thomas Laboratory, Department of Molecular Biology, Princeton University, Washington Road, Princeton, NJ 08544, USA
- Center for Infectious Disease Control, National Institute for Public Health and the Environment (RIVM), Antonie van Leeuwenhoeklaan 9, Bilthoven 3721 MA, the Netherlands
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6
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Rigby C, Sabsay K, Bisht K, Eggink D, Jalal H, te Velthuis AJ. Evolution of transient RNA structure-RNA polymerase interactions in respiratory RNA virus genomes. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.05.25.542331. [PMID: 37292879 PMCID: PMC10245964 DOI: 10.1101/2023.05.25.542331] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/10/2023]
Abstract
RNA viruses are important human pathogens that cause seasonal epidemics and occasional pandemics. Examples are influenza A viruses (IAV) and coronaviruses (CoV). When emerging IAV and CoV spill over to humans, they adapt to evade immune responses and optimize their replication and spread in human cells. In IAV, adaptation occurs in all viral proteins, including the viral ribonucleoprotein (RNP) complex. RNPs consists of a copy of the viral RNA polymerase, a double-helical coil of nucleoprotein, and one of the eight segments of the IAV RNA genome. The RNA segments and their transcripts are partially structured to coordinate the packaging of the viral genome and modulate viral mRNA translation. In addition, RNA structures can affect the efficiency of viral RNA synthesis and the activation of host innate immune response. Here, we investigated if RNA structures that modulate IAV replication processivity, so called template loops (t-loops), vary during the adaptation of pandemic and emerging IAV to humans. Using cell culture-based replication assays and in silico sequence analyses, we find that the sensitivity of the IAV H3N2 RNA polymerase to t-loops increased between isolates from 1968 and 2017, whereas the total free energy of t-loops in the IAV H3N2 genome was reduced. This reduction is particularly prominent in the PB1 gene. In H1N1 IAV, we find two separate reductions in t-loop free energy, one following the 1918 pandemic and one following the 2009 pandemic. No destabilization of t-loops is observed in the IBV genome, whereas analysis of SARS-CoV-2 isolates reveals destabilization of viral RNA structures. Overall, we propose that a loss of free energy in the RNA genome of emerging respiratory RNA viruses may contribute to the adaption of these viruses to the human population.
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Affiliation(s)
- Charlotte Rigby
- Lewis Thomas Laboratory, Department of Molecular Biology, Princeton University, 08544 New Jersey, United States
- University of Cambridge, Department of Pathology, Addenbrooke’s Hospital, Cambridge CB2 2QQ, United Kingdom
- Public Health England, Addenbrooke’s Hospital, Cambridge CB2 2QQ, United Kingdom
| | - Kimberly Sabsay
- Lewis Thomas Laboratory, Department of Molecular Biology, Princeton University, 08544 New Jersey, United States
- Sigler Institute, Princeton University, Princeton, NJ 08544, United States
| | - Karishma Bisht
- Lewis Thomas Laboratory, Department of Molecular Biology, Princeton University, 08544 New Jersey, United States
| | - Dirk Eggink
- Department of Medical Microbiology, Amsterdam UMC, Amsterdam, The Netherlands
- Center for Infectious Disease Control, National Institute for Public Health and the Environment (RIVM), Bilthoven, the Netherlands
| | - Hamid Jalal
- Public Health England, Addenbrooke’s Hospital, Cambridge CB2 2QQ, United Kingdom
| | - Aartjan J.W. te Velthuis
- Lewis Thomas Laboratory, Department of Molecular Biology, Princeton University, 08544 New Jersey, United States
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7
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Le Sage V, Kanarek JP, Lakdawala SS, Lee N. Local changes in viral RNA sequence drive global changes in influenza nucleoprotein binding. J Med Virol 2023; 95:e28896. [PMID: 37386887 PMCID: PMC10878429 DOI: 10.1002/jmv.28896] [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: 05/30/2023] [Accepted: 06/03/2023] [Indexed: 07/01/2023]
Abstract
The genome of influenza A viruses (IAV) consists of eight negative-sense RNA segments that are coated by viral nucleoprotein (NP). Until recently, it was assumed that NP binds viral genomic RNA (vRNA) uniformly along the entire segment. However, genome-wide studies have revised the original model in that NP instead binds preferentially to certain regions of vRNA, while others are depleted for NP binding. Even strains with high sequence similarity exhibit distinct NP-binding profiles. Thus, it remains unknown how NP-binding specificity to vRNA is established. Here we introduced nucleotide changes to vRNA to examine whether primary sequence can affect NP binding. Our findings demonstrate that NP binding is indeed susceptible to sequence alterations, as NP peaks can be lost or appear de novo at mutated sites. Unexpectedly, nucleotide changes not only affect NP binding locally at the site of mutation, but also impact NP binding at distal regions that have not been modified. Taken together, our results suggest that NP binding is not regulated by primary sequence alone, but that a network formed by multiple segments governs the deposition of NP on vRNA.
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Affiliation(s)
- Valerie Le Sage
- University of Pittsburgh School of Medicine, Department of Microbiology and Molecular Genetics, 450 Technology Drive, Pittsburgh, PA 15219, USA
| | - Jack P. Kanarek
- University of Pittsburgh School of Medicine, Department of Microbiology and Molecular Genetics, 450 Technology Drive, Pittsburgh, PA 15219, USA
| | - Seema S. Lakdawala
- Emory University School of Medicine, Department of Microbiology and Immunology, 1510 Clifton Rd., Atlanta, GA 30322
| | - Nara Lee
- University of Pittsburgh School of Medicine, Department of Microbiology and Molecular Genetics, 450 Technology Drive, Pittsburgh, PA 15219, USA
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8
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Jakob C, Paul-Stansilaus R, Schwemmle M, Marquet R, Bolte H. The influenza A virus genome packaging network - complex, flexible and yet unsolved. Nucleic Acids Res 2022; 50:9023-9038. [PMID: 35993811 PMCID: PMC9458418 DOI: 10.1093/nar/gkac688] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2022] [Revised: 07/19/2022] [Accepted: 08/18/2022] [Indexed: 12/24/2022] Open
Abstract
The genome of influenza A virus (IAV) consists of eight unique viral RNA segments. This genome organization allows genetic reassortment between co-infecting IAV strains, whereby new IAVs with altered genome segment compositions emerge. While it is known that reassortment events can create pandemic IAVs, it remains impossible to anticipate reassortment outcomes with pandemic prospects. Recent research indicates that reassortment is promoted by a viral genome packaging mechanism that delivers the eight genome segments as a supramolecular complex into the virus particle. This finding holds promise of predicting pandemic IAVs by understanding the intermolecular interactions governing this genome packaging mechanism. Here, we critically review the prevailing mechanistic model postulating that IAV genome packaging is orchestrated by a network of intersegmental RNA-RNA interactions. Although we find supporting evidence, including segment-specific packaging signals and experimentally proposed RNA-RNA interaction networks, this mechanistic model remains debatable due to a current shortage of functionally validated intersegmental RNA-RNA interactions. We speculate that identifying such functional intersegmental RNA-RNA contacts might be hampered by limitations of the utilized probing techniques and the inherent complexity of the genome packaging mechanism. Nevertheless, we anticipate that improved probing strategies combined with a mutagenesis-based validation could facilitate their discovery.
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Affiliation(s)
| | | | - Martin Schwemmle
- To whom correspondence should be addressed. Tel: +49 761 203 6526; Fax: +49 761 203 6626;
| | - Roland Marquet
- Correspondence may also be addressed to Roland Marquet. Tel: +33 3 88 41 70 54; Fax: +33 3 88 60 22 18;
| | - Hardin Bolte
- Institute of Virology, Medical Center – University of Freiburg, 79104 Freiburg, Germany,Faculty of Medicine, University of Freiburg, 79110 Freiburg, Germany
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9
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de Bruin ACM, Funk M, Spronken MI, Gultyaev AP, Fouchier RAM, Richard M. Hemagglutinin Subtype Specificity and Mechanisms of Highly Pathogenic Avian Influenza Virus Genesis. Viruses 2022; 14:1566. [PMID: 35891546 PMCID: PMC9321182 DOI: 10.3390/v14071566] [Citation(s) in RCA: 19] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2022] [Revised: 07/08/2022] [Accepted: 07/11/2022] [Indexed: 02/04/2023] Open
Abstract
Highly Pathogenic Avian Influenza Viruses (HPAIVs) arise from low pathogenic precursors following spillover from wild waterfowl into poultry populations. The main virulence determinant of HPAIVs is the presence of a multi-basic cleavage site (MBCS) in the hemagglutinin (HA) glycoprotein. The MBCS allows for HA cleavage and, consequently, activation by ubiquitous proteases, which results in systemic dissemination in terrestrial poultry. Since 1959, 51 independent MBCS acquisition events have been documented, virtually all in HA from the H5 and H7 subtypes. In the present article, data from natural LPAIV to HPAIV conversions and experimental in vitro and in vivo studies were reviewed in order to compile recent advances in understanding HA cleavage efficiency, protease usage, and MBCS acquisition mechanisms. Finally, recent hypotheses that might explain the unique predisposition of the H5 and H7 HA sequences to obtain an MBCS in nature are discussed.
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Affiliation(s)
- Anja C. M. de Bruin
- Department of Viroscience, Erasmus Medical Center, 3000 CA Rotterdam, The Netherlands; (A.C.M.d.B.); (M.F.); (M.I.S.); (A.P.G.); (R.A.M.F.)
| | - Mathis Funk
- Department of Viroscience, Erasmus Medical Center, 3000 CA Rotterdam, The Netherlands; (A.C.M.d.B.); (M.F.); (M.I.S.); (A.P.G.); (R.A.M.F.)
| | - Monique I. Spronken
- Department of Viroscience, Erasmus Medical Center, 3000 CA Rotterdam, The Netherlands; (A.C.M.d.B.); (M.F.); (M.I.S.); (A.P.G.); (R.A.M.F.)
| | - Alexander P. Gultyaev
- Department of Viroscience, Erasmus Medical Center, 3000 CA Rotterdam, The Netherlands; (A.C.M.d.B.); (M.F.); (M.I.S.); (A.P.G.); (R.A.M.F.)
- Group Imaging and Bioinformatics, Leiden Institute of Advanced Computer Science (LIACS), Leiden University, 2300 RA Leiden, The Netherlands
| | - Ron A. M. Fouchier
- Department of Viroscience, Erasmus Medical Center, 3000 CA Rotterdam, The Netherlands; (A.C.M.d.B.); (M.F.); (M.I.S.); (A.P.G.); (R.A.M.F.)
| | - Mathilde Richard
- Department of Viroscience, Erasmus Medical Center, 3000 CA Rotterdam, The Netherlands; (A.C.M.d.B.); (M.F.); (M.I.S.); (A.P.G.); (R.A.M.F.)
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10
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Zhou Y, Sotcheff SL, Routh AL. Next-generation sequencing: A new avenue to understand viral RNA-protein interactions. J Biol Chem 2022; 298:101924. [PMID: 35413291 PMCID: PMC8994257 DOI: 10.1016/j.jbc.2022.101924] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2021] [Revised: 04/01/2022] [Accepted: 04/02/2022] [Indexed: 10/25/2022] Open
Abstract
The genomes of RNA viruses present an astonishing source of both sequence and structural diversity. From intracellular viral RNA-host interfaces to interactions between the RNA genome and structural proteins in virus particles themselves, almost the entire viral lifecycle is accompanied by a myriad of RNA-protein interactions that are required to fulfill their replicative potential. It is therefore important to characterize such rich and dynamic collections of viral RNA-protein interactions to understand virus evolution and their adaptation to their hosts and environment. Recent advances in next-generation sequencing technologies have allowed the characterization of viral RNA-protein interactions, including both transient and conserved interactions, where molecular and structural approaches have fallen short. In this review, we will provide a methodological overview of the high-throughput techniques used to study viral RNA-protein interactions, their biochemical mechanisms, and how they evolved from classical methods as well as one another. We will discuss how different techniques have fueled virus research to characterize how viral RNA and proteins interact, both locally and on a global scale. Finally, we will present examples on how these techniques influence the studies of clinically important pathogens such as HIV-1 and SARS-CoV-2.
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Affiliation(s)
- Yiyang Zhou
- Department of Biochemistry and Molecular Biology, The University of Texas Medical Branch, Galveston, Texas, USA.
| | - Stephanea L Sotcheff
- Department of Biochemistry and Molecular Biology, The University of Texas Medical Branch, Galveston, Texas, USA
| | - Andrew L Routh
- Department of Biochemistry and Molecular Biology, The University of Texas Medical Branch, Galveston, Texas, USA; Sealy Center for Structural Biology and Molecular Biophysics, The University of Texas Medical Branch, Galveston, Texas, USA; Institute for Human Infections and Immunity, University of Texas Medical Branch, Galveston, Texas, USA
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11
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Secondary Structure of Influenza A Virus Genomic Segment 8 RNA Folded in a Cellular Environment. Int J Mol Sci 2022; 23:ijms23052452. [PMID: 35269600 PMCID: PMC8910647 DOI: 10.3390/ijms23052452] [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: 12/06/2021] [Revised: 02/05/2022] [Accepted: 02/17/2022] [Indexed: 11/17/2022] Open
Abstract
Influenza A virus (IAV) is a member of the single-stranded RNA (ssRNA) family of viruses. The most recent global pandemic caused by the SARS-CoV-2 virus has shown the major threat that RNA viruses can pose to humanity. In comparison, influenza has an even higher pandemic potential as a result of its high rate of mutations within its relatively short (<13 kbp) genome, as well as its capability to undergo genetic reassortment. In light of this threat, and the fact that RNA structure is connected to a broad range of known biological functions, deeper investigation of viral RNA (vRNA) structures is of high interest. Here, for the first time, we propose a secondary structure for segment 8 vRNA (vRNA8) of A/California/04/2009 (H1N1) formed in the presence of cellular and viral components. This structure shows similarities with prior in vitro experiments. Additionally, we determined the location of several well-defined, conserved structural motifs of vRNA8 within IAV strains with possible functionality. These RNA motifs appear to fold independently of regional nucleoprotein (NP)-binding affinity, but a low or uneven distribution of NP in each motif region is noted. This research also highlights several accessible sites for oligonucleotide tools and small molecules in vRNA8 in a cellular environment that might be a target for influenza A virus inhibition on the RNA level.
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Jones JE, Le Sage V, Padovani GH, Calderon M, Wright ES, Lakdawala SS. Parallel evolution between genomic segments of seasonal human influenza viruses reveals RNA-RNA relationships. eLife 2021; 10:66525. [PMID: 34448455 PMCID: PMC8523153 DOI: 10.7554/elife.66525] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2021] [Accepted: 08/23/2021] [Indexed: 11/22/2022] Open
Abstract
The influenza A virus (IAV) genome consists of eight negative-sense viral RNA (vRNA) segments that are selectively assembled into progeny virus particles through RNA-RNA interactions. To explore putative intersegmental RNA-RNA relationships, we quantified similarity between phylogenetic trees comprising each vRNA segment from seasonal human IAV. Intersegmental tree similarity differed between subtype and lineage. While intersegmental relationships were largely conserved over time in H3N2 viruses, they diverged in H1N1 strains isolated before and after the 2009 pandemic. Surprisingly, intersegmental relationships were not driven solely by protein sequence, suggesting that IAV evolution could also be driven by RNA-RNA interactions. Finally, we used confocal microscopy to determine that colocalization of highly coevolved vRNA segments is enriched over other assembly intermediates at the nuclear periphery during productive viral infection. This study illustrates how putative RNA interactions underlying selective assembly of IAV can be interrogated with phylogenetics. The viruses responsible for influenza evolve rapidly during infection. Changes typically emerge in two key ways: through random mutations in the genetic sequence of the virus, or by reassortment. Reassortment can occur when two or more strains infect the same cell. Once in a cell, viral particles ‘open up’ to release their genetic material so it can make copies of itself using the cell’s machinery. The new copies of the genetic material of the virus are used to make new viral particles, which then envelop the genetic material and are released from the cell to infect other cells. If several strains of a virus infect the same cell, a new viral particle may pick up genetic segments from each of the infecting strains, creating a new strain via reassortment. Several factors are known to affect the success of the reassortment process. For example, if the new strain acquires a genetic defect that hinders its replication cycle, it is likely to die out quickly. Other times, this trading of genetic information can create a strain that is more resistant to the human immune system, allowing it to sweep across the globe and cause a deadly pandemic. However, a key part of the reassortment process that still remains unclear is how genome segments from two different influenza strains recognize each other before merging together to create hybrid daughter viruses. To explore this further, Jones et al. used a technique called fluorescence microscopy. They found that genome segments that evolved along similar paths were more likely to cluster in the same area inside infected cells, and therefore, more likely to be reassorted together into a new strain during assembly of daughter viruses. This suggests that assembly may guide the evolutionary path taken by individual genomic segments. Jones et al. also looked at the evolution of different genome segments collected from patients suffering from seasonal influenza, and found that these segments had a distinct evolutionary path to those in pandemic-causing strains. This research provides new insights into the role of reassortment in the evolution of influenza viruses during infection. In particular, it suggests that how the genome segments interact with one another may have a previously unknown and important role in guiding this evolution. These insights could be used to predict future reassortment events based on evolutionary relationships between influenza virus genomic segments, and may in the future be used as part of risk assessment tools to predict the emergence of new pandemic strains.
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Affiliation(s)
- Jennifer E Jones
- Department of Microbiology & Molecular Genetics, University of Pittsburgh, Pittsburgh, United States.,Center for Evolutionary Biology and Medicine, University of Pittsburgh, Pittsburgh, United States.,Center for Vaccine Research, University of Pittsburgh School of Medicine, Pittsburgh, United States
| | - Valerie Le Sage
- Department of Microbiology & Molecular Genetics, University of Pittsburgh, Pittsburgh, United States.,Center for Vaccine Research, University of Pittsburgh School of Medicine, Pittsburgh, United States
| | - Gabriella H Padovani
- Department of Microbiology & Molecular Genetics, University of Pittsburgh, Pittsburgh, United States.,Center for Vaccine Research, University of Pittsburgh School of Medicine, Pittsburgh, United States
| | - Michael Calderon
- Department of Cell Biology, Center for Biologic Imaging, University of Pittsburgh, Pittsburgh, United States
| | - Erik S Wright
- Center for Evolutionary Biology and Medicine, University of Pittsburgh, Pittsburgh, United States.,Department of Biomedical Informatics, University of Pittsburgh, Pittsburgh, United States
| | - Seema S Lakdawala
- Department of Microbiology & Molecular Genetics, University of Pittsburgh, Pittsburgh, United States.,Center for Vaccine Research, University of Pittsburgh School of Medicine, Pittsburgh, United States
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Le Sage V, Kanarek JP, Snyder DJ, Cooper VS, Lakdawala SS, Lee N. Mapping of Influenza Virus RNA-RNA Interactions Reveals a Flexible Network. Cell Rep 2021; 31:107823. [PMID: 32610124 DOI: 10.1016/j.celrep.2020.107823] [Citation(s) in RCA: 44] [Impact Index Per Article: 14.7] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2019] [Revised: 04/20/2020] [Accepted: 06/04/2020] [Indexed: 11/25/2022] Open
Abstract
Selective assembly of influenza virus segments into virions is proposed to be mediated through intersegmental RNA-RNA interactions. Here, we developed a method called 2CIMPL that includes proximity ligation under native conditions to identify genome-wide RNA duplexes. Interactions between all eight segments were observed at multiple sites along a given segment and are concentrated at hotspots. Furthermore, synonymous nucleotide changes in a hotspot decreased the formation of RNA-RNA interactions at this site and resulted in a genome-wide rearrangement without a loss in replicative fitness. These results indicate that the viral RNA interaction network is flexible to account for nucleotide evolution. Moreover, comparative analysis of RNA-RNA interaction sites with viral nucleoprotein (NP) binding to the genome revealed that RNA junctions can also occur adjacent to NP peaks, suggesting that NP association does not exclude RNA duplex formation. Overall, 2CIMPL is a versatile technique to map in vivo RNA-RNA interactions.
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Affiliation(s)
- Valerie Le Sage
- Department of Microbiology and Molecular Genetics, University of Pittsburgh School of Medicine, 450 Technology Drive, Pittsburgh, PA 15219, USA
| | - Jack P Kanarek
- Department of Microbiology and Molecular Genetics, University of Pittsburgh School of Medicine, 450 Technology Drive, Pittsburgh, PA 15219, USA
| | - Dan J Snyder
- Department of Microbiology and Molecular Genetics, University of Pittsburgh School of Medicine, 450 Technology Drive, Pittsburgh, PA 15219, USA
| | - Vaughn S Cooper
- Department of Microbiology and Molecular Genetics, University of Pittsburgh School of Medicine, 450 Technology Drive, Pittsburgh, PA 15219, USA
| | - Seema S Lakdawala
- Department of Microbiology and Molecular Genetics, University of Pittsburgh School of Medicine, 450 Technology Drive, Pittsburgh, PA 15219, USA; Center for Vaccine Research, University of Pittsburgh School of Medicine, 450 Technology Drive, Pittsburgh, PA 15219, USA.
| | - Nara Lee
- Department of Microbiology and Molecular Genetics, University of Pittsburgh School of Medicine, 450 Technology Drive, Pittsburgh, PA 15219, USA.
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Li X, Gu M, Zheng Q, Gao R, Liu X. Packaging signal of influenza A virus. Virol J 2021; 18:36. [PMID: 33596956 PMCID: PMC7890907 DOI: 10.1186/s12985-021-01504-4] [Citation(s) in RCA: 29] [Impact Index Per Article: 9.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2020] [Accepted: 02/02/2021] [Indexed: 12/15/2022] Open
Abstract
Influenza A virus (IAV) contains a genome with eight single-stranded, negative-sense RNA segments that encode 17 proteins. During its assembly, all eight separate viral RNA (vRNA) segments are incorporated into virions in a selective manner. Evidence suggested that the highly selective genome packaging mechanism relies on RNA-RNA or protein-RNA interactions. The specific structures of each vRNA that contribute to mediating the packaging of the vRNA into virions have been described and identified as packaging signals. Abundant research indicated that sequences required for genome incorporation are not series and are varied among virus genotypes. The packaging signals play important roles in determining the virus replication, genome incorporation and genetic reassortment of influenza A virus. In this review, we discuss recent studies on influenza A virus packaging signals to provide an overview of their characteristics and functions.
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Affiliation(s)
- Xiuli Li
- Animal Infectious Disease Laboratory, College of Veterinary Medicine, Yangzhou University, 48 East Wenhui Road, Yangzhou, Jiangsu, China
| | - Min Gu
- Animal Infectious Disease Laboratory, College of Veterinary Medicine, Yangzhou University, 48 East Wenhui Road, Yangzhou, Jiangsu, China
| | - Qinmei Zheng
- Animal Infectious Disease Laboratory, College of Veterinary Medicine, Yangzhou University, 48 East Wenhui Road, Yangzhou, Jiangsu, China
| | - Ruyi Gao
- Animal Infectious Disease Laboratory, College of Veterinary Medicine, Yangzhou University, 48 East Wenhui Road, Yangzhou, Jiangsu, China
| | - Xiufan Liu
- Animal Infectious Disease Laboratory, College of Veterinary Medicine, Yangzhou University, 48 East Wenhui Road, Yangzhou, Jiangsu, China.
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15
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Wandzik JM, Kouba T, Karuppasamy M, Pflug A, Drncova P, Provaznik J, Azevedo N, Cusack S. A Structure-Based Model for the Complete Transcription Cycle of Influenza Polymerase. Cell 2020; 181:877-893.e21. [PMID: 32304664 DOI: 10.1016/j.cell.2020.03.061] [Citation(s) in RCA: 82] [Impact Index Per Article: 20.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2019] [Revised: 02/18/2020] [Accepted: 03/26/2020] [Indexed: 11/16/2022]
Abstract
Influenza polymerase uses unique mechanisms to synthesize capped and polyadenylated mRNAs from the genomic viral RNA (vRNA) template, which is packaged inside ribonucleoprotein particles (vRNPs). Here, we visualize by cryoelectron microscopy the conformational dynamics of the polymerase during the complete transcription cycle from pre-initiation to termination, focusing on the template trajectory. After exiting the active site cavity, the template 3' extremity rebinds into a specific site on the polymerase surface. Here, it remains sequestered during all subsequent transcription steps, forcing the template to loop out as it further translocates. At termination, the strained connection between the bound template 5' end and the active site results in polyadenylation by stuttering at uridine 17. Upon product dissociation, further conformational changes release the trapped template, allowing recycling back into the pre-initiation state. Influenza polymerase thus performs transcription while tightly binding to and protecting both template ends, allowing efficient production of multiple mRNAs from a single vRNP.
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Affiliation(s)
- Joanna M Wandzik
- European Molecular Biology Laboratory, 71 Avenue des Martyrs, CS 90181, 38042 Grenoble Cedex 9, France
| | - Tomas Kouba
- European Molecular Biology Laboratory, 71 Avenue des Martyrs, CS 90181, 38042 Grenoble Cedex 9, France
| | - Manikandan Karuppasamy
- European Molecular Biology Laboratory, 71 Avenue des Martyrs, CS 90181, 38042 Grenoble Cedex 9, France
| | - Alexander Pflug
- European Molecular Biology Laboratory, 71 Avenue des Martyrs, CS 90181, 38042 Grenoble Cedex 9, France
| | - Petra Drncova
- European Molecular Biology Laboratory, 71 Avenue des Martyrs, CS 90181, 38042 Grenoble Cedex 9, France
| | - Jan Provaznik
- European Molecular Biology Laboratory, GeneCore, Meyerhofstraße 1, 69117 Heidelberg, Germany
| | - Nayara Azevedo
- European Molecular Biology Laboratory, GeneCore, Meyerhofstraße 1, 69117 Heidelberg, Germany
| | - Stephen Cusack
- European Molecular Biology Laboratory, 71 Avenue des Martyrs, CS 90181, 38042 Grenoble Cedex 9, France.
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Shafiuddin M, Boon ACM. RNA Sequence Features Are at the Core of Influenza A Virus Genome Packaging. J Mol Biol 2019; 431:4217-4228. [PMID: 30914291 PMCID: PMC6756997 DOI: 10.1016/j.jmb.2019.03.018] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2019] [Revised: 02/18/2019] [Accepted: 03/11/2019] [Indexed: 11/23/2022]
Abstract
The influenza A virus (IAV), a respiratory pathogen for humans, poses serious medical and economic challenges to global healthcare systems. The IAV genome, consisting of eight single-stranded viral RNA segments, is incorporated into virions by a complex process known as genome packaging. Specific RNA sequences within the viral RNA segments serve as signals that are necessary for genome packaging. Although efficient packaging is a prerequisite for viral infectivity, many of the mechanistic details about this process are still missing. In this review, we discuss the recent advances toward the understanding of IAV genome packaging and focus on the RNA features that play a role in this process.
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Affiliation(s)
- Md Shafiuddin
- Department of Internal Medicine, Washington University in Saint Louis School of Medicine, St. Louis, MO 63110, USA
| | - Adrianus C M Boon
- Department of Internal Medicine, Washington University in Saint Louis School of Medicine, St. Louis, MO 63110, USA; Department of Molecular Microbiology and Microbial Pathogenesis, Washington University in Saint Louis School of Medicine, St. Louis, MO 63110, USA; Department of Pathology and Immunology, Washington University in Saint Louis School of Medicine, St. Louis, MO 63110, USA.
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mSphere of Influence: Redefining an Influenza Virus-How Different Are Influenza Viruses and Extracellular Vesicles? mSphere 2019; 4:4/5/e00563-19. [PMID: 31484743 PMCID: PMC6731533 DOI: 10.1128/msphere.00563-19] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Seema Lakdawala works in the field of influenza virology. In this mSphere of Influence article, she reflects on how the article “Conserved and host-specific features of influenza virion architecture” by Edward C. Seema Lakdawala works in the field of influenza virology. In this mSphere of Influence article, she reflects on how the article “Conserved and host-specific features of influenza virion architecture” by Edward C. Hutchinson et al. (Nat Commun 5:4816, 2014, https://doi.org/10.1038/ncomms5816) made an impact on her thinking about what constitutes an infectious virus and how influenza viruses can spread within and among hosts.
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18
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Newburn LR, White KA. Trans-Acting RNA-RNA Interactions in Segmented RNA Viruses. Viruses 2019; 11:v11080751. [PMID: 31416187 PMCID: PMC6723669 DOI: 10.3390/v11080751] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2019] [Revised: 08/08/2019] [Accepted: 08/11/2019] [Indexed: 12/18/2022] Open
Abstract
RNA viruses represent a large and important group of pathogens that infect a broad range of hosts. Segmented RNA viruses are a subclass of this group that encode their genomes in two or more molecules and package all of their RNA segments in a single virus particle. These divided genomes come in different forms, including double-stranded RNA, coding-sense single-stranded RNA, and noncoding single-stranded RNA. Genera that possess these genome types include, respectively, Orbivirus (e.g., Bluetongue virus), Dianthovirus (e.g., Red clover necrotic mosaic virus) and Alphainfluenzavirus (e.g., Influenza A virus). Despite their distinct genomic features and diverse host ranges (i.e., animals, plants, and humans, respectively) each of these viruses uses trans-acting RNA–RNA interactions (tRRIs) to facilitate co-packaging of their segmented genome. The tRRIs occur between different viral genome segments and direct the selective packaging of a complete genome complement. Here we explore the current state of understanding of tRRI-mediated co-packaging in the abovementioned viruses and examine other known and potential functions for this class of RNA–RNA interaction.
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Affiliation(s)
- Laura R Newburn
- Department of Biology, York University, Toronto, ON M3J 1P3, Canada
| | - K Andrew White
- Department of Biology, York University, Toronto, ON M3J 1P3, Canada.
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19
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Simon LM, Morandi E, Luganini A, Gribaudo G, Martinez-Sobrido L, Turner DH, Oliviero S, Incarnato D. In vivo analysis of influenza A mRNA secondary structures identifies critical regulatory motifs. Nucleic Acids Res 2019; 47:7003-7017. [PMID: 31053845 PMCID: PMC6648356 DOI: 10.1093/nar/gkz318] [Citation(s) in RCA: 45] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2019] [Revised: 04/15/2019] [Accepted: 04/23/2019] [Indexed: 02/05/2023] Open
Abstract
The influenza A virus (IAV) is a continuous health threat to humans as well as animals due to its recurring epidemics and pandemics. The IAV genome is segmented and the eight negative-sense viral RNAs (vRNAs) are transcribed into positive sense complementary RNAs (cRNAs) and viral messenger RNAs (mRNAs) inside infected host cells. A role for the secondary structure of IAV mRNAs has been hypothesized and debated for many years, but knowledge on the structure mRNAs adopt in vivo is currently missing. Here we solve, for the first time, the in vivo secondary structure of IAV mRNAs in living infected cells. We demonstrate that, compared to the in vitro refolded structure, in vivo IAV mRNAs are less structured but exhibit specific locally stable elements. Moreover, we show that the targeted disruption of these high-confidence structured domains results in an extraordinary attenuation of IAV replicative capacity. Collectively, our data provide the first comprehensive map of the in vivo structural landscape of IAV mRNAs, hence providing the means for the development of new RNA-targeted antivirals.
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Affiliation(s)
- Lisa Marie Simon
- Dipartimento di Scienze della Vita e Biologia dei Sistemi, Università di Torino, Via Accademia Albertina 13, 10123 Torino, Italy
| | - Edoardo Morandi
- Dipartimento di Scienze della Vita e Biologia dei Sistemi, Università di Torino, Via Accademia Albertina 13, 10123 Torino, Italy
| | - Anna Luganini
- Dipartimento di Scienze della Vita e Biologia dei Sistemi, Università di Torino, Via Accademia Albertina 13, 10123 Torino, Italy
| | - Giorgio Gribaudo
- Dipartimento di Scienze della Vita e Biologia dei Sistemi, Università di Torino, Via Accademia Albertina 13, 10123 Torino, Italy
| | - Luis Martinez-Sobrido
- Department of Microbiology and Immunology, University of Rochester Medical Center, 601 Elmwood Avenue, Rochester, NY 14642, USA
| | - Douglas H Turner
- Department of Chemistry and Center for RNA Biology, University of Rochester, Rochester, NY 14627, USA
| | - Salvatore Oliviero
- Dipartimento di Scienze della Vita e Biologia dei Sistemi, Università di Torino, Via Accademia Albertina 13, 10123 Torino, Italy
| | - Danny Incarnato
- Dipartimento di Scienze della Vita e Biologia dei Sistemi, Università di Torino, Via Accademia Albertina 13, 10123 Torino, Italy
- Department of Molecular Genetics, Groningen Biomolecular Sciences and Biotechnology Institute (GBB), University of Groningen, Nijenborgh 7, 9747 AG, Groningen, the Netherlands
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Lakdawala SS, Brooke CB. What's New with Flu? An Overview. Viruses 2019; 11:v11050433. [PMID: 31083357 PMCID: PMC6563513 DOI: 10.3390/v11050433] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2019] [Accepted: 05/06/2019] [Indexed: 12/11/2022] Open
Affiliation(s)
- Seema S Lakdawala
- Department of Microbiology & Molecular Genetics, University of Pittsburgh School of Medicine, Pittsburgh, PA 15219, USA.
- Center for Vaccine Research, University of Pittsburgh School of Medicine, Pittsburgh, PA 15219, USA.
| | - Christopher B Brooke
- Department of Microbiology, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA.
- Carl R. Woese Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA.
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Lakdawala SS, Lee N, Brooke CB. Teaching an Old Virus New Tricks: A Review on New Approaches to Study Age-Old Questions in Influenza Biology. J Mol Biol 2019; 431:4247-4258. [PMID: 31051174 DOI: 10.1016/j.jmb.2019.04.038] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2019] [Revised: 04/12/2019] [Accepted: 04/23/2019] [Indexed: 01/31/2023]
Abstract
Influenza viruses have been studied for over 80 years, yet much about the basic viral lifecycle remain unknown. However, new imaging, biochemical, and sequencing techniques have revealed significant insight into many age-old questions of influenza virus biology. In this review, we will cover the role of imaging techniques to describe unique aspects of influenza virus assembly, biochemical techniques to study viral genomic organization, and next-generation sequencing to explore influenza genomic evolution. Our goal is to provide a brief overview of how emerging techniques are being used to answer basic questions about influenza viruses. This is not a comprehensive list of emerging techniques, rather ones that we feel will continue to make significant contributions to field of influenza biology.
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Affiliation(s)
- Seema S Lakdawala
- Department of Microbiology and Molecular Genetics, University of Pittsburgh, School of Medicine Pittsburgh, PA 15219, USA.
| | - Nara Lee
- Department of Microbiology and Molecular Genetics, University of Pittsburgh, School of Medicine Pittsburgh, PA 15219, USA.
| | - Christopher B Brooke
- Department of Microbiology, University of Illinois at Urbana-Champaign, Champaign, IL 61801, USA; Carl R. Woese Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Champaign, IL 61801, USA.
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Lakdawala SS, Nair N, Hutchinson E. Educational Material about Influenza Viruses. Viruses 2019; 11:E231. [PMID: 30866478 PMCID: PMC6466267 DOI: 10.3390/v11030231] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2019] [Revised: 03/04/2019] [Accepted: 03/05/2019] [Indexed: 12/25/2022] Open
Abstract
To supplement a special edition of the journal Viruses, entitled "What's New with Flu?", influenza virus researchers have worked together to generate simple educational material to communicate their science to school students. Educational materials suitable for a range of ages are included, from coloring exercises for younger students through to explanations of cutting-edge science in straightforward language for older students. This article contains a handout with influenza facts, a coloring page, a glossary and word find and a connect-the-dots exercise explaining the ideas behind recently published scientific papers. Together, these materials are intended to make research on influenza viruses more accessible to students and teachers.
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Affiliation(s)
- Seema S Lakdawala
- Department of Microbiology and Molecular Genetics, University of Pittsburgh, Pittsburgh, PA, 15219 USA.
| | - Naina Nair
- School of Simulation and Visualisation, The Glasgow School of Art, 167 Renfrew Street, Glasgow G3 6RQ, UK.
- MRC-University of Glasgow Centre for Virus Research, 464 Bearsden Road, Glasgow G61 1QH, UK.
| | - Edward Hutchinson
- MRC-University of Glasgow Centre for Virus Research, 464 Bearsden Road, Glasgow G61 1QH, UK.
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