1
|
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: 7] [Impact Index Per Article: 3.5] [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.
Collapse
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
| |
Collapse
|
2
|
Tejus A, Mathur A, Pradhan S, Malik S, Salmani MF. Drug update - Baloxavir marboxil: Latest entrant into the arena of pharmacotherapy of influenza. Med J Armed Forces India 2021; 78:125-130. [PMID: 35463549 PMCID: PMC9023778 DOI: 10.1016/j.mjafi.2021.09.005] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2018] [Accepted: 09/21/2021] [Indexed: 11/17/2022] Open
Abstract
Influenza is a frequent cause of clinically significant human disease, with seasonal epidemics and occasional pandemics. Uncomplicated influenza in healthy individuals is managed symptomatically. Vaccination against influenza plays a vital role in the control of infection in humans. The currently available antivirals include adamantanes, neuraminidase inhibitors, and ribavirin. Baloxavir marboxil, the prodrug of baloxavir, is the latest addition to the family of anti-influenza drugs, and it received US-FDA approval on October 24, 2018. Baloxavir acts through a novel mechanism of inhibiting Cap-dependent endonuclease (CEN), the vital step in the transcription of viral RNA, and prevents further spread of the virus.
Collapse
Affiliation(s)
- A. Tejus
- Classified Specialist (Pharmacology), Medical Officer, HQ IMTRAT, C/o 99 APO, India
- Corresponding author.
| | | | - Sapna Pradhan
- Professor (Pharmacology), Army College of Medical Sciences, Delhi Cantt, India
| | - Salma Malik
- Demonstrator (Pharmacology), Army College of Medical Sciences, Delhi Cantt, India
| | - Md Fadil Salmani
- Demonstrator (Pharmacology), Army College of Medical Sciences, Delhi Cantt, India
| |
Collapse
|
3
|
Host factor Rab11a is critical for efficient assembly of influenza A virus genomic segments. PLoS Pathog 2021; 17:e1009517. [PMID: 33970958 PMCID: PMC8136845 DOI: 10.1371/journal.ppat.1009517] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2021] [Revised: 05/20/2021] [Accepted: 04/19/2021] [Indexed: 11/30/2022] Open
Abstract
It is well documented that influenza A viruses selectively package 8 distinct viral ribonucleoprotein complexes (vRNPs) into each virion; however, the role of host factors in genome assembly is not completely understood. To evaluate the significance of cellular factors in genome assembly, we generated a reporter virus carrying a tetracysteine tag in the NP gene (NP-Tc virus) and assessed the dynamics of vRNP localization with cellular components by fluorescence microscopy. At early time points, vRNP complexes were preferentially exported to the MTOC; subsequently, vRNPs associated on vesicles positive for cellular factor Rab11a and formed distinct vRNP bundles that trafficked to the plasma membrane on microtubule networks. In Rab11a deficient cells, however, vRNP bundles were smaller in the cytoplasm with less co-localization between different vRNP segments. Furthermore, Rab11a deficiency increased the production of non-infectious particles with higher RNA copy number to PFU ratios, indicative of defects in specific genome assembly. These results indicate that Rab11a+ vesicles serve as hubs for the congregation of vRNP complexes and enable specific genome assembly through vRNP:vRNP interactions, revealing the importance of Rab11a as a critical host factor for influenza A virus genome assembly. The influenza A virus (IAV) genome is composed of 8 distinct RNA segments. It has remained unclear how these 8 individual RNA segments are assembled together to form infectious virus particles. Our study shows that Rab11a+ vesicles serve as platforms for the congregation and assembly of 8 individual viral RNA segments needed to form infectious virus particles. However, in cells lacking Rab11a, viral RNA segments fail to congregate together, resulting in increased production of defective virus particles, likely due to misassembling of viral RNA segments. Thus, our study reveals the important role for Rab11a in influenza virus genome assembly and production of infectious virus particles.
Collapse
|
4
|
Selective flexible packaging pathways of the segmented genome of influenza A virus. Nat Commun 2020; 11:4355. [PMID: 32859915 PMCID: PMC7455735 DOI: 10.1038/s41467-020-18108-1] [Citation(s) in RCA: 20] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2019] [Accepted: 07/30/2020] [Indexed: 12/20/2022] Open
Abstract
The genome of influenza A viruses (IAV) is encoded in eight distinct viral ribonucleoproteins (vRNPs) that consist of negative sense viral RNA (vRNA) covered by the IAV nucleoprotein. Previous studies strongly support a selective packaging model by which vRNP segments are bundling to an octameric complex, which is integrated into budding virions. However, the pathway(s) generating a complete genome bundle is not known. We here use a multiplexed FISH assay to monitor all eight vRNAs in parallel in human lung epithelial cells. Analysis of 3.9 × 105 spots of colocalizing vRNAs provides quantitative insights into segment composition of vRNP complexes and, thus, implications for bundling routes. The complexes rarely contain multiple copies of a specific segment. The data suggest a selective packaging mechanism with limited flexibility by which vRNPs assemble into a complete IAV genome. We surmise that this flexibility forms an essential basis for the development of reassortant viruses with pandemic potential.
Collapse
|
5
|
Morris AK, Wang Z, Ivey AL, Xie Y, Hill PS, Schey KL, Ren Y. Cellular mRNA export factor UAP56 recognizes nucleic acid binding site of influenza virus NP protein. Biochem Biophys Res Commun 2020; 525:259-264. [PMID: 32085897 DOI: 10.1016/j.bbrc.2020.02.059] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/03/2020] [Accepted: 02/09/2020] [Indexed: 02/06/2023]
Abstract
Influenza A virus nucleoprotein (NP) is a structural component that encapsulates the viral genome into the form of ribonucleoprotein complexes (vRNPs). Efficient assembly of vRNPs is critical for the virus life cycle. The assembly route from RNA-free NP to the NP-RNA polymer in vRNPs has been suggested to require a cellular factor UAP56, but the mechanism is poorly understood. Here, we characterized the interaction between NP and UAP56 using recombinant proteins and showed that UAP56 features two NP binding sites. In addition to the UAP56 core comprised of two RecA domains, we identified the N-terminal extension (NTE) of UAP56 as a previously unknown NP binding site. In particular, UAP56-NTE recognizes the nucleic acid binding region of NP. This corroborates our observation that binding of UAP56-NTE and RNA to NP is mutually exclusive. Collectively, our results reveal the molecular basis for how UAP56 acts on RNA-free NP, and provide new insights into NP-mediated influenza genome packaging.
Collapse
Affiliation(s)
- Andrew K Morris
- Department of Biochemistry, Vanderbilt University School of Medicine, Nashville, TN, 37232, USA
| | - Zhen Wang
- Department of Biochemistry, Vanderbilt University School of Medicine, Nashville, TN, 37232, USA; Mass Spectrometry Research Center, Vanderbilt University School of Medicine, Nashville, TN, 37232, USA
| | - Austin L Ivey
- Department of Biochemistry, Vanderbilt University School of Medicine, Nashville, TN, 37232, USA
| | - Yihu Xie
- Department of Biochemistry, Vanderbilt University School of Medicine, Nashville, TN, 37232, USA
| | - Pate S Hill
- Department of Biochemistry, Vanderbilt University School of Medicine, Nashville, TN, 37232, USA
| | - Kevin L Schey
- Department of Biochemistry, Vanderbilt University School of Medicine, Nashville, TN, 37232, USA; Mass Spectrometry Research Center, Vanderbilt University School of Medicine, Nashville, TN, 37232, USA
| | - Yi Ren
- Department of Biochemistry, Vanderbilt University School of Medicine, Nashville, TN, 37232, USA.
| |
Collapse
|
6
|
Yamagata Y, Muramoto Y, Miyamoto S, Shindo K, Nakano M, Noda T. Generation of a purely clonal defective interfering influenza virus. Microbiol Immunol 2019; 63:164-171. [PMID: 30997933 DOI: 10.1111/1348-0421.12681] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2018] [Revised: 04/09/2019] [Accepted: 04/10/2019] [Indexed: 11/29/2022]
Abstract
Defective interfering (DI) influenza viruses carry a large deletion in a gene segment that interferes with the replication of infectious virus; thus, such viruses have potential for antiviral therapy. However, because DI viruses cannot replicate autonomously without the aid of an infectious helper virus, clonal DI virus stocks that are not contaminated with helper virus have not yet been generated. To overcome this problem, we used reverse genetics to generate a clonal DI virus with a PB2 DI gene, amplified the clonal DI virus using a cell line stably expressing the PB2 protein, and confirmed its ability to interfere with infectious virus replication in vitro. Thus, our approach is suitable for obtaining purely clonal DI viruses, will contribute to the understanding of DI virus interference mechanisms and can be used to develop DI virus-based antivirals.
Collapse
Affiliation(s)
- Yutaro Yamagata
- Laboratory of Ultrastructural Virology, Institute for Frontier Life and Medical Sciences, Kyoto University, Sakyo-ku, Kyoto, Japan.,Laboratory of Ultrastructural Virology, Graduate School of Biostudies, Kyoto University, Sakyo-ku, Kyoto, Japan
| | - Yukiko Muramoto
- Laboratory of Ultrastructural Virology, Institute for Frontier Life and Medical Sciences, Kyoto University, Sakyo-ku, Kyoto, Japan
| | - Sho Miyamoto
- Laboratory of Ultrastructural Virology, Institute for Frontier Life and Medical Sciences, Kyoto University, Sakyo-ku, Kyoto, Japan.,Department of Molecular Virology, Graduate School of Medicine, Kyoto University, Kyoto, Japan
| | - Keiko Shindo
- Laboratory of Ultrastructural Virology, Institute for Frontier Life and Medical Sciences, Kyoto University, Sakyo-ku, Kyoto, Japan
| | - Masahiro Nakano
- Laboratory of Ultrastructural Virology, Institute for Frontier Life and Medical Sciences, Kyoto University, Sakyo-ku, Kyoto, Japan.,Laboratory of Ultrastructural Virology, Graduate School of Biostudies, Kyoto University, Sakyo-ku, Kyoto, Japan
| | - Takeshi Noda
- Laboratory of Ultrastructural Virology, Institute for Frontier Life and Medical Sciences, Kyoto University, Sakyo-ku, Kyoto, Japan.,Laboratory of Ultrastructural Virology, Graduate School of Biostudies, Kyoto University, Sakyo-ku, Kyoto, Japan
| |
Collapse
|
7
|
Metal-Tagging Transmission Electron Microscopy and Immunogold Labeling on Tokuyasu Cryosections to Image Influenza A Virus Ribonucleoprotein Transport and Packaging. Methods Mol Biol 2019; 1836:281-301. [PMID: 30151579 DOI: 10.1007/978-1-4939-8678-1_14] [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] [Indexed: 02/17/2023]
Abstract
Transmission electron microscopy (TEM) has been instrumental for studying viral infections. In particular, methods for labeling macromolecules at the ultrastructural level, by integrating biochemistry, molecular biology, and morphology, have allowed to study the functions of viral macromolecular complexes within the cellular context. Here, we describe a strategy for imaging influenza virus ribonucleoproteins in infected cells with two complementary labeling methods, metal-tagging transmission electron microscopy or METTEM, a highly sensitive technique based on the use of a metal-binding protein as a clonable tag, and immunogold labeling on thawed cryosections, a very specific labeling method that allows to study the distribution of different proteins simultaneously. The combination of both labeling methods offers new possibilities for TEM analysis of viral components in cells.
Collapse
|
8
|
Takizawa N, Ogura Y, Fujita Y, Noda T, Shigematsu H, Hayashi T, Kurokawa K. Local structural changes of the influenza A virus ribonucleoprotein complex by single mutations in the specific residues involved in efficient genome packaging. Virology 2019; 531:126-140. [PMID: 30875489 DOI: 10.1016/j.virol.2019.03.004] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2018] [Revised: 03/05/2019] [Accepted: 03/06/2019] [Indexed: 11/15/2022]
Abstract
The influenza A virus genome consists of eight single-stranded negative-sense RNA segments. The noncoding regions located at the 3'- and 5'- ends of each segment are necessary for genome packaging, and the terminal coding regions are required to precisely bundle the eight segments. However, the nucleotide residues important for genome bundling are not defined. Here, we introduced premature termination codons in the hemagglutinin (HA) or matrix protein 2 (M2) gene and constructed virus libraries containing random sequences in the terminal coding regions. Using these virus libraries, we identified nucleotide residues involved in efficient virus propagation. Viral genome packaging was impaired in viruses that contained single mutations at these identified residues. Furthermore, these single mutations altered the local structure of the viral ribonucleoprotein complex. Our results show that specific nucleotide residues in the viral protein coding region are involved in forming the precise structure of the viral ribonucleoprotein complex.
Collapse
Affiliation(s)
- Naoki Takizawa
- Laboratory of Virology, Institute of Microbial Chemistry (BIKAKEN), Tokyo, Japan.
| | - Yoshitoshi Ogura
- Department of Bacteriology, Faculty of Medical Sciences, Kyushu University, Fukuoka, Japan
| | - Yoko Fujita
- Laboratory of Ultrastructural Virology, Institute for Frontier Life and Medical Sciences, Kyoto University, Kyoto, Japan; Laboratory of Ultrastructural Virology, Division of Integrated Life Science, Graduate School of Biostudies, Kyoto University, Kyoto, Japan
| | - Takeshi Noda
- Laboratory of Ultrastructural Virology, Institute for Frontier Life and Medical Sciences, Kyoto University, Kyoto, Japan; Laboratory of Ultrastructural Virology, Division of Integrated Life Science, Graduate School of Biostudies, Kyoto University, Kyoto, Japan
| | - Hideki Shigematsu
- Life Science Research Infrastructure Group, RIKEN SPring-8 Center, Hyogo, Japan
| | - Tetsuya Hayashi
- Department of Bacteriology, Faculty of Medical Sciences, Kyushu University, Fukuoka, Japan
| | - Ken Kurokawa
- Center for Information Biology, National Institute of Genetics, Shizuoka, Japan
| |
Collapse
|
9
|
Bolte H, Rosu ME, Hagelauer E, García-Sastre A, Schwemmle M. Packaging of the Influenza Virus Genome Is Governed by a Plastic Network of RNA- and Nucleoprotein-Mediated Interactions. J Virol 2019; 93:e01861-18. [PMID: 30463968 PMCID: PMC6363987 DOI: 10.1128/jvi.01861-18] [Citation(s) in RCA: 26] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2018] [Accepted: 11/15/2018] [Indexed: 11/20/2022] Open
Abstract
The genome of influenza A virus is organized into eight ribonucleoproteins, each composed of a distinct RNA segment bound by the viral polymerase and oligomeric viral nucleoprotein. Packaging sequences unique to each RNA segment together with specific nucleoprotein amino acids are thought to ensure the precise incorporation of these eight ribonucleoproteins into single virus particles, and yet the underlying interaction network remains largely unexplored. We show here that the genome packaging mechanism of an H7N7 subtype influenza A virus widely tolerates the mutation of individual packaging sequences in three different RNA segments. However, combinations of these modified RNA segments cause distinct genome packaging defects, marked by the absence of specific RNA segment subsets from the viral particles. Furthermore, we find that combining a single mutated packaging sequence with sets of specific nucleoprotein amino acid substitutions greatly impairs the viral genome packaging process. Along with previous reports, our data propose that influenza A virus uses a redundant and plastic network of RNA-RNA and potentially RNA-nucleoprotein interactions to coordinately incorporate its segmented genome into virions.IMPORTANCE The genome of influenza A virus is organized into eight viral ribonucleoproteins (vRNPs); this provides evolutionary advantages but complicates genome packaging. Although it has been shown that RNA packaging sequences and specific amino acids in the viral nucleoprotein (NP), both components of each vRNP, ensure selective packaging of one copy of each vRNP per virus particle, the required RNA-RNA and RNA-NP interactions remain largely elusive. We identified that the genome packaging mechanism tolerates the mutation of certain individual RNA packaging sequences, while their combined mutation provokes distinct genome packaging defects. Moreover, we found that seven specific amino acid substitutions in NP impair the function of RNA packaging sequences and that this defect is partially restored by another NP amino acid change. Collectively, our data indicate that packaging of the influenza A virus genome is controlled by a redundant and plastic network of RNA/protein interactions, which may facilitate natural reassortment processes.
Collapse
Affiliation(s)
- Hardin Bolte
- Institute of Virology, Medical Center University of Freiburg, Freiburg, Germany
- Spemann Graduate School of Biology and Medicine, University of Freiburg, Freiburg, Germany
- Faculty of Biology, University of Freiburg, Freiburg, Germany
- Faculty of Medicine, University of Freiburg, Freiburg, Germany
| | - Miruna E Rosu
- Institute of Virology, Medical Center University of Freiburg, Freiburg, Germany
- Department of Viroscience, Postgraduate School Molecular Medicine, Erasmus Medical Center, Rotterdam, The Netherlands
| | - Elena Hagelauer
- Institute of Virology, Medical Center University of Freiburg, Freiburg, Germany
- Faculty of Biology, University of Freiburg, Freiburg, Germany
- Faculty of Medicine, University of Freiburg, Freiburg, Germany
| | - Adolfo García-Sastre
- Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York, New York, USA
- Global Health and Emerging Pathogens Institute, Icahn School of Medicine at Mount Sinai, New York, New York, USA
- Department of Medicine, Division of Infectious Diseases, Icahn School of Medicine at Mount Sinai, New York, New York, USA
| | - Martin Schwemmle
- Institute of Virology, Medical Center University of Freiburg, Freiburg, Germany
- Faculty of Medicine, University of Freiburg, Freiburg, Germany
| |
Collapse
|
10
|
Amorim MJ. A Comprehensive Review on the Interaction Between the Host GTPase Rab11 and Influenza A Virus. Front Cell Dev Biol 2019; 6:176. [PMID: 30687703 PMCID: PMC6333742 DOI: 10.3389/fcell.2018.00176] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2018] [Accepted: 12/17/2018] [Indexed: 12/20/2022] Open
Abstract
This year marks the 100th anniversary of one of the deadliest pandemic outbreaks, commonly referred as the Spanish Flu, that was caused by influenza A virus (IAV). Since then, IAV has been in governmental agendas worldwide, and a lot of effort has been put into understanding the pathogen's lifecycle, predict and mitigate the emergence of the strains that provoke yearly epidemics and pandemic events. Despite decades of research and seminal contributions there is still a lot to be investigated. In particular for this review, IAV lifecycle that takes place inside the host cell is not fully understood. Two steps that need clarification include genome transport to budding sites and genome assembly, the latter a complex process challenged by the nature of IAV genome that is divided into eight distinct parts. Assembly of such segmented genome is crucial to form fully infectious viral particles but is also critical for the emergence of viruses with pandemic potential that arise when avian and human IAV strains co-infect a host. The host GTPase Rab11 was separately implicated in both steps, and, interestingly these processes are beginning to emerge as being intimately related. Rab11 was initially proposed to be involved in the budding/release of IAV virions. It was subsequently shown to transport progeny genome, and later proposed to promote assembly of viral genome, but the underlying bridging mechanism the two is far from clear. For simplicity, this Rab11-centric review provides an initial separate account of Rab11 involvement in genome transport and in assembly. IAV genome assembly is a complicated molecular biology process, and therefore earned a dedicated section on how/if the viral genome forms a genomic supramolecular complex. Both topics present intricate challenges, outstanding questions, and unique controversies. At the end of the review, I will explore possible mechanisms intertwining IAV vRNP transport and genome assembly. Importantly, Rab11 has recently emerged as a key factor subverted by evolutionary unrelated viral families (Paramyxo, Bunya, and Orthomyxoviruses, among many others) and bacteria (Salmonella and Shigella) relevant to human health. This review provides a framework to identify common biological principles among the lifecycles of these pathogens.
Collapse
Affiliation(s)
- Maria João Amorim
- Cell Biology of Viral Infection Lab, Instituto Gulbenkian de Ciência, Oeiras, Portugal
| |
Collapse
|
11
|
Wichgers Schreur PJ, Kormelink R, Kortekaas J. Genome packaging of the Bunyavirales. Curr Opin Virol 2018; 33:151-155. [PMID: 30227361 DOI: 10.1016/j.coviro.2018.08.011] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2018] [Revised: 08/17/2018] [Accepted: 08/28/2018] [Indexed: 11/18/2022]
Abstract
The order Bunyavirales comprises nine families of enveloped, negative-strand RNA viruses. Depending on the family and genus, bunyaviruses (i.e. now referring to all members of the Bunyavirales) contain genomes consisting of two to six segments. Each genome segment is encapsidated by multiple copies of the nucleocapsid (N) protein and one or a few molecules of the viral polymerase, forming so-called ribonucleoproteins (RNPs). Incorporation of RNPs into virions is mediated by the interaction of N with the cytoplasmic tails of the structural glycoproteins. Although some selectivity exists in the packaging of RNPs into virions, which seems to be driven by the 5' and 3'-untranslated regions of the genomic RNA segments, evidence is accumulating that bunyavirus genome packaging is a stochastic process.
Collapse
Affiliation(s)
| | - Richard Kormelink
- Laboratory of Virology, Wageningen University, Droevendaalsesteeg 1, 6708 PB Wageningen, The Netherlands
| | - Jeroen Kortekaas
- Wageningen Bioveterinary Research, Houtribweg 39, 8221 RA Lelystad, The Netherlands; Laboratory of Virology, Wageningen University, Droevendaalsesteeg 1, 6708 PB Wageningen, The Netherlands
| |
Collapse
|
12
|
Noda T, Murakami S, Nakatsu S, Imai H, Muramoto Y, Shindo K, Sagara H, Kawaoka Y. Importance of the 1+7 configuration of ribonucleoprotein complexes for influenza A virus genome packaging. Nat Commun 2018; 9:54. [PMID: 29302061 PMCID: PMC5754346 DOI: 10.1038/s41467-017-02517-w] [Citation(s) in RCA: 40] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2017] [Accepted: 12/06/2017] [Indexed: 12/31/2022] Open
Abstract
The influenza A virus genome is composed of eight single-stranded negative-sense RNAs. Eight distinct viral RNA segments (vRNAs) are selectively packaged into progeny virions, with eight vRNAs in ribonucleoprotein complexes (RNPs) arranged in a specific “1+7” pattern, that is, one central RNP surrounded by seven RNPs. Here we report the genome packaging of an artificially generated seven-segment virus that lacks the hemagglutinin (HA) vRNA. Electron microscopy shows that, even in the presence of only seven vRNAs, the virions efficiently package eight RNPs arranged in the same “1+7” pattern as wild-type virions. Next-generation sequencing reveals that the virions specifically incorporate host-derived 18S and 28S ribosomal RNAs (rRNAs) seemingly as the eighth RNP in place of the HA vRNA. These findings highlight the importance of the assembly of eight RNPs into a specific “1+7” configuration for genome packaging in progeny virions and suggest a potential role for cellular RNAs in viral genome packaging. Influenza A virus (IAV) packages its eight genomic RNA segments in a specific “1+7” pattern. Here, the authors generate IAV that lack one RNA segment and show that ribosomal RNA is packaged in place of the eighth segment, suggesting that the 1+7 pattern is important for particle production.
Collapse
Affiliation(s)
- Takeshi Noda
- Division of Virology, Department of Microbiology and Immunology, Institute of Medical Science, University of Tokyo, 4-6-1 Shirokanedai, Minato-ku, Tokyo, 108-8639, Japan. .,International Research Center for Infectious Diseases, Institute of Medical Science, University of Tokyo, 4-6-1 Shirokanedai, Minato-ku, Tokyo, 108-8639, Japan. .,PRESTO, Japan Science and Technology Agency, 4-1-8 Honcho, Kawaguchi, Saitama, 332-0012, Japan. .,Laboratory of Ultrastructural Virology, Institute for Frontier Life and Medical Sciences, Kyoto University, 53 Shogoin Kawahara-cho, Sakyo-ku, Kyoto, 606-8507, Japan. .,Laboratory of Ultrastructural Virology, Graduate School of Biostudies, Kyoto University, 53 Shogoin Kawahara-cho, Sakyo-ku, Kyoto, 606-8507, Japan.
| | - Shin Murakami
- Division of Virology, Department of Microbiology and Immunology, Institute of Medical Science, University of Tokyo, 4-6-1 Shirokanedai, Minato-ku, Tokyo, 108-8639, Japan.,Department of Veterinary Microbiology, Graduate School of Agricultural and Life Sciences, The University of Tokyo, 1-1-1 Yayoi, Bunkyo-ku, Tokyo, 113-8657, Japan
| | - Sumiho Nakatsu
- Division of Virology, Department of Microbiology and Immunology, Institute of Medical Science, University of Tokyo, 4-6-1 Shirokanedai, Minato-ku, Tokyo, 108-8639, Japan
| | - Hirotaka Imai
- Division of Virology, Department of Microbiology and Immunology, Institute of Medical Science, University of Tokyo, 4-6-1 Shirokanedai, Minato-ku, Tokyo, 108-8639, Japan.,Department of Biological Informatics and Experimental Therapeutics, Graduate School of Medicine, Akita University, Akita, 010-8543, Japan
| | - Yukiko Muramoto
- Division of Virology, Department of Microbiology and Immunology, Institute of Medical Science, University of Tokyo, 4-6-1 Shirokanedai, Minato-ku, Tokyo, 108-8639, Japan.,Laboratory of Ultrastructural Virology, Institute for Frontier Life and Medical Sciences, Kyoto University, 53 Shogoin Kawahara-cho, Sakyo-ku, Kyoto, 606-8507, Japan
| | - Keiko Shindo
- Laboratory of Ultrastructural Virology, Institute for Frontier Life and Medical Sciences, Kyoto University, 53 Shogoin Kawahara-cho, Sakyo-ku, Kyoto, 606-8507, Japan
| | - Hiroshi Sagara
- Medical Proteomics Laboratory, Institute of Medical Science, University of Tokyo, 4-6-1 Shirokanedai, Minato-ku, Tokyo, 108-8639, Japan
| | - Yoshihiro Kawaoka
- Division of Virology, Department of Microbiology and Immunology, Institute of Medical Science, University of Tokyo, 4-6-1 Shirokanedai, Minato-ku, Tokyo, 108-8639, Japan. .,International Research Center for Infectious Diseases, Institute of Medical Science, University of Tokyo, 4-6-1 Shirokanedai, Minato-ku, Tokyo, 108-8639, Japan. .,Department of Pathological Sciences, School of Veterinary Medicine, University of Wisconsin-Madison, Madison, WI, 53771, USA.
| |
Collapse
|
13
|
Influenza virus genome reaches the plasma membrane via a modified endoplasmic reticulum and Rab11-dependent vesicles. Nat Commun 2017; 8:1396. [PMID: 29123131 PMCID: PMC5680169 DOI: 10.1038/s41467-017-01557-6] [Citation(s) in RCA: 58] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2017] [Accepted: 09/27/2017] [Indexed: 12/05/2022] Open
Abstract
Transport of neo-synthesized influenza A virus (IAV) viral ribonucleoproteins (vRNPs) from the nucleus to the plasma membrane involves Rab 11 but the precise mechanism remains poorly understood. We used metal-tagging and immunolabeling to visualize viral proteins and cellular endomembrane markers by electron microscopy of IAV-infected cells. Unexpectedly, we provide evidence that the vRNP components and the Rab11 protein are present at the membrane of a modified, tubulated endoplasmic reticulum (ER) that extends all throughout the cell, and on irregularly coated vesicles (ICVs). Some ICVs are found very close to the ER and to the plasma membrane. ICV formation is observed only in infected cells and requires an active Rab11 GTPase. Against the currently accepted model in which vRNPs are carried onto Rab11-positive recycling endosomes across the cytoplasm, our findings reveal that the endomembrane organelle that is primarily involved in the transport of vRNPs is the ER. Transport of neo-synthesized influenza A virus viral ribonucleoproteins (vRNPs) from the nucleus to the plasma membrane involves Rab 11 but the mechanism is unclear. Here the authors show that vRNPs are transported through a modified Rab11-positive endoplasmic reticulum and Rab11-dependent vesicles.
Collapse
|
14
|
Ramos-Nascimento A, Kellen B, Ferreira F, Alenquer M, Vale-Costa S, Raposo G, Delevoye C, Amorim MJ. KIF13A mediates trafficking of influenza A virus ribonucleoproteins. J Cell Sci 2017; 130:4038-4050. [PMID: 29061883 DOI: 10.1242/jcs.210807] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2017] [Accepted: 10/18/2017] [Indexed: 01/18/2023] Open
Abstract
Influenza A is a rapidly evolving virus that is successful in provoking periodic epidemics and occasional pandemics in humans. Viral assembly is complex as the virus incorporates an eight-partite genome of RNA (in the form of viral ribonucleoproteins, vRNPs), and viral genome assembly - with its implications to public health - is not completely understood. It has previously been reported that vRNPs are transported to the cell surface on Rab11-containing vesicles by using microtubules but, so far, no molecular motor has been assigned to the process. Here, we have identified KIF13A, a member of the kinesin-3 family, as the first molecular motor to efficiently transport vRNP-Rab11 vesicles during infection with influenza A. Depletion of KIF13A resulted in reduced viral titers and less accumulation of vRNPs at the cell surface, without interfering with the levels of other viral proteins at sites of viral assembly. In addition, when overexpressed and following two separate approaches to displace vRNP-Rab11 vesicles, KIF13A increased levels of vRNP at the plasma membrane. Together, our results show that KIF13A plays an important role in the transport of influenza A vRNPs, a crucial step for viral assembly.This article has an associated First Person interview with the first author of the paper.
Collapse
Affiliation(s)
- Ana Ramos-Nascimento
- Cell Biology of Viral Infection Lab, Instituto Gulbenkian de Ciência (IGC), 2780-156 Oeiras, Portugal.,Institute of Virology, Hannover Medical School, 30625 Hannover, Germany
| | - Bárbara Kellen
- Science4U, MARL Espaços CC02 e CC03, São Julião do Tojal, 2660-421, Loures, Portugal
| | - Filipe Ferreira
- Cell Biology of Viral Infection Lab, Instituto Gulbenkian de Ciência (IGC), 2780-156 Oeiras, Portugal
| | - Marta Alenquer
- Cell Biology of Viral Infection Lab, Instituto Gulbenkian de Ciência (IGC), 2780-156 Oeiras, Portugal
| | - Sílvia Vale-Costa
- Cell Biology of Viral Infection Lab, Instituto Gulbenkian de Ciência (IGC), 2780-156 Oeiras, Portugal
| | - Graça Raposo
- Institut Curie, PSL Research University, CNRS, UMR144, Structure and Membrane Compartments, 75005 Paris, France
| | - Cédric Delevoye
- Institut Curie, PSL Research University, CNRS, UMR144, Structure and Membrane Compartments, 75005 Paris, France
| | - Maria João Amorim
- Cell Biology of Viral Infection Lab, Instituto Gulbenkian de Ciência (IGC), 2780-156 Oeiras, Portugal
| |
Collapse
|
15
|
Affiliation(s)
- Anice C. Lowen
- Department of Microbiology and Immunology, Emory University School of Medicine, Atlanta, Georgia 30322
| |
Collapse
|
16
|
Spronken MI, van de Sandt CE, de Jongh EP, Vuong O, van der Vliet S, Bestebroer TM, Olsthoorn RCL, Rimmelzwaan GF, Fouchier RAM, Gultyaev AP. A compensatory mutagenesis study of a conserved hairpin in the M gene segment of influenza A virus shows its role in virus replication. RNA Biol 2017; 14:1606-1616. [PMID: 28662365 PMCID: PMC5785231 DOI: 10.1080/15476286.2017.1338243] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022] Open
Abstract
RNA structures are increasingly recognized to be of importance during influenza A virus replication. Here, we investigated a predicted conserved hairpin in the M gene segment (nt 967-994) within the region of the vRNA 5′ packaging signal. The existence of this RNA structure and its possible role in virus replication was investigated using a compensatory mutagenesis approach. Mutations were introduced in the hairpin stem, based on natural variation. Virus replication properties were studied for the mutant viruses with disrupted and restored RNA structures. Viruses with structure-disrupting mutations had lower virus titers and a significantly reduced median plaque size when compared with the wild-type (WT) virus, while viruses with structure restoring-mutations replicated comparable to WT. Moreover, virus replication was also reduced when mutations were introduced in the hairpin loop, suggesting its involvement in RNA interactions. Northern blot and FACS experiments were performed to study differences in RNA levels as well as production of M1 and M2 proteins, expressed via alternative splicing. Stem-disruptive mutants caused lower vRNA and M2 mRNA levels and reduced M2 protein production at early time-points. When the RNA structure was restored, vRNA, M2 mRNA and M2 protein levels were increased, demonstrating a compensatory effect. Thus, this study provides evidence for functional importance of the predicted M RNA structure and suggests its role in splicing regulation.
Collapse
Affiliation(s)
- M I Spronken
- a Department of Viroscience , Erasmus Medical Centre , Rotterdam , the Netherlands
| | - C E van de Sandt
- a Department of Viroscience , Erasmus Medical Centre , Rotterdam , the Netherlands
| | - E P de Jongh
- a Department of Viroscience , Erasmus Medical Centre , Rotterdam , the Netherlands
| | - O Vuong
- a Department of Viroscience , Erasmus Medical Centre , Rotterdam , the Netherlands
| | - S van der Vliet
- a Department of Viroscience , Erasmus Medical Centre , Rotterdam , the Netherlands
| | - T M Bestebroer
- a Department of Viroscience , Erasmus Medical Centre , Rotterdam , the Netherlands
| | - R C L Olsthoorn
- c Group Supramolecular and Biomaterials Chemistry, Leiden Institute of Chemistry, Leiden University , Leiden , the Netherlands
| | - G F Rimmelzwaan
- a Department of Viroscience , Erasmus Medical Centre , Rotterdam , the Netherlands
| | - R A M Fouchier
- a Department of Viroscience , Erasmus Medical Centre , Rotterdam , the Netherlands
| | - A P Gultyaev
- a Department of Viroscience , Erasmus Medical Centre , Rotterdam , the Netherlands.,b Group Imaging and Bioinformatics, Leiden Institute of Advanced Computer Science, Leiden University , Leiden , the Netherlands
| |
Collapse
|
17
|
Suzuki Y. Co-evolution in a putative bundling signal of bluetongue and epizootic hemorrhagic disease viruses. Genes Genet Syst 2017; 91:283-288. [PMID: 27853052 DOI: 10.1266/ggs.16-00035] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022] Open
Abstract
Bluetongue virus (BTV) and epizootic hemorrhagic disease virus (EHDV) possess a genome of 10 segmented RNAs (S1-S10), one copy of each of which is considered to be packaged in a virion. This selective packaging is thought to be mediated by supramolecular complex formation of the 10 RNAs, through intermolecular base pairing of complementary nucleotide sequences termed the bundling signal. Here, the whole genomic sequences of BTV and EHDV isolates were analyzed to identify co-evolving pairs of complementary nucleotide sequences within and between genomic segments. One co-evolving pair was identified within S5 and another between S5 and S10. The co-evolving pair between S5 and S10, consisting of six bases in each segment, was a candidate for a bundling signal and was identical to one of two putative bundling signals reported in a previous experimental study, validating the effectiveness of the method used in the present study. The six bases in S10 were confirmed to be located in a loop at the end of a stable stem. Although the six bases in S5 were located in a loop at the end of a stem of only four bases long, the complementary nucleotide sequences constituting this stem were, remarkably, the co-evolving pair within S5. These results highlight the importance not only of loops but also of stems in the intermolecular base pairing of bundling signals.
Collapse
|
18
|
Pflug A, Lukarska M, Resa-Infante P, Reich S, Cusack S. Structural insights into RNA synthesis by the influenza virus transcription-replication machine. Virus Res 2017; 234:103-117. [PMID: 28115197 DOI: 10.1016/j.virusres.2017.01.013] [Citation(s) in RCA: 119] [Impact Index Per Article: 17.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2016] [Revised: 12/31/2016] [Accepted: 01/13/2017] [Indexed: 12/22/2022]
Abstract
Influenza virus is a segmented, negative strand RNA virus with each genome segment being packaged in a distinct ribonucleoprotein particle (RNP). The RNP consists of the heterotrimeric viral RNA-dependent RNA polymerase bound to the conserved 5' and 3' ends of the genome segment (the viral promoter) with the rest of the viral RNA (vRNA) being covered by multiple copies of nucleoprotein. This review focusses on the new insights that recent crystal structures have given into the detailed molecular mechanisms by which the polymerase performs both transcription and replication of the vRNA genome. Promoter binding, in particular that of 5' end, is essential to allosterically activate all polymerase functions. Transcription is initiated by the hijacking of nascent, capped host transcripts by the process of 'cap-snatching', for which the viral polymerase makes an essential interaction with the C-terminal domain (CTD) of cellular RNA polymerase II. The structures allow a coherent mechanistic model of the subsequent cap-snatching, cap-dependent priming, elongation and self-polyadenylation steps of viral mRNA synthesis. During replication, the vRNA is copied without modification into complementary RNA (cRNA) which is packaged into cRNPs. A priming loop located in the polymerase active site is required for the unprimed synthesis of cRNA from vRNA, but is not required for cRNA to vRNA replication due to differences in the mode of initiation of RNA synthesis. Overall a picture emerges of influenza polymerase being a highly complex, flexible and dynamic machine. The challenge remains to understand in more detail how it functions within the RNP and how interacting host factors modulate its activity in the cellular context. Finally, these detailed insights have opened up new opportunities for structure-based antiviral drug design targeting multiple aspects of polymerase function.
Collapse
Affiliation(s)
- Alexander Pflug
- European Molecular Biology Laboratory, Grenoble Outstation, 71 Avenue des Martyrs, CS 90181, 38042 Grenoble Cedex 9, France
| | - Maria Lukarska
- European Molecular Biology Laboratory, Grenoble Outstation, 71 Avenue des Martyrs, CS 90181, 38042 Grenoble Cedex 9, France
| | - Patricia Resa-Infante
- European Molecular Biology Laboratory, Grenoble Outstation, 71 Avenue des Martyrs, CS 90181, 38042 Grenoble Cedex 9, France
| | - Stefan Reich
- European Molecular Biology Laboratory, Grenoble Outstation, 71 Avenue des Martyrs, CS 90181, 38042 Grenoble Cedex 9, France
| | - Stephen Cusack
- European Molecular Biology Laboratory, Grenoble Outstation, 71 Avenue des Martyrs, CS 90181, 38042 Grenoble Cedex 9, France.
| |
Collapse
|
19
|
Isel C, Munier S, Naffakh N. Experimental Approaches to Study Genome Packaging of Influenza A Viruses. Viruses 2016; 8:v8080218. [PMID: 27517951 PMCID: PMC4997580 DOI: 10.3390/v8080218] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2016] [Revised: 07/26/2016] [Accepted: 08/01/2016] [Indexed: 11/16/2022] Open
Abstract
The genome of influenza A viruses (IAV) consists of eight single-stranded negative sense viral RNAs (vRNAs) encapsidated into viral ribonucleoproteins (vRNPs). It is now well established that genome packaging (i.e., the incorporation of a set of eight distinct vRNPs into budding viral particles), follows a specific pathway guided by segment-specific cis-acting packaging signals on each vRNA. However, the precise nature and function of the packaging signals, and the mechanisms underlying the assembly of vRNPs into sub-bundles in the cytoplasm and their selective packaging at the viral budding site, remain largely unknown. Here, we review the diverse and complementary methods currently being used to elucidate these aspects of the viral cycle. They range from conventional and competitive reverse genetics, single molecule imaging of vRNPs by fluorescence in situ hybridization (FISH) and high-resolution electron microscopy and tomography of budding viral particles, to solely in vitro approaches to investigate vRNA-vRNA interactions at the molecular level.
Collapse
Affiliation(s)
- Catherine Isel
- Architecture et Réactivité de l'ARN, Université de Strasbourg, Centre National de la Recherche Scientifique (CNRS), Institut de Biologie Moléculaire et Cellulaire (IBMC), 15 rue René Descartes, 67084 Strasbourg, France.
- Département de Virologie, Unité de Génétique Moléculaire des Virus à ARN, Institut Pasteur, 75015 Paris, France.
| | - Sandie Munier
- Département de Virologie, Unité de Génétique Moléculaire des Virus à ARN, Institut Pasteur, 75015 Paris, France.
- Centre National de la Recherche Scientifique (CNRS), Unité Mixte de Recherche 3569, 75016 Paris, France.
- Unité de Génétique Moléculaire des Virus à ARN, Sorbonne Paris Cité, Université Paris Diderot, 75013 Paris, France.
| | - Nadia Naffakh
- Département de Virologie, Unité de Génétique Moléculaire des Virus à ARN, Institut Pasteur, 75015 Paris, France.
- Centre National de la Recherche Scientifique (CNRS), Unité Mixte de Recherche 3569, 75016 Paris, France.
- Unité de Génétique Moléculaire des Virus à ARN, Sorbonne Paris Cité, Université Paris Diderot, 75013 Paris, France.
| |
Collapse
|