1
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Takizawa N, Kawaguchi RK. Comprehensive in virio structure probing analysis of the influenza A virus identifies functional RNA structures involved in viral genome replication. Comput Struct Biotechnol J 2023; 21:5259-5272. [PMID: 37954152 PMCID: PMC10632597 DOI: 10.1016/j.csbj.2023.10.036] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2023] [Revised: 10/17/2023] [Accepted: 10/17/2023] [Indexed: 11/14/2023] Open
Abstract
The influenza A virus genome is segmented into eight viral RNAs (vRNA). Secondary structures of vRNA are known to be involved in the viral proliferation process. Comprehensive vRNA structures in vitro, in virio, and in cellulo have been analyzed. However, the resolution of the structure map can be improved by comparative analysis and statistical modeling. Construction of a more high-resolution and reliable RNA structure map can identify uncharacterized functional structure motifs on vRNA in virion. Here, we establish the global map of the vRNA secondary structure in virion using the combination of dimethyl sulfate (DMS)-seq and selective 2'-hydroxyl acylation analyzed by primer extension (SHAPE)-seq with a robust statistical analysis. Our high-resolution analysis identified a stem-loop structure at nucleotide positions 39 - 60 of segment 6 and further validated the structure at nucleotide positions 87 - 130 of segment 5 that was previously predicted to form a pseudoknot structure in silico. Notably, when the cells were infected with recombinant viruses which possess the mutations to disrupt the structure, the replication and packaging of the viral genome were drastically decreased. Our results provide comprehensive and high-resolution information on the influenza A virus genome structures in virion and evidence that the functional RNA structure motifs on the influenza A virus genome are associated with appropriate replication and packaging of the viral genome.
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Affiliation(s)
- Naoki Takizawa
- Laboratory of Virology, Institute of Microbial Chemistry (BIKAKEN), Tokyo, Japan
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2
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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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3
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Whelan M, Pelchat M. Role of RNA Polymerase II Promoter-Proximal Pausing in Viral Transcription. Viruses 2022; 14:v14092029. [PMID: 36146833 PMCID: PMC9503719 DOI: 10.3390/v14092029] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2022] [Revised: 09/09/2022] [Accepted: 09/11/2022] [Indexed: 11/16/2022] Open
Abstract
The promoter-proximal pause induced by the binding of the DRB sensitivity-inducing factor (DSIF) and the negative elongation factor (NELF) to RNAP II is a key step in the regulation of metazoan gene expression. It helps maintain a permissive chromatin landscape and ensures a quick transcriptional response from stimulus-responsive pathways such as the innate immune response. It is also involved in the biology of several RNA viruses such as the human immunodeficiency virus (HIV), the influenza A virus (IAV) and the hepatitis delta virus (HDV). HIV uses the pause as one of its mechanisms to enter and maintain latency, leading to the creation of viral reservoirs resistant to antiretrovirals. IAV, on the other hand, uses the pause to acquire the capped primers necessary to initiate viral transcription through cap-snatching. Finally, the HDV RNA genome is transcribed directly by RNAP II and requires the small hepatitis delta antigen to displace NELF from the polymerase and overcome the transcriptional block caused by RNAP II promoter-proximal pausing. In this review, we will discuss the RNAP II promoter-proximal pause and the roles it plays in the life cycle of RNA viruses such as HIV, IAV and HDV.
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4
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Takizawa N, Takada H, Umekita M, Igarashi M, Takahashi Y. Anti-influenza Virus Activity of Methylthio-Formycin Distinct From That of T-705. Front Microbiol 2022; 13:802671. [PMID: 35250924 PMCID: PMC8894184 DOI: 10.3389/fmicb.2022.802671] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2021] [Accepted: 01/28/2022] [Indexed: 11/13/2022] Open
Abstract
Seasonal influenza virus epidemics result in severe illness, and occasionally influenza pandemics cause significant morbidity and mortality, although vaccines and anti-influenza virus drugs are available. By screening an in-house library, we identified methylthio-formycin (SMeFM), an adenosine analog, as a potent inhibitor of influenza virus propagation. SMeFM inhibited the propagation of influenza A and B viruses (IC50: 34.1 and 37.9 nM, respectively) and viruses showing reduced susceptibility to baloxavir and neuraminidase inhibitors but not T-705 (Favipiravir). However, the combination of T-705 and SMeFM inhibited the propagation of the influenza virus not in an antagonistic but in a slightly synergistic manner, suggesting that SMeFM has targets distinct from that of T-705. SMeFM induced A-to-C transversion mutations in virus genome RNA, and SMeFM triphosphate did not inhibit in vitro viral RNA synthesis. Our results show that SMeFM inhibits the propagation of the influenza virus by a mechanism different from that of T-705 and is a potential drug candidate to develop for anti-influenza drug.
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5
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Frazzini S, Riva F, Amadori M. Therapeutic and Prophylactic Use of Oral, Low-Dose IFNs in Species of Veterinary Interest: Back to the Future. Vet Sci 2021; 8:109. [PMID: 34208413 PMCID: PMC8231284 DOI: 10.3390/vetsci8060109] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2021] [Revised: 06/02/2021] [Accepted: 06/10/2021] [Indexed: 12/17/2022] Open
Abstract
Cytokines are important molecules that orchestrate the immune response. Given their role, cytokines have been explored as drugs in immunotherapy in the fight against different pathological conditions such as bacterial and viral infections, autoimmune diseases, transplantation and cancer. One of the problems related to their administration consists in the definition of the correct dose to avoid severe side effects. In the 70s and 80s different studies demonstrated the efficacy of cytokines in veterinary medicine, but soon the investigations were abandoned in favor of more profitable drugs such as antibiotics. Recently, the World Health Organization has deeply discouraged the use of antibiotics in order to reduce the spread of multi-drug resistant microorganisms. In this respect, the use of cytokines to prevent or ameliorate infectious diseases has been highlighted, and several studies show the potential of their use in therapy and prophylaxis also in the veterinary field. In this review we aim to review the principles of cytokine treatments, mainly IFNs, and to update the experiences encountered in animals.
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Affiliation(s)
- Sara Frazzini
- Gastroenterology and Endoscopy Unit, Fondazione IRCCS Cà Granda, Ospedale Maggiore Policlinico, 20122 Milan, Italy;
| | - Federica Riva
- Dipartimento di Medicina Veterinaria, Università degli Studi di Milano, 26900 Lodi, Italy
| | - Massimo Amadori
- Rete Nazionale di Immunologia Veterinaria, 25125 Brescia, Italy;
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6
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Bae JY, Kim JI, Park MS, Lee GE, Park H, Song KJ, Park MS. The Immune Correlates of Orthohantavirus Vaccine. Vaccines (Basel) 2021; 9:vaccines9050518. [PMID: 34069997 PMCID: PMC8157935 DOI: 10.3390/vaccines9050518] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2021] [Revised: 05/01/2021] [Accepted: 05/10/2021] [Indexed: 01/09/2023] Open
Abstract
Zoonotic transmission of orthohantaviruses from rodent reservoirs to humans has been the cause of severe fatalities. Human infections are reported worldwide, but vaccines have been approved only in China and Korea. Orthohantavirus vaccine development has been pursued with no sense of urgency due to the relative paucity of cases in countries outside China and Korea. However, the orthohantaviruses continuously evolve in hosts and thus the current vaccine may not work as well against some variants. Therefore, a more effective vaccine should be prepared against the orthohantaviruses. In this review, we discuss the issues caused by the orthohantavirus vaccine. Given the pros and cons of the orthohantavirus vaccine, we suggest strategies for the development of better vaccines in terms of pandemic preparedness.
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7
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Tang YS, Xu S, Chen YW, Wang JH, Shaw PC. Crystal structures of influenza nucleoprotein complexed with nucleic acid provide insights into the mechanism of RNA interaction. Nucleic Acids Res 2021; 49:4144-4154. [PMID: 33784403 PMCID: PMC8053115 DOI: 10.1093/nar/gkab203] [Citation(s) in RCA: 23] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2021] [Revised: 03/09/2021] [Accepted: 03/29/2021] [Indexed: 01/05/2023] Open
Abstract
The nucleoprotein (NP) of influenza virus is the core component of the ribonucleoprotein (RNP) and performs multiple structural and functional roles. Structures of the influenza A, B and D NP molecules have been solved previously, but structural information on how NP interacts with RNA remains elusive. Here we present the crystal structure of an obligate monomer of H5N1 NP in complex with RNA nucleotides to 2.3 Å, and a C-terminal truncation of this mutant, also in complex with RNA nucleotides, to 3 Å. In both structures, three nucleotides were identified near two positive grooves of NP suggested to be important for RNA binding. Structural evidence supports that conformational changes of flexible loops and the C-terminal tail both play important roles in the binding of RNA. Based on the structure, we propose a mechanism by which NP captures RNA by flexible loops and transfers it onto the positive binding grooves. Binding of RNA by NP is a crucial step for template re-encapsidation during transcription and replication and cRNP formation. Our structures thus provide insights into the molecular virology of the influenza virus.
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Affiliation(s)
- Yun-Sang Tang
- Centre for Protein Science and Crystallography, School of Life Sciences, The Chinese University of Hong Kong, Hong Kong SAR, China
| | - Shutong Xu
- Department of Medical Oncology and Department of Cancer Biology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA 02115, USA.,College of Life Science and Technology, Huazhong Agricultural University, Wuhan, China
| | - Yu-Wai Chen
- Department of Applied Biology and Chemical Technology, The Hong Kong Polytechnic University, Hong Kong SAR, China
| | - Jia-Huai Wang
- Department of Medical Oncology and Department of Cancer Biology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA 02115, USA
| | - Pang-Chui Shaw
- Centre for Protein Science and Crystallography, School of Life Sciences, The Chinese University of Hong Kong, Hong Kong SAR, China.,Li Dak Sum Yip Yio Chin R & D Centre for Chinese Medicine, The Chinese University of Hong Kong, Hong Kong SAR, China
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8
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Modeling the
Influenza A
NP-vRNA-Polymerase Complex in Atomic Detail. Biomolecules 2021; 11:biom11010124. [PMID: 33477938 PMCID: PMC7833383 DOI: 10.3390/biom11010124] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2020] [Revised: 01/07/2021] [Accepted: 01/13/2021] [Indexed: 11/17/2022] Open
Abstract
Seasonal flu is an acute respiratory disease that exacts a massive toll on human populations, healthcare systems and economies. The disease is caused by an enveloped Influenza virus containing eight ribonucleoprotein (RNP) complexes. Each RNP incorporates multiple copies of nucleoprotein (NP), a fragment of the viral genome (vRNA), and a viral RNA-dependent RNA polymerase (POL), and is responsible for packaging the viral genome and performing critical functions including replication and transcription. A complete model of an Influenza RNP in atomic detail can elucidate the structural basis for viral genome functions, and identify potential targets for viral therapeutics. In this work we construct a model of a complete Influenza A RNP complex in atomic detail using multiple sources of structural and sequence information and a series of homology-modeling techniques, including a motif-matching fragment assembly method. Our final model provides a rationale for experimentally-observed changes to viral polymerase activity in numerous mutational assays. Further, our model reveals specific interactions between the three primary structural components of the RNP, including potential targets for blocking POL-binding to the NP-vRNA complex. The methods developed in this work open the possibility of elucidating other functionally-relevant atomic-scale interactions in additional RNP structures and other biomolecular complexes.
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9
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Zhu W, Feng Z, Chen Y, Yang L, Liu J, Li X, Liu S, Zhou L, Wei H, Gao R, Wang D, Shu Y. Mammalian-adaptive mutation NP-Q357K in Eurasian H1N1 Swine Influenza viruses determines the virulence phenotype in mice. Emerg Microbes Infect 2019; 8:989-999. [PMID: 31267843 PMCID: PMC6609330 DOI: 10.1080/22221751.2019.1635873] [Citation(s) in RCA: 21] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/03/2022]
Abstract
It has recently been proposed that the Eurasian avian-like H1N1 (EA H1N1) swine influenza virus (SIV) is one of the most likely zoonotic viruses to cause the next influenza pandemic. Two main genotypes EA H1N1 viruses have been recognized to be infected humans in China. Our study finds that one of the genotypes JS1-like viruses are avirulent in mice. However, the other are HuN-like viruses and are virulent in mice. The molecular mechanism underlying this difference shows that the NP gene determines the virulence of the EA H1N1 viruses in mice. In addition, a single substitution, Q357K, in the NP protein of the EA H1N1 viruses alters the virulence phenotype. This substitution is a typical human signature marker, which is prevalent in human viruses but rarely detected in avian influenza viruses. The NP-Q357K substitution is readily to be occurred when avian influenza viruses circulate in pigs, and may facilitate their infection of humans and allow viruses also carrying NP-357K to circulate in humans. Our study demonstrates that the substitution Q357K in the NP protein plays a key role in the virulence phenotype of EA H1N1 SIVs, and provides important information for evaluating the pandemic risk of field influenza strains.
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Affiliation(s)
- Wenfei Zhu
- a National Institute for Viral Disease Control and Prevention, Collaboration Innovation Center for Diagnosis and Treatment of Infectious Diseases , Chinese Center for Disease Control and Prevention , Beijing , People's Republic of China.,b Key Laboratory for Medical Virology , National Health and Family Planning Commission , Beijing , People's Republic of China
| | - Zhaomin Feng
- a National Institute for Viral Disease Control and Prevention, Collaboration Innovation Center for Diagnosis and Treatment of Infectious Diseases , Chinese Center for Disease Control and Prevention , Beijing , People's Republic of China.,b Key Laboratory for Medical Virology , National Health and Family Planning Commission , Beijing , People's Republic of China
| | - Yongkun Chen
- c School of Public Health (Shenzhen) , Sun Yat-sen University , Guangdong , People's Republic of China
| | - Lei Yang
- a National Institute for Viral Disease Control and Prevention, Collaboration Innovation Center for Diagnosis and Treatment of Infectious Diseases , Chinese Center for Disease Control and Prevention , Beijing , People's Republic of China.,b Key Laboratory for Medical Virology , National Health and Family Planning Commission , Beijing , People's Republic of China
| | - Jia Liu
- a National Institute for Viral Disease Control and Prevention, Collaboration Innovation Center for Diagnosis and Treatment of Infectious Diseases , Chinese Center for Disease Control and Prevention , Beijing , People's Republic of China.,b Key Laboratory for Medical Virology , National Health and Family Planning Commission , Beijing , People's Republic of China
| | - Xiyan Li
- a National Institute for Viral Disease Control and Prevention, Collaboration Innovation Center for Diagnosis and Treatment of Infectious Diseases , Chinese Center for Disease Control and Prevention , Beijing , People's Republic of China.,b Key Laboratory for Medical Virology , National Health and Family Planning Commission , Beijing , People's Republic of China
| | - Suli Liu
- c School of Public Health (Shenzhen) , Sun Yat-sen University , Guangdong , People's Republic of China
| | - Lijuan Zhou
- a National Institute for Viral Disease Control and Prevention, Collaboration Innovation Center for Diagnosis and Treatment of Infectious Diseases , Chinese Center for Disease Control and Prevention , Beijing , People's Republic of China.,b Key Laboratory for Medical Virology , National Health and Family Planning Commission , Beijing , People's Republic of China
| | - Hejiang Wei
- a National Institute for Viral Disease Control and Prevention, Collaboration Innovation Center for Diagnosis and Treatment of Infectious Diseases , Chinese Center for Disease Control and Prevention , Beijing , People's Republic of China.,b Key Laboratory for Medical Virology , National Health and Family Planning Commission , Beijing , People's Republic of China
| | - Rongbao Gao
- a National Institute for Viral Disease Control and Prevention, Collaboration Innovation Center for Diagnosis and Treatment of Infectious Diseases , Chinese Center for Disease Control and Prevention , Beijing , People's Republic of China.,b Key Laboratory for Medical Virology , National Health and Family Planning Commission , Beijing , People's Republic of China
| | - Dayan Wang
- a National Institute for Viral Disease Control and Prevention, Collaboration Innovation Center for Diagnosis and Treatment of Infectious Diseases , Chinese Center for Disease Control and Prevention , Beijing , People's Republic of China.,b Key Laboratory for Medical Virology , National Health and Family Planning Commission , Beijing , People's Republic of China
| | - Yuelong Shu
- a National Institute for Viral Disease Control and Prevention, Collaboration Innovation Center for Diagnosis and Treatment of Infectious Diseases , Chinese Center for Disease Control and Prevention , Beijing , People's Republic of China.,b Key Laboratory for Medical Virology , National Health and Family Planning Commission , Beijing , People's Republic of China.,c School of Public Health (Shenzhen) , Sun Yat-sen University , Guangdong , People's Republic of China
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10
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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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11
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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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12
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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.
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Affiliation(s)
- Maria João Amorim
- Cell Biology of Viral Infection Lab, Instituto Gulbenkian de Ciência, Oeiras, Portugal
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13
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Takizawa N, Kimura T, Watanabe T, Shibasaki M. Anti-influenza virus activity of a salcomine derivative mediated by inhibition of viral RNA synthesis. Arch Virol 2018; 163:1607-1614. [PMID: 29497849 DOI: 10.1007/s00705-018-3779-9] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2017] [Accepted: 01/19/2018] [Indexed: 12/25/2022]
Abstract
Influenza virus infection is a major threat to global health. Although vaccines and anti-influenza virus drugs are available, annual influenza virus epidemics result in severe illness, and an influenza pandemic occurs every 20-30 years. To identify candidate anti-influenza virus compounds, we screened approximately 5,000 compounds in an in-house library. We identified MZ7465, a salcomine derivative, as a potent inhibitor of influenza virus propagation. We analyzed the antiviral propagation mechanism of the hit compound by determining the amounts of viral proteins and RNA in infected cells treated with or without the hit compound. Treatment of infected cells with MZ7465 decreased both viral protein and RNA synthesis. In addition, an in vitro assay showed that viral RNA synthesis was directly inhibited by MZ7465. These results suggest that salcomine and its derivatives are potential candidates for the treatment of influenza virus infections.
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MESH Headings
- Animals
- Antiviral Agents/chemistry
- Antiviral Agents/pharmacology
- Bronchi/drug effects
- Bronchi/pathology
- Bronchi/virology
- Cell Line
- Dogs
- Epithelial Cells/drug effects
- Epithelial Cells/pathology
- Epithelial Cells/virology
- Gene Expression Regulation, Viral
- HEK293 Cells
- High-Throughput Screening Assays
- Humans
- Influenza A Virus, H1N1 Subtype/drug effects
- Influenza A Virus, H1N1 Subtype/genetics
- Influenza A Virus, H1N1 Subtype/growth & development
- Influenza A Virus, H3N2 Subtype/drug effects
- Influenza A Virus, H3N2 Subtype/genetics
- Influenza A Virus, H3N2 Subtype/growth & development
- Madin Darby Canine Kidney Cells
- Organometallic Compounds/chemistry
- Organometallic Compounds/pharmacology
- RNA, Viral/antagonists & inhibitors
- RNA, Viral/biosynthesis
- RNA, Viral/genetics
- Small Molecule Libraries/chemistry
- Small Molecule Libraries/pharmacology
- Structure-Activity Relationship
- Viral Proteins/antagonists & inhibitors
- Viral Proteins/biosynthesis
- Viral Proteins/genetics
- Virus Replication/drug effects
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Affiliation(s)
- Naoki Takizawa
- Laboratory of Virology, Institute of Microbial Chemistry (BIKAKEN), Tokyo, Japan.
| | - Tomoyuki Kimura
- Laboratory of Synthetic Organic Chemistry, Institute of Microbial Chemistry (BIKAKEN), Tokyo, Japan
| | - Takumi Watanabe
- Laboratory of Synthetic Organic Chemistry, Institute of Microbial Chemistry (BIKAKEN), Tokyo, Japan
| | - Masakatsu Shibasaki
- Laboratory of Virology, Institute of Microbial Chemistry (BIKAKEN), Tokyo, Japan
- Laboratory of Synthetic Organic Chemistry, Institute of Microbial Chemistry (BIKAKEN), Tokyo, Japan
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14
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Williams GD, Townsend D, Wylie KM, Kim PJ, Amarasinghe GK, Kutluay SB, Boon ACM. Nucleotide resolution mapping of influenza A virus nucleoprotein-RNA interactions reveals RNA features required for replication. Nat Commun 2018; 9:465. [PMID: 29386621 PMCID: PMC5792457 DOI: 10.1038/s41467-018-02886-w] [Citation(s) in RCA: 53] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2017] [Accepted: 01/04/2018] [Indexed: 02/03/2023] Open
Abstract
Influenza A virus nucleoprotein (NP) association with viral RNA (vRNA) is essential for packaging, but the pattern of NP binding to vRNA is unclear. Here we applied photoactivatable ribonucleoside enhanced cross-linking and immunoprecipitation (PAR-CLIP) to assess the native-state of NP-vRNA interactions in infected human cells. NP binds short fragments of RNA (~12 nucleotides) non-uniformly and without apparent sequence specificity. Moreover, NP binding is reduced at specific locations within the viral genome, including regions previously identified as required for viral genome segment packaging. Synonymous mutations designed to alter the predicted RNA structures in these low-NP-binding regions impact genome packaging and result in virus attenuation, whereas control mutations or mutagenesis of NP-bound regions have no effect. Finally, we demonstrate that the sequence conservation of low-NP-binding regions is required in multiple genome segments for propagation of diverse mammalian and avian IAV in host cells.
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Affiliation(s)
- Graham D Williams
- Department of Medicine at Washington University School of Medicine, St Louis, MO, 63110, USA
- Department of Molecular Microbiology at Washington University School of Medicine, St Louis, MO, 63110, USA
| | - Dana Townsend
- Department of Molecular Microbiology at Washington University School of Medicine, St Louis, MO, 63110, USA
| | - Kristine M Wylie
- Department of Pediatrics at Washington University School of Medicine, St Louis, MO, 63110, USA
- The McDonnell Genome Institute at Washington University School of Medicine, St Louis, MO, 63110, USA
| | - Preston J Kim
- Department of Pathology and Immunology at Washington University School of Medicine, St Louis, MO, 63110, USA
| | - Gaya K Amarasinghe
- Department of Pathology and Immunology at Washington University School of Medicine, St Louis, MO, 63110, USA
- Department of Biochemistry and Biophysics at Washington University School of Medicine, St Louis, MO, 63110, USA
| | - Sebla B Kutluay
- Department of Molecular Microbiology at Washington University School of Medicine, St Louis, MO, 63110, USA
| | - Adrianus C M Boon
- Department of Medicine at Washington University School of Medicine, St Louis, MO, 63110, USA.
- Department of Molecular Microbiology at Washington University School of Medicine, St Louis, MO, 63110, USA.
- Department of Pathology and Immunology at Washington University School of Medicine, St Louis, MO, 63110, USA.
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15
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Abstract
Influenza is a negative-sense single-stranded RNA virus with segmented genome. Each segment is encapsidated by a ribonucleoprotein (RNP) complex composed of RNA-dependent RNA polymerase (RdRP) and multiple copies of nucleoprotein (NP). The RNP complex plays a crucial role in viral life cycle, supporting and regulating transcription and replication of viral genome in infected cells. The structural characterization of RdRP and RNP in recent years has shed light on its functions and mechanism of action. In this review, we summarize current understanding on the structure of RNP complex, as well as the structure of each subunit. Crucial functions of RNP are also discussed.
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Affiliation(s)
- Chun-Yeung Lo
- Centre for Protein Science and Crystallography, School of Life Sciences, The Chinese University of Hong Kong, Shatin, N.T, Hong Kong, China
| | - Yun-Sang Tang
- Centre for Protein Science and Crystallography, School of Life Sciences, The Chinese University of Hong Kong, Shatin, N.T, Hong Kong, China
| | - Pang-Chui Shaw
- Centre for Protein Science and Crystallography, School of Life Sciences, The Chinese University of Hong Kong, Shatin, N.T, Hong Kong, China.
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16
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Assembly and remodeling of viral DNA and RNA replicons regulated by cellular molecular chaperones. Biophys Rev 2017; 10:445-452. [PMID: 29170971 DOI: 10.1007/s12551-017-0333-z] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2017] [Accepted: 11/07/2017] [Indexed: 12/12/2022] Open
Abstract
A variety of cellular reactions mediated by interactions among proteins and nucleic acids requires a series of proteins called molecular chaperones. The viral genome encodes relatively few kinds of viral proteins and, therefore, host-derived cellular factors are required for virus proliferation. Here we discuss those cellular proteins known as molecular chaperones, which are essential for the assembly of functional viral DNA/RNA replicons. The function of these molecular chaperones in the cellular context is also discussed.
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17
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Cellular splicing factor UAP56 stimulates trimeric NP formation for assembly of functional influenza viral ribonucleoprotein complexes. Sci Rep 2017; 7:14053. [PMID: 29070793 PMCID: PMC5656576 DOI: 10.1038/s41598-017-13784-4] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2017] [Accepted: 10/02/2017] [Indexed: 12/02/2022] Open
Abstract
The influenza virus RNA genome exists as a ribonucleoprotein (RNP) complex by interacting with NP, one of virus-encoded RNA binding proteins. It is proposed that trimeric NP is a functional form, but it is not clear how trimeric NP is formed and transferred to RNA. UAP56, a cellular splicing factor, functions as a molecular chaperone for NP and is required for the replication-coupled RNP formation of newly synthesized viral genome, but the details of NP transfer to viral RNA by UAP56 is unclear. Here we found that UAP56 is complexed with trimeric NP, but not monomeric NP. Gel filtration analysis and atomic force microscopy analysis indicated that the complex consists of two trimeric NP connected by UAP56. We also found that UAP56 stimulates trimeric NP formation from monomeric NP even at physiological salt concentrations. Thus, UAP56 facilitates the transfer of NP to viral RNA since trimeric NP has higher RNA binding activity than monomeric NP. Further, UAP56 represses the binding of excess amount of NP to RNA possibly by transferring trimeric NP. Collectively, we propose that UAP56 stimulates viral RNP formation through promotion of the assembly of trimeric NP and is important for the structural integrity of NP-RNA complex.
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18
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Generation of a Genetically Stable High-Fidelity Influenza Vaccine Strain. J Virol 2017; 91:JVI.01073-16. [PMID: 28053101 DOI: 10.1128/jvi.01073-16] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2016] [Accepted: 12/24/2016] [Indexed: 12/20/2022] Open
Abstract
Vaccination is considered the most effective preventive means for influenza control. The development of a master virus with high growth and genetic stability, which may be used for the preparation of vaccine viruses by gene reassortment, is crucial for the enhancement of vaccine performance and efficiency of production. Here, we describe the generation of a high-fidelity and high-growth influenza vaccine master virus strain with a single V43I amino acid change in the PB1 polymerase of the high-growth A/Puerto Rico/8/1934 (PR8) master virus. The PB1-V43I mutation was introduced to increase replication fidelity in order to design an H1N1 vaccine strain with a low error rate. The PR8-PB1-V43I virus exhibited good replication compared with that of the parent PR8 virus. In order to compare the efficiency of egg adaptation and the occurrence of gene mutations leading to antigenic alterations, we constructed 6:2 genetic reassortant viruses between the A(H1N1)pdm09 and the PR8-PB1-V43I viruses; hemagglutinin (HA) and neuraminidase (NA) were from the A(H1N1)pdm09 virus, and the other genes were from the PR8 virus. Mutations responsible for egg adaptation mutations occurred in the HA of the PB1-V43I reassortant virus during serial egg passages; however, in contrast, antigenic mutations were introduced into the HA gene of the 6:2 reassortant virus possessing the wild-type PB1. This study shows that the mutant PR8 virus possessing the PB1 polymerase with the V43I substitution may be utilized as a master virus for the generation of high-growth vaccine viruses with high polymerase fidelity, low error rates of gene replication, and reduced antigenic diversity during virus propagation in eggs for vaccine production.IMPORTANCE Vaccination represents the most effective prophylactic option against influenza. The threat of emergence of influenza pandemics necessitates the ability to generate vaccine viruses rapidly. However, as the influenza virus exhibits a high mutation rate, vaccines must be updated to ensure a good match of the HA and NA antigens between the vaccine and the circulating strain. Here, we generated a genetically stable master virus of the A/Puerto Rico/8/1934 (H1N1) backbone encoding an engineered high-fidelity viral polymerase. Importantly, following the application of the high-fidelity PR8 backbone, no mutation resulting in antigenic change was introduced into the HA gene during propagation of the A(H1N1)pdm09 candidate vaccine virus. The low error rate of the present vaccine virus should decrease the risk of generating mutant viruses with increased virulence. Therefore, our findings are expected to be useful for the development of prepandemic vaccines and live attenuated vaccines with higher safety than that of the present candidate vaccines.
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Pre-mRNA Processing Factor Prp18 Is a Stimulatory Factor of Influenza Virus RNA Synthesis and Possesses Nucleoprotein Chaperone Activity. J Virol 2017; 91:JVI.01398-16. [PMID: 27852861 DOI: 10.1128/jvi.01398-16] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2016] [Accepted: 11/13/2016] [Indexed: 11/20/2022] Open
Abstract
The genome of influenza virus (viral RNA [vRNA]) is associated with the nucleoprotein (NP) and viral RNA-dependent RNA polymerases and forms helical viral ribonucleoprotein (vRNP) complexes. The NP-vRNA complex is the biologically active template for RNA synthesis by the viral polymerase. Previously, we identified human pre-mRNA processing factor 18 (Prp18) as a stimulatory factor for viral RNA synthesis using a Saccharomyces cerevisiae replicon system and a single-gene deletion library of Saccharomyces cerevisiae (T. Naito, Y. Kiyasu, K. Sugiyama, A. Kimura, R. Nakano, A. Matsukage, and K. Nagata, Proc Natl Acad Sci USA, 104:18235-18240, 2007, https://doi.org/10.1073/pnas.0705856104). In infected Prp18 knockdown (KD) cells, the synthesis of vRNA, cRNA, and viral mRNAs was reduced. Prp18 was found to stimulate in vitro viral RNA synthesis through its interaction with NP. Analyses using in vitro RNA synthesis reactions revealed that Prp18 dissociates newly synthesized RNA from the template after the early elongation step to stimulate the elongation reaction. We found that Prp18 functions as a chaperone for NP to facilitate the formation of NP-RNA complexes. Based on these results, it is suggested that Prp18 accelerates influenza virus RNA synthesis as an NP chaperone for the processive elongation reaction. IMPORTANCE Templates for viral RNA synthesis of negative-stranded RNA viruses are not naked RNA but rather RNA encapsidated by viral nucleocapsid proteins forming vRNP complexes. However, viral basic proteins tend to aggregate under physiological ionic strength without chaperones. We identified the pre-mRNA processing factor Prp18 as a stimulatory factor for influenza virus RNA synthesis. We found that one of the targets of Prp18 is NP. Prp18 facilitates the elongation reaction of viral polymerases by preventing the deleterious annealing of newly synthesized RNA to the template. Prp18 functions as a chaperone for NP to stimulate the formation of NP-RNA complexes. Based on these results, we propose that Prp18 may be required to maintain the structural integrity of vRNP for processive template reading.
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20
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Subtype-specific structural constraints in the evolution of influenza A virus hemagglutinin genes. Sci Rep 2016; 6:38892. [PMID: 27966593 PMCID: PMC5155281 DOI: 10.1038/srep38892] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2016] [Accepted: 11/14/2016] [Indexed: 11/08/2022] Open
Abstract
The influenza A virus genome consists of eight RNA segments. RNA structures within these segments and complementary (cRNA) and protein-coding mRNAs may play a role in virus replication. Here, conserved putative secondary structures that impose significant evolutionary constraints on the gene segment encoding the surface glycoprotein hemagglutinin (HA) were investigated using available sequence data on tens of thousands of virus strains. Structural constraints were identified by analysis of covariations of nucleotides suggested to be paired by structure prediction algorithms. The significance of covariations was estimated by mutual information calculations and tracing multiple covariation events during virus evolution. Covariation patterns demonstrated that structured domains in HA RNAs were mostly subtype-specific, whereas some structures were conserved in several subtypes. The influence of RNA folding on virus replication was studied by plaque assays of mutant viruses with disrupted structures. The results suggest that over the whole length of the HA segment there are local structured domains which contribute to the virus fitness but individually are not essential for the virus. Existence of subtype-specific structured regions in the segments of the influenza A virus genome is apparently an important factor in virus evolution and reassortment of its genes.
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21
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Secondary structure model of the naked segment 7 influenza A virus genomic RNA. Biochem J 2016; 473:4327-4348. [PMID: 27694388 DOI: 10.1042/bcj20160651] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/04/2016] [Revised: 09/25/2016] [Accepted: 09/30/2016] [Indexed: 11/17/2022]
Abstract
The influenza A virus (IAV) genome comprises eight negative-sense viral (v)RNA segments. The seventh segment of the genome encodes two essential viral proteins and is specifically packaged alongside the other seven vRNAs. To gain insights into the possible roles of RNA structure both within and without virions, a secondary structure model of a naked (protein-free) segment 7 vRNA (vRNA7) has been determined using chemical mapping and thermodynamic energy minimization. The proposed structure model was validated using microarray mapping, RNase H cleavage and comparative sequence analysis. Additionally, the detailed structures of three vRNA7 fragment constructs - comprising independently folded subdomains - were determined. Much of the proposed vRNA7 structure is preserved between IAV strains, suggesting their importance in the influenza replication cycle. Possible structure rearrangements, which allow or preclude long-range RNA interactions, are also proposed.
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22
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Highly sensitive detection of influenza virus by boron-doped diamond electrode terminated with sialic acid-mimic peptide. Proc Natl Acad Sci U S A 2016; 113:8981-4. [PMID: 27457924 DOI: 10.1073/pnas.1603609113] [Citation(s) in RCA: 47] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
The progression of influenza varies according to age and the presence of an underlying disease; appropriate treatment is therefore required to prevent severe disease. Anti-influenza therapy, such as with neuraminidase inhibitors, is effective, but diagnosis at an early phase of infection before viral propagation is critical. Here, we show that several dozen plaque-forming units (pfu) of influenza virus (IFV) can be detected using a boron-doped diamond (BDD) electrode terminated with a sialic acid-mimic peptide. The peptide was used instead of the sialyloligosaccharide receptor, which is the common receptor of influenza A and B viruses required during the early phase of infection, to capture IFV particles. The peptide, which was previously identified by phage-display technology, was immobilized by click chemistry on the BDD electrode, which has excellent electrochemical characteristics such as low background current and weak adsorption of biomolecules. Electrochemical impedance spectroscopy revealed that H1N1 and H3N2 IFVs were detectable in the range of 20-500 pfu by using the peptide-terminated BDD electrode. Our results demonstrate that the BDD device integrated with the receptor-mimic peptide has high sensitivity for detection of a low number of virus particles in the early phase of infection.
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23
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Kobayashi Y, Dadonaite B, van Doremalen N, Suzuki Y, Barclay WS, Pybus OG. Computational and molecular analysis of conserved influenza A virus RNA secondary structures involved in infectious virion production. RNA Biol 2016; 13:883-94. [PMID: 27399914 DOI: 10.1080/15476286.2016.1208331] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/21/2022] Open
Abstract
As well as encoding viral proteins, genomes of RNA viruses harbor secondary and tertiary RNA structures that have been associated with functions essential for successful replication and propagation. Here, we identified stem-loop structures that are extremely conserved among 1,884 M segment sequences of influenza A virus (IAV) strains from various subtypes and host species using computational and evolutionary methods. These structures were predicted within the 3' and 5' ends of the coding regions of M1 and M2, respectively, where packaging signals have been previously proposed to exist. These signals are thought to be required for the incorporation of a single copy of 8 different negative-strand RNA segments (vRNAs) into an IAV particle. To directly test the functionality of conserved stem-loop structures, we undertook reverse genetic experiments to introduce synonymous mutations designed to disrupt secondary structures predicted at 3 locations and found them to attenuate infectivity of recombinant virus. In one mutant, predicted to disrupt stem loop structure at nucleotide positions 219-240, attenuation was more evident at increased temperature and was accompanied by an increase in the production of defective virus particles. Our results suggest that the conserved secondary structures predicted in the M segment are involved in the production of infectious viral particles during IAV replication.
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Affiliation(s)
- Yuki Kobayashi
- a Nihon University Veterinary Research Center , Fujisawa , Kanagawa , Japan.,b Department of Zoology , University of Oxford , Oxford , UK
| | - Bernadeta Dadonaite
- c Section of Virology, Department of Medicine, Imperial College London , London , UK
| | - Neeltje van Doremalen
- c Section of Virology, Department of Medicine, Imperial College London , London , UK.,d Laboratory of Virology, Division of Intramural Research, National Institute of Allergy and Infectious Diseases, National Institutes of Health , Hamilton , MT , USA
| | - Yoshiyuki Suzuki
- e Graduate School of Natural Sciences, Nagoya City University , Nagoya , Japan
| | - Wendy S Barclay
- c Section of Virology, Department of Medicine, Imperial College London , London , UK
| | - Oliver G Pybus
- b Department of Zoology , University of Oxford , Oxford , UK
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24
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Lenartowicz E, Kesy J, Ruszkowska A, Soszynska-Jozwiak M, Michalak P, Moss WN, Turner DH, Kierzek R, Kierzek E. Self-Folding of Naked Segment 8 Genomic RNA of Influenza A Virus. PLoS One 2016; 11:e0148281. [PMID: 26848969 PMCID: PMC4743857 DOI: 10.1371/journal.pone.0148281] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2015] [Accepted: 01/15/2016] [Indexed: 01/10/2023] Open
Abstract
Influenza A is a negative sense RNA virus that kills hundreds of thousands of humans each year. Base pairing in RNA is very favorable, but possibilities for RNA secondary structure of the influenza genomic RNA have not been investigated. This work presents the first experimentally-derived exploration of potential secondary structure in an influenza A naked (protein-free) genomic segment. Favorable folding regions are revealed by in vitro chemical structure mapping, thermodynamics, bioinformatics, and binding to isoenergetic microarrays of an entire natural sequence of the 875 nt segment 8 vRNA and of a smaller fragment. Segment 8 has thermodynamically stable and evolutionarily conserved RNA structure and encodes essential viral proteins NEP and NS1. This suggests that vRNA self-folding may generate helixes and loops that are important at one or more stages of the influenza life cycle.
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Affiliation(s)
- Elzbieta Lenartowicz
- Institute of Bioorganic Chemistry, Polish Academy of Sciences, Noskowskiego 12/14, 61–704 Poznan, Poland
| | - Julita Kesy
- Institute of Bioorganic Chemistry, Polish Academy of Sciences, Noskowskiego 12/14, 61–704 Poznan, Poland
| | - Agnieszka Ruszkowska
- Institute of Bioorganic Chemistry, Polish Academy of Sciences, Noskowskiego 12/14, 61–704 Poznan, Poland
| | - Marta Soszynska-Jozwiak
- Institute of Bioorganic Chemistry, Polish Academy of Sciences, Noskowskiego 12/14, 61–704 Poznan, Poland
| | - Paula Michalak
- Institute of Bioorganic Chemistry, Polish Academy of Sciences, Noskowskiego 12/14, 61–704 Poznan, Poland
| | - Walter N. Moss
- Department of Chemistry, University of Rochester, Rochester, New York, 14627, United States of America
| | - Douglas H. Turner
- Department of Chemistry, University of Rochester, Rochester, New York, 14627, United States of America
| | - Ryszard Kierzek
- Institute of Bioorganic Chemistry, Polish Academy of Sciences, Noskowskiego 12/14, 61–704 Poznan, Poland
| | - Elzbieta Kierzek
- Institute of Bioorganic Chemistry, Polish Academy of Sciences, Noskowskiego 12/14, 61–704 Poznan, Poland
- * E-mail:
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25
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Mondal A, Potts GK, Dawson AR, Coon JJ, Mehle A. Phosphorylation at the homotypic interface regulates nucleoprotein oligomerization and assembly of the influenza virus replication machinery. PLoS Pathog 2015; 11:e1004826. [PMID: 25867750 PMCID: PMC4395114 DOI: 10.1371/journal.ppat.1004826] [Citation(s) in RCA: 49] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/26/2014] [Accepted: 03/21/2015] [Indexed: 11/22/2022] Open
Abstract
Negative-sense RNA viruses assemble large ribonucleoprotein (RNP) complexes that direct replication and transcription of the viral genome. Influenza virus RNPs contain the polymerase, genomic RNA and multiple copies of nucleoprotein (NP). During RNP assembly, monomeric NP oligomerizes along the length of the genomic RNA. Regulated assembly of the RNP is essential for virus replication, but how NP is maintained as a monomer that subsequently oligomerizes to form RNPs is poorly understood. Here we elucidate a mechanism whereby NP phosphorylation regulates oligomerization. We identified new evolutionarily conserved phosphorylation sites on NP and demonstrated that phosphorylation of NP decreased formation of higher-order complexes. Two phosphorylation sites were located on opposite sides of the NP:NP interface. In both influenza A and B virus, mutating or mimicking phosphorylation at these residues blocked homotypic interactions and drove NP towards a monomeric form. Highlighting the central role of this process during infection, these mutations impaired RNP formation, polymerase activity and virus replication. Thus, dynamic phosphorylation of NP regulates RNP assembly and modulates progression through the viral life cycle. Replication and transcription by negative-sense RNA viruses occurs in large macromolecular complexes. These complexes contain the viral polymerase, genomic RNA, and multiple copies of nucleoprotein that bind RNA and oligomerize to coat the genome. For influenza virus, nucleoprotein (NP) non-specifically binds nucleic acids and spontaneously oligomerizes. It is essential that a portion of NP be maintained as a monomer so that it can selectively oligomerize into replication complexes. Despite the fact that this process must be tightly regulated during the viral life cycle, how this regulation is achieved is largely unknown. Here we show that phosphorylation of NP negatively regulates assembly of the influenza virus replication machinery. We identified two phosphorylation sites on opposite sides of the NP:NP interface and showed that phosphorylation at either site blocks homotypic interactions, distorting the monomer:oligomer balance of NP in cells and severely impairing virus replication. Our findings show that the phospho-regulated conversion of NP between mono- and oligomeric states is important for RNP formation, gene expression and viral replication. Moreover, we showed that these critical phosphorylation sites play the same role in influenza B virus and are likely present in influenza C and D viruses, suggesting our results are broadly applicable across viral strains and genera and reveal a global regulatory strategy for Orthomyxoviridae.
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Affiliation(s)
- Arindam Mondal
- Medical Microbiology and Immunology, University of Wisconsin, Madison, Wisconsin, United States of America
| | - Gregory K. Potts
- Department of Chemistry, University of Wisconsin, Madison, Wisconsin, United States of America
| | - Anthony R. Dawson
- Medical Microbiology and Immunology, University of Wisconsin, Madison, Wisconsin, United States of America
- Cellular and Molecular Biology Graduate Program, University of Wisconsin, Madison, Wisconsin, United States of America
| | - Joshua J. Coon
- Department of Chemistry, University of Wisconsin, Madison, Wisconsin, United States of America
- Department of Biomolecular Chemistry, University of Wisconsin, Madison, Wisconsin, United States of America
| | - Andrew Mehle
- Medical Microbiology and Immunology, University of Wisconsin, Madison, Wisconsin, United States of America
- * E-mail:
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26
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Abstract
Influenza A viral ribonucleoprotein (vRNP) complexes comprise the eight genomic negative-sense RNAs, each of which is bound to multiple copies of the vRNP and a trimeric viral polymerase complex. The influenza virus life cycle centres on the vRNPs, which in turn rely on host cellular processes to carry out functions that are necessary for the successful completion of the virus life cycle. In this Review, we discuss our current knowledge about vRNP trafficking within host cells and the function of these complexes in the context of the virus life cycle, highlighting how structure contributes to function and the crucial interactions with host cell pathways, as well as on the information gaps that remain. An improved understanding of how vRNPs use host cell pathways is essential to identify mechanisms of virus pathogenicity, host adaptation and, ultimately, new targets for antiviral intervention.
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27
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Deep sequencing reveals the eight facets of the influenza A/HongKong/1/1968 (H3N2) virus cap-snatching process. Sci Rep 2014; 4:6181. [PMID: 25154590 PMCID: PMC4143772 DOI: 10.1038/srep06181] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2014] [Accepted: 07/31/2014] [Indexed: 11/08/2022] Open
Abstract
The influenza A virus RNA polymerase cleaves the 5′ end of host pre-mRNAs and uses the capped RNA fragments as primers for viral mRNA synthesis. We performed deep sequencing of the 5′ ends of viral mRNAs from all genome segments transcribed in both human (A549) and mouse (M-1) cells infected with the influenza A/HongKong/1/1968 (H3N2) virus. In addition to information on RNA motifs present, our results indicate that the host primers are divergent between the viral transcripts. We observed differences in length distributions, nucleotide motifs and the identity of the host primers between the viral mRNAs. Mapping the reads to known transcription start sites indicates that the virus targets the most abundant host mRNAs, which is likely caused by the higher expression of these genes. Our findings suggest negligible competition amongst RdRp:vRNA complexes for individual host mRNA templates during cap-snatching and provide a better understanding of the molecular mechanism governing the first step of transcription of this influenza strain.
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28
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Gultyaev AP, Tsyganov-Bodounov A, Spronken MIJ, van der Kooij S, Fouchier RAM, Olsthoorn RCL. RNA structural constraints in the evolution of the influenza A virus genome NP segment. RNA Biol 2014; 11:942-52. [PMID: 25180940 DOI: 10.4161/rna.29730] [Citation(s) in RCA: 38] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022] Open
Abstract
Conserved RNA secondary structures were predicted in the nucleoprotein (NP) segment of the influenza A virus genome using comparative sequence and structure analysis. A number of structural elements exhibiting nucleotide covariations were identified over the whole segment length, including protein-coding regions. Calculations of mutual information values at the paired nucleotide positions demonstrate that these structures impose considerable constraints on the virus genome evolution. Functional importance of a pseudoknot structure, predicted in the NP packaging signal region, was confirmed by plaque assays of the mutant viruses with disrupted structure and those with restored folding using compensatory substitutions. Possible functions of the conserved RNA folding patterns in the influenza A virus genome are discussed.
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Affiliation(s)
- Alexander P Gultyaev
- Department of Viroscience, Erasmus Medical Center, The Netherlands; Leiden Institute of Advanced Computer Science (LIACS), Leiden University, Niels Bohrweg 1, The Netherlands
| | - Anton Tsyganov-Bodounov
- Leiden Institute of Chemistry, Leiden University, P.O.Box 9502, 2300 RA Leiden, The Netherlands;; Current address: Illumina UK Ltd., Chesterford Research Park, Little Chesterford, Essex, UK
| | | | - Sander van der Kooij
- Department of Viroscience, Erasmus Medical Center, The Netherlands; Current address: BaseClear B.V., Einsteinweg, The Netherlands
| | - Ron A M Fouchier
- Department of Viroscience, Erasmus Medical Center, The Netherlands
| | - René C L Olsthoorn
- Leiden Institute of Chemistry, Leiden University, P.O.Box 9502, 2300 RA Leiden, The Netherlands
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29
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Khaperskyy DA, Emara MM, Johnston BP, Anderson P, Hatchette TF, McCormick C. Influenza a virus host shutoff disables antiviral stress-induced translation arrest. PLoS Pathog 2014; 10:e1004217. [PMID: 25010204 PMCID: PMC4092144 DOI: 10.1371/journal.ppat.1004217] [Citation(s) in RCA: 98] [Impact Index Per Article: 9.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2014] [Accepted: 05/14/2014] [Indexed: 12/22/2022] Open
Abstract
Influenza A virus (IAV) polymerase complexes function in the nucleus of infected cells, generating mRNAs that bear 5′ caps and poly(A) tails, and which are exported to the cytoplasm and translated by host machinery. Host antiviral defences include mechanisms that detect the stress of virus infection and arrest cap-dependent mRNA translation, which normally results in the formation of cytoplasmic aggregates of translationally stalled mRNA-protein complexes known as stress granules (SGs). It remains unclear how IAV ensures preferential translation of viral gene products while evading stress-induced translation arrest. Here, we demonstrate that at early stages of infection both viral and host mRNAs are sensitive to drug-induced translation arrest and SG formation. By contrast, at later stages of infection, IAV becomes partially resistant to stress-induced translation arrest, thereby maintaining ongoing translation of viral gene products. To this end, the virus deploys multiple proteins that block stress-induced SG formation: 1) non-structural protein 1 (NS1) inactivates the antiviral double-stranded RNA (dsRNA)-activated kinase PKR, thereby preventing eIF2α phosphorylation and SG formation; 2) nucleoprotein (NP) inhibits SG formation without affecting eIF2α phosphorylation; 3) host-shutoff protein polymerase-acidic protein-X (PA-X) strongly inhibits SG formation concomitant with dramatic depletion of cytoplasmic poly(A) RNA and nuclear accumulation of poly(A)-binding protein. Recombinant viruses with disrupted PA-X host shutoff function fail to effectively inhibit stress-induced SG formation. The existence of three distinct mechanisms of IAV-mediated SG blockade reveals the magnitude of the threat of stress-induced translation arrest during viral replication. Like all viruses, Influenza A virus (IAV) is absolutely dependent on host-cell protein synthesis machinery. This dependence makes the virus vulnerable to the innate ability of cells to inhibit protein synthesis in response to various types of stress. This inhibition, termed translation arrest, helps cells survive adverse conditions by re-dedicating their energy to stress responses. When cells arrest translation, they form stress granules: depots of untranslated mRNAs and associated proteins. Translation arrest and formation of stress granules can be induced pharmacologically, and in this work we sought to determine whether stress granule induction would be effective in blocking IAV replication. Here we demonstrate that treatment of cells with inducers of stress granules at early times after infection resulted in blockade of viral protein synthesis and stopped viral replication. At later times post-infection, by contrast, IAV proteins prevented pharmacological induction of stress granules. We identified three viral proteins – more than in any virus to date – that work in concert to prevent stress granule formation. Taken together, our studies reveal a multipronged approach for viral suppression of translation arrest, and identify a window of opportunity early in infection when pharmacological induction of stress granules has a strong antiviral effect.
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Affiliation(s)
- Denys A. Khaperskyy
- Department of Microbiology and Immunology, Dalhousie University, Halifax, Nova Scotia, Canada
| | - Mohamed M. Emara
- Laboratory of Stem Cell Research, Qatar Biomedical Research Institute, Doha, Qatar
- Department of Virology, School of Veterinary Medicine, Cairo University, Giza, Egypt
- Division of Rheumatology, Immunology and Allergy, Brigham and Women's Hospital, Harvard Medical School, Boston, Massachusetts, United States of America
| | - Benjamin P. Johnston
- Department of Microbiology and Immunology, Dalhousie University, Halifax, Nova Scotia, Canada
| | - Paul Anderson
- Division of Rheumatology, Immunology and Allergy, Brigham and Women's Hospital, Harvard Medical School, Boston, Massachusetts, United States of America
| | - Todd F. Hatchette
- Department of Microbiology and Immunology, Dalhousie University, Halifax, Nova Scotia, Canada
| | - Craig McCormick
- Department of Microbiology and Immunology, Dalhousie University, Halifax, Nova Scotia, Canada
- * E-mail:
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Gerber M, Isel C, Moules V, Marquet R. Selective packaging of the influenza A genome and consequences for genetic reassortment. Trends Microbiol 2014; 22:446-55. [PMID: 24798745 DOI: 10.1016/j.tim.2014.04.001] [Citation(s) in RCA: 94] [Impact Index Per Article: 9.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/11/2014] [Revised: 03/25/2014] [Accepted: 04/02/2014] [Indexed: 10/25/2022]
Abstract
Influenza A viruses package their segmented RNA genome in a selective manner. Electron tomography, biochemical assays, and replication assays of viruses produced by reverse genetics recently unveiled molecular details of this mechanism, whereby different influenza viral strains form different and unique networks of direct intermolecular RNA-RNA interactions. Together with detailed views of the three-dimensional structure of the viral ribonucleoparticles, these recent advances help us understand the rules that govern genome packaging. They also have deep implications for the genetic reassortment processes, which are responsible for devastating pandemics.
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Affiliation(s)
- Marie Gerber
- Architecture et Réactivité de l'ARN, Université de Strasbourg, Centre National de Recherche Scientifique (CNRS), Institut de Biologie Moléculaire et Cellulaire (IBMC), 15 rue René Descartes, 67084 Strasbourg, France
| | - Catherine Isel
- Architecture et Réactivité de l'ARN, Université de Strasbourg, Centre National de Recherche Scientifique (CNRS), Institut de Biologie Moléculaire et Cellulaire (IBMC), 15 rue René Descartes, 67084 Strasbourg, France
| | - Vincent Moules
- Virologie et Pathologie Humaine, Université Lyon 1, EA4610, Faculté de Médecine RTH Laennec, 69008 Lyon, France; VirNext, Université Lyon 1, EA4610, Faculté de Médecine RTH Laennec, 69008 Lyon, France
| | - Roland Marquet
- Architecture et Réactivité de l'ARN, Université de Strasbourg, Centre National de Recherche Scientifique (CNRS), Institut de Biologie Moléculaire et Cellulaire (IBMC), 15 rue René Descartes, 67084 Strasbourg, France.
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31
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Abstract
The influenza A viruses cause yearly epidemics and occasional pandemics of respiratory disease, which constitute a serious health and economic burden. Their genome consists of eight single-stranded, negative-polarity RNAs that associate to the RNA polymerase and many nucleoprotein monomers to form ribonucleoprotein complexes (RNPs). Here, we focus on the organization of these RNPs, as well as on the structure and interactions of its constitutive elements and we discuss the mechanisms by which the RNPs transcribe and replicate the viral genome.
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32
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Zheng W, Olson J, Vakharia V, Tao YJ. The crystal structure and RNA-binding of an orthomyxovirus nucleoprotein. PLoS Pathog 2013; 9:e1003624. [PMID: 24068932 PMCID: PMC3771910 DOI: 10.1371/journal.ppat.1003624] [Citation(s) in RCA: 34] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2013] [Accepted: 07/31/2013] [Indexed: 12/23/2022] Open
Abstract
Genome packaging for viruses with segmented genomes is often a complex problem. This is particularly true for influenza viruses and other orthomyxoviruses, whose genome consists of multiple negative-sense RNAs encapsidated as ribonucleoprotein (RNP) complexes. To better understand the structural features of orthomyxovirus RNPs that allow them to be packaged, we determined the crystal structure of the nucleoprotein (NP) of a fish orthomyxovirus, the infectious salmon anemia virus (ISAV) (genus Isavirus). As the major protein component of the RNPs, ISAV-NP possesses a bi-lobular structure similar to the influenza virus NP. Because both RNA-free and RNA-bound ISAV NP forms stable dimers in solution, we were able to measure the NP RNA binding affinity as well as the stoichiometry using recombinant proteins and synthetic oligos. Our RNA binding analysis revealed that each ISAV-NP binds ∼12 nts of RNA, shorter than the 24–28 nts originally estimated for the influenza A virus NP based on population average. The 12-nt stoichiometry was further confirmed by results from electron microscopy and dynamic light scattering. Considering that RNPs of ISAV and the influenza viruses have similar morphologies and dimensions, our findings suggest that NP-free RNA may exist on orthomyxovirus RNPs, and selective RNP packaging may be accomplished through direct RNA-RNA interactions. Orthomyxoviruses are a family of RNA viruses that include the various types of influenza viruses. The genome of orthomyxoviruses consists of multiple segments of negative-sense, single-stranded RNA molecules, each packaged in the form of rod-shaped, double-helical ribonucleoprotein (RNP) complexes. How different RNPs interact with each other to ensure specific genome packaging is a long-standing question and crucial to our understanding of orthomyxovirus replication and influenza virus gene reassortment. Our study of a fish orthomyxovirus, the infectious salmon anemia virus (ISAV), shows that its nucleoprotein (NP), which forms the protein scaffold backbone of the viral RNP, has a bi-lobular structure like the influenza virus NP. Because ISAV-NP forms stable dimers in solution, we were able to determine ISAV-NP RNA binding stoichiometry by biochemical assays, electron microscopy and dynamic light scattering. Our results indicate that each ISAV-NP binds ∼12-nt RNA, shorter than the 24–28 nts originally estimated for the influenza A virus based on population average. We propose that NP-free RNA exists on orthomyxovirus RNPs, and such RNA regions likely mediate specific RNP-RNP interactions during genome packaging. Further elucidation of the RNA-mediated RNP-RNP interactions will help us determine the molecular basis of gene reassortment by orthomyxoviruses including the influenza viruses.
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Affiliation(s)
- Wenjie Zheng
- Department of Biochemistry and Cell Biology, Rice University, Houston, Texas, United States of America
| | - John Olson
- Department of Biochemistry and Cell Biology, Rice University, Houston, Texas, United States of America
| | - Vikram Vakharia
- Department of Marine Biotechnology, University of Maryland Baltimore County, Institute of Marine and Environmental Technology, Baltimore, Maryland, United States of America
| | - Yizhi Jane Tao
- Department of Biochemistry and Cell Biology, Rice University, Houston, Texas, United States of America
- * E-mail:
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Turrell L, Lyall JW, Tiley LS, Fodor E, Vreede FT. The role and assembly mechanism of nucleoprotein in influenza A virus ribonucleoprotein complexes. Nat Commun 2013; 4:1591. [PMID: 23481399 PMCID: PMC4168216 DOI: 10.1038/ncomms2589] [Citation(s) in RCA: 92] [Impact Index Per Article: 8.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2012] [Accepted: 02/08/2013] [Indexed: 12/04/2022] Open
Abstract
The nucleoprotein of negative strand RNA viruses forms a major component of the ribonucleoprotein complex that is responsible for viral transcription and replication. However, the precise role of nucleoprotein in viral RNA transcription and replication is not clear. Here we show that nucleoprotein of influenza A virus is entirely dispensable for replication and transcription of short viral RNA-like templates in vivo, suggesting that nucleoprotein represents an elongation factor for the viral RNA polymerase. We also find that the recruitment of nucleoprotein to nascent ribonucleoprotein complexes during replication of full length viral genes is mediated through nucleoprotein-nucleoprotein homo-oligomerisation in a “tail loop-first” orientation and is independent of RNA binding. This work demonstrates that nucleoprotein does not regulate the initiation and termination of transcription and replication by the viral polymerase in vivo and provides new mechanistic insights into the assembly and regulation of viral ribonucleoprotein complexes.
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Affiliation(s)
- Lauren Turrell
- Sir William Dunn School of Pathology, University of Oxford, South Parks Road, Oxford OX1 3RE, UK
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34
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Structure and assembly of the influenza A virus ribonucleoprotein complex. FEBS Lett 2013; 587:1206-14. [PMID: 23499938 DOI: 10.1016/j.febslet.2013.02.048] [Citation(s) in RCA: 52] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2013] [Revised: 02/26/2013] [Accepted: 02/26/2013] [Indexed: 11/20/2022]
Abstract
The genome of influenza A viruses consists of eight segments of single-stranded, negative-sense RNA that are encapsidated as individual rod-shaped ribonucleoprotein complexes (RNPs). Each RNP contains a viral RNA, a viral polymerase and multiple copies of the viral nucleoprotein (NP). Influenza A virus RNPs play important roles during virus infection by directing viral RNA replication and transcription, intracellular transport of the viral RNA, gene reassortment as well as viral genome packaging into progeny particles. As a unique genomic entity, the influenza A virus RNP has been extensively studied since the 1960s. Recently, exciting progress has been made in studying the RNP structure and its assembly, leading to a better understanding of the structural basis of various RNP functions.
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35
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Fournier E, Moules V, Essere B, Paillart JC, Sirbat JD, Cavalier A, Rolland JP, Thomas D, Lina B, Isel C, Marquet R. Interaction network linking the human H3N2 influenza A virus genomic RNA segments. Vaccine 2012; 30:7359-67. [PMID: 23063835 DOI: 10.1016/j.vaccine.2012.09.079] [Citation(s) in RCA: 65] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2011] [Revised: 04/24/2012] [Accepted: 09/28/2012] [Indexed: 12/14/2022]
Abstract
The genome of influenza A viruses is comprised of eight negative-sense viral RNAs (vRNAs) that form viral ribonucleoproteins (vRNPs). In order to be infectious, an influenza A viral particle must encapsidate at least one copy of each of the vRNAs. Thus, even though genome segmentation is evolutionary advantageous, it undeniably complicates viral assembly, which is believed to occur through a selective mechanism that still remains to be understood. Using electron tomography 3D-reconstructions, we show that the eight vRNPs of an influenza A Moscow/10/99 (H3N2) virus are interconnected within a star-like structure as they emerge from a unique "transition zone" at the budding tip of the virions. Notably, this "transition zone" is thick enough to accommodate all described packaging signals. We also report that, in vitro, each vRNA segment is involved in a direct contact with at least one other vRNA partner, in a single network of intermolecular interactions. We show that in several cases, the regions involved in vRNA/vRNA interactions overlap with previously identified packaging signals. Our results thus provide support for the involvement of RNA/RNA interactions in the selection and specific packaging of influenza A genomic RNAs, which appear embedded into an organised supramolecular complex likely held together by direct base-pairings between packaging signals.
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Affiliation(s)
- Emilie Fournier
- Architecture et Réactivité de l'ARN, Université de Strasbourg, CNRS, IBMC, 15 rue René Descartes, 67084 Strasbourg, France.
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36
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Terrier O, Moules V, Carron C, Cartet G, Frobert E, Yver M, Traversier A, Wolff T, Riteau B, Naffakh N, Lina B, Diaz JJ, Rosa-Calatrava M. The influenza fingerprints: NS1 and M1 proteins contribute to specific host cell ultrastructure signatures upon infection by different influenza A viruses. Virology 2012; 432:204-18. [PMID: 22770924 DOI: 10.1016/j.virol.2012.05.019] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2012] [Revised: 05/02/2012] [Accepted: 05/21/2012] [Indexed: 12/22/2022]
Abstract
Influenza A are nuclear replicating viruses which hijack host machineries in order to achieve optimal infection. Numerous functional virus-host interactions have now been characterized, but little information has been gathered concerning their link to the virally induced remodeling of the host cellular architecture. In this study, we infected cells with several human and avian influenza viruses and we have analyzed their ultrastructural modifications by using electron and confocal microscopy. We discovered that infections lead to a major and systematic disruption of nucleoli and the formation of a large number of diverse viral structures showing specificity that depended on the subtype origin and genomic composition of viruses. We identified NS1 and M1 proteins as the main actors in the remodeling of the host ultra-structure and our results suggest that each influenza A virus strain could be associated with a specific cellular fingerprint, possibly correlated to the functional properties of their viral components.
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Affiliation(s)
- Olivier Terrier
- Equipe VirCell, Laboratoire de Virologie et Pathologie Humaine, VirPath EMR 4610, Université de Lyon, Université Claude Bernard Lyon 1, Hospices Civils de Lyon, Faculté de médecine RTH Laennec, rue Guillaume Paradin, F-69008 Lyon, France
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37
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Combining RNA–DNA swapping and quantitative polymerase chain reaction for the detection of influenza A nucleoprotein. Anal Biochem 2012; 420:121-6. [DOI: 10.1016/j.ab.2011.09.009] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2011] [Revised: 09/08/2011] [Accepted: 09/09/2011] [Indexed: 12/25/2022]
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38
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Tarus B, Bakowiez O, Chenavas S, Duchemin L, Estrozi LF, Bourdieu C, Lejal N, Bernard J, Moudjou M, Chevalier C, Delmas B, Ruigrok RWH, Di Primo C, Slama-Schwok A. Oligomerization paths of the nucleoprotein of influenza A virus. Biochimie 2011; 94:776-85. [PMID: 22155087 DOI: 10.1016/j.biochi.2011.11.009] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2011] [Accepted: 11/22/2011] [Indexed: 10/14/2022]
Abstract
The influenza viruses contain a segmented, negative strand RNA genome. Each RNA segment is covered by multiple copies of the nucleoprotein (NP) and is associated with the polymerase complex into ribonucleoprotein (RNP) particles. Despite its importance in the virus life cycle, the interactions between the NP and the genome are not well understood. Here, we studied the assembly process of NP-RNA oligomers and analyzed how the oligomeric/monomeric status of RNA-free NP affects RNA binding and oligomerization. Recombinant wild-type NP purified in low salt concentrations and a derived mutant engineered for oligomerization deficiency (R416A) were mainly monomeric in RNA-free solutions as shown by biochemical and electron microscopy techniques. NP monomer formed with RNA a fast 1/1 complex characterized by surface plasmon resonance. In a subsequent and slow process that depended on the RNA length, oligomerization of NP was mediated by RNA binding. In contrast, preparations of wild-type NP purified in high salt concentrations as well as mutant Y148A engineered for deficiency in nucleic acid binding were partly or totally oligomeric in RNA-free solutions. These trimer/tetramer NP oligomers bind directly as oligomers to RNA with a higher affinity than that of the monomers. Both oligomerization routes we characterized could be exploited by cellular or viral factors to modulate or control viral RNA encapsidation by NP.
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Affiliation(s)
- B Tarus
- Virologie et Immunologie Moléculaires, UR 892, INRA, Centre de Jouy en Josas, Domaine de Vilvert, Jouy en Josas 78350, France
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39
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Fournier E, Moules V, Essere B, Paillart JC, Sirbat JD, Isel C, Cavalier A, Rolland JP, Thomas D, Lina B, Marquet R. A supramolecular assembly formed by influenza A virus genomic RNA segments. Nucleic Acids Res 2011; 40:2197-209. [PMID: 22075989 PMCID: PMC3300030 DOI: 10.1093/nar/gkr985] [Citation(s) in RCA: 134] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022] Open
Abstract
The influenza A virus genome consists of eight viral RNAs (vRNAs) that form viral ribonucleoproteins (vRNPs). Even though evidence supporting segment-specific packaging of vRNAs is accumulating, the mechanism ensuring selective packaging of one copy of each vRNA into the viral particles remains largely unknown. We used electron tomography to show that the eight vRNPs emerge from a common ‘transition zone’ located underneath the matrix layer at the budding tip of the virions, where they appear to be interconnected and often form a star-like structure. This zone appears as a platform in 3D surface rendering and is thick enough to contain all known packaging signals. In vitro, all vRNA segments are involved in a single network of intermolecular interactions. The regions involved in the strongest interactions were identified and correspond to known packaging signals. A limited set of nucleotides in the 5′ region of vRNA 7 was shown to interact with vRNA 6 and to be crucial for packaging of the former vRNA. Collectively, our findings support a model in which the eight genomic RNA segments are selected and packaged as an organized supramolecular complex held together by direct base pairing of the packaging signals.
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Affiliation(s)
- Emilie Fournier
- Architecture et Réactivité de l'ARN, Université de Strasbourg, CNRS, IBMC, 15 rue René Descartes, 67084 Strasbourg, France
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40
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Jiang H, Yang H, Kapczynski DR. Chicken interferon alpha pretreatment reduces virus replication of pandemic H1N1 and H5N9 avian influenza viruses in lung cell cultures from different avian species. Virol J 2011; 8:447. [PMID: 21939525 PMCID: PMC3197513 DOI: 10.1186/1743-422x-8-447] [Citation(s) in RCA: 46] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2011] [Accepted: 09/22/2011] [Indexed: 12/20/2022] Open
Abstract
BACKGROUND Type I interferons, including interferon alpha (IFN-α), represent one of the first lines of innate immune defense against influenza virus infection. Following natural infection of chickens with avian influenza virus (AIV), transcription of IFN-α is quickly up regulated along with multiple other immune-related genes. Chicken IFN-α up regulates a number of important anti-viral response genes and has been demonstrated to be an important cytokine to establish anti-viral immunity. However, the mechanisms by which interferon inhibit virus replication in avian species remains unknown as does the biological activity of chicken interferon in other avian species. METHODS In these studies, we assessed the protective potential of exogenous chicken IFN-α applied to chicken, duck, and turkey primary lung cell cultures prior to infection with the pandemic H1N1 virus (A/turkey/Virginia/SEP-4/2009) and an established avian H5N9 virus (A/turkey/Wisconsin/1968). Growth kinetics and induction of select immune response genes, including IFN-α and myxovirus-resistance gene I (Mx), as well as proinflammatory cytokines (IL-1β and IL-6), were measured in response to chicken IFN-α and viral infection over time. RESULTS Results demonstrate that pretreatment with chicken IFN-α before AIV infection significantly reduced virus replication in both chicken-and turkey-origin lung cells and to a lesser degree the duck-origin cells. Virus growth was reduced by approximately 200-fold in chicken and turkey cells and 30-fold in duck cells after 48 hours of incubation. Interferon treatment also significantly decreased the interferon and proinflammatory response during viral infection. In general, infection with the H1N1 virus resulted in an attenuated interferon and proinflammatory response in these cell lines, compared to the H5N9 virus. CONCLUSIONS Taken together, these studies show that chicken IFN-α reduces virus replication, lower host innate immune response following infection, and is biologically active in other avian species.
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Affiliation(s)
- Haijun Jiang
- Key Laboratory of Zoonosis of Ministry of Agriculture, College of Veterinary Medicine and State Key Laboratory of Agrobiotechnology, China Agricultural University, Beijing, People's Republic of China
- Exotic and Emerging Avian Disease Unit, Southeast Poultry Research Laboratory, Agricultural Research Service, USDA, 934 College Station Road, Athens, GA, 30605, USA
| | - Hanchun Yang
- Key Laboratory of Zoonosis of Ministry of Agriculture, College of Veterinary Medicine and State Key Laboratory of Agrobiotechnology, China Agricultural University, Beijing, People's Republic of China
| | - Darrell R Kapczynski
- Exotic and Emerging Avian Disease Unit, Southeast Poultry Research Laboratory, Agricultural Research Service, USDA, 934 College Station Road, Athens, GA, 30605, USA
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41
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Stabilization of influenza virus replication intermediates is dependent on the RNA-binding but not the homo-oligomerization activity of the viral nucleoprotein. J Virol 2011; 85:12073-8. [PMID: 21917965 DOI: 10.1128/jvi.00695-11] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
The influenza virus nucleoprotein (NP) is believed to play a central role in directing a switch from RNA genome transcription to replication by the viral RNA polymerase. However, this role has recently been disputed with the proposal of alternative regulatory mechanisms. It has been suggested that the expression of viral polymerase and NP allows genome replication by stabilization of cRNA replication intermediates and complementary ribonucleoprotein (cRNP) assembly. Here, we demonstrate that the RNA-binding activity of NP is necessary for stabilization of cRNA, whereas, surprisingly, homo-oligomerization of NP is not essential. However, both RNA binding and homo-oligomerization activities are essential for genome replication.
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42
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Wang Z, Liu X, Zhao Z, Xu C, Zhang K, Chen C, Sun L, Gao GF, Ye X, Liu W. Cyclophilin E functions as a negative regulator to influenza virus replication by impairing the formation of the viral ribonucleoprotein complex. PLoS One 2011; 6:e22625. [PMID: 21887220 PMCID: PMC3160840 DOI: 10.1371/journal.pone.0022625] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2011] [Accepted: 06/27/2011] [Indexed: 12/23/2022] Open
Abstract
Background The nucleoprotein (NP) of influenza A virus is a multifunctional protein that plays a critical role in the replication and transcription of the viral genome. Therefore, examining host factors that interact with NP may shed light on the mechanism of host restriction barriers and the tissue tropism of influenza A virus. Here, Cyclophilin E (CypE), a member of the peptidyl-propyl cis-trans isomerase (PPIase) family, was found to bind to NP and inhibit viral replication and transcription. Methodology/Principal Findings In the present study, CypE was found to interact with NP but not with the other components of the viral ribonucleoprotein complex (vRNP): PB1, PB2, and PA. Mutagenesis data revealed that the CypE domain comprised of residues 137–186 is responsible for its binding to NP. Functional analysis results indicated that CypE is a negative regulator in the influenza virus life cycle. Furthermore, knock-down of CypE resulted in increased levels of three types of viral RNA, suggesting that CypE negatively affects viral replication and transcription. Moreover, up-regulation of CypE inhibited the activity of influenza viral polymerase. We determined that the molecular mechanism by which CypE negatively regulates influenza virus replication and transcription is by interfering with NP self-association and the NP-PB1 and NP-PB2 interactions. Conclusions/Significance CypE is a host restriction factor that inhibits the functions of NP, as well as viral replication and transcription, by impairing the formation of the vRNP. The data presented here will help us to better understand the molecular mechanisms of host restriction barriers, host adaptation, and tissue tropism of influenza A virus.
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Affiliation(s)
- Zengfu Wang
- Center for Molecular Virology, Chinese Academy of Sciences Key Laboratory of Pathogenic Microbiology and Immunology, Institute of Microbiology, Chinese Academy of Sciences, Beijing, China
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43
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Replication-coupled and host factor-mediated encapsidation of the influenza virus genome by viral nucleoprotein. J Virol 2011; 85:6197-204. [PMID: 21507964 DOI: 10.1128/jvi.00277-11] [Citation(s) in RCA: 51] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022] Open
Abstract
The influenza virus RNA-dependent RNA polymerase is capable of initiating replication but mainly catalyzes abortive RNA synthesis in the absence of viral and host regulatory factors. Previously, we reported that IREF-1/minichromosome maintenance (MCM) complex stimulates a de novo initiated replication reaction by stabilizing an initiated replication complex through scaffolding between the viral polymerase and nascent cRNA to which MCM binds. In addition, several lines of genetic and biochemical evidence suggest that viral nucleoprotein (NP) is involved in successful replication. Here, using cell-free systems, we have shown the precise stimulatory mechanism of virus genome replication by NP. Stepwise cell-free replication reactions revealed that exogenously added NP free of RNA activates the viral polymerase during promoter escape while it is incapable of encapsidating the nascent cRNA. However, we found that a previously identified cellular protein, RAF-2p48/NPI-5/UAP56, facilitates replication reaction-coupled encapsidation as an NP molecular chaperone. These findings demonstrate that replication of the virus genome is followed by its encapsidation by NP in collaboration with its chaperone.
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44
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Resa-Infante P, Jorba N, Coloma R, Ortin J. The influenza virus RNA synthesis machine: advances in its structure and function. RNA Biol 2011; 8:207-15. [PMID: 21358279 DOI: 10.4161/rna.8.2.14513] [Citation(s) in RCA: 151] [Impact Index Per Article: 11.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/29/2023] Open
Abstract
The influenza A viruses are the causative agents of respiratory disease that occurs as yearly epidemics and occasional pandemics. These viruses are endemic in wild avian species and can sometimes break the species barrier to infect and generate new virus lineages in humans. The influenza A virus genome consists of eight single-stranded, negative-polarity RNAs that form ribonucleoprotein complexes by association to the RNA polymerase and the nucleoprotein. In this review we focus on the structure of this RNA-synthesis machines and the included RNA polymerase, and on the mechanisms by which they express their genetic information as mRNAs and generate progeny ribonucleoproteins that will become incorporated into new infectious virions. New structural, biochemical and genetic data are rapidly accumulating in this very active area of research. We discuss these results and attempt to integrate the information into structural and functional models that may help the design of new experiments and further our knowledge on virus RNA replication and gene expression. This interplay between structural and functional data will eventually provide new targets for controlled attenuation or antiviral therapy.
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Human importin alpha and RNA do not compete for binding to influenza A virus nucleoprotein. Virology 2010; 409:84-90. [PMID: 20974480 DOI: 10.1016/j.virol.2010.10.001] [Citation(s) in RCA: 26] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2010] [Revised: 08/23/2010] [Accepted: 10/01/2010] [Indexed: 11/20/2022]
Abstract
Influenza virus has a segmented genome composed of eight negative stranded RNA segments. Each segment is covered with NP forming ribonucleoproteins (vRNPs) and carries a copy of the heterotrimeric polymerase complex. As a rare phenomenon among the RNA viruses, the viral replication occurs in the nucleus and therefore implies interactions between host and viral factors, such as between importin alpha and nucleoprotein. In the present study we report that through binding with the human nuclear receptor importin α5 (Impα5), the viral NP is no longer oligomeric but maintained as a monomer inside the complex. In this regard, Impα5 acts as a chaperone until NP is delivered in the nucleus for viral RNA encapsidation. Moreover, we show that the association of NP with the host transporter does not impair the binding of NP to RNA. The complex human Impα5-NP binds RNA with the same affinity as wt NP alone, whereas engineered monomeric NP through point mutations binds RNA with a strongly reduced affinity.
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Gultyaev AP, Fouchier RAM, Olsthoorn RCL. Influenza virus RNA structure: unique and common features. Int Rev Immunol 2010; 29:533-56. [PMID: 20923332 DOI: 10.3109/08830185.2010.507828] [Citation(s) in RCA: 40] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
The influenza A virus genome consists of eight negative-sense RNA segments. Here we review the currently available data on structure-function relationships in influenza virus RNAs. Various ideas and hypotheses about the roles of influenza virus RNA folding in the virus replication are also discussed in relation to other viruses.
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Matsubara T, Onishi A, Saito T, Shimada A, Inoue H, Taki T, Nagata K, Okahata Y, Sato T. Sialic Acid-Mimic Peptides As Hemagglutinin Inhibitors for Anti-Influenza Therapy. J Med Chem 2010; 53:4441-9. [DOI: 10.1021/jm1002183] [Citation(s) in RCA: 90] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Teruhiko Matsubara
- Department of Biosciences and Informatics, Keio University, Yokohama 223-8522, Japan
| | - Ai Onishi
- Department of Biosciences and Informatics, Keio University, Yokohama 223-8522, Japan
| | - Tomomi Saito
- Department of Biosciences and Informatics, Keio University, Yokohama 223-8522, Japan
| | - Aki Shimada
- Department of Biosciences and Informatics, Keio University, Yokohama 223-8522, Japan
| | - Hiroki Inoue
- Department of Biomolecular Engineering, Tokyo Institute of Technology, Yokohama 226-8501, Japan
| | - Takao Taki
- Molecular Medical Science Institute, Otsuka Pharmaceutical Co. Ltd., Tokushima 771-0192, Japan
| | - Kyosuke Nagata
- Department of Infection Biology, Graduate School of Comprehensive Human Sciences, University of Tsukuba, Tsukuba 305-8575, Japan
| | - Yoshio Okahata
- Department of Biomolecular Engineering, Tokyo Institute of Technology, Yokohama 226-8501, Japan
| | - Toshinori Sato
- Department of Biosciences and Informatics, Keio University, Yokohama 223-8522, Japan
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[Function of influenza virus RNA polymerase based on structure]. Uirusu 2009; 59:1-11. [PMID: 19927983 DOI: 10.2222/jsv.59.1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/19/2022]
Abstract
Studies using cell-free RNA synthesis systems and reverse genetics have been contributing to understanding of the molecular mechanism of replication and transcription of the influenza virus genome, which is the most essential process through the virus life cycle. Recently, it is noted that this mechanism is also involved in host range determination of the virus. In the light of the fact that viruses resistant to previously developed anti-influenza virus drugs emerge, establishment of a rational screening strategy of drugs for novel molecular targets is highly required. Further to clarify the detailed function of viral factors involved in replication and transcription of the virus genome and to devise anti-viral methods, determination of the 3D structures of viral factors should give a breakthrough. In this review, we summarize the recent accumulating information on the 3D structures of viral factors and discuss their function based on their structures.
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The structure of a biologically active influenza virus ribonucleoprotein complex. PLoS Pathog 2009; 5:e1000491. [PMID: 19557158 PMCID: PMC2695768 DOI: 10.1371/journal.ppat.1000491] [Citation(s) in RCA: 158] [Impact Index Per Article: 10.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2009] [Accepted: 05/28/2009] [Indexed: 12/21/2022] Open
Abstract
The influenza viruses contain a segmented, single-stranded RNA genome of negative polarity. Each RNA segment is encapsidated by the nucleoprotein and the polymerase complex into ribonucleoprotein particles (RNPs), which are responsible for virus transcription and replication. Despite their importance, information about the structure of these RNPs is scarce. We have determined the three-dimensional structure of a biologically active recombinant RNP by cryo-electron microscopy. The structure shows a nonameric nucleoprotein ring (at 12 Angstrom resolution) with two monomers connected to the polymerase complex (at 18 Angstrom resolution). Docking the atomic structures of the nucleoprotein and polymerase domains, as well as mutational analyses, has allowed us to define the interactions between the functional elements of the RNP and to propose the location of the viral RNA. Our results provide the first model for a functional negative-stranded RNA virus ribonucleoprotein complex. The structure reported here will serve as a framework to generate a quasi-atomic model of the molecular machine responsible for viral RNA synthesis and to test new models for virus RNA replication and transcription.
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Ng AKL, Wang JH, Shaw PC. Structure and sequence analysis of influenza A virus nucleoprotein. ACTA ACUST UNITED AC 2009; 52:439-49. [PMID: 19471866 DOI: 10.1007/s11427-009-0064-x] [Citation(s) in RCA: 37] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2009] [Accepted: 04/18/2009] [Indexed: 10/20/2022]
Abstract
Influenza A virus nucleoprotein (NP) forms homo-oligomers and multiple copies of NP wrap around genomic RNA, along with a trimeric polymerase making up ribonucleoprotein (RNP) complex. Sequence comparison of more than 2500 influenza A NP showed that this protein contains 30.1 % of polymorphic residues. NP is composed of a head and a body domain and a tail loop/ linker region. The head domain is more conserved than the body domain, as revealed from the structure-based sequence alignment. NP oligomerization is mediated by the insertion of the non-polymorphic and structurally conserved tail loop of one NP molecule to a groove of another NP. The different form of NP oligomers is due to the flexibility of the polymorphic linkers that join the tail loop to the rest of the protein. The RNA binding property of NP is known to involve the protruding element and the flexible basic loop between the head and body domains, both having high degree of primary sequence conservation. To bind RNA, NP may first capture the RNA by the flexible basic loop and then the RNA is clamped by the protruding element.
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Affiliation(s)
- Andy Ka-Leung Ng
- Molecular Biotechnology Programme, Department of Biochemistry and Centre for Protein Science and Crystallography, The Chinese University of Hong Kong, Shatin, Hong Kong SAR, China
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