1
|
Zhang M, Zeng Y, Wang F, Feng H, Liu Q, Li F, Zhao S, Zhao J, Liu Z, Zheng F, Liu H. Effects of the Nonstructural Protein-Nucleolar and Coiled-Body Phosphoprotein 1 Protein Interaction on rRNA Synthesis Through Telomeric Repeat-Binding Factor 2 Regulation Under Nucleolar Stress. AIDS Res Hum Retroviruses 2024; 40:408-416. [PMID: 38062753 DOI: 10.1089/aid.2023.0067] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/14/2024] Open
Abstract
To investigate the effects and underlying molecular mechanisms of the interaction between the non-structural protein 1 (NS1) and nucleolar and coiled-body phosphoprotein 1 (NOLC1) on rRNA synthesis through nucleolar telomeric repeat-binding factor 2 (TRF2) under nucleolar stress in avian influenza A virus infection. The analysis of TRF2 ties into the exploration of ribosomal protein L11 (RPL11) and mouse double minute 2 (MDM2) because TRF2 has been found to interact with NOLC1, and the RPL11-MDM2 pathway plays an important role in nucleolar regulation and cellular processes. Both human embryonic kidney 293T cells and human lung adenocarcinoma A549 cells were transfected with the plasmids pCAGGS-HA and pCAGGS-HA-NS1, respectively. In addition, A549 cells were transfected with the plasmids pEGFP-N1, pEGFP-N1-NS1, and pDsRed2-N1-TRF2. The cell cycle was detected by flow cytometry, and coimmunoprecipitation was applied to examine the interactions between different proteins. The effect of NS1 on TRF2 was detected by immunoprecipitation, and the colocalization of NOLC1 and TRF2 or NS1 and TRF2 was visualized by immunofluorescence. Quantitative real-time PCR was conducted to detect the expression of the TRF2 and p21. There is a strong interaction between NOLC1 and TRF2, and the colocalization of NOLC1 and TRF2 in the nucleus. The protein expression of NOLC1 in A549-HA-NS1 cells was lower than that in A549-HA cells, which was accompanied by the upregulated protein expression of p53 in A549-HA-NS1 cells (all p < .05). TRF2 was scattered throughout the nucleus without clear nucleolar aggregation. RPL11 specifically interacted with MDM2 in the NS1 group, and expression of the p21 gene was significantly increased in the HA-NS1 group compared with the HA group (p < .01). NS1 protein can lead to the reduced aggregation of TRF2 in the nucleolus, inhibition of rRNA expression, and cell cycle blockade by interfering with the NOLC1 protein and generating nucleolar stress.
Collapse
Affiliation(s)
- Man Zhang
- School of Life Science, Liaoning University, Shenyang, China
| | - Yingyue Zeng
- School of Life Science, Liaoning University, Shenyang, China
- Key Laboratory of Computational Simulation and Information Processing of Biomacromolecules of Liaoning, Shenyang, China
- Shenyang Key Laboratory of Computational Simulation and Information Processing of Biological Macromolecules, Shenyang, China
| | - Fengchao Wang
- School of Life Science, Liaoning University, Shenyang, China
| | - Huawei Feng
- Key Laboratory of Computational Simulation and Information Processing of Biomacromolecules of Liaoning, Shenyang, China
- Shenyang Key Laboratory of Computational Simulation and Information Processing of Biological Macromolecules, Shenyang, China
- School of Pharmacy, Liaoning University, Shenyang, China
- Liaoning Provincial Engineering Laboratory of Molecular Modeling and Design for Drug, Shenyang, China
| | - Qingqing Liu
- School of Life Science, Liaoning University, Shenyang, China
| | - Feng Li
- School of Life Science, Liaoning University, Shenyang, China
| | - Shan Zhao
- School of Life Science, Liaoning University, Shenyang, China
| | - Jian Zhao
- School of Life Science, Liaoning University, Shenyang, China
- Key Laboratory of Computational Simulation and Information Processing of Biomacromolecules of Liaoning, Shenyang, China
- Shenyang Key Laboratory of Computational Simulation and Information Processing of Biological Macromolecules, Shenyang, China
- School of Pharmacy, Liaoning University, Shenyang, China
- Liaoning Provincial Engineering Laboratory of Molecular Modeling and Design for Drug, Shenyang, China
| | - Zhikui Liu
- Liaoning Huikang Testing and Evaluation Technology Co., Shenyang, China
| | - Fangliang Zheng
- School of Life Science, Liaoning University, Shenyang, China
| | - Hongsheng Liu
- Key Laboratory of Computational Simulation and Information Processing of Biomacromolecules of Liaoning, Shenyang, China
- Shenyang Key Laboratory of Computational Simulation and Information Processing of Biological Macromolecules, Shenyang, China
- School of Pharmacy, Liaoning University, Shenyang, China
- Liaoning Provincial Engineering Laboratory of Molecular Modeling and Design for Drug, Shenyang, China
| |
Collapse
|
2
|
Bougon J, Kadijk E, Gallot-Lavallee L, Curtis BA, Landers M, Archibald JM, Khaperskyy DA. Influenza A virus NS1 effector domain is required for PA-X-mediated host shutoff in infected cells. J Virol 2024; 98:e0190123. [PMID: 38629840 PMCID: PMC11092343 DOI: 10.1128/jvi.01901-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2023] [Accepted: 03/28/2024] [Indexed: 05/15/2024] Open
Abstract
Many viruses inhibit general host gene expression to limit innate immune responses and gain preferential access to the cellular translational apparatus for their protein synthesis. This process is known as host shutoff. Influenza A viruses (IAVs) encode two host shutoff proteins: nonstructural protein 1 (NS1) and polymerase acidic X (PA-X). NS1 inhibits host nuclear pre-messenger RNA maturation and export, and PA-X is an endoribonuclease that preferentially cleaves host spliced nuclear and cytoplasmic messenger RNAs. Emerging evidence suggests that in circulating human IAVs NS1 and PA-X co-evolve to ensure optimal magnitude of general host shutoff without compromising viral replication that relies on host cell metabolism. However, the functional interplay between PA-X and NS1 remains unexplored. In this study, we sought to determine whether NS1 function has a direct effect on PA-X activity by analyzing host shutoff in A549 cells infected with wild-type or mutant IAVs with NS1 effector domain deletion. This was done using conventional quantitative reverse transcription polymerase chain reaction techniques and direct RNA sequencing using nanopore technology. Our previous research on the molecular mechanisms of PA-X function identified two prominent features of IAV-infected cells: nuclear accumulation of cytoplasmic poly(A) binding protein (PABPC1) and increase in nuclear poly(A) RNA abundance relative to the cytoplasm. Here we demonstrate that NS1 effector domain function augments PA-X host shutoff and is necessary for nuclear PABPC1 accumulation. By contrast, nuclear poly(A) RNA accumulation is not dependent on either NS1 or PA-X-mediated host shutoff and is accompanied by nuclear retention of viral transcripts. Our study demonstrates for the first time that NS1 and PA-X may functionally interact in mediating host shutoff.IMPORTANCERespiratory viruses including the influenza A virus continue to cause annual epidemics with high morbidity and mortality due to the limited effectiveness of vaccines and antiviral drugs. Among the strategies evolved by viruses to evade immune responses is host shutoff-a general blockade of host messenger RNA and protein synthesis. Disabling influenza A virus host shutoff is being explored in live attenuated vaccine development as an attractive strategy for increasing their effectiveness by boosting antiviral responses. Influenza A virus encodes two proteins that function in host shutoff: the nonstructural protein 1 (NS1) and the polymerase acidic X (PA-X). We and others have characterized some of the NS1 and PA-X mechanisms of action and the additive effects that these viral proteins may have in ensuring the blockade of host gene expression. In this work, we examined whether NS1 and PA-X functionally interact and discovered that NS1 is required for PA-X to function effectively. This work significantly advances our understanding of influenza A virus host shutoff and identifies new potential targets for therapeutic interventions against influenza and further informs the development of improved live attenuated vaccines.
Collapse
Affiliation(s)
- Juliette Bougon
- Department of Microbiology & Immunology, Dalhousie University, Halifax, Nova Scotia, Canada
| | - Eileigh Kadijk
- Department of Microbiology & Immunology, Dalhousie University, Halifax, Nova Scotia, Canada
| | - Lucie Gallot-Lavallee
- Department of Biochemistry & Molecular Biology, Institute for Comparative Genomics, Dalhousie University, Halifax, Nova Scotia, Canada
| | - Bruce A. Curtis
- Department of Biochemistry & Molecular Biology, Institute for Comparative Genomics, Dalhousie University, Halifax, Nova Scotia, Canada
| | - Matthew Landers
- Department of Microbiology & Immunology, Dalhousie University, Halifax, Nova Scotia, Canada
| | - John M. Archibald
- Department of Biochemistry & Molecular Biology, Institute for Comparative Genomics, Dalhousie University, Halifax, Nova Scotia, Canada
| | - Denys A. Khaperskyy
- Department of Microbiology & Immunology, Dalhousie University, Halifax, Nova Scotia, Canada
| |
Collapse
|
3
|
Zabrodskaya Y, Tsvetkov V, Shurygina AP, Vasyliev K, Shaldzhyan A, Gorshkov A, Kuklin A, Fedorova N, Egorov V. How the immune mousetrap works: Structural evidence for the immunomodulatory action of a peptide from influenza NS1 protein. Biophys Chem 2024; 307:107176. [PMID: 38219420 DOI: 10.1016/j.bpc.2024.107176] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2023] [Accepted: 01/08/2024] [Indexed: 01/16/2024]
Abstract
One of the critical stages of the T-cell immune response is the dimerization of the intramembrane domains of T-cell receptors (TCR). Structural similarities between the immunosuppressive domains of viral proteins and the transmembrane domains of TCR have led several authors to hypothesize the mechanism of immune response suppression by highly pathogenic viruses: viral proteins embed themselves in the membrane and act on the intramembrane domain of the TCRalpha subunit, hindering its functional oligomerization. It has also been suggested that this mechanism is used by influenza A virus in NS1-mediated immunosuppression. We have shown that the peptide corresponding to the primary structure of the potential immunosuppressive domain of NS1 protein (G51) can reduce concanavalin A-induced proliferation of PBMC cells, as well as in vitro, G51 can affect the oligomerization of the core peptide corresponding to the intramembrane domain of TCR, using AFM and small-angle neutron scattering. The results obtained using in cellulo and in vitro model systems suggest the presence of functional interaction between the NS1 fragment and the intramembrane domain of the TCR alpha subunit. We have proposed a possible scheme for such interaction obtained by computer modeling. This suggests the existence of another NS1-mediated mechanism of immunosuppression in influenza.
Collapse
Affiliation(s)
- Yana Zabrodskaya
- Institute of Biomedical Systems and Biotechnology, Peter the Great Saint Petersburg Polytechnic University, 29 Ulitsa Polytechnicheskaya, St. Petersburg 194064, Russia; Smorodintsev Research Institute of Influenza, Russian Ministry of Health, 15/17 Ulitsa Prof. Popova, St. Petersburg 197376, Russia.
| | - Vladimir Tsvetkov
- Smorodintsev Research Institute of Influenza, Russian Ministry of Health, 15/17 Ulitsa Prof. Popova, St. Petersburg 197376, Russia; Federal Research and Clinical Center for Physical Chemical Medicine, 1a Ulitsa Malaya Pirogovskaya, Moscow 119435, Russia; Center for Mathematical Modeling in Drug Development, I.M. Sechenov First Moscow State Medical University, Moscow 119146, Russia
| | - Anna-Polina Shurygina
- Smorodintsev Research Institute of Influenza, Russian Ministry of Health, 15/17 Ulitsa Prof. Popova, St. Petersburg 197376, Russia
| | - Kirill Vasyliev
- Smorodintsev Research Institute of Influenza, Russian Ministry of Health, 15/17 Ulitsa Prof. Popova, St. Petersburg 197376, Russia
| | - Aram Shaldzhyan
- Smorodintsev Research Institute of Influenza, Russian Ministry of Health, 15/17 Ulitsa Prof. Popova, St. Petersburg 197376, Russia
| | - Andrey Gorshkov
- Smorodintsev Research Institute of Influenza, Russian Ministry of Health, 15/17 Ulitsa Prof. Popova, St. Petersburg 197376, Russia
| | - Alexander Kuklin
- International Intergovernmental Organization Joint Institute for Nuclear Research, 6 Ulitsa Joliot-Curie, Dubna 141980, Russia; Moscow Institute of Physics and Technology (State University), 9 Institutskiy pereulok, 141701 Dolgoprudny, Moscow Region, Russia
| | - Natalya Fedorova
- Petersburg Nuclear Physics Institute Named by B. P. Konstantinov of National Research Center, Kurchatov Institute, 1 mkr. Orlova Roshcha, Gatchina 188300, Russia
| | - Vladimir Egorov
- Institute of Experimental Medicine, 12 Ulitsa Akademika Pavlova, St. Petersburg 197376, Russia
| |
Collapse
|
4
|
Li R, Gao S, Chen H, Zhang X, Yang X, Zhao J, Wang Z. Virus usurps alternative splicing to clear the decks for infection. Virol J 2023; 20:131. [PMID: 37340420 DOI: 10.1186/s12985-023-02098-9] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2023] [Accepted: 06/12/2023] [Indexed: 06/22/2023] Open
Abstract
Since invasion, there will be a tug-of-war between host and virus to scramble cellular resources, for either restraining or facilitating infection. Alternative splicing (AS) is a conserved and critical mechanism of processing pre-mRNA into mRNAs to increase protein diversity in eukaryotes. Notably, this kind of post-transcriptional regulatory mechanism has gained appreciation since it is widely involved in virus infection. Here, we highlight the important roles of AS in regulating viral protein expression and how virus in turn hijacks AS to antagonize host immune response. This review will widen the understandings of host-virus interactions, be meaningful to innovatively elucidate viral pathogenesis, and provide novel targets for developing antiviral drugs in the future.
Collapse
Affiliation(s)
- Ruixue Li
- College of Veterinary Medicine, Henan Agricultural University, Zhengzhou, People's Republic of China
| | - Shenyan Gao
- College of Veterinary Medicine, Henan Agricultural University, Zhengzhou, People's Republic of China
| | - Huayuan Chen
- College of Veterinary Medicine, Henan Agricultural University, Zhengzhou, People's Republic of China
| | - Xiaozhan Zhang
- College of Veterinary Medicine, Henan University of Animal Husbandry and Economy, Zhengzhou, People's Republic of China
| | - Xia Yang
- College of Veterinary Medicine, Henan Agricultural University, Zhengzhou, People's Republic of China
| | - Jun Zhao
- College of Veterinary Medicine, Henan Agricultural University, Zhengzhou, People's Republic of China
| | - Zeng Wang
- College of Veterinary Medicine, Henan Agricultural University, Zhengzhou, People's Republic of China.
| |
Collapse
|
5
|
Zhu Y, Wang R, Zou J, Tian S, Yu L, Zhou Y, Ran Y, Jin M, Chen H, Zhou H. N6-methyladenosine reader protein YTHDC1 regulates influenza A virus NS segment splicing and replication. PLoS Pathog 2023; 19:e1011305. [PMID: 37053288 PMCID: PMC10146569 DOI: 10.1371/journal.ppat.1011305] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2022] [Revised: 04/28/2023] [Accepted: 03/20/2023] [Indexed: 04/15/2023] Open
Abstract
N6-methyladenosine (m6A) modification on viral RNAs has a profound impact on infectivity. m6A is also a highly pervasive modification for influenza viral RNAs. However, its role in virus mRNA splicing is largely unknown. Here, we identify the m6A reader protein YTHDC1 as a host factor that associates with influenza A virus NS1 protein and modulates viral mRNA splicing. YTHDC1 levels are enhanced by IAV infection. We demonstrate that YTHDC1 inhibits NS splicing by binding to an NS 3' splicing site and promotes IAV replication and pathogenicity in vitro and in vivo. Our results provide a mechanistic understanding of IAV-host interactions, a potential therapeutic target for blocking influenza virus infection, and a new avenue for the development of attenuated vaccines.
Collapse
Affiliation(s)
- Yinxing Zhu
- State Key Laboratory of Agricultural Microbiology, College of Veterinary Medicine, Huazhong Agricultural University, Wuhan, China
- Key Laboratory of Preventive Veterinary Medicine in Hubei Province, Cooperative Innovation Center for Sustainable Pig Production, Wuhan, China
| | - Ruifang Wang
- State Key Laboratory of Agricultural Microbiology, College of Veterinary Medicine, Huazhong Agricultural University, Wuhan, China
- Key Laboratory of Preventive Veterinary Medicine in Hubei Province, Cooperative Innovation Center for Sustainable Pig Production, Wuhan, China
| | - Jiahui Zou
- State Key Laboratory of Agricultural Microbiology, College of Veterinary Medicine, Huazhong Agricultural University, Wuhan, China
- Key Laboratory of Preventive Veterinary Medicine in Hubei Province, Cooperative Innovation Center for Sustainable Pig Production, Wuhan, China
| | - Shan Tian
- State Key Laboratory of Agricultural Microbiology, College of Veterinary Medicine, Huazhong Agricultural University, Wuhan, China
- Key Laboratory of Preventive Veterinary Medicine in Hubei Province, Cooperative Innovation Center for Sustainable Pig Production, Wuhan, China
| | - Luyao Yu
- State Key Laboratory of Agricultural Microbiology, College of Veterinary Medicine, Huazhong Agricultural University, Wuhan, China
- Key Laboratory of Preventive Veterinary Medicine in Hubei Province, Cooperative Innovation Center for Sustainable Pig Production, Wuhan, China
| | - Yuanbao Zhou
- State Key Laboratory of Agricultural Microbiology, College of Veterinary Medicine, Huazhong Agricultural University, Wuhan, China
- Key Laboratory of Preventive Veterinary Medicine in Hubei Province, Cooperative Innovation Center for Sustainable Pig Production, Wuhan, China
| | - Ying Ran
- State Key Laboratory of Agricultural Microbiology, College of Veterinary Medicine, Huazhong Agricultural University, Wuhan, China
- Key Laboratory of Preventive Veterinary Medicine in Hubei Province, Cooperative Innovation Center for Sustainable Pig Production, Wuhan, China
| | - Meilin Jin
- State Key Laboratory of Agricultural Microbiology, College of Veterinary Medicine, Huazhong Agricultural University, Wuhan, China
- Key Laboratory of Preventive Veterinary Medicine in Hubei Province, Cooperative Innovation Center for Sustainable Pig Production, Wuhan, China
| | - Huanchun Chen
- State Key Laboratory of Agricultural Microbiology, College of Veterinary Medicine, Huazhong Agricultural University, Wuhan, China
- Key Laboratory of Preventive Veterinary Medicine in Hubei Province, Cooperative Innovation Center for Sustainable Pig Production, Wuhan, China
| | - Hongbo Zhou
- State Key Laboratory of Agricultural Microbiology, College of Veterinary Medicine, Huazhong Agricultural University, Wuhan, China
- Key Laboratory of Preventive Veterinary Medicine in Hubei Province, Cooperative Innovation Center for Sustainable Pig Production, Wuhan, China
| |
Collapse
|
6
|
Han YJ, Lee KM, Wu GH, Gong YN, Dutta A, Shih SR. Targeting influenza A virus by splicing inhibitor herboxidiene reveals the importance of subtype-specific signatures around splice sites. J Biomed Sci 2023; 30:10. [PMID: 36737756 PMCID: PMC9895974 DOI: 10.1186/s12929-023-00897-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2022] [Accepted: 01/05/2023] [Indexed: 02/05/2023] Open
Abstract
BACKGROUND The association between M segment splicing and pathogenicity remains ambiguous in human influenza A viruses. In this study, we aimed to investigate M splicing in various human influenza A viruses and characterize its physiological roles by applying the splicing inhibitor, herboxidiene. METHODS We examined the M splicing of human H1N1 and H3N2 viruses by comparing three H1N1 and H3N2 strains, respectively, through reverse transcriptase-polymerase chain reaction (RT-PCR) analyses. We randomly selected M sequences of human H1N1, H2N2, and H3N2 viruses isolated from 1933 to 2020 and examined their phylogenetic relationships. Next, we determined the effects of single nucleotide variations on M splicing by generating mutant viruses harboring the 55C/T variant through reverse genetics. To confirm the importance of M2 splicing in the replication of H1N1 and H3N2, we treated infected cells with splicing inhibitor herboxidiene and analyzed the viral growth using plaque assay. To explore the physiological role of the various levels of M2 protein in pathogenicity, we challenged C57BL/6 mice with the H1N1 WSN wild-type strain, mutant H1N1 (55T), and chimeric viruses including H1N1 + H3wt and H1N1 + H3mut. One-tailed paired t-test was used for virus titer calculation and multiple comparisons between groups were performed using two-way analysis of variance. RESULTS M sequence splice site analysis revealed an evolutionarily conserved single nucleotide variant C55T in H3N2, which impaired M2 expression and was accompanied by collinear M1 and mRNA3 production. Aberrant M2 splicing resulted from splice-site selection rather than a general defect in the splicing process. The C55T substitution significantly reduced both M2 mRNA and protein levels regardless of the virus subtype. Consequently, herboxidiene treatment dramatically decreased both the H1N1 and H3N2 virus titers. However, a lower M2 expression only attenuated H1N1 virus replication and in vivo pathogenicity. This attenuated phenotype was restored by M replacement of H3N2 M in a chimeric H1N1 virus, despite low M2 levels. CONCLUSIONS The discrepancy in M2-dependence emphasizes the importance of M2 in human influenza A virus pathogenicity, which leads to subtype-specific evolution. Our findings provide insights into virus adaptation processes in humans and highlights splicing regulation as a potential antiviral target.
Collapse
Affiliation(s)
- Yi-Ju Han
- grid.145695.a0000 0004 1798 0922Graduate Institute of Biomedical Science, College of Medicine, Chang Gung University, Taoyuan, Taiwan ,grid.145695.a0000 0004 1798 0922Research Center of Emerging Virus Infection, Division of Biotechnology, College of Medicine, Chang Gung University, Taoyuan, Taiwan
| | - Kuo-Ming Lee
- grid.145695.a0000 0004 1798 0922Research Center of Emerging Virus Infection, Division of Biotechnology, College of Medicine, Chang Gung University, Taoyuan, Taiwan ,grid.145695.a0000 0004 1798 0922International Master Degree Program for Molecular Medicine in Emerging Viral Infections, College of Medicine, Chang Gung University, Taoyuan, Taiwan ,grid.454211.70000 0004 1756 999XDivision of Infectious Diseases, Department of Pediatrics, Linkou Chang Gung Memorial Hospital, Taoyuan, Taiwan
| | - Guan-Hong Wu
- grid.145695.a0000 0004 1798 0922Graduate Institute of Biomedical Science, College of Medicine, Chang Gung University, Taoyuan, Taiwan ,grid.145695.a0000 0004 1798 0922Research Center of Emerging Virus Infection, Division of Biotechnology, College of Medicine, Chang Gung University, Taoyuan, Taiwan
| | - Yu-Nong Gong
- grid.145695.a0000 0004 1798 0922Research Center of Emerging Virus Infection, Division of Biotechnology, College of Medicine, Chang Gung University, Taoyuan, Taiwan ,grid.454211.70000 0004 1756 999XDivision of Infectious Diseases, Department of Pediatrics, Linkou Chang Gung Memorial Hospital, Taoyuan, Taiwan ,grid.454211.70000 0004 1756 999XDepartment of Laboratory Science, Linkou Chang Gung Memorial Hospital, Taoyuan, Taiwan
| | - Avijit Dutta
- grid.454211.70000 0004 1756 999XDivision of Infectious Diseases, Department of Medicine, Linkou Chang Gung Memorial Hospital, Taoyuan, Taiwan
| | - Shin-Ru Shih
- Research Center of Emerging Virus Infection, Division of Biotechnology, College of Medicine, Chang Gung University, Taoyuan, Taiwan. .,Department of Laboratory Science, Linkou Chang Gung Memorial Hospital, Taoyuan, Taiwan. .,Department of Medical Biotechnology and Laboratory Science, College of Medicine, Chang Gung University, Taoyuan, Taiwan. .,Research Center for Chinese Herbal Medicine, Chang Gung University of Science and Technology, Taoyuan, Taiwan. .,Research Center for Food and Cosmetic Safety, Chang Gung University of Science and Technology, Taoyuan, Taiwan. .,Graduate Institute of Health Industry Technology, College of Human Ecology, Chang Gung University of Science and Technology, Taoyuan, Taiwan.
| |
Collapse
|
7
|
Wang X, Lin L, Yu Y, Yan Y, Ojha NK, Zhou J. The N-terminal residual arginine 19 of influenza A virus NS1 protein is required for its nuclear localization and RNA binding. Vet Microbiol 2020; 251:108895. [PMID: 33126184 DOI: 10.1016/j.vetmic.2020.108895] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2020] [Accepted: 10/11/2020] [Indexed: 11/30/2022]
Abstract
RNA binding ability and cellular distribution are important for nonstructural protein 1 (NS1) of influenza A virus to act as a viral regulatory factor to control virus life cycle. In this study, we identified that the N-terminal residues 19-21 of NS1 are a highly conserved motif depending on all the available NS1 full length sequence of H5N1 influenza A virus from NCBI database. Site-directed mutation analysis demonstrated that the R19 residue of NS1 is critical for its RNA binding and nuclear localization. Furthermore, the residue R19 of NS1 was identified to be critical for regulating M1 mRNA splicing and NS1 nuclear export. Biological analysis of the rescued viruses indicated that the R19A mutation of NS1 did not interfere the replication of H5N1 virus during infection and attenuated the virulence of H5N1 virus in mice.
Collapse
Affiliation(s)
- Xingbo Wang
- MOA Key Laboratory of Animal Virology, Center for Veterinary Sciences, Zhejiang University, Hangzhou, 310058, PR China
| | - Lulu Lin
- MOA Key Laboratory of Animal Virology, Center for Veterinary Sciences, Zhejiang University, Hangzhou, 310058, PR China
| | - Yang Yu
- MOA Key Laboratory of Animal Virology, Center for Veterinary Sciences, Zhejiang University, Hangzhou, 310058, PR China
| | - Yan Yan
- MOA Key Laboratory of Animal Virology, Center for Veterinary Sciences, Zhejiang University, Hangzhou, 310058, PR China
| | - Nishant Kumar Ojha
- MOA Key Laboratory of Animal Virology, Center for Veterinary Sciences, Zhejiang University, Hangzhou, 310058, PR China
| | - Jiyong Zhou
- MOA Key Laboratory of Animal Virology, Center for Veterinary Sciences, Zhejiang University, Hangzhou, 310058, PR China; State Key Laboratory for Diagnosis and Treatment of Infectious Diseases, First Affiliated Hospital, Zhejiang University, Hangzhou, 310003, PR China.
| |
Collapse
|
8
|
Nahand JS, Jamshidi S, Hamblin MR, Mahjoubin-Tehran M, Vosough M, Jamali M, Khatami A, Moghoofei M, Baghi HB, Mirzaei H. Circular RNAs: New Epigenetic Signatures in Viral Infections. Front Microbiol 2020; 11:1853. [PMID: 32849445 PMCID: PMC7412987 DOI: 10.3389/fmicb.2020.01853] [Citation(s) in RCA: 43] [Impact Index Per Article: 10.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2020] [Accepted: 07/15/2020] [Indexed: 12/20/2022] Open
Abstract
Covalent closed circular RNAs (circRNAs) can act as a bridge between non-coding RNAs and coding messenger RNAs. CircRNAs are generated by a back-splicing mechanism during post-transcriptional processing and are abundantly expressed in eukaryotic cells. CircRNAs can act via the modulation of RNA transcription and protein production, and by the sponging of microRNAs (miRNAs). CircRNAs are now thought to be involved in many different biological and pathological processes. Some studies have suggested that the expression of host circRNAs is dysregulated in several types of virus-infected cells, compared to control cells. It is highly likely that viruses can use these molecules for their own purposes. In addition, some viral genes are able to produce viral circRNAs (VcircRNA) by a back-splicing mechanism. However, the viral genes that encode VcircRNAs, and their functions, are poorly studied. In this review, we highlight some new findings about the interaction of host circRNAs and viral infection. Moreover, the potential of VcircRNAs derived from the virus itself, to act as biomarkers and therapeutic targets is summarized.
Collapse
Affiliation(s)
- Javid Sadri Nahand
- Department of Virology, Faculty of Medicine, Iran University of Medical Sciences, Tehran, Iran.,Student Research Committee, Iran University of Medical Sciences, Tehran, Iran
| | - Sogol Jamshidi
- Department of Virology, Faculty of Medicine, Iran University of Medical Sciences, Tehran, Iran
| | - Michael R Hamblin
- Wellman Center for Photomedicine, Massachusetts General Hospital, Boston, MA, United States.,Department of Dermatology, Harvard Medical School, Boston, MA, United States.,Laser Research Centre, Faculty of Health Science, University of Johannesburg, Doornfontein, South Africa
| | - Maryam Mahjoubin-Tehran
- Student Research Committee, Mashhad University of Medical Sciences, Mashhad, Iran.,Department of Medical Biotechnology, Faculty of Medicine, Mashhad University of Medical Sciences, Mashhad, Iran
| | - Massoud Vosough
- Department of Regenerative Medicine, Cell Science Research Center, Royan Institute for Stem Cell Biology and Technology, ACECR, Tehran, Iran
| | - Marzieh Jamali
- Department of Gynecology and Obstetrics, Mahdieh Hospital, Shahid Beheshti University of Medical Sciences, Tehran, Iran
| | - Alireza Khatami
- Department of Virology, Faculty of Medicine, Iran University of Medical Sciences, Tehran, Iran.,Student Research Committee, Iran University of Medical Sciences, Tehran, Iran
| | - Mohsen Moghoofei
- Department of Microbiology, Faculty of Medicine, Kermanshah University of Medical Sciences, Kermanshah, Iran
| | - Hossein Bannazadeh Baghi
- Infectious and Tropical Diseases Research Center, Tabriz University of Medical Sciences, Tabriz, Iran.,Immunology Research Center, Tabriz University of Medical Sciences, Tabriz, Iran
| | - Hamed Mirzaei
- Research Center for Biochemistry and Nutrition in Metabolic Diseases, Kashan University of Medical Sciences, Kashan, Iran
| |
Collapse
|
9
|
Differential Modulation of Innate Immune Responses in Human Primary Cells by Influenza A Viruses Carrying Human or Avian Nonstructural Protein 1. J Virol 2019; 94:JVI.00999-19. [PMID: 31597767 PMCID: PMC6912104 DOI: 10.1128/jvi.00999-19] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2019] [Accepted: 09/29/2019] [Indexed: 12/22/2022] Open
Abstract
Influenza A viruses (IAVs) cause seasonal epidemics which result in an important health and economic burden. Wild aquatic birds are the natural host of IAV. However, IAV can infect diverse hosts, including humans, domestic poultry, pigs, and others. IAVs circulating in animals occasionally cross the species barrier, infecting humans, which results in mild to very severe disease. In some cases, these viruses can acquire the ability to be transmitted among humans and initiate a pandemic. The nonstructural 1 (NS1) protein of IAV is an important antagonist of the innate immune response. In this study, using recombinant viruses and primary human cells, we show that NS1 proteins from human and avian hosts show intrinsic differences in the modulation of the innate immunity in human dendritic cells and epithelial cells, as well as different cellular localization dynamics in infected cells. The influenza A virus (IAV) nonstructural protein 1 (NS1) contributes to disease pathogenesis through the inhibition of host innate immune responses. Dendritic cells (DCs) release interferons (IFNs) and proinflammatory cytokines and promote adaptive immunity upon viral infection. In order to characterize the strain-specific effects of IAV NS1 on human DC activation, we infected human DCs with a panel of recombinant viruses with the same backbone (A/Puerto Rico/08/1934) expressing different NS1 proteins from human and avian origin. We found that these viruses induced a clearly distinct phenotype in DCs. Specifically, viruses expressing NS1 from human IAV (either H1N1 or H3N2) induced higher levels of expression of type I (IFN-α and IFN-β) and type III (IFN-λ1 to IFNλ3) IFNs than viruses expressing avian IAV NS1 proteins (H5N1, H7N9, and H7N2), but the differences observed in the expression levels of proinflammatory cytokines like tumor necrosis factor alpha (TNF-α) or interleukin-6 (IL-6) were not significant. In addition, using imaging flow cytometry, we found that human and avian NS1 proteins segregate based on their subcellular trafficking dynamics, which might be associated with the different innate immune profile induced in DCs by viruses expressing those NS1 proteins. Innate immune responses induced by our panel of IAV recombinant viruses were also characterized in normal human bronchial epithelial cells, and the results were consistent with those in DCs. Altogether, our results reveal an increased ability of NS1 from avian viruses to antagonize innate immune responses in human primary cells compared to the ability of NS1 from human viruses, which could contribute to the severe disease induced by avian IAV in humans. IMPORTANCE Influenza A viruses (IAVs) cause seasonal epidemics which result in an important health and economic burden. Wild aquatic birds are the natural host of IAV. However, IAV can infect diverse hosts, including humans, domestic poultry, pigs, and others. IAVs circulating in animals occasionally cross the species barrier, infecting humans, which results in mild to very severe disease. In some cases, these viruses can acquire the ability to be transmitted among humans and initiate a pandemic. The nonstructural 1 (NS1) protein of IAV is an important antagonist of the innate immune response. In this study, using recombinant viruses and primary human cells, we show that NS1 proteins from human and avian hosts show intrinsic differences in the modulation of the innate immunity in human dendritic cells and epithelial cells, as well as different cellular localization dynamics in infected cells.
Collapse
|
10
|
Bogdanow B, Wang X, Eichelbaum K, Sadewasser A, Husic I, Paki K, Budt M, Hergeselle M, Vetter B, Hou J, Chen W, Wiebusch L, Meyer IM, Wolff T, Selbach M. The dynamic proteome of influenza A virus infection identifies M segment splicing as a host range determinant. Nat Commun 2019; 10:5518. [PMID: 31797923 PMCID: PMC6892822 DOI: 10.1038/s41467-019-13520-8] [Citation(s) in RCA: 31] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2018] [Accepted: 11/12/2019] [Indexed: 12/16/2022] Open
Abstract
Pandemic influenza A virus (IAV) outbreaks occur when strains from animal reservoirs acquire the ability to infect and spread among humans. The molecular basis of this species barrier is incompletely understood. Here we combine metabolic pulse labeling and quantitative proteomics to monitor protein synthesis upon infection of human cells with a human- and a bird-adapted IAV strain and observe striking differences in viral protein synthesis. Most importantly, the matrix protein M1 is inefficiently produced by the bird-adapted strain. We show that impaired production of M1 from bird-adapted strains is caused by increased splicing of the M segment RNA to alternative isoforms. Strain-specific M segment splicing is controlled by the 3' splice site and functionally important for permissive infection. In silico and biochemical evidence shows that avian-adapted M segments have evolved different conserved RNA structure features than human-adapted sequences. Thus, we identify M segment RNA splicing as a viral host range determinant.
Collapse
Affiliation(s)
- Boris Bogdanow
- Max Delbrück Center for Molecular Medicine, Robert-Rössle-Strasse 10, 13125, Berlin, Germany
- Unit 17 "Influenza and other Respiratory Viruses", Robert Koch Institut, Seestrase 10, 13353, Berlin, Germany
- Structural Interactomics, Leibniz-Forschungsinstitut für Molekulare Pharmakologie, Robert-Rössle-Strasse 10, 13125, Berlin, Germany
| | - Xi Wang
- Max Delbrück Center for Molecular Medicine, Robert-Rössle-Strasse 10, 13125, Berlin, Germany
- Division of Theoretical Systems Biology, German Cancer Research Center, 69120, Heidelberg, Germany
| | - Katrin Eichelbaum
- Max Delbrück Center for Molecular Medicine, Robert-Rössle-Strasse 10, 13125, Berlin, Germany
| | - Anne Sadewasser
- Unit 17 "Influenza and other Respiratory Viruses", Robert Koch Institut, Seestrase 10, 13353, Berlin, Germany
| | - Immanuel Husic
- Max Delbrück Center for Molecular Medicine, Robert-Rössle-Strasse 10, 13125, Berlin, Germany
| | - Katharina Paki
- Unit 17 "Influenza and other Respiratory Viruses", Robert Koch Institut, Seestrase 10, 13353, Berlin, Germany
| | - Matthias Budt
- Unit 17 "Influenza and other Respiratory Viruses", Robert Koch Institut, Seestrase 10, 13353, Berlin, Germany
| | - Martha Hergeselle
- Max Delbrück Center for Molecular Medicine, Robert-Rössle-Strasse 10, 13125, Berlin, Germany
| | - Barbara Vetter
- Labor für Pädiatrische Molekularbiologie, Charité Universitätsmedizin Berlin, Augustenburger Platz 1, 13353, Berlin, Germany
| | - Jingyi Hou
- Max Delbrück Center for Molecular Medicine, Robert-Rössle-Strasse 10, 13125, Berlin, Germany
| | - Wei Chen
- Max Delbrück Center for Molecular Medicine, Robert-Rössle-Strasse 10, 13125, Berlin, Germany
- Department of Biology, Southern University of Science and Technology, Xuanyuan Road 1088, 518055, Shenzhen, China
| | - Lüder Wiebusch
- Labor für Pädiatrische Molekularbiologie, Charité Universitätsmedizin Berlin, Augustenburger Platz 1, 13353, Berlin, Germany
| | - Irmtraud M Meyer
- Max Delbrück Center for Molecular Medicine, Robert-Rössle-Strasse 10, 13125, Berlin, Germany
- Freie Universität Berlin, Department of Biology, Chemistry, Pharmacy Institute of Chemistry and Biochemistry, Thielallee 63, 14195, Berlin, Germany
| | - Thorsten Wolff
- Unit 17 "Influenza and other Respiratory Viruses", Robert Koch Institut, Seestrase 10, 13353, Berlin, Germany
| | - Matthias Selbach
- Max Delbrück Center for Molecular Medicine, Robert-Rössle-Strasse 10, 13125, Berlin, Germany.
- Charité Universitätsmedizin Berlin, 10117, Berlin, Germany.
| |
Collapse
|
11
|
Mezhenskaya D, Isakova-Sivak I, Rudenko L. M2e-based universal influenza vaccines: a historical overview and new approaches to development. J Biomed Sci 2019; 26:76. [PMID: 31629405 PMCID: PMC6800501 DOI: 10.1186/s12929-019-0572-3] [Citation(s) in RCA: 69] [Impact Index Per Article: 13.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2019] [Accepted: 10/01/2019] [Indexed: 01/04/2023] Open
Abstract
The influenza A virus was isolated for the first time in 1931, and the first attempts to develop a vaccine against the virus began soon afterwards. In addition to causing seasonal epidemics, influenza viruses can cause pandemics at random intervals, which are very hard to predict. Vaccination is the most effective way of preventing the spread of influenza infection. However, seasonal vaccination is ineffective against pandemic influenza viruses because of antigenic differences, and it takes approximately six months from isolation of a new virus to develop an effective vaccine. One of the possible ways to fight the emergence of pandemics may be by using a new type of vaccine, with a long and broad spectrum of action. The extracellular domain of the M2 protein (M2e) of influenza A virus is a conservative region, and an attractive target for a universal influenza vaccine. This review gives a historical overview of the study of M2 protein, and summarizes the latest developments in the preparation of M2e-based universal influenza vaccines.
Collapse
Affiliation(s)
- Daria Mezhenskaya
- Department of Virology, Institute of Experimental Medicine, 12 Acad. Pavlov Street, St. Petersburg, 197376, Russia
| | - Irina Isakova-Sivak
- Department of Virology, Institute of Experimental Medicine, 12 Acad. Pavlov Street, St. Petersburg, 197376, Russia.
| | - Larisa Rudenko
- Department of Virology, Institute of Experimental Medicine, 12 Acad. Pavlov Street, St. Petersburg, 197376, Russia
| |
Collapse
|
12
|
Species-Specific Host-Virus Interactions: Implications for Viral Host Range and Virulence. Trends Microbiol 2019; 28:46-56. [PMID: 31597598 DOI: 10.1016/j.tim.2019.08.007] [Citation(s) in RCA: 56] [Impact Index Per Article: 11.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2019] [Revised: 08/11/2019] [Accepted: 08/19/2019] [Indexed: 01/09/2023]
Abstract
A growing number of studies indicate that host species-specific and virus strain-specific interactions of viral molecules with the host innate immune system play a pivotal role in determining virus host range and virulence. Because interacting proteins are likely constrained in their evolution, mutations that are selected to improve virus replication in one species may, by chance, alter the ability of a viral antagonist to inhibit immune responses in hosts the virus has not yet encountered. Based on recent findings of host-species interactions of poxvirus, herpesvirus, and influenza virus proteins, we propose a model for viral fitness and host range which considers the full interactome between a specific host species and a virus, resulting from the combination of all interactions, positive and negative, that influence whether a virus can productively infect a cell and cause disease in different hosts.
Collapse
|
13
|
Artarini A, Meyer M, Shin YJ, Huber K, Hilz N, Bracher F, Eros D, Orfi L, Keri G, Goedert S, Neuenschwander M, von Kries J, Domovich-Eisenberg Y, Dekel N, Szabadkai I, Lebendiker M, Horváth Z, Danieli T, Livnah O, Moncorgé O, Frise R, Barclay W, Meyer TF, Karlas A. Regulation of influenza A virus mRNA splicing by CLK1. Antiviral Res 2019; 168:187-196. [PMID: 31176694 DOI: 10.1016/j.antiviral.2019.06.003] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2018] [Revised: 06/04/2019] [Accepted: 06/06/2019] [Indexed: 10/26/2022]
Abstract
Influenza A virus carries eight negative single-stranded RNAs and uses spliced mRNAs to increase the number of proteins produced from them. Several genome-wide screens for essential host factors for influenza A virus replication revealed a necessity for splicing and splicing-related factors, including Cdc-like kinase 1 (CLK1). This CLK family kinase plays a role in alternative splicing regulation through phosphorylation of serine-arginine rich (SR) proteins. To examine the influence that modulation of splicing regulation has on influenza infection, we analyzed the effect of CLK1 knockdown and inhibition. CLK1 knockdown in A549 cells reduced influenza A/WSN/33 virus replication and increased the level of splicing of segment 7, which encodes the viral M1 and M2 proteins. CLK1-/- mice infected with influenza A/England/195/2009 (H1N1pdm09) virus supported lower levels of virus replication than wild-type mice. Screening of newly developed CLK inhibitors revealed several compounds that have an effect on the level of splicing of influenza A gene segment M in different models and decrease influenza A/WSN/33 virus replication in A549 cells. The promising inhibitor KH-CB19, an indole-based enaminonitrile with unique binding mode for CLK1, and its even more selective analogue NIH39 showed high specificity towards CLK1 and had a similar effect on influenza mRNA splicing regulation. Taken together, our findings indicate that targeting host factors that regulate splicing of influenza mRNAs may represent a novel therapeutic approach.
Collapse
Affiliation(s)
- Anita Artarini
- Max Planck Institute for Infection Biology, Department of Molecular Biology, Charitéplatz 1, 10117, Berlin, Germany
| | - Michael Meyer
- Steinbeis Innovation, Center for Systems Biomedicine, 14612, Falkensee, Germany
| | - Yu Jin Shin
- Max Planck Institute for Infection Biology, Department of Molecular Biology, Charitéplatz 1, 10117, Berlin, Germany
| | - Kilian Huber
- Department of Pharmacy, Center for Drug Research, Ludwig-Maximilians-University, Butenandtstrasse 5-13, 81377, Munich, Germany
| | - Nikolaus Hilz
- Department of Pharmacy, Center for Drug Research, Ludwig-Maximilians-University, Butenandtstrasse 5-13, 81377, Munich, Germany
| | - Franz Bracher
- Department of Pharmacy, Center for Drug Research, Ludwig-Maximilians-University, Butenandtstrasse 5-13, 81377, Munich, Germany
| | - Daniel Eros
- Vichem Chemie Research Ltd., Herman Ottó 15, H-1022, Budapest, Hungary
| | - Laszlo Orfi
- Vichem Chemie Research Ltd., Herman Ottó 15, H-1022, Budapest, Hungary; Department of Pharmaceutical Chemistry, Semmelweis University, Budapest, 1092, Hungary
| | - Gyorgy Keri
- Vichem Chemie Research Ltd., Herman Ottó 15, H-1022, Budapest, Hungary
| | - Sigrid Goedert
- Max Planck Institute for Infection Biology, Department of Molecular Biology, Charitéplatz 1, 10117, Berlin, Germany
| | - Martin Neuenschwander
- Leibniz Institute for Molecular Pharmacology, Robert-Roessle Str. 10, D-13125, Berlin, Germany
| | - Jens von Kries
- Leibniz Institute for Molecular Pharmacology, Robert-Roessle Str. 10, D-13125, Berlin, Germany
| | - Yael Domovich-Eisenberg
- The Wolfson Centre for Applied Structural Biology, The Hebrew University of Jerusalem, Edmond J. Safra Campus at Givat Ram, 91904, Jerusalem, Israel
| | - Noa Dekel
- The Wolfson Centre for Applied Structural Biology, The Hebrew University of Jerusalem, Edmond J. Safra Campus at Givat Ram, 91904, Jerusalem, Israel
| | - István Szabadkai
- Vichem Chemie Research Ltd., Herman Ottó 15, H-1022, Budapest, Hungary
| | - Mario Lebendiker
- The Wolfson Centre for Applied Structural Biology, The Hebrew University of Jerusalem, Edmond J. Safra Campus at Givat Ram, 91904, Jerusalem, Israel
| | - Zoltán Horváth
- Vichem Chemie Research Ltd., Herman Ottó 15, H-1022, Budapest, Hungary
| | - Tsafi Danieli
- The Wolfson Centre for Applied Structural Biology, The Hebrew University of Jerusalem, Edmond J. Safra Campus at Givat Ram, 91904, Jerusalem, Israel
| | - Oded Livnah
- The Wolfson Centre for Applied Structural Biology, The Hebrew University of Jerusalem, Edmond J. Safra Campus at Givat Ram, 91904, Jerusalem, Israel
| | - Olivier Moncorgé
- Imperial College London, Section of Virology, Faculty of Medicine, St. Mary's Campus, Norfolk Place, London, W2 1PG, UK
| | - Rebecca Frise
- Imperial College London, Section of Virology, Faculty of Medicine, St. Mary's Campus, Norfolk Place, London, W2 1PG, UK
| | - Wendy Barclay
- Imperial College London, Section of Virology, Faculty of Medicine, St. Mary's Campus, Norfolk Place, London, W2 1PG, UK
| | - Thomas F Meyer
- Max Planck Institute for Infection Biology, Department of Molecular Biology, Charitéplatz 1, 10117, Berlin, Germany.
| | - Alexander Karlas
- Max Planck Institute for Infection Biology, Department of Molecular Biology, Charitéplatz 1, 10117, Berlin, Germany.
| |
Collapse
|
14
|
Thompson MG, Lynch KW. Functional and Mechanistic Interplay of Host and Viral Alternative Splicing Regulation during Influenza Infection. COLD SPRING HARBOR SYMPOSIA ON QUANTITATIVE BIOLOGY 2019; 84:123-131. [PMID: 32703803 DOI: 10.1101/sqb.2019.84.039040] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
Abstract
Alternative splicing is a pervasive gene regulatory mechanism utilized by both mammalian cells and viruses to expand their genomic coding capacity. The process of splicing and the RNA sequences that guide this process are the same in mammalian and viral transcripts; however, viruses lack the splicing machinery and therefore must usurp both the host spliceosome and many of the associated regulatory proteins in order to correctly process their genes. Here, we use the example of the influenza A virus to both describe how viruses utilize host splicing factors to regulate their own splicing and provide examples of how viral infection can, in turn, alter host splicing. Importantly, we show that at least some of the viral-induced changes in host splicing occur in genes that alter the efficiency of influenza replication. We emphasize the importance of increased understanding of the mechanistic interplay between host and viral splicing, and its functional consequences, in uncovering potential antiviral vulnerabilities.
Collapse
Affiliation(s)
- Matthew G Thompson
- Department of Biochemistry and Biophysics Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania 19104, USA
| | - Kristen W Lynch
- Department of Biochemistry and Biophysics Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania 19104, USA
| |
Collapse
|
15
|
Dou D, Revol R, Östbye H, Wang H, Daniels R. Influenza A Virus Cell Entry, Replication, Virion Assembly and Movement. Front Immunol 2018; 9:1581. [PMID: 30079062 PMCID: PMC6062596 DOI: 10.3389/fimmu.2018.01581] [Citation(s) in RCA: 295] [Impact Index Per Article: 49.2] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2018] [Accepted: 06/26/2018] [Indexed: 12/20/2022] Open
Abstract
Influenza viruses replicate within the nucleus of the host cell. This uncommon RNA virus trait provides influenza with the advantage of access to the nuclear machinery during replication. However, it also increases the complexity of the intracellular trafficking that is required for the viral components to establish a productive infection. The segmentation of the influenza genome makes these additional trafficking requirements especially challenging, as each viral RNA (vRNA) gene segment must navigate the network of cellular membrane barriers during the processes of entry and assembly. To accomplish this goal, influenza A viruses (IAVs) utilize a combination of viral and cellular mechanisms to coordinate the transport of their proteins and the eight vRNA gene segments in and out of the cell. The aim of this review is to present the current mechanistic understanding for how IAVs facilitate cell entry, replication, virion assembly, and intercellular movement, in an effort to highlight some of the unanswered questions regarding the coordination of the IAV infection process.
Collapse
Affiliation(s)
- Dan Dou
- Department of Biochemistry and Biophysics, Stockholm University, Stockholm, Sweden
| | - Rebecca Revol
- Department of Biochemistry and Biophysics, Stockholm University, Stockholm, Sweden
| | - Henrik Östbye
- Department of Biochemistry and Biophysics, Stockholm University, Stockholm, Sweden
| | - Hao Wang
- Department of Biochemistry and Biophysics, Stockholm University, Stockholm, Sweden
| | - Robert Daniels
- Department of Biochemistry and Biophysics, Stockholm University, Stockholm, Sweden
| |
Collapse
|
16
|
Sheng Z, Liu R, Yu J, Ran Z, Newkirk SJ, An W, Li F, Wang D. Identification and characterization of viral defective RNA genomes in influenza B virus. J Gen Virol 2018; 99:475-488. [PMID: 29458654 DOI: 10.1099/jgv.0.001018] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023] Open
Abstract
Influenza B virus (FLUBV) is an important pathogen that infects humans and causes seasonal influenza epidemics. To date, little is known about defective genomes of FLUBV and their roles in viral replication. In this study, by using a next-generation sequencing approach, we analyzed total mRNAs extracted from A549 cells infected with B/Brisbane/60/2008 virus (Victoria lineage), and identified four defective FLUBV genomes with two (PB1∆A and PB1∆B) from the polymerase basic subunit 1 (PB1) segment and the other two (M∆A and M∆B) from the matrix (M) protein-encoding segment. These defective genomes contained significant deletions in the central regions with each having the potential for encoding a novel polypeptide. Significantly, each of the discovered defective RNAs can potently inhibit the replication of B/Yamanashi/166/98 (Yamagata lineage). Furthermore, PB1∆A was able to interfere modestly with influenza A virus (FLUAV) replication. In summary, our study provides important initial insights into FLUBV defective-interfering genomes, which can be further explored to achieve better understanding of the replication, pathogenesis and evolution of FLUBV.
Collapse
Affiliation(s)
- Zizhang Sheng
- Department of Biochemistry and Molecular Biophysics, Columbia University, New York, NY, USA
| | - Runxia Liu
- Department of Biology and Microbiology, South Dakota State University, Brookings, SD, USA
| | - Jieshi Yu
- Department of Biology and Microbiology, South Dakota State University, Brookings, SD, USA
| | - Zhiguang Ran
- Department of Biology and Microbiology, South Dakota State University, Brookings, SD, USA.,Department of Veterinary and Biomedical Sciences, South Dakota State University, Brookings, SD, USA
| | - Simon J Newkirk
- Department of Pharmaceutical Sciences, South Dakota State University, Brookings, SD, USA
| | - Wenfeng An
- Department of Pharmaceutical Sciences, South Dakota State University, Brookings, SD, USA
| | - Feng Li
- Department of Biology and Microbiology, South Dakota State University, Brookings, SD, USA.,Department of Veterinary and Biomedical Sciences, South Dakota State University, Brookings, SD, USA.,BioSystems Networks and Translational Research (BioSNTR), Brookings, SD, USA
| | - Dan Wang
- BioSystems Networks and Translational Research (BioSNTR), Brookings, SD, USA.,Department of Biology and Microbiology, South Dakota State University, Brookings, SD, USA
| |
Collapse
|
17
|
Influenza A Virus NS1 Protein Promotes Efficient Nuclear Export of Unspliced Viral M1 mRNA. J Virol 2017; 91:JVI.00528-17. [PMID: 28515301 PMCID: PMC5651720 DOI: 10.1128/jvi.00528-17] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2017] [Accepted: 05/10/2017] [Indexed: 01/08/2023] Open
Abstract
Influenza A virus mRNAs are transcribed by the viral RNA-dependent RNA polymerase in the cell nucleus before being exported to the cytoplasm for translation. Segment 7 produces two major transcripts: an unspliced mRNA that encodes the M1 matrix protein and a spliced transcript that encodes the M2 ion channel. Export of both mRNAs is dependent on the cellular NXF1/TAP pathway, but it is unclear how they are recruited to the export machinery or how the intron-containing but unspliced M1 mRNA bypasses the normal quality-control checkpoints. Using fluorescent in situ hybridization to monitor segment 7 mRNA localization, we found that cytoplasmic accumulation of unspliced M1 mRNA was inefficient in the absence of NS1, both in the context of segment 7 RNPs reconstituted by plasmid transfection and in mutant virus-infected cells. This effect was independent of any major effect on steady-state levels of segment 7 mRNA or splicing but corresponded to a ∼5-fold reduction in the accumulation of M1. A similar defect in intronless hemagglutinin (HA) mRNA nuclear export was seen with an NS1 mutant virus. Efficient export of M1 mRNA required both an intact NS1 RNA-binding domain and effector domain. Furthermore, while wild-type NS1 interacted with cellular NXF1 and also increased the interaction of segment 7 mRNA with NXF1, mutant NS1 polypeptides unable to promote mRNA export did neither. Thus, we propose that NS1 facilitates late viral gene expression by acting as an adaptor between viral mRNAs and the cellular nuclear export machinery to promote their nuclear export.IMPORTANCE Influenza A virus is a major pathogen of a wide variety of mammalian and avian species that threatens public health and food security. A fuller understanding of the virus life cycle is important to aid control strategies. The virus has a small genome that encodes relatively few proteins that are often multifunctional. Here, we characterize a new function for the NS1 protein, showing that, as well as previously identified roles in antagonizing the innate immune defenses of the cell and directly upregulating translation of viral mRNAs, it also promotes the nuclear export of the viral late gene mRNAs by acting as an adaptor between the viral mRNAs and the cellular mRNA nuclear export machinery.
Collapse
|
18
|
Huang X, Zheng M, Wang P, Mok BWY, Liu S, Lau SY, Chen P, Liu YC, Liu H, Chen Y, Song W, Yuen KY, Chen H. An NS-segment exonic splicing enhancer regulates influenza A virus replication in mammalian cells. Nat Commun 2017; 8:14751. [PMID: 28323816 PMCID: PMC5364394 DOI: 10.1038/ncomms14751] [Citation(s) in RCA: 42] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2016] [Accepted: 01/26/2017] [Indexed: 01/04/2023] Open
Abstract
Influenza virus utilizes host splicing machinery to process viral mRNAs expressed from both M and NS segments. Through genetic analysis and functional characterization, we here show that the NS segment of H7N9 virus contains a unique G540A substitution, located within a previously undefined exonic splicing enhancer (ESE) motif present in the NEP mRNA of influenza A viruses. G540A supports virus replication in mammalian cells while retaining replication ability in avian cells. Host splicing regulator, SF2, interacts with this ESE to regulate splicing of NEP/NS1 mRNA and G540A substitution affects SF2–ESE interaction. The NS1 protein directly interacts with SF2 in the nucleus and modulates splicing of NS mRNAs during virus replication. We demonstrate that splicing of NEP/NS1 mRNA is regulated through a cis NEP-ESE motif and suggest a unique NEP-ESE may contribute to provide H7N9 virus with the ability to both circulate efficiently in avian hosts and replicate in mammalian cells. Some circulating avian influenza A viruses can infect humans, but the mechanism enabling species jump is poorly understood. Here, Huang et al. identify a nucleotide in NEP of avian H7N9 viruses that affects splicing efficiency of the NS segment and supports virus replication in avian and mammalian cells.
Collapse
Affiliation(s)
- Xiaofeng Huang
- State Key Laboratory for Emerging Infectious Diseases, Department of Microbiology, The University of Hong Kong, Hong Kong SAR, China.,Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, The University of Hong Kong, Hong Kong SAR, China
| | - Min Zheng
- State Key Laboratory for Emerging Infectious Diseases, Department of Microbiology, The University of Hong Kong, Hong Kong SAR, China.,Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, The University of Hong Kong, Hong Kong SAR, China
| | - Pui Wang
- State Key Laboratory for Emerging Infectious Diseases, Department of Microbiology, The University of Hong Kong, Hong Kong SAR, China.,Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, The University of Hong Kong, Hong Kong SAR, China
| | - Bobo Wing-Yee Mok
- State Key Laboratory for Emerging Infectious Diseases, Department of Microbiology, The University of Hong Kong, Hong Kong SAR, China.,Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, The University of Hong Kong, Hong Kong SAR, China
| | - Siwen Liu
- State Key Laboratory for Emerging Infectious Diseases, Department of Microbiology, The University of Hong Kong, Hong Kong SAR, China.,Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, The University of Hong Kong, Hong Kong SAR, China
| | - Siu-Ying Lau
- State Key Laboratory for Emerging Infectious Diseases, Department of Microbiology, The University of Hong Kong, Hong Kong SAR, China
| | - Pin Chen
- State Key Laboratory for Emerging Infectious Diseases, Department of Microbiology, The University of Hong Kong, Hong Kong SAR, China.,Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, The University of Hong Kong, Hong Kong SAR, China
| | - Yen-Chin Liu
- State Key Laboratory for Emerging Infectious Diseases, Department of Microbiology, The University of Hong Kong, Hong Kong SAR, China.,Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, The University of Hong Kong, Hong Kong SAR, China
| | - Honglian Liu
- State Key Laboratory for Emerging Infectious Diseases, Department of Microbiology, The University of Hong Kong, Hong Kong SAR, China.,Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, The University of Hong Kong, Hong Kong SAR, China
| | - Yixin Chen
- National Institute of Diagnostics and Vaccine Development in Infectious Diseases, State Key Laboratory of Molecular Vaccinology and Molecular Diagnostics, School of Public Health, Xiamen University, Xiamen 361005, China
| | - Wenjun Song
- State Key Laboratory for Emerging Infectious Diseases, Department of Microbiology, The University of Hong Kong, Hong Kong SAR, China.,Department of Biotechnology, College of Life Science and Technology, Jinan University, 601 Huangpu Avenue West, Guangzhou 510632, China
| | - Kwok-Yung Yuen
- State Key Laboratory for Emerging Infectious Diseases, Department of Microbiology, The University of Hong Kong, Hong Kong SAR, China.,Department of Biotechnology, College of Life Science and Technology, Jinan University, 601 Huangpu Avenue West, Guangzhou 510632, China
| | - Honglin Chen
- State Key Laboratory for Emerging Infectious Diseases, Department of Microbiology, The University of Hong Kong, Hong Kong SAR, China.,Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, The University of Hong Kong, Hong Kong SAR, China.,National Institute of Diagnostics and Vaccine Development in Infectious Diseases, State Key Laboratory of Molecular Vaccinology and Molecular Diagnostics, School of Public Health, Xiamen University, Xiamen 361005, China
| |
Collapse
|
19
|
Lipsitch M, Barclay W, Raman R, Russell CJ, Belser JA, Cobey S, Kasson PM, Lloyd-Smith JO, Maurer-Stroh S, Riley S, Beauchemin CA, Bedford T, Friedrich TC, Handel A, Herfst S, Murcia PR, Roche B, Wilke CO, Russell CA. Viral factors in influenza pandemic risk assessment. eLife 2016; 5. [PMID: 27834632 PMCID: PMC5156527 DOI: 10.7554/elife.18491] [Citation(s) in RCA: 68] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2016] [Accepted: 11/03/2016] [Indexed: 12/13/2022] Open
Abstract
The threat of an influenza A virus pandemic stems from continual virus spillovers from reservoir species, a tiny fraction of which spark sustained transmission in humans. To date, no pandemic emergence of a new influenza strain has been preceded by detection of a closely related precursor in an animal or human. Nonetheless, influenza surveillance efforts are expanding, prompting a need for tools to assess the pandemic risk posed by a detected virus. The goal would be to use genetic sequence and/or biological assays of viral traits to identify those non-human influenza viruses with the greatest risk of evolving into pandemic threats, and/or to understand drivers of such evolution, to prioritize pandemic prevention or response measures. We describe such efforts, identify progress and ongoing challenges, and discuss three specific traits of influenza viruses (hemagglutinin receptor binding specificity, hemagglutinin pH of activation, and polymerase complex efficiency) that contribute to pandemic risk.
Collapse
Affiliation(s)
- Marc Lipsitch
- Center for Communicable Disease Dynamics, Harvard T. H Chan School of Public Health, Boston, United States.,Department of Epidemiology, Harvard T. H. Chan School of Public Health, Boston, United States.,Department of Immunology and Infectious Diseases, Harvard T. H. Chan School of Public Health, Boston, United States
| | - Wendy Barclay
- Division of Infectious Disease, Faculty of Medicine, Imperial College, London, United Kingdom
| | - Rahul Raman
- Department of Biological Engineering, Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, United States
| | - Charles J Russell
- Department of Infectious Diseases, St. Jude Children's Research Hospital, Memphis, United States
| | - Jessica A Belser
- Centers for Disease Control and Prevention, Atlanta, United States
| | - Sarah Cobey
- Department of Ecology and Evolutionary Biology, University of Chicago, Chicago, United States
| | - Peter M Kasson
- Department of Biomedical Engineering, University of Virginia, Charlottesville, United States.,Department of Molecular Physiology and Biological Physics, University of Virginia, Charlottesville, United States
| | - James O Lloyd-Smith
- Department of Ecology and Evolutionary Biology, University of California, Los Angeles, Los Angeles, United States.,Fogarty International Center, National Institutes of Health, Bethesda, United States
| | - Sebastian Maurer-Stroh
- Bioinformatics Institute, Agency for Science Technology and Research, Singapore, Singapore.,National Public Health Laboratory, Communicable Diseases Division, Ministry of Health, Singapore, Singapore.,School of Biological Sciences, Nanyang Technological University, Singapore, Singapore
| | - Steven Riley
- MRC Centre for Outbreak Analysis and Modelling, School of Public Health, Imperial College London, London, United Kingdom.,Department of Infectious Disease Epidemiology, School of Public Health, Imperial College London, London, United Kingdom
| | | | - Trevor Bedford
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Research Center, Seattle, United States
| | - Thomas C Friedrich
- Department of Pathobiological Sciences, University of Wisconsin School of Veterinary Medicine, Madison, United States
| | - Andreas Handel
- Department of Epidemiology and Biostatistics, College of Public Health, University of Georgia, Athens, United States
| | - Sander Herfst
- Department of Viroscience, Erasmus Medical Center, Rotterdam, Netherlands
| | - Pablo R Murcia
- MRC-University of Glasgow Centre For Virus Research, Glasgow, United Kingdom
| | | | - Claus O Wilke
- Center for Computational Biology and Bioinformatics, Institute for Cellular and Molecular Biology, The University of Texas at Austin, Austin, United States.,Department of Integrative Biology, The University of Texas at Austin, Austin, United States
| | - Colin A Russell
- Department of Veterinary Medicine, University of Cambridge, Cambridge, United Kingdom
| |
Collapse
|
20
|
Kerviel A, Dash S, Moncorgé O, Panthu B, Prchal J, Décimo D, Ohlmann T, Lina B, Favard C, Decroly E, Ottmann M, Roingeard P, Muriaux D. Involvement of an Arginine Triplet in M1 Matrix Protein Interaction with Membranes and in M1 Recruitment into Virus-Like Particles of the Influenza A(H1N1)pdm09 Virus. PLoS One 2016; 11:e0165421. [PMID: 27814373 PMCID: PMC5096668 DOI: 10.1371/journal.pone.0165421] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2016] [Accepted: 10/11/2016] [Indexed: 11/18/2022] Open
Abstract
The influenza A(H1N1)pdm09 virus caused the first influenza pandemic of the 21st century. In this study, we wanted to decipher the role of conserved basic residues of the viral M1 matrix protein in virus assembly and release. M1 plays many roles in the influenza virus replication cycle. Specifically, it participates in viral particle assembly, can associate with the viral ribonucleoprotein complexes and can bind to the cell plasma membrane and/or the cytoplasmic tail of viral transmembrane proteins. M1 contains an N-terminal domain of 164 amino acids with two basic domains: the nuclear localization signal on helix 6 and an arginine triplet (R76/77/78) on helix 5. To investigate the role of these two M1 basic domains in influenza A(H1N1)pdm09 virus molecular assembly, we analyzed M1 attachment to membranes, virus-like particle (VLP) production and virus infectivity. In vitro, M1 binding to large unilamellar vesicles (LUVs), which contain negatively charged lipids, decreased significantly when the M1 R76/77/78 motif was mutated. In cells, M1 alone was mainly observed in the nucleus (47%) and in the cytosol (42%). Conversely, when co-expressed with the viral proteins NS1/NEP and M2, M1 was relocated to the cell membranes (55%), as shown by subcellular fractionation experiments. This minimal system allowed the production of M1 containing-VLPs. However, M1 with mutations in the arginine triplet accumulated in intracellular clusters and its incorporation in VLPs was strongly diminished. M2 over-expression was essential for M1 membrane localization and VLP production, whereas the viral trans-membrane proteins HA and NA seemed dispensable. These results suggest that the M1 arginine triplet participates in M1 interaction with membranes. This R76/77/78 motif is essential for M1 incorporation in virus particles and the importance of this motif was confirmed by reverse genetic demonstrating that its mutation is lethal for the virus. These results highlight the molecular mechanism of M1-membrane interaction during the formation of influenza A(H1N1)pdm09 virus particles which is essential for infectivity.
Collapse
Affiliation(s)
- Adeline Kerviel
- Centre d'études d'agents Pathogènes et Biotechnologies pour la Santé (CPBS), CNRS & Université of Montpellier, Montpellier, France
| | - Shantoshini Dash
- Centre d'études d'agents Pathogènes et Biotechnologies pour la Santé (CPBS), CNRS & Université of Montpellier, Montpellier, France
| | - Olivier Moncorgé
- Centre d'études d'agents Pathogènes et Biotechnologies pour la Santé (CPBS), CNRS & Université of Montpellier, Montpellier, France
| | | | - Jan Prchal
- Centre d'études d'agents Pathogènes et Biotechnologies pour la Santé (CPBS), CNRS & Université of Montpellier, Montpellier, France
| | - Didier Décimo
- CIRI, INSERM U 1111, France & ENS de Lyon, Lyon, France
| | | | - Bruno Lina
- Université de Lyon, Université Lyon 1, Faculté de Médecine Lyon Est, Laboratoire de Virologie et Pathologie Humaine, EA 4610, Lyon, France
| | - Cyril Favard
- Centre d'études d'agents Pathogènes et Biotechnologies pour la Santé (CPBS), CNRS & Université of Montpellier, Montpellier, France
| | - Etienne Decroly
- Aix-Marseille Université & CNRS, AFMB UMR 7257, 163 Avenue de Luminy, 13288 Marseille cedex 09, France
| | - Michèle Ottmann
- Université de Lyon, Université Lyon 1, Faculté de Médecine Lyon Est, Laboratoire de Virologie et Pathologie Humaine, EA 4610, Lyon, France
| | - Philippe Roingeard
- INSERM U966, Université François Rabelais & CHRU de Tours, Tours, France
| | - Delphine Muriaux
- Centre d'études d'agents Pathogènes et Biotechnologies pour la Santé (CPBS), CNRS & Université of Montpellier, Montpellier, France
- * E-mail:
| |
Collapse
|
21
|
Te Velthuis AJW, Fodor E. Influenza virus RNA polymerase: insights into the mechanisms of viral RNA synthesis. Nat Rev Microbiol 2016; 14:479-93. [PMID: 27396566 DOI: 10.1038/nrmicro.2016.87] [Citation(s) in RCA: 292] [Impact Index Per Article: 36.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
The genomes of influenza viruses consist of multiple segments of single-stranded negative-sense RNA. Each of these segments is bound by the heterotrimeric viral RNA-dependent RNA polymerase and multiple copies of nucleoprotein, which form viral ribonucleoprotein (vRNP) complexes. It is in the context of these vRNPs that the viral RNA polymerase carries out transcription of viral genes and replication of the viral RNA genome. In this Review, we discuss our current knowledge of the structure of the influenza virus RNA polymerase, and insights that have been gained into the molecular mechanisms of viral transcription and replication, and their regulation by viral and host factors. Furthermore, we discuss how advances in our understanding of the structure and function of polymerases could help in identifying new antiviral targets.
Collapse
Affiliation(s)
- Aartjan J W Te Velthuis
- Sir William Dunn School of Pathology, University of Oxford, South Parks Road, Oxford OX1 3RE, UK
| | - Ervin Fodor
- Sir William Dunn School of Pathology, University of Oxford, South Parks Road, Oxford OX1 3RE, UK
| |
Collapse
|
22
|
Mor A, White A, Zhang K, Thompson M, Esparza M, Muñoz-Moreno R, Koide K, Lynch KW, García-Sastre A, Fontoura BM. Influenza virus mRNA trafficking through host nuclear speckles. Nat Microbiol 2016; 1:16069. [PMID: 27572970 PMCID: PMC4917225 DOI: 10.1038/nmicrobiol.2016.69] [Citation(s) in RCA: 69] [Impact Index Per Article: 8.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2015] [Accepted: 04/20/2016] [Indexed: 12/26/2022]
Abstract
Influenza A virus is a human pathogen with a genome composed of eight viral RNA segments that replicate in the nucleus. Two viral mRNAs are alternatively spliced. The unspliced M1 mRNA is translated into the matrix M1 protein, while the ion channel M2 protein is generated after alternative splicing. These proteins are critical mediators of viral trafficking and budding. We show that the influenza virus uses nuclear speckles to promote post-transcriptional splicing of its M1 mRNA. We assign previously unknown roles for the viral NS1 protein and cellular factors to an intranuclear trafficking pathway that targets the viral M1 mRNA to nuclear speckles, mediates splicing at these nuclear bodies and exports the spliced M2 mRNA from the nucleus. Given that nuclear speckles are storage sites for splicing factors, which leave these sites to splice cellular pre-mRNAs at transcribing genes, we reveal a functional subversion of nuclear speckles to promote viral gene expression.
Collapse
Affiliation(s)
- Amir Mor
- Department of Cell Biology, University of Texas Southwestern Medical Center, Dallas, TX 75390-9039, USA
| | - Alexander White
- Department of Cell Biology, University of Texas Southwestern Medical Center, Dallas, TX 75390-9039, USA
| | - Ke Zhang
- Department of Cell Biology, University of Texas Southwestern Medical Center, Dallas, TX 75390-9039, USA
| | - Matthew Thompson
- Department of Biochemistry and Biophysics, University of Pennsylvania School of Medicine, Philadelphia, PA 19104-6059, USA
| | - Matthew Esparza
- Department of Cell Biology, University of Texas Southwestern Medical Center, Dallas, TX 75390-9039, USA
| | - Raquel Muñoz-Moreno
- Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
- Global Health and Emerging Pathogens Institute, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Kazunori Koide
- Department of Chemistry, University of Pittsburgh, Pittsburgh, PA 15260, USA
| | - Kristen W. Lynch
- Department of Biochemistry and Biophysics, University of Pennsylvania School of Medicine, Philadelphia, PA 19104-6059, USA
| | - Adolfo García-Sastre
- Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
- Global Health and Emerging Pathogens Institute, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
- Department of Medicine, Division of Infectious Diseases, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Beatriz M.A. Fontoura
- Department of Cell Biology, University of Texas Southwestern Medical Center, Dallas, TX 75390-9039, USA
| |
Collapse
|
23
|
Thulasi Raman SN, Zhou Y. Networks of Host Factors that Interact with NS1 Protein of Influenza A Virus. Front Microbiol 2016; 7:654. [PMID: 27199973 PMCID: PMC4855030 DOI: 10.3389/fmicb.2016.00654] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2016] [Accepted: 04/19/2016] [Indexed: 11/13/2022] Open
Abstract
Pigs are an important host of influenza A viruses due to their ability to generate reassortant viruses with pandemic potential. NS1 protein of influenza A viruses is a key virulence factor and a major antagonist of innate immune responses. It is also involved in enhancing viral mRNA translation and regulation of virus replication. Being a protein with pleiotropic functions, NS1 has a variety of cellular interaction partners. Hence, studies on swine influenza viruses (SIV) and identification of swine influenza NS1-interacting host proteins is of great interest. Here, we constructed a recombinant SIV carrying a Strep-tag in the NS1 protein and infected primary swine respiratory epithelial cells (SRECs) with this virus. The Strep-tag sequence in the NS1 protein enabled us to purify intact, the NS1 protein and its interacting protein complex specifically. We identified cellular proteins present in the purified complex by liquid chromatography-tandem mass spectrometry (LC-MS/MS) and generated a dataset of these proteins. 445 proteins were identified by LC-MS/MS and among them 192 proteins were selected by setting up a threshold based on MS parameters. The selected proteins were analyzed by bioinformatics and were categorized as belonging to different functional groups including translation, RNA processing, cytoskeleton, innate immunity, and apoptosis. Protein interaction networks were derived using these data and the NS1 interactions with some of the specific host factors were verified by immunoprecipitation. The novel proteins and the networks revealed in our study will be the potential candidates for targeted study of the molecular interaction of NS1 with host proteins, which will provide insights into the identification of new therapeutic targets to control influenza infection and disease pathogenesis.
Collapse
Affiliation(s)
- Sathya N Thulasi Raman
- Vaccine and Infectious Disease Organization - International Vaccine Centre, University of Saskatchewan, SaskatoonSK, Canada; Vaccinology and Immunotherapeutics Program, School of Public Health, University of Saskatchewan, SaskatoonSK, Canada
| | - Yan Zhou
- Vaccine and Infectious Disease Organization - International Vaccine Centre, University of Saskatchewan, SaskatoonSK, Canada; Vaccinology and Immunotherapeutics Program, School of Public Health, University of Saskatchewan, SaskatoonSK, Canada
| |
Collapse
|
24
|
Kuo RL, Li ZH, Li LH, Lee KM, Tam EH, Liu HM, Liu HP, Shih SR, Wu CC. Interactome Analysis of the NS1 Protein Encoded by Influenza A H1N1 Virus Reveals a Positive Regulatory Role of Host Protein PRP19 in Viral Replication. J Proteome Res 2016; 15:1639-48. [PMID: 27096427 DOI: 10.1021/acs.jproteome.6b00103] [Citation(s) in RCA: 28] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Influenza A virus, which can cause severe respiratory illnesses in infected individuals, is responsible for worldwide human pandemics. The NS1 protein encoded by this virus plays a crucial role in regulating the host antiviral response through various mechanisms. In addition, it has been reported that NS1 can modulate cellular pre-mRNA splicing events. To investigate the biological processes potentially affected by the NS1 protein in host cells, NS1-associated protein complexes in human cells were identified using coimmunoprecipitation combined with GeLC-MS/MS. By employing software to build biological process and protein-protein interaction networks, NS1-interacting cellular proteins were found to be related to RNA splicing/processing, cell cycle, and protein folding/targeting cellular processes. By monitoring spliced and unspliced RNAs of a reporter plasmid, we further validated that NS1 can interfere with cellular pre-mRNA splicing. One of the identified proteins, pre-mRNA-processing factor 19 (PRP19), was confirmed to interact with the NS1 protein in influenza A virus-infected cells. Importantly, depletion of PRP19 in host cells reduced replication of influenza A virus. In summary, the interactome of influenza A virus NS1 in host cells was comprehensively profiled, and our findings reveal a novel regulatory role for PRP19 in viral replication.
Collapse
Affiliation(s)
| | | | | | | | | | - Helene M Liu
- Department of Clinical Laboratory Sciences and Medical Technology, College of Medicine, National Taiwan University , Taipei 10617, Taiwan
| | - Hao-Ping Liu
- Department of Veterinary Medicine, National Chung Hsing University , Taichung 40227, Taiwan
| | | | | |
Collapse
|
25
|
An A14U Substitution in the 3' Noncoding Region of the M Segment of Viral RNA Supports Replication of Influenza Virus with an NS1 Deletion by Modulating Alternative Splicing of M Segment mRNAs. J Virol 2015. [PMID: 26223635 PMCID: PMC4580205 DOI: 10.1128/jvi.00919-15] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022] Open
Abstract
The NS1 protein of influenza virus has multiple functions and is a determinant of virulence. Influenza viruses with NS1 deletions (DelNS1 influenza viruses) are a useful tool for studying virus replication and can serve as effective live attenuated vaccines, but deletion of NS1 severely diminishes virus replication, hampering functional studies and vaccine production. We found that WSN-DelNS1 viruses passaged in cells consistently adapted to gain an A14U substitution in the 3′ noncoding region of the M segment of viral RNA (vRNA) which restored replicative ability. DelNS1-M-A14U viruses cannot inhibit interferon expression in virus infected-cells, providing an essential model for studying virus replication in the absence of the NS1 protein. Characterization of DelNS1-M-A14U virus showed that the lack of NS1 has no apparent effect on expression of other viral proteins, with the exception of M mRNAs. Expression of the M transcripts, M1, M2, mRNA3, and mRNA4, is regulated by alternative splicing. The A14U substitution changes the splicing donor site consensus sequence of mRNA3, altering expression of M transcripts, with M2 expression significantly increased and mRNA3 markedly suppressed in DelNS1-M-A14U, but not DelNS1-M-WT, virus-infected cells. Further analysis revealed that the A14U substitution also affects promoter function during replication of the viral genome. The M-A14U mutation increases M vRNA synthesis in DelNS1 virus infection and enhances alternative splicing of M2 mRNA in the absence of other viral proteins. The findings demonstrate that NS1 is directly involved in influenza virus replication through modulation of alternative splicing of M transcripts and provide strategic information important to construction of vaccine strains with NS1 deletions. IMPORTANCE Nonstructural protein (NS1) of influenza virus has multiple functions. Besides its role in antagonizing host antiviral activity, NS1 is also believed to be involved in regulating virus replication, but mechanistic details are not clear. The NS1 protein is a virulence determinant which inhibits both innate and adaptive immunity and live attenuated viruses with NS1 deletions show promise as effective vaccines. However, deletion of NS1 causes severe attenuation of virus replication during infection, impeding functional studies and vaccine development. We characterized a replication-competent DelNS1 virus which carries an A14U substitution in the 3′ noncoding region of the vRNA M segment. We found that M-A14U mutation supports virus replication through modulation of alternative splicing of mRNAs transcribed from the M segment. Our findings give insight into the role of NS1 in influenza virus replication and provide an approach for constructing replication-competent strains with NS1 deletions for use in functional and vaccine studies.
Collapse
|
26
|
Marc D. Influenza virus non-structural protein NS1: interferon antagonism and beyond. J Gen Virol 2014; 95:2594-2611. [PMID: 25182164 DOI: 10.1099/vir.0.069542-0] [Citation(s) in RCA: 102] [Impact Index Per Article: 10.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022] Open
Abstract
Most viruses express one or several proteins that counter the antiviral defences of the host cell. This is the task of non-structural protein NS1 in influenza viruses. Absent in the viral particle, but highly expressed in the infected cell, NS1 dramatically inhibits cellular gene expression and prevents the activation of key players in the IFN system. In addition, NS1 selectively enhances the translation of viral mRNAs and may regulate the synthesis of viral RNAs. Our knowledge of the virus and of NS1 has increased dramatically during the last 15 years. The atomic structure of NS1 has been determined, many cellular partners have been identified and its multiple activities have been studied in depth. This review presents our current knowledge, and attempts to establish relationships between the RNA sequence, the structure of the protein, its ligands, its activities and the pathogenicity of the virus. A better understanding of NS1 could help in elaborating novel antiviral strategies, based on either live vaccines with altered NS1 or on small-compound inhibitors of NS1.
Collapse
Affiliation(s)
- Daniel Marc
- Université François Rabelais, UMR1282 Infectiologie et Santé Publique, 37000 Tours, France.,Pathologie et Immunologie Aviaire, INRA, UMR1282 Infectiologie et Santé Publique, 37380 Nouzilly, France
| |
Collapse
|
27
|
Larsen S, Bui S, Perez V, Mohammad A, Medina-Ramirez H, Newcomb LL. Influenza polymerase encoding mRNAs utilize atypical mRNA nuclear export. Virol J 2014; 11:154. [PMID: 25168591 PMCID: PMC4158059 DOI: 10.1186/1743-422x-11-154] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2014] [Accepted: 08/12/2014] [Indexed: 11/14/2022] Open
Abstract
BACKGROUND Influenza is a segmented negative strand RNA virus. Each RNA segment is encapsulated by influenza nucleoprotein and bound by the viral RNA dependent RNA polymerase (RdRP) to form viral ribonucleoproteins responsible for RNA synthesis in the nucleus of the host cell. Influenza transcription results in spliced mRNAs (M2 and NS2), intron-containing mRNAs (M1 and NS1), and intron-less mRNAs (HA, NA, NP, PB1, PB2, and PA), all of which undergo nuclear export into the cytoplasm for translation. Most cellular mRNA nuclear export is Nxf1-mediated, while select mRNAs utilize Crm1. METHODS Here we inhibited Nxf1 and Crm1 nuclear export prior to infection with influenza A/Udorn/307/1972(H3N2) virus and analyzed influenza intron-less mRNAs using cellular fractionation and reverse transcription-quantitative polymerase chain reaction (RT-qPCR). We examined direct interaction between Nxf1 and influenza intron-less mRNAs using immuno purification of Nxf1 and RT-PCR of associated RNA. RESULTS Inhibition of Nxf1 resulted in less influenza intron-less mRNA export into the cytoplasm for HA and NA influenza mRNAs in both human embryonic kidney cell line (293 T) and human lung adenocarcinoma epithelial cell line (A549). However, in 293 T cells no change was observed for mRNAs encoding the components of the viral ribonucleoproteins; NP, PA, PB1, and PB2, while in A549 cells, only PA, PB1, and PB2 mRNAs, encoding the RdRP, remained unaffected; NP mRNA was reduced in the cytoplasm. In A549 cells NP, NA, HA, mRNAs were found associated with Nxf1 but PA, PB1, and PB2 mRNAs were not. Crm1 inhibition also resulted in no significant difference in PA, PB1, and PB2 mRNA nuclear export. CONCLUSIONS These results further confirm Nxf1-mediated nuclear export is functional during the influenza life cycle and hijacked for select influenza mRNA nuclear export. We reveal a cell type difference for Nxf1-mediated nuclear export of influenza NP mRNA, a reminder that cell type can influence molecular mechanisms. Importantly, we conclude that in both A549 and 293 T cells, PA, PB1, and PB2 mRNA nuclear export is Nxf1 and Crm1 independent. Our data support the hypothesis that PA, PB1, and PB2 mRNAs, encoding the influenza RdRP, utilize atypical mRNA nuclear export.
Collapse
MESH Headings
- Active Transport, Cell Nucleus
- Antibiotics, Antineoplastic/pharmacology
- Cell Line
- Fatty Acids, Unsaturated/pharmacology
- Gene Expression Regulation
- Humans
- Influenza A Virus, H3N2 Subtype/genetics
- Influenza A Virus, H3N2 Subtype/metabolism
- Karyopherins/antagonists & inhibitors
- Karyopherins/genetics
- Karyopherins/metabolism
- Nucleocytoplasmic Transport Proteins/antagonists & inhibitors
- Nucleocytoplasmic Transport Proteins/genetics
- Nucleocytoplasmic Transport Proteins/metabolism
- RNA, Messenger/genetics
- RNA, Messenger/metabolism
- RNA, Viral/genetics
- RNA, Viral/metabolism
- RNA-Binding Proteins/antagonists & inhibitors
- RNA-Binding Proteins/genetics
- RNA-Binding Proteins/metabolism
- Receptors, Cytoplasmic and Nuclear/antagonists & inhibitors
- Receptors, Cytoplasmic and Nuclear/genetics
- Receptors, Cytoplasmic and Nuclear/metabolism
- Virus Replication
- Exportin 1 Protein
Collapse
Affiliation(s)
- Sean Larsen
- Department of Biology, California State University San Bernardino, 5500 University Parkway, San Bernardino, CA 92407 USA
| | - Steven Bui
- Department of Biology, California State University San Bernardino, 5500 University Parkway, San Bernardino, CA 92407 USA
| | - Veronica Perez
- Department of Biology, California State University San Bernardino, 5500 University Parkway, San Bernardino, CA 92407 USA
| | - Adeba Mohammad
- Department of Biology, California State University San Bernardino, 5500 University Parkway, San Bernardino, CA 92407 USA
| | - Hilario Medina-Ramirez
- Department of Biology, California State University San Bernardino, 5500 University Parkway, San Bernardino, CA 92407 USA
| | - Laura L Newcomb
- Department of Biology, California State University San Bernardino, 5500 University Parkway, San Bernardino, CA 92407 USA
| |
Collapse
|
28
|
Jiang T, Kennedy SD, Moss WN, Kierzek E, Turner DH. Secondary structure of a conserved domain in an intron of influenza A M1 mRNA. Biochemistry 2014; 53:5236-48. [PMID: 25026548 PMCID: PMC4139153 DOI: 10.1021/bi500611j] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
Influenza A virus utilizes RNA throughout infection. Little is known, however, about the roles of RNA structures. A previous bioinformatics survey predicted multiple regions of influenza A virus that are likely to generate evolutionarily conserved and stable RNA structures. One predicted conserved structure is in the pre-mRNA coding for essential proteins, M1 and M2. This structure starts 79 nucleotides downstream of the M2 mRNA 5' splice site. Here, a combination of biochemical structural mapping, mutagenesis, and NMR confirms the predicted three-way multibranch structure of this RNA. Imino proton NMR spectra reveal no change in secondary structure when 80 mM KCl is supplemented with 4 mM MgCl2. Optical melting curves in 1 M NaCl and in 100 mM KCl with 10 mM MgCl2 are very similar, with melting temperatures ∼14 °C higher than that for 100 mM KCl alone. These results provide a firm basis for designing experiments and potential therapeutics to test for function in cell culture.
Collapse
Affiliation(s)
- Tian Jiang
- Department of Chemistry and Center for RNA Biology, University of Rochester , Rochester, New York 14627, United States
| | | | | | | | | |
Collapse
|
29
|
Recruitment of RED-SMU1 complex by Influenza A Virus RNA polymerase to control Viral mRNA splicing. PLoS Pathog 2014; 10:e1004164. [PMID: 24945353 PMCID: PMC4055741 DOI: 10.1371/journal.ppat.1004164] [Citation(s) in RCA: 41] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2014] [Accepted: 04/21/2014] [Indexed: 12/21/2022] Open
Abstract
Influenza A viruses are major pathogens in humans and in animals, whose genome consists of eight single-stranded RNA segments of negative polarity. Viral mRNAs are synthesized by the viral RNA-dependent RNA polymerase in the nucleus of infected cells, in close association with the cellular transcriptional machinery. Two proteins essential for viral multiplication, the exportin NS2/NEP and the ion channel protein M2, are produced by splicing of the NS1 and M1 mRNAs, respectively. Here we identify two human spliceosomal factors, RED and SMU1, that control the expression of NS2/NEP and are required for efficient viral multiplication. We provide several lines of evidence that in infected cells, the hetero-trimeric viral polymerase recruits a complex formed by RED and SMU1 through interaction with its PB2 and PB1 subunits. We demonstrate that the splicing of the NS1 viral mRNA is specifically affected in cells depleted of RED or SMU1, leading to a decreased production of the spliced mRNA species NS2, and to a reduced NS2/NS1 protein ratio. In agreement with the exportin function of NS2, these defects impair the transport of newly synthesized viral ribonucleoproteins from the nucleus to the cytoplasm, and strongly reduce the production of infectious influenza virions. Overall, our results unravel a new mechanism of viral subversion of the cellular splicing machinery, by establishing that the human splicing factors RED and SMU1 act jointly as key regulators of influenza virus gene expression. In addition, our data point to a central role of the viral RNA polymerase in coupling transcription and alternative splicing of the viral mRNAs.
Collapse
|
30
|
Trapp S, Soubieux D, Marty H, Esnault E, Hoffmann TW, Chandenier M, Lion A, Kut E, Quéré P, Larcher T, Ledevin M, Munier S, Naffakh N, Marc D. Shortening the unstructured, interdomain region of the non-structural protein NS1 of an avian H1N1 influenza virus increases its replication and pathogenicity in chickens. J Gen Virol 2014; 95:1233-1243. [DOI: 10.1099/vir.0.063776-0] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022] Open
Abstract
Currently circulating H5N1 influenza viruses have undergone a complex evolution since the appearance of their progenitor A/Goose/Guangdong/1/96 in 1996. After the eradication of the H5N1 viruses that emerged in Hong Kong in 1997 (HK/97 viruses), new genotypes of H5N1 viruses emerged in the same region in 2000 that were more pathogenic for both chickens and mice than HK/97 viruses. These, as well as virtually all highly pathogenic H5N1 viruses since 2000, harbour a deletion of aa 80–84 in the unstructured region of the non-structural (NS) protein NS1 linking its RNA-binding domain to its effector domain. NS segments harbouring this mutation have since been found in non-H5N1 viruses and we asked whether this 5 aa deletion could have a general effect not limited to the NS1 of H5N1 viruses. We genetically engineered this deletion in the NS segment of a duck-origin avian H1N1 virus, and compared the in vivo and in vitro properties of the WT and NSdel8084 viruses. In experimentally infected chickens, the NSdel8084 virus showed both an increased replication potential and an increased pathogenicity. This in vivo phenotype was correlated with a higher replicative efficiency in vitro, both in embryonated eggs and in a chicken lung epithelial cell line. Our data demonstrated that the increased replicative potential conferred by this small deletion was a general feature not restricted to NS1 from H5N1 viruses and suggested that viruses acquiring this mutation may be selected positively in the future.
Collapse
Affiliation(s)
- Sascha Trapp
- UMR1282 Infectiologie et Santé Publique, Université François Rabelais de Tours, 37000 Tours, France
- Equipe PIA, UMR1282 Infectiologie et Santé Publique, INRA, 37380 Nouzilly, France
| | - Denis Soubieux
- Equipe BioVA, UMR1282 Infectiologie et Santé Publique, Institut National de la Recherche Agronomique, 37380 Nouzilly, France
- UMR1282 Infectiologie et Santé Publique, Université François Rabelais de Tours, 37000 Tours, France
- Equipe PIA, UMR1282 Infectiologie et Santé Publique, INRA, 37380 Nouzilly, France
| | - Hélène Marty
- UMR1282 Infectiologie et Santé Publique, Université François Rabelais de Tours, 37000 Tours, France
- Equipe PIA, UMR1282 Infectiologie et Santé Publique, INRA, 37380 Nouzilly, France
| | - Evelyne Esnault
- UMR1282 Infectiologie et Santé Publique, Université François Rabelais de Tours, 37000 Tours, France
- Equipe PIA, UMR1282 Infectiologie et Santé Publique, INRA, 37380 Nouzilly, France
| | - Thomas W. Hoffmann
- Equipe BioVA, UMR1282 Infectiologie et Santé Publique, Institut National de la Recherche Agronomique, 37380 Nouzilly, France
- UMR1282 Infectiologie et Santé Publique, Université François Rabelais de Tours, 37000 Tours, France
| | - Margaux Chandenier
- Equipe BioVA, UMR1282 Infectiologie et Santé Publique, Institut National de la Recherche Agronomique, 37380 Nouzilly, France
- UMR1282 Infectiologie et Santé Publique, Université François Rabelais de Tours, 37000 Tours, France
| | - Adrien Lion
- UMR1282 Infectiologie et Santé Publique, Université François Rabelais de Tours, 37000 Tours, France
- Equipe PIA, UMR1282 Infectiologie et Santé Publique, INRA, 37380 Nouzilly, France
| | - Emmanuel Kut
- UMR1282 Infectiologie et Santé Publique, Université François Rabelais de Tours, 37000 Tours, France
- Equipe PIA, UMR1282 Infectiologie et Santé Publique, INRA, 37380 Nouzilly, France
| | - Pascale Quéré
- UMR1282 Infectiologie et Santé Publique, Université François Rabelais de Tours, 37000 Tours, France
- Equipe PIA, UMR1282 Infectiologie et Santé Publique, INRA, 37380 Nouzilly, France
| | - Thibaut Larcher
- LUNAM Université, École Nationale Vétérinaire, agro-alimentaire et de l’alimentation Nantes-Atlantique (Oniris), 44307 Nantes, France
- INRA UMR 703, APEX, Oniris-La Chantrerie, 44307 Nantes, France
| | - Mireille Ledevin
- LUNAM Université, École Nationale Vétérinaire, agro-alimentaire et de l’alimentation Nantes-Atlantique (Oniris), 44307 Nantes, France
- INRA UMR 703, APEX, Oniris-La Chantrerie, 44307 Nantes, France
| | - Sandie Munier
- Université Paris Diderot, Sorbonne Paris Cité, Unité de Génétique Moléculaire des Virus à ARN, EA302, 75015 Paris, France
- CNRS, UMR3569, 75015 Paris, France
- Institut Pasteur, Unité de Génétique Moléculaire des Virus à ARN, Département de Virologie, 75015 Paris, France
| | - Nadia Naffakh
- Université Paris Diderot, Sorbonne Paris Cité, Unité de Génétique Moléculaire des Virus à ARN, EA302, 75015 Paris, France
- CNRS, UMR3569, 75015 Paris, France
- Institut Pasteur, Unité de Génétique Moléculaire des Virus à ARN, Département de Virologie, 75015 Paris, France
| | - Daniel Marc
- Equipe BioVA, UMR1282 Infectiologie et Santé Publique, Institut National de la Recherche Agronomique, 37380 Nouzilly, France
- UMR1282 Infectiologie et Santé Publique, Université François Rabelais de Tours, 37000 Tours, France
- Equipe PIA, UMR1282 Infectiologie et Santé Publique, INRA, 37380 Nouzilly, France
| |
Collapse
|
31
|
Abstract
During their nuclear replication stage, influenza viruses hijack the host splicing machinery to process some of their RNA segments, the M and NS segments. In this review, we provide an overview of the current knowledge gathered on this interplay between influenza viruses and the cellular spliceosome, with a particular focus on influenza A viruses (IAV). These viruses have developed accurate regulation mechanisms to reassign the host spliceosome to alter host cellular expression and enable an optimal expression of specific spliced viral products throughout infection. Moreover, IAV segments undergoing splicing display high levels of similarity with human consensus splice sites and their viral transcripts show noteworthy secondary structures. Sequence alignments and consensus analyses, along with recently published studies, suggest both conservation and evolution of viral splice site sequences and structure for improved adaptation to the host. Altogether, these results emphasize the ability of IAV to be well adapted to the host's splicing machinery, and further investigations may contribute to a better understanding of splicing regulation with regard to viral replication, host range, and pathogenesis.
Collapse
|
32
|
Vasin AV, Temkina OA, Egorov VV, Klotchenko SA, Plotnikova MA, Kiselev OI. Molecular mechanisms enhancing the proteome of influenza A viruses: an overview of recently discovered proteins. Virus Res 2014; 185:53-63. [PMID: 24675275 DOI: 10.1016/j.virusres.2014.03.015] [Citation(s) in RCA: 118] [Impact Index Per Article: 11.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2013] [Revised: 02/19/2014] [Accepted: 03/11/2014] [Indexed: 12/11/2022]
Abstract
Influenza A virus is one of the major human pathogens. Despite numerous efforts to produce absolutely effective anti-influenza drugs or vaccines, no such agent has been developed yet. One of the main reasons for this complication is the high mutation rate and the specific structure of influenza A viruses genome. For more than 25 years since the first mapping of the viral genome, it was believed that its 8 genome segments encode 10 proteins. However, the proteome of influenza A viruses has turned out to be much more complex than previously thought. In 2001, the first accessory protein, PB1-F2, translated from the alternative open reading frame, was discovered. Subsequently, six more proteins, PB1-N40, PA-X, PA-N155, PA-N182, M42, and NS3, have been found. It is important to pay close attention to these novel proteins in order to evaluate their role in the pathogenesis of influenza, especially in the case of outbreaks of human infections with new avian viruses, such as H5N1 or H7N9. In this review we summarize the data on the molecular mechanisms used by influenza A viruses to expand their proteome and on the possible functions of the recently discovered viral proteins.
Collapse
Affiliation(s)
- A V Vasin
- Laboratory of Structural and Functional Proteomics, Research Institute of Influenza, St-Petersburg 197376, Russia.
| | - O A Temkina
- Laboratory of Structural and Functional Proteomics, Research Institute of Influenza, St-Petersburg 197376, Russia
| | - V V Egorov
- Laboratory of Structural and Functional Proteomics, Research Institute of Influenza, St-Petersburg 197376, Russia
| | - S A Klotchenko
- Laboratory of Structural and Functional Proteomics, Research Institute of Influenza, St-Petersburg 197376, Russia
| | - M A Plotnikova
- Laboratory of Structural and Functional Proteomics, Research Institute of Influenza, St-Petersburg 197376, Russia
| | - O I Kiselev
- Laboratory of Structural and Functional Proteomics, Research Institute of Influenza, St-Petersburg 197376, Russia
| |
Collapse
|
33
|
Kuss SK, Mata MA, Zhang L, Fontoura BMA. Nuclear imprisonment: viral strategies to arrest host mRNA nuclear export. Viruses 2013; 5:1824-49. [PMID: 23872491 PMCID: PMC3738964 DOI: 10.3390/v5071824] [Citation(s) in RCA: 45] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2013] [Revised: 06/27/2013] [Accepted: 07/11/2013] [Indexed: 12/15/2022] Open
Abstract
Viruses possess many strategies to impair host cellular responses to infection. Nuclear export of host messenger RNAs (mRNA) that encode antiviral factors is critical for antiviral protein production and control of viral infections. Several viruses have evolved sophisticated strategies to inhibit nuclear export of host mRNAs, including targeting mRNA export factors and nucleoporins to compromise their roles in nucleo-cytoplasmic trafficking of cellular mRNA. Here, we present a review of research focused on suppression of host mRNA nuclear export by viruses, including influenza A virus and vesicular stomatitis virus, and the impact of this viral suppression on host antiviral responses.
Collapse
Affiliation(s)
- Sharon K Kuss
- Department of Cell Biology, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA.
| | | | | | | |
Collapse
|
34
|
Cellular RNA binding proteins NS1-BP and hnRNP K regulate influenza A virus RNA splicing. PLoS Pathog 2013; 9:e1003460. [PMID: 23825951 PMCID: PMC3694860 DOI: 10.1371/journal.ppat.1003460] [Citation(s) in RCA: 67] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2013] [Accepted: 05/12/2013] [Indexed: 01/19/2023] Open
Abstract
Influenza A virus is a major human pathogen with a genome comprised of eight single-strand, negative-sense, RNA segments. Two viral RNA segments, NS1 and M, undergo alternative splicing and yield several proteins including NS1, NS2, M1 and M2 proteins. However, the mechanisms or players involved in splicing of these viral RNA segments have not been fully studied. Here, by investigating the interacting partners and function of the cellular protein NS1-binding protein (NS1-BP), we revealed novel players in the splicing of the M1 segment. Using a proteomics approach, we identified a complex of RNA binding proteins containing NS1-BP and heterogeneous nuclear ribonucleoproteins (hnRNPs), among which are hnRNPs involved in host pre-mRNA splicing. We found that low levels of NS1-BP specifically impaired proper alternative splicing of the viral M1 mRNA segment to yield the M2 mRNA without affecting splicing of mRNA3, M4, or the NS mRNA segments. Further biochemical analysis by formaldehyde and UV cross-linking demonstrated that NS1-BP did not interact directly with viral M1 mRNA but its interacting partners, hnRNPs A1, K, L, and M, directly bound M1 mRNA. Among these hnRNPs, we identified hnRNP K as a major mediator of M1 mRNA splicing. The M1 mRNA segment generates the matrix protein M1 and the M2 ion channel, which are essential proteins involved in viral trafficking, release into the cytoplasm, and budding. Thus, reduction of NS1-BP and/or hnRNP K levels altered M2/M1 mRNA and protein ratios, decreasing M2 levels and inhibiting virus replication. Thus, NS1-BP-hnRNPK complex is a key mediator of influenza A virus gene expression. Influenza A virus is a major human pathogen, which causes approximately 500,000 deaths/year worldwide. In pandemic years, influenza infection can lead to even higher mortality rates, as in 1918, when ∼30–50 million deaths occurred worldwide. In this manuscript, we identified a novel function for the cellular protein termed NS1-BP as a regulator of the influenza A virus life cycle. We found that NS1-BP, together with other host factors, mediates the expression of a key viral protein termed M2. NS1-BP and its interacting partner hnRNP K specifically regulate alternative splicing of the viral M1 mRNA segment, which generates the M2 mRNA that is translated into the essential viral M2 protein. The M2 protein is key for viral uncoating and entry into the host cell cytoplasm. Altogether, inhibition of NS1-BP and hnRNP K functions regulate influenza A virus gene expression and replication. In sum, these studies revealed new functions for the cellular proteins NS1-BP and hnRNP K during viral RNA expression, which facilitate the influenza A virus life cycle.
Collapse
|
35
|
York A, Fodor E. Biogenesis, assembly, and export of viral messenger ribonucleoproteins in the influenza A virus infected cell. RNA Biol 2013; 10:1274-82. [PMID: 23807439 PMCID: PMC3817148 DOI: 10.4161/rna.25356] [Citation(s) in RCA: 43] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022] Open
Abstract
The flow of genetic information from sites of transcription within the nucleus to the cytoplasmic translational machinery of eukaryotic cells is obstructed by a physical blockade, the nuclear double membrane, which must be overcome in order to adhere to the central dogma of molecular biology, DNA makes RNA makes protein. Advancement in the field of cellular and molecular biology has painted a detailed picture of the molecular mechanisms from transcription of genes to mRNAs and their processing that is closely coupled to export from the nucleus. The rules that govern delivering messenger transcripts from the nucleus must be obeyed by influenza A virus, a member of the Orthomyxoviridae that has adopted a nuclear replication cycle. The negative-sense genome of influenza A virus is segmented into eight individual viral ribonucleoprotein (vRNP) complexes containing the viral RNA-dependent RNA polymerase and single-stranded RNA encapsidated in viral nucleoprotein. Influenza A virus mRNAs fall into three major categories, intronless, intron-containing unspliced and spliced. During evolutionary history, influenza A virus has conceived a way of negotiating the passage of viral transcripts from the nucleus to cytoplasmic sites of protein synthesis. The major mRNA nuclear export NXF1 pathway is increasingly implicated in viral mRNA export and this review considers and discusses the current understanding of how influenza A virus exploits the host mRNA export pathway for replication.
Collapse
Affiliation(s)
- Ashley York
- Sir William Dunn School of Pathology; University of Oxford; Oxford, United Kingdom
| | | |
Collapse
|
36
|
Komarova AV, Combredet C, Sismeiro O, Dillies MA, Jagla B, Sanchez David RY, Vabret N, Coppée JY, Vidalain PO, Tangy F. Identification of RNA partners of viral proteins in infected cells. RNA Biol 2013; 10:944-56. [PMID: 23595062 PMCID: PMC4111734 DOI: 10.4161/rna.24453] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2013] [Revised: 03/20/2013] [Accepted: 03/26/2013] [Indexed: 12/20/2022] Open
Abstract
RNA viruses exhibit small-sized genomes encoding few proteins, but still establish complex networks of protein-protein and RNA-protein interactions within a cell to achieve efficient replication and spreading. Deciphering these interactions is essential to reach a comprehensive understanding of the viral infection process. To study RNA-protein complexes directly in infected cells, we developed a new approach based on recombinant viruses expressing tagged viral proteins that were purified together with their specific RNA partners. High-throughput sequencing was then used to identify these RNA molecules. As a proof of principle, this method was applied to measles virus nucleoprotein (MV-N). It revealed that in addition to full-length genomes, MV-N specifically interacted with a unique population of 5' copy-back defective interfering RNA genomes that we characterized. Such RNA molecules were able to induce strong activation of interferon-stimulated response element promoter preferentially via the cytoplasmic pattern recognition receptor RIG-I protein, demonstrating their biological functionality. Thus, this method provides a new platform to explore biologically active RNA-protein networks that viruses establish within infected cells.
Collapse
Affiliation(s)
- Anastassia V. Komarova
- Unité de Génomique virale et Vaccination; Institut Pasteur; CNRS URA-3015; Paris, France
| | - Chantal Combredet
- Unité de Génomique virale et Vaccination; Institut Pasteur; CNRS URA-3015; Paris, France
| | - Odile Sismeiro
- Plateforme Transcriptome et Epigénome – Génopole; Institut Pasteur; Paris, France
| | - Marie-Agnès Dillies
- Plateforme Transcriptome et Epigénome – Génopole; Institut Pasteur; Paris, France
| | - Bernd Jagla
- Plateforme Transcriptome et Epigénome – Génopole; Institut Pasteur; Paris, France
| | | | - Nicolas Vabret
- Unité de Génomique virale et Vaccination; Institut Pasteur; CNRS URA-3015; Paris, France
| | - Jean-Yves Coppée
- Plateforme Transcriptome et Epigénome – Génopole; Institut Pasteur; Paris, France
| | | | - Frédéric Tangy
- Unité de Génomique virale et Vaccination; Institut Pasteur; CNRS URA-3015; Paris, France
| |
Collapse
|
37
|
Yin J, Liu S, Zhu Y. An overview of the highly pathogenic H5N1 influenza virus. Virol Sin 2013; 28:3-15. [PMID: 23325419 PMCID: PMC7090813 DOI: 10.1007/s12250-013-3294-9] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2012] [Accepted: 12/31/2012] [Indexed: 11/17/2022] Open
Abstract
Since the first human case of H5N1 avian influenza virus infection was reported in 1997, this highly pathogenic virus has infected hundreds of people around the world and resulted in many deaths. The ability of H5N1 to cross species boundaries, and the presence of polymorphisms that enhance virulence, present challenges to developing clear strategies to prevent the pandemic spread of this highly pathogenic avian influenza (HPAI) virus. This review summarizes the current understanding of, and recent research on, the avian influenza H5N1 virus, including transmission, virulence, pathogenesis, clinical characteristics, treatment and prevention.
Collapse
Affiliation(s)
- Jingchuan Yin
- The State Key laboratory of Virology and College of Life Sciences, Wuhan University, Wuhan 430072, China
| | | | | |
Collapse
|
38
|
Wise HM, Hutchinson EC, Jagger BW, Stuart AD, Kang ZH, Robb N, Schwartzman LM, Kash JC, Fodor E, Firth AE, Gog JR, Taubenberger JK, Digard P. Identification of a novel splice variant form of the influenza A virus M2 ion channel with an antigenically distinct ectodomain. PLoS Pathog 2012; 8:e1002998. [PMID: 23133386 PMCID: PMC3486900 DOI: 10.1371/journal.ppat.1002998] [Citation(s) in RCA: 165] [Impact Index Per Article: 13.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2011] [Accepted: 09/13/2012] [Indexed: 01/25/2023] Open
Abstract
Segment 7 of influenza A virus produces up to four mRNAs. Unspliced transcripts encode M1, spliced mRNA2 encodes the M2 ion channel, while protein products from spliced mRNAs 3 and 4 have not previously been identified. The M2 protein plays important roles in virus entry and assembly, and is a target for antiviral drugs and vaccination. Surprisingly, M2 is not essential for virus replication in a laboratory setting, although its loss attenuates the virus. To better understand how IAV might replicate without M2, we studied the reversion mechanism of an M2-null virus. Serial passage of a virus lacking the mRNA2 splice donor site identified a single nucleotide pseudoreverting mutation, which restored growth in cell culture and virulence in mice by upregulating mRNA4 synthesis rather than by reinstating mRNA2 production. We show that mRNA4 encodes a novel M2-related protein (designated M42) with an antigenically distinct ectodomain that can functionally replace M2 despite showing clear differences in intracellular localisation, being largely retained in the Golgi compartment. We also show that the expression of two distinct ion channel proteins is not unique to laboratory-adapted viruses but, most notably, was also a feature of the 1983 North American outbreak of H5N2 highly pathogenic avian influenza virus. In identifying a 14th influenza A polypeptide, our data reinforce the unexpectedly high coding capacity of the viral genome and have implications for virus evolution, as well as for understanding the role of M2 in the virus life cycle. Influenza A virus is a pathogen capable of infecting a wide range of avian and mammalian hosts, causing seasonal epidemics and pandemics in humans. In recent years, the unexpected coding capacity of the virus has begun to be unravelled, with the identification of three more protein products (PB1-F2, PB1-N40 and PA-X) on top of the 10 viral proteins originally identified 30 years ago. Here, we identify a 14th primary translation product, made from segment 7. Previously established protein products from segment 7 include the matrix (M1) and ion channel (M2) proteins. M2, made from a spliced transcript, has multiple roles in the virus lifecycle including in entry and budding. In a laboratory setting, it is possible to generate M2 deficient viruses, but these are highly attenuated. However, upon serial passage a virus lacking the M2 splice donor site quickly recovered wild type growth properties, without reverting the original mutation. Instead we found a compensatory single nucleotide mutation had upregulated another segment 7 mRNA. This mRNA encoded a novel M2-like protein with a variant extracellular domain, which we called M42. M42 compensated for loss of M2 in tissue culture cells and animals, although it displayed some differences in subcellular localisation. Our study therefore identifies a further novel influenza protein and gives insights into the evolution of the virus.
Collapse
MESH Headings
- Alternative Splicing
- Animals
- Birds
- Cell Line, Tumor
- Disease Outbreaks
- Dogs
- Humans
- Influenza A Virus, H5N2 Subtype/genetics
- Influenza A Virus, H5N2 Subtype/metabolism
- Influenza in Birds/epidemiology
- Influenza in Birds/genetics
- Influenza in Birds/metabolism
- Influenza, Human/epidemiology
- Influenza, Human/genetics
- Influenza, Human/metabolism
- Mice
- Mice, Inbred BALB C
- North America/epidemiology
- RNA, Messenger/biosynthesis
- RNA, Messenger/genetics
- RNA, Viral/biosynthesis
- RNA, Viral/genetics
- Viral Matrix Proteins/biosynthesis
- Viral Matrix Proteins/genetics
Collapse
Affiliation(s)
- Helen M. Wise
- Division of Virology, Department of Pathology, University of Cambridge, Cambridge, United Kingdom
- The Roslin Institute, University of Edinburgh, Easter Bush, Midlothian, United Kingdom
| | - Edward C. Hutchinson
- Division of Virology, Department of Pathology, University of Cambridge, Cambridge, United Kingdom
| | - Brett W. Jagger
- Division of Virology, Department of Pathology, University of Cambridge, Cambridge, United Kingdom
- Viral Pathogenesis and Evolution Section, Laboratory of Infectious Diseases, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, Maryland, United States of America
| | - Amanda D. Stuart
- Division of Virology, Department of Pathology, University of Cambridge, Cambridge, United Kingdom
| | - Zi H. Kang
- Division of Virology, Department of Pathology, University of Cambridge, Cambridge, United Kingdom
| | - Nicole Robb
- Sir William Dunn School of Pathology, University of Oxford, Oxford, United Kingdom
| | - Louis M. Schwartzman
- Viral Pathogenesis and Evolution Section, Laboratory of Infectious Diseases, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, Maryland, United States of America
| | - John C. Kash
- Viral Pathogenesis and Evolution Section, Laboratory of Infectious Diseases, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, Maryland, United States of America
| | - Ervin Fodor
- Sir William Dunn School of Pathology, University of Oxford, Oxford, United Kingdom
| | - Andrew E. Firth
- Division of Virology, Department of Pathology, University of Cambridge, Cambridge, United Kingdom
| | - Julia R. Gog
- DAMTP, Centre for Mathematical Sciences, University of Cambridge, Cambridge, United Kingdom
| | - Jeffery K. Taubenberger
- Viral Pathogenesis and Evolution Section, Laboratory of Infectious Diseases, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, Maryland, United States of America
| | - Paul Digard
- Division of Virology, Department of Pathology, University of Cambridge, Cambridge, United Kingdom
- The Roslin Institute, University of Edinburgh, Easter Bush, Midlothian, United Kingdom
- * E-mail:
| |
Collapse
|
39
|
Moss WN, Dela-Moss LI, Priore SF, Turner DH. The influenza A segment 7 mRNA 3' splice site pseudoknot/hairpin family. RNA Biol 2012; 9:1305-10. [PMID: 23064116 PMCID: PMC3597570 DOI: 10.4161/rna.22343] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022] Open
Abstract
The 3′ splice site of the influenza A segment 7 transcript is utilized to produce mRNA for the critical M2 ion-channel protein. In solution a 63 nt fragment that includes this region can adopt two conformations: a pseudoknot and a hairpin. In each conformation, the splice site, a binding site for the SF2/ASF exonic splicing enhancer and a polypyrimidine tract, each exists in a different structural context. The most dramatic difference occurs for the splice site. In the hairpin the splice site is between two residues that are involved in a 2 by 2 nucleotide internal loop. In the pseudoknot, however, these bases are canonically paired within one of the pseudoknotted helices. The conformational switching observed in this region has implications for the regulation of splicing of the segment 7 mRNA. A measure of stability of the structures also shows interesting trends with respect to host specificity: avian strains tend to be the most stable, followed by swine and then human.
Collapse
Affiliation(s)
- Walter N Moss
- Department of Chemistry and Center for RNA Biology, University of Rochester; Rochester, NY, USA
| | | | | | | |
Collapse
|
40
|
Mutations in the M-gene segment can substantially increase replication efficiency of NS1 deletion influenza A virus in MDCK cells. J Virol 2012; 86:12341-50. [PMID: 22951840 DOI: 10.1128/jvi.01725-12] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Influenza viruses unable to express NS1 protein (delNS1) replicate poorly and induce large amounts of interferon (IFN). They are therefore considered candidate viruses for live-attenuated influenza vaccines. Their attenuated replication is generally assumed to result from the inability to counter the antiviral host response, as delNS1 viruses replicate efficiently in Vero cells, which lack IFN expression. In this study, delNS1 virus was parallel passaged on IFN-competent MDCK cells, which resulted in two strains that were able to replicate to high virus titers in MDCK cells due to adaptive mutations especially in the M-gene segment but also in the NP and NS gene segments. Most notable were clustered U-to-C mutations in the M segment of both strains and clustered A-to-G mutations in the NS segment of one strain, which presumably resulted from host cell-mediated RNA editing. The M segment mutations in both strains changed the ratio of M1 to M2 expression, probably by affecting splicing efficiency. In one virus, 2 amino acid substitutions in M1 additionally enhanced virus replication, possibly through changes in the M1 distribution between the nucleus and the cytoplasm. Both adapted viruses induced levels of IFN equal to that of the original delNS1 virus. These results show that the increased replication of the adapted viruses is not primarily due to altered IFN induction but rather is related to changes in M1 expression or localization. The mutations identified in this paper may be used to enhance delNS1 virus replication for vaccine production.
Collapse
|
41
|
Moss WN, Dela-Moss LI, Kierzek E, Kierzek R, Priore SF, Turner DH. The 3' splice site of influenza A segment 7 mRNA can exist in two conformations: a pseudoknot and a hairpin. PLoS One 2012; 7:e38323. [PMID: 22685560 PMCID: PMC3369869 DOI: 10.1371/journal.pone.0038323] [Citation(s) in RCA: 37] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2012] [Accepted: 05/03/2012] [Indexed: 12/29/2022] Open
Abstract
The 3′ splice site of influenza A segment 7 is used to produce mRNA for the M2 ion-channel protein, which is critical to the formation of viable influenza virions. Native gel analysis, enzymatic/chemical structure probing, and oligonucleotide binding studies of a 63 nt fragment, containing the 3′ splice site, key residues of an SF2/ASF splicing factor binding site, and a polypyrimidine tract, provide evidence for an equilibrium between pseudoknot and hairpin structures. This equilibrium is sensitive to multivalent cations, and can be forced towards the pseudoknot by addition of 5 mM cobalt hexammine. In the two conformations, the splice site and other functional elements exist in very different structural environments. In particular, the splice site is sequestered in the middle of a double helix in the pseudoknot conformation, while in the hairpin it resides in a two-by-two nucleotide internal loop. The results suggest that segment 7 mRNA splicing can be controlled by a conformational switch that exposes or hides the splice site.
Collapse
Affiliation(s)
- Walter N. Moss
- Department of Chemistry, Center for RNA Biology, University of Rochester, Rochester, New York, United States of America
| | - Lumbini I. Dela-Moss
- Department of Chemistry, Center for RNA Biology, University of Rochester, Rochester, New York, United States of America
| | - Elzbieta Kierzek
- Institute of Bioorganic Chemistry, Polish Academy of Sciences, Poznan, Noskowskiego, Poland
| | - Ryszard Kierzek
- Institute of Bioorganic Chemistry, Polish Academy of Sciences, Poznan, Noskowskiego, Poland
| | - Salvatore F. Priore
- Department of Chemistry, Center for RNA Biology, University of Rochester, Rochester, New York, United States of America
| | - Douglas H. Turner
- Department of Chemistry, Center for RNA Biology, University of Rochester, Rochester, New York, United States of America
- * E-mail:
| |
Collapse
|
42
|
Forbes NE, Ping J, Dankar SK, Jia JJ, Selman M, Keleta L, Zhou Y, Brown EG. Multifunctional adaptive NS1 mutations are selected upon human influenza virus evolution in the mouse. PLoS One 2012; 7:e31839. [PMID: 22363747 PMCID: PMC3283688 DOI: 10.1371/journal.pone.0031839] [Citation(s) in RCA: 40] [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: 11/04/2011] [Accepted: 01/12/2012] [Indexed: 02/06/2023] Open
Abstract
The role of the NS1 protein in modulating influenza A virulence and host range was assessed by adapting A/Hong Kong/1/1968 (H3N2) (HK-wt) to increased virulence in the mouse. Sequencing the NS genome segment of mouse-adapted variants revealed 11 mutations in the NS1 gene and 4 in the overlapping NEP gene. Using the HK-wt virus and reverse genetics to incorporate mutant NS gene segments, we demonstrated that all NS1 mutations were adaptive and enhanced virus replication (up to 100 fold) in mouse cells and/or lungs. All but one NS1 mutant was associated with increased virulence measured by survival and weight loss in the mouse. Ten of twelve NS1 mutants significantly enhanced IFN-β antagonism to reduce the level of IFN β production relative to HK-wt in infected mouse lungs at 1 day post infection, where 9 mutants induced viral yields in the lung that were equivalent to or significantly greater than HK-wt (up to 16 fold increase). Eight of 12 NS1 mutants had reduced or lost the ability to bind the 30 kDa cleavage and polyadenylation specificity factor (CPSF30) thus demonstrating a lack of correlation with reduced IFN β production. Mutant NS1 genes resulted in increased viral mRNA transcription (10 of 12 mutants), and protein production (6 of 12 mutants) in mouse cells. Increased transcription activity was demonstrated in the influenza mini-genome assay for 7 of 11 NS1 mutants. Although we have shown gain-of-function properties for all mutant NS genes, the contribution of the NEP mutations to phenotypic changes remains to be assessed. This study demonstrates that NS1 is a multifunctional virulence factor subject to adaptive evolution.
Collapse
Affiliation(s)
- Nicole E. Forbes
- Department of Biochemistry, Microbiology and Immunology, Faculty of Medicine, University of Ottawa, Ottawa, Ontario, Canada
- Emerging Pathogens Research Centre, Faculty of Medicine, University of Ottawa, Ottawa, Ontario, Canada
| | - Jihui Ping
- Department of Biochemistry, Microbiology and Immunology, Faculty of Medicine, University of Ottawa, Ottawa, Ontario, Canada
- Emerging Pathogens Research Centre, Faculty of Medicine, University of Ottawa, Ottawa, Ontario, Canada
| | - Samar K. Dankar
- Department of Biochemistry, Microbiology and Immunology, Faculty of Medicine, University of Ottawa, Ottawa, Ontario, Canada
- Emerging Pathogens Research Centre, Faculty of Medicine, University of Ottawa, Ottawa, Ontario, Canada
| | - Jian-Jun Jia
- Department of Biochemistry, Microbiology and Immunology, Faculty of Medicine, University of Ottawa, Ottawa, Ontario, Canada
- Emerging Pathogens Research Centre, Faculty of Medicine, University of Ottawa, Ottawa, Ontario, Canada
| | - Mohammed Selman
- Department of Biochemistry, Microbiology and Immunology, Faculty of Medicine, University of Ottawa, Ottawa, Ontario, Canada
- Emerging Pathogens Research Centre, Faculty of Medicine, University of Ottawa, Ottawa, Ontario, Canada
| | - Liya Keleta
- Department of Biochemistry, Microbiology and Immunology, Faculty of Medicine, University of Ottawa, Ottawa, Ontario, Canada
- Emerging Pathogens Research Centre, Faculty of Medicine, University of Ottawa, Ottawa, Ontario, Canada
| | - Yan Zhou
- Vaccine and Infectious Disease Organization, University of Saskatchewan, Saskatoon, Saskatchewan, Canada
- Canadian Institutes of Health Research (CIHR) Canadian Influenza Pathogenesis Team, University of Ottawa, Ottawa, Ontario, Canada
| | - Earl G. Brown
- Department of Biochemistry, Microbiology and Immunology, Faculty of Medicine, University of Ottawa, Ottawa, Ontario, Canada
- Emerging Pathogens Research Centre, Faculty of Medicine, University of Ottawa, Ottawa, Ontario, Canada
- Canadian Institutes of Health Research (CIHR) Canadian Influenza Pathogenesis Team, University of Ottawa, Ottawa, Ontario, Canada
| |
Collapse
|