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Rigby CV, Sabsay KR, Bisht K, Eggink D, Jalal H, te Velthuis AJW. Evolution of transient RNA structure-RNA polymerase interactions in respiratory RNA virus genomes. Virus Evol 2023; 9:vead056. [PMID: 37692892 PMCID: PMC10492445 DOI: 10.1093/ve/vead056] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2023] [Revised: 08/02/2023] [Accepted: 08/24/2023] [Indexed: 09/12/2023] Open
Abstract
RNA viruses are important human pathogens that cause seasonal epidemics and occasional pandemics. Examples are influenza A viruses (IAV) and coronaviruses (CoV). When emerging IAV and CoV spill over to humans, they adapt to evade immune responses and optimize their replication and spread in human cells. In IAV, adaptation occurs in all viral proteins, including the viral ribonucleoprotein (RNP) complex. RNPs consist of a copy of the viral RNA polymerase, a double-helical coil of nucleoprotein, and one of the eight segments of the IAV RNA genome. The RNA segments and their transcripts are partially structured to coordinate the packaging of the viral genome and modulate viral mRNA translation. In addition, RNA structures can affect the efficiency of viral RNA synthesis and the activation of host innate immune response. Here, we investigated if RNA structures that modulate IAV replication processivity, so-called template loops (t-loops), vary during the adaptation of pandemic and emerging IAV to humans. Using cell culture-based replication assays and in silico sequence analyses, we find that the sensitivity of the IAV H3N2 RNA polymerase to t-loops increased between isolates from 1968 and 2017, whereas the total free energy of t-loops in the IAV H3N2 genome was reduced. This reduction is particularly prominent in the PB1 gene. In H1N1 IAV, we find two separate reductions in t-loop free energy, one following the 1918 pandemic and one following the 2009 pandemic. No destabilization of t-loops is observed in the influenza B virus genome, whereas analysis of SARS-CoV-2 isolates reveals destabilization of viral RNA structures. Overall, we propose that a loss of free energy in the RNA genome of emerging respiratory RNA viruses may contribute to the adaption of these viruses to the human population.
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Affiliation(s)
- Charlotte V Rigby
- Lewis Thomas Laboratory, Department of Molecular Biology, Princeton University, Washington Road, Princeton, NJ 08544, USA
- Department of Pathology, Addenbrooke’s Hospital, University of Cambridge, Hills Road, Cambridge CB2 2QQ, UK
- Addenbrooke’s Hospital, Public Health England, Hills Road, Cambridge CB2 2QQ, UK
| | - Kimberly R Sabsay
- Lewis Thomas Laboratory, Department of Molecular Biology, Princeton University, Washington Road, Princeton, NJ 08544, USA
- Carl Icahn Laboratory, Lewis-Sigler Institute, Princeton University, South Drive, Princeton, NJ 08544, USA
| | - Karishma Bisht
- Lewis Thomas Laboratory, Department of Molecular Biology, Princeton University, Washington Road, Princeton, NJ 08544, USA
| | - Dirk Eggink
- Department of Medical Microbiology, Amsterdam UMC, Meibergdreef 9, Amsterdam 1105 AZ, The Netherlands
| | - Hamid Jalal
- Addenbrooke’s Hospital, Public Health England, Hills Road, Cambridge CB2 2QQ, UK
| | - Aartjan J W te Velthuis
- Lewis Thomas Laboratory, Department of Molecular Biology, Princeton University, Washington Road, Princeton, NJ 08544, USA
- Center for Infectious Disease Control, National Institute for Public Health and the Environment (RIVM), Antonie van Leeuwenhoeklaan 9, Bilthoven 3721 MA, the Netherlands
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2
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Rigby C, Sabsay K, Bisht K, Eggink D, Jalal H, te Velthuis AJ. Evolution of transient RNA structure-RNA polymerase interactions in respiratory RNA virus genomes. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.05.25.542331. [PMID: 37292879 PMCID: PMC10245964 DOI: 10.1101/2023.05.25.542331] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/10/2023]
Abstract
RNA viruses are important human pathogens that cause seasonal epidemics and occasional pandemics. Examples are influenza A viruses (IAV) and coronaviruses (CoV). When emerging IAV and CoV spill over to humans, they adapt to evade immune responses and optimize their replication and spread in human cells. In IAV, adaptation occurs in all viral proteins, including the viral ribonucleoprotein (RNP) complex. RNPs consists of a copy of the viral RNA polymerase, a double-helical coil of nucleoprotein, and one of the eight segments of the IAV RNA genome. The RNA segments and their transcripts are partially structured to coordinate the packaging of the viral genome and modulate viral mRNA translation. In addition, RNA structures can affect the efficiency of viral RNA synthesis and the activation of host innate immune response. Here, we investigated if RNA structures that modulate IAV replication processivity, so called template loops (t-loops), vary during the adaptation of pandemic and emerging IAV to humans. Using cell culture-based replication assays and in silico sequence analyses, we find that the sensitivity of the IAV H3N2 RNA polymerase to t-loops increased between isolates from 1968 and 2017, whereas the total free energy of t-loops in the IAV H3N2 genome was reduced. This reduction is particularly prominent in the PB1 gene. In H1N1 IAV, we find two separate reductions in t-loop free energy, one following the 1918 pandemic and one following the 2009 pandemic. No destabilization of t-loops is observed in the IBV genome, whereas analysis of SARS-CoV-2 isolates reveals destabilization of viral RNA structures. Overall, we propose that a loss of free energy in the RNA genome of emerging respiratory RNA viruses may contribute to the adaption of these viruses to the human population.
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Affiliation(s)
- Charlotte Rigby
- Lewis Thomas Laboratory, Department of Molecular Biology, Princeton University, 08544 New Jersey, United States
- University of Cambridge, Department of Pathology, Addenbrooke’s Hospital, Cambridge CB2 2QQ, United Kingdom
- Public Health England, Addenbrooke’s Hospital, Cambridge CB2 2QQ, United Kingdom
| | - Kimberly Sabsay
- Lewis Thomas Laboratory, Department of Molecular Biology, Princeton University, 08544 New Jersey, United States
- Sigler Institute, Princeton University, Princeton, NJ 08544, United States
| | - Karishma Bisht
- Lewis Thomas Laboratory, Department of Molecular Biology, Princeton University, 08544 New Jersey, United States
| | - Dirk Eggink
- Department of Medical Microbiology, Amsterdam UMC, Amsterdam, The Netherlands
- Center for Infectious Disease Control, National Institute for Public Health and the Environment (RIVM), Bilthoven, the Netherlands
| | - Hamid Jalal
- Public Health England, Addenbrooke’s Hospital, Cambridge CB2 2QQ, United Kingdom
| | - Aartjan J.W. te Velthuis
- Lewis Thomas Laboratory, Department of Molecular Biology, Princeton University, 08544 New Jersey, United States
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3
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Zhao N, Ho JSY, Meng F, Zheng S, Kurland AP, Tian L, Rea-Moreno M, Song X, Seo JS, Kaniskan HÜ, Te Velthuis AJW, Tortorella D, Chen YW, Johnson JR, Jin J, Marazzi I. Generation of host-directed and virus-specific antivirals using targeted protein degradation promoted by small molecules and viral RNA mimics. Cell Host Microbe 2023; 31:1154-1169.e10. [PMID: 37339625 PMCID: PMC10528416 DOI: 10.1016/j.chom.2023.05.030] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2022] [Revised: 04/24/2023] [Accepted: 05/30/2023] [Indexed: 06/22/2023]
Abstract
Targeted protein degradation (TPD), as exemplified by proteolysis-targeting chimera (PROTAC), is an emerging drug discovery platform. PROTAC molecules, which typically contain a target protein ligand linked to an E3 ligase ligand, recruit a target protein to the E3 ligase to induce its ubiquitination and degradation. Here, we applied PROTAC approaches to develop broad-spectrum antivirals targeting key host factors for many viruses and virus-specific antivirals targeting unique viral proteins. For host-directed antivirals, we identified a small-molecule degrader, FM-74-103, that elicits selective degradation of human GSPT1, a translation termination factor. FM-74-103-mediated GSPT1 degradation inhibits both RNA and DNA viruses. Among virus-specific antivirals, we developed viral RNA oligonucleotide-based bifunctional molecules (Destroyers). As a proof of principle, RNA mimics of viral promoter sequences were used as heterobifunctional molecules to recruit and target influenza viral polymerase for degradation. This work highlights the broad utility of TPD to rationally design and develop next-generation antivirals.
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Affiliation(s)
- Nan Zhao
- 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, USA
| | - Jessica Sook Yuin Ho
- Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Fanye Meng
- Mount Sinai Center for Therapeutics Discovery, Departments of Pharmacological Sciences and Oncological Sciences, Tisch Cancer Institute, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Simin Zheng
- Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Andrew P Kurland
- Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Lu Tian
- Department of Otolaryngology, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Martha Rea-Moreno
- Department of Otolaryngology, Master of Science in Biomedical Science Program, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Xiangyang Song
- Mount Sinai Center for Therapeutics Discovery, Departments of Pharmacological Sciences and Oncological Sciences, Tisch Cancer Institute, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Ji-Seon Seo
- Department of Biological Chemistry, University of California, Irvine, Irvine, CA 92697, USA
| | - H Ümit Kaniskan
- Mount Sinai Center for Therapeutics Discovery, Departments of Pharmacological Sciences and Oncological Sciences, Tisch Cancer Institute, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Aartjan J W Te Velthuis
- Lewis Thomas Laboratory, Department of Molecular Biology, Princeton University, Princeton, NJ 08544, USA
| | - Domenico Tortorella
- Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Ya-Wen Chen
- Department of Otolaryngology, Department of Cell, Developmental and Regenerative Biology, Black Family Stem Cell Institute, Institute for Airway Sciences, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Jeffrey R Johnson
- Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Jian Jin
- Mount Sinai Center for Therapeutics Discovery, Departments of Pharmacological Sciences and Oncological Sciences, Tisch Cancer Institute, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA.
| | - Ivan Marazzi
- 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, USA; Department of Biological Chemistry, University of California, Irvine, Irvine, CA 92697, USA.
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4
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Pan M, Zhang W, Xiao Y, Lai Y, Cao M, Wang J, Deng T. The Hierarchical Sequence Requirements of the H1 Subtype-Specific Noncoding Regions of Influenza A Virus. Microbiol Spectr 2022; 10:e0315322. [PMID: 36287543 PMCID: PMC9769845 DOI: 10.1128/spectrum.03153-22] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2022] [Accepted: 09/16/2022] [Indexed: 01/10/2023] Open
Abstract
The genome of influenza A virus consists of eight single-stranded viral RNA (vRNA) segments. The nonconserved noncoding regions (NCRs) at the 3' and 5' termini of each segment show extremely low divergence and mutation rate. They appear as segment specific among the eight segments and also subtype specific among different subtype-determinant hemagglutinin (HA) and neuraminidase (NA) segments. In order to acquire in-depth knowledge on the sequence requirements of the segment-specific or subtype-specific NCRs (ssNCRs), we, in the context of WSN (H1N1) reverse genetics, designed a virus random nucleotide selection assay (vRNSA) in which we generated pHW2000-HA plasmid libraries with random nucleotides in each grouped nucleotide positions in the 3' and 5' H1-ssNCRs, followed by virus rescue, serial passage, and deep sequencing. The resulting sequence logos present a visualized dynamic overview of the hierarchical sequence requirements of the 3' and 5' H1-ssNCRs. It showed that, in the process of continuous passage, the 3' H1-ssNCR, in general, stabilized more quickly than the 5' H1-ssNCR. The nucleotides close to the highly conserved 3' and 5' promoter regions showed higher sequence stringency than nucleotides away from the promoter regions. All stabilized sequences displayed a common feature of high A/U ratios. Especially with our mutational function analyses, we demonstrate that the 3' promoter-proximal nucleotides could cooperatively exert a direct effect on the transcription and replication of the HA segment. Together, these results provide in-depth knowledge for understanding the NCRs of influenza A virus. IMPORTANCE The segment-specific and subtype-specific nonconserved noncoding regions (ssNCRs) at both 3' and 5' ends of viral RNA segments of influenza A virus are largely conserved among the same segments of different viruses. However, the function-related sequence requirements of these ssNCRs remain unclear. In this study, through a novel self-designed vRNSA approach, we present a visualized dynamic overview diagram directly reflecting the hierarchical sequence requirements within and between the 3' and 5' H1-ssNCRs. The in-depth functional mutagenesis analyses further revealed that specific nucleotides in the 3' promoter-proximal region could cooperatively exert a direct effect on viral RNA transcription and replication. This work further advanced our knowledge in understanding the nonconserved noncoding regions of influenza A viruses.
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Affiliation(s)
- Minglei Pan
- NHC Key Laboratory of Systems Biology of Pathogens, Institute of Pathogen Biology, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Wenyu Zhang
- NHC Key Laboratory of Systems Biology of Pathogens, Institute of Pathogen Biology, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Yue Xiao
- NHC Key Laboratory of Systems Biology of Pathogens, Institute of Pathogen Biology, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Yuerong Lai
- CAS Key Laboratory of Pathogen Microbiology and Immunology, Institute of Microbiology, Chinese Academy of Sciences, Beijing, China
| | - Mengmeng Cao
- NHC Key Laboratory of Systems Biology of Pathogens, Institute of Pathogen Biology, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Jianwei Wang
- NHC Key Laboratory of Systems Biology of Pathogens, Institute of Pathogen Biology, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Tao Deng
- NHC Key Laboratory of Systems Biology of Pathogens, Institute of Pathogen Biology, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
- CAS Key Laboratory of Pathogen Microbiology and Immunology, Institute of Microbiology, Chinese Academy of Sciences, Beijing, China
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5
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de Rozières CM, Pequeno A, Shahabi S, Lucas TM, Godula K, Ghosh G, Joseph S. PABP1 Drives the Selective Translation of Influenza A Virus mRNA. J Mol Biol 2022; 434:167460. [PMID: 35074482 PMCID: PMC8897273 DOI: 10.1016/j.jmb.2022.167460] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2021] [Revised: 12/22/2021] [Accepted: 01/13/2022] [Indexed: 11/26/2022]
Abstract
Influenza A virus (IAV) is a human-infecting pathogen with a history of causing seasonal epidemics and on several occasions worldwide pandemics. Infection by IAV causes a dramatic decrease in host mRNA translation, whereas viral mRNAs are efficiently translated. The IAV mRNAs have a highly conserved 5'-untranslated region (5'UTR) that is rich in adenosine residues. We show that the human polyadenylate binding protein 1 (PABP1) binds to the 5'UTR of the viral mRNAs. The interaction of PABP1 with the viral 5'UTR makes the translation of viral mRNAs more resistant to canonical cap-dependent translation inhibition than model mRNAs. Additionally, PABP1 bound to the viral 5'UTR can recruit eIF4G in an eIF4E-independent manner. These results indicate that PABP1 bound to the viral 5'UTR may promote eIF4E-independent translation initiation.
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Affiliation(s)
- Cyrus M de Rozières
- Department of Chemistry and Biochemistry, University of California, San Diego, La Jolla, CA 92093-0314, USA
| | - Alberto Pequeno
- Department of Chemistry and Biochemistry, University of California, San Diego, La Jolla, CA 92093-0314, USA
| | - Shandy Shahabi
- Department of Chemistry and Biochemistry, University of California, San Diego, La Jolla, CA 92093-0314, USA
| | - Taryn M Lucas
- Department of Chemistry and Biochemistry, University of California, San Diego, La Jolla, CA 92093-0314, USA
| | - Kamil Godula
- Department of Chemistry and Biochemistry, University of California, San Diego, La Jolla, CA 92093-0314, USA
| | - Gourisankar Ghosh
- Department of Chemistry and Biochemistry, University of California, San Diego, La Jolla, CA 92093-0314, USA
| | - Simpson Joseph
- Department of Chemistry and Biochemistry, University of California, San Diego, La Jolla, CA 92093-0314, USA.
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6
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Abstract
Influenza A virus has long been known to encode 10 major polypeptides, produced, almost without exception, by every natural isolate of the virus. These polypeptides are expressed in readily detectable amounts during infection and are either fully essential or their loss severely attenuates virus replication. More recent work has shown that this core proteome is elaborated by expression of a suite of accessory gene products that tend to be expressed at lower levels through noncanonical transcriptional and/or translational events. Expression and activity of these accessory proteins varies between virus strains and is nonessential (sometimes inconsequential) for virus replication in cell culture, but in many cases has been shown to affect virulence and/or transmission in vivo. This review describes, when known, the expression mechanisms and functions of this influenza A virus accessory proteome and discusses its significance and evolution.
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Affiliation(s)
- Rute M Pinto
- The Roslin Institute, University of Edinburgh, Midlothian EH25 9RG, United Kingdom
| | - Samantha Lycett
- The Roslin Institute, University of Edinburgh, Midlothian EH25 9RG, United Kingdom
| | - Eleanor Gaunt
- The Roslin Institute, University of Edinburgh, Midlothian EH25 9RG, United Kingdom
| | - Paul Digard
- The Roslin Institute, University of Edinburgh, Midlothian EH25 9RG, United Kingdom
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7
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Bamunuarachchi G, Pushparaj S, Liu L. Interplay between host non-coding RNAs and influenza viruses. RNA Biol 2021; 18:767-784. [PMID: 33404285 PMCID: PMC8078518 DOI: 10.1080/15476286.2021.1872170] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2020] [Revised: 12/28/2020] [Accepted: 01/01/2021] [Indexed: 01/20/2023] Open
Abstract
Influenza virus infection through seasonal epidemics and occasional pandemics has been a major public health concern for decades. Incomplete protection from vaccination and increased antiviral resistance due to frequent mutations of influenza viruses have led to a continuous need for new therapeutic options. The functional significance of host protein and influenza virus interactions has been established, but relatively less is known about the interaction of host noncoding RNAs, including microRNAs and long noncoding RNAs, with influenza viruses. In this review, we summarize host noncoding RNA profiles during influenza virus infection and the regulation of influenza virus infection by host noncoding RNAs. Influenza viral non-coding RNAs are briefly discussed. Increased understanding of the molecular regulation of influenza viral replication will be beneficial in identifying potential therapeutic targets against the influenza virus.
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Affiliation(s)
- Gayan Bamunuarachchi
- Oklahoma Center for Respiratory and Infectious Diseases, Oklahoma State University, Stillwater, Oklahoma, USA
- Lundberg-Kienlen Lung Biology and Toxicology Laboratory, Department of Physiological Sciences, Oklahoma State University, Stillwater, USA
- Department of Physiological Sciences, Oklahoma State University, Stillwater, USA
| | - Samuel Pushparaj
- Oklahoma Center for Respiratory and Infectious Diseases, Oklahoma State University, Stillwater, Oklahoma, USA
- Lundberg-Kienlen Lung Biology and Toxicology Laboratory, Department of Physiological Sciences, Oklahoma State University, Stillwater, USA
- Department of Physiological Sciences, Oklahoma State University, Stillwater, USA
| | - Lin Liu
- Oklahoma Center for Respiratory and Infectious Diseases, Oklahoma State University, Stillwater, Oklahoma, USA
- Lundberg-Kienlen Lung Biology and Toxicology Laboratory, Department of Physiological Sciences, Oklahoma State University, Stillwater, USA
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8
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Li X, Gu M, Zheng Q, Gao R, Liu X. Packaging signal of influenza A virus. Virol J 2021; 18:36. [PMID: 33596956 PMCID: PMC7890907 DOI: 10.1186/s12985-021-01504-4] [Citation(s) in RCA: 28] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2020] [Accepted: 02/02/2021] [Indexed: 12/15/2022] Open
Abstract
Influenza A virus (IAV) contains a genome with eight single-stranded, negative-sense RNA segments that encode 17 proteins. During its assembly, all eight separate viral RNA (vRNA) segments are incorporated into virions in a selective manner. Evidence suggested that the highly selective genome packaging mechanism relies on RNA-RNA or protein-RNA interactions. The specific structures of each vRNA that contribute to mediating the packaging of the vRNA into virions have been described and identified as packaging signals. Abundant research indicated that sequences required for genome incorporation are not series and are varied among virus genotypes. The packaging signals play important roles in determining the virus replication, genome incorporation and genetic reassortment of influenza A virus. In this review, we discuss recent studies on influenza A virus packaging signals to provide an overview of their characteristics and functions.
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Affiliation(s)
- Xiuli Li
- Animal Infectious Disease Laboratory, College of Veterinary Medicine, Yangzhou University, 48 East Wenhui Road, Yangzhou, Jiangsu, China
| | - Min Gu
- Animal Infectious Disease Laboratory, College of Veterinary Medicine, Yangzhou University, 48 East Wenhui Road, Yangzhou, Jiangsu, China
| | - Qinmei Zheng
- Animal Infectious Disease Laboratory, College of Veterinary Medicine, Yangzhou University, 48 East Wenhui Road, Yangzhou, Jiangsu, China
| | - Ruyi Gao
- Animal Infectious Disease Laboratory, College of Veterinary Medicine, Yangzhou University, 48 East Wenhui Road, Yangzhou, Jiangsu, China
| | - Xiufan Liu
- Animal Infectious Disease Laboratory, College of Veterinary Medicine, Yangzhou University, 48 East Wenhui Road, Yangzhou, Jiangsu, China.
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9
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Rodriguez P, Marcos-Villar L, Zamarreño N, Yángüez E, Nieto A. Mutations of the segment-specific nucleotides at the 3' end of influenza virus NS segment control viral replication. Virology 2019; 539:104-113. [PMID: 31706162 DOI: 10.1016/j.virol.2019.10.015] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2019] [Revised: 10/25/2019] [Accepted: 10/28/2019] [Indexed: 11/28/2022]
Abstract
The vRNAs of influenza A viruses contain 12 and 13 nucleotide-long sequences at their 3' and 5' termini respectively that are highly conserved and constitute the vRNA promoter. These sequences and the next three segment-specific nucleotides show inverted partial complementarity and are followed by several unpaired nucleotides of poorly characterized function at the 3' end. We have performed systematic point-mutations at the segment-specific nucleotides 15-18 of the 3'-end of a NS-like vRNA segment. All NS-like vRNAs containing mutations at position 15, and some at positions 16-18 showed reduced transcription/replication efficiency in a transfection/infection system. In addition, the replication of recombinant viruses containing mutations at position 15 was impaired both in single and multi-cycle experiments. This reduction was the consequence of a decreased expression of the NS segment. The data indicate that NS1 plays a role in the transcription/replication of its own segment, which elicits a global defect on virus replication.
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Affiliation(s)
- Paloma Rodriguez
- Centro Nacional de Biotecnología, C.S.I.C. Darwin 3, Cantoblanco, 28049, Madrid, Spain; CIBER de Enfermedades Respiratorias CIBERES, Spain
| | - Laura Marcos-Villar
- Centro Nacional de Biotecnología, C.S.I.C. Darwin 3, Cantoblanco, 28049, Madrid, Spain; CIBER de Enfermedades Respiratorias CIBERES, Spain
| | - Noelia Zamarreño
- Centro Nacional de Biotecnología, C.S.I.C. Darwin 3, Cantoblanco, 28049, Madrid, Spain; CIBER de Enfermedades Respiratorias CIBERES, Spain
| | - Emilio Yángüez
- Centro Nacional de Biotecnología, C.S.I.C. Darwin 3, Cantoblanco, 28049, Madrid, Spain; CIBER de Enfermedades Respiratorias CIBERES, Spain
| | - Amelia Nieto
- Centro Nacional de Biotecnología, C.S.I.C. Darwin 3, Cantoblanco, 28049, Madrid, Spain; CIBER de Enfermedades Respiratorias CIBERES, Spain.
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10
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Analysis of the Variability in the Non-Coding Regions of Influenza A Viruses. Vet Sci 2018; 5:vetsci5030076. [PMID: 30149635 PMCID: PMC6165000 DOI: 10.3390/vetsci5030076] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/04/2018] [Revised: 08/14/2018] [Accepted: 08/22/2018] [Indexed: 01/20/2023] Open
Abstract
The genomes of influenza A viruses (IAVs) comprise eight negative-sense single-stranded RNA segments. In addition to the protein-coding region, each segment possesses 5′ and 3′ non-coding regions (NCR) that are important for transcription, replication and packaging. The NCRs contain both conserved and segment-specific sequences, and the impacts of variability in the NCRs are not completely understood. Full NCRs have been determined from some viruses, but a detailed analysis of potential variability in these regions among viruses from different host groups and locations has not been performed. To evaluate the degree of conservation in NCRs among different viruses, we sequenced the NCRs of IAVs isolated from different wild bird host groups (ducks, gulls and seabirds). We then extended our study to include NCRs available from the National Center for Biotechnology Information (NCBI) Influenza Virus Database, which allowed us to analyze a wider variety of host species and more HA and NA subtypes. We found that the amount of variability within the NCRs varies among segments, with the greatest variation found in the HA and NA and the least in the M and NS segments. Overall, variability in NCR sequences was correlated with the coding region phylogeny, suggesting vertical coevolution of the (coding sequence) CDS and NCR regions.
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11
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Levina AS, Repkova MN, Chelobanov BP, Bessudnova EV, Mazurkova NA, Stetsenko DA, Zarytova VF. Impact of delivery method on antiviral activity of phosphodiester, phosphorothioate, and phosphoryl guanidine oligonucleotides in MDCK cells infected with H5N1 bird flu virus. Mol Biol 2017. [DOI: 10.1134/s0026893317040136] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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12
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Panthu B, Terrier O, Carron C, Traversier A, Corbin A, Balvay L, Lina B, Rosa-Calatrava M, Ohlmann T. The NS1 Protein from Influenza Virus Stimulates Translation Initiation by Enhancing Ribosome Recruitment to mRNAs. J Mol Biol 2017; 429:3334-3352. [PMID: 28433538 DOI: 10.1016/j.jmb.2017.04.007] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2016] [Revised: 03/24/2017] [Accepted: 04/11/2017] [Indexed: 12/20/2022]
Abstract
The non-structural protein NS1 of influenza A viruses exerts pleiotropic functions during infection. Among these functions, NS1 was shown to be involved in the control of both viral and cellular translation; however, the mechanism by which this occurs remains to be determined. Thus, we have revisited the role of NS1 in translation by using a combination of influenza infection, mRNA reporter transfection, and in vitro functional and biochemical assays. Our data show that the NS1 protein is able to enhance the translation of virtually all tested mRNAs with the exception of constructs bearing the Dicistroviruses Internal ribosome entry segment (IRESes) (DCV and CrPV), suggesting a role at the level of translation initiation. The domain of NS1 required for translation stimulation was mapped to the RNA binding amino-terminal motif of the protein with residues R38 and K41 being critical for activity. Although we show that NS1 can bind directly to mRNAs, it does not correlate with its ability to stimulate translation. This activity rather relies on the property of NS1 to associate with ribosomes and to recruit them to target mRNAs.
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Affiliation(s)
- Baptiste Panthu
- CIRI, International Center for Infectiology Research, Université de Lyon, 69364 Lyon, France; Inserm, U1111, 69364 Lyon, France; Ecole Normale Supérieure de Lyon, 69364 Lyon, France; Université Lyon 1, Centre International de Recherche en Infectiologie, 69364 Lyon, France; CNRS, UMR5308, 69364 Lyon, France
| | - Olivier Terrier
- CIRI, International Center for Infectiology Research, Université de Lyon, 69364 Lyon, France; Inserm, U1111, 69364 Lyon, France; Ecole Normale Supérieure de Lyon, 69364 Lyon, France; Université Lyon 1, Centre International de Recherche en Infectiologie, 69364 Lyon, France; CNRS, UMR5308, 69364 Lyon, France; Laboratoire de Virologie et Pathologie Humaine VirPath, Université Claude Bernard Lyon 1, Hospices Civils de Lyon, Faculté de médecine RTH Laennec, rue Guillaume Paradin, F-69008 Lyon, France
| | - Coralie Carron
- CIRI, International Center for Infectiology Research, Université de Lyon, 69364 Lyon, France; Inserm, U1111, 69364 Lyon, France; Ecole Normale Supérieure de Lyon, 69364 Lyon, France; Université Lyon 1, Centre International de Recherche en Infectiologie, 69364 Lyon, France; CNRS, UMR5308, 69364 Lyon, France; Laboratoire de Virologie et Pathologie Humaine VirPath, Université Claude Bernard Lyon 1, Hospices Civils de Lyon, Faculté de médecine RTH Laennec, rue Guillaume Paradin, F-69008 Lyon, France
| | - Aurélien Traversier
- CIRI, International Center for Infectiology Research, Université de Lyon, 69364 Lyon, France; Inserm, U1111, 69364 Lyon, France; Ecole Normale Supérieure de Lyon, 69364 Lyon, France; Université Lyon 1, Centre International de Recherche en Infectiologie, 69364 Lyon, France; CNRS, UMR5308, 69364 Lyon, France; Laboratoire de Virologie et Pathologie Humaine VirPath, Université Claude Bernard Lyon 1, Hospices Civils de Lyon, Faculté de médecine RTH Laennec, rue Guillaume Paradin, F-69008 Lyon, France
| | - Antoine Corbin
- CIRI, International Center for Infectiology Research, Université de Lyon, 69364 Lyon, France; Inserm, U1111, 69364 Lyon, France; Ecole Normale Supérieure de Lyon, 69364 Lyon, France; Université Lyon 1, Centre International de Recherche en Infectiologie, 69364 Lyon, France; CNRS, UMR5308, 69364 Lyon, France
| | - Laurent Balvay
- CIRI, International Center for Infectiology Research, Université de Lyon, 69364 Lyon, France; Inserm, U1111, 69364 Lyon, France; Ecole Normale Supérieure de Lyon, 69364 Lyon, France; Université Lyon 1, Centre International de Recherche en Infectiologie, 69364 Lyon, France; CNRS, UMR5308, 69364 Lyon, France
| | - Bruno Lina
- CIRI, International Center for Infectiology Research, Université de Lyon, 69364 Lyon, France; Inserm, U1111, 69364 Lyon, France; Ecole Normale Supérieure de Lyon, 69364 Lyon, France; Université Lyon 1, Centre International de Recherche en Infectiologie, 69364 Lyon, France; CNRS, UMR5308, 69364 Lyon, France; Laboratoire de Virologie et Pathologie Humaine VirPath, Université Claude Bernard Lyon 1, Hospices Civils de Lyon, Faculté de médecine RTH Laennec, rue Guillaume Paradin, F-69008 Lyon, France
| | - Manuel Rosa-Calatrava
- CIRI, International Center for Infectiology Research, Université de Lyon, 69364 Lyon, France; Inserm, U1111, 69364 Lyon, France; Ecole Normale Supérieure de Lyon, 69364 Lyon, France; Université Lyon 1, Centre International de Recherche en Infectiologie, 69364 Lyon, France; CNRS, UMR5308, 69364 Lyon, France; Laboratoire de Virologie et Pathologie Humaine VirPath, Université Claude Bernard Lyon 1, Hospices Civils de Lyon, Faculté de médecine RTH Laennec, rue Guillaume Paradin, F-69008 Lyon, France
| | - Théophile Ohlmann
- CIRI, International Center for Infectiology Research, Université de Lyon, 69364 Lyon, France; Inserm, U1111, 69364 Lyon, France; Ecole Normale Supérieure de Lyon, 69364 Lyon, France; Université Lyon 1, Centre International de Recherche en Infectiologie, 69364 Lyon, France; CNRS, UMR5308, 69364 Lyon, France.
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13
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Dual Roles of the Hemagglutinin Segment-Specific Noncoding Nucleotides in the Extended Duplex Region of the Influenza A Virus RNA Promoter. J Virol 2016; 91:JVI.01931-16. [PMID: 27795444 DOI: 10.1128/jvi.01931-16] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2016] [Accepted: 10/18/2016] [Indexed: 01/28/2023] Open
Abstract
We recently reported that the segment-specific noncoding regions (NCRs) of the hemagglutinin (HA) and neuraminidase (NA) segments are subtype specific, varying significantly in sequence and length at both the 3' and 5' ends. Interestingly, we found that nucleotides CC at positions 13 and 14 at the 3' end and GUG at positions 14 to 16 at the 5' end (termed 14' and 16' to distinguish them from 3' positions) are absolutely conserved among all HA subtype-specific NCRs. These HA segment-specific NCR nucleotides are located in the extended duplex region of the viral RNA promoter. In order to understand the significance of these highly conserved HA segment-specific NCR nucleotides in the virus life cycle, we performed extensive mutagenesis on the HA segment-specific NCR nucleotides and studied their functional significance in regulating influenza A virus replication in the context of the HA segment with both RNP reconstitution and virus infection systems. We found that the base pairing of the 3'-end 13 position with the 5'-end 14' position (3'13-5'14') position is critical for RNA promoter activity while the identity of the base pair is critical in determining HA segment packaging. Moreover, the identity of the residue at the 3'-end 14 position is functionally more important in regulating virus genome packaging than in regulating viral RNA synthesis. Taken together, these results demonstrated that the HA segment-specific NCR nucleotides in the extended duplex region of the promoter not only form part of the promoter but also play a key role in controlling virus selective genome packaging. IMPORTANCE The segment-specific complementary nucleotides (13 to 15 in the 3' end and 14' to 16' in the 5' end) in the extended duplex region of the influenza virus RNA promoter vary significantly among different segments and have rarely been studied. Here, we performed mutagenesis analysis of the highly conserved HA segment-specific nucleotides in the extended duplex region and examined their effects on virus replication in the context of the influenza A/WSN/33 (WSN) virus infection. We found that these HA segment-specific nucleotides not only act as a part of the RNA promoter but also play a critical role in HA segment packaging. Therefore, we showed experimentally, for the first time, the requirement of the nucleotides in the extended duplex region for the RNA promoter and also identified specific noncoding residues in regulating HA segment packaging. This work has implications for the development of attenuated vaccine strains and for elucidation the mechanisms of the virus genome packaging.
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14
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Koire A, Gilbert BE, Sucgang R, Zechiedrich L. Repurposed Transcriptomic Data Reveal Small Viral RNA Produced by Influenza Virus during Infection in Mice. PLoS One 2016; 11:e0165729. [PMID: 27788253 PMCID: PMC5082947 DOI: 10.1371/journal.pone.0165729] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2016] [Accepted: 10/17/2016] [Indexed: 11/27/2022] Open
Abstract
Influenza virus, a highly infectious ssRNA virus, replicates in the nucleus of host cells. This unusual feature brings the possibility that the virus may hijack host small noncoding RNA metabolism. Influenza small viral RNA production has been examined in vitro but has not yet been studied in an in vivo setting. We assessed small RNA species from influenza virus during mouse infection by mining publicly available mouse small RNA transcriptome data. We uncovered 26 nt reads corresponding to svRNA, a small viral RNA previously detected in vitro that regulates the transition from transcription to replication during infection, and found a strong positive correlation between svRNA production and host susceptibility to influenza virus infection. We also detected significant overrepresentation of a non-coding 23 nt sequence that we speculate may behave like a miRNA and work with influenza protein NS1 to prevent the transcription and maturation of interferon-stimulated mRNAs.
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Affiliation(s)
- Amanda Koire
- Program in Structural and Computational Biology and Molecular Biophysics, Baylor College of Medicine, Houston, Texas, United States of America
| | - Brian E. Gilbert
- Department of Molecular Virology and Microbiology, Baylor College of Medicine, Houston, Texas, United States of America
| | - Richard Sucgang
- Verna and Marrs McLean Department of Biochemistry and Molecular Biology, Baylor College of Medicine, Houston, Texas, United States of America
| | - Lynn Zechiedrich
- Program in Structural and Computational Biology and Molecular Biophysics, Baylor College of Medicine, Houston, Texas, United States of America
- Department of Molecular Virology and Microbiology, Baylor College of Medicine, Houston, Texas, United States of America
- Verna and Marrs McLean Department of Biochemistry and Molecular Biology, Baylor College of Medicine, Houston, Texas, United States of America
- Department of Pharmacology, Baylor College of Medicine, Houston, Texas, United States of America
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15
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Levina AS, Repkova MN, Bessudnova EV, Filippova EI, Mazurkova NA, Zarytova VF. High antiviral effect of TiO 2·PL-DNA nanocomposites targeted to conservative regions of (-)RNA and (+)RNA of influenza A virus in cell culture. BEILSTEIN JOURNAL OF NANOTECHNOLOGY 2016; 7:1166-1173. [PMID: 27826491 PMCID: PMC5082348 DOI: 10.3762/bjnano.7.108] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/01/2016] [Accepted: 07/20/2016] [Indexed: 05/22/2023]
Abstract
Background: The development of new antiviral drugs based on nucleic acids is under scrutiny. An important problem in this aspect is to find the most vulnerable conservative regions in the viral genome as targets for the action of these agents. Another challenge is the development of an efficient system for their delivery into cells. To solve this problem, we proposed a TiO2·PL-DNA nanocomposite consisting of titanium dioxide nanoparticles and polylysine (PL)-containing oligonucleotides. Results: The TiO2·PL-DNA nanocomposites bearing the DNA fragments targeted to different conservative regions of (-)RNA and (+)RNA of segment 5 of influenza A virus (IAV) were studied for their antiviral activity in MDCK cells infected with the H1N1, H5N1, and H3N2 virus subtypes. Within the negative strand of each of the studied strains, the efficiency of DNA fragments increased in the direction of its 3'-end. Thus, the DNA fragment aimed at the 3'-noncoding region of (-)RNA was the most efficient and inhibited the reproduction of different IAV subtypes by 3-4 orders of magnitude. Although to a lesser extent, the DNA fragments targeted at the AUG region of (+)RNA and the corresponding region of (-)RNA were also active. For all studied viral subtypes, the nanocomposites bearing the DNA fragments targeted to (-)RNA appeared to be more efficient than those containing fragments aimed at the corresponding (+)RNA regions. Conclusion: The proposed TiO2·PL-DNA nanocomposites can be successfully used for highly efficient and site-specific inhibition of influenza A virus of different subtypes. Some patterns of localization of the most vulnerable regions in IAV segment 5 for the action of DNA-based drugs were found. The (-)RNA strand of IAV segment 5 appeared to be more sensitive as compared to (+)RNA.
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Affiliation(s)
- Asya S Levina
- Institute of Chemical Biology and Fundamental Medicine, Siberian Branch of Russian Academy of Sciences, pr. Lavrent’eva 8, Novosibirsk, 630090, Russia
| | - Marina N Repkova
- Institute of Chemical Biology and Fundamental Medicine, Siberian Branch of Russian Academy of Sciences, pr. Lavrent’eva 8, Novosibirsk, 630090, Russia
| | - Elena V Bessudnova
- Institute of Catalysis, Siberian Branch of Russian Academy of Sciences, pr. Lavrent’eva 5, Novosibirsk, 630090, Russia
| | - Ekaterina I Filippova
- FBRI State Research Center of Virology and Biotechnology "Vector", Koltsovo, Novosibirsk region, 630559, Russia
| | - Natalia A Mazurkova
- FBRI State Research Center of Virology and Biotechnology "Vector", Koltsovo, Novosibirsk region, 630559, Russia
| | - Valentina F Zarytova
- Institute of Chemical Biology and Fundamental Medicine, Siberian Branch of Russian Academy of Sciences, pr. Lavrent’eva 8, Novosibirsk, 630090, Russia
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16
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Levina AS, Repkova MN, Mazurkova NA, Makarevich EV, Ismagilov ZR, Zarytova VF. Knockdown of different influenza A virus subtypes in cell culture by a single antisense oligodeoxyribonucleotide. Int J Antimicrob Agents 2015; 46:125-8. [PMID: 25963340 DOI: 10.1016/j.ijantimicag.2015.03.004] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2014] [Revised: 02/04/2015] [Accepted: 03/06/2015] [Indexed: 11/17/2022]
Abstract
Influenza is a heavy socially significant viral infection that affects humans, birds, and wild and domestic animals. The threat of existing and new highly pathogenic subtypes of influenza A virus (IAV) makes it necessary to develop an effective drug that may affect different IAV strains. For this purpose, oligodeoxynucleotides (DNA fragments) attached to titanium dioxide (TiO2) nanoparticles through a polylysine linker, forming TiO2·PL-DNA nanocomposites, that penetrated into cells without transfection agents were used. For the first time, efficient (≥99.9%) suppression of the reproduction of different subtypes of IAV, including highly pathogenic H5N1 and H1N1, was achieved. These results were obtained using the TiO2·PL-DNA nanocomposite bearing a single antisense oligodeoxynucleotide (0.1μM) targeted to the conserved 3'-noncoding region of RNA segment 5, which is common to all tested strains. Very efficient suppression of the reproduction of different subtypes of IAV was probably achieved due to the use of the proposed delivery system for oligonucleotides in the form of the TiO2·PL-DNA nanocomposites. These results indicate the possibility of creating an efficient drug to affect existing and newly emerging pathogenic IAV strains.
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Affiliation(s)
- Asya S Levina
- Institute of Chemical Biology and Fundamental Medicine, Siberian Branch of Russian Academy of Sciences, pr. Lavrent'eva 8, Novosibirsk 630090, Russia
| | - Marina N Repkova
- Institute of Chemical Biology and Fundamental Medicine, Siberian Branch of Russian Academy of Sciences, pr. Lavrent'eva 8, Novosibirsk 630090, Russia
| | - Natalia A Mazurkova
- FBRI State Research Center of Virology and Biotechnology, 'Vector', Koltsovo, Novosibirsk 630559, Russia
| | - Elena V Makarevich
- FBRI State Research Center of Virology and Biotechnology, 'Vector', Koltsovo, Novosibirsk 630559, Russia
| | - Zinfer R Ismagilov
- Institute of Catalysis, Siberian Branch of Russian Academy of Sciences, pr. Lavrent'eva 5, Novosibirsk 630090, Russia
| | - Valentina F Zarytova
- Institute of Chemical Biology and Fundamental Medicine, Siberian Branch of Russian Academy of Sciences, pr. Lavrent'eva 8, Novosibirsk 630090, Russia.
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17
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Díaz A, García K, Navarrete A, Higuera G, Romero J. Virtual screening of gene expression regulatory sites in non-coding regions of the infectious salmon anemia virus. BMC Res Notes 2014; 7:477. [PMID: 25069483 PMCID: PMC4132239 DOI: 10.1186/1756-0500-7-477] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2014] [Accepted: 07/09/2014] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Members of the Orthomyxoviridae family, which contains an important fish pathogen called the infectious salmon anemia virus (ISAV), have a genome consisting of eight segments of single-stranded RNA that encode different viral proteins. Each of these segments is flanked by non-coding regions (NCRs). In other Orthomyxoviruses, sequences have been shown within these NCRs that regulate gene expression and virulence; however, only the sequences of these regions are known in ISAV, and a biological role has not yet been attributed to these regions. This study aims to determine possible functions of the NCRs of ISAV. RESULTS The results suggested an association between the molecular architecture of NCR regions and their role in the viral life cycle. The available NCR sequences from ISAV isolates were compiled, alignments were performed to obtain a consensus sequence, and conserved regions were identified in this consensus sequence. To determine the molecular structure adopted by these NCRs, various bioinformatics tools, including RNAfold, RNAstructure, Sfold, and Mfold, were used. This hypothetical structure, together with a comparison with influenza, yielded reliable secondary structure models that lead to the identification of conserved nucleotide positions on an intergenus level. These models determined which nucleotide positions are involved in the recognition of the vRNA/cRNA by RNA-dependent RNA polymerase (RdRp) or mRNA by the ribosome. CONCLUSIONS The information obtained in this work allowed the proposal of previously unknown sites that are involved in the regulation of different stages of the viral cycle, leading to the identification of new viral targets that may assist future antiviral strategies.
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Affiliation(s)
| | | | | | | | - Jaime Romero
- Instituto de Nutrición y Tecnología de los Alimentos, INTA, Universidad de Chile, Avenida El Líbano #5524, Macul, Santiago, Chile.
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Rapid sequencing of influenza A virus vRNA, cRNA and mRNA non-coding regions. J Virol Methods 2013; 195:26-33. [PMID: 24096269 DOI: 10.1016/j.jviromet.2013.09.005] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2012] [Revised: 09/05/2013] [Accepted: 09/20/2013] [Indexed: 01/17/2023]
Abstract
Characterizing the genomic sequences of influenza A viruses is important for pathophysiological and evolutionary studies. Noncoding regions (NCR) of influenza A virus have been shown to play critical roles in replication and transcription but their sequences are infrequently determined. In this study, a method employing poly(A) addition and SMART (switching mechanism at 5' end of RNA transcript) technology is described for directly determining and discriminating both NCR ends of viral RNA (vRNA), complementary RNA (cRNA), or NCR and cap sequences from viral mRNA. This modified method may also be used to characterize the NCRs of influenza A virus samples in which the RNA has been degraded.
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Surveillance of human influenza A(H3N2) virus from 1999 to 2009 in southern Italy. Epidemiol Infect 2013; 142:933-9. [PMID: 23967903 DOI: 10.1017/s095026881300201x] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
The aim of this study was to evaluate the presence of influenza virus co-infections in humans and changes in the genetic variability of A(H3N2) virus strains in southern Italy from 1999 to 2009. A partial sequence of the haemagglutinin (HA) gene by human influenza H3N2 strains identified in oropharyngeal swabs from patients with influenza-like illness was analysed by DNA sequencing and a phylogenetic analysis was performed. During the seasons 1999-2000, 2002-2003, 2004-2005 and 2008-2009, the influenza viruses circulating belonged to subtype H3N2. However, A(H1N1) subtype virus and B type were respectively prevalent during the 2000-2001, 2006-2007, 2007-2008 and 2001-2002, 2003-2004, 2005-2006 seasons. The HA sequences appeared to be closely related to the sequence of the influenza A vaccine strain. Only the 2002-2003 season was characterized by co-circulation of two viral lineages: A/New York/55/01(H3N2)-like virus of the previous season and A/Fujian/411/02(H3N2)-like virus, a new H3 variant. In this study, over the decade analysed, no significant change was seen in the sequences of the HA gene of H3 viruses isolated.
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Impact of the segment-specific region of the 3'-untranslated region of the influenza A virus PB1 segment on protein expression. Virus Genes 2013; 47:429-38. [PMID: 23949786 DOI: 10.1007/s11262-013-0969-0] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2013] [Accepted: 08/05/2013] [Indexed: 10/26/2022]
Abstract
The 12 and 13 terminal nucleotides in the 3'- and 5'-untranslated regions (UTRs) of the influenza A virus genome, respectively, are important for the transcription of the viral RNA and the translation of mRNA. However, the functions of the segment-specific regions of the UTRs are not well known. We utilized an enhanced green fluorescent protein (eGFP) flanked at both ends by different UTRs (from the eight segments of H1N1 PR8/34) as a reporter gene to evaluate the effects of these UTRs on protein expression in vitro. The results showed that the protein expression levels of NP-eGFP, NS-eGFP, and HA-eGFP were higher than those of the other reporters and that the protein level of PB1-eGFP remained at a relatively low amount 48-h post-transfection. The results revealed that the UTRs of all segments differently affected the protein expression levels and that the effect of the UTRs of PB1 segment on protein expression was significant. The deletion of "UAAA" and "UAAACU" motifs in the PB1-3'-UTR significantly increased the protein expression level by 49.8 and 142.6%, respectively. This finding suggests that the "UAAACU" motif in the PB1-3'-UTR is at least partly responsible for the low protein expression level. By introducing the "UAAACU" motif into other 3'-UTRs (PA, NS, NP, and HA) at similar locations, the eGFP expression was reduced as expected by 56, 61, 22, and 22%, respectively. This result further confirmed that the "UAAACU" motif of the PB1-3'-UTR can inhibit protein expression. Our findings suggest that the segment-specific regions in the UTRs and not just the conserved regions of the UTRs play an important role in the viral protein expression. Additionally, the reported findings may also shed light on novel regulatory mechanism for the influenza A virus genome.
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21
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Adaptation of avian influenza A virus polymerase in mammals to overcome the host species barrier. J Virol 2013; 87:7200-9. [PMID: 23616660 DOI: 10.1128/jvi.00980-13] [Citation(s) in RCA: 170] [Impact Index Per Article: 15.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Avian influenza A viruses, such as the highly pathogenic avian H5N1 viruses, sporadically enter the human population but often do not transmit between individuals. In rare cases, however, they establish a new lineage in humans. In addition to well-characterized barriers to cell entry, one major hurdle which avian viruses must overcome is their poor polymerase activity in human cells. There is compelling evidence that these viruses overcome this obstacle by acquiring adaptive mutations in the polymerase subunits PB1, PB2, and PA and the nucleoprotein (NP) as well as in the novel polymerase cofactor nuclear export protein (NEP). Recent findings suggest that synthesis of the viral genome may represent the major defect of avian polymerases in human cells. While the precise mechanisms remain to be unveiled, it appears that a broad spectrum of polymerase adaptive mutations can act collectively to overcome this defect. Thus, identification and monitoring of emerging adaptive mutations that further increase polymerase activity in human cells are critical to estimate the pandemic potential of avian viruses.
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22
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Suzuki Y, Kobayashi Y. Evolution of complementary nucleotides in 5' and 3' untranslated regions of influenza A virus genomic segments. INFECTION GENETICS AND EVOLUTION 2012; 13:175-9. [PMID: 23146832 DOI: 10.1016/j.meegid.2012.10.007] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/07/2012] [Revised: 09/29/2012] [Accepted: 10/08/2012] [Indexed: 10/27/2022]
Abstract
The genome of influenza A virus comprises 8 segments (segments 1-8) of single-stranded RNA (virion RNA: vRNA) with negative-polarity. All vRNAs share 13 and 12 terminal nucleotides in the 5' and 3' untranslated regions (UTRs), respectively, which are partially complementary and constitute panhandle and corkscrew structures. Here, it is shown, from the analysis of genomic sequences for 506 strains of influenza A virus, that the number of contiguous complementary nucleotides in the 5' and 3' UTRs varies from 4 to 7 among segments. Complementary nucleotides were segment specific and highly conserved in all segments except for segment 6, where in the phylogenetic analysis co-evolution was observed to have occurred between and within subtypes of neuraminidase (NA). Mutations in the terminal sequences sometimes appeared to have caused convergence between subtypes, involving changes in multiple nucleotide positions. These observations suggest that intra-segmental (homologous) recombinations may have taken place for transferring terminal sequences in segment 6.
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Affiliation(s)
- Yoshiyuki Suzuki
- Graduate School of Natural Sciences, Nagoya City University, 1 Yamanohata, Nagoya-shi, Aichi-ken 467-8501, Japan.
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