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RPLP1 and RPLP2 Are Essential Flavivirus Host Factors That Promote Early Viral Protein Accumulation. J Virol 2017; 91:JVI.01706-16. [PMID: 27974556 DOI: 10.1128/jvi.01706-16] [Citation(s) in RCA: 57] [Impact Index Per Article: 8.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2016] [Accepted: 12/06/2016] [Indexed: 12/11/2022] Open
Abstract
The Flavivirus genus contains several arthropod-borne viruses that pose global health threats, including dengue viruses (DENV), yellow fever virus (YFV), and Zika virus (ZIKV). In order to understand how these viruses replicate in human cells, we previously conducted genome-scale RNA interference screens to identify candidate host factors. In these screens, we identified ribosomal proteins RPLP1 and RPLP2 (RPLP1/2) to be among the most crucial putative host factors required for DENV and YFV infection. RPLP1/2 are phosphoproteins that bind the ribosome through interaction with another ribosomal protein, RPLP0, to form a structure termed the ribosomal stalk. RPLP1/2 were validated as essential host factors for DENV, YFV, and ZIKV infection in two human cell lines: A549 lung adenocarcinoma and HuH-7 hepatoma cells, and for productive DENV infection of Aedes aegypti mosquitoes. Depletion of RPLP1/2 caused moderate cell-line-specific effects on global protein synthesis, as determined by metabolic labeling. In A549 cells, global translation was increased, while in HuH-7 cells it was reduced, albeit both of these effects were modest. In contrast, RPLP1/2 knockdown strongly reduced early DENV protein accumulation, suggesting a requirement for RPLP1/2 in viral translation. Furthermore, knockdown of RPLP1/2 reduced levels of DENV structural proteins expressed from an exogenous transgene. We postulate that these ribosomal proteins are required for efficient translation elongation through the viral open reading frame. In summary, this work identifies RPLP1/2 as critical flaviviral host factors required for translation. IMPORTANCE Flaviviruses cause important diseases in humans. Examples of mosquito-transmitted flaviviruses include dengue, yellow fever and Zika viruses. Viruses require a plethora of cellular factors to infect cells, and the ribosome plays an essential role in all viral infections. The ribosome is a complex macromolecular machine composed of RNA and proteins and it is responsible for protein synthesis. We identified two specific ribosomal proteins that are strictly required for flavivirus infection of human cells and mosquitoes: RPLP1 and RPLP2 (RPLP1/2). These proteins are part of a structure known as the ribosomal stalk and help orchestrate the elongation phase of translation. We show that flaviviruses are particularly dependent on the function of RPLP1/2. Our findings suggest that ribosome composition is an important factor for virus translation and may represent a regulatory layer for translation of specific cellular mRNAs.
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Liu ZY, Li XF, Jiang T, Deng YQ, Ye Q, Zhao H, Yu JY, Qin CF. Viral RNA switch mediates the dynamic control of flavivirus replicase recruitment by genome cyclization. eLife 2016; 5. [PMID: 27692070 PMCID: PMC5101012 DOI: 10.7554/elife.17636] [Citation(s) in RCA: 58] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2016] [Accepted: 09/30/2016] [Indexed: 12/23/2022] Open
Abstract
Viral replicase recruitment and long-range RNA interactions are essential for RNA virus replication, yet the mechanism of their interplay remains elusive. Flaviviruses include numerous important human pathogens, e.g., dengue virus (DENV) and Zika virus (ZIKV). Here, we revealed a highly conserved, conformation-tunable cis-acting element named 5′-UAR-flanking stem (UFS) in the flavivirus genomic 5′ terminus. We demonstrated that the UFS was critical for efficient NS5 recruitment and viral RNA synthesis in different flaviviruses. Interestingly, stabilization of the DENV UFS impaired both genome cyclization and vRNA replication. Moreover, the UFS unwound in response to genome cyclization, leading to the decreased affinity of NS5 for the viral 5′ end. Thus, we propose that the UFS is switched by genome cyclization to regulate dynamic RdRp binding for vRNA replication. This study demonstrates that the UFS enables communication between flavivirus genome cyclization and RdRp recruitment, highlighting the presence of switch-like mechanisms among RNA viruses. DOI:http://dx.doi.org/10.7554/eLife.17636.001 Flaviviruses include a large family of viruses that are harmful to human health, such as dengue virus, West Nile virus and Zika virus. Understanding the details of the life cycle of these viruses is important for better controlling and treating the diseases that they cause. The genetic information of flaviviruses is stored in single-stranded molecules of RNA. To form new copies of a virus, the RNA must be replicated in a process that involves two critical steps. First, an enzyme called viral RNA polymerase NS5 must be recruited to a specific end of the RNA strand (known as the 5′ end). Then, the ends of the RNA strand bind together to form a circular loop. However, little is known about whether these two processes are linked, or how they are regulated. Using bioinformatics, biochemical and reverse genetics approaches, Liu et al. have now identified a new section of RNA in the 5′ end of the flavivirus RNA, named the 5′-UAR-flanking stem (or UFS for short), which is critical for viral replication. The UFS plays an important role in efficiently recruiting the NS5 viral RNA polymerase to the 5′ end of the flavivirus RNA. After the RNA forms a circle, the UFS unwinds. This makes the NS5 polymerase less likely to bind to the 5′ end of the RNA. Stabilizing the structure of the UFS impairs the ability of the RNA strand to form a circle, and hence reduces the ability of the RNA to replicate. Thus, the UFS links and enables communication between the processes that form the flavivirus RNA into a circle and that recruit the viral RNA polymerase to the RNA. The structural basis of the interaction between the flavivirus RNA 5′ end, including the UFS element, and the viral RNA polymerase now deserves further investigation. It will be also important to explore whether other types of viruses regulate their replication via a similar mechanism. DOI:http://dx.doi.org/10.7554/eLife.17636.002
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Affiliation(s)
- Zhong-Yu Liu
- Department of Virology, Beijing Institute of Microbiology and Epidemiology, Beijing, China.,State Key Laboratory of Pathogen and Biosecurity, Beijing, China
| | - Xiao-Feng Li
- Department of Virology, Beijing Institute of Microbiology and Epidemiology, Beijing, China.,State Key Laboratory of Pathogen and Biosecurity, Beijing, China
| | - Tao Jiang
- Department of Virology, Beijing Institute of Microbiology and Epidemiology, Beijing, China.,State Key Laboratory of Pathogen and Biosecurity, Beijing, China
| | - Yong-Qiang Deng
- Department of Virology, Beijing Institute of Microbiology and Epidemiology, Beijing, China.,State Key Laboratory of Pathogen and Biosecurity, Beijing, China
| | - Qing Ye
- Department of Virology, Beijing Institute of Microbiology and Epidemiology, Beijing, China
| | - Hui Zhao
- Department of Virology, Beijing Institute of Microbiology and Epidemiology, Beijing, China
| | - Jiu-Yang Yu
- Department of Virology, Beijing Institute of Microbiology and Epidemiology, Beijing, China
| | - Cheng-Feng Qin
- Department of Virology, Beijing Institute of Microbiology and Epidemiology, Beijing, China.,State Key Laboratory of Pathogen and Biosecurity, Beijing, China
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Garcia-Blanco MA, Vasudevan SG, Bradrick SS, Nicchitta C. Flavivirus RNA transactions from viral entry to genome replication. Antiviral Res 2016; 134:244-249. [PMID: 27666184 DOI: 10.1016/j.antiviral.2016.09.010] [Citation(s) in RCA: 55] [Impact Index Per Article: 6.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2016] [Revised: 09/16/2016] [Accepted: 09/22/2016] [Indexed: 11/16/2022]
Abstract
Upon release of the ∼11 kb single-stranded positive polarity dengue virus genomic RNA (gRNA) into the cytoplasm of an infected cell, it serves as the template for translation of the viral polyprotein, which is cleaved into three structural and seven non-structural proteins. The structural organization of the viral replication complex and RNA is not known but it is increasingly becoming evident that the viral gRNA and replication intermediates adopt unique structural features and localize to discrete regions in the infected cell. Both structure and location play multiple roles ranging from evasion of innate immune response to recruitment of viral and host proteins for translation and replication of the message. This review visits the various transactions that the viral gRNA undergoes between entry and RNA synthesis with the view that some of these events may be targeted by antiviral compounds. This article forms part of a symposium on flavivirus drug discovery in Antiviral Research.
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Affiliation(s)
- Mariano A Garcia-Blanco
- Programme of Emerging Infectious Diseases, Duke-NUS Medical School, Singapore; Department of Biochemistry and Molecular Biology, University of Texas Medical Branch, Galveston, TX, USA.
| | - Subhash G Vasudevan
- Programme of Emerging Infectious Diseases, Duke-NUS Medical School, Singapore.
| | - Shelton S Bradrick
- Department of Biochemistry and Molecular Biology, University of Texas Medical Branch, Galveston, TX, USA
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Viktorovskaya OV, Greco TM, Cristea IM, Thompson SR. Identification of RNA Binding Proteins Associated with Dengue Virus RNA in Infected Cells Reveals Temporally Distinct Host Factor Requirements. PLoS Negl Trop Dis 2016; 10:e0004921. [PMID: 27556644 PMCID: PMC4996428 DOI: 10.1371/journal.pntd.0004921] [Citation(s) in RCA: 48] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2016] [Accepted: 07/22/2016] [Indexed: 12/14/2022] Open
Abstract
BACKGROUND There are currently no vaccines or antivirals available for dengue virus infection, which can cause dengue hemorrhagic fever and death. A better understanding of the host pathogen interaction is required to develop effective therapies to treat DENV. In particular, very little is known about how cellular RNA binding proteins interact with viral RNAs. RNAs within cells are not naked; rather they are coated with proteins that affect localization, stability, translation and (for viruses) replication. METHODOLOGY/PRINCIPAL FINDINGS Seventy-nine novel RNA binding proteins for dengue virus (DENV) were identified by cross-linking proteins to dengue viral RNA during a live infection in human cells. These cellular proteins were specific and distinct from those previously identified for poliovirus, suggesting a specialized role for these factors in DENV amplification. Knockdown of these proteins demonstrated their function as viral host factors, with evidence for some factors acting early, while others late in infection. Their requirement by DENV for efficient amplification is likely specific, since protein knockdown did not impair the cell fitness for viral amplification of an unrelated virus. The protein abundances of these host factors were not significantly altered during DENV infection, suggesting their interaction with DENV RNA was due to specific recruitment mechanisms. However, at the global proteome level, DENV altered the abundances of proteins in particular classes, including transporter proteins, which were down regulated, and proteins in the ubiquitin proteasome pathway, which were up regulated. CONCLUSIONS/SIGNIFICANCE The method for identification of host factors described here is robust and broadly applicable to all RNA viruses, providing an avenue to determine the conserved or distinct mechanisms through which diverse viruses manage the viral RNA within cells. This study significantly increases the number of cellular factors known to interact with DENV and reveals how DENV modulates and usurps cellular proteins for efficient amplification.
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Affiliation(s)
- Olga V. Viktorovskaya
- Department of Microbiology, University of Alabama at Birmingham, Birmingham, Alabama, United States of America
| | - Todd M. Greco
- Department of Molecular Biology, Princeton University, Princeton, New Jersey, United States of America
| | - Ileana M. Cristea
- Department of Molecular Biology, Princeton University, Princeton, New Jersey, United States of America
| | - Sunnie R. Thompson
- Department of Microbiology, University of Alabama at Birmingham, Birmingham, Alabama, United States of America
- * E-mail:
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Jan E, Mohr I, Walsh D. A Cap-to-Tail Guide to mRNA Translation Strategies in Virus-Infected Cells. Annu Rev Virol 2016; 3:283-307. [PMID: 27501262 DOI: 10.1146/annurev-virology-100114-055014] [Citation(s) in RCA: 94] [Impact Index Per Article: 11.8] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
Although viruses require cellular functions to replicate, their absolute dependence upon the host translation machinery to produce polypeptides indispensable for their reproduction is most conspicuous. Despite their incredible diversity, the mRNAs produced by all viruses must engage cellular ribosomes. This has proven to be anything but a passive process and has revealed a remarkable array of tactics for rapidly subverting control over and dominating cellular regulatory pathways that influence translation initiation, elongation, and termination. Besides enforcing viral mRNA translation, these processes profoundly impact host cell-intrinsic immune defenses at the ready to deny foreign mRNA access to ribosomes and block protein synthesis. Finally, genome size constraints have driven the evolution of resourceful strategies for maximizing viral coding capacity. Here, we review the amazing strategies that work to regulate translation in virus-infected cells, highlighting both virus-specific tactics and the tremendous insight they provide into fundamental translational control mechanisms in health and disease.
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Affiliation(s)
- Eric Jan
- Department of Biochemistry and Molecular Biology, University of British Columbia, Vancouver, British Columbia V6T 1Z3, Canada;
| | - Ian Mohr
- Department of Microbiology and New York University Cancer Institute, New York University School of Medicine, New York, NY 10016;
| | - Derek Walsh
- Department of Microbiology-Immunology, Feinberg School of Medicine, Northwestern University, Chicago, Illinois 60611;
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Zhu Z, Chan JFW, Tee KM, Choi GKY, Lau SKP, Woo PCY, Tse H, Yuen KY. Comparative genomic analysis of pre-epidemic and epidemic Zika virus strains for virological factors potentially associated with the rapidly expanding epidemic. Emerg Microbes Infect 2016; 5:e22. [PMID: 26980239 PMCID: PMC4820678 DOI: 10.1038/emi.2016.48] [Citation(s) in RCA: 142] [Impact Index Per Article: 17.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2016] [Accepted: 03/03/2016] [Indexed: 12/21/2022]
Abstract
Less than 20 sporadic cases of human Zika virus (ZIKV) infection were reported in Africa and Asia before 2007, but large outbreaks involving up to 73% of the populations on the Pacific islands have started since 2007, and spread to the Americas in 2014. Moreover, the clinical manifestation of ZIKV infection has apparently changed, as evident by increasing reports of neurological complications, such as Guillain-Barré syndrome in adults and congenital anomalies in neonates. We comprehensively compared the genome sequences of pre-epidemic and epidemic ZIKV strains with complete genome or complete polyprotein sequences available in GenBank. Besides the reported phylogenetic clustering of the epidemic strains with the Asian lineage, we found that the topology of phylogenetic tree of all coding regions is the same except that of the non-structural 2B (NS2B) coding region. This finding was confirmed by bootscan analysis and multiple sequence alignment, which suggested the presence of a fragment of genetic recombination at NS2B with that of Spondweni virus. Moreover, the representative epidemic strain possesses one large bulge of nine bases instead of an external loop on the first stem-loop structure at the 3'-untranslated region just distal to the stop codon of the NS5 in the 1947 pre-epidemic prototype strain. Fifteen amino acid substitutions are found in the epidemic strains when compared with the pre-epidemic strains. As mutations in other flaviviruses can be associated with changes in virulence, replication efficiency, antigenic epitopes and host tropism, further studies would be important to ascertain the biological significance of these genomic changes.
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Affiliation(s)
- Zheng Zhu
- Department of Microbiology, The University of Hong Kong, Hong Kong, China
| | - Jasper Fuk-Woo Chan
- Department of Microbiology, The University of Hong Kong, Hong Kong, China
- State Key Laboratory of Emerging Infectious Diseases, The University of Hong Kong, Hong Kong, China
- Research Centre of Infection and Immunology, The University of Hong Kong, Hong Kong, China
- Carol Yu Centre for Infection, The University of Hong Kong, Hong Kong, China
| | - Kah-Meng Tee
- Department of Microbiology, The University of Hong Kong, Hong Kong, China
| | - Garnet Kwan-Yue Choi
- Research Centre of Infection and Immunology, The University of Hong Kong, Hong Kong, China
| | - Susanna Kar-Pui Lau
- Department of Microbiology, The University of Hong Kong, Hong Kong, China
- State Key Laboratory of Emerging Infectious Diseases, The University of Hong Kong, Hong Kong, China
- Research Centre of Infection and Immunology, The University of Hong Kong, Hong Kong, China
- Carol Yu Centre for Infection, The University of Hong Kong, Hong Kong, China
| | - Patrick Chiu-Yat Woo
- Department of Microbiology, The University of Hong Kong, Hong Kong, China
- State Key Laboratory of Emerging Infectious Diseases, The University of Hong Kong, Hong Kong, China
- Research Centre of Infection and Immunology, The University of Hong Kong, Hong Kong, China
- Carol Yu Centre for Infection, The University of Hong Kong, Hong Kong, China
| | - Herman Tse
- Department of Microbiology, The University of Hong Kong, Hong Kong, China
- State Key Laboratory of Emerging Infectious Diseases, The University of Hong Kong, Hong Kong, China
- Research Centre of Infection and Immunology, The University of Hong Kong, Hong Kong, China
- Carol Yu Centre for Infection, The University of Hong Kong, Hong Kong, China
| | - Kwok-Yung Yuen
- Department of Microbiology, The University of Hong Kong, Hong Kong, China
- State Key Laboratory of Emerging Infectious Diseases, The University of Hong Kong, Hong Kong, China
- Research Centre of Infection and Immunology, The University of Hong Kong, Hong Kong, China
- Carol Yu Centre for Infection, The University of Hong Kong, Hong Kong, China
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57
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Son M, Choi H, Kim KH. Specific binding of Fusarium graminearum Hex1 protein to untranslated regions of the genomic RNA of Fusarium graminearum virus 1 correlates with increased accumulation of both strands of viral RNA. Virology 2016; 489:202-11. [PMID: 26773381 DOI: 10.1016/j.virol.2015.12.013] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2015] [Revised: 12/14/2015] [Accepted: 12/22/2015] [Indexed: 11/25/2022]
Abstract
The HEX1 gene of Fusarium graminearum was previously reported to be required for the efficient accumulation of Fusarium graminearum virus 1 (FgV1) RNA in its host. To investigate the molecular mechanism underlying the production of FgHEX1 and the replication of FgV1 viral RNA, we conducted electrophoretic mobility shift assays (EMSA) with recombinant FgHex1 protein and RNA sequences derived from various regions of FgV1 genomic RNA. These analyses demonstrated that FgHex1 and both the 5'- and 3'-untranslated regions of plus-strand FgV1 RNA formed complexes. To determine whether FgHex1 protein affects FgV1 replication, we quantified accumulation viral RNAs in protoplasts and showed that both (+)- and (-)-strands of FgV1 RNAs were increased in the over-expression mutant and decreased in the deletion mutant. These results indicate that the FgHex1 functions in the synthesis of both strands of FgV1 RNA and therefore in FgV1 replication probably by specifically binding to the FgV1 genomic RNA.
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Affiliation(s)
- Moonil Son
- Department of Agricultural Biotechnology, Seoul National University, Seoul, Korea; Center for Fungal Pathogenesis, Seoul National University, Seoul, Korea; Research Institute of Agriculture and Life Sciences, Seoul National University, Seoul, Korea
| | - Hoseong Choi
- Department of Agricultural Biotechnology, Seoul National University, Seoul, Korea
| | - Kook-Hyung Kim
- Department of Agricultural Biotechnology, Seoul National University, Seoul, Korea; Center for Fungal Pathogenesis, Seoul National University, Seoul, Korea; Research Institute of Agriculture and Life Sciences, Seoul National University, Seoul, Korea; Plant Genomics and Breeding Institute, Seoul National University, Seoul, Korea.
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58
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Characterization of RyDEN (C19orf66) as an Interferon-Stimulated Cellular Inhibitor against Dengue Virus Replication. PLoS Pathog 2016; 12:e1005357. [PMID: 26735137 PMCID: PMC4703206 DOI: 10.1371/journal.ppat.1005357] [Citation(s) in RCA: 72] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2015] [Accepted: 12/02/2015] [Indexed: 12/13/2022] Open
Abstract
Dengue virus (DENV) is one of the most important arthropod-borne pathogens that cause life-threatening diseases in humans. However, no vaccine or specific antiviral is available for dengue. As seen in other RNA viruses, the innate immune system plays a key role in controlling DENV infection and disease outcome. Although the interferon (IFN) response, which is central to host protective immunity, has been reported to limit DENV replication, the molecular details of how DENV infection is modulated by IFN treatment are elusive. In this study, by employing a gain-of-function screen using a type I IFN-treated cell-derived cDNA library, we identified a previously uncharacterized gene, C19orf66, as an IFN-stimulated gene (ISG) that inhibits DENV replication, which we named Repressor of yield of DENV (RyDEN). Overexpression and gene knockdown experiments revealed that expression of RyDEN confers resistance to all serotypes of DENV in human cells. RyDEN expression also limited the replication of hepatitis C virus, Kunjin virus, Chikungunya virus, herpes simplex virus type 1, and human adenovirus. Importantly, RyDEN was considered to be a crucial effector molecule in the IFN-mediated anti-DENV response. When affinity purification-mass spectrometry analysis was performed, RyDEN was revealed to form a complex with cellular mRNA-binding proteins, poly(A)-binding protein cytoplasmic 1 (PABPC1), and La motif-related protein 1 (LARP1). Interestingly, PABPC1 and LARP1 were found to be positive modulators of DENV replication. Since RyDEN influenced intracellular events on DENV replication and, suppression of protein synthesis from DENV-based reporter construct RNA was also observed in RyDEN-expressing cells, our data suggest that RyDEN is likely to interfere with the translation of DENV via interaction with viral RNA and cellular mRNA-binding proteins, resulting in the inhibition of virus replication in infected cells.
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Identification of Proteins Bound to Dengue Viral RNA In Vivo Reveals New Host Proteins Important for Virus Replication. mBio 2016; 7:e01865-15. [PMID: 26733069 PMCID: PMC4725007 DOI: 10.1128/mbio.01865-15] [Citation(s) in RCA: 57] [Impact Index Per Article: 7.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022] Open
Abstract
Dengue virus is the most prevalent cause of arthropod-borne infection worldwide. Due to the limited coding capacity of the viral genome and the complexity of the viral life cycle, host cell proteins play essential roles throughout the course of viral infection. Host RNA-binding proteins mediate various aspects of virus replication through their physical interactions with viral RNA. Here we describe a technique designed to identify such interactions in the context of infected cells using UV cross-linking followed by antisense-mediated affinity purification and mass spectrometry. Using this approach, we identified interactions, several of them novel, between host proteins and dengue viral RNA in infected Huh7 cells. Most of these interactions were subsequently validated using RNA immunoprecipitation. Using small interfering RNA (siRNA)-mediated gene silencing, we showed that more than half of these host proteins are likely involved in regulating virus replication, demonstrating the utility of this method in identifying biologically relevant interactions that may not be identified using traditional in vitro approaches. Dengue virus is the most prevalent cause of arthropod-borne infection worldwide. Viral RNA molecules physically interact with cellular RNA-binding proteins (RBPs) throughout the course of infection; the identification of such interactions will lead to the elucidation of the molecular mechanisms of virus replication. Until now, the identification of host proteins bound to dengue viral RNA has been accomplished using in vitro strategies. Here, we used a method for the specific purification of dengue viral ribonucleoprotein (RNP) complexes from infected cells and subsequently identified the associated proteins by mass spectrometry. We then validated a functional role for the majority of these proteins in mediating efficient virus replication. This approach has broad relevance to virology and RNA biology, as it could theoretically be used to purify any viral RNP complex of interest.
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60
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Phillips SL, Garcia-Blanco MA, Bradrick SS. Antisense-mediated affinity purification of dengue virus ribonucleoprotein complexes from infected cells. Methods 2015; 91:13-19. [PMID: 26276314 DOI: 10.1016/j.ymeth.2015.08.008] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2015] [Revised: 08/10/2015] [Accepted: 08/11/2015] [Indexed: 10/23/2022] Open
Abstract
The identification of RNA-binding proteins that physically associate with viral RNA molecules during infection can provide insight into the molecular mechanisms of RNA virus replication. Until recently, such RNA-protein interactions have been identified predominantly with the use of in vitro assays that may not accurately reflect associations that occur in the context of a living cell. Here we describe a method for the specific affinity purification of dengue virus RNA and associated proteins using in vivo cross-linking followed by antisense-mediated affinity purification. RNA-binding proteins that specifically co-purify with viral RNA using this method can be identified en masse by mass spectrometry. This strategy can potentially be adapted to the purification of any viral RNA species of interest.
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Affiliation(s)
- Stacia L Phillips
- Department of Biochemistry and Molecular Biology, University of Texas Medical Branch, 301 University Blvd., Galveston, TX 77555-1055, United States; Department of Microbiology and Molecular Genetics, Center for RNA Biology and Department of Medicine, Duke University, 213 Research Drive, Durham, NC 27710, United States
| | - Mariano A Garcia-Blanco
- Department of Biochemistry and Molecular Biology, University of Texas Medical Branch, 301 University Blvd., Galveston, TX 77555-1055, United States; Department of Microbiology and Molecular Genetics, Center for RNA Biology and Department of Medicine, Duke University, 213 Research Drive, Durham, NC 27710, United States
| | - Shelton S Bradrick
- Department of Biochemistry and Molecular Biology, University of Texas Medical Branch, 301 University Blvd., Galveston, TX 77555-1055, United States; Department of Microbiology and Molecular Genetics, Center for RNA Biology and Department of Medicine, Duke University, 213 Research Drive, Durham, NC 27710, United States.
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Katsarou K, Rao ALN, Tsagris M, Kalantidis K. Infectious long non-coding RNAs. Biochimie 2015; 117:37-47. [PMID: 25986218 DOI: 10.1016/j.biochi.2015.05.005] [Citation(s) in RCA: 28] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2015] [Accepted: 05/07/2015] [Indexed: 02/06/2023]
Abstract
Long non protein coding RNAs (lncRNAs) constitute a large category of the RNA world, able to regulate different biological processes. In this review we are focusing on infectious lncRNAs, their classification, pathogenesis and impact on the infected organisms. Here they are presented in two separate groups: 'dependent lncRNAs' (comprising satellites RNA, Hepatitis D virus and lncRNAs of viral origin) which need a helper virus and 'independent lncRNAs' (viroids) that can self-replicate. Even though these lncRNA do not encode any protein, their structure and/or sequence comprise all the necessary information to drive specific interactions with host factors and regulate several cellular functions. These new data that have emerged during the last few years concerning lncRNAs modify the way we understand molecular biology's 'central dogma' and give new perspectives for applications and potential therapeutic strategies.
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Affiliation(s)
- Konstantina Katsarou
- Institute of Molecular Biology and Biotechnology, Foundation for Research and Technology, Heraklion, Crete, Greece
| | - A L N Rao
- Department of Plant Pathology and Microbiology, University of California, Riverside, CA, 92521-01222, USA
| | - Mina Tsagris
- Department of Biology, University of Crete, Heraklion, Crete, Greece
| | - Kriton Kalantidis
- Institute of Molecular Biology and Biotechnology, Foundation for Research and Technology, Heraklion, Crete, Greece; Department of Biology, University of Crete, Heraklion, Crete, Greece.
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Griseri P, Pagès G. Control of pro-angiogenic cytokine mRNA half-life in cancer: the role of AU-rich elements and associated proteins. J Interferon Cytokine Res 2015; 34:242-54. [PMID: 24697202 DOI: 10.1089/jir.2013.0140] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023] Open
Abstract
Control of mRNA half-life plays a central role in normal development and disease. Several pathological conditions, such as inflammation and cancer, tightly correlate with deregulation in mRNA stability of pro-inflammatory genes. Among these, pro-angiogenesis cytokines, which play a crucial role in the formation of new blood vessels, normally show rapid mRNA decay patterns. The mRNA half-life of these genes appears to be regulated by mRNA-binding proteins that interact with AU-rich elements (AREs) in the 3'-untranslated region of mRNAs. Some of these RNA-binding proteins, such as tristetraprolin (TTP), ARE RNA-binding protein 1, and KH-type splicing regulatory protein, normally promote mRNA degradation. Conversely, other proteins, such as embryonic lethal abnormal vision-like protein 1 (HuR) and polyadenylate-binding protein-interacting protein 2, act as antagonists, stabilizing the mRNA. The steady state levels of mRNA-binding proteins and their relative ratio is often perturbed in human cancers and associated with invasion and aggressiveness. Compelling evidence also suggests that underexpression of TTP and overexpression of HuR may be a useful prognostic and predictive marker in breast, colon, prostate, and brain cancers, indicating a potential therapeutic approach for these tumors. In this review, we summarize the main mechanisms involved in the regulation of mRNA decay of pro-angiogenesis cytokines in different cancers and discuss the interactions between the AU-rich-binding proteins and their mRNA targets.
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Affiliation(s)
- Paola Griseri
- 1 U.O.C Medical Genetics, Institute Giannina Gaslini , Genoa, Italy
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63
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Dong Y, Yang J, Ye W, Wang Y, Miao Y, Ding T, Xiang C, Lei Y, Xu Z. LSm1 binds to the Dengue virus RNA 3' UTR and is a positive regulator of Dengue virus replication. Int J Mol Med 2015; 35:1683-9. [PMID: 25872476 DOI: 10.3892/ijmm.2015.2169] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2014] [Accepted: 02/25/2015] [Indexed: 11/06/2022] Open
Abstract
Dengue virus (DENV) is a mosquito-transmitted flavivirus that can cause severe disease in humans. The DENV positive strand RNA genome contains 5' and 3' untranslated regions (UTRs) that have been shown to be required for virus replication and interaction with host cell proteins. In the present study LSm1 was identified as a host cellular protein involved in DENV RNA replication. By using two independent methodologies, we demonstrated a critical interaction between LSm1 and the 3' UTR of DENV. Furthermore, the confocal immunofluorescence analysis showed that the interaction between LSm1 and viral RNA is located in P-body around nucleoli in the cytoplasm. LSm1 knockdown by siRNA specifically reduced the levels of viral RNA in DENV-infected cells and infectious DENV particles in the supernatant. These results provide evidence that LSm1 binding to the DENV RNA 3' UTR positively regulates DENV RNA replication.
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Affiliation(s)
- Yangchao Dong
- Department of Microbiology, Faculty of Preclinical Medicine, The Fourth Military Medical University, Xi'an, Shaanxi 710032, P.R. China
| | - Jing Yang
- Department of Microbiology, Faculty of Preclinical Medicine, The Fourth Military Medical University, Xi'an, Shaanxi 710032, P.R. China
| | - Wei Ye
- Department of Microbiology, Faculty of Preclinical Medicine, The Fourth Military Medical University, Xi'an, Shaanxi 710032, P.R. China
| | - Yuan Wang
- Department of Microbiology, Faculty of Preclinical Medicine, The Fourth Military Medical University, Xi'an, Shaanxi 710032, P.R. China
| | - Yunbo Miao
- Department of Microbiology, Faculty of Preclinical Medicine, The Fourth Military Medical University, Xi'an, Shaanxi 710032, P.R. China
| | - Tianbing Ding
- Department of Microbiology, Faculty of Preclinical Medicine, The Fourth Military Medical University, Xi'an, Shaanxi 710032, P.R. China
| | - Chen Xiang
- Department of Orthopaedics, Tangdu Hospital, The Fourth Military Medical University, Xi'an, Shaanxi 710038, P.R. China
| | - Yingfeng Lei
- Department of Microbiology, Faculty of Preclinical Medicine, The Fourth Military Medical University, Xi'an, Shaanxi 710032, P.R. China
| | - Zhikai Xu
- Department of Microbiology, Faculty of Preclinical Medicine, The Fourth Military Medical University, Xi'an, Shaanxi 710032, P.R. China
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Lloyd RE. Nuclear proteins hijacked by mammalian cytoplasmic plus strand RNA viruses. Virology 2015; 479-480:457-74. [PMID: 25818028 PMCID: PMC4426963 DOI: 10.1016/j.virol.2015.03.001] [Citation(s) in RCA: 59] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2014] [Revised: 01/12/2015] [Accepted: 03/03/2015] [Indexed: 01/18/2023]
Abstract
Plus strand RNA viruses that replicate in the cytoplasm face challenges in supporting the numerous biosynthetic functions required for replication and propagation. Most of these viruses are genetically simple and rely heavily on co-opting cellular proteins, particularly cellular RNA-binding proteins, into new roles for support of virus infection at the level of virus-specific translation, and building RNA replication complexes. In the course of infectious cycles many nuclear-cytoplasmic shuttling proteins of mostly nuclear distribution are detained in the cytoplasm by viruses and re-purposed for their own gain. Many mammalian viruses hijack a common group of the same factors. This review summarizes recent gains in our knowledge of how cytoplasmic RNA viruses use these co-opted host nuclear factors in new functional roles supporting virus translation and virus RNA replication and common themes employed between different virus groups. Nuclear shuttling host proteins are commonly hijacked by RNA viruses to support replication. A limited group of ubiquitous RNA binding proteins are commonly hijacked by a broad range of viruses. Key virus proteins alter roles of RNA binding proteins in different stages of virus replication.
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Affiliation(s)
- Richard E Lloyd
- Department of Molecular Virology and Microbiology, Baylor College of Medicine, Houston, TX 77030, United States.
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65
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Suresh Babu S, Joladarashi D, Jeyabal P, Thandavarayan RA, Krishnamurthy P. RNA-stabilizing proteins as molecular targets in cardiovascular pathologies. Trends Cardiovasc Med 2015; 25:676-83. [PMID: 25801788 DOI: 10.1016/j.tcm.2015.02.006] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/09/2014] [Revised: 01/31/2015] [Accepted: 02/13/2015] [Indexed: 01/08/2023]
Abstract
The stability of mRNA has emerged as a key step in the regulation of eukaryotic gene expression and function. RNA stabilizing proteins (RSPs) contain several RNA recognition motifs, and selectively bind to adenylate-uridylate-rich elements in the 3' untranslated region of several mRNAs leading to altered processing, stability, and translation. These post-transcriptional gene regulations play a critical role in cellular homeostasis; therefore act as molecular switch between 'normal cell' and 'disease state.' Many mRNA binding proteins have been discovered to date, which either stabilize (HuR/HuA, HuB, HuC, HuD) or destabilize (AUF1, tristetraprolin, KSRP) the target transcripts. Although the function of RSPs has been widely studied in cancer biology, its role in cardiovascular pathologies is only beginning to evolve. The current review provides an overall understanding of the potential role of RSPs, specifically HuR-mediated mRNA stability in myocardial infarction, hypertension and hypertrophy. Also, the effect of RSPs on various cellular processes including inflammation, fibrosis, angiogenesis, cell-death, and proliferation and its relevance to cardiovascular pathophysiological processes is presented. We also discuss the potential clinical implications of RSPs as therapeutic targets in cardiovascular diseases.
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Affiliation(s)
- Sahana Suresh Babu
- Department of Cardiovascular Sciences, Center for Cardiovascular Regeneration, Houston Methodist Research Institute, Houston, TX
| | - Darukeshwara Joladarashi
- Department of Cardiovascular Sciences, Center for Cardiovascular Regeneration, Houston Methodist Research Institute, Houston, TX
| | - Prince Jeyabal
- Department of Cardiovascular Sciences, Center for Cardiovascular Regeneration, Houston Methodist Research Institute, Houston, TX
| | - Rajarajan A Thandavarayan
- Department of Cardiovascular Sciences, Center for Cardiovascular Regeneration, Houston Methodist Research Institute, Houston, TX
| | - Prasanna Krishnamurthy
- Department of Cardiovascular Sciences, Center for Cardiovascular Regeneration, Houston Methodist Research Institute, Houston, TX.
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66
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Brinton MA, Basu M. Functions of the 3' and 5' genome RNA regions of members of the genus Flavivirus. Virus Res 2015; 206:108-19. [PMID: 25683510 DOI: 10.1016/j.virusres.2015.02.006] [Citation(s) in RCA: 60] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2015] [Accepted: 02/04/2015] [Indexed: 11/26/2022]
Abstract
The positive sense genomes of members of the genus Flavivirus in the family Flaviviridae are ∼ 11 kb in length and have a 5' type I cap but no 3' poly-A. The 3' and 5' terminal regions contain short conserved sequences that are proposed to be repeated remnants of an ancient sequence. However, the functions of most of these conserved sequences have not yet been determined. The terminal regions of the genome also contain multiple conserved RNA structures. Functional data for many of these structures have been obtained. Three sets of complementary 3' and 5' terminal region sequences, some of which are located in conserved RNA structures, interact to form a panhandle structure that is required for initiation of minus strand RNA synthesis with the 5' terminal structure functioning as the promoter. How the switch from the terminal RNA structure base pairing to the long distance RNA-RNA interaction is triggered and regulated is not well understood but evidence suggests involvement of a cell protein binding to three sites on the 3' terminal RNA structures and a cis-acting metastable 3' RNA element in the 3' terminal RNA structure. Cell proteins may also be involved in facilitating exponential replication of nascent genomic RNA within replication vesicles at later times of the infection cycle. Other conserved RNA structures and/or sequences in the 3' and 5' terminal regions have been proposed to regulate genome translation. Additional functions of the 3' and 5' terminal sequences have also been reported.
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Affiliation(s)
- Margo A Brinton
- Department of Biology, Georgia State University, Atlanta, GA, USA.
| | - Mausumi Basu
- Department of Biology, Georgia State University, Atlanta, GA, USA
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67
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Tuplin A. Diverse roles and interactions of RNA structures during the replication of positive-stranded RNA viruses of humans and animals. J Gen Virol 2015; 96:1497-503. [PMID: 25626680 DOI: 10.1099/vir.0.000066] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/20/2023] Open
Abstract
Positive-stranded RNA viruses include important human, animal and plant pathogens. Their genomes are able to fold into complex structures stabilized by base pairing between individual nucleotides, many of which are highly conserved and have essential functions during virus replication. With new studies and technological advances the diversity of roles, mechanisms and interactions in which such structured viral RNA functions is becoming increasingly clear. It is also evident that many RNA structures do not function as discrete elements but through mechanisms involving multiple, long-range and often dynamic RNARNA interactions. Through a range of examples and recent advances, this review illustrates the diverse roles and mechanisms of structured viral RNA during the replication of positive-stranded RNA viruses infecting humans and animals.
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Affiliation(s)
- Andrew Tuplin
- School of Molecular and Cellular Biology, Faculty of Biological Sciences, University of Leeds, Leeds, LS2 9JT, UK
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68
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Tahiri-Alaoui A, Zhao Y, Sadigh Y, Popplestone J, Kgosana L, Smith LP, Nair V. Poly(A) binding protein 1 enhances cap-independent translation initiation of neurovirulence factor from avian herpesvirus. PLoS One 2014; 9:e114466. [PMID: 25503397 PMCID: PMC4263670 DOI: 10.1371/journal.pone.0114466] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2014] [Accepted: 11/07/2014] [Indexed: 11/19/2022] Open
Abstract
Poly(A) binding protein 1 (PABP1) plays a central role in mRNA translation and stability and is a target by many viruses in diverse manners. We report a novel viral translational control strategy involving the recruitment of PABP1 to the 5' leader internal ribosome entry site (5L IRES) of an immediate-early (IE) bicistronic mRNA that encodes the neurovirulence protein (pp14) from the avian herpesvirus Marek's disease virus serotype 1 (MDV1). We provide evidence for the interaction between an internal poly(A) sequence within the 5L IRES and PABP1 which may occur concomitantly with the recruitment of PABP1 to the poly(A) tail. RNA interference and reverse genetic mutagenesis results show that a subset of virally encoded-microRNAs (miRNAs) targets the inhibitor of PABP1, known as paip2, and therefore plays an indirect role in PABP1 recruitment strategy by increasing the available pool of active PABP1. We propose a model that may offer a mechanistic explanation for the cap-independent enhancement of the activity of the 5L IRES by recruitment of a bona fide initiation protein to the 5' end of the message and that is, from the affinity binding data, still compatible with the formation of 'closed loop' structure of mRNA.
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Affiliation(s)
- Abdessamad Tahiri-Alaoui
- The Pirbright Institute, Ash Road, Pirbright, Woking, Surrey, United Kingdom
- * E-mail: (ATA); (VN)
| | - Yuguang Zhao
- The Division of Structural Biology, The Wellcome Trust Centre for Human Genetics, Oxford University, Oxford, United Kingdom
| | - Yashar Sadigh
- The Pirbright Institute, Ash Road, Pirbright, Woking, Surrey, United Kingdom
| | - James Popplestone
- The Pirbright Institute, Ash Road, Pirbright, Woking, Surrey, United Kingdom
| | - Lydia Kgosana
- The Pirbright Institute, Ash Road, Pirbright, Woking, Surrey, United Kingdom
| | - Lorraine P. Smith
- The Pirbright Institute, Ash Road, Pirbright, Woking, Surrey, United Kingdom
| | - Venugopal Nair
- The Pirbright Institute, Ash Road, Pirbright, Woking, Surrey, United Kingdom
- * E-mail: (ATA); (VN)
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Abstract
Flaviviruses are a genus of (+)ssRNA (positive ssRNA) enveloped viruses that replicate in the cytoplasm of cells of diverse species from arthropods to mammals. Many are important human pathogens such as DENV-1-4 (dengue virus types 1-4), WNV (West Nile virus), YFV (yellow fever virus), JEV (Japanese encephalitis virus) and TBEV (tick-borne encephalitis). Given their RNA genomes it is not surprising that flaviviral life cycles revolve around critical RNA transactions. It is these we highlight in the present article. First, we summarize the mechanisms governing flaviviral replication and the central role of conserved RNA elements and viral protein-RNA interactions in RNA synthesis, translation and packaging. Secondly, we focus on how host RNA-binding proteins both benefit and inhibit flaviviral replication at different stages of their life cycle in mammalian hosts. Thirdly, we cover recent studies on viral non-coding RNAs produced in flavivirus-infected cells and how these RNAs affect various aspects of cellular RNA metabolism. Together, the article puts into perspective the central role of flaviviral RNAs in modulating both viral and cellular functions.
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70
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Selisko B, Wang C, Harris E, Canard B. Regulation of Flavivirus RNA synthesis and replication. Curr Opin Virol 2014; 9:74-83. [PMID: 25462437 DOI: 10.1016/j.coviro.2014.09.011] [Citation(s) in RCA: 67] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2014] [Revised: 09/18/2014] [Accepted: 09/26/2014] [Indexed: 01/21/2023]
Abstract
RNA synthesis and replication of the members of the Flavivirus genus (including dengue, West Nile and Japanese encephalitis viruses) is regulated by a wide variety of mechanisms and actors. These include the sequestration of the RNA-dependent RNA polymerase (RdRp) for functions other than RNA synthesis, regulatory interactions with other viral and host proteins within the replication complex (RC), and regulatory elements within the RNA genome itself. In this review, we discuss our current knowledge of the multiple levels at which Flavivirus RNA synthesis is controlled. We aim to bring together two active research fields: the structural and functional biology of individual proteins of the RC and the impressive wealth of knowledge acquired regarding the viral genomic RNA.
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Affiliation(s)
- Barbara Selisko
- Aix-Marseille Université, AFMB UMR 7257, 13288 Marseille, France; CNRS, AFMB UMR 7257, 13288 Marseille, France
| | - Chunling Wang
- Division of Infectious Diseases and Vaccinology, School of Public Health, University of California, Berkeley, 185 Li Ka Shing Center, Berkeley, CA 94720-3370, USA
| | - Eva Harris
- Division of Infectious Diseases and Vaccinology, School of Public Health, University of California, Berkeley, 185 Li Ka Shing Center, Berkeley, CA 94720-3370, USA
| | - Bruno Canard
- Aix-Marseille Université, AFMB UMR 7257, 13288 Marseille, France; CNRS, AFMB UMR 7257, 13288 Marseille, France.
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71
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Eliseeva IA, Lyabin DN, Ovchinnikov LP. Poly(A)-binding proteins: structure, domain organization, and activity regulation. BIOCHEMISTRY (MOSCOW) 2014; 78:1377-91. [PMID: 24490729 DOI: 10.1134/s0006297913130014] [Citation(s) in RCA: 59] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
Abstract
RNA-binding proteins are of vital importance for mRNA functioning. Among these, poly(A)-binding proteins (PABPs) are of special interest due to their participation in virtually all mRNA-dependent events that is caused by their high affinity for A-rich mRNA sequences. Apart from mRNAs, PABPs interact with many proteins, thus promoting their involvement in cellular events. In the nucleus, PABPs play a role in polyadenylation, determine the length of the poly(A) tail, and may be involved in mRNA export. In the cytoplasm, they participate in regulation of translation initiation and either protect mRNAs from decay through binding to their poly(A) tails or stimulate this decay by promoting mRNA interactions with deadenylase complex proteins. This review presents modern notions of the role of PABPs in mRNA-dependent events; peculiarities of regulation of PABP amount in the cell and activities are also discussed.
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Affiliation(s)
- I A Eliseeva
- Institute of Protein Research, Russian Academy of Sciences, Pushchino, Moscow Region, 142290, Russia.
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72
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Charley PA, Wilusz J. Sponging of cellular proteins by viral RNAs. Curr Opin Virol 2014; 9:14-8. [PMID: 25233339 DOI: 10.1016/j.coviro.2014.09.001] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2014] [Accepted: 09/01/2014] [Indexed: 12/14/2022]
Abstract
Viral RNAs accumulate to high levels during infection and interact with a variety of cellular factors including miRNAs and RNA-binding proteins. Although many of these interactions exist to directly modulate replication, translation and decay of viral transcripts, evidence is emerging that abundant viral RNAs may in certain cases serve as a sponge to sequester host non-coding RNAs and proteins. By effectively reducing the ability of cellular RNA binding proteins to regulate host cell gene expression, viral RNAs can alter the response to infection and favor viral replication. This review focuses on the potential contribution that sequestration of cellular proteins by viral RNAs makes to viral replication and cytopathology.
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Affiliation(s)
- Phillida A Charley
- Colorado State University, Department of Microbiology, Immunology and Pathology, 1682 Campus Delivery, Fort Collins, CO 80523, United States
| | - Jeffrey Wilusz
- Colorado State University, Department of Microbiology, Immunology and Pathology, 1682 Campus Delivery, Fort Collins, CO 80523, United States.
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Abstract
Dengue virus (DENV) is an emerging mosquito-borne human pathogen that affects millions of individuals each year by causing severe and potentially fatal syndromes. Despite intense research efforts, no approved vaccine or antiviral therapy is yet available. Overcoming this limitation requires detailed understanding of the intimate relationship between the virus and its host cell, providing the basis to devise optimal prophylactic and therapeutic treatment options. With the advent of novel high-throughput technologies including functional genomics, transcriptomics, proteomics, and lipidomics, new important insights into the DENV replication cycle and the interaction of this virus with its host cell have been obtained. In this chapter, we provide a comprehensive overview on the current status of the DENV research field, covering every step of the viral replication cycle with a particular focus on virus-host cell interaction. We will also review specific chemical inhibitors targeting cellular factors and processes of relevance for the DENV replication cycle and their possible exploitation for the development of next generation antivirals.
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74
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Chapman EG, Moon SL, Wilusz J, Kieft JS. RNA structures that resist degradation by Xrn1 produce a pathogenic Dengue virus RNA. eLife 2014; 3:e01892. [PMID: 24692447 PMCID: PMC3968743 DOI: 10.7554/elife.01892] [Citation(s) in RCA: 149] [Impact Index Per Article: 14.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2013] [Accepted: 02/25/2014] [Indexed: 12/16/2022] Open
Abstract
Dengue virus is a growing global health threat. Dengue and other flaviviruses commandeer the host cell's RNA degradation machinery to generate the small flaviviral RNA (sfRNA), a noncoding RNA that induces cytopathicity and pathogenesis. Host cell exonuclease Xrn1 likely loads on the 5' end of viral genomic RNA and degrades processively through ∼10 kB of RNA, halting near the 3' end of the viral RNA. The surviving RNA is the sfRNA. We interrogated the architecture of the complete Dengue 2 sfRNA, identifying five independently-folded RNA structures, two of which quantitatively confer Xrn1 resistance. We developed an assay for real-time monitoring of Xrn1 resistance that we used with mutagenesis and RNA folding experiments to show that Xrn1-resistant RNAs adopt a specific fold organized around a three-way junction. Disrupting the junction's fold eliminates the buildup of disease-related sfRNAs in human cells infected with a flavivirus, directly linking RNA structure to sfRNA production. DOI: http://dx.doi.org/10.7554/eLife.01892.001.
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Affiliation(s)
- Erich G Chapman
- Department of Biochemistry and Molecular Genetics, Howard Hughes Medical Institute, University of Colorado Denver School of Medicine, Aurora, United States
| | - Stephanie L Moon
- Department of Microbiology, Immunology and Pathology, Colorado State University, Fort Collins, United States
| | - Jeffrey Wilusz
- Department of Microbiology, Immunology and Pathology, Colorado State University, Fort Collins, United States
| | - Jeffrey S Kieft
- Department of Biochemistry and Molecular Genetics, Howard Hughes Medical Institute, University of Colorado Denver School of Medicine, Aurora, United States
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75
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Sagar V, Murray KE. The mammalian orthoreovirus bicistronic M3 mRNA initiates translation using a 5' end-dependent, scanning mechanism that does not require interaction of 5'-3' untranslated regions. Virus Res 2014; 183:30-40. [PMID: 24486484 DOI: 10.1016/j.virusres.2014.01.018] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2013] [Revised: 01/15/2014] [Accepted: 01/16/2014] [Indexed: 12/12/2022]
Abstract
Mammalian orthoreovirus mRNAs possess short 5' UTR, lack 3' poly(A) tails, and may lack 5' cap structures at late times post-infection. As such, the mechanisms by which these viral mRNAs recruit ribosomes remain completely unknown. Toward addressing this question, we used bicistronic MRV M3 mRNA to analyze the role of 5' and 3' UTRs during MRV protein synthesis. The 5' UTR was found to be dispensable for translation initiation; however, reducing its length promoted increased downstream initiation. Modifying start site Kozak context altered the ratio of upstream to downstream initiation, whereas mutations in the 3' UTR did not. Moreover, an M3 mRNA lacking a 3' UTR was able to rescue MRV infection to WT levels in an siRNA trans-complementation assay. Together, these data allow us to propose a model in which the MRV M3 mRNA initiates translation using a 5' end-dependent, scanning mechanism that does not require the viral mRNA 3' UTR or 5'-3' UTRs interaction.
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Affiliation(s)
- Vidya Sagar
- Department of Biological Sciences, Florida International University, Miami, FL 33199, United States.
| | - Kenneth E Murray
- Department of Biological Sciences, Florida International University, Miami, FL 33199, United States
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76
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Roby JA, Pijlman GP, Wilusz J, Khromykh AA. Noncoding subgenomic flavivirus RNA: multiple functions in West Nile virus pathogenesis and modulation of host responses. Viruses 2014; 6:404-27. [PMID: 24473339 PMCID: PMC3939463 DOI: 10.3390/v6020404] [Citation(s) in RCA: 116] [Impact Index Per Article: 11.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2013] [Revised: 01/13/2014] [Accepted: 01/15/2014] [Indexed: 12/11/2022] Open
Abstract
Flaviviruses are a large group of positive strand RNA viruses transmitted by arthropods that include many human pathogens such as West Nile virus (WNV), Japanese encephalitis virus (JEV), yellow fever virus, dengue virus, and tick-borne encephalitis virus. All members in this genus tested so far are shown to produce a unique subgenomic flavivirus RNA (sfRNA) derived from the 3' untranslated region (UTR). sfRNA is a product of incomplete degradation of genomic RNA by the cell 5'–3' exoribonuclease XRN1 which stalls at highly ordered secondary RNA structures at the beginning of the 3'UTR. Generation of sfRNA results in inhibition of XRN1 activity leading to an increase in stability of many cellular mRNAs. Mutant WNV deficient in sfRNA generation was highly attenuated displaying a marked decrease in cytopathicity in cells and pathogenicity in mice. sfRNA has also been shown to inhibit the antiviral activity of IFN-α/β by yet unknown mechanism and of the RNAi pathway by likely serving as a decoy substrate for Dicer. Thus, sfRNA is involved in modulating multiple cellular pathways to facilitate viral pathogenicity; however the overlying mechanism linking all these multiple functions of sfRNA remains to be elucidated.
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Affiliation(s)
- Justin A Roby
- Australian Infectious Disease Research Centre, School of Chemistry and Molecular Biosciences, The University of Queensland, St. Lucia, Brisbane 4072, Australia.
| | - Gorben P Pijlman
- Laboratory of Virology, Wageningen University, Wageningen, 6708NW, The Netherlands.
| | - Jeffrey Wilusz
- Department of Microbiology, Immunology & Pathology, Colorado State University Fort Collins, CO 80523, USA;.
| | - Alexander A Khromykh
- Australian Infectious Disease Research Centre, School of Chemistry and Molecular Biosciences, The University of Queensland, St. Lucia, Brisbane 4072, Australia.
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77
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Replication cycle and molecular biology of the West Nile virus. Viruses 2013; 6:13-53. [PMID: 24378320 PMCID: PMC3917430 DOI: 10.3390/v6010013] [Citation(s) in RCA: 95] [Impact Index Per Article: 8.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2013] [Revised: 12/12/2013] [Accepted: 12/12/2013] [Indexed: 12/27/2022] Open
Abstract
West Nile virus (WNV) is a member of the genus Flavivirus in the family Flaviviridae. Flaviviruses replicate in the cytoplasm of infected cells and modify the host cell environment. Although much has been learned about virion structure and virion-endosomal membrane fusion, the cell receptor(s) used have not been definitively identified and little is known about the early stages of the virus replication cycle. Members of the genus Flavivirus differ from members of the two other genera of the family by the lack of a genomic internal ribosomal entry sequence and the creation of invaginations in the ER membrane rather than double-membrane vesicles that are used as the sites of exponential genome synthesis. The WNV genome 3' and 5' sequences that form the long distance RNA-RNA interaction required for minus strand initiation have been identified and contact sites on the 5' RNA stem loop for NS5 have been mapped. Structures obtained for many of the viral proteins have provided information relevant to their functions. Viral nonstructural protein interactions are complex and some may occur only in infected cells. Although interactions between many cellular proteins and virus components have been identified, the functions of most of these interactions have not been delineated.
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78
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Balinsky CA, Schmeisser H, Ganesan S, Singh K, Pierson TC, Zoon KC. Nucleolin interacts with the dengue virus capsid protein and plays a role in formation of infectious virus particles. J Virol 2013; 87:13094-106. [PMID: 24027323 PMCID: PMC3838225 DOI: 10.1128/jvi.00704-13] [Citation(s) in RCA: 75] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2013] [Accepted: 09/03/2013] [Indexed: 01/24/2023] Open
Abstract
Dengue virus (DENV) is a mosquito-transmitted flavivirus that can cause severe disease in humans and is considered a reemerging pathogen of significant importance to public health. The DENV capsid (C) protein functions as a structural component of the infectious virion; however, it may have additional functions in the virus replicative cycle. Here, we show that the DENV C protein interacts and colocalizes with the multifunctional host protein nucleolin (NCL). Furthermore, we demonstrate that this interaction can be disrupted by the addition of an NCL binding aptamer (AS1411). Knockdown of NCL with small interfering RNA (siRNA) or treatment of cells with AS1411 results in a significant reduction of viral titers after DENV infection. Western blotting and quantitative RT-PCR (qRT-PCR) analysis revealed no differences in viral RNA or protein levels at early time points postinfection, suggesting a role for NCL in viral morphogenesis. We support this hypothesis by showing that treatment with AS1411 alters the migration characteristics of the viral capsid, as visualized by native electrophoresis. Here, we identify a critical interaction between DENV C protein and NCL that represents a potential new target for the development of antiviral therapeutics.
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Affiliation(s)
- Corey A. Balinsky
- Cytokine Biology Section, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, Maryland, USA
| | - Hana Schmeisser
- Cytokine Biology Section, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, Maryland, USA
| | - Sundar Ganesan
- Biological Imaging Section, Research Technologies Branch, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, Maryland, USA
| | - Kavita Singh
- Structural Biology Unit, Research Technologies Branch, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, Maryland, USA
| | - Theodore C. Pierson
- Viral Pathogenesis Section, Laboratory of Viral Diseases, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, Maryland, USA
| | - Kathryn C. Zoon
- Cytokine Biology Section, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, Maryland, USA
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79
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Norovirus genome circularization and efficient replication are facilitated by binding of PCBP2 and hnRNP A1. J Virol 2013; 87:11371-87. [PMID: 23946460 DOI: 10.1128/jvi.03433-12] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022] Open
Abstract
Sequences and structures within the terminal genomic regions of plus-strand RNA viruses are targets for the binding of host proteins that modulate functions such as translation, RNA replication, and encapsidation. Using murine norovirus 1 (MNV-1), we describe the presence of long-range RNA-RNA interactions that were stabilized by cellular proteins. The proteins potentially responsible for the stabilization were selected based on their ability to bind the MNV-1 genome and/or having been reported to be involved in the stabilization of RNA-RNA interactions. Cell extracts were preincubated with antibodies against the selected proteins and used for coprecipitation reactions. Extracts treated with antibodies to poly(C) binding protein 2 (PCBP2) and heterogeneous nuclear ribonucleoprotein (hnRNP) A1 significantly reduced the 5'-3' interaction. Both PCBP2 and hnRNP A1 recombinant proteins stabilized the 5'-3' interactions and formed ribonucleoprotein complexes with the 5' and 3' ends of the MNV-1 genomic RNA. Mutations within the 3' complementary sequences (CS) that disrupt the 5'-3'-end interactions resulted in a significant reduction of the viral titer, suggesting that the integrity of the 3'-end sequence and/or the lack of complementarity with the 5' end is important for efficient virus replication. Small interfering RNA-mediated knockdown of PCBP2 or hnRNP A1 resulted in a reduction in virus yield, confirming a role for the observed interactions in efficient viral replication. PCBP2 and hnRNP A1 induced the circularization of MNV-1 RNA, as revealed by electron microscopy. This study provides evidence that PCBP2 and hnRNP A1 bind to the 5' and 3' ends of the MNV-1 viral RNA and contribute to RNA circularization, playing a role in the virus life cycle.
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80
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Bai Y, Zhou K, Doudna JA. Hepatitis C virus 3'UTR regulates viral translation through direct interactions with the host translation machinery. Nucleic Acids Res 2013; 41:7861-74. [PMID: 23783572 PMCID: PMC3763534 DOI: 10.1093/nar/gkt543] [Citation(s) in RCA: 56] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/11/2023] Open
Abstract
The 3′ untranslated region (3′UTR) of hepatitis C virus (HCV) messenger RNA stimulates viral translation by an undetermined mechanism. We identified a high affinity interaction, conserved among different HCV genotypes, between the HCV 3′UTR and the host ribosome. The 3′UTR interacts with 40S ribosomal subunit proteins residing primarily in a localized region on the 40S solvent-accessible surface near the messenger RNA entry and exit sites. This region partially overlaps with the site where the HCV internal ribosome entry site was found to bind, with the internal ribosome entry site-40S subunit interaction being dominant. Despite its ability to bind to 40S subunits independently, the HCV 3′UTR only stimulates translation in cis, without affecting the first round translation rate. These observations support a model in which the HCV 3′UTR retains ribosome complexes during translation termination to facilitate efficient initiation of subsequent rounds of translation.
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Affiliation(s)
- Yun Bai
- Department of Molecular and Cell Biology, University of California, Berkeley, CA 94720, USA, Howard Hughes Medical Institute, University of California, Berkeley, CA 94720, USA, Department of Chemistry, University of California, Berkeley, CA 94720, USA and Physical Biosciences Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA
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81
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Lott WB, Doran MR. Do RNA viruses require genome cyclisation for replication? Trends Biochem Sci 2013; 38:350-5. [PMID: 23768999 DOI: 10.1016/j.tibs.2013.04.005] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2013] [Revised: 04/18/2013] [Accepted: 04/29/2013] [Indexed: 11/15/2022]
Abstract
Complementary sequences at the 5' and 3' ends of the dengue virus RNA genome are essential for viral replication, and are believed to cyclise the genome through long-range base pairing in cis. Although consistent with evidence in the literature, this view neglects possible biologically active multimeric forms that are equally consistent with the data. Here, we propose alternative multimeric structures, and suggest that multigenome noncovalent concatemers are more likely to exist under cellular conditions than single cyclised monomers. Concatemers provide a plausible mechanism for the dengue virus to overcome the single-stranded (+)-sense RNA virus dilemma, and can potentially assist genome transport from the virus-induced vesicles into the cytosol.
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Affiliation(s)
- William B Lott
- Cells and Tissue Domain, Infectious Diseases Program, Institute of Health and Biomedical Innovation, Queensland University of Technology, Brisbane, Australia.
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82
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Differential RNA sequence requirement for dengue virus replication in mosquito and mammalian cells. J Virol 2013; 87:9365-72. [PMID: 23760236 DOI: 10.1128/jvi.00567-13] [Citation(s) in RCA: 39] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Dengue virus cycles between mosquitoes and humans. Each host provides a different environment for viral replication, imposing different selective pressures. We identified a sequence in the dengue virus genome that is essential for viral replication in mosquito cells but not in mammalian cells. This sequence is located at the viral 3' untranslated region and folds into a small hairpin structure. A systematic mutational analysis using dengue virus infectious clones and reporter viruses allowed the determination of two putative functions in this cis-acting RNA motif, one linked to the structure and the other linked to the nucleotide sequence. We found that single substitutions that did not alter the hairpin structure did not affect dengue virus replication in mammalian cells but abolished replication in mosquito cells. This is the first sequence identified in a flavivirus genome that is exclusively required for viral replication in insect cells.
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83
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Oral cavity tumors in younger patients show a poor prognosis and do not contain viral RNA. Oral Oncol 2013; 49:525-33. [DOI: 10.1016/j.oraloncology.2013.02.003] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/26/2012] [Accepted: 02/06/2013] [Indexed: 12/12/2022]
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84
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Japanese encephalitis virus non-coding RNA inhibits activation of interferon by blocking nuclear translocation of interferon regulatory factor 3. Vet Microbiol 2013; 166:11-21. [PMID: 23755934 DOI: 10.1016/j.vetmic.2013.04.026] [Citation(s) in RCA: 76] [Impact Index Per Article: 6.9] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2012] [Revised: 04/26/2013] [Accepted: 04/30/2013] [Indexed: 12/24/2022]
Abstract
Noncoding RNA (ncRNA) plays a critical role in modulating a broad range of diseases. All arthropod-borne flaviviruses produce short fragment ncRNA (sfRNA) collinear with highly conserved regions of the 3'-untranslated region (UTR) in the viral genome. We show that the molar ratio of sfRNA to genomic RNA in Japanese encephalitis virus (JEV) persistently infected cells is greater than that in acutely infected cells, indicating an sfRNA role in establishing persistent infection. Transfecting excess quantities of sfRNA into JEV-infected cells reduced interferon-β (IFN-β) promoter activity by 57% and IFN-β mRNA levels by 52%, compared to mock-transfected cells. Transfection of sfRNA into JEV-infected cells also reduced phosphorylation of interferon regulatory factor-3 (IRF-3), the IFN-β upstream regulator, and blocked roughly 30% of IRF-3 nuclear localization. Furthermore, JEV-infected sfRNA transfected cells produced 23% less IFN-β-stimulated apoptosis than mock-transfected groups did. Taken together, these results suggest that sfRNA plays a role against host-cell antiviral responses, prevents cells from undergoing apoptosis, and thus contributes to viral persistence.
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85
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Abstract
The 3' ends of two large noncoding RNAs, MALAT1 (metastasis-associated lung adenocarcinoma transcript 1) and MEN β, are formed by cleavage by RNase P and are capped but not polyadenylated. In the November 1, 2012, issue of Genes & Development, Wilusz and colleagues (pp. 2392-2407) show that when these 3' ends are formed on a GFP reporter, the resulting mRNA is exported to the cytoplasm and translated. The 3' end forms a novel triple-helical structure that supports export and translation as well as a poly(A) tail does.
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Affiliation(s)
- William F Marzluff
- Program in Molecular Biology, Department of Biochemistry and Biophysics, University of North Carolina, Chapel Hill, North Carolina 27599, USA.
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86
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Walsh D, Mathews MB, Mohr I. Tinkering with translation: protein synthesis in virus-infected cells. Cold Spring Harb Perspect Biol 2013; 5:a012351. [PMID: 23209131 DOI: 10.1101/cshperspect.a012351] [Citation(s) in RCA: 178] [Impact Index Per Article: 16.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
Viruses are obligate intracellular parasites, and their replication requires host cell functions. Although the size, composition, complexity, and functions encoded by their genomes are remarkably diverse, all viruses rely absolutely on the protein synthesis machinery of their host cells. Lacking their own translational apparatus, they must recruit cellular ribosomes in order to translate viral mRNAs and produce the protein products required for their replication. In addition, there are other constraints on viral protein production. Crucially, host innate defenses and stress responses capable of inactivating the translation machinery must be effectively neutralized. Furthermore, the limited coding capacity of the viral genome needs to be used optimally. These demands have resulted in complex interactions between virus and host that exploit ostensibly virus-specific mechanisms and, at the same time, illuminate the functioning of the cellular protein synthesis apparatus.
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Affiliation(s)
- Derek Walsh
- Department of Microbiology, New York University School of Medicine, New York, NY 10016, USA.
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87
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Abstract
Viruses have adapted a broad range of unique mechanisms to modulate the cellular translational machinery to ensure viral translation at the expense of cellular protein synthesis. Many of these promote virus-specific translation by use of molecular tags on viral mRNA such as internal ribosome entry sites (IRES) and genome-linked viral proteins (VPg) that bind translation machinery components in unusual ways and promote RNA circularization. This review describes recent advances in understanding some of the mechanisms in which animal virus mRNAs gain an advantage over cellular transcripts, including new structural and biochemical insights into IRES function and novel proteins that function as alternate met-tRNAimet carriers in translation initiation. Comparisons between animal and plant virus mechanisms that promote translation of viral mRNAs are discussed.
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Affiliation(s)
- Lucas C Reineke
- Department of Molecular Virology and Microbiology, Baylor College of Medicine, Houston, TX 77030, USA
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88
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Poly(A)-binding protein facilitates translation of an uncapped/nonpolyadenylated viral RNA by binding to the 3' untranslated region. J Virol 2012; 86:7836-49. [PMID: 22593149 DOI: 10.1128/jvi.00538-12] [Citation(s) in RCA: 36] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022] Open
Abstract
Viruses employ an alternative translation mechanism to exploit cellular resources at the expense of host mRNAs and to allow preferential translation. Plant RNA viruses often lack both a 5' cap and a 3' poly(A) tail in their genomic RNAs. Instead, cap-independent translation enhancer elements (CITEs) located in the 3' untranslated region (UTR) mediate their translation. Although eukaryotic translation initiation factors (eIFs) or ribosomes have been shown to bind to the 3'CITEs, our knowledge is still limited for the mechanism, especially for cellular factors. Here, we searched for cellular factors that stimulate the 3'CITE-mediated translation of Red clover necrotic mosaic virus (RCNMV) RNA1 using RNA aptamer-based one-step affinity chromatography, followed by mass spectrometry analysis. We identified the poly(A)-binding protein (PABP) as one of the key players in the 3'CITE-mediated translation of RCNMV RNA1. We found that PABP binds to an A-rich sequence (ARS) in the viral 3' UTR. The ARS is conserved among dianthoviruses. Mutagenesis and a tethering assay revealed that the PABP-ARS interaction stimulates 3'CITE-mediated translation of RCNMV RNA1. We also found that both the ARS and 3'CITE are important for the recruitment of the plant eIF4F and eIFiso4F factors to the 3' UTR and of the 40S ribosomal subunit to the viral mRNA. Our results suggest that dianthoviruses have evolved the ARS and 3'CITE as substitutes for the 3' poly(A) tail and the 5' cap of eukaryotic mRNAs for the efficient recruitment of eIFs, PABP, and ribosomes to the uncapped/nonpolyadenylated viral mRNA.
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89
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Composition of the sequence downstream of the dengue virus 5' cyclization sequence (dCS) affects viral RNA replication. Virology 2011; 422:346-56. [PMID: 22137186 DOI: 10.1016/j.virol.2011.10.025] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2011] [Revised: 08/11/2011] [Accepted: 10/28/2011] [Indexed: 12/31/2022]
Abstract
RNA replication of dengue virus (DENV) requires an RNA-RNA mediated circularization of the viral genome, which includes at least three sets of complementary RNA sequences on both ends of the genome. The 5' and the 3' untranslated regions form several additional RNA elements that are involved in regulation of translation and required for RNA replication. Communication between the genomic termini results in a structural reorganization of the RNA elements, forming a functional RNA panhandle structure. Here we report that the sequence composition downstream of the 5' CS element in the capsid gene, designated as downstream CS (dCS) sequence - but not the capsid protein - also influences the ability of the viral genome to circularize and hence replicate by modulating the topology of the 5' end. These results provide insights for the design of reporter sub-genomic and genomic mosquito-borne flavivirus constructs and contribute to the understanding of viral RNA replication.
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90
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Fan YH, Nadar M, Chen CC, Weng CC, Lin YT, Chang RY. Small noncoding RNA modulates Japanese encephalitis virus replication and translation in trans. Virol J 2011; 8:492. [PMID: 22040380 PMCID: PMC3221644 DOI: 10.1186/1743-422x-8-492] [Citation(s) in RCA: 36] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/27/2011] [Accepted: 11/01/2011] [Indexed: 12/14/2022] Open
Abstract
Background Sequence and structural elements in the 3'-untranslated region (UTR) of Japanese encephalitis virus (JEV) are known to regulate translation and replication. We previously reported an abundant accumulation of small subgenomic flaviviral RNA (sfRNA) which is collinear with the highly conserved regions of the 3'-UTR in JEV-infected cells. However, function of the sfRNA in JEV life cycle remains unknown. Results Northern blot and real-time RT-PCR analyses indicated that the sfRNA becomes apparent at the time point at which minus-strand RNA (antigenome) reaches a plateau suggesting a role for sfRNA in the regulation of antigenome synthesis. Transfection of minus-sense sfRNA into JEV-infected cells, in order to counter the effects of plus-sense sfRNA, resulted in higher levels of antigenome suggesting that the presence of the sfRNA inhibits antigenome synthesis. Trans-acting effect of sfRNA on JEV translation was studied using a reporter mRNA containing the luciferase gene fused to partial coding regions of JEV and flanked by the respective JEV UTRs. In vivo and in vitro translation revealed that sfRNA inhibited JEV translation. Conclusions Our results indicate that sfRNA modulates viral translation and replication in trans.
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Affiliation(s)
- Yi-Hsin Fan
- Department of Life Science and Institute of Biotechnology, National Dong Hwa University, Hualien 97401, Taiwan
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91
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Le Breton M, Meyniel-Schicklin L, Deloire A, Coutard B, Canard B, de Lamballerie X, Andre P, Rabourdin-Combe C, Lotteau V, Davoust N. Flavivirus NS3 and NS5 proteins interaction network: a high-throughput yeast two-hybrid screen. BMC Microbiol 2011; 11:234. [PMID: 22014111 PMCID: PMC3215679 DOI: 10.1186/1471-2180-11-234] [Citation(s) in RCA: 77] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2011] [Accepted: 10/20/2011] [Indexed: 01/20/2023] Open
Abstract
Background The genus Flavivirus encompasses more than 50 distinct species of arthropod-borne viruses, including several major human pathogens, such as West Nile virus, yellow fever virus, Japanese encephalitis virus and the four serotypes of dengue viruses (DENV type 1-4). Each year, flaviviruses cause more than 100 million infections worldwide, some of which lead to life-threatening conditions such as encephalitis or haemorrhagic fever. Among the viral proteins, NS3 and NS5 proteins constitute the major enzymatic components of the viral replication complex and are essential to the flavivirus life cycle. Results We report here the results of a high-throughput yeast two-hybrid screen to identify the interactions between human host proteins and the flavivirus NS3 and NS5 proteins. Using our screen results and literature curation, we performed a global analysis of the NS3 and NS5 cellular targets based on functional annotation with the Gene Ontology features. We finally created the first flavivirus NS3 and NS5 proteins interaction network and analysed the topological features of this network. Our proteome mapping screen identified 108 human proteins interacting with NS3 or NS5 proteins or both. The global analysis of the cellular targets revealed the enrichment of host proteins involved in RNA binding, transcription regulation, vesicular transport or innate immune response regulation. Conclusions We proposed that the selective disruption of these newly identified host/virus interactions could represent a novel and attractive therapeutic strategy in treating flavivirus infections. Our virus-host interaction map provides a basis to unravel fundamental processes about flavivirus subversion of the host replication machinery and/or immune defence strategy.
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92
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Chritton JJ, Wickens M. A role for the poly(A)-binding protein Pab1p in PUF protein-mediated repression. J Biol Chem 2011; 286:33268-78. [PMID: 21768112 DOI: 10.1074/jbc.m111.264572] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
PUF proteins regulate translation and mRNA stability throughout eukaryotes. Using a cell-free translation assay, we examined the mechanisms of translational repression of PUF proteins in the budding yeast Saccharomyces cerevisiae. We demonstrate that the poly(A)-binding protein Pab1p is required for PUF-mediated translational repression for two distantly related PUF proteins: S. cerevisiae Puf5p and Caenorhabditis elegans FBF-2. Pab1p interacts with oligo(A) tracts in the HO 3'-UTR, a target of Puf5p, to dramatically enhance the efficiency of Puf5p repression. Both the Pab1p ability to activate translation and interact with eukaryotic initiation factor 4G (eIF4G) were required to observe maximal repression by Puf5p. Repression was also more efficient when Pab1p was bound in close proximity to Puf5p. Puf5p may disrupt translation initiation by interfering with the interaction between Pab1p and eIF4G. Finally, we demonstrate two separable mechanisms of translational repression employed by Puf5p: a Pab1p-dependent mechanism and a Pab1p-independent mechanism.
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Affiliation(s)
- Jacqueline J Chritton
- Department of Genetics, University of Wisconsin-Madison, Madison, Wisconsin 53706, USA
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93
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Manzano M, Reichert ED, Polo S, Falgout B, Kasprzak W, Shapiro BA, Padmanabhan R. Identification of cis-acting elements in the 3'-untranslated region of the dengue virus type 2 RNA that modulate translation and replication. J Biol Chem 2011; 286:22521-34. [PMID: 21515677 PMCID: PMC3121397 DOI: 10.1074/jbc.m111.234302] [Citation(s) in RCA: 81] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2011] [Revised: 04/21/2011] [Indexed: 12/30/2022] Open
Abstract
Using the massively parallel genetic algorithm for RNA folding, we show that the core region of the 3'-untranslated region of the dengue virus (DENV) RNA can form two dumbbell structures (5'- and 3'-DBs) of unequal frequencies of occurrence. These structures have the propensity to form two potential pseudoknots between identical five-nucleotide terminal loops 1 and 2 (TL1 and TL2) and their complementary pseudoknot motifs, PK2 and PK1. Mutagenesis using a DENV2 replicon RNA encoding the Renilla luciferase reporter indicated that all four motifs and the conserved sequence 2 (CS2) element within the 3'-DB are important for replication. However, for translation, mutation of TL1 alone does not have any effect; TL2 mutation has only a modest effect in translation, but translation is reduced by ∼60% in the TL1/TL2 double mutant, indicating that TL1 exhibits a cooperative synergy with TL2 in translation. Despite the variable contributions of individual TL and PK motifs in translation, WT levels are achieved when the complementarity between TL1/PK2 and TL2/PK1 is maintained even under conditions of inhibition of the translation initiation factor 4E function mediated by LY294002 via a noncanonical pathway. Taken together, our results indicate that the cis-acting RNA elements in the core region of DENV2 RNA that include two DB structures are required not only for RNA replication but also for optimal translation.
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Affiliation(s)
- Mark Manzano
- From the Department of Microbiology and Immunology, Georgetown University School of Medicine, Washington, D. C. 20057
| | - Erin D. Reichert
- From the Department of Microbiology and Immunology, Georgetown University School of Medicine, Washington, D. C. 20057
| | - Stephanie Polo
- the Center for Biologics Evaluation and Review, Food and Drug Administration, Bethesda, Maryland 20892
| | - Barry Falgout
- the Center for Biologics Evaluation and Review, Food and Drug Administration, Bethesda, Maryland 20892
| | | | - Bruce A. Shapiro
- the Center for Cancer Research Nanobiology Program, NCI-Frederick, National Institutes of Health, Frederick, Maryland 21702
| | - Radhakrishnan Padmanabhan
- From the Department of Microbiology and Immunology, Georgetown University School of Medicine, Washington, D. C. 20057
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94
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Abstract
The regulation of translation has emerged as a major determinant of gene expression and is critical for both normal cellular function and the development of disease. Numerous studies have highlighted the diverse, and sometimes related, mechanisms which underlie the regulation of global translation rates and the translational control of specific mRNAs. In the present paper, we discuss the emerging roles of the basal translation factor PABP [poly(A)-binding protein] in mRNA-specific translational control in metazoa which suggest that PABP function is more complex than first recognized.
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95
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Ribosome binding to a 5' translational enhancer is altered in the presence of the 3' untranslated region in cap-independent translation of turnip crinkle virus. J Virol 2011; 85:4638-53. [PMID: 21389125 DOI: 10.1128/jvi.00005-11] [Citation(s) in RCA: 48] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022] Open
Abstract
Plus-strand RNA viruses without 5' caps require noncanonical mechanisms for ribosome recruitment. A translational enhancer in the 3' untranslated region (UTR) of Turnip crinkle virus (TCV) contains an internal T-shaped structure (TSS) that binds to 60S ribosomal subunits. We now report that the 63-nucleotide (nt) 5' UTR of TCV contains a 19-nt pyrimidine-rich element near the initiation codon that supports translation of an internal open reading frame (ORF) independent of upstream 5' UTR sequences. Addition of 80S ribosomes to the 5' UTR reduced the flexibility of the polypyrimidine residues and generated a toeprint consistent with binding to this region. Binding of salt-washed 40S ribosomal subunits was reduced 6-fold when the pyrimidine-rich sequence was mutated. 40S subunit binding generated the same toeprint as 80S ribosomes but also additional ones near the 5' end. Generation of out-of-frame AUGs upstream of the polypyrimidine region reduced translation, which suggests that 5'-terminal entry of 40S subunits is followed by scanning and that the polypyrimidine region is needed for an alternative function that requires ribosome binding. No evidence for RNA-RNA interactions between 5' and 3' sequences was found, suggesting that TCV utilizes an alternative means for circularizing its genome. Combining 5' and 3' UTR fragments in vitro had no discernible effect on the structures of the RNAs. In contrast, when 80S ribosomes were added to both fragments, structural changes were found in the 5' UTR polypyrimidine tract that were not evident when ribosomes interacted with the individual fragments. This suggests that ribosomes can promote an interaction between the 5' and 3' UTRs of TCV.
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96
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Malys N, McCarthy JEG. Translation initiation: variations in the mechanism can be anticipated. Cell Mol Life Sci 2011; 68:991-1003. [PMID: 21076851 PMCID: PMC11115079 DOI: 10.1007/s00018-010-0588-z] [Citation(s) in RCA: 71] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2010] [Revised: 10/25/2010] [Accepted: 10/28/2010] [Indexed: 01/05/2023]
Abstract
Translation initiation is a critical step in protein synthesis. Previously, two major mechanisms of initiation were considered as essential: prokaryotic, based on SD interaction; and eukaryotic, requiring cap structure and ribosomal scanning. Although discovered decades ago, cap-independent translation has recently been acknowledged as a widely spread mechanism in viruses, which may take place in some cellular mRNA translations. Moreover, it has become evident that translation can be initiated on the leaderless mRNA in all three domains of life. New findings demonstrate that other distinguishable types of initiation exist, including SD-independent in Bacteria and Archaea, and various modifications of 5' end-dependent and internal initiation mechanisms in Eukarya. Since translation initiation has developed through the loss, acquisition, and modification of functional elements, all of which have been elevated by competition with viral translation in a large number of organisms of different complexity, more variation in initiation mechanisms can be anticipated.
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Affiliation(s)
- Naglis Malys
- Manchester Centre for Integrative Systems Biology, Faculty of Life Sciences, Manchester Interdisciplinary Biocentre, The University of Manchester, UK.
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97
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Bronzoni RVM, Madrid MCFS, Duarte DVB, Pellegrini VOA, Pacca CC, Carmo ACV, Zanelli CF, Valentini SR, Santacruz-Pérez C, Barbosa JARG, Lutz CS, Rahal P, Nogueira ML. The small nuclear ribonucleoprotein U1A interacts with NS5 from yellow fever virus. Arch Virol 2011; 156:931-8. [PMID: 21298455 DOI: 10.1007/s00705-011-0927-x] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2010] [Accepted: 01/18/2011] [Indexed: 10/18/2022]
Abstract
The flavivirus NS5 protein is one of the most important proteins of the replication complex, and cellular proteins can interact with it. This study shows for the first time that the yellow fever virus (YFV) NS5 protein is able to interact with U1A, a protein involved in splicing and polyadenylation. We confirmed this interaction by GST-pulldown assay and by co-immunoprecipitation in YFV-infected cells. A region between amino acids 368 and 448 was identified as the site of interaction of the NS5 protein with U1A. This region was conserved among some flaviviruses of medical importance. The implications of this interaction for flavivirus replication are discussed.
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Affiliation(s)
- Roberta V M Bronzoni
- Departamento de Doenças Dermatológicas, Infecciosas e Parasitárias, Faculdade de Medicina de Rio Preto, São José do Rio Preto 15090-000, Brazil
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98
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Lei Y, Huang Y, Zhang H, Yu L, Zhang M, Dayton A. Functional interaction between cellular p100 and the dengue virus 3' UTR. J Gen Virol 2010; 92:796-806. [PMID: 21148275 DOI: 10.1099/vir.0.028597-0] [Citation(s) in RCA: 45] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/12/2023] Open
Abstract
Host factors interacting with the dengue virus (DENV) 3' UTR are involved in virus replication, but their roles remain poorly understood. We used RNA affinity capture and mass spectrometry to identify p100 as a host cellular protein associated with the DENV 3' UTR. By using RNA immunoprecipitation and confocal immunofluorescence analysis we demonstrated an interaction between p100 and the 3' UTR in DENV-infected cells. We identified the A4 region (the extensive stem-loop structure at the 3' end) as the binding site of p100 by studying deletion mutants. p100 knockdown specifically reduced the levels of viral RNA and viral protein in DENV-infected cells. Furthermore, downregulation of p100 reduced the expression of a heterologously expressed luciferase-3' UTR(DENV) mRNA in an A4-dependent manner, confirming the binding data and the effects of p100 knockdown on viral replication. These results provide evidence that p100 interacts with the 3' UTR of DENV and is required for normal DENV replication.
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Affiliation(s)
- Yingfeng Lei
- Laboratory of Molecular Virology, Center for Biologics Evaluation and Research, Food and Drug Administration, 1401 Rockville Pike, Rockville, MD 20852, USA
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99
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Urcuqui-Inchima S, Patiño C, Torres S, Haenni AL, Díaz FJ. Recent developments in understanding dengue virus replication. Adv Virus Res 2010; 77:1-39. [PMID: 20951868 DOI: 10.1016/b978-0-12-385034-8.00001-6] [Citation(s) in RCA: 34] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
Dengue is the most important cause of mosquito-borne virus diseases in tropical and subtropical regions in the world. Severe clinical outcomes such as dengue hemorrhagic fever and dengue shock syndrome are potentially fatal. The epidemiology of dengue has undergone profound changes in recent years, due to several factors such as expansion of the geographical distribution of the insect vector, increase in traveling, and demographic pressure. As a consequence, the incidence of dengue has increased dramatically. Since mosquito control has not been successful and since no vaccine or antiviral treatment is available, new approaches to this problem are needed. Consequently, an in-depth understanding of the molecular and cellular biology of the virus should be helpful to design efficient strategies for the control of dengue. Here, we review the recently acquired knowledge on the molecular and cell biology of the dengue virus life cycle based on newly developed molecular biology technologies.
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Affiliation(s)
- Silvio Urcuqui-Inchima
- Grupo de Inmunoviología, Sede de Investigación Universitaria, Universidad de Antioquia, Medellín, Colombia
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Vera-Otarola J, Soto-Rifo R, Ricci EP, Ohlmann T, Darlix JL, López-Lastra M. The 3' untranslated region of the Andes hantavirus small mRNA functionally replaces the poly(A) tail and stimulates cap-dependent translation initiation from the viral mRNA. J Virol 2010; 84:10420-4. [PMID: 20660206 PMCID: PMC2937818 DOI: 10.1128/jvi.01270-10] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2010] [Accepted: 07/10/2010] [Indexed: 12/26/2022] Open
Abstract
In the process of translation of eukaryotic mRNAs, the 5' cap and the 3' poly(A) tail interact synergistically to stimulate protein synthesis. Unlike its cellular counterparts, the small mRNA (SmRNA) of Andes hantavirus (ANDV), a member of the Bunyaviridae, lacks a 3' poly(A) tail. Here we report that the 3' untranslated region (3'UTR) of the ANDV SmRNA functionally replaces a poly(A) tail and synergistically stimulates cap-dependent translation initiation from the viral mRNA. Stimulation of translation by the 3'UTR of the ANDV SmRNA was found to be independent of viral proteins and of host poly(A)-binding protein.
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Affiliation(s)
- Jorge Vera-Otarola
- Laboratorio de Virología Molecular, Núcleo Milenio de Inmunología e Inmunoterapia, Centro de Investigaciones Médicas, Facultad de Medicina, Pontificia Universidad Católica de Chile, Marcoleta 391, Santiago, Chile, TEV, LaboRetro, Unité de Virologie Humaine, INSERM 758, IFR 128, ENS de Lyon, 46 allée d'Italie, 69364 Lyon, France
| | - Ricardo Soto-Rifo
- Laboratorio de Virología Molecular, Núcleo Milenio de Inmunología e Inmunoterapia, Centro de Investigaciones Médicas, Facultad de Medicina, Pontificia Universidad Católica de Chile, Marcoleta 391, Santiago, Chile, TEV, LaboRetro, Unité de Virologie Humaine, INSERM 758, IFR 128, ENS de Lyon, 46 allée d'Italie, 69364 Lyon, France
| | - Emiliano P. Ricci
- Laboratorio de Virología Molecular, Núcleo Milenio de Inmunología e Inmunoterapia, Centro de Investigaciones Médicas, Facultad de Medicina, Pontificia Universidad Católica de Chile, Marcoleta 391, Santiago, Chile, TEV, LaboRetro, Unité de Virologie Humaine, INSERM 758, IFR 128, ENS de Lyon, 46 allée d'Italie, 69364 Lyon, France
| | - Théophile Ohlmann
- Laboratorio de Virología Molecular, Núcleo Milenio de Inmunología e Inmunoterapia, Centro de Investigaciones Médicas, Facultad de Medicina, Pontificia Universidad Católica de Chile, Marcoleta 391, Santiago, Chile, TEV, LaboRetro, Unité de Virologie Humaine, INSERM 758, IFR 128, ENS de Lyon, 46 allée d'Italie, 69364 Lyon, France
| | - Jean-Luc Darlix
- Laboratorio de Virología Molecular, Núcleo Milenio de Inmunología e Inmunoterapia, Centro de Investigaciones Médicas, Facultad de Medicina, Pontificia Universidad Católica de Chile, Marcoleta 391, Santiago, Chile, TEV, LaboRetro, Unité de Virologie Humaine, INSERM 758, IFR 128, ENS de Lyon, 46 allée d'Italie, 69364 Lyon, France
| | - Marcelo López-Lastra
- Laboratorio de Virología Molecular, Núcleo Milenio de Inmunología e Inmunoterapia, Centro de Investigaciones Médicas, Facultad de Medicina, Pontificia Universidad Católica de Chile, Marcoleta 391, Santiago, Chile, TEV, LaboRetro, Unité de Virologie Humaine, INSERM 758, IFR 128, ENS de Lyon, 46 allée d'Italie, 69364 Lyon, France
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