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Sang L, Gong X, Huang Y, Zhang L, Sun J. Immunotherapeutic implications on targeting the cytokines produced in rhinovirus-induced immunoreactions. FRONTIERS IN ALLERGY 2024; 5:1427762. [PMID: 38859875 PMCID: PMC11163110 DOI: 10.3389/falgy.2024.1427762] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2024] [Accepted: 05/13/2024] [Indexed: 06/12/2024] Open
Abstract
Rhinovirus is a widespread virus associated with several respiratory diseases, especially asthma exacerbation. Currently, there are no accurate therapies for rhinovirus. Encouragingly, it is found that during rhinovirus-induced immunoreactions the levels of certain cytokines in patients' serum will alter. These cytokines may have pivotal pro-inflammatory or anti-inflammatory effects via their specific mechanisms. Thus far, studies have shown that inhibitions of cytokines such as IL-1, IL-4, IL-5, IL-6, IL-13, IL-18, IL-25, and IL-33 may attenuate rhinovirus-induced immunoreactions, thereby relieving rhinovirus infection. Furthermore, such therapeutics for rhinovirus infection can be applied to viruses of other species, with certain practicability.
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Affiliation(s)
- Le Sang
- Department of Medicine, Shaoxing University, Shaoxing City, Zhejiang Province, China
| | - Xia Gong
- Department of Medicine, Shaoxing University, Shaoxing City, Zhejiang Province, China
| | - Yunlei Huang
- Department of Medicine, Shaoxing University, Shaoxing City, Zhejiang Province, China
| | - Linling Zhang
- Department of Respiratory Medicine, Shaoxing People’s Hospital, Shaoxing City, Zhejiang Province, China
| | - Jian Sun
- Department of Respiratory Medicine, Shaoxing People’s Hospital, Shaoxing City, Zhejiang Province, China
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2
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Amin PH, Carlson KR, Wek RC. An RNA stem-loop functions in conjunction with an upstream open reading frame to direct preferential translation in the integrated stress response. J Biol Chem 2023; 299:102864. [PMID: 36596357 PMCID: PMC9971878 DOI: 10.1016/j.jbc.2022.102864] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2022] [Revised: 11/30/2022] [Accepted: 12/28/2022] [Indexed: 01/02/2023] Open
Abstract
In response to environmental stresses, cells invoke translational control to conserve resources and rapidly reprogram gene expression for optimal adaptation. A central mechanism for translational control involves phosphorylation of the α subunit of eIF2 (p-eIF2α), which reduces delivery of initiator tRNA to ribosomes. Because p-eIF2α is invoked by multiple protein kinases, each responding to distinct stresses, this pathway is named the integrated stress response (ISR). While p-eIF2α lowers bulk translation initiation, many stress-related mRNAs are preferentially translated. The process by which ribosomes delineate gene transcripts for preferential translation is known to involve upstream open reading frames (uORFs) embedded in the targeted mRNAs. In this study, we used polysome analyses and reporter assays to address the mechanisms directing preferential translation of human IBTKα in the ISR. The IBTKα mRNA encodes four uORFs, with only 5'-proximal uORF1 and uORF2 being translated. Of importance, the 5'-leader of IBTKα mRNA also contains a phylogenetically conserved stem-loop of moderate stability that is situated 11 nucleotides downstream of uORF2. The uORF2 is well translated and functions in combination with the stem-loop to effectively lower translation reinitiation at the IBTKα coding sequence. Upon stress-induced p-eIF2α, the uORF2/stem loop element can be bypassed to enhance IBTKα translation by a mechanism that may involve the modestly translated uORF1. Our study demonstrates that uORFs in conjunction with RNA secondary structures can be critical elements that serve as the "bar code" by which scanning ribosomes can delineate which mRNAs are preferentially translated in the ISR.
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Affiliation(s)
- Parth H Amin
- Department of Biochemistry and Molecular Biology, Indiana University School of Medicine, Indianapolis, Indiana, USA
| | - Kenneth R Carlson
- Department of Biochemistry and Molecular Biology, Indiana University School of Medicine, Indianapolis, Indiana, USA
| | - Ronald C Wek
- Department of Biochemistry and Molecular Biology, Indiana University School of Medicine, Indianapolis, Indiana, USA.
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3
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Sawaged S, Mota T, Piplani H, Thakur R, Lall D, McCabe E, Seo S, Sutterwala FS, Feuer R, Gottlieb RA, Sin J. TBK1 and GABARAP family members suppress Coxsackievirus B infection by limiting viral production and promoting autophagic degradation of viral extracellular vesicles. PLoS Pathog 2022; 18:e1010350. [PMID: 36044516 PMCID: PMC9469980 DOI: 10.1371/journal.ppat.1010350] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2022] [Revised: 09/13/2022] [Accepted: 08/18/2022] [Indexed: 11/23/2022] Open
Abstract
Host-pathogen dynamics are constantly at play during enteroviral infection. Coxsackievirus B (CVB) is a common juvenile enterovirus that infects multiple organs and drives inflammatory diseases including acute pancreatitis and myocarditis. Much like other enteroviruses, CVB is capable of manipulating host machinery to hijack and subvert autophagy for its benefit. We have previously reported that CVB triggers the release of infectious extracellular vesicles (EVs) which originate from autophagosomes. These EVs facilitate efficient dissemination of infectious virus. Here, we report that TBK1 (Tank-binding kinase 1) suppresses release of CVB-induced EVs. TBK1 is a multimeric kinase that directly activates autophagy adaptors for efficient cargo recruitment and induces type-1 interferons during viral-mediated STING recruitment. Positioning itself at the nexus of pathogen elimination, we hypothesized that loss of TBK1 could exacerbate CVB infection due to its specific role in autophagosome trafficking. Here we report that infection with CVB during genetic TBK1 knockdown significantly increases viral load and potentiates the bulk release of viral EVs. Similarly, suppressing TBK1 with small interfering RNA (siRNA) caused a marked increase in intracellular virus and EV release, while treatment in vivo with the TBK1-inhibitor Amlexanox exacerbated viral pancreatitis and EV spread. We further demonstrated that viral EV release is mediated by the autophagy modifier proteins GABARAPL1 and GABARAPL2 which facilitate autophagic flux. We observe that CVB infection stimulates autophagy and increases the release of GABARAPL1/2-positive EVs. We conclude that TBK1 plays additional antiviral roles by inducing autophagic flux during CVB infection independent of interferon signaling, and the loss of TBK1 better allows CVB-laden autophagosomes to circumvent lysosomal degradation, increasing the release of virus-laden EVs. This discovery sheds new light on the mechanisms involved in viral spread and EV propagation during acute enteroviral infection and highlights novel intracellular trafficking protein targets for antiviral therapy. Coxsackievirus B (CVB) is a significant human enterovirus that can cause myocarditis, meningitis, and pancreatitis. The subversion of host immunity and mechanisms of viral dissemination are critical factors which promote pathogenesis. We had previously reported that following infection, CVB becomes engulfed by autophagosomes which evade lysosomal degradation and instead get released as infectious extracellular vesicles (EVs). In this current study, we report that in addition to its traditional role in interferon-mediated antiviral signaling, TANK-binding kinase (TBK1) is crucial in limiting viral production and EV-based viral egress through the autophagy pathway. Indeed, in the absence of TBK1, we observe (i) a disruption in autophagic flux, (ii) significant increases in intracellular viral burden and viral EV release, and (iii) elevated viral load in both in vitro and in vivo models of infection. EVs isolated from TBK1-deficient cells or mice treated with the TBK1-inhibitor Amlexanox were more infectious compared to controls. In all, the dual role TBK1 plays in suppressing viral escape in addition to mediating antiviral immunity makes it a promising therapeutic target for the treatment of CVB infection.
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Affiliation(s)
- Savannah Sawaged
- The Smidt Heart Institute, Cedars-Sinai Medical Center, Los Angeles, California, United States of America
| | - Thomas Mota
- The Center for Neural Science and Medicine, Regenerative Medicine Institute, Cedars-Sinai Medical Center, Los Angeles, California, United States of America
| | - Honit Piplani
- The Smidt Heart Institute, Cedars-Sinai Medical Center, Los Angeles, California, United States of America
| | - Reetu Thakur
- The Smidt Heart Institute, Cedars-Sinai Medical Center, Los Angeles, California, United States of America
| | - Deepti Lall
- The Center for Neural Science and Medicine, Regenerative Medicine Institute, Cedars-Sinai Medical Center, Los Angeles, California, United States of America
| | - Elizabeth McCabe
- Department of Biological Sciences, University of Alabama, Tuscaloosa, Alabama, United States of America
| | - Soojung Seo
- Department of Biological Sciences, University of Alabama, Tuscaloosa, Alabama, United States of America
| | - Fayyaz S. Sutterwala
- Department of Medicine, Women’s Guild Lung Institute, Cedars-Sinai Medical Center, Los Angeles, California, United States of America
| | - Ralph Feuer
- The Integrated Regenerative Research Institute at San Diego State University, San Diego, California, United States of America
| | - Roberta A. Gottlieb
- The Smidt Heart Institute, Cedars-Sinai Medical Center, Los Angeles, California, United States of America
| | - Jon Sin
- The Smidt Heart Institute, Cedars-Sinai Medical Center, Los Angeles, California, United States of America
- Department of Biological Sciences, University of Alabama, Tuscaloosa, Alabama, United States of America
- * E-mail:
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4
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Insights from structural studies of the Cardiovirus 2A protein. Biosci Rep 2022; 42:230648. [PMID: 35022657 PMCID: PMC8777194 DOI: 10.1042/bsr20210406] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2021] [Revised: 01/10/2022] [Accepted: 01/10/2022] [Indexed: 11/24/2022] Open
Abstract
Cardioviruses are single-stranded RNA viruses of the family Picornaviridae. In addition to being the first example of internal ribosome entry site (IRES) utilization, cardioviruses also employ a series of alternative translation strategies, such as Stop-Go translation and programmed ribosome frameshifting. Here, we focus on cardiovirus 2A protein, which is not only a primary virulence factor, but also exerts crucial regulatory functions during translation, including activation of viral ribosome frameshifting and inhibition of host cap-dependent translation. Only recently, biochemical and structural studies have allowed us to close the gaps in our knowledge of how cardiovirus 2A is able to act in diverse translation-related processes as a novel RNA-binding protein. This review will summarize these findings, which ultimately may lead to the discovery of other RNA-mediated gene expression strategies across a broad range of RNA viruses.
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Akdad M, Moujane S, Bouadid I, Benlyas M, Eddouks M. Phytocompounds from Anvillea radiata as promising anti-Covid-19 drugs: in silico studies and in vivo safety assessment. JOURNAL OF ENVIRONMENTAL SCIENCE AND HEALTH. PART A, TOXIC/HAZARDOUS SUBSTANCES & ENVIRONMENTAL ENGINEERING 2022; 56:1512-1523. [PMID: 34978275 DOI: 10.1080/10934529.2021.2020029] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/03/2021] [Revised: 11/04/2021] [Accepted: 11/09/2021] [Indexed: 06/14/2023]
Abstract
As an alternative strategy in combating the COVID-19 pandemic, phytoconstituents from medicinal plants are getting attention worldwide. The current investigation focused on the efficacy of the essential phytocompounds identified in Anvillea radiata to target the main protease (Mpro) of SARS-COV-2 through molecular docking and dynamic analyses; in addition to the safety assessment of this herb in vivo. In silico, the 6LU7 structure of Mpro was prepared as a target by Discovery Studio 2020. The virtual screening of phytocompounds from Anvillea radiata was performed through iGEMDOCK program, followed by an evaluation of the potential inhibitors based on the docking scores calculated using AutoDock Vina and MGL Tools programs, as well as complexes stability assessment through MD simulation. In vivo toxicity studies of Anvillea radiata aqueous extract were also conducted in Wistar rats. Among the phytocompounds evaluated in this study, 3,5-Dicaffeoylquinic acid, Spinacetin, 9α-Epoxyparthenolide, Hispidulin, Quercetin, jaceosidin, Nepetin, and isorhamnetin were predicted to have the highest binding affinity for the Main protease (Mpro) target of SARS-CoV-2. The aqueous extract of Anvillea radiata did not induce any signs of toxicity. 3,5-Dicaffeoylquinic acid, Spinacetin, 9α-Epoxyparthenolide, jaceosidin, and isorhamnetin from Anvillea radiata were selected as potential inhibitors of SARS-Cov-2 to develop new drugs anti-COVID-19.
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Affiliation(s)
- Mourad Akdad
- Team of Ethnopharmacology and Pharmacognosy, Faculty of Sciences and Techniques Errachidia, Moulay Ismail University of Meknes, Errachidia, Morocco
| | - Soumia Moujane
- Biochemistry of Natural Substances, Faculty of Sciences and Techniques, Errachidia, Moulay Ismail University of Meknes, Errachidia, Morocco
| | - Ismail Bouadid
- Team of Ethnopharmacology and Pharmacognosy, Faculty of Sciences and Techniques Errachidia, Moulay Ismail University of Meknes, Errachidia, Morocco
| | - Mohamed Benlyas
- Biochemistry of Natural Substances, Faculty of Sciences and Techniques, Errachidia, Moulay Ismail University of Meknes, Errachidia, Morocco
| | - Mohamed Eddouks
- Team of Ethnopharmacology and Pharmacognosy, Faculty of Sciences and Techniques Errachidia, Moulay Ismail University of Meknes, Errachidia, Morocco
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6
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Dabrowska A, Milewska A, Ner-Kluza J, Suder P, Pyrc K. Mass Spectrometry versus Conventional Techniques of Protein Detection: Zika Virus NS3 Protease Activity towards Cellular Proteins. Molecules 2021; 26:molecules26123732. [PMID: 34207340 PMCID: PMC8234618 DOI: 10.3390/molecules26123732] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2021] [Revised: 06/11/2021] [Accepted: 06/15/2021] [Indexed: 11/30/2022] Open
Abstract
Mass spectrometry (MS) used in proteomic approaches is able to detect hundreds of proteins in a single assay. Although undeniable high analytical power of MS, data acquired sometimes lead to confusing results, especially during a search of very selective, unique interactions in complex biological matrices. Here, we would like to show an example of such confusing data, providing an extensive discussion on the observed phenomenon. Our investigations focus on the interaction between the Zika virus NS3 protease, which is essential for virus replication. This enzyme is known for helping to remodel the microenvironment of the infected cells. Several reports show that this protease can process cellular substrates and thereby modify cellular pathways that are important for the virus. Herein, we explored some of the targets of NS3, clearly shown by proteomic techniques, as processed during infection. Unfortunately, we could not confirm the biological relevance of protein targets for viral infections detected by MS. Thus, although mass spectrometry is highly sensitive and useful in many instances, also being able to show directions where cell/virus interaction occurs, we believe that deep recognition of their biological role is essential to receive complete insight into the investigated process.
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Affiliation(s)
- Agnieszka Dabrowska
- Virogenetics Laboratory of Virology, Malopolska Centre of Biotechnology, Jagiellonian University, Gronostajowa 7a, 30-387 Krakow, Poland; (A.D.); (A.M.)
- Microbiology Department, Faculty of Biochemistry, Biophysics and Biotechnology, Jagiellonian University, Gronostajowa 7a, 30-387 Krakow, Poland
| | - Aleksandra Milewska
- Virogenetics Laboratory of Virology, Malopolska Centre of Biotechnology, Jagiellonian University, Gronostajowa 7a, 30-387 Krakow, Poland; (A.D.); (A.M.)
- Microbiology Department, Faculty of Biochemistry, Biophysics and Biotechnology, Jagiellonian University, Gronostajowa 7a, 30-387 Krakow, Poland
| | - Joanna Ner-Kluza
- Department of Analytical Chemistry and Biochemistry, Faculty of Materials Science and Ceramics, AGH University of Science and Technology, Mickiewicza 30, 30-059 Krakow, Poland;
| | - Piotr Suder
- Department of Analytical Chemistry and Biochemistry, Faculty of Materials Science and Ceramics, AGH University of Science and Technology, Mickiewicza 30, 30-059 Krakow, Poland;
- Correspondence: (P.S.); (K.P.); Tel.: +48-12-617-50-83 (P.S.); +48-12-664-61-21 (K.P.)
| | - Krzysztof Pyrc
- Virogenetics Laboratory of Virology, Malopolska Centre of Biotechnology, Jagiellonian University, Gronostajowa 7a, 30-387 Krakow, Poland; (A.D.); (A.M.)
- Correspondence: (P.S.); (K.P.); Tel.: +48-12-617-50-83 (P.S.); +48-12-664-61-21 (K.P.)
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7
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Rhinovirus and Cell Death. Viruses 2021; 13:v13040629. [PMID: 33916958 PMCID: PMC8067602 DOI: 10.3390/v13040629] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2021] [Revised: 03/29/2021] [Accepted: 03/29/2021] [Indexed: 12/27/2022] Open
Abstract
Rhinoviruses (RVs) are the etiological agents of upper respiratory tract infections, particularly the common cold. Infections in the lower respiratory tract is shown to cause severe disease and exacerbations in asthma and COPD patients. Viruses being obligate parasites, hijack host cell pathways such as programmed cell death to suppress host antiviral responses and prolong viral replication and propagation. RVs are non-enveloped positive sense RNA viruses with a lifecycle fully contained within the cytoplasm. Despite decades of study, the details of how RVs exit the infected cell are still unclear. There are some diverse studies that suggest a possible role for programmed cell death. In this review, we aimed to consolidate current literature on the impact of RVs on cell death to inform future research on the topic. We searched peer reviewed English language literature in the past 21 years for studies on the interaction with and modulation of cell death pathways by RVs, placing it in the context of the broader knowledge of these interconnected pathways from other systems. Our review strongly suggests a role for necroptosis and/or autophagy in RV release, with the caveat that all the literature is based on RV-A and RV-B strains, with no studies to date examining the interaction of RV-C strains with cell death pathways.
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8
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Kumar V, Kancharla S, Jena MK. In silico virtual screening-based study of nutraceuticals predicts the therapeutic potentials of folic acid and its derivatives against COVID-19. Virusdisease 2021; 32:29-37. [PMID: 33532517 PMCID: PMC7843005 DOI: 10.1007/s13337-020-00643-6] [Citation(s) in RCA: 18] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2020] [Accepted: 11/11/2020] [Indexed: 12/12/2022] Open
Abstract
The recent outbreak of the novel coronavirus (SARS-CoV-2) in the Wuhan province of China has taken millions of lives worldwide. In this pandemic situation and absence of known drugs and vaccines against novel coronavirus disease (COVID-19), there is an urgent need for the repurposing of the existing drugs against it. So, here we have examined a safe and cheap alternative against this virus by screening hundreds of nutraceuticals compounds against known therapeutic targets of SARS-COV-2 by molecular docking. The virtual screening results were then analyzed for binding energy and interactive residues and compared with some already known hits in the best binding pose. All these analyses of this study strongly predicted the potential of Folic acid and its derivates like Tetrahydrofolic acid and 5-methyl tetrahydrofolic acid against SARS-COV-2. The strong and stable binding affinity of this water-soluble vitamin and its derivatives against the SARS-COV-2, indicating that they could be valuable drugs against the management of this COVID-19 pandemic. This study could serve as the starting point for further investigation of these molecules through in vitro and in vivo assays.
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Affiliation(s)
- Vipul Kumar
- Department of Biotechnology, School of Bioengineering and Biosciences, Lovely Professional University, Phagwara, Punjab 144411 India
| | | | - Manoj Kumar Jena
- Department of Biotechnology, School of Bioengineering and Biosciences, Lovely Professional University, Phagwara, Punjab 144411 India
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9
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Boersma S, Rabouw HH, Bruurs LJM, Pavlovič T, van Vliet ALW, Beumer J, Clevers H, van Kuppeveld FJM, Tanenbaum ME. Translation and Replication Dynamics of Single RNA Viruses. Cell 2020; 183:1930-1945.e23. [PMID: 33188777 PMCID: PMC7664544 DOI: 10.1016/j.cell.2020.10.019] [Citation(s) in RCA: 34] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2020] [Revised: 08/14/2020] [Accepted: 10/11/2020] [Indexed: 01/09/2023]
Abstract
RNA viruses are among the most prevalent pathogens and are a major burden on society. Although RNA viruses have been studied extensively, little is known about the processes that occur during the first several hours of infection because of a lack of sensitive assays. Here we develop a single-molecule imaging assay, virus infection real-time imaging (VIRIM), to study translation and replication of individual RNA viruses in live cells. VIRIM uncovered a striking heterogeneity in replication dynamics between cells and revealed extensive coordination between translation and replication of single viral RNAs. Furthermore, using VIRIM, we identify the replication step of the incoming viral RNA as a major bottleneck of successful infection and identify host genes that are responsible for inhibition of early virus replication. Single-molecule imaging of virus infection is a powerful tool to study virus replication and virus-host interactions that may be broadly applicable to RNA viruses.
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Affiliation(s)
- Sanne Boersma
- Oncode Institute, Hubrecht Institute-KNAW and University Medical Center Utrecht, 3584 CT Utrecht, the Netherlands
| | - Huib H Rabouw
- Oncode Institute, Hubrecht Institute-KNAW and University Medical Center Utrecht, 3584 CT Utrecht, the Netherlands; Virology Division, Department of Infectious Diseases and Immunology, Faculty of Veterinary Medicine, Utrecht University, 3584 CL Utrecht, the Netherlands
| | - Lucas J M Bruurs
- Oncode Institute, Hubrecht Institute-KNAW and University Medical Center Utrecht, 3584 CT Utrecht, the Netherlands
| | - Tonja Pavlovič
- Oncode Institute, Hubrecht Institute-KNAW and University Medical Center Utrecht, 3584 CT Utrecht, the Netherlands
| | - Arno L W van Vliet
- Virology Division, Department of Infectious Diseases and Immunology, Faculty of Veterinary Medicine, Utrecht University, 3584 CL Utrecht, the Netherlands
| | - Joep Beumer
- Oncode Institute, Hubrecht Institute-KNAW and University Medical Center Utrecht, 3584 CT Utrecht, the Netherlands
| | - Hans Clevers
- Oncode Institute, Hubrecht Institute-KNAW and University Medical Center Utrecht, 3584 CT Utrecht, the Netherlands
| | - Frank J M van Kuppeveld
- Virology Division, Department of Infectious Diseases and Immunology, Faculty of Veterinary Medicine, Utrecht University, 3584 CL Utrecht, the Netherlands.
| | - Marvin E Tanenbaum
- Oncode Institute, Hubrecht Institute-KNAW and University Medical Center Utrecht, 3584 CT Utrecht, the Netherlands.
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10
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Marine RL, Magaña LC, Castro CJ, Zhao K, Montmayeur AM, Schmidt A, Diez-Valcarce M, Ng TFF, Vinjé J, Burns CC, Nix WA, Rota PA, Oberste MS. Comparison of Illumina MiSeq and the Ion Torrent PGM and S5 platforms for whole-genome sequencing of picornaviruses and caliciviruses. J Virol Methods 2020; 280:113865. [PMID: 32302601 PMCID: PMC9119587 DOI: 10.1016/j.jviromet.2020.113865] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2019] [Revised: 02/04/2020] [Accepted: 04/06/2020] [Indexed: 02/06/2023]
Abstract
Next-generation sequencing is a powerful tool for virological surveillance. While Illumina® and Ion Torrent® sequencing platforms are used extensively for generating viral RNA genome sequences, there is limited data comparing different platforms. The Illumina MiSeq, Ion Torrent PGM and Ion Torrent S5 platforms were evaluated using a panel of sixteen specimens containing picornaviruses and human caliciviruses (noroviruses and sapoviruses). The specimens were processed, using combinations of three library preparation and five sequencing kits, to assess the quality and completeness of assembled viral genomes, and an estimation of cost per sample to generate the data was calculated. The choice of library preparation kit and sequencing platform was found to impact the breadth of genome coverage and accuracy of consensus viral genomes. The Ion Torrent S5 510 chip runs produced more reads at a lower cost per sample than the highest output Ion Torrent PGM 318 chip run, and generated the highest proportion of reads for enterovirus D68 samples. However, indels at homopolymer regions impacted the accuracy of consensus genome sequences. For lower throughput sequencing runs (i.e., Ion Torrent 510 and Illumina MiSeq Nano V2), the cost per sample was lower on the MiSeq platform, whereas with higher throughput runs (Ion Torrent 530 and Illumina MiSeq V2) there is less of a difference in the cost per sample between the two sequencing platforms ($5.47-$10.25 more per sample for an Ion Torrent 530 chip run when multiplexing 24 samples). These findings suggest that the Ion Torrent S5 and Illumina MiSeq platforms are both viable options for genomic sequencing of RNA viruses, each with specific advantages and tradeoffs.
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Affiliation(s)
- Rachel L Marine
- Division of Viral Diseases, Centers for Disease Control and Prevention, Atlanta, GA, USA.
| | - Laura C Magaña
- Division of Viral Diseases, Centers for Disease Control and Prevention, Atlanta, GA, USA; Oak Ridge Institute for Science and Education, Oak Ridge, Tennessee, USA
| | - Christina J Castro
- Division of Viral Diseases, Centers for Disease Control and Prevention, Atlanta, GA, USA; Oak Ridge Institute for Science and Education, Oak Ridge, Tennessee, USA
| | - Kun Zhao
- Division of Viral Diseases, Centers for Disease Control and Prevention, Atlanta, GA, USA
| | | | | | - Marta Diez-Valcarce
- Division of Viral Diseases, Centers for Disease Control and Prevention, Atlanta, GA, USA; Oak Ridge Institute for Science and Education, Oak Ridge, Tennessee, USA
| | - Terry Fei Fan Ng
- Division of Viral Diseases, Centers for Disease Control and Prevention, Atlanta, GA, USA
| | - Jan Vinjé
- Division of Viral Diseases, Centers for Disease Control and Prevention, Atlanta, GA, USA
| | - Cara C Burns
- Division of Viral Diseases, Centers for Disease Control and Prevention, Atlanta, GA, USA
| | - W Allan Nix
- Division of Viral Diseases, Centers for Disease Control and Prevention, Atlanta, GA, USA
| | - Paul A Rota
- Division of Viral Diseases, Centers for Disease Control and Prevention, Atlanta, GA, USA
| | - M Steven Oberste
- Division of Viral Diseases, Centers for Disease Control and Prevention, Atlanta, GA, USA
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11
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D'Andrea L, Pérez-Rodríguez FJ, de Castellarnau M, Guix S, Ribes E, Quer J, Gregori J, Bosch A, Pintó RM. The Critical Role of Codon Composition on the Translation Efficiency Robustness of the Hepatitis A Virus Capsid. Genome Biol Evol 2020; 11:2439-2456. [PMID: 31290967 PMCID: PMC6735747 DOI: 10.1093/gbe/evz146] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 07/08/2019] [Indexed: 12/13/2022] Open
Abstract
Hepatoviruses show an intriguing deviated codon usage, suggesting an evolutionary signature. Abundant and rare codons in the cellular genome are scarce in the human hepatitis A virus (HAV) genome, while intermediately abundant host codons are abundant in the virus. Genotype–phenotype maps, or fitness landscapes, are a means of representing a genotype position in sequence space and uncovering how genotype relates to phenotype and fitness. Using genotype–phenotype maps of the translation efficiency, we have shown the critical role of the HAV capsid codon composition in regulating translation and determining its robustness. Adaptation to an environmental perturbation such as the artificial induction of cellular shutoff—not naturally occurring in HAV infection—involved movements in the sequence space and dramatic changes of the translation efficiency. Capsid rare codons, including abundant and rare codons of the cellular genome, slowed down the translation efficiency in conditions of no cellular shutoff. In contrast, rare capsid codons that are abundant in the cellular genome were efficiently translated in conditions of shutoff. Capsid regions very rich in slowly translated codons adapt to shutoff through sequence space movements from positions with highly robust translation to others with diminished translation robustness. These movements paralleled decreases of the capsid physical and biological robustness, and resulted in the diversification of capsid phenotypes. The deviated codon usage of extant hepatoviruses compared with that of their hosts may suggest the occurrence of a virus ancestor with an optimized codon usage with respect to an unknown ancient host.
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Affiliation(s)
- Lucía D'Andrea
- Enteric Virus Laboratory, Department of Genetics, Microbiology and Statistics, School of Biology, and Institute of Nutrition and Safety, University of Barcelona, Spain
| | - Francisco-Javier Pérez-Rodríguez
- Enteric Virus Laboratory, Department of Genetics, Microbiology and Statistics, School of Biology, and Institute of Nutrition and Safety, University of Barcelona, Spain
| | - Montserrat de Castellarnau
- Enteric Virus Laboratory, Department of Genetics, Microbiology and Statistics, School of Biology, and Institute of Nutrition and Safety, University of Barcelona, Spain
| | - Susana Guix
- Enteric Virus Laboratory, Department of Genetics, Microbiology and Statistics, School of Biology, and Institute of Nutrition and Safety, University of Barcelona, Spain
| | - Enric Ribes
- Enteric Virus Laboratory, Department of Cell Biology, Physiology and Immunology, School of Biology, University of Barcelona, Spain
| | - Josep Quer
- Liver Unit, Internal Medicine, Hepatic Diseases Laboratory, Vall d'Hebron Research Institute-Hospital Universitari Vall d'Hebron (VHIR-HUVH), Barcelona, Spain.,Centre of the Biomedical Research Network (CIBER) for Hepatic and Digestive Diseases (CIBERehd), Instituto de Salud Carlos III
| | - Josep Gregori
- Liver Unit, Internal Medicine, Hepatic Diseases Laboratory, Vall d'Hebron Research Institute-Hospital Universitari Vall d'Hebron (VHIR-HUVH), Barcelona, Spain.,Roche Diagnostics SL, Barcelona, Spain
| | - Albert Bosch
- Enteric Virus Laboratory, Department of Genetics, Microbiology and Statistics, School of Biology, and Institute of Nutrition and Safety, University of Barcelona, Spain
| | - Rosa M Pintó
- Enteric Virus Laboratory, Department of Genetics, Microbiology and Statistics, School of Biology, and Institute of Nutrition and Safety, University of Barcelona, Spain
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12
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Bouin A, Gretteau PA, Wehbe M, Renois F, N'Guyen Y, Lévêque N, Vu MN, Tracy S, Chapman NM, Bruneval P, Fornes P, Semler BL, Andreoletti L. Enterovirus Persistence in Cardiac Cells of Patients With Idiopathic Dilated Cardiomyopathy Is Linked to 5' Terminal Genomic RNA-Deleted Viral Populations With Viral-Encoded Proteinase Activities. Circulation 2020; 139:2326-2338. [PMID: 30755025 DOI: 10.1161/circulationaha.118.035966] [Citation(s) in RCA: 21] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
BACKGROUND Group B enteroviruses are common causes of acute myocarditis, which can be a precursor of chronic myocarditis and dilated cardiomyopathy, leading causes of heart transplantation. To date, the specific viral functions involved in the development of dilated cardiomyopathy remain unclear. METHODS Total RNA from cardiac tissue of patients with dilated cardiomyopathy was extracted, and sequences corresponding to the 5' termini of enterovirus RNAs were identified. After next-generation RNA sequencing, viral cDNA clones mimicking the enterovirus RNA sequences found in patient tissues were generated in vitro, and their replication and impact on host cell functions were assessed on primary human cardiac cells in culture. RESULTS Major enterovirus B populations characterized by 5' terminal genomic RNA deletions ranging from 17 to 50 nucleotides were identified either alone or associated with low proportions of intact 5' genomic termini. In situ hybridization and immunohistological assays detected these persistent genomes in clusters of cardiomyocytes. Transfection of viral RNA into primary human cardiomyocytes demonstrated that deleted forms of genomic RNAs displayed early replication activities in the absence of detectable viral plaque formation, whereas mixed deleted and complete forms generated particles capable of inducing cytopathic effects at levels distinct from those observed with full-length forms alone. Moreover, deleted or full-length and mixed forms of viral RNA were capable of directing translation and production of proteolytically active viral proteinase 2A in human cardiomyocytes. CONCLUSIONS We demonstrate that persistent viral forms are composed of B-type enteroviruses harboring a 5' terminal deletion in their genomic RNAs and that these viruses alone or associated with full-length populations of helper RNAs could impair cardiomyocyte functions by the proteolytic activity of viral proteinase 2A in cases of unexplained dilated cardiomyopathy. These results provide a better understanding of the molecular mechanisms that underlie the persistence of EV forms in human cardiac tissues and should stimulate the development of new therapeutic strategies based on specific inhibitors of the coxsackievirus B proteinase 2A activity for acute and chronic cardiac infections.
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Affiliation(s)
- Alexis Bouin
- EA-4684 Cardiovir, Faculty of Medicine, University of Reims Champagne-Ardenne, Reims, France (A.B., P.-A.G., M.W., F.R., Y.N., A.R., P.F., L.A.).,Department of Microbiology and Molecular Genetics, School of Medicine, University of California, Irvine (A.B., M.N.V., B.L.S.)
| | - Paul-Antoine Gretteau
- EA-4684 Cardiovir, Faculty of Medicine, University of Reims Champagne-Ardenne, Reims, France (A.B., P.-A.G., M.W., F.R., Y.N., A.R., P.F., L.A.)
| | - Michel Wehbe
- EA-4684 Cardiovir, Faculty of Medicine, University of Reims Champagne-Ardenne, Reims, France (A.B., P.-A.G., M.W., F.R., Y.N., A.R., P.F., L.A.).,Centre AZM pour la recherche en biotechnologie et ses applications, Université Libanaise, Tripoli, Lebanon (M.W.)
| | - Fanny Renois
- EA-4684 Cardiovir, Faculty of Medicine, University of Reims Champagne-Ardenne, Reims, France (A.B., P.-A.G., M.W., F.R., Y.N., A.R., P.F., L.A.).,LUNAM University, Oniris, LABERCA, UMR INRA 1329, Nantes, France (F.R.).,CHU Robert Debré, Laboratoire de Virologie Médicale et Moléculaire, Reims, France (F.R., Y.N., N.L., P.F., L.A.)
| | - Yohan N'Guyen
- EA-4684 Cardiovir, Faculty of Medicine, University of Reims Champagne-Ardenne, Reims, France (A.B., P.-A.G., M.W., F.R., Y.N., A.R., P.F., L.A.).,CHU Robert Debré, Laboratoire de Virologie Médicale et Moléculaire, Reims, France (F.R., Y.N., N.L., P.F., L.A.)
| | - Nicolas Lévêque
- CHU Robert Debré, Laboratoire de Virologie Médicale et Moléculaire, Reims, France (F.R., Y.N., N.L., P.F., L.A.).,EA-4331 LITEC, Faculty of Medicine and Pharmacy, University Hospital of Poitiers, France (N.L.)
| | - Michelle N Vu
- Department of Microbiology and Molecular Genetics, School of Medicine, University of California, Irvine (A.B., M.N.V., B.L.S.)
| | - Steven Tracy
- Department of Pathology and Microbiology, University of Nebraska Medical Center, Omaha (S.T., N.M.C.)
| | - Nora M Chapman
- Department of Pathology and Microbiology, University of Nebraska Medical Center, Omaha (S.T., N.M.C.)
| | - Patrick Bruneval
- Service d'Anatomie Pathologique, Hôpital Européen Georges Pompidou, Paris, France (P.B.)
| | - Paul Fornes
- EA-4684 Cardiovir, Faculty of Medicine, University of Reims Champagne-Ardenne, Reims, France (A.B., P.-A.G., M.W., F.R., Y.N., A.R., P.F., L.A.)
| | - Bert L Semler
- Department of Microbiology and Molecular Genetics, School of Medicine, University of California, Irvine (A.B., M.N.V., B.L.S.)
| | - Laurent Andreoletti
- EA-4684 Cardiovir, Faculty of Medicine, University of Reims Champagne-Ardenne, Reims, France (A.B., P.-A.G., M.W., F.R., Y.N., A.R., P.F., L.A.)
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13
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Woods Acevedo MA, Erickson AK, Pfeiffer JK. The Antibiotic Neomycin Enhances Coxsackievirus Plaque Formation. mSphere 2019; 4:e00632-18. [PMID: 30787120 PMCID: PMC6382971 DOI: 10.1128/msphere.00632-18] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2018] [Accepted: 01/31/2019] [Indexed: 01/06/2023] Open
Abstract
Coxsackievirus typically infects humans via the gastrointestinal tract, which has a large number of microorganisms collectively referred to as the microbiota. To study how the intestinal microbiota influences enteric virus infection, several groups have used an antibiotic regimen in mice to deplete bacteria. These studies have shown that bacteria promote infection with several enteric viruses. However, very little is known about whether antibiotics influence viruses in a microbiota-independent manner. In this study, we sought to determine the effects of antibiotics on coxsackievirus B3 (CVB3) using an in vitro cell culture model in the absence of bacteria. We determined that an aminoglycoside antibiotic, neomycin, enhanced the plaque size of CVB3 strain Nancy. Neomycin treatment did not alter viral attachment, translation, or replication. However, we found that the positive charge of neomycin and other positively charged compounds enhanced viral diffusion by overcoming the negative inhibitory effect of sulfated polysaccharides present in agar overlays. Neomycin and the positively charged compound protamine also enhanced plaque formation of reovirus. Overall, these data provide further evidence that antibiotics can play noncanonical roles in viral infections and that this should be considered when studying enteric virus-microbiota interactions.IMPORTANCE Coxsackieviruses primarily infect the gastrointestinal tract of humans, but they can disseminate systemically and cause severe disease. Using antibiotic treatment regimens to deplete intestinal microbes in mice, several groups have shown the bacteria promote infection with a variety of enteric viruses. However, it is possible that antibiotics have microbiota-independent effects on viruses. Here we show that an aminoglycoside antibiotic, neomycin, can influence quantification of coxsackievirus in cultured cells in the absence of bacteria.
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Affiliation(s)
- Mikal A Woods Acevedo
- Department of Microbiology, University of Texas Southwestern Medical Center, Dallas, Texas, USA
| | - Andrea K Erickson
- Department of Microbiology, University of Texas Southwestern Medical Center, Dallas, Texas, USA
| | - Julie K Pfeiffer
- Department of Microbiology, University of Texas Southwestern Medical Center, Dallas, Texas, USA
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14
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Wang Y, Ma L, Stipkovits L, Szathmary S, Li X, Liu Y. The Strategy of Picornavirus Evading Host Antiviral Responses: Non-structural Proteins Suppress the Production of IFNs. Front Microbiol 2018; 9:2943. [PMID: 30619109 PMCID: PMC6297142 DOI: 10.3389/fmicb.2018.02943] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2018] [Accepted: 11/15/2018] [Indexed: 12/22/2022] Open
Abstract
Viral infections trigger the innate immune system to produce interferons (IFNs), which play important role in host antiviral responses. Co-evolution of viruses with their hosts has favored development of various strategies to evade the effects of IFNs, enabling viruses to survive inside host cells. One such strategy involves inhibition of IFN signaling pathways by non-structural proteins. In this review, we provide a brief overview of host signaling pathways inducing IFN production and their suppression by picornavirus non-structural proteins. Using this strategy, picornaviruses can evade the host immune response and replicate inside host cells.
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Affiliation(s)
- Yining Wang
- State Key Laboratory of Veterinary Etiological Biology, Lanzhou Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Lanzhou, China
| | - Lina Ma
- State Key Laboratory of Veterinary Etiological Biology, Lanzhou Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Lanzhou, China
| | | | | | - Xuerui Li
- State Key Laboratory of Veterinary Etiological Biology, Lanzhou Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Lanzhou, China
| | - Yongsheng Liu
- State Key Laboratory of Veterinary Etiological Biology, Lanzhou Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Lanzhou, China
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15
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Flather D, Nguyen JHC, Semler BL, Gershon PD. Exploitation of nuclear functions by human rhinovirus, a cytoplasmic RNA virus. PLoS Pathog 2018; 14:e1007277. [PMID: 30142213 PMCID: PMC6126879 DOI: 10.1371/journal.ppat.1007277] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2018] [Revised: 09/06/2018] [Accepted: 08/11/2018] [Indexed: 12/17/2022] Open
Abstract
Protein production, genomic RNA replication, and virion assembly during infection by picornaviruses like human rhinovirus and poliovirus take place in the cytoplasm of infected human cells, making them the quintessential cytoplasmic pathogens. However, a growing body of evidence suggests that picornavirus replication is promoted by a number of host proteins localized normally within the host cell nucleus. To systematically identify such nuclear proteins, we focused on those that appear to re-equilibrate from the nucleus to the cytoplasm during infection of HeLa cells with human rhinovirus via quantitative protein mass spectrometry. Our analysis revealed a highly selective re-equilibration of proteins with known mRNA splicing and transport-related functions over nuclear proteins of all other functional classes. The multifunctional splicing factor proline and glutamine rich (SFPQ) was identified as one such protein. We found that SFPQ is targeted for proteolysis within the nucleus by viral proteinase 3CD/3C, and a fragment of SFPQ was shown to migrate to the cytoplasm at mid-to-late times of infection. Cells knocked down for SFPQ expression showed significantly reduced rhinovirus titers, viral protein production, and viral RNA accumulation, consistent with SFPQ being a pro-viral factor. The SFPQ fragment that moved into the cytoplasm was able to bind rhinovirus RNA either directly or indirectly. We propose that the truncated form of SFPQ promotes viral RNA stability or replication, or virion morphogenesis. More broadly, our findings reveal dramatic changes in protein compartmentalization during human rhinovirus infection, allowing the virus to systematically hijack the functions of proteins not normally found at its cytoplasmic site of replication. We explored the dynamics of host cell protein relocalization from the nucleus to the cytoplasm during an infection by human rhinovirus using quantitative mass spectrometry, confocal imaging, and Western blot analysis. We discovered a highly selective re-equilibration of proteins with known mRNA splicing and transport-related functions, including splicing factor proline and glutamine rich (SFPQ). Using RNAi experiments and viral replication assays, we demonstrated that SFPQ is a pro-viral factor required for rhinovirus growth. Our studies provide new insights into how this cytoplasmic RNA virus is able to alter and hijack the functions of host proteins that normally reside in the nucleus.
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Affiliation(s)
- Dylan Flather
- Department of Microbiology and Molecular Genetics, School of Medicine, University of California, Irvine, California, United States of America
- Center for Virus Research, University of California, Irvine, California, United States of America
| | - Joseph H. C. Nguyen
- Department of Microbiology and Molecular Genetics, School of Medicine, University of California, Irvine, California, United States of America
- Center for Virus Research, University of California, Irvine, California, United States of America
| | - Bert L. Semler
- Department of Microbiology and Molecular Genetics, School of Medicine, University of California, Irvine, California, United States of America
- Center for Virus Research, University of California, Irvine, California, United States of America
- * E-mail: (BLS); (PDG)
| | - Paul D. Gershon
- Center for Virus Research, University of California, Irvine, California, United States of America
- Department of Molecular Biology and Biochemistry, University of California, Irvine, California, United States of America
- * E-mail: (BLS); (PDG)
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16
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Corona Velazquez A, Corona AK, Klein KA, Jackson WT. Poliovirus induces autophagic signaling independent of the ULK1 complex. Autophagy 2018; 14:1201-1213. [PMID: 29929428 PMCID: PMC6103675 DOI: 10.1080/15548627.2018.1458805] [Citation(s) in RCA: 42] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2017] [Revised: 12/07/2017] [Accepted: 03/26/2018] [Indexed: 12/31/2022] Open
Abstract
Poliovirus (PV), like many positive-strand RNA viruses, subverts the macroautophagy/autophagy pathway to promote its own replication. Here, we investigate whether the virus uses the canonical autophagic signaling complex, consisting of the ULK1/2 kinases, ATG13, RB1CC1, and ATG101, to activate autophagy. We find that the virus sends autophagic signals independent of the ULK1 complex, and that the members of the autophagic complex are not required for normal levels of viral replication. We also show that the SQSTM1/p62 receptor protein is not degraded in a conventional manner during infection, but is likely cleaved in a manner similar to that shown for coxsackievirus B3. This means that SQSTM1, normally used to monitor autophagic degradation, cannot be used to accurately monitor degradation during poliovirus infection. In fact, autophagic degradation may be affected by the loss of SQSTM1 at the same time as autophagic signals are being sent. Finally, we demonstrate that ULK1 and ULK2 protein levels are greatly reduced during PV infection, and ATG13, RB1CC1, and ATG101 protein levels are reduced as well. Surprisingly, autophagic signaling appears to increase as ULK1 levels decrease. Overexpression of wild-type or dominant-negative ULK1 constructs does not affect virus replication, indicating that ULK1 degradation may be a side effect of the ULK1-independent signaling mechanism used by PV, inducing complex instability. This demonstration of ULK1-independent autophagic signaling is novel and leads to a model by which the virus is signaling to generate autophagosomes downstream of ULK1, while at the same time, cleaving cargo receptors, which may affect cargo loading and autophagic degradative flux. Our data suggest that PV has a finely-tuned relationship with the autophagic machinery, generating autophagosomes without using the primary autophagy signaling pathway. ABBREVIATIONS ACTB - actin beta; ATG13 - autophagy related 13; ATG14 - autophagy related 14; ATG101 - autophagy related 101; BECN1 - beclin 1; CVB3 - coxsackievirus B3; DMV - double-membraned vesicles; EM - electron microscopy; EMCV - encephalomyocarditis virus; EV-71 - enterovirus 71; FMDV - foot and mouth disease virus; GFP - green fluorescent protein; MAP1LC3B/LC3B - microtubule associated protein 1 light chain 3 beta; MOI - multiplicity of infection; MTOR - mechanistic target of rapamycin kinase; PIK3C3 - phosphatidylinositol 3-kinase catalytic subunit type 3; PRKAA2 - protein kinase AMP-activated catalytic subunit alpha 2; PSMG1 - proteasome assembly chaperone 1; PSMG2 - proteasome assembly chaperone 2PV - poliovirus; RB1CC1 - RB1 inducible coiled-coil 1; SQSTM1 - sequestosome 1; ULK1 - unc-51 like autophagy activating kinase 1; ULK2 - unc-51 like autophagy activating kinase 2; WIPI1 - WD repeat domain, phosphoinositide interacting 1.
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Affiliation(s)
- Angel Corona Velazquez
- Department of Microbiology and Immunology, University of Maryland School of Medicine, Baltimore, MD, USA
| | - Abigail K. Corona
- Department of Microbiology and Immunology, University of Maryland School of Medicine, Baltimore, MD, USA
| | - Kathryn A. Klein
- Department of Microbiology and Molecular Genetics, Medical College of Wisconsin, Milwaukee, WI, USA
| | - William T. Jackson
- Department of Microbiology and Immunology, University of Maryland School of Medicine, Baltimore, MD, USA
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17
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Rodamilans B, Shan H, Pasin F, García JA. Plant Viral Proteases: Beyond the Role of Peptide Cutters. FRONTIERS IN PLANT SCIENCE 2018; 9:666. [PMID: 29868107 PMCID: PMC5967125 DOI: 10.3389/fpls.2018.00666] [Citation(s) in RCA: 26] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/15/2018] [Accepted: 04/30/2018] [Indexed: 05/23/2023]
Abstract
Almost half of known plant viral species rely on proteolytic cleavages as key co- and post-translational modifications throughout their infection cycle. Most of these viruses encode their own endopeptidases, proteases with high substrate specificity that internally cleave large polyprotein precursors for the release of functional sub-units. Processing of the polyprotein, however, is not an all-or-nothing process in which endopeptidases act as simple peptide cutters. On the contrary, spatial-temporal modulation of these polyprotein cleavage events is crucial for a successful viral infection. In this way, the processing of the polyprotein coordinates viral replication, assembly and movement, and has significant impact on pathogen fitness and virulence. In this mini-review, we give an overview of plant viral proteases emphasizing their importance during viral infections and the varied functionalities that result from their proteolytic activities.
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Affiliation(s)
- Bernardo Rodamilans
- Departamento de Genética Molecular de Plantas, Centro Nacional de Biotecnología, Consejo Superior de Investigaciones Científicas, Universidad Autónoma de Madrid, Madrid, Spain
| | - Hongying Shan
- Departamento de Genética Molecular de Plantas, Centro Nacional de Biotecnología, Consejo Superior de Investigaciones Científicas, Universidad Autónoma de Madrid, Madrid, Spain
| | - Fabio Pasin
- Agricultural Biotechnology Research Center, Academia Sinica, Taipei, Taiwan
| | - Juan Antonio García
- Departamento de Genética Molecular de Plantas, Centro Nacional de Biotecnología, Consejo Superior de Investigaciones Científicas, Universidad Autónoma de Madrid, Madrid, Spain
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18
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Maciejewski S, Ullmer W, Semler BL. VPg unlinkase/TDP2 in cardiovirus infected cells: Re-localization and proteolytic cleavage. Virology 2018; 516:139-146. [PMID: 29353210 DOI: 10.1016/j.virol.2018.01.010] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2017] [Revised: 01/05/2018] [Accepted: 01/09/2018] [Indexed: 10/18/2022]
Abstract
Cardioviruses cause diseases in many animals including, in rare cases, humans. Although they share common features with all picornaviruses, cardioviruses have unique properties that distinguish them from other family members, including enteroviruses. One feature shared by all picornaviruses is the covalent attachment of VPg to the 5' end of genomic RNA via a phosphotyrosyl linkage. For enteroviruses, this linkage is cleaved by a host cell protein, TDP2. Since TDP2 is divergently required during enterovirus infections, we determined if TDP2 is necessary during infection by the prototype cardiovirus, EMCV. We found that EMCV yields are reduced in the absence of TDP2. We observed a decrease in viral protein accumulation and viral RNA replication in the absence of TDP2. In contrast to enterovirus infections, we found that TDP2 is modified at peak times of EMCV infection. This finding suggests a unique mechanism for cardioviruses to regulate TDP2 activity during infection.
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Affiliation(s)
- Sonia Maciejewski
- Department of Microbiology and Molecular Genetics, School of Medicine, University of California, Irvine, CA 92697, USA
| | - Wendy Ullmer
- Department of Microbiology and Molecular Genetics, School of Medicine, University of California, Irvine, CA 92697, USA
| | - Bert L Semler
- Department of Microbiology and Molecular Genetics, School of Medicine, University of California, Irvine, CA 92697, USA.
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Lim CS, Brown CM. Know Your Enemy: Successful Bioinformatic Approaches to Predict Functional RNA Structures in Viral RNAs. Front Microbiol 2018; 8:2582. [PMID: 29354101 PMCID: PMC5758548 DOI: 10.3389/fmicb.2017.02582] [Citation(s) in RCA: 20] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2017] [Accepted: 12/11/2017] [Indexed: 12/14/2022] Open
Abstract
Structured RNA elements may control virus replication, transcription and translation, and their distinct features are being exploited by novel antiviral strategies. Viral RNA elements continue to be discovered using combinations of experimental and computational analyses. However, the wealth of sequence data, notably from deep viral RNA sequencing, viromes, and metagenomes, necessitates computational approaches being used as an essential discovery tool. In this review, we describe practical approaches being used to discover functional RNA elements in viral genomes. In addition to success stories in new and emerging viruses, these approaches have revealed some surprising new features of well-studied viruses e.g., human immunodeficiency virus, hepatitis C virus, influenza, and dengue viruses. Some notable discoveries were facilitated by new comparative analyses of diverse viral genome alignments. Importantly, comparative approaches for finding RNA elements embedded in coding and non-coding regions differ. With the exponential growth of computer power we have progressed from stem-loop prediction on single sequences to cutting edge 3D prediction, and from command line to user friendly web interfaces. Despite these advances, many powerful, user friendly prediction tools and resources are underutilized by the virology community.
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Affiliation(s)
- Chun Shen Lim
- Department of Biochemistry, School of Biomedical Sciences, University of Otago, Dunedin, New Zealand
| | - Chris M Brown
- Department of Biochemistry, School of Biomedical Sciences, University of Otago, Dunedin, New Zealand
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20
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Foot-and-mouth disease virus 5'-terminal S fragment is required for replication and modulation of the innate immune response in host cells. Virology 2017; 512:132-143. [PMID: 28961454 DOI: 10.1016/j.virol.2017.08.036] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2017] [Revised: 08/30/2017] [Accepted: 08/31/2017] [Indexed: 11/20/2022]
Abstract
The S fragment of the FMDV 5' UTR is predicted to fold into a long stem-loop structure and it has been implicated in virus-host protein interactions. In this study, we report the minimal S fragment sequence required for virus viability and show a direct correlation between the extent of the S fragment deletion mutations and attenuated phenotypes. Furthermore, we provide novel insight into the role of the S fragment in modulating the host innate immune response. Importantly, in an FMDV mouse model system, all animals survive the inoculation with the live A24 FMDV-S4 mutant, containing a 164 nucleotide deletion in the upper S fragment loop, at a dose 1000 higher than the one causing lethality by parental A24 FMDV, indicating that the A24 FMDV-S4 virus is highly attenuated in vivo. Additionally, mice exposed to high doses of live A24 FMDV-S4 virus are fully protected when challenged with parental A24 FMDV virus.
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21
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Interaction of 2A proteinase of human rhinovirus genetic group A with eIF4E is required for eIF4G cleavage during infection. Virology 2017; 511:123-134. [DOI: 10.1016/j.virol.2017.08.020] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2017] [Revised: 08/11/2017] [Accepted: 08/14/2017] [Indexed: 01/04/2023]
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22
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Nonstructural Protein NSs of Schmallenberg Virus Is Targeted to the Nucleolus and Induces Nucleolar Disorganization. J Virol 2016; 91:JVI.01263-16. [PMID: 27795408 PMCID: PMC5165206 DOI: 10.1128/jvi.01263-16] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2016] [Accepted: 10/04/2016] [Indexed: 01/04/2023] Open
Abstract
Schmallenberg virus (SBV) was discovered in Germany in late 2011 and then spread rapidly to many European countries. SBV is an orthobunyavirus that causes abortion and congenital abnormalities in ruminants. A virus-encoded nonstructural protein, termed NSs, is a major virulence factor of SBV, and it is known to promote the degradation of Rpb1, a subunit of the RNA polymerase II (Pol II) complex, and therefore hampers global cellular transcription. In this study, we found that NSs is mainly localized in the nucleus of infected cells and specifically appears to target the nucleolus through a nucleolar localization signal (NoLS) localized between residues 33 and 51 of the protein. NSs colocalizes with nucleolar markers such as B23 (nucleophosmin) and fibrillarin. We observed that in SBV-infected cells, B23 undergoes a nucleolus-to-nucleoplasm redistribution, evocative of virus-induced nucleolar disruption. In contrast, the nucleolar pattern of B23 was unchanged upon infection with an SBV recombinant mutant with NSs lacking the NoLS motif (SBVΔNoLS). Interestingly, unlike wild-type SBV, the inhibitory activity of SBVΔNoLS toward RNA Pol II transcription is impaired. Overall, our results suggest that a putative link exists between NSs-induced nucleolar disruption and its inhibitory function on cellular transcription, which consequently precludes the cellular antiviral response and/or induces cell death. IMPORTANCE Schmallenberg virus (SBV) is an emerging arbovirus of ruminants that spread in Europe between 2011 and 2013. SBV induces fetal abnormalities during gestation, with the central nervous system being one of the most affected organs. The virus-encoded NSs protein acts as a virulence factor by impairing host cell transcription. Here, we show that NSs contains a nucleolar localization signal (NoLS) and induces disorganization of the nucleolus. The NoLS motif in the SBV NSs is absolutely necessary for virus-induced inhibition of cellular transcription. To our knowledge, this is the first report of nucleolar functions for NSs within the Bunyaviridae family.
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23
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Walker E, Jensen L, Croft S, Wei K, Fulcher AJ, Jans DA, Ghildyal R. Rhinovirus 16 2A Protease Affects Nuclear Localization of 3CD during Infection. J Virol 2016; 90:11032-11042. [PMID: 27681132 PMCID: PMC5126362 DOI: 10.1128/jvi.00974-16] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2016] [Accepted: 09/11/2016] [Indexed: 01/08/2023] Open
Abstract
The human rhinovirus (HRV) 3C and 2A proteases (3Cpro and 2Apro, respectively) are critical in HRV infection, as they are required for viral polyprotein processing as well as proteolysing key host factors to facilitate virus replication. Early in infection, 3Cpro is present as its precursor 3CD, which, although the mechanism of subcellular targeting is unknown, is found in the nucleus as well as the cytoplasm. In this study, we use transfected and infected cell systems to show that 2Apro activity is required for 3CD nuclear localization. Using green fluorescent protein (GFP)-tagged forms of 3Cpro, 3D, and mutant derivatives thereof, we show that 3Cpro is located in the cytoplasm and the nucleus, whereas 3CD and 3D are localized predominantly in the cytoplasm, implying that 3D lacks nuclear targeting ability and that 3Cpro activity within 3CD is not sufficient to allow the larger protein into the nucleus. Importantly, by coexpressing mCherry-2Apro fusion proteins, we demonstrate formally that 2Apro activity is required to allow HRV 3CD access to the nucleus. In contrast, mCherry-3Cpro is insufficient to allow 3CD access to the nucleus. Finally, we confirm the relevance of these results to HRV infection by demonstrating that nuclear localization of 3CD correlates with 2Apro activity and not 3Cpro activity, which is observed only later in infection. The results thus define the temporal activities of 2Apro and 3CD/3Cpro activities in HRV serotype16 infection. IMPORTANCE The human rhinovirus genome encodes two proteases, 2A and 3C, as well as a precursor protease, 3CD. These proteases are essential for efficient virus replication. The 3CD protein is found in the nucleus early during infection, though the mechanism of subcellular localization is unknown. Here we show that 2A protease is required for this localization, the 3C protease activity of 3CD is not sufficient to allow 3CD entry into the nucleus, and 3D lacks nuclear targeting ability. This study demonstrates that both 2A and 3C proteases are required for the correct localization of proteins during infection and defines the temporal regulation of 2A and 3CD/3C protease activities during HRV16 infection.
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Affiliation(s)
- Erin Walker
- Centre for Research in Therapeutic Solutions, University of Canberra, Canberra, Australian Capital Territory, Australia
| | - Lora Jensen
- Centre for Research in Therapeutic Solutions, University of Canberra, Canberra, Australian Capital Territory, Australia
| | - Sarah Croft
- Centre for Research in Therapeutic Solutions, University of Canberra, Canberra, Australian Capital Territory, Australia
| | - Kejun Wei
- Centre for Research in Therapeutic Solutions, University of Canberra, Canberra, Australian Capital Territory, Australia
| | - Alex J Fulcher
- Department of Biochemistry and Molecular Biology, Monash University, Clayton, Victoria, Australia
- Monash Micro Imaging, Monash University, Clayton, Victoria, Australia
| | - David A Jans
- Department of Biochemistry and Molecular Biology, Monash University, Clayton, Victoria, Australia
| | - Reena Ghildyal
- Centre for Research in Therapeutic Solutions, University of Canberra, Canberra, Australian Capital Territory, Australia
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24
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High-Throughput Next-Generation Sequencing of Polioviruses. J Clin Microbiol 2016; 55:606-615. [PMID: 27927929 DOI: 10.1128/jcm.02121-16] [Citation(s) in RCA: 53] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2016] [Accepted: 12/05/2016] [Indexed: 01/30/2023] Open
Abstract
The poliovirus (PV) is currently targeted for worldwide eradication and containment. Sanger-based sequencing of the viral protein 1 (VP1) capsid region is currently the standard method for PV surveillance. However, the whole-genome sequence is sometimes needed for higher resolution global surveillance. In this study, we optimized whole-genome sequencing protocols for poliovirus isolates and FTA cards using next-generation sequencing (NGS), aiming for high sequence coverage, efficiency, and throughput. We found that DNase treatment of poliovirus RNA followed by random reverse transcription (RT), amplification, and the use of the Nextera XT DNA library preparation kit produced significantly better results than other preparations. The average viral reads per total reads, a measurement of efficiency, was as high as 84.2% ± 15.6%. PV genomes covering >99 to 100% of the reference length were obtained and validated with Sanger sequencing. A total of 52 PV genomes were generated, multiplexing as many as 64 samples in a single Illumina MiSeq run. This high-throughput, sequence-independent NGS approach facilitated the detection of a diverse range of PVs, especially for those in vaccine-derived polioviruses (VDPV), circulating VDPV, or immunodeficiency-related VDPV. In contrast to results from previous studies on other viruses, our results showed that filtration and nuclease treatment did not discernibly increase the sequencing efficiency of PV isolates. However, DNase treatment after nucleic acid extraction to remove host DNA significantly improved the sequencing results. This NGS method has been successfully implemented to generate PV genomes for molecular epidemiology of the most recent PV isolates. Additionally, the ability to obtain full PV genomes from FTA cards will aid in facilitating global poliovirus surveillance.
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25
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Napthine S, Treffers EE, Bell S, Goodfellow I, Fang Y, Firth AE, Snijder EJ, Brierley I. A novel role for poly(C) binding proteins in programmed ribosomal frameshifting. Nucleic Acids Res 2016; 44:5491-503. [PMID: 27257056 PMCID: PMC4937337 DOI: 10.1093/nar/gkw480] [Citation(s) in RCA: 38] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2016] [Accepted: 05/18/2016] [Indexed: 01/16/2023] Open
Abstract
Translational control through programmed ribosomal frameshifting (PRF) is exploited widely by viruses and increasingly documented in cellular genes. Frameshifting is induced by mRNA secondary structures that compromise ribosome fidelity during decoding of a heptanucleotide 'slippery' sequence. The nsp2 PRF signal of porcine reproductive and respiratory syndrome virus is distinctive in directing both -2 and -1 PRF and in its requirement for a trans-acting protein factor, the viral replicase subunit nsp1β. Here we show that the the trans-activation of frameshifting is carried out by a protein complex composed of nsp1β and a cellular poly(C) binding protein (PCBP). From the results of in vitro translation and electrophoretic mobility shift assays, we demonstrate that a PCBP/nsp1β complex binds to a C-rich sequence downstream of the slippery sequence and here mimics the activity of a structured mRNA stimulator of PRF. This is the first description of a role for a trans-acting cellular protein in PRF. The discovery broadens the repertoire of activities associated with poly(C) binding proteins and prototypes a new class of virus-host interactions.
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Affiliation(s)
- Sawsan Napthine
- Department of Pathology, University of Cambridge, Cambridge, CB2 1QP, UK
| | - Emmely E Treffers
- Department of Medical Microbiology, Leiden University Medical Center, P.O. Box 9600, 2300 RC Leiden, The Netherlands
| | - Susanne Bell
- Department of Pathology, University of Cambridge, Cambridge, CB2 1QP, UK
| | - Ian Goodfellow
- Department of Pathology, University of Cambridge, Cambridge, CB2 1QP, UK
| | - Ying Fang
- College of Veterinary Medicine, Kansas State University, Manhattan, KS 66506-5705, USA
| | - Andrew E Firth
- Department of Pathology, University of Cambridge, Cambridge, CB2 1QP, UK
| | - Eric J Snijder
- Department of Medical Microbiology, Leiden University Medical Center, P.O. Box 9600, 2300 RC Leiden, The Netherlands
| | - Ian Brierley
- Department of Pathology, University of Cambridge, Cambridge, CB2 1QP, UK
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26
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Construction of a subgenomic CV-B3 replicon expressing emerald green fluorescent protein to assess viral replication of a cardiotropic enterovirus strain in cultured human cells. J Virol Methods 2016; 230:1-8. [PMID: 26800776 DOI: 10.1016/j.jviromet.2016.01.005] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2015] [Revised: 01/13/2016] [Accepted: 01/15/2016] [Indexed: 11/21/2022]
Abstract
Coxsackieviruses B (CV-B) (Picornaviridae) are a common infectious cause of acute myocarditis in children and young adults, a disease, which is a precursor to 10-20% of chronic myocarditis and dilated cardiomyopathy (DCM) cases. The mechanisms involved in the disease progression from acute to chronic myocarditis phase and toward the DCM clinical stage are not fully understood but are influenced by both viral and host factors. Subgenomic replicons of CV-B can be used to assess viral replication mechanisms in human cardiac cells and evaluate the effects of potential antiviral drugs on viral replication activities. Our objectives were to generate a reporter replicon from a cardiotropic prototype CV-B3/28 strain and to characterize its replication properties into human cardiac primary cells. To obtain this replicon, a cDNA plasmid containing the full CV-B3/28 genome flanked by a hammerhead ribozyme sequence and an MluI restriction site was generated and used as a platform for the insertion of sequences encoding emerald green fluorescent protein (EmGFP) in place of those encoding VP3. In vitro transcribed RNA from this plasmid was transfected into HeLa cells and human primary cardiac cells and was able to produce EmGFP and VP1-containing polypeptides. Moreover, non-structural protein biological activity was assessed by the specific cleavage of eIF4G1 by viral 2A(pro). Viral RNA replication was indirectly demonstrated by inhibition assays, fluoxetine was added to cell culture and prevented the EmGFP synthesis. Our results indicated that the EmGFP CV-B3 replicon was able to replicate and translate as well as the CV-B3/28 prototype strain. Our EmGFP CV-B3 replicon will be a valuable tool to readily investigate CV-B3 replication activities in human target cell models.
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27
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Maciejewski S, Nguyen JHC, Gómez-Herreros F, Cortés-Ledesma F, Caldecott KW, Semler BL. Divergent Requirement for a DNA Repair Enzyme during Enterovirus Infections. mBio 2015; 7:e01931-15. [PMID: 26715620 PMCID: PMC4725011 DOI: 10.1128/mbio.01931-15] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2015] [Accepted: 11/09/2015] [Indexed: 01/13/2023] Open
Abstract
UNLABELLED Viruses of the Enterovirus genus of picornaviruses, including poliovirus, coxsackievirus B3 (CVB3), and human rhinovirus, commandeer the functions of host cell proteins to aid in the replication of their small viral genomic RNAs during infection. One of these host proteins is a cellular DNA repair enzyme known as 5' tyrosyl-DNA phosphodiesterase 2 (TDP2). TDP2 was previously demonstrated to mediate the cleavage of a unique covalent linkage between a viral protein (VPg) and the 5' end of picornavirus RNAs. Although VPg is absent from actively translating poliovirus mRNAs, the removal of VPg is not required for the in vitro translation and replication of the RNA. However, TDP2 appears to be excluded from replication and encapsidation sites during peak times of poliovirus infection of HeLa cells, suggesting a role for TDP2 during the viral replication cycle. Using a mouse embryonic fibroblast cell line lacking TDP2, we found that TDP2 is differentially required among enteroviruses. Our single-cycle viral growth analysis shows that CVB3 replication has a greater dependency on TDP2 than does poliovirus or human rhinovirus replication. During infection, CVB3 protein accumulation is undetectable (by Western blot analysis) in the absence of TDP2, whereas poliovirus protein accumulation is reduced but still detectable. Using an infectious CVB3 RNA with a reporter, CVB3 RNA could still be replicated in the absence of TDP2 following transfection, albeit at reduced levels. Overall, these results indicate that TDP2 potentiates viral replication during enterovirus infections of cultured cells, making TDP2 a potential target for antiviral development for picornavirus infections. IMPORTANCE Picornaviruses are one of the most prevalent groups of viruses that infect humans and livestock worldwide. These viruses include the human pathogens belonging to the Enterovirus genus, such as poliovirus, coxsackievirus B3 (CVB3), and human rhinovirus. Diseases caused by enteroviruses pose a major problem for public health and have significant economic impact. Poliovirus can cause paralytic poliomyelitis. CVB3 can cause hand, foot, and mouth disease and myocarditis. Human rhinovirus is the causative agent of the common cold, which has a severe economic impact due to lost productivity and severe health consequences in individuals with respiratory dysfunction, such as asthma. By gaining a better understanding of the enterovirus replication cycle, antiviral drugs against enteroviruses may be developed. Here, we report that the absence of the cellular enzyme TDP2 can significantly decrease viral yields of poliovirus, CVB3, and human rhinovirus, making TDP2 a potential target for an antiviral against enterovirus infections.
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Affiliation(s)
- Sonia Maciejewski
- Department of Microbiology and Molecular Genetics, School of Medicine, University of California, Irvine, California, USA
| | - Joseph H C Nguyen
- Department of Microbiology and Molecular Genetics, School of Medicine, University of California, Irvine, California, USA
| | - Fernando Gómez-Herreros
- School of Life Sciences, Genome Damage and Stability Centre, University of Sussex, Brighton, United Kingdom
| | - Felipe Cortés-Ledesma
- School of Life Sciences, Genome Damage and Stability Centre, University of Sussex, Brighton, United Kingdom
| | - Keith W Caldecott
- School of Life Sciences, Genome Damage and Stability Centre, University of Sussex, Brighton, United Kingdom
| | - Bert L Semler
- Department of Microbiology and Molecular Genetics, School of Medicine, University of California, Irvine, California, USA
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28
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Martin TM, Plautz SA, Pannier AK. Temporal endogenous gene expression profiles in response to polymer-mediated transfection and profile comparison to lipid-mediated transfection. J Gene Med 2015; 17:33-53. [PMID: 25663627 DOI: 10.1002/jgm.2822] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2014] [Revised: 02/01/2015] [Accepted: 02/03/2015] [Indexed: 12/12/2022] Open
Abstract
BACKGROUND Design of efficient nonviral gene delivery systems is limited by the rudimentary understanding of specific molecules that facilitate transfection. METHODS Polyplexes using 25-kDa polyethylenimine (PEI) and plasmid-encoding green fluorescent protein (GFP) were delivered to HEK 293T cells. After treating cells with polyplexes, microarrays were used to identify endogenous genes differentially expressed between treated and untreated cells (2 h of exposure) or between flow-separated transfected cells (GFP+) and treated, untransfected cells (GFP-) at 8, 16 and 24 h after lipoplex treatment. Cell priming studies were conducted using pharmacologic agents to alter endogenous levels of the identified differentially expressed genes to determine effect on transfection levels. Differentially expressed genes in polyplex-mediated transfection were compared with those differentially expressed in lipoplex transfection to identify DNA carrier-dependent molecular factors. RESULTS Differentially expressed genes were RGS1, ARHGAP24, PDZD2, SNX24, GSN and IGF2BP1 after 2 h; RAP1A and ACTA1 after 8 h; RAP1A, WDR78 and ACTA1 after 16 h; and RAP1A, SCG5, ATF3, IREB2 and ACTA1 after 24 h. Pharmacologic studies altering endogenous levels for ARHGAP24, GSN, IGF2BP1, PDZD2 and RGS1 were able to increase or decrease transgene production. Comparing differentially expressed genes for polyplexes and lipoplexes, no common genes were identified at the 2-h time point, whereas, after the 8-h time point, RAP1A, ATF3 and HSPA6 were similarly expressed. SCG5 and PGAP1 were only upregulated in polyplex-transfected cells. CONCLUSIONS The identified genes and pharmacologic agents provide targets for improving transfection systems, although polyplex or lipoplex dependencies must be considered.
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Affiliation(s)
- Timothy M Martin
- Department of Pharmaceutical Sciences, Durham Research Center II, University of Nebraska-Medical Center, Omaha, NE, USA
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29
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Kim Y, Kankanamalage ACG, Damalanka VC, Weerawarna PM, Groutas WC, Chang KO. Potent inhibition of enterovirus D68 and human rhinoviruses by dipeptidyl aldehydes and α-ketoamides. Antiviral Res 2015; 125:84-91. [PMID: 26658373 PMCID: PMC4698184 DOI: 10.1016/j.antiviral.2015.11.010] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/04/2015] [Revised: 10/21/2015] [Accepted: 11/23/2015] [Indexed: 01/17/2023]
Abstract
Enterovirus D68 (EV-D68) is an emerging pathogen responsible for mild to severe respiratory infections that occur mostly in infants, children and teenagers. EV-D68, one of more than 100 non-polio enteroviruses, is acid-labile and biologically similar to human rhinoviruses (HRV) (originally classified as HRV87). However, there is no approved preventive or therapeutic measure against EV-D68, HRV, or other enteroviruses. In this study, we evaluated the antiviral activity of series of dipeptidyl compounds against EV-D68 and HRV strains, and demonstrated that several peptidyl aldehyde and α-ketoamide peptidyl compounds are potent inhibitors of EV-D68 and HRV strains with high in-vitro therapeutic indices (>1000). One of the α-ketoamide compounds is shown to have favorable pharmacokinetics profiles, including a favorable oral bioavailability in rats. Recent successful development of α-ketoamide protease inhibitors against hepatitis C virus suggests these compounds may have a high potential for further optimization and development against emerging EV-D68, as well as HRV. Series of dipeptidyl aldehyde or ketomide compounds were highly effective against enterovirus-D68 and human rhinoviruses. The highly effective ketoamide compound is shown to have favorable pharmacokinetics profiles. These may have a high potential for further antiviral development against emerging enterovirus-D68 and human rhinoviruses.
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Affiliation(s)
- Yunjeong Kim
- Department of Diagnostic Medicine and Pathobiology, College of Veterinary Medicine, Kansas State University, Manhattan, KS, USA
| | | | | | | | - William C Groutas
- Department of Chemistry, Wichita State University, Wichita, KS, USA.
| | - Kyeong-Ok Chang
- Department of Diagnostic Medicine and Pathobiology, College of Veterinary Medicine, Kansas State University, Manhattan, KS, USA.
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30
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Wen X, Cheng A, Wang M, Jia R, Zhu D, Chen S, Liu M, Sun K, Yang Q, Wu Y, Chen X. Recent advances from studies on the role of structural proteins in enterovirus infection. Future Microbiol 2015; 10:1529-42. [DOI: 10.2217/fmb.15.62] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022] Open
Abstract
Enteroviruses are a large group of small nonenveloped viruses that cause common and debilitating illnesses affecting humans and animals worldwide. The capsid composed by viral structural proteins packs the RNA genome. It is becoming apparent that structural proteins of enteroviruses play versatile roles in the virus–host interaction in the viral life cycle, more than just a shell. Furthermore, structural proteins to some extent may be associated with viral virulence and pathogenesis. Better understanding the roles of structural proteins in enterovirus infection may lead to the development of potential antiviral strategies. Here, we discuss recent advances from studies on the role of structural proteins in enterovirus infection and antiviral therapeutics targeted structural proteins.
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Affiliation(s)
- Xingjian Wen
- Institute of Preventive Veterinary Medicine, Sichuan Agricultural University, Wenjiang, Chengdu City, Sichuan 611130, PR China
- Avian Disease Research Center, College of Veterinary Medicine of Sichuan Agricultural University, Wenjiang, Chengdu City, Sichuan 611130, PR China
- Key Laboratory of Animal Disease & Human Health of Sichuan Province, Sichuan Agricultural University, Wenjiang, Chengdu City, Sichuan 611130, PR China
| | - Anchun Cheng
- Institute of Preventive Veterinary Medicine, Sichuan Agricultural University, Wenjiang, Chengdu City, Sichuan 611130, PR China
- Avian Disease Research Center, College of Veterinary Medicine of Sichuan Agricultural University, Wenjiang, Chengdu City, Sichuan 611130, PR China
- Key Laboratory of Animal Disease & Human Health of Sichuan Province, Sichuan Agricultural University, Wenjiang, Chengdu City, Sichuan 611130, PR China
- Engineering & Technology Center for Laboratory Animals of Sichuan Agricultural University, Ya'an, Sichuan 625014, China
| | - Mingshu Wang
- Institute of Preventive Veterinary Medicine, Sichuan Agricultural University, Wenjiang, Chengdu City, Sichuan 611130, PR China
- Avian Disease Research Center, College of Veterinary Medicine of Sichuan Agricultural University, Wenjiang, Chengdu City, Sichuan 611130, PR China
- Key Laboratory of Animal Disease & Human Health of Sichuan Province, Sichuan Agricultural University, Wenjiang, Chengdu City, Sichuan 611130, PR China
| | - Renyong Jia
- Institute of Preventive Veterinary Medicine, Sichuan Agricultural University, Wenjiang, Chengdu City, Sichuan 611130, PR China
- Avian Disease Research Center, College of Veterinary Medicine of Sichuan Agricultural University, Wenjiang, Chengdu City, Sichuan 611130, PR China
- Key Laboratory of Animal Disease & Human Health of Sichuan Province, Sichuan Agricultural University, Wenjiang, Chengdu City, Sichuan 611130, PR China
| | - Dekang Zhu
- Avian Disease Research Center, College of Veterinary Medicine of Sichuan Agricultural University, Wenjiang, Chengdu City, Sichuan 611130, PR China
- Key Laboratory of Animal Disease & Human Health of Sichuan Province, Sichuan Agricultural University, Wenjiang, Chengdu City, Sichuan 611130, PR China
| | - Shun Chen
- Institute of Preventive Veterinary Medicine, Sichuan Agricultural University, Wenjiang, Chengdu City, Sichuan 611130, PR China
- Avian Disease Research Center, College of Veterinary Medicine of Sichuan Agricultural University, Wenjiang, Chengdu City, Sichuan 611130, PR China
- Key Laboratory of Animal Disease & Human Health of Sichuan Province, Sichuan Agricultural University, Wenjiang, Chengdu City, Sichuan 611130, PR China
| | - Mafeng Liu
- Institute of Preventive Veterinary Medicine, Sichuan Agricultural University, Wenjiang, Chengdu City, Sichuan 611130, PR China
- Avian Disease Research Center, College of Veterinary Medicine of Sichuan Agricultural University, Wenjiang, Chengdu City, Sichuan 611130, PR China
- Key Laboratory of Animal Disease & Human Health of Sichuan Province, Sichuan Agricultural University, Wenjiang, Chengdu City, Sichuan 611130, PR China
| | - Kunfeng Sun
- Institute of Preventive Veterinary Medicine, Sichuan Agricultural University, Wenjiang, Chengdu City, Sichuan 611130, PR China
- Avian Disease Research Center, College of Veterinary Medicine of Sichuan Agricultural University, Wenjiang, Chengdu City, Sichuan 611130, PR China
- Key Laboratory of Animal Disease & Human Health of Sichuan Province, Sichuan Agricultural University, Wenjiang, Chengdu City, Sichuan 611130, PR China
| | - Qiao Yang
- Institute of Preventive Veterinary Medicine, Sichuan Agricultural University, Wenjiang, Chengdu City, Sichuan 611130, PR China
- Avian Disease Research Center, College of Veterinary Medicine of Sichuan Agricultural University, Wenjiang, Chengdu City, Sichuan 611130, PR China
- Key Laboratory of Animal Disease & Human Health of Sichuan Province, Sichuan Agricultural University, Wenjiang, Chengdu City, Sichuan 611130, PR China
| | - Ying Wu
- Institute of Preventive Veterinary Medicine, Sichuan Agricultural University, Wenjiang, Chengdu City, Sichuan 611130, PR China
- Avian Disease Research Center, College of Veterinary Medicine of Sichuan Agricultural University, Wenjiang, Chengdu City, Sichuan 611130, PR China
- Key Laboratory of Animal Disease & Human Health of Sichuan Province, Sichuan Agricultural University, Wenjiang, Chengdu City, Sichuan 611130, PR China
| | - Xiaoyue Chen
- Avian Disease Research Center, College of Veterinary Medicine of Sichuan Agricultural University, Wenjiang, Chengdu City, Sichuan 611130, PR China
- Key Laboratory of Animal Disease & Human Health of Sichuan Province, Sichuan Agricultural University, Wenjiang, Chengdu City, Sichuan 611130, PR China
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31
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The heat shock response restricts virus infection in Drosophila. Sci Rep 2015; 5:12758. [PMID: 26234525 PMCID: PMC4522674 DOI: 10.1038/srep12758] [Citation(s) in RCA: 73] [Impact Index Per Article: 8.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2015] [Accepted: 07/09/2015] [Indexed: 01/02/2023] Open
Abstract
Innate immunity is the first line of defence against pathogens and is essential for survival of the infected host. The fruit fly Drosophila melanogaster is an emerging model to study viral pathogenesis, yet antiviral defence responses remain poorly understood. Here, we describe the heat shock response, a cellular mechanism that prevents proteotoxicity, as a component of the antiviral immune response in Drosophila. Transcriptome analyses of Drosophila S2 cells and adult flies revealed strong induction of the heat shock response upon RNA virus infection. Dynamic induction patterns of heat shock pathway components were characterized in vitro and in vivo following infection with different classes of viruses. The heat shock transcription factor (Hsf), as well as active viral replication, were necessary for the induction of the response. Hsf-deficient adult flies were hypersensitive to virus infection, indicating a role of the heat shock response in antiviral defence. In accordance, transgenic activation of the heat shock response prolonged survival time after infection and enabled long-term control of virus replication to undetectable levels. Together, our results establish the heat shock response as an important constituent of innate antiviral immunity in Drosophila.
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32
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Rawlinson SM, Moseley GW. The nucleolar interface of
RNA
viruses. Cell Microbiol 2015; 17:1108-20. [DOI: 10.1111/cmi.12465] [Citation(s) in RCA: 39] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2015] [Revised: 05/27/2015] [Accepted: 06/01/2015] [Indexed: 02/06/2023]
Affiliation(s)
- Stephen M. Rawlinson
- Viral Pathogenesis Laboratory Department of Biochemistry and Molecular Biology Bio21 Molecular Science and Biotechnology Institute The University of Melbourne Melbourne Australia
| | - Gregory W. Moseley
- Viral Pathogenesis Laboratory Department of Biochemistry and Molecular Biology Bio21 Molecular Science and Biotechnology Institute The University of Melbourne Melbourne Australia
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Piñeiro D, Fernandez-Chamorro J, Francisco-Velilla R, Martinez-Salas E. Gemin5: A Multitasking RNA-Binding Protein Involved in Translation Control. Biomolecules 2015; 5:528-44. [PMID: 25898402 PMCID: PMC4496684 DOI: 10.3390/biom5020528] [Citation(s) in RCA: 28] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2015] [Revised: 04/01/2015] [Accepted: 04/09/2015] [Indexed: 12/31/2022] Open
Abstract
Gemin5 is a RNA-binding protein (RBP) that was first identified as a peripheral component of the survival of motor neurons (SMN) complex. This predominantly cytoplasmic protein recognises the small nuclear RNAs (snRNAs) through its WD repeat domains, allowing assembly of the SMN complex into small nuclear ribonucleoproteins (snRNPs). Additionally, the amino-terminal end of the protein has been reported to possess cap-binding capacity and to interact with the eukaryotic initiation factor 4E (eIF4E). Gemin5 was also shown to downregulate translation, to be a substrate of the picornavirus L protease and to interact with viral internal ribosome entry site (IRES) elements via a bipartite non-canonical RNA-binding site located at its carboxy-terminal end. These features link Gemin5 with translation control events. Thus, beyond its role in snRNPs biogenesis, Gemin5 appears to be a multitasking protein cooperating in various RNA-guided processes. In this review, we will summarise current knowledge of Gemin5 functions. We will discuss the involvement of the protein on translation control and propose a model to explain how the proteolysis fragments of this RBP in picornavirus-infected cells could modulate protein synthesis.
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Affiliation(s)
- David Piñeiro
- Medical Research Council Toxicology Unit, Lancaster Rd, Leicester LE1 9HN, UK.
| | - Javier Fernandez-Chamorro
- Centro de Biología Molecular Severo Ochoa, Consejo Superior de Investigaciones Científicas-Universidad Autónoma de Madrid, Nicolas Cabrera 1, Madrid 28049, Spain.
| | - Rosario Francisco-Velilla
- Centro de Biología Molecular Severo Ochoa, Consejo Superior de Investigaciones Científicas-Universidad Autónoma de Madrid, Nicolas Cabrera 1, Madrid 28049, Spain.
| | - Encarna Martinez-Salas
- Centro de Biología Molecular Severo Ochoa, Consejo Superior de Investigaciones Científicas-Universidad Autónoma de Madrid, Nicolas Cabrera 1, Madrid 28049, Spain.
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34
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Martínez-Salas E, Francisco-Velilla R, Fernandez-Chamorro J, Lozano G, Diaz-Toledano R. Picornavirus IRES elements: RNA structure and host protein interactions. Virus Res 2015; 206:62-73. [PMID: 25617758 DOI: 10.1016/j.virusres.2015.01.012] [Citation(s) in RCA: 96] [Impact Index Per Article: 10.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2014] [Revised: 01/05/2015] [Accepted: 01/12/2015] [Indexed: 01/26/2023]
Abstract
Internal ribosome entry site (IRES) elements were discovered in picornaviruses. These elements are cis-acting RNA sequences that adopt diverse three-dimensional structures and recruit the translation machinery using a 5' end-independent mechanism assisted by a subset of translation initiation factors and various RNA binding proteins termed IRES transacting factors (ITAFs). Many of these factors suffer important modifications during infection including cleavage by picornavirus proteases, changes in the phosphorylation level and/or redistribution of the protein from the nuclear to the cytoplasm compartment. Picornavirus IRES are amongst the most potent elements described so far. However, given their large diversity and complexity, the mechanistic basis of its mode of action is not yet fully understood. This review is focused to describe recent advances on the studies of RNA structure and RNA-protein interactions modulating picornavirus IRES activity.
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Affiliation(s)
- Encarnación Martínez-Salas
- Centro de Biología Molecular Severo Ochoa, Consejo Superior de Investigaciones Científicas - Universidad Autónoma de Madrid, Nicolas Cabrera 1, 28049 Madrid, Spain.
| | - Rosario Francisco-Velilla
- Centro de Biología Molecular Severo Ochoa, Consejo Superior de Investigaciones Científicas - Universidad Autónoma de Madrid, Nicolas Cabrera 1, 28049 Madrid, Spain
| | - Javier Fernandez-Chamorro
- Centro de Biología Molecular Severo Ochoa, Consejo Superior de Investigaciones Científicas - Universidad Autónoma de Madrid, Nicolas Cabrera 1, 28049 Madrid, Spain
| | - Gloria Lozano
- Centro de Biología Molecular Severo Ochoa, Consejo Superior de Investigaciones Científicas - Universidad Autónoma de Madrid, Nicolas Cabrera 1, 28049 Madrid, Spain
| | - Rosa Diaz-Toledano
- Centro de Biología Molecular Severo Ochoa, Consejo Superior de Investigaciones Científicas - Universidad Autónoma de Madrid, Nicolas Cabrera 1, 28049 Madrid, Spain
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Abstract
Human rhinoviruses (HRV) are the major etiological agents of the common cold and asthma exacerbations, with significant worldwide health and economic impact. Although large-scale population vaccination has proved successful in limiting or even eradicating many viruses, the more than 100 distinct serotypes mean that conventional vaccination is not a feasible strategy to combat HRV. An alternative strategy is to target conserved viral proteins such as the HRV proteases, 2A(pro) and 3C(pro), the focus of this review. Necessary for host cell shutoff, virus replication, and pathogenesis, 2A(pro) and 3C(pro) are clearly viable drug targets, and indeed, 3C(pro) has been successfully targeted for treating the common cold in experimental infection. 2A(pro) and 3C(pro) are crucial for virus replication due to their role in polyprotein processing as well as cleavage of key cellular proteins to inhibit cellular transcription and translation. Intriguingly, the action of the HRV proteases also disrupts nucleocytoplasmic trafficking, contributing to HRV cytopathic effects. Improved understanding of the protease-cell interactions should enable new therapeutic approaches to be identified for drug development.
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Affiliation(s)
- Lora M Jensen
- Faculty of Education, Science, Technology and Mathematics, Centre for Research in Therapeutic Solutions, University of Canberra, 1 Kirinari Street, Bruce, Canberra, ACT, 2601, Australia
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36
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Greninger AL. Picornavirus–Host Interactions to Construct Viral Secretory Membranes. PROGRESS IN MOLECULAR BIOLOGY AND TRANSLATIONAL SCIENCE 2015; 129:189-212. [DOI: 10.1016/bs.pmbts.2014.10.007] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
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37
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Human rhinovirus 16 causes Golgi apparatus fragmentation without blocking protein secretion. J Virol 2014; 88:11671-85. [PMID: 25100828 PMCID: PMC4178721 DOI: 10.1128/jvi.01170-14] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/31/2023] Open
Abstract
The replication of picornaviruses has been described to cause fragmentation of the Golgi apparatus that blocks the secretory pathway. The inhibition of major histocompatibility complex class I upregulation and cytokine, chemokine and interferon secretion may have important implications for host defense. Previous studies have shown that disruption of the secretory pathway can be replicated by expression of individual nonstructural proteins; however the situation with different serotypes of human rhinovirus (HRV) is unclear. The expression of 3A protein from HRV14 or HRV2 did not cause Golgi apparatus disruption or a block in secretion, whereas other studies showed that infection of cells with HRV1A did cause Golgi apparatus disruption which was replicated by the expression of 3A. HRV16 is the serotype most widely used in clinical HRV challenge studies; consequently, to address the issue of Golgi apparatus disruption for HRV16, we have systematically and quantitatively examined the effect of HRV16 on both Golgi apparatus fragmentation and protein secretion in HeLa cells. First, we expressed each individual nonstructural protein and examined their cellular localization and their disruption of endoplasmic reticulum and Golgi apparatus architecture. We quantified their effects on the secretory pathway by measuring secretion of the reporter protein Gaussia luciferase. Finally, we examined the same outcomes following infection of cells with live virus. We demonstrate that expression of HRV16 3A and 3AB and, to a lesser extent, 2B caused dispersal of the Golgi structure, and these three nonstructural proteins also inhibited protein secretion. The infection of cells with HRV16 also caused significant Golgi apparatus dispersal; however, this did not result in the inhibition of protein secretion. IMPORTANCE The ability of replicating picornaviruses to influence the function of the secretory pathway has important implications for host defense. However, there appear to be differences between different members of the family and inconsistent results when comparing infection with live virus to expression of individual nonstructural proteins. We demonstrate that individual nonstructural HRV16 proteins, when expressed in HeLa cells, can both fragment the Golgi apparatus and block secretion, whereas viral infection fragments the Golgi apparatus without blocking secretion. This has major implications for how we interpret mechanistic evidence derived from the expression of single viral proteins.
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38
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Feng Q, Langereis MA, van Kuppeveld FJM. Induction and suppression of innate antiviral responses by picornaviruses. Cytokine Growth Factor Rev 2014; 25:577-85. [PMID: 25086453 PMCID: PMC7172595 DOI: 10.1016/j.cytogfr.2014.07.003] [Citation(s) in RCA: 47] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2014] [Accepted: 07/03/2014] [Indexed: 12/24/2022]
Abstract
The family Picornaviridae comprises of small, non-enveloped, positive-strand RNA viruses and contains many human and animal pathogens including enteroviruses (e.g. poliovirus, coxsackievirus, enterovirus 71 and rhinovirus), cardioviruses (e.g. encephalomyocarditis virus), hepatitis A virus and foot-and-mouth disease virus. Picornavirus infections activate a cytosolic RNA sensor, MDA5, which in turn, induces a type I interferon response, a crucial component of antiviral immunity. Moreover, picornaviruses activate the formation of stress granules (SGs), large aggregates of preassembled mRNPs (messenger ribonucleoprotein particles) to temporarily store these molecules upon cellular stress. Meanwhile, picornaviruses actively suppress these antiviral responses to ensure efficient replication. In this review we provide an overview of the induction and suppression of the MDA5-mediated IFN-α/β response and the cellular stress pathway by picornaviruses.
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Affiliation(s)
- Qian Feng
- Virology Division, Department of Infectious Diseases and Immunology, Faculty of Veterinary Medicine, University of Utrecht, 3584CL Utrecht, The Netherlands
| | - Martijn A Langereis
- Virology Division, Department of Infectious Diseases and Immunology, Faculty of Veterinary Medicine, University of Utrecht, 3584CL Utrecht, The Netherlands
| | - Frank J M van Kuppeveld
- Virology Division, Department of Infectious Diseases and Immunology, Faculty of Veterinary Medicine, University of Utrecht, 3584CL Utrecht, The Netherlands.
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39
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Amorim R, Costa SM, Cavaleiro NP, da Silva EE, da Costa LJ. HIV-1 transcripts use IRES-initiation under conditions where Cap-dependent translation is restricted by poliovirus 2A protease. PLoS One 2014; 9:e88619. [PMID: 24520405 PMCID: PMC3919812 DOI: 10.1371/journal.pone.0088619] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2013] [Accepted: 01/14/2014] [Indexed: 11/18/2022] Open
Abstract
The 30 different species of mRNAs synthesized during the HIV-1 replication cycle are all capped and polyadenilated. Internal ribosome entry sites have been recognized in the 5' untranslated region of some mRNA species of HIV-1, which would contribute to an alternative mechanism of initiation of mRNA translation. However, the Cap-dependent translation is assumed to be the main mechanism driving the initiation of HIV-1 protein synthesis. In this work, we describe a cell system in which lower to higher levels of transient expression of the poliovirus 2A protease strongly inhibited cellular Cap-dependent translation with no toxic effect to the cells during a 72-hour time frame. In this system, the synthesis of HIV-1 proteins was inhibited in a temporal dose-dependent way. Higher levels of 2A protease expression severely inhibited HIV-1 protein synthesis during the first 24 hours of infection consequently inhibiting viral production and infectivity. Intermediate to lower levels of 2A Protease expression caused the inhibition of viral protein synthesis only during the first 48 hours of viral replication. After this period both protein synthesis and viral release were recovered to the control levels. However, the infectivity of viral progeny was still partially inhibited. These results indicate that two mechanisms of mRNA translation initiation contribute to the synthesis of HIV-1 proteins; during the first 24-48 hours of viral replication HIV-1 protein synthesis is strongly dependent on Cap-initiation, while at later time points IRES-driven translation initiation is sufficient to produce high amounts of viral particles.
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Affiliation(s)
- Raquel Amorim
- Instituto de Microbiologia, Departamento de Virologia, Universidade Federal do Rio de Janeiro, Rio de Janeiro, Brazil
| | - Sara Mesquita Costa
- Instituto de Microbiologia, Departamento de Virologia, Universidade Federal do Rio de Janeiro, Rio de Janeiro, Brazil
| | - Nathalia Pereira Cavaleiro
- Instituto de Microbiologia, Departamento de Virologia, Universidade Federal do Rio de Janeiro, Rio de Janeiro, Brazil
| | - Edson Elias da Silva
- Laboratório de Enterovírus, Instituto Oswaldo Cruz, Fundação Oswaldo Cruz, Rio de Janeiro, Brazil
| | - Luciana Jesus da Costa
- Instituto de Microbiologia, Departamento de Virologia, Universidade Federal do Rio de Janeiro, Rio de Janeiro, Brazil
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Cathcart AL, Rozovics JM, Semler BL. Cellular mRNA decay protein AUF1 negatively regulates enterovirus and human rhinovirus infections. J Virol 2013; 87:10423-34. [PMID: 23903828 PMCID: PMC3807403 DOI: 10.1128/jvi.01049-13] [Citation(s) in RCA: 55] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2013] [Accepted: 07/19/2013] [Indexed: 01/12/2023] Open
Abstract
To successfully complete their replication cycles, picornaviruses modify several host proteins to alter the cellular environment to favor virus production. One such target of viral proteinase cleavage is AU-rich binding factor 1 (AUF1), a cellular protein that binds to AU-rich elements, or AREs, in the 3' noncoding regions (NCRs) of mRNAs to affect the stability of the RNA. Previous studies found that, during poliovirus or human rhinovirus infection, AUF1 is cleaved by the viral proteinase 3CD and that AUF1 can interact with the long 5' NCR of these viruses in vitro. Here, we expand on these initial findings to demonstrate that all four isoforms of AUF1 bind directly to stem-loop IV of the poliovirus 5' NCR, an interaction that is inhibited through proteolytic cleavage of AUF1 by the viral proteinase 3CD. Endogenous AUF1 was observed to relocalize to the cytoplasm of infected cells in a viral protein 2A-driven manner and to partially colocalize with the viral protein 3CD. We identify a negative role for AUF1 in poliovirus infection, as AUF1 inhibited viral translation and, ultimately, overall viral titers. Our findings also demonstrate that AUF1 functions as an antiviral factor during infection by coxsackievirus or human rhinovirus, suggesting a common mechanism that targets these related picornaviruses.
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Affiliation(s)
- Andrea L Cathcart
- Department of Microbiology and Molecular Genetics, School of Medicine, University of California, Irvine, CA 92697 USA
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Presentation overrides specificity: probing the plasticity of alphaviral proteolytic activity through mutational analysis. J Virol 2013; 87:10207-20. [PMID: 23864614 DOI: 10.1128/jvi.01485-13] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Semliki Forest virus (genus Alphavirus) is an important model for studying regulated nonstructural (ns) polyprotein processing. In this study, we evaluated the strictness of the previously outlined cleavage rules, accounting for the timing and outcome of each of three cleavages within the ns polyprotein P1234, and assessed the significance of residues P6 to P4 within the cleavage sites using an alanine scanning approach. The processing of the 1/2 and 3/4 sites was most strongly affected following changes in residues P5 and P4, respectively. However, none of the mutations had a detectable effect on the processing of the 2/3 site. An analysis of recombinant viruses bearing combinations of mutations in cleavage sites revealed tolerance toward the cooccurrence of native and mutated cleavage sites within the same polyprotein, suggesting a remarkable plasticity of the protease recognition pocket. Even in a virus in which all of the cleavage sequences were replaced with alanines in the P6, P5, and P4 positions, the processing pattern was largely preserved, without leading to reversion of cleavage site mutations. Instead, the emergence of second-site mutations was identified, among which Q706R/L in nsP2 was confirmed to be associated with the recognition of the P4 position within the modified cleavage sites. Our results imply that the spatial arrangement of the viral replication complex inherently contributes to scissile-site presentation for the protease, alleviating stringent sequence recognition requirements yet ensuring the precision and the correct order of processing events. Obtaining a proper understanding of the consequences of cleavage site manipulations may provide new tools for taming alphaviruses.
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Abstract
The autophagic degradation pathway is a powerful tool in the host cell arsenal against cytosolic pathogens. Contents trapped inside cytosolic vesicles, termed autophagosomes, are delivered to the lysosome for degradation. In spite of the degradative nature of the pathway, some pathogens are able to subvert autophagy for their benefit. In many cases, these pathogens have developed strategies to induce the autophagic signaling pathway while inhibiting the associated degradation activity. One surprising finding from recent literature is that some viruses do not impede degradation but instead promote the generation of degradative autolysosomes, which are the endpoint compartments of autophagy. Dengue virus, poliovirus, and hepatitis C virus, all positive-strand RNA viruses, utilize the maturation of autophagosomes into acidic and ultimately degradative compartments to promote their replication. While the benefits that each virus reaps from autophagosome maturation are unique, the parallels between the viruses indicate a complex relationship between cytosolic viruses and host cell degradation vesicles.
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