1
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Kitano T, Inagaki H, Hoshino SI. The impact of single-stranded RNAs on the dimerization of double-stranded RNA-dependent protein kinase PKR. Biochem Biophys Res Commun 2024; 719:150103. [PMID: 38761636 DOI: 10.1016/j.bbrc.2024.150103] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2024] [Accepted: 05/10/2024] [Indexed: 05/20/2024]
Abstract
The RNA-binding protein PKR serves as a crucial antiviral innate immune factor that globally suppresses translation by sensing viral double-stranded RNA (dsRNA) and by phosphorylating the translation initiation factor eIF2α. Recent findings have unveiled that single-stranded RNAs (ssRNAs), including in vitro transcribed (IVT) mRNA, can also bind to and activate PKR. However, the precise mechanism underlying PKR activation by ssRNAs, remains incompletely understood. Here, we developed a NanoLuc Binary Technology (NanoBiT)-based in vitro PKR dimerization assay to assess the impact of ssRNAs on PKR dimerization. Our findings demonstrate that, akin to double-stranded polyinosinic:polycytidylic acid (polyIC), an encephalomyocarditis virus (EMCV) RNA, as well as NanoLuc luciferase (Nluc) mRNA, can induce PKR dimerization. Conversely, homopolymeric RNA lacking secondary structure fails to promote PKR dimerization, underscoring the significance of secondary structure in this process. Furthermore, adenovirus VA RNA 1, another ssRNA, impedes PKR dimerization by competing with Nluc mRNA. Additionally, we observed structured ssRNAs capable of forming G-quadruplexes induce PKR dimerization. Collectively, our results indicate that ssRNAs have the ability to either induce or inhibit PKR dimerization, thus representing potential targets for the development of antiviral and anti-inflammatory agents.
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Affiliation(s)
- Tomoya Kitano
- Department of Biological Chemistry, Graduate School of Pharmaceutical Sciences, Nagoya City University, Nagoya, 467-8603, Japan
| | - Hiroto Inagaki
- Department of Biological Chemistry, Graduate School of Pharmaceutical Sciences, Nagoya City University, Nagoya, 467-8603, Japan
| | - Shin-Ichi Hoshino
- Department of Biological Chemistry, Graduate School of Pharmaceutical Sciences, Nagoya City University, Nagoya, 467-8603, Japan.
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2
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Boone M, Zappa F. Signaling plasticity in the integrated stress response. Front Cell Dev Biol 2023; 11:1271141. [PMID: 38143923 PMCID: PMC10740175 DOI: 10.3389/fcell.2023.1271141] [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: 08/01/2023] [Accepted: 11/29/2023] [Indexed: 12/26/2023] Open
Abstract
The Integrated Stress Response (ISR) is an essential homeostatic signaling network that controls the cell's biosynthetic capacity. Four ISR sensor kinases detect multiple stressors and relay this information to downstream effectors by phosphorylating a common node: the alpha subunit of the eukaryotic initiation factor eIF2. As a result, general protein synthesis is repressed while select transcripts are preferentially translated, thus remodeling the proteome and transcriptome. Mounting evidence supports a view of the ISR as a dynamic signaling network with multiple modulators and feedback regulatory features that vary across cell and tissue types. Here, we discuss updated views on ISR sensor kinase mechanisms, how the subcellular localization of ISR components impacts signaling, and highlight ISR signaling differences across cells and tissues. Finally, we consider crosstalk between the ISR and other signaling pathways as a determinant of cell health.
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3
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McLaughlin T, Wang J, Jia L, Wu F, Wang Y, Wang JJ, Mu X, Zhang SX. Neuronal p58 IPK Protects Retinal Ganglion Cells Independently of Macrophage/Microglia Activation in Ocular Hypertension. Cells 2023; 12:1558. [PMID: 37371028 PMCID: PMC10297187 DOI: 10.3390/cells12121558] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2022] [Revised: 01/10/2023] [Accepted: 01/12/2023] [Indexed: 06/29/2023] Open
Abstract
p58IPK is a multifaceted endoplasmic reticulum (ER) chaperone and a regulator of eIF2α kinases involved in a wide range of cellular processes including protein synthesis, ER stress response, and macrophage-mediated inflammation. Systemic deletion of p58IPK leads to age-related loss of retinal ganglion cells (RGC) and exacerbates RGC damage induced by ischemia/reperfusion and increased intraocular pressure (IOP), suggesting a protective role of p58IPK in the retina. However, the mechanisms remain elusive. Herein, we investigated the cellular mechanisms underlying the neuroprotection action of p58IPK using conditional knockout (cKO) mouse lines where p58IPK is deleted in retinal neurons (Chx10-p58IPK cKO) or in myeloid cells (Lyz2-p58IPK cKO). In addition, we overexpressed p58IPK by adeno-associated virus (AAV) in the retina to examine the effect of p58IPK on RGC survival after ocular hypertension (OHT) in wild type (WT) mice. Our results show that overexpression of p58IPK by AAV significantly improved RGC survival after OHT in WT mice, suggesting a protective effect of p58IPK on reducing RGC injury. Conditional knockout of p58IPK in retinal neurons or in myeloid cells did not alter retinal structure or cellular composition. However, a significant reduction in the b wave of light-adapted electroretinogram (ERG) was observed in Chx10-p58IPK cKO mice. Deletion of p58IPK in retinal neurons exacerbates RGC loss at 14 days after OHT. In contrast, deficiency of p58IPK in myeloid cells increased the microglia/macrophage activation but had no effect on RGC loss. We conclude that deletion of p58IPK in macrophages increases their activation, but does not influence RGC survival. These results suggest that the neuroprotective action of p58IPK is mediated by its expression in retinal neurons, but not in macrophages. Therefore, targeting p58IPK specifically in retinal neurons is a promising approach for the treatment of neurodegenerative retinal diseases including glaucoma.
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Affiliation(s)
- Todd McLaughlin
- Department of Ophthalmology and Ross Eye Institute, Jacobs School of Medicine and Biomedical Sciences, University at Buffalo, State University of New York, Buffalo, NY 14203, USA
| | - Jinli Wang
- Department of Ophthalmology and Ross Eye Institute, Jacobs School of Medicine and Biomedical Sciences, University at Buffalo, State University of New York, Buffalo, NY 14203, USA
| | - Liyun Jia
- Department of Ophthalmology and Ross Eye Institute, Jacobs School of Medicine and Biomedical Sciences, University at Buffalo, State University of New York, Buffalo, NY 14203, USA
- Beijing Tongren Hospital, Capital Medical University, Beijing 100005, China
| | - Fuguo Wu
- Department of Ophthalmology and Ross Eye Institute, Jacobs School of Medicine and Biomedical Sciences, University at Buffalo, State University of New York, Buffalo, NY 14203, USA
| | - Yaqin Wang
- Department of Ophthalmology and Ross Eye Institute, Jacobs School of Medicine and Biomedical Sciences, University at Buffalo, State University of New York, Buffalo, NY 14203, USA
- Taihe Hospital, Hubei University of Medicine, Shiyan 442005, China
| | - Joshua J. Wang
- Department of Ophthalmology and Ross Eye Institute, Jacobs School of Medicine and Biomedical Sciences, University at Buffalo, State University of New York, Buffalo, NY 14203, USA
| | - Xiuqian Mu
- Department of Ophthalmology and Ross Eye Institute, Jacobs School of Medicine and Biomedical Sciences, University at Buffalo, State University of New York, Buffalo, NY 14203, USA
- Department of Biochemistry, University at Buffalo, State University of New York, Buffalo, NY 14203, USA
| | - Sarah X. Zhang
- Department of Ophthalmology and Ross Eye Institute, Jacobs School of Medicine and Biomedical Sciences, University at Buffalo, State University of New York, Buffalo, NY 14203, USA
- Department of Biochemistry, University at Buffalo, State University of New York, Buffalo, NY 14203, USA
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4
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Lažetić V, Troemel ER. Conservation lost: host-pathogen battles drive diversification and expansion of gene families. FEBS J 2021; 288:5289-5299. [PMID: 33190369 PMCID: PMC10901648 DOI: 10.1111/febs.15627] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2020] [Revised: 10/29/2020] [Accepted: 11/12/2020] [Indexed: 11/30/2022]
Abstract
One of the strongest drivers in evolution is the struggle to survive a host-pathogen battle. This pressure selects for diversity among the factors directly involved in this battle, including virulence factors deployed by pathogens, their corresponding host targets, and host immune factors. A logical outcome of this diversification is that over time, the sequence of many immune factors will not be evolutionarily conserved across a broad range of species. Thus, while universal sequence conservation is often hailed as the hallmark of the importance of a particular gene, the immune system does not necessarily play by these rules when defending against co-evolving pathogens. This loss of sequence conservation is in contrast to many signaling pathways in development and basic cell biology that are not targeted by pathogens. In addition to diversification, another consequence of host-pathogen battles can be an amplification in gene number, thus leading to large gene families that have sequence relatively specific to a particular strain, species, or clade. Here we highlight this general theme across a variety of pathogen virulence factors and host immune factors. We summarize the wide range and number across species of these expanded, lineage-specific host-pathogen factors including ubiquitin ligases, nucleotide-binding leucine-rich repeat receptors, GTPases, and proteins without obvious biochemical function but that nonetheless play key roles in immunity.
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Affiliation(s)
- Vladimir Lažetić
- Division of Biological Sciences, University of California, San Diego, La Jolla, CA, USA
| | - Emily R Troemel
- Division of Biological Sciences, University of California, San Diego, La Jolla, CA, USA
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5
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Cesaro T, Hayashi Y, Borghese F, Vertommen D, Wavreil F, Michiels T. PKR activity modulation by phosphomimetic mutations of serine residues located three aminoacids upstream of double-stranded RNA binding motifs. Sci Rep 2021; 11:9188. [PMID: 33911136 PMCID: PMC8080564 DOI: 10.1038/s41598-021-88610-z] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/04/2020] [Accepted: 04/12/2021] [Indexed: 11/28/2022] Open
Abstract
Eukaryotic translation initiation factor 2 alpha kinase 2 (EIF2AK2), better known as PKR, plays a key role in the response to viral infections and cellular homeostasis by regulating mRNA translation. Upon binding dsRNA, PKR is activated through homodimerization and subsequent autophosphorylation on residues Thr446 and Thr451. In this study, we identified a novel PKR phosphorylation site, Ser6, located 3 amino acids upstream of the first double-stranded RNA binding motif (DRBM1). Another Ser residue occurs in PKR at position 97, the very same position relative to the DRBM2. Ser or Thr residues also occur 3 amino acids upstream DRBMs of other proteins such as ADAR1 or DICER. Phosphoinhibiting mutations (Ser-to-Ala) introduced at Ser6 and Ser97 spontaneously activated PKR. In contrast, phosphomimetic mutations (Ser-to-Asp) inhibited PKR activation following either poly (I:C) transfection or virus infection. These mutations moderately affected dsRNA binding or dimerization, suggesting a model where negative charges occurring at position 6 and 97 tighten the interaction of DRBMs with the kinase domain, thus keeping PKR in an inactive closed conformation even in the presence of dsRNA. This study provides new insights on PKR regulation mechanisms and identifies Ser6 and Ser97 as potential targets to modulate PKR activity for therapeutic purposes.
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Affiliation(s)
- Teresa Cesaro
- de Duve Institute, Université Catholique de Louvain, VIRO B1.74.07, 74, Avenue Hippocrate, 1200, Brussels, Belgium
| | - Yohei Hayashi
- de Duve Institute, Université Catholique de Louvain, VIRO B1.74.07, 74, Avenue Hippocrate, 1200, Brussels, Belgium.,Frontier Sciences Unit, Department of Medical Innovations, Otsuka Pharmaceutical Co., Ltd., Tokushima, Japan
| | - Fabian Borghese
- de Duve Institute, Université Catholique de Louvain, VIRO B1.74.07, 74, Avenue Hippocrate, 1200, Brussels, Belgium
| | - Didier Vertommen
- PHOS Unit and MASSPROT Platform, de Duve Institute, Université Catholique de Louvain, Brussels, Belgium
| | - Fanny Wavreil
- de Duve Institute, Université Catholique de Louvain, VIRO B1.74.07, 74, Avenue Hippocrate, 1200, Brussels, Belgium
| | - Thomas Michiels
- de Duve Institute, Université Catholique de Louvain, VIRO B1.74.07, 74, Avenue Hippocrate, 1200, Brussels, Belgium.
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6
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Emanuelli G, Nassehzadeh-Tabriz N, Morrell NW, Marciniak SJ. The integrated stress response in pulmonary disease. Eur Respir Rev 2020; 29:29/157/200184. [PMID: 33004527 PMCID: PMC7116220 DOI: 10.1183/16000617.0184-2020] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2020] [Accepted: 07/15/2020] [Indexed: 02/07/2023] Open
Abstract
The respiratory tract and its resident immune cells face daily exposure
to stress, both from without and from within. Inhaled pathogens, including
severe acute respiratory syndrome coronavirus 2, and toxins from pollution
trigger a cellular defence system that reduces protein synthesis to minimise
viral replication or the accumulation of misfolded proteins. Simultaneously, a
gene expression programme enhances antioxidant and protein folding machineries
in the lung. Four kinases (PERK, PKR, GCN2 and HRI) sense a diverse range of
stresses to trigger this “integrated stress response”. Here we review recent
advances identifying the integrated stress response as a critical pathway in the
pathogenesis of pulmonary diseases, including pneumonias, thoracic malignancy,
pulmonary fibrosis and pulmonary hypertension. Understanding the integrated
stress response provides novel targets for the development of therapies.
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Affiliation(s)
- Giulia Emanuelli
- Cambridge Institute for Medical Research (CIMR), University of Cambridge, Cambridge, UK.,Division of Respiratory Medicine, Dept of Medicine, University of Cambridge, Cambridge, UK.,Equal first authors
| | - Nikou Nassehzadeh-Tabriz
- Cambridge Institute for Medical Research (CIMR), University of Cambridge, Cambridge, UK.,Equal first authors
| | - Nick W Morrell
- Division of Respiratory Medicine, Dept of Medicine, University of Cambridge, Cambridge, UK
| | - Stefan J Marciniak
- Cambridge Institute for Medical Research (CIMR), University of Cambridge, Cambridge, UK .,Division of Respiratory Medicine, Dept of Medicine, University of Cambridge, Cambridge, UK
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7
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Poxvirus encoded eIF2α homolog, K3 family proteins, is a key determinant of poxvirus host species specificity. Virology 2019; 541:101-112. [PMID: 32056708 DOI: 10.1016/j.virol.2019.12.008] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2019] [Revised: 12/17/2019] [Accepted: 12/17/2019] [Indexed: 11/24/2022]
Abstract
Protein kinase R plays a key role in innate antiviral immune responses of vertebrate animals. Most mammalian poxviruses encode two PKR antagonists, E3 (dsRNA binding) and K3 (eIF2α homolog) proteins. In this study, the role of K3 family proteins from poxviruses with distinct host tropisms in determining the virus host range was examined in a vaccinia E3L deletion mutant virus. It was found that K3 orthologs from the species-specific poxviruses (taterapox virus, sheeppox virus, myxoma virus, swinepox virus and yaba monkey tumor virus) restored the virus replication competency in cells derived from their natural hosts or related animal species. Further, it was found that the residues located in the helix insert region of the protein, K45 of vaccinia K3 and Y47 of the sheep poxvirus ortholog 011, are critical for the virus host species specificity. These observations demonstrate that poxvirus K3 proteins are major determinants of the virus host specificity.
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8
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Lee YS, Kunkeaw N, Lee YS. Protein kinase R and its cellular regulators in cancer: An active player or a surveillant? WILEY INTERDISCIPLINARY REVIEWS-RNA 2019; 11:e1558. [PMID: 31231984 DOI: 10.1002/wrna.1558] [Citation(s) in RCA: 29] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/09/2019] [Revised: 05/24/2019] [Accepted: 05/28/2019] [Indexed: 12/12/2022]
Abstract
Protein kinase R (PKR), originally known as an antiviral protein, senses various stresses as well as pathogen-driven double-stranded RNAs. Thereby activated PKR provokes diverse downstream events, including eIF2α phosphorylation and nuclear factor kappa-light-chain-enhancer of activated B cells activation. Consequently, PKR induces apoptosis and inflammation, both of which are highly important in cancer as much as its original antiviral role. Therefore, cellular proteins and RNAs should tightly control PKR activity. PKR and its regulators are often dysregulated in cancer and it is undoubted that such dysregulation contributes to tumorigenesis. However, PKR's precise role in cancer is still in debate, due to incomprehensible and even contradictory data. In this review, we introduce important cellular PKR regulators and discuss about their roles in cancer. Among them, we pay particular attention to nc886, a PKR repressor noncoding RNA that has been identified relatively recently, because its expression pattern in cancer can explain interesting yet obscure oncologic aspects of PKR. Based on nc886 and its regulation of PKR, we have proposed a tumor surveillance model, which reconciles contradictory data about PKR in cancer. This article is categorized under: Regulatory RNAs/RNAi/Riboswitches > Regulatory RNAs RNA Interactions with Proteins and Other Molecules > Protein-RNA Interactions: Functional Implications.
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Affiliation(s)
- Yong Sun Lee
- Department of Cancer Biomedical Science, Graduate School of Cancer Science and Policy, National Cancer Center, Goyang, Korea
| | - Nawapol Kunkeaw
- Institute of Molecular Biosciences, Mahidol University, Nakhon Pathom, Thailand
| | - Yeon-Su Lee
- Division of Clinical Research, Research Institute, National Cancer Center, Goyang, Korea
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9
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Meade N, DiGiuseppe S, Walsh D. Translational control during poxvirus infection. WILEY INTERDISCIPLINARY REVIEWS-RNA 2018; 10:e1515. [PMID: 30381906 DOI: 10.1002/wrna.1515] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/19/2018] [Revised: 08/31/2018] [Accepted: 10/01/2018] [Indexed: 02/06/2023]
Abstract
Poxviruses are an unusual family of large double-stranded (ds) DNA viruses that exhibit an incredible degree of self-sufficiency and complexity in their replication and immune evasion strategies. Indeed, amongst their approximately 200 open reading frames (ORFs), poxviruses encode approximately 100 immunomodulatory proteins to counter host responses along with complete DNA synthesis, transcription, mRNA processing and cytoplasmic redox systems that enable them to replicate exclusively in the cytoplasm of infected cells. However, like all other viruses poxviruses do not encode ribosomes and therefore remain completely dependent on gaining access to the host translational machinery in order to synthesize viral proteins. Early studies of these intriguing viruses helped discover the mRNA cap and polyadenylated (polyA) tail that we now know to be present on most eukaryotic messages and which play fundamental roles in mRNA translation, while more recent studies have begun to reveal the remarkable lengths poxviruses go to in order to control both host and viral protein synthesis. Here, we discuss some of the central strategies used by poxviruses and the broader battle that ensues with the host cell to control the translation system, the outcome of which ultimately dictates the fate of infection. This article is categorized under: Translation > Translation Regulation.
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Affiliation(s)
- Nathan Meade
- Department of Microbiology-Immunology, Feinberg School of Medicine, Northwestern University, Chicago, Illinois
| | - Stephen DiGiuseppe
- Department of Microbiology-Immunology, Feinberg School of Medicine, Northwestern University, Chicago, Illinois
| | - Derek Walsh
- Department of Microbiology-Immunology, Feinberg School of Medicine, Northwestern University, Chicago, Illinois
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10
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Matz KM, Guzman RM, Goodman AG. The Role of Nucleic Acid Sensing in Controlling Microbial and Autoimmune Disorders. INTERNATIONAL REVIEW OF CELL AND MOLECULAR BIOLOGY 2018; 345:35-136. [PMID: 30904196 PMCID: PMC6445394 DOI: 10.1016/bs.ircmb.2018.08.002] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
Innate immunity, the first line of defense against invading pathogens, is an ancient form of host defense found in all animals, from sponges to humans. During infection, innate immune receptors recognize conserved molecular patterns, such as microbial surface molecules, metabolites produces during infection, or nucleic acids of the microbe's genome. When initiated, the innate immune response activates a host defense program that leads to the synthesis proteins capable of pathogen killing. In mammals, the induction of cytokines during the innate immune response leads to the recruitment of professional immune cells to the site of infection, leading to an adaptive immune response. While a fully functional innate immune response is crucial for a proper host response and curbing microbial infection, if the innate immune response is dysfunctional and is activated in the absence of infection, autoinflammation and autoimmune disorders can develop. Therefore, it follows that the innate immune response must be tightly controlled to avoid an autoimmune response from host-derived molecules, yet still unencumbered to respond to infection. In this review, we will focus on the innate immune response activated from cytosolic nucleic acids, derived from the microbe or host itself. We will depict how viruses and bacteria activate these nucleic acid sensing pathways and their mechanisms to inhibit the pathways. We will also describe the autoinflammatory and autoimmune disorders that develop when these pathways are hyperactive. Finally, we will discuss gaps in knowledge with regard to innate immune response failure and identify where further research is needed.
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Affiliation(s)
- Keesha M Matz
- School of Molecular Biosciences, College of Veterinary Medicine, Washington State University, Pullman, WA, United States
| | - R Marena Guzman
- School of Molecular Biosciences, College of Veterinary Medicine, Washington State University, Pullman, WA, United States
| | - Alan G Goodman
- School of Molecular Biosciences, College of Veterinary Medicine, Washington State University, Pullman, WA, United States; Paul G. Allen School for Global Animal Health, College of Veterinary Medicine, Washington State University, Pullman, WA, United States.
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11
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Auto-phosphorylation Represses Protein Kinase R Activity. Sci Rep 2017; 7:44340. [PMID: 28281686 PMCID: PMC5345052 DOI: 10.1038/srep44340] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2017] [Accepted: 02/07/2017] [Indexed: 12/11/2022] Open
Abstract
The central role of protein kinases in controlling disease processes has spurred efforts to develop pharmaceutical regulators of their activity. A rational strategy to achieve this end is to determine intrinsic auto-regulatory processes, then selectively target these different states of kinases to repress their activation. Here we investigate auto-regulation of the innate immune effector protein kinase R, which phosphorylates the eukaryotic initiation factor 2α to inhibit global protein translation. We demonstrate that protein kinase R activity is controlled by auto-inhibition via an intra-molecular interaction. Part of this mechanism of control had previously been reported, but was then controverted. We account for the discrepancy and extend our understanding of the auto-inhibitory mechanism by identifying that auto-inhibition is paradoxically instigated by incipient auto-phosphorylation. Phosphor-residues at the amino-terminus instigate an intra-molecular interaction that enlists both of the N-terminal RNA-binding motifs of the protein with separate surfaces of the C-terminal kinase domain, to co-operatively inhibit kinase activation. These findings identify an innovative mechanism to control kinase activity, providing insight for strategies to better regulate kinase activity.
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12
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Tsalikis J, Croitoru DO, Philpott DJ, Girardin SE. Nutrient sensing and metabolic stress pathways in innate immunity. Cell Microbiol 2013; 15:1632-41. [PMID: 23834352 DOI: 10.1111/cmi.12165] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2013] [Revised: 06/25/2013] [Accepted: 07/01/2013] [Indexed: 01/13/2023]
Abstract
Cells monitor nutrient availability through several highly conserved pathways that include the mTOR signalling axis regulated by AKT/PI3K, HIF and AMPK, as well as the GCN2/eIF2α integrated stress response pathway that provides cellular adaptation to amino acid starvation. Recent evidence has identified a critical interplay between these nutrient sensing pathways and innate immunity to bacterial pathogens, viruses and parasites. These observations suggest that, in addition to the well-characterized pro-inflammatory signalling mediated by pattern recognition molecules, a metabolic stress programme contributes to shape the global response to pathogens.
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Affiliation(s)
- Jessica Tsalikis
- Department of Laboratory Medicine and Pathobiologyy, University of Toronto, Toronto, M5S 1A8, Canada
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13
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Jiang P, Wen J, Song H, Chen X, Sun Y, Huo X, Zhang D. Characterization of porcine P58IPK gene and its up-regulation after H1N1 or H3N2 influenza virus infection. J Clin Virol 2013; 58:120-6. [PMID: 23827789 DOI: 10.1016/j.jcv.2013.06.007] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2013] [Revised: 05/27/2013] [Accepted: 06/04/2013] [Indexed: 12/25/2022]
Abstract
BACKGROUND The 58-kDa inhibitor of the interferon-induced double-stranded RNA-activated protein kinase (P58IPK) is a cellular protein that is activated during influenza virus infection. Although the function of human P58IPK has been studied for a long time, porcine P58IPK (pP58IPK) has little been studied except for its cloning. OBJECTIVE In this study, we aimed to investigate the characteristics of the pP58IPK gene, determine its subcellular localization, and find its expression change during H1N1 or H3N2 infection. STUDY DESIGN First, the sequence and structure of pP58IPK were analyzed. Second, pP58IPK gene was cloned into pEGFP-N1 and pEGFP-C1 vectors, respectively, which were transfected into cells to determine its subcellular localization. Third, Lung tissues of piglets from H1N1 infected, H3N2 infected and control groups were analyzed using histopathology, real-time PCR, and immunohistochemistry. RESULTS The sequence and structure of pP58IPK was highly similar to the counterpart of human. pP58IPK protein distributed only in the cytoplasm. Lung tissues of piglets infected by H1N1 or H3N2 appeared obvious pathological changes, and the expression of pP58IPK in both mRNA and protein level was up-regulated by approximate 1.5-fold in piglets infected by H1N1 or H3N2 comparing with control piglets. CONCLUSIONS We analyzed the characteristics of the pP58IPK gene, constructed a phylogenetic tree, determined its subcellular localization, and investigated its expression changes during H1N1 or H3N2 infection. The fundamental data accumulated in this study provides a potential medical model for investigating the function of P58IPK during influenza A viruses infection.
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Affiliation(s)
- Pengfei Jiang
- MOA Key Laboratory of Animal Biotechnology of National Ministry of Agriculture, Institute of Veterinary Immunology, Northwest A&F University, Yangling, 712100, Xi'an City, Shaanxi Province, PR China
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14
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Sequence and phylogenetic analysis of host-range (E3L, K3L, and C7L) and structural protein (B5R) genes of buffalopox virus isolates from buffalo, cattle, and human in India. Virus Genes 2012; 45:488-98. [PMID: 22872567 DOI: 10.1007/s11262-012-0788-8] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2011] [Accepted: 07/10/2012] [Indexed: 10/28/2022]
Abstract
Buffalopox virus (BPXV), a close variant of vaccinia virus (VACV) has emerged as a zoonotic pathogen. The host tropism of poxviruses is governed by host-range genes. Among the host-range genes: E3L, K3L, and C7L are essential for virus replication by preventing interferon resistance, whereas B5R is essential for spread of the virus and evasion from the host's immune response as in VACV. We report sequence analysis of host-range genes: E3L, K3L, C7L, and membrane protein gene (B5R) of BPXVs from buffalo, cattle, and human from recent outbreaks in India-their phylogenetic relationship with reference strain (BP4) and other Orthopoxviruses. BPXVs revealed a sequence homology with VACVs including zoonotic Brazilian VACV-like viruses. The aa sequences of E3L and K3L genes were 100 % similar in buffalo, cattle, and human isolates. However, four significant point mutations (I11K; N12K and S36F in C7L gene and D249G in B5R gene) were observed specific to buffalo isolate only. This signifies that different strains of BPXV were circulated during the outbreak. The mutations in C7L and B5R could play an important role in adaptation of BPXV in human and cattle which needs further functional studies. The strain of BPXV isolated from buffalo may not be adopted in human and cow. Various point mutations were observed in the host-range genes of reference strain (BPXV-BP4) which may be due to several passages of virus in cell culture. The phylogeny constructed based on concatenated gene sequences revealed that BPXVs are not as closely related to vaccine strain (Lister and Lister-derived strain-LC16m8), as hypothesized earlier, rather they are more closely related to reference strain (BPXV-BP4) and other vaccinia and vaccinia-like viruses such as Passatempo and Aracatuba viruses. The availability of information regarding host tropism determinants would allow us to understand molecular mechanism of species tropism of poxviruses which would be useful in unveiling new strategies to control zoonotic poxviral infections.
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Dalton LE, Healey E, Irving J, Marciniak SJ. Phosphoproteins in stress-induced disease. PROGRESS IN MOLECULAR BIOLOGY AND TRANSLATIONAL SCIENCE 2012; 106:189-221. [PMID: 22340719 DOI: 10.1016/b978-0-12-396456-4.00003-1] [Citation(s) in RCA: 36] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
The integrated stress response (ISR) is an evolutionarily conserved homeostatic program activated by specific pathological states. These include amino acid deprivation, viral infection, iron deficiency, and the misfolding of proteins within the endoplasmic reticulum (ER), the so-called ER stress. Although apparently disparate, each of these stresses induces phosphorylation of a translation initiation factor, eIF2α, to attenuate new protein translation while simultaneously triggering a transcriptional program. This is achieved by four homologous stress-sensing kinases: GCN2, PKR, HRI, and PERK. In addition to these kinases, mammals possess two specific eIF2α phosphatases, GADD34 and CReP, which play crucial roles in the recovery of protein synthesis following the initial insult. They are not only important in embryonic development but also appear to play important roles in disease, particularly cancer. In this chapter, we discuss each of the eIF2α kinases, in turn, with particular emphasis on their regulation and the new insights provided by recent structural studies. We also discuss the potential for developing novel drug therapies that target the ISR.
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Affiliation(s)
- Lucy E Dalton
- Division of Respiratory Medicine, Department of Medicine, University of Cambridge, Cambridge Institute for Medical Research, Cambridge, United Kingdom
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16
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Svärd M, Biterova EI, Bourhis JM, Guy JE. The crystal structure of the human co-chaperone P58(IPK). PLoS One 2011; 6:e22337. [PMID: 21799829 PMCID: PMC3143134 DOI: 10.1371/journal.pone.0022337] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2011] [Accepted: 06/24/2011] [Indexed: 12/02/2022] Open
Abstract
P58IPK is one of the endoplasmic reticulum- (ER-) localised DnaJ (ERdj) proteins which interact with the chaperone BiP, the mammalian ER ortholog of Hsp70, and are thought to contribute to the specificity and regulation of its diverse functions. P58IPK, expression of which is upregulated in response to ER stress, has been suggested to act as a co-chaperone, binding un- or misfolded proteins and delivering them to BiP. In order to give further insights into the functions of P58IPK, and the regulation of BiP by ERdj proteins, we have determined the crystal structure of human P58IPK to 3.0 Å resolution using a combination of molecular replacement and single wavelength anomalous diffraction. The structure shows the human P58IPK monomer to have a very elongated overall shape. In addition to the conserved J domain, P58IPK contains nine N-terminal tetratricopeptide repeat motifs, divided into three subdomains of three motifs each. The J domain is attached to the C-terminal end via a flexible linker, and the structure shows the conserved Hsp70-binding histidine-proline-aspartate (HPD) motif to be situated on the very edge of the elongated protein, 100 Å from the putative binding site for unfolded protein substrates. The residues that comprise the surface surrounding the HPD motif are highly conserved in P58IPK from other organisms but more varied between the human ERdj proteins, supporting the view that their regulation of different BiP functions is facilitated by differences in BiP-binding.
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Affiliation(s)
- Maria Svärd
- Department of Medical Biochemistry and Biophysics, Karolinska Institutet, Stockholm, Sweden
| | - Ekaterina I. Biterova
- Department of Medical Biochemistry and Biophysics, Karolinska Institutet, Stockholm, Sweden
| | - Jean-Marie Bourhis
- Department of Medical Biochemistry and Biophysics, Karolinska Institutet, Stockholm, Sweden
| | - Jodie E. Guy
- Department of Medical Biochemistry and Biophysics, Karolinska Institutet, Stockholm, Sweden
- * E-mail:
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17
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Tao J, Sha B. Structural insight into the protective role of P58(IPK) during unfolded protein response. Methods Enzymol 2011; 490:259-70. [PMID: 21266255 DOI: 10.1016/b978-0-12-385114-7.00015-5] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Abstract
P58(IPK) has been identified as an ER molecular chaperone to maintain protein-folding homeostasis. P58(IPK) expression can be significantly upregulated during unfolded protein responses (UPR), and it may play important roles in suppressing the ER protein aggregations. To investigate the mechanism how P58(IPK) functions to promote protein folding within ER, we have determined the crystal structure of P58(IPK) TPR domain at 2.5Å resolution. P58(IPK) contains nine TPR motifs and a C-terminal J domain within its primary sequence. The crystal structure of P58(IPK) revealed three subdomains (I, II, and III) with similar folds and each domain contains three TPR motifs. Our data also showed that P58(IPK) acts as a molecular chaperone by interacting with the unfolded proteins such as luciferase, rhodanese, and insulin. The P58(IPK) structure reveals a conserved hydrophobic patch located in subdomain I that may be involved in binding the misfolded polypeptides. We have proposed a working model for P58(IPK) to act together with Bip to prevent protein aggregations and promote protein foldings within ER.
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Affiliation(s)
- Jiahui Tao
- Department of Cell Biology, University of Alabama at Birmingham, Birmingham, Alabama, USA
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18
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Guan Z, Liu D, Mi S, Zhang J, Ye Q, Wang M, Gao GF, Yan J. Interaction of Hsp40 with influenza virus M2 protein: implications for PKR signaling pathway. Protein Cell 2010; 1:944-55. [PMID: 21204021 PMCID: PMC4875119 DOI: 10.1007/s13238-010-0115-x] [Citation(s) in RCA: 34] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2010] [Accepted: 10/09/2010] [Indexed: 12/14/2022] Open
Abstract
Influenza virus contains three integral membrane proteins: haemagglutinin, neuraminidase, and matrix protein (M1 and M2). Among them, M2 protein functions as an ion channel, important for virus uncoating in endosomes of virus-infected cells and essential for virus replication. In an effort to explore potential new functions of M2 in the virus life cycle, we used yeast two-hybrid system to search for M2-associated cellular proteins. One of the positive clones was identified as human Hsp40/Hdj1, a DnaJ/Hsp40 family protein. Here, we report that both BM2 (M2 of influenza B virus) and A/M2 (M2 of influenza A virus) interacted with Hsp40 in vitro and in vivo. The region of M2-Hsp40 interaction has been mapped to the CTD1 domain of Hsp40. Hsp40 has been reported to be a regulator of PKR signaling pathway by interacting with p58(IPK) that is a cellular inhibitor of PKR. PKR is a crucial component of the host defense response against virus infection. We therefore attempted to understand the relationship among M2, Hsp40 and p58(IPK) by further experimentation. The results demonstrated that both A/M2 and BM2 are able to bind to p58(IPK) in vitro and in vivo and enhance PKR autophosphorylation probably via forming a stable complex with Hsp40 and P58(IPK), and consequently induce cell death. These results suggest that influenza virus M2 protein is involved in p58(IPK) mediated PKR regulation during influenza virus infection, therefore affecting infected-cell life cycle and virus replication.
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Affiliation(s)
- Zhenhong Guan
- College of Veterinary Medicine, China Agricultural University, Beijing, 100094 China
- CAS Key Laboratory of Pathogenic Microbiology and Immunology, Institute of Microbiology, Chinese Academy of Sciences, Beijing, 100101 China
| | - Di Liu
- CAS Key Laboratory of Pathogenic Microbiology and Immunology, Institute of Microbiology, Chinese Academy of Sciences, Beijing, 100101 China
| | - Shuofu Mi
- CAS Key Laboratory of Pathogenic Microbiology and Immunology, Institute of Microbiology, Chinese Academy of Sciences, Beijing, 100101 China
| | - Jie Zhang
- CAS Key Laboratory of Pathogenic Microbiology and Immunology, Institute of Microbiology, Chinese Academy of Sciences, Beijing, 100101 China
| | - Qinong Ye
- Beijing Institute of Biotechnology, Beijing, 100850 China
| | - Ming Wang
- College of Veterinary Medicine, China Agricultural University, Beijing, 100094 China
| | - George F. Gao
- College of Veterinary Medicine, China Agricultural University, Beijing, 100094 China
- CAS Key Laboratory of Pathogenic Microbiology and Immunology, Institute of Microbiology, Chinese Academy of Sciences, Beijing, 100101 China
- Beijing Institutes of Life Science, Chinese Academy of Sciences, Beijing, 100101 China
| | - Jinghua Yan
- CAS Key Laboratory of Pathogenic Microbiology and Immunology, Institute of Microbiology, Chinese Academy of Sciences, Beijing, 100101 China
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Roberts LO, Jopling CL, Jackson RJ, Willis AE. Viral strategies to subvert the mammalian translation machinery. PROGRESS IN MOLECULAR BIOLOGY AND TRANSLATIONAL SCIENCE 2009; 90:313-67. [PMID: 20374746 PMCID: PMC7102724 DOI: 10.1016/s1877-1173(09)90009-6] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 01/06/2023]
Abstract
Viruses do not carry their own protein biosynthesis machinery and the translation of viral proteins therefore requires that the virus usurps the machinery of the host cell. To allow optimal translation of viral proteins at the expense of cellular proteins, virus families have evolved a variety of methods to repress the host translation machinery, while allowing effective viral protein synthesis. Many viruses use noncanonical mechanisms that permit translation of their own RNAs under these conditions. Viruses have also developed mechanisms to evade host innate immune responses that would repress translation under conditions of viral infection, in particular PKR activation in response to double-stranded RNA (dsRNA). Importantly, the study of viral translation mechanisms has enormously enhanced our understanding of many aspects of the cellular protein biosynthesis pathway and its components. A number of unusual mechanisms of translation initiation that were first discovered in viruses have since been observed in cellular mRNAs, and it has become apparent that a diverse range of translation mechanisms operates in eukaryotes, allowing subtle regulation of this essential process.
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Affiliation(s)
- Lisa O Roberts
- Faculty of Health and Medical Sciences, University of Surrey, Guildford, United Kingdom
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20
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Goodman AG, Fornek JL, Medigeshi GR, Perrone LA, Peng X, Dyer MD, Proll SC, Knoblaugh SE, Carter VS, Korth MJ, Nelson JA, Tumpey TM, Katze MG. P58(IPK): a novel "CIHD" member of the host innate defense response against pathogenic virus infection. PLoS Pathog 2009; 5:e1000438. [PMID: 19461876 PMCID: PMC2677460 DOI: 10.1371/journal.ppat.1000438] [Citation(s) in RCA: 35] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2009] [Accepted: 04/21/2009] [Indexed: 12/26/2022] Open
Abstract
To support their replication, viruses take advantage of numerous cellular factors and processes. Recent large-scale screens have identified hundreds of such factors, yet little is known about how viruses exploit any of these. Influenza virus infection post-translationally activates P58(IPK), a cellular inhibitor of the interferon-induced, dsRNA-activated eIF2alpha kinase, PKR. Here, we report that infection of P58(IPK) knockout mice with influenza virus resulted in increased lung pathology, immune cell apoptosis, PKR activation, and mortality. Analysis of lung transcriptional profiles, including those induced by the reconstructed 1918 pandemic virus, revealed increased expression of genes associated with the cell death, immune, and inflammatory responses. These experiments represent the first use of a mammalian infection model to demonstrate the role of P58(IPK) in the antiviral response. Our results suggest that P58(IPK) represents a new class of molecule, a cellular inhibitor of the host defense (CIHD), as P58(IPK) is activated during virus infection to inhibit virus-induced apoptosis and inflammation to prolong host survival, even while prolonging viral replication.
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Affiliation(s)
- Alan G. Goodman
- Department of Microbiology, University of Washington, Seattle, Washington, United States of America
- Graduate Program in Bioengineering, University of Washington, Seattle, Washington, United States of America
| | - Jamie L. Fornek
- Department of Microbiology, University of Washington, Seattle, Washington, United States of America
| | - Guruprasad R. Medigeshi
- Vaccine and Gene Therapy Institute, Oregon Health and Science University, Beaverton, Oregon, United States of America
| | - Lucy A. Perrone
- Influenza Division, National Center for Immunization and Respiratory Diseases, Centers for Disease Control and Prevention, Atlanta, Georgia, United States of America
| | - Xinxia Peng
- Department of Microbiology, University of Washington, Seattle, Washington, United States of America
| | - Matthew D. Dyer
- Department of Microbiology, University of Washington, Seattle, Washington, United States of America
| | - Sean C. Proll
- Department of Microbiology, University of Washington, Seattle, Washington, United States of America
| | - Sue E. Knoblaugh
- Animal Health Shared Resources, Fred Hutchinson Cancer Research Center, Seattle, Washington, United States of America
| | - Victoria S. Carter
- Department of Microbiology, University of Washington, Seattle, Washington, United States of America
| | - Marcus J. Korth
- Department of Microbiology, University of Washington, Seattle, Washington, United States of America
| | - Jay A. Nelson
- Vaccine and Gene Therapy Institute, Oregon Health and Science University, Beaverton, Oregon, United States of America
| | - Terrence M. Tumpey
- Influenza Division, National Center for Immunization and Respiratory Diseases, Centers for Disease Control and Prevention, Atlanta, Georgia, United States of America
| | - Michael G. Katze
- Department of Microbiology, University of Washington, Seattle, Washington, United States of America
- Washington National Primate Research Center, Seattle, Washington, United States of America
- * E-mail:
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21
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22
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Protein kinase PKR mutants resistant to the poxvirus pseudosubstrate K3L protein. Proc Natl Acad Sci U S A 2008; 105:16894-9. [PMID: 18971339 DOI: 10.1073/pnas.0805524105] [Citation(s) in RCA: 26] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
As part of the mammalian cell innate immune response, the double-stranded RNA activated protein kinase PKR phosphorylates the translation initiation factor eIF2alpha to inhibit protein synthesis and thus block viral replication. Poxviruses including vaccinia and smallpox viruses express PKR inhibitors such as the vaccinia virus K3L protein that resembles the N-terminal substrate-targeting domain of eIF2alpha. Whereas high-level expression of human PKR was toxic in yeast, this growth inhibition was suppressed by coexpression of the K3L protein. We used this yeast assay to screen for PKR mutants that are resistant to K3L inhibition, and we identified 12 mutations mapping to the C-terminal lobe of the PKR kinase domain. The PKR mutations specifically conferred resistance to the K3L protein both in yeast and in vitro. Consistently, the PKR-D486V mutation led to nearly a 15-fold decrease in K3L binding affinity yet did not impair eIF2alpha phosphorylation. Our results support the identification of the eIF2alpha-binding site on an extensive face of the C-terminal lobe of the kinase domain, and they indicate that subtle changes to the PKR kinase domain can drastically impact pseudosubstrate inhibition while leaving substrate phosphorylation intact. We propose that these paradoxical effects of the PKR mutations on pseudosubstrate vs. substrate interactions reflect differences between the rigid K3L protein and the plastic nature of eIF2alpha around the Ser-51 phosphorylation site.
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23
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Affiliation(s)
- Jason T Blackard
- Division of Digestive Diseases, University of Cincinnati College of Medicine, Cincinnati, OH, USA
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24
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García MA, Gil J, Ventoso I, Guerra S, Domingo E, Rivas C, Esteban M. Impact of protein kinase PKR in cell biology: from antiviral to antiproliferative action. Microbiol Mol Biol Rev 2007; 70:1032-60. [PMID: 17158706 PMCID: PMC1698511 DOI: 10.1128/mmbr.00027-06] [Citation(s) in RCA: 599] [Impact Index Per Article: 35.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022] Open
Abstract
The double-stranded RNA-dependent protein kinase PKR is a critical mediator of the antiproliferative and antiviral effects exerted by interferons. Not only is PKR an effector molecule on the cellular response to double-stranded RNA, but it also integrates signals in response to Toll-like receptor activation, growth factors, and diverse cellular stresses. In this review, we provide a detailed picture on how signaling downstream of PKR unfolds and what are the ultimate consequences for the cell fate. PKR activation affects both transcription and translation. PKR phosphorylation of the alpha subunit of eukaryotic initiation factor 2 results in a blockade on translation initiation. However, PKR cannot avoid the translation of some cellular and viral mRNAs bearing special features in their 5' untranslated regions. In addition, PKR affects diverse transcriptional factors such as interferon regulatory factor 1, STATs, p53, activating transcription factor 3, and NF-kappaB. In particular, how PKR triggers a cascade of events involving IKK phosphorylation of IkappaB and NF-kappaB nuclear translocation has been intensively studied. At the cellular and organism levels PKR exerts antiproliferative effects, and it is a key antiviral agent. A point of convergence in both effects is that PKR activation results in apoptosis induction. The extent and strength of the antiviral action of PKR are clearly understood by the findings that unrelated viral proteins of animal viruses have evolved to inhibit PKR action by using diverse strategies. The case for the pathological consequences of the antiproliferative action of PKR is less understood, but therapeutic strategies aimed at targeting PKR are beginning to offer promising results.
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Affiliation(s)
- M A García
- Department of Molecular and Cellular Biology, Centro Nacional de Biotecnología, Ciudad Universitaria Cantoblanco, 28049 Madrid, Spain
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25
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Toth AM, Zhang P, Das S, George CX, Samuel CE. Interferon action and the double-stranded RNA-dependent enzymes ADAR1 adenosine deaminase and PKR protein kinase. ACTA ACUST UNITED AC 2007; 81:369-434. [PMID: 16891177 DOI: 10.1016/s0079-6603(06)81010-x] [Citation(s) in RCA: 74] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [MESH Headings] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Affiliation(s)
- Ann M Toth
- Department of Molecular, Cellular, and Developmental Biology, University of California, Santa Barbara, California 93106, USA
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26
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Goodman AG, Smith JA, Balachandran S, Perwitasari O, Proll SC, Thomas MJ, Korth MJ, Barber GN, Schiff LA, Katze MG. The cellular protein P58IPK regulates influenza virus mRNA translation and replication through a PKR-mediated mechanism. J Virol 2006; 81:2221-30. [PMID: 17166899 PMCID: PMC1865913 DOI: 10.1128/jvi.02151-06] [Citation(s) in RCA: 70] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022] Open
Abstract
We previously hypothesized that efficient translation of influenza virus mRNA requires the recruitment of P58(IPK), the cellular inhibitor of PKR, an interferon-induced kinase that targets the eukaryotic translation initiation factor eIF2alpha. P58(IPK) also inhibits PERK, an eIF2alpha kinase that is localized in the endoplasmic reticulum (ER) and induced during ER stress. The ability of P58(IPK) to interact with and inhibit multiple eIF2alpha kinases suggests it is a critical regulator of both cellular and viral mRNA translation. In this study, we sought to definitively define the role of P58(IPK) during viral infection of mammalian cells. Using mouse embryo fibroblasts from P58(IPK-/-) mice, we demonstrated that the absence of P58(IPK) led to an increase in eIF2alpha phosphorylation and decreased influenza virus mRNA translation. The absence of P58(IPK) also resulted in decreased vesicular stomatitis virus replication but enhanced reovirus yields. In cells lacking the P58(IPK) target, PKR, the trends were reversed-eIF2alpha phosphorylation was decreased, and influenza virus mRNA translation was increased. Although P58(IPK) also inhibits PERK, the presence or absence of this kinase had little effect on influenza virus mRNA translation, despite reduced levels of eIF2alpha phosphorylation in cells lacking PERK. Finally, we showed that influenza virus protein synthesis and viral mRNA levels decrease in cells that express a constitutively active, nonphosphorylatable eIF2alpha. Taken together, our results support a model in which P58(IPK) regulates influenza virus mRNA translation and infection through a PKR-mediated mechanism which is independent of PERK.
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Affiliation(s)
- Alan G Goodman
- Department of Microbiology, University of Washington, Box 358070, Seattle, WA 98195-8070, USA
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Feng Z, Cerveny M, Yan Z, He B. The VP35 protein of Ebola virus inhibits the antiviral effect mediated by double-stranded RNA-dependent protein kinase PKR. J Virol 2006; 81:182-92. [PMID: 17065211 PMCID: PMC1797262 DOI: 10.1128/jvi.01006-06] [Citation(s) in RCA: 141] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
The VP35 protein of Ebola virus is a viral antagonist of interferon. It acts to block virus or double-stranded RNA-mediated activation of interferon regulatory factor 3, a transcription factor that facilitates the expression of interferon and interferon-stimulated genes. In this report, we show that the VP35 protein is also able to inhibit the antiviral response induced by alpha interferon. This depends on the VP35 function that interferes with the pathway regulated by double-stranded RNA-dependent protein kinase PKR. When expressed in a heterologous system, the VP35 protein enhanced viral polypeptide synthesis and growth in Vero cells pretreated with alpha/beta interferon, displaying an interferon-resistant phenotype. In correlation, phosphorylation of PKR and eIF-2alpha was suppressed in cells expressing the VP35 protein. This activity of the VP35 protein was required for efficient viral replication in PKR+/+ but not PKR-/- mouse embryo fibroblasts. Furthermore, VP35 appears to be a RNA binding protein. Notably, a deletion of amino acids 1 to 200, but not R312A substitution in the RNA binding motif, abolished the ability of the VP35 protein to confer viral resistance to interferon. However, the R312A substitution rendered the VP35 protein unable to inhibit the induction of the beta interferon promoter mediated by virus infection. Together, these results show that the VP35 protein targets multiple pathways of the interferon system.
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Affiliation(s)
- Zongdi Feng
- Department of Microbiology and Immunology (M/C 790), College of Medicine, The University of Illinois at Chicago, 835 South Wolcott Avenue, Chicago, IL 60612, USA
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28
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Hakki M, Marshall EE, De Niro KL, Geballe AP. Binding and nuclear relocalization of protein kinase R by human cytomegalovirus TRS1. J Virol 2006; 80:11817-26. [PMID: 16987971 PMCID: PMC1642616 DOI: 10.1128/jvi.00957-06] [Citation(s) in RCA: 92] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
The human cytomegalovirus (HCMV) TRS1 and IRS1 genes block the phosphorylation of the alpha subunit of eukaryotic initiation factor 2 (eIF2alpha) and the consequent shutoff of cellular protein synthesis that occur during infection with vaccinia virus (VV) deleted of the double-stranded RNA binding protein gene E3L (VVDeltaE3L). To further define the underlying mechanism, we first evaluated the effect of pTRS1 on protein kinase R (PKR), the double-stranded RNA (dsRNA)-dependent eIF2alpha kinase. Immunoblot analyses revealed that pTRS1 expression in the context of a VVDeltaE3L recombinant decreased levels of PKR in the cytoplasm and increased its levels in the nucleus of infected cells, an effect not seen with wild-type VV or a VVDeltaE3L recombinant virus expressing E3L. This effect of pTRS1 was confirmed by visualizing the nuclear relocalization of PKR-EGFP expressed by transient transfection. PKR present in both the nuclear and cytoplasmic fractions was nonphosphorylated, indicating that it was unactivated when TRS1 was present. PKR also accumulated in the nucleus during HCMV infection as determined by indirect immunofluorescence and immunoblot analysis. Binding assays revealed that pTRS1 interacted with PKR in mammalian cells and in vitro. This interaction required the same carboxy-terminal region of pTRS1 that is necessary to rescue VVDeltaE3L replication in HeLa cells. The carboxy terminus of pIRS1 was also required for rescue of VVDeltaE3L and for mediating an interaction of pIRS1 with PKR. These results suggest that these HCMV genes directly interact with PKR and inhibit its activation by sequestering it in the nucleus, away from both its activator, cytoplasmic dsRNA, and its substrate, eIF2alpha.
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Affiliation(s)
- Morgan Hakki
- Division of Human Biology, Fred Hutchinson Cancer Research Center, 1100 Fairview Ave. N., Seattle, WA 98109, USA
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29
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Kash JC, Goodman AG, Korth MJ, Katze MG. Hijacking of the host-cell response and translational control during influenza virus infection. Virus Res 2006; 119:111-20. [PMID: 16630668 DOI: 10.1016/j.virusres.2005.10.013] [Citation(s) in RCA: 37] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2005] [Revised: 09/23/2005] [Accepted: 10/20/2005] [Indexed: 11/17/2022]
Abstract
Influenza virus is a major public health problem with annual deaths in the US of 36,000 with pandemic outbreaks, such as in 1918, resulting in deaths exceeding 20 million worldwide. Recently, there is much concern over the introduction of highly pathogenic avian influenza H5N1 viruses into the human population. Influenza virus has evolved complex translational control strategies that utilize cap-dependent translation initiation mechanisms and involve the recruitment of both viral and host-cell proteins to preferentially synthesize viral proteins and prevent activation of antiviral responses. Influenza virus is a member of the Orthomyxoviridae family of negative-stranded, segmented RNA viruses and represents a particularly attractive model system as viral replication strategies are closely intertwined with normal cellular processes including the host defense and stress pathways. In this chapter, we review the parallels between translational control in influenza virus infected cells and in stressed cells with a focus on selective translation of viral mRNAs and the antagonism of the dsRNA and host antiviral responses. Moreover, we will discuss how the use of genomic technologies such as DNA microarrays and high through-put proteomics can be used to gain new insights into the control of protein synthesis during viral infection and provide a near comprehensive view of virus-host interactions.
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Affiliation(s)
- John C Kash
- Department of Microbiology, University of Washington School of Medicine, Box 358070, Seattle, WA 98195-8070, USA.
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30
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Hiasa Y, Blackard JT, Lin W, Kamegaya Y, Horiike N, Onji M, Schmidt EV, Chung RT. Cell-based models of sustained, interferon-sensitive hepatitis C virus genotype 1 replication. J Virol Methods 2005; 132:195-203. [PMID: 16313977 PMCID: PMC2865175 DOI: 10.1016/j.jviromet.2005.10.014] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2005] [Revised: 09/18/2005] [Accepted: 10/03/2005] [Indexed: 10/25/2022]
Abstract
We have previously reported hepatitis C virus (HCV) replication using a novel binary expression system in which mammalian cells were transfected with a T7 polymerase-driven full-length genotype 1a HCV cDNA plasmid (pT7-flHCV-Rz) and infected with vaccinia-T7 polymerase. We hypothesized that the use of replication-defective adenoviral vectors expressing T7 (Ad-T7pol) or cell lines stably transfected with T7 (Huh-T7) would alleviate cell toxicity and allow for more sustained HCV replication. CV-1, Huh7, and Huh-T7 cells were transfected with pT7-flHCV-Rz and treated with Ad-T7pol (CV-1 and Huh7 only). Protein and RNA were harvested from cells on days 1, 2, 3, 5, 7, and 9 post-infection. No cytotoxicity was observed at 9 days post-infection in any cell type. HCV positive- and negative-strand RNA expression were strongest during days 1-3 post-infection; however, HCV RNA remained detectable throughout the 9-day observation period. Furthermore, transfection with a replication-incompetent plasmid suggested that efficient HCV replication is dependent upon NS5B gene expression. Finally, after 1-2 days of IFN treatment, HCV positive-strand levels decreased significantly compared to HCV-infected but untreated samples (p<0.05). In conclusion, these refined binary systems offer more durable and authentic models for identification of host cellular processes critical to HCV replication and will permit longer-term analysis of virus-host interactions critical to HCV pathogenesis and the treatment of genotype 1 infections.
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Affiliation(s)
- Yoichi Hiasa
- Gastrointestinal Unit, Massachusetts General Hospital and Harvard Medical School, GRJ 816, 55 Fruit Street, Boston, MA 02114, USA
- Department of Medicine, Harvard Medical School, Boston, MA, USA
- Third Department of Internal Medicine, Ehime University School of Medicine, Shitsukawa, Toon-shi, Ehime 791-0295, Japan
| | - Jason T. Blackard
- Gastrointestinal Unit, Massachusetts General Hospital and Harvard Medical School, GRJ 816, 55 Fruit Street, Boston, MA 02114, USA
- Department of Medicine, Harvard Medical School, Boston, MA, USA
| | - Wenyu Lin
- Gastrointestinal Unit, Massachusetts General Hospital and Harvard Medical School, GRJ 816, 55 Fruit Street, Boston, MA 02114, USA
- Department of Medicine, Harvard Medical School, Boston, MA, USA
| | - Yoshitaka Kamegaya
- Gastrointestinal Unit, Massachusetts General Hospital and Harvard Medical School, GRJ 816, 55 Fruit Street, Boston, MA 02114, USA
- Department of Medicine, Harvard Medical School, Boston, MA, USA
| | - Norio Horiike
- Third Department of Internal Medicine, Ehime University School of Medicine, Shitsukawa, Toon-shi, Ehime 791-0295, Japan
| | - Morikazu Onji
- Third Department of Internal Medicine, Ehime University School of Medicine, Shitsukawa, Toon-shi, Ehime 791-0295, Japan
| | - Emmett V. Schmidt
- Cancer Center, Massachusetts General Hospital and Harvard Medical School, Building149, 55 Fruit Street, Boston, MA 02114, USA
- Hospital for Children, Massachusetts General Hospital, Boston, MA, USA
- Department of Pediatrics, Harvard Medical School, Boston, MA, USA
| | - Raymond T. Chung
- Gastrointestinal Unit, Massachusetts General Hospital and Harvard Medical School, GRJ 816, 55 Fruit Street, Boston, MA 02114, USA
- Department of Medicine, Harvard Medical School, Boston, MA, USA
- Corresponding author. Tel.: +1 617 724 7562; fax: +1 617 726 5895
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31
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Hsiao JC, Chung CS, Drillien R, Chang W. The cowpox virus host range gene, CP77, affects phosphorylation of eIF2 alpha and vaccinia viral translation in apoptotic HeLa cells. Virology 2004; 329:199-212. [PMID: 15476887 DOI: 10.1016/j.virol.2004.07.032] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/02/2004] [Revised: 04/09/2004] [Accepted: 07/12/2004] [Indexed: 10/26/2022]
Abstract
Host restriction of vaccinia virus has been previously described in CHO and RK13 cells in which a cowpox virus CP77 gene rescues vaccinia virus growth at the viral protein translation level. Here we investigate the restrictive stage of vaccinia virus in HeLa cells using a vaccinia mutant virus (VV-hr) that contains a deletion of 18-kb genome sequences resulting in no growth in HeLa cells. Insertion of CP77 gene into VV-hr generated a recombinant virus (VV-36hr) that multiplied well in HeLa cells. Both viruses could enter cells, initiate viral DNA replication and intermediate gene transcription. However, translation of viral intermediate gene was only detected in cells infected with VV-36hr, indicating that CP77 relieves host restriction at the intermediate gene translation stage in HeLa cells. Caspase-2 and -3 activation was observed in HeLa cells infected with VV-hr coupled with dramatic morphological alterations and cleavage of the translation initiation factor eIF4G. Caspase activation was reduced in HeLa cells infected with VV-36hr, indicating that CP77 acts upstream of caspase activation. Enhanced phosphorylation of PKR and eIF2alpha was also observed in cells infected with VV-hr and was suppressed by CP77. Suppression of eIF4G cleavage with the caspase inhibitor ZVAD did not rescue virus translation, whereas expression of a mutant eIF2alpha protein with an alanine substitution of serine at amino acid position 51 (eIF2alphaS51A) partially restored viral translation and moderately increased virus growth in HeLa cells.
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Affiliation(s)
- Jye-Chian Hsiao
- Graduate Institute of Life Science, National Defense Medical Center, National Defense University, Taipei, Taiwan, ROC
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32
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Whitham SA, Wang Y. Roles for host factors in plant viral pathogenicity. CURRENT OPINION IN PLANT BIOLOGY 2004; 7:365-71. [PMID: 15231257 DOI: 10.1016/j.pbi.2004.04.006] [Citation(s) in RCA: 90] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/20/2023]
Abstract
The simple, obligate nature of viruses requires them to usurp or divert cellular resources, including host factors, away from their normal functions. The characterization of host proteins, membranes, and nucleic acids that are implicated in viral infection cycles, together with other recent discoveries, is providing fundamental clues about the molecular bases of viral susceptibility. As viruses invade susceptible plants, they create conditions that favor systemic infections by suppressing multiple layers of innate host defenses. When viruses meddle in these defense mechanisms, which are interlinked with basic cellular functions, phenotypic changes can result that contribute to disease symptoms.
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Affiliation(s)
- Steven A Whitham
- Iowa State University, Department of Plant Pathology, Ames, Iowa 50011-1020, USA.
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33
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Dave RS, Pomerantz RJ. RNA interference: on the road to an alternate therapeutic strategy! Rev Med Virol 2004; 13:373-85. [PMID: 14625885 DOI: 10.1002/rmv.407] [Citation(s) in RCA: 57] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Abstract
RNA interference (RNAi) is a newly described natural biological phenomenon mediated by small interfering RNA (siRNA) molecules which target viral mRNA for degradation by cellular enzymes. RNAi has become a method of choice for studying gene function, especially in mammalian systems. With proof-of-concept studies already presented against a wide variety of human pathogens and several innovative methods of delivering the siRNA to a wide variety of primary cells available, the role for siRNA as a potential therapeutic strategy is becoming increasingly clear. This review presents recent advances in this direction.
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Affiliation(s)
- Rajnish S Dave
- Center for Human Virology and Biodefense, Division of Infectious Diseases and Environmental Medicine, Thomas Jefferson University, Philadelphia, PA 19107, USA
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34
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Hiasa Y, Kamegaya Y, Nuriya H, Onji M, Kohara M, Schmidt EV, Chung RT. Protein kinase R is increased and is functional in hepatitis C virus-related hepatocellular carcinoma. Am J Gastroenterol 2003; 98:2528-34. [PMID: 14638359 DOI: 10.1111/j.1572-0241.2003.08663.x] [Citation(s) in RCA: 19] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
OBJECTIVE Protein kinase R (PKR) interacts with dsRNA and phosphorylates eukaryotic initiation factor-2 (eIF2alpha), which in turn inhibits host translation initiation as well as hepatitis C virus (HCV) translation. Because PKR inhibits host cell growth and proliferation, it has also been proposed to act as a eukaryotic tumor suppressor. To evaluate the role of PKR in HCV-related hepatocellular carcinoma (HCC), we compared PKR and related protein expression in paired tumor (T) and surrounding nontumor (NT) tissue. METHODS Tissue samples were obtained from 12 HCV-infected HCCs. To determine PKR and related protein expression, Western blotting and semiquantitative reverse transcriptase-polymerase chain reaction were performed. RESULTS PKR protein levels were consistently increased in HCV-related HCC compared with NT (p=0.001); similar increases were seen in total eIF2alpha and the PKR inhibitor p58IPK in T compared with NT (p=0.022, p=0.048, respectively). Relative increases in phosphorylated eIF2alpha (peIF2alpha) were also seen, and the ratio of peIF2alpha/total eIF2alpha did not change in T compared with NT, suggesting that PKR remains functional within T. Cytoplasmic levels of HCV RNA within T were decreased compared with NT. CONCLUSIONS These findings indicate that PKR has increased activity in human HCC compared with LC, and suggest that PKR acts as a growth inducer in HCC.
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Affiliation(s)
- Yoichi Hiasa
- Gastrointestinal Unit, Cancer Center and Hospital for Children, Massachusetts General Hospital, Boston, Massachusetts 02114, USA
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35
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Bilgin DD, Liu Y, Schiff M, Dinesh-Kumar SP. P58(IPK), a plant ortholog of double-stranded RNA-dependent protein kinase PKR inhibitor, functions in viral pathogenesis. Dev Cell 2003; 4:651-61. [PMID: 12737801 DOI: 10.1016/s1534-5807(03)00125-4] [Citation(s) in RCA: 84] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/12/2023]
Abstract
P58(IPK) is a cellular inhibitor of the mammalian double-stranded RNA-activated protein kinase (PKR). Here we provide evidence for the existence of its homolog in plants and its role in viral infection at the organism level. Viral infection of P58(IPK)-silenced Nicotiana benthamiana and Arabidopsis knockouts leads to host death. This host cell death is associated with phosphorylation of the alpha subunit of eukaryotic translation initiation factor (eIF-2alpha). Loss of P58(IPK) leads to reduced virus titer, suggesting that wild-type P58(IPK) protein plays an important role in viral pathogenesis. Although our complementation results using mammalian P58(IPK) suggest conservation of the P58(IPK) pathway in plants and animals, its biological significance seems to be different in these two systems. In animals, P58(IPK) is recruited by the influenza virus to limit PKR-mediated innate antiviral response. In plants, P58(IPK) is required by viruses for virulence and therefore functions as a susceptibility factor.
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Affiliation(s)
- Damla D Bilgin
- Department of Molecular, Cellular and Developmental Biology, Yale University, New Haven, CT 06520, USA
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36
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Main ERG, Xiong Y, Cocco MJ, D'Andrea L, Regan L. Design of stable alpha-helical arrays from an idealized TPR motif. Structure 2003; 11:497-508. [PMID: 12737816 DOI: 10.1016/s0969-2126(03)00076-5] [Citation(s) in RCA: 217] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/27/2022]
Abstract
The tetratricopeptide repeat (TPR) is a 34-amino acid alpha-helical motif that occurs in over 300 different proteins. In the different proteins, three to sixteen or more TPR motifs occur in tandem arrays and function to mediate protein-protein interactions. The binding specificity of each TPR protein is different, although the underlying structural motif is the same. Here we describe a statistical approach to the design of an idealized TPR motif. We present the high-resolution X-ray crystal structures (to 1.55 and 1.6 A) of designed TPR proteins and describe their solution properties and stability. A detailed analysis of these structures provides an understanding of the TPR motif, how it is repeated to give helical arrays with different superhelical twists, and how a very stable framework may be constructed for future functional designs.
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Affiliation(s)
- Ewan R G Main
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT 06520, USA
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37
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Affiliation(s)
- C Jungwirth
- Institute for Virology and Immunobiology, University of Würzburg, D-97078 Würzburg, Germany
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38
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Ramelot TA, Cort JR, Yee AA, Liu F, Goshe MB, Edwards AM, Smith RD, Arrowsmith CH, Dever TE, Kennedy MA. Myxoma virus immunomodulatory protein M156R is a structural mimic of eukaryotic translation initiation factor eIF2alpha. J Mol Biol 2002; 322:943-54. [PMID: 12367520 DOI: 10.1016/s0022-2836(02)00858-6] [Citation(s) in RCA: 40] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
Abstract
Phosphorylation of the translation initiation factor eIF2 on Ser51 of its alpha subunit is a key event for regulation of protein synthesis in all eukaryotes. M156R, the product of the myxoma virus M156R open reading frame, has sequence similarity to eIF2alpha as well as to a family of viral proteins that bind to the interferon-induced protein kinase PKR and inhibit phosphorylation of eIF2alpha. In this study, we demonstrate that, like eIF2alpha. M156R is an efficient substrate for phosphorylation by PKR and can compete with eIF2alpha. To gain insights into the substrate specificity of the eIF2alpha kinases, we have determined the nuclear magnetic resonance (NMR) structure of M156R, the first structure of a myxoma virus protein. The fold consists of a five-stranded antiparallel beta-barrel with two of the strands connected by a loop and an alpha-helix. The similarity between M156R and the beta-barrel structure in the N terminus of eIF2alpha suggests that the viral homologs mimic eIF2alpha structure in order to compete for binding to PKR. A homology-modeled structure of the well-studied vaccinia virus K3L was generated on the basis of alignment with M156R. Comparison of the structures of the K3L model, M156R, and human eIF2alpha indicated that residues important for binding to PKR are located at conserved positions on the surface of the beta-barrel and in the mobile loop, identifying the putative PKR recognition motif.
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Affiliation(s)
- Theresa A Ramelot
- Environmental Molecular Sciences Laboratory, Pacific Northwest National Laboratory, Richland, WA 99352, USA
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39
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Tan SL, Tareen SU, Melville MW, Blakely CM, Katze MG. The direct binding of the catalytic subunit of protein phosphatase 1 to the PKR protein kinase is necessary but not sufficient for inactivation and disruption of enzyme dimer formation. J Biol Chem 2002; 277:36109-17. [PMID: 12138106 DOI: 10.1074/jbc.m205109200] [Citation(s) in RCA: 33] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022] Open
Abstract
The PKR protein kinase is among the best-studied effectors of the host interferon (IFN)-induced antiviral and antiproliferative response system. In response to stress signals, including virus infection, the normally latent PKR becomes activated through autophosphorylation and dimerization and phosphorylates the eIF2alpha translation initiation factor subunit, leading to an inhibition of mRNA translation initiation. While numerous virally encoded or modulated proteins that bind and inhibit PKR during virus infection have been studied, little is known about the cellular proteins that counteract PKR activity in uninfected cells. Overexpression of PKR in yeast also leads to an inhibition of eIF2alpha-dependent protein synthesis, resulting in severe growth suppression. Screening of a human cDNA library for clones capable of counteracting the PKR-mediated growth defect in yeast led to the identification of the catalytic subunit (PP1(C)) of protein phosphatase 1alpha. PP1(C) reduced double-stranded RNA-mediated auto-activation of PKR and inhibited PKR transphosphorylation activities. A specific and direct interaction between PP1(C) and PKR was detected, with PP1(C) binding to the N-terminal regulatory region regardless of the double-stranded RNA-binding activity of PKR. Importantly, a consensus motif shared by many PP1(C)-interacting proteins was necessary for PKR binding to PP1(C). The PKR-interactive site was mapped to a C-terminal non-catalytic region that is conserved in the PP1(C)2 isoform. Indeed, co-expression of PP1(C) or PP1(C)2 inhibited PKR dimer formation in Escherichia coli. Interestingly, co-expression of a PP1(C) mutant lacking the catalytic domain, despite retaining its ability to bind PKR, did not prevent PKR dimerization. Our findings suggest that PP1(C) modulates PKR activity via protein dephosphorylation and subsequent disruption of PKR dimers.
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Affiliation(s)
- Seng-Lai Tan
- Department of Microbiology, School of Medicine, University of Washington, Seattle, Washington, 98195, USA.
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40
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Dar AC, Sicheri F. X-ray crystal structure and functional analysis of vaccinia virus K3L reveals molecular determinants for PKR subversion and substrate recognition. Mol Cell 2002; 10:295-305. [PMID: 12191475 DOI: 10.1016/s1097-2765(02)00590-7] [Citation(s) in RCA: 72] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
The vaccinia virus protein K3L subverts the mammalian antiviral defense mechanism by inhibiting the RNA-dependent protein kinase PKR. K3L is a structural mimic of PKR's natural substrate, the translation initiation factor eIF2alpha. To further our understanding of K3L inhibitory function and PKR substrate recognition, we have solved the 1.8 A X-ray crystal structure of K3L. The structure consists of a five-strand beta barrel with an intervening helix insert region similar in topology to the functionally divergent S1 domain. Mutational analysis identifies two proximal regions of the K3L structure as possessing specialized PKR binding and inhibitory function. Further analysis reveals that PKR dimerization composes a key switch that regulates both its catalytic activation and its molecular recognition of K3L and eIF2alpha.
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Affiliation(s)
- Arvin C Dar
- Program in Molecular Biology and Cancer, Samuel Lunenfeld Research Institute, Mount Sinai Hospital, Toronto, Ontario, Canada
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41
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García-Sastre A. Mechanisms of inhibition of the host interferon alpha/beta-mediated antiviral responses by viruses. Microbes Infect 2002; 4:647-55. [PMID: 12048034 DOI: 10.1016/s1286-4579(02)01583-6] [Citation(s) in RCA: 104] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Complex multicellular organisms have evolved sophisticated mechanisms to prevent and control infection by pathogens. Among these mechanisms, the type I interferon or interferon alpha/beta system represents one of the first lines of defense against viral infections. Typically, viral infection induces the synthesis and secretion of interferon alpha/beta by the infected cell, which in turn activates signaling pathways leading to an antiviral state. As a counter measure, many viruses have developed intriguing mechanisms to evade the interferon alpha/beta system of the host. In this review, we will summarize recent research developments in this interesting field of virus-host cell interactions.
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Affiliation(s)
- Adolfo García-Sastre
- Department of Microbiology, Box 1124, Mount Sinai School of Medicine, 1 Gustave L. Levy Place, New York, NY 10029, USA.
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42
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Clemens MJ. Initiation factor eIF2 alpha phosphorylation in stress responses and apoptosis. PROGRESS IN MOLECULAR AND SUBCELLULAR BIOLOGY 2002; 27:57-89. [PMID: 11575161 DOI: 10.1007/978-3-662-09889-9_3] [Citation(s) in RCA: 169] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
The alpha subunit of polypeptide chain initiation factor eIF2 can be phosphorylated by a number of related protein kinases which are activated in response to cellular stresses. Physiological conditions which result in eIF2 alpha phosphorylation include virus infection, heat shock, iron deficiency, nutrient deprivation, changes in intracellular calcium, accumulation of unfolded or denatured proteins and the induction of apoptosis. Phosphorylated eIF2 acts as a dominant inhibitor of the guanine nucleotide exchange factor eIF2B and prevents the recycling of eIF2 between successive rounds of protein synthesis. Extensive phosphorylation of eIF2 alpha and strong inhibition of eIF2B activity can result in the downregulation of the overall rate of protein synthesis; less marked changes may lead to alterations in the selective translation of alternative open reading frames in polycistronic mRNAs, as demonstrated in yeast. These mechanisms can provide a signal transduction pathway linking eukaryotic cellular stress responses to alterations in the control of gene expression at the translational level.
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Affiliation(s)
- M J Clemens
- Department of Biochemistry and Immunology, St George's Hospital Medical School, University of London, Cranmer Terrace, London SW17 0RE, UK
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43
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Abstract
Molecular chaperones assist protein folding, and some chaperones are induced by heat, nutrient depletion, or pathogen invasion. This study investigates the role played by Hsp90 in the life cycle of vaccinia virus. The titer of vaccinia intracellular mature virions (IMV) was reduced by 2 orders of magnitude in RK13 cells treated with geldanamycin (GA), which blocks the ATPase activity of Hsp90. GA does not affect expression from the viral early promoter, but treatment with GA delays DNA replication and intermediate gene transcription and reduces expression from the viral late promoter. Vaccinia virus infection does not induce Hsp90 expression; however, intracellular distribution of Hsp90 is altered in virus-infected cells. Hsp90 is restricted to the cytoplasm of mock-infected cells; in contrast, Hsp90 is transiently associated with virosomes in virus-infected cells although it is not incorporated into IMV. In addition, Hsp90 interacts with viral core protein 4a, the mature form of the A10L gene product, in virus-infected cells. In conclusion, these results suggest that a cellular chaperone protein, Hsp90, is important for vaccinia virus growth in cultured cells and that viral core protein 4a associates with Hsp90-containing complexes in the infected cells.
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Affiliation(s)
- Jan-Jong Hung
- Institute of Molecular Biology, Academia Sinica, Taipei, Taiwan, Republic of China
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44
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Essbauer S, Bremont M, Ahne W. Comparison of the eIF-2alpha homologous proteins of seven ranaviruses (Iridoviridae). Virus Genes 2001; 23:347-59. [PMID: 11778703 DOI: 10.1023/a:1012533625571] [Citation(s) in RCA: 28] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
Abstract
The alpha-subunit of the eukaryotic initiation factor 2 (eIF-2alpha) is a key component of the translation machinery of the cell. In response to cellular stress such as viral infections, eIF-2alpha is phosphorylated by double-stranded RNA-dependent protein kinase (PKR) leading to the inhibition of cellular protein synthesis. The importance of eIF-2alpha as a regulatory mechanism for protein synthesis is illustrated by the wide variety of strategies employed by viruses to down-regulate PKR. Thus, Vaccinia virus encodes K3L protein, which resembles eIF-2alpha and acts as a pseudo-substrate inhibitor of PKR. Nucleotide sequencing of the genome of epizootic haematopoietic necrosis virus (EHNV), a member of the genus ranavirus of Iridoviridae, has revealed an eIF-2alpha equivalent gene. We have cloned and sequenced eIF-2alpha genes of several iridoviruses of fishes and frogs. The eIF-2alpha open reading frames and deduced proteins of the iridoviruses investigated exhibit a high degree of homology of both nucleotide and amino acid sequences. At the N-terminus, the iridoviral eIF-2alpha shows significant homology to the N-termini of cellular initiation factor 2-alpha of various species, to full-length poxviral eIF-2alpha proteins, and to the S1 domain of ribosomal proteins. Comparison of amino acid sequences of corresponding iridoviral proteins with eIF-2alpha homologous proteins of poxviruses and eukaryotes has revealed a high conservation of motifs. A phylogenetic analysis of eukaryotic eIF-2alpha and poxvirus and iridovirus eIF-2alpha sequences has demonstrated the relationship of these iridoviruses. In order to investigate the role of the eIF-2alpha equivalent, respective genes have been expressed in prokaryotic and eukaryotic (insect, fish and chicken cell) systems. The iridoviral eIF-2alpha protein has a molecular weight of 31 kDa and is cytoplasmic. The cellular and viral protein synthesis of iridoviruses is probably regulated by a mechanism similar to that of Vaccinia virus. Frog-virus 3, the type species of the genus ranavirus of Iridoviridae, has a unique translational efficiency and, moreover, down-regulates the cellular protein synthesis of infected cells.
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Affiliation(s)
- S Essbauer
- Institute of Zoology, Fishery Biology and Fish Diseases, LMU University of Munich, Muenchen, Germany.
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45
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Parker LM, Fierro-Monti I, Mathews MB. Nuclear factor 90 is a substrate and regulator of the eukaryotic initiation factor 2 kinase double-stranded RNA-activated protein kinase. J Biol Chem 2001; 276:32522-30. [PMID: 11438540 DOI: 10.1074/jbc.m104408200] [Citation(s) in RCA: 75] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/12/2023] Open
Abstract
Nuclear factor 90 (NF90) is a member of an expanding family of double-stranded (ds) RNA-binding proteins thought to be involved in gene expression. Originally identified in complex with nuclear factor 45 (NF45) as a sequence-specific DNA-binding protein, NF90 contains two double stranded RNA-binding motifs (dsRBMs) and interacts with highly structured RNAs as well as the dsRNA-activated protein kinase, PKR. In this report, we characterize the biochemical interactions between these two dsRBM containing proteins. NF90 binds to PKR through two independent mechanisms: an RNA-independent interaction occurs between the N terminus of NF90 and the C-terminal region of PKR, and an RNA-dependent interaction is mediated by the dsRBMs of the two proteins. Co-immunoprecipitation analysis demonstrates that NF90, NF45, and PKR form a complex in both nuclear and cytosolic extracts, and both proteins serve as substrates for PKR in vitro. NF90 is phosphorylated by PKR in its RNA-binding domain, and this reaction is partially blocked by the NF90 N-terminal region. The C-terminal region also inhibits PKR function, probably through competitive binding to dsRNA. A model for NF90-PKR interactions is proposed.
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Affiliation(s)
- L M Parker
- Department of Biochemistry and Molecular Biology, New Jersey Medical School, University of Medicine and Dentistry, New Jersey, Newark, New Jersey 07103-2714, USA
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46
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Ung TL, Cao C, Lu J, Ozato K, Dever TE. Heterologous dimerization domains functionally substitute for the double-stranded RNA binding domains of the kinase PKR. EMBO J 2001; 20:3728-37. [PMID: 11447114 PMCID: PMC125533 DOI: 10.1093/emboj/20.14.3728] [Citation(s) in RCA: 92] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022] Open
Abstract
The protein kinase PKR (dsRNA-dependent protein kinase) phosphorylates the eukaryotic translation initiation factor eIF2alpha to downregulate protein synthesis in virus-infected cells. Two double-stranded RNA binding domains (dsRBDs) in the N-terminal half of PKR are thought to bind the activator double-stranded RNA, mediate dimerization of the protein and target PKR to the ribosome. To investigate further the importance of dimerization for PKR activity, fusion proteins were generated linking the PKR kinase domain to heterologous dimerization domains. Whereas the isolated PKR kinase domain (KD) was non-functional in vivo, expression of a glutathione S-transferase-KD fusion, or co-expression of KD fusions containing the heterodimerization domains of the Xlim-1 and Ldb1 proteins, restored PKR activity in yeast cells. Finally, coumermycin-mediated dimerization of a GyrB-KD fusion protein increased eIF2alpha phosphorylation and inhibited reporter gene translation in mammalian cells. These results demonstrate the critical importance of dimerization for PKR activity in vivo, and suggest that a primary function of double-stranded RNA binding to the dsRBDs of native PKR is to promote dimerization and activation of the kinase domain.
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Affiliation(s)
| | | | - Jianming Lu
- Laboratories of Gene Regulation and Development and
Molecular Growth Regulation, National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, MD 20892, USA Corresponding author e-mail:
| | - Keiko Ozato
- Laboratories of Gene Regulation and Development and
Molecular Growth Regulation, National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, MD 20892, USA Corresponding author e-mail:
| | - Thomas E. Dever
- Laboratories of Gene Regulation and Development and
Molecular Growth Regulation, National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, MD 20892, USA Corresponding author e-mail:
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47
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García-Sastre A. Inhibition of interferon-mediated antiviral responses by influenza A viruses and other negative-strand RNA viruses. Virology 2001; 279:375-84. [PMID: 11162793 DOI: 10.1006/viro.2000.0756] [Citation(s) in RCA: 244] [Impact Index Per Article: 10.6] [Reference Citation Analysis] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/22/2023]
Affiliation(s)
- A García-Sastre
- Department of Microbiology, Mount Sinai School of Medicine, New York, New York 10029, USA.
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48
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Kawagishi-Kobayashi M, Cao C, Lu J, Ozato K, Dever TE. Pseudosubstrate inhibition of protein kinase PKR by swine pox virus C8L gene product. Virology 2000; 276:424-34. [PMID: 11040133 DOI: 10.1006/viro.2000.0561] [Citation(s) in RCA: 38] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
The interferon-induced protein kinase PKR is activated upon binding double-stranded RNA and phosphorylates the translation initiation factor eIF2alpha on Ser-51 to inhibit protein synthesis in virally infected cells. Swinepox virus C8L and vaccinia virus K3L gene products structurally resemble the amino-terminal third of eIF2alpha. We demonstrate that the C8L protein, like the K3L protein, can reverse the toxic effects caused by high level expression of human PKR in yeast cells. In addition, expression of either the K3L or C8L gene product was found to reverse the inhibition of reporter gene translation caused by PKR expression in mammalian cells. The inhibitory function of the K3L and C8L gene products in these assays was found to be critically dependent on residues near the carboxyl-termini of the proteins including a sequence motif shared among eIF2alpha and the C8L and K3L gene products. Thus, despite significant sequence differences both the C8L and K3L proteins function as pseudosubstrate inhibitors of PKR.
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Affiliation(s)
- M Kawagishi-Kobayashi
- Laboratory of Eukaryotic Gene Regulation, National Institute of Child Health and Human Development, Bethesda, Maryland, 20892-2716, USA
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49
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Abstract
As obligate intracellular parasites, viruses rely exclusively on the translational machinery of the host cell for the synthesis of viral proteins. This relationship has imposed numerous challenges on both the infecting virus and the host cell. Importantly, viruses must compete with the endogenous transcripts of the host cell for the translation of viral mRNA. Eukaryotic viruses have thus evolved diverse mechanisms to ensure translational efficiency of viral mRNA above and beyond that of cellular mRNA. Mechanisms that facilitate the efficient and selective translation of viral mRNA may be inherent in the structure of the viral nucleic acid itself and can involve the recruitment and/or modification of specific host factors. These processes serve to redirect the translation apparatus to favor viral transcripts, and they often come at the expense of the host cell. Accordingly, eukaryotic cells have developed antiviral countermeasures to target the translational machinery and disrupt protein synthesis during the course of virus infection. Not to be outdone, many viruses have answered these countermeasures with their own mechanisms to disrupt cellular antiviral pathways, thereby ensuring the uncompromised translation of virion proteins. Here we review the varied and complex translational programs employed by eukaryotic viruses. We discuss how these translational strategies have been incorporated into the virus life cycle and examine how such programming contributes to the pathogenesis of the host cell.
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Affiliation(s)
- M Gale
- University of Texas Southwestern Medical Center, Dallas, Texas, USA.
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Coolidge CJ, Patton JG. A new double-stranded RNA-binding protein that interacts with PKR. Nucleic Acids Res 2000; 28:1407-17. [PMID: 10684936 PMCID: PMC111047 DOI: 10.1093/nar/28.6.1407] [Citation(s) in RCA: 26] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/1999] [Revised: 01/26/2000] [Accepted: 01/26/2000] [Indexed: 11/13/2022] Open
Abstract
We have identified a 74 kDa double-stranded (ds)RNA-binding protein that shares extensive homology with the mouse spermatid perinuclear RNA-binding (Spnr) protein. p74 contains two dsRNA-binding motifs (dsRBMs) that are essential for preferential binding to dsRNA. Previously, dsRNA-binding proteins were shown to undergo homo- and heterodimerization, raising the possibility that regulation of activity could be controlled by interactions between different family members. Homodimerization is required to activate the dsRNA-dependent protein kinase PKR, whereas hetero-dimerization between PKR and other dsRNA-binding proteins can inhibit kinase activity. We have found that p74 also interacts with PKR, both the wild-type enzyme and a catalytically defective mutant (K296R). While co-expression of p74 and wild-type PKR in the yeast Saccharomyces cerevisiae did not alter PKR activity, co-expression of p74 and the catalytically defective K296R mutant surprisingly resulted in abnormal morphology and cell death in transformants that maintained a high level of p74 expression. These transformants could be rescued by overexpression of the alpha-subunit of wild-type eukaryotic translation initiation factor 2 (eIF2alpha), one of the known substrates for PKR. We hypothesize that competing heterodimers between p74-K296R PKR and eIF2alpha-K296R PKR may control cell growth such that stabilization of the p74-K296R PKR heterodimer induces abnormal morphology and cell death.
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Affiliation(s)
- C J Coolidge
- Department of Molecular Biology, Box 1820, Station B, Vanderbilt University, Nashville, TN 37235, USA
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