51
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Sales PCM, Williams BRG, Silva AM. Regulation of double-stranded RNA dependent protein kinase expression and attenuation of protein synthesis induced by bacterial toll-like receptors agonists in the absence of interferon. J Interferon Cytokine Res 2012; 32:495-504. [PMID: 22873641 DOI: 10.1089/jir.2012.0019] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/28/2022] Open
Abstract
Double-stranded RNA dependent protein kinase (PKR) is a host defense enzyme whose expression is up-regulated in response to interferons (IFNs) and during viral infections. Increased levels of PKR can result in its activation, which, in turn, inhibits global cellular protein synthesis. Despite growing evidence suggesting the involvement of PKR in bacterial infections, little is known about its expression, regulation and cellular role in nonviral infections. The aim of this work was to determine the expression and regulation of PKR in response to stimulation of human THP-1 monocytes with bacterial agonists of TLR2/4. Treatment of cells with Pam3CSK4 or lipopolyssacharide (LPS) resulted in an increase in PKR mRNA and protein levels. Robust PKR expression at later times correlated with a decrease in global protein synthesis. PKR was also required to regulate the inhibition of protein synthesis triggered by LPS in mouse splenocytes. Surprisingly, no increase of IFN-β or IFN-α mRNA levels was detected after treatment of THP-1 cells with toll-like receptor (TLR) agonists. In accordance with this, the supernatants from LPS or Pam3CSK4-treated cells lacked the ability to activate the PKR and ISG56 promoters in gene reporter assays carried out in HEK293T cells. The expression of PKR induced by TLRs agonists was dramatically impaired when cells were treated in the presence of tosyl-phenylalanyl chloromethylketone or Mithramycin, suggesting that NF-κB and Sp1 transcription factors, but not those activated by IFNs, regulate the expression of PKR in human monocytes.
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Affiliation(s)
- Paula C M Sales
- Laboratory of Inflammatory Genes, Institute of Biological Sciences, Federal University of Minas Gerais, Belo Horizonte, Brazil
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52
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Singh M, Patel RC. Increased interaction between PACT molecules in response to stress signals is required for PKR activation. J Cell Biochem 2012; 113:2754-64. [DOI: 10.1002/jcb.24152] [Citation(s) in RCA: 34] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/11/2023]
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53
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Byrne EH, Prosser I, Muttucumaru N, Curtis TY, Wingler A, Powers S, Halford NG. Overexpression of GCN2-type protein kinase in wheat has profound effects on free amino acid concentration and gene expression. PLANT BIOTECHNOLOGY JOURNAL 2012; 10:328-40. [PMID: 22070093 DOI: 10.1111/j.1467-7652.2011.00665.x] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/05/2023]
Abstract
A key point of regulation of protein synthesis and amino acid homoeostasis in eukaryotes is the phosphorylation of the α subunit of eukaryotic translation initiation factor 2 (eIF2α) by protein kinase general control nonderepressible (GCN)-2. In this study, a GCN2-type PCR product (TaGCN2) was amplified from wheat (Triticum aestivum) RNA, while a wheat eIF2α homologue was identified in wheat genome data and found to contain a conserved target site for phosphorylation by GCN2. TaGCN2 overexpression in transgenic wheat resulted in significant decreases in total free amino acid concentration in the grain, with free asparagine concentration in particular being much lower than in controls. There were significant increases in the expression of eIF2α and protein phosphatase PP2A, as well as a nitrate reductase gene and genes encoding phosphoserine phosphatase and dihydrodipicolinate synthase, while the expression of an asparagine synthetase (AS1) gene and genes encoding cystathionine gamma-synthase and sulphur-deficiency-induced-1 all decreased significantly. Sulphur deficiency-induced activation of these genes occurred in wild-type plants but not in TaGCN2 overexpressing lines. Under sulphur deprivation, the expression of genes encoding aspartate kinase/homoserine dehydrogenase and 3-deoxy-D-arabino-heptulosonate-7-phosphate synthase was also lower than in controls. The study demonstrates that TaGCN2 plays an important role in the regulation of genes encoding enzymes of amino acid biosynthesis in wheat and is the first to implicate GCN2-type protein kinases so clearly in sulphur signalling in any organism. It shows that manipulation of TaGCN2 gene expression could be used to reduce free asparagine accumulation in wheat grain and the risk of acrylamide formation in wheat products.
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Affiliation(s)
- Edward H Byrne
- Department of Plant Science, Rothamsted Research, Harpenden, Hertfordshire, UK
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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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55
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Elbahesh H, Scherbik SV, Brinton MA. West Nile virus infection does not induce PKR activation in rodent cells. Virology 2011; 421:51-60. [PMID: 21982595 DOI: 10.1016/j.virol.2011.08.008] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2011] [Revised: 05/21/2011] [Accepted: 08/14/2011] [Indexed: 11/16/2022]
Abstract
dsRNA-activated protein kinase (PKR) is activated by viral dsRNAs and phosphorylates eIF2a reducing translation of host and viral mRNA. Although infection with a chimeric West Nile virus (WNV) efficiently induced PKR and eIF2a phosphorylation, infections with natural lineage 1 or 2 strains did not. Investigation of the mechanism of suppression showed that among the cellular PKR inhibitor proteins tested, only Nck, known to interact with inactive PKR, colocalized and co-immunoprecipitated with PKR in WNV-infected cells and PKR phosphorylation did not increase in infected Nck1,2-/- cells. Several WNV stem-loop RNAs efficiently activated PKR in vitro but not in infected cells. WNV infection did not interfere with intracellular PKR activation by poly(I:C) and similar virus yields were produced by control and PKR-/- cells. The results indicate that PKR phosphorylation is not actively suppressed in WNV-infected cells but that PKR is not activated by the viral dsRNA in infected cells.
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Affiliation(s)
- H Elbahesh
- Department of Biology, Georgia State University, Atlanta, GA 30303, USA
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56
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Pfaller CK, Li Z, George CX, Samuel CE. Protein kinase PKR and RNA adenosine deaminase ADAR1: new roles for old players as modulators of the interferon response. Curr Opin Immunol 2011; 23:573-82. [PMID: 21924887 PMCID: PMC3190076 DOI: 10.1016/j.coi.2011.08.009] [Citation(s) in RCA: 110] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2011] [Accepted: 08/24/2011] [Indexed: 12/20/2022]
Abstract
Double-stranded RNA (dsRNA) plays a centrally important role in antiviral innate immunity, both for the production of interferon (IFN) and also in the actions of IFN. Among the IFN-inducible gene products are the protein kinase regulated by RNA (PKR) and the adenosine deaminase acting on RNA 1 (ADAR1). PKR is an established key player in the antiviral actions of IFN, through dsRNA-dependent activation and subsequent phosphorylation of protein synthesis initiation factor eIF2α thereby altering the translational pattern in cells. In addition, PKR plays an important role as a positive effector that amplifies the production of IFN. ADAR1 catalyzes the deamination of adenosine (A) in RNA with double-stranded (ds) character, leading to the destabilization of RNA duplex structures and genetic recoding. By contrast to the antiviral and proapoptotic functions associated with PKR, the actions of ADAR1 in some instances are proviral and cell protective as ADAR1 functions as a suppressor of dsRNA-mediated antiviral responses including activation of PKR and interferon regulatory factor 3.
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Affiliation(s)
- Christian K Pfaller
- Department of Molecular, Cellular and Developmental Biology, University of California, Santa Barbara, CA 93106, USA
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57
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Singh M, Castillo D, Patel CV, Patel RC. Stress-induced phosphorylation of PACT reduces its interaction with TRBP and leads to PKR activation. Biochemistry 2011; 50:4550-60. [PMID: 21526770 DOI: 10.1021/bi200104h] [Citation(s) in RCA: 50] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/13/2023]
Abstract
PACT is a stress-modulated activator of interferon (IFN)-induced double-stranded (ds) RNA-activated protein kinase (PKR) and is an important regulator of PKR-dependent signaling pathways. Stress-induced phosphorylation of PACT is essential for PACT's association with PKR leading to PKR activation. PKR activation by PACT leads to phosphorylation of translation initiation factor eIF2α, inhibition of protein synthesis, and apoptosis. In addition to positive regulation by PACT, PKR activity in cells is also negatively regulated by TRBP. In this study, we demonstrate for the first time that stress-induced phosphorylation at serine 287 significantly increases PACT's ability to activate PKR by weakening PACT's interaction with TRBP. A non-phosphorylatable alanine substitution mutant at this position causes enhanced interaction of PACT with TRBP and leads to a loss of PKR activation. Furthermore, TRBP overexpression in cells is unable to block apoptosis induced by a phospho-mimetic, constitutively active PACT mutant. These results demonstrate for the first time that stress-induced PACT phosphorylation functions to free PACT from the inhibitory interaction with TRBP and also to enhance its interaction with PKR.
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Affiliation(s)
- Madhurima Singh
- Department of Biological Sciences, Developmental Biology and Anatomy, School of Medicine, University of South Carolina, Columbia, SC 29208, USA
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58
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Cui W, Li J, Ron D, Sha B. The structure of the PERK kinase domain suggests the mechanism for its activation. ACTA CRYSTALLOGRAPHICA. SECTION D, BIOLOGICAL CRYSTALLOGRAPHY 2011; 67:423-8. [PMID: 21543844 PMCID: PMC3087621 DOI: 10.1107/s0907444911006445] [Citation(s) in RCA: 99] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/17/2011] [Accepted: 02/20/2011] [Indexed: 11/10/2022]
Abstract
The endoplasmic reticulum (ER) unfolded protein response (UPR) is comprised of several intracellular signaling pathways that alleviate ER stress. The ER-localized transmembrane kinase PERK is one of three major ER stress transducers. Oligomerization of PERK's N-terminal ER luminal domain by ER stress promotes PERK trans-autophosphorylation of the C-terminal cytoplasmic kinase domain at multiple residues including Thr980 on the kinase activation loop. Activated PERK phosphorylates Ser51 of the α-subunit of translation initiation factor 2 (eIF2α), which inhibits initiation of protein synthesis and reduces the load of unfolded proteins entering the ER. The crystal structure of PERK's kinase domain has been determined to 2.8 Å resolution. The structure resembles the back-to-back dimer observed in the related eIF2α kinase PKR. Phosphorylation of Thr980 stabilizes both the activation loop and helix αG in the C-terminal lobe, preparing the latter for eIF2α binding. The structure suggests conservation in the mode of activation of eIF2α kinases and is consistent with a `line-up' model for PERK activation triggered by oligomerization of its luminal domain.
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Affiliation(s)
- Wenjun Cui
- Department of Cell Biology, University of Alabama at Birmingham, Birmingham, AL 35294, USA
| | - Jingzhi Li
- Department of Cell Biology, University of Alabama at Birmingham, Birmingham, AL 35294, USA
| | - David Ron
- Institute of Metabolic Science, University of Cambridge, Cambridge CB2 0QQ, England
| | - Bingdong Sha
- Department of Cell Biology, University of Alabama at Birmingham, Birmingham, AL 35294, USA
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59
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Rothenburg S, Chinchar VG, Dever TE. Characterization of a ranavirus inhibitor of the antiviral protein kinase PKR. BMC Microbiol 2011; 11:56. [PMID: 21418572 PMCID: PMC3068933 DOI: 10.1186/1471-2180-11-56] [Citation(s) in RCA: 37] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2010] [Accepted: 03/18/2011] [Indexed: 01/06/2023] Open
Abstract
Background Ranaviruses (family Iridoviridae) are important pathogens of lower vertebrates. However, little is known about how they circumvent the immune response of their hosts. Many ranaviruses contain a predicted protein, designated vIF2α, which shows homology with the eukaryotic translation initiation factor 2α. In analogy to distantly related proteins found in poxviruses vIF2α might act as an inhibitor of the antiviral protein kinase PKR. Results We have characterized the function of vIF2α from Rana catesbeiana virus Z (RCV-Z). Multiple sequence alignments and secondary structure prediction revealed homology of vIF2α with eIF2α throughout the S1-, helical- and C-terminal domains. Genetic and biochemical analyses showed that vIF2α blocked the toxic effects of human and zebrafish PKR in a heterologous yeast system. Rather than complementing eIF2α function, vIF2α acted in a manner comparable to the vaccinia virus (VACV) K3L protein (K3), a pseudosubstrate inhibitor of PKR. Both vIF2α and K3 inhibited human PKR-mediated eIF2α phosphorylation, but not PKR autophosphorylation on Thr446. In contrast the E3L protein (E3), another poxvirus inhibitor of PKR, inhibited both Thr446 and eIF2α Ser51 phosphorylation. Interestingly, phosphorylation of eIF2α by zebrafish PKR was inhibited by vIF2α and E3, but not by K3. Effective inhibition of PKR activity coincided with increased PKR expression levels, indicative of relieved autoinhibition of PKR expression. Experiments with vIF2α deletion constructs, showed that both the N-terminal and helical domains were sufficient for inhibition of PKR, whereas the C-terminal domain was dispensable. Conclusions Our results show that RCV-Z vIF2α is a functional inhibitor of human and zebrafish PKR, and probably functions in similar fashion as VACV K3. This constitutes an important step in understanding the interaction of ranaviruses and the host innate immune system.
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Affiliation(s)
- Stefan Rothenburg
- Laboratory of Gene Regulation and Development, NICHD, National Institutes of Health, Bethesda, MD 20892, USA.
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60
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Cho H, Mukherjee S, Palasuberniam P, Pillow L, Bilgin B, Nezich C, Walton SP, Feig M, Chan C. Molecular mechanism by which palmitate inhibits PKR autophosphorylation. Biochemistry 2011; 50:1110-9. [PMID: 21192654 DOI: 10.1021/bi101923r] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
PKR (double-stranded RNA-activated protein kinase) is an important component of the innate immunity, antiviral, and apoptotic pathways. Recently, our group found that palmitate, a saturated fatty acid, is involved in apoptosis by reducing the autophosphorylation of PKR at the Thr451 residue; however, the molecular mechanism by which palmitate reduces PKR autophosphorylation is not known. Thus, we investigated how palmitate affects the phosphorylation of the PKR protein at the molecular and biophysical levels. Biochemical and computational studies show that palmitate binds to PKR, near the ATP-binding site, thereby inhibiting its autophosphorylation at Thr451 and Thr446. Mutation studies suggest that Lys296 and Asp432 in the ATP-binding site on the PKR protein are important for palmitate binding. We further confirmed that palmitate also interacts with other kinases, due to the conserved ATP-binding site. A better understanding of how palmitate interacts with the PKR protein, as well as other kinases, could shed light onto possible mechanisms by which palmitate mediates kinase signaling pathways that could have implications on the efficacy of current drug therapies that target kinases.
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Affiliation(s)
- Hyunju Cho
- Department of Chemical Engineering and Materials Science, Michigan State University, East Lansing, Michigan 48824, United States
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61
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Pindel A, Sadler A. The Role of Protein Kinase R in the Interferon Response. J Interferon Cytokine Res 2011; 31:59-70. [DOI: 10.1089/jir.2010.0099] [Citation(s) in RCA: 125] [Impact Index Per Article: 9.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023] Open
Affiliation(s)
- Agnieszka Pindel
- Centre for Cancer Research, Monash Institute of Medical Research, Monash University, Melbourne, Australia
| | - Anthony Sadler
- Centre for Cancer Research, Monash Institute of Medical Research, Monash University, Melbourne, Australia
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Ranji A, Shkriabai N, Kvaratskhelia M, Musier-Forsyth K, Boris-Lawrie K. Features of double-stranded RNA-binding domains of RNA helicase A are necessary for selective recognition and translation of complex mRNAs. J Biol Chem 2010; 286:5328-37. [PMID: 21123178 DOI: 10.1074/jbc.m110.176339] [Citation(s) in RCA: 39] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
The DExH protein RNA helicase A (RHA) plays numerous roles in cell physiology, and post-transcriptional activation of gene expression is a major role among them. RHA selectively activates translation of complex cellular and retroviral mRNAs. Although RHA requires interaction with structural features of the 5'-UTR of these target mRNAs, the molecular basis of their translation activation by RHA is poorly understood. RHA contains a conserved ATPase-dependent helicase core that is flanked by two α-β-β-β-α double-stranded RNA-binding domains at the N terminus and repeated arginine-glycine residues at the C terminus. The individual recombinant N-terminal, central helicase, and C-terminal domains were evaluated for their ability to specifically interact with cognate RNAs by in vitro biochemical measurements and mRNA translation assays in cells. The results demonstrate that N-terminal residues confer selective interaction with retroviral and junD target RNAs. Conserved lysine residues in the distal α-helix of the double-stranded RNA-binding domains are necessary to engage structural features of retroviral and junD 5'-UTRs. Exogenous expression of the N terminus coprecipitates junD mRNA and inhibits the translation activity of endogenous RHA. The results indicate that the molecular basis for the activation of translation by RHA is recognition of target mRNA by the N-terminal domain that tethers the ATP-dependent helicase for rearrangement of the complex 5'-UTR.
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Affiliation(s)
- Arnaz Ranji
- Center for Retrovirus Research, Department of Veterinary Biosciences, Ohio State University, Columbus, Ohio 43210, USA
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63
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Wostenberg C, Quarles KA, Showalter SA. Dynamic origins of differential RNA binding function in two dsRBDs from the miRNA "microprocessor" complex. Biochemistry 2010; 49:10728-36. [PMID: 21073201 DOI: 10.1021/bi1015716] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
MicroRNAs (miRNAs) affect gene regulation by base pairing with mRNA and contribute to the control of cellular homeostasis. The first step in miRNA maturation is conducted in the nucleus by the "microprocessor" complex made up of an RNase III enzyme, Drosha, that contains one dsRNA binding domain (dsRBD), and DGCR8, that contains two dsRBDs in tandem. The crystal structure of DGCR8-Core (493-720), containing both dsRBDs, and the NMR solution structure of Drosha-dsRBD (1259-1337) have been reported, but the solution dynamics have not been explored for any of these dsRBDs. To better define the mechanism of dsRNA binding and thus the nuclear maturation step of miRNA processing, we report NMR spin relaxation and MD simulations of Drosha-dsRBD (1259-1337) and DGCR8-dsRBD1 (505-583). The study was motivated by electrophoretic mobility shift assays (EMSAs) of the two dsRBDs, which showed that Drosha-dsRBD does not bind a representative miRNA but isolated DGCR8-dsRBD1 does (K(d) = 9.4 ± 0.4 μM). Our results show that loop 2 in both dsRBDs is highly dynamic but the pattern of the correlations observed in MD is different for the two proteins. Additionally, the extended loop 1 of Drosha-dsRBD is more flexible than the corresponding loop in DGCR8-dsRBD1 but shows no correlation with loop 2, which potentially explains the lack of dsRNA binding by Drosha-dsRBD in the absence of the RNase III domains. The results presented in this study provide key structural and dynamic features of dsRBDs that contribute to the binding mechanism of these domains to dsRNA.
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Affiliation(s)
- Christopher Wostenberg
- Department of Chemistry, The Pennsylvania State University, 104 Chemistry Building, University Park, Pennsylvania 16802, United States
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64
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Sadler AJ. Orchestration of the activation of protein kinase R by the RNA-binding motif. J Interferon Cytokine Res 2010; 30:195-204. [PMID: 20377414 DOI: 10.1089/jir.2010.0005] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023] Open
Abstract
The protein kinase R (PKR) constitutes part of the host antiviral response. PKR activation is regulated by the N-terminus of protein, which encodes tandem RNA-binding motifs (RBMs). The full capabilities of RBMs from PKR and other proteins have surpassed the narrow specificities initially determined as merely binding double-stranded RNA. Recognition of the increased affinity of the RBM for additional RNA species has established an immunological distinction by which PKR can detect exogenous RNAs, as well as identified PKR-mediated expression of specific endogenous genes. Furthermore, as RBMs also mediate interactions with other proteins, including PKR itself, this motif connects PKR to the broader RNA metabolism. Given the fundamental importance of protein-RNA interactions, not only in the innate immune response to intracellular pathogens, but also to coordinate the cellular replication machinery, there is considerable interest in the mechanisms by which proteins recognize and respond to RNA. This review appraises our understanding of how PKR activity is modulated by the RBMs.
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Affiliation(s)
- Anthony J Sadler
- Monash Institute of Medical Research, Monash University, Melbourne, Australia
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65
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Li XL, Ezelle HJ, Hsi TY, Hassel BA. A central role for RNA in the induction and biological activities of type 1 interferons. WILEY INTERDISCIPLINARY REVIEWS-RNA 2010; 2:58-78. [PMID: 21956969 DOI: 10.1002/wrna.32] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
In mammals the type 1 interferon (IFN) system functions as the primary innate antiviral defense and more broadly as a stress response and regulator of diverse homeostatic mechanisms. RNA plays a central role in the induction of IFN and in its biologic activities. Cellular toll-like receptors (TLR), RIG-I-like receptors (RLR), and nucleotide organization domain-like receptors (NLR) sense pathogen- and danger-associated RNAs as nonself based on structural features and subcellular location that distinguish them from ubiquitous host RNAs. Detection of nonself RNAs activates signaling pathways to induce IFN transcription and secretion. In turn, IFN binds cell surface receptors to initiate signaling that results in the induction of IFN-stimulated genes (ISGs) that mediate its biologic activities. RNA also plays a critical role in this effector phase of the IFN system, serving as an activator of enzyme activity for protein kinase RNA-dependent (PKR) and oligoadenylate synthetase (OAS), and as a substrate for 2('), 5(') -linked oligoadenylate dependant-endoribonuclease (RNase-L). In contrast to the transcriptional response induced by RNA receptors, these key ISGs mediate their activities primarily through post transcriptional mechanisms to regulate the translation and stability of host and microbial RNAs. Together RNA-sensing and RNA-effector molecules comprise a network of coordinately regulated proteins with integrated feedback and feed-forward loops that tightly regulate the cellular response to RNA. This stringent regulation is essential to prevent deleterious effects of uncontrolled IFN expression and effector activation. In light of this extensive crosstalk, targeting key mediators of the cellular response to RNA represents a viable strategy for therapeutic modulation of immune function and treatment of diseases in which this response is dysregulated (e.g., cancer).
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Affiliation(s)
- Xiao-Ling Li
- Marlene and Stewart Greenebaum Cancer Center, University of Maryland School of Medicine, Baltimore, MD, USA
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66
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Abstract
The lack of an efficacious HIV-1 vaccine and the continued emergence of drug-resistant HIV-1 strains have pushed the research community to explore novel avenues for AIDS therapy. Over the last decade, one new avenue that has been realized involves cellular HIV-1 restriction factors, defined as host cellular proteins or factors that restrict or inhibit HIV-1 replication. Many of these factors are interferon-induced and inhibit specific stages of the HIV-1 lifecycle that are not targeted by current AIDS therapies. Our understanding of the molecular mechanisms underlying HIV-1 restriction is far from complete, but our current knowledge of these factors offers hope for the future development of novel therapeutic ideas.
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Affiliation(s)
- Stephen D Barr
- Department of Microbiology & Immunology, The University of Western Ontario, London, ON, Canada
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67
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Martel C, Dugré-Brisson S, Boulay K, Breton B, Lapointe G, Armando S, Trépanier V, Duchaîne T, Bouvier M, Desgroseillers L. Multimerization of Staufen1 in live cells. RNA (NEW YORK, N.Y.) 2010; 16:585-97. [PMID: 20075165 PMCID: PMC2822923 DOI: 10.1261/rna.1664210] [Citation(s) in RCA: 38] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/08/2023]
Abstract
Transport of mRNA is an efficient mechanism to target proteins to specific regions of a cell. Although it is well documented that mRNAs are transported in ribonucleoprotein (RNP) complexes, several of the mechanisms involved in complex formation and localization are poorly understood. Staufen (Stau) 1, a double-stranded RNA-binding protein, is a well accepted marker of mRNA transport complexes. In this manuscript, we provide evidence that Stau1 self-associates in live cells using immunoprecipitation and bioluminescence resonance energy transfer (BRET) assays. The double-stranded RNA-binding domains dsRBD3 and dsRBD4 contributed about half of the signal, suggesting that Stau1 RNA-binding activity is involved in Stau1 self-association. Protein-protein interaction also occurred, via dsRBD5 and dsRBD2, as shown by in vitro pull-down, yeast two-hybrid, and BRET assays in live cells. Interestingly, Stau1 self-association contributes to the formation of oligomeric complexes as evidenced by the coexpression of split Renilla luciferase halves covalently linked to Stau1 in a protein complementation assay (PCA) combined with a BRET assay with Stau1-YFP. Moreover, we showed that these higher-order Stau1-containing complexes carry RNAs when the RNA stain SYTO 14 was used as the energy acceptor in the PCA/BRET assay. The oligomeric composition of Stau1-containing complexes and the presence of specific mRNAs have been confirmed by biochemical approaches involving two successive immunoprecipitations of Stau1-tagged molecules followed by qRT-PCR amplification. Altogether, these results indicate that Stau1 self-associates in mRNPs via its multiple functional domains that can select mRNAs to be transported and establish protein-protein interaction.
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Affiliation(s)
- Catherine Martel
- Département de Biochimie, Université de Montréal, Montréal, Québec H3C 3J7, Canada
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68
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Abstract
Many extracellular stresses cause inhibition of translation initiation by triggering phosphorylation of the initiation factor, eIF-2alpha. A major protein kinase responsible for this phosphorylation is PKR, a latent kinase which itself needs to be activated by autophosphorylation. In stressed cells, this activation occurs when PACT, a PKR-binding protein, is phosphorylated and activates PKR. We have previously demonstrated that the presence of specific residues in domain 3 of PACT is necessary for its ability to activate PKR in vivo. Here, we analyze the biochemical properties of the inactive PACT mutants by assessing their ability to bind and activate PKR in vitro. Among the essential residues, two serines need to be phosphorylated in vivo for PACT's ability to activate PKR. We substituted those serines with aspartic acids, mimics of phosphoserines, and investigated the properties of the corresponding mutant PACTs. In vitro, they activate PKR more efficiently because they bind to PKR more tightly. These results indicate that stress-induced phosphorylation of specific serine residues in domain 3 of PACT increases its affinity for PKR, which leads to better activation of PKR and resultant eIF-2alpha phosphorylation.
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Affiliation(s)
- Gregory A Peters
- Department of Molecular Genetics, Lerner Research Institute, The Cleveland Clinic Foundation, Cleveland, Ohio 44195, USA
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69
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Inhibition of protein kinase R activation and upregulation of GADD34 expression play a synergistic role in facilitating coronavirus replication by maintaining de novo protein synthesis in virus-infected cells. J Virol 2009; 83:12462-72. [PMID: 19776135 DOI: 10.1128/jvi.01546-09] [Citation(s) in RCA: 78] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022] Open
Abstract
A diversity of strategies is evolved by RNA viruses to manipulate the host translation machinery in order to create an optimal environment for viral replication and progeny production. One of the common viral targets is the alpha subunit of eukaryotic initiation factor 2 (eIF-2alpha). In this report, we show that phosphorylation of eIF-2alpha was severely suppressed in human and animal cells infected with the coronavirus infectious bronchitis virus (IBV). To understand whether this suppression is through inhibition of protein kinase R (PKR), the double-stranded-RNA-dependent kinase that is one of the main kinases responsible for phosphorylation of eIF-2alpha, cells infected with IBV were analyzed by Western blotting. The results showed that the level of phosphorylated PKR was greatly reduced in IBV-infected cells. Overexpression of IBV structural and nonstructural proteins (nsp) demonstrated that nsp2 is a weak PKR antagonist. Furthermore, GADD34, a component of the protein phosphatase 1 (PP1) complex, which dephosphorylates eIF-2alpha, was significantly induced in IBV-infected cells. Inhibition of the PP1 activity by okadaic acid and overexpression of GADD34, eIF-2alpha, and PKR, as well as their mutant constructs in virus-infected cells, showed that these viral regulatory strategies played a synergistic role in facilitating coronavirus replication. Taken together, these results confirm that IBV has developed a combination of two mechanisms, i.e., blocking PKR activation and inducing GADD34 expression, to maintain de novo protein synthesis in IBV-infected cells and, meanwhile, to enhance viral replication.
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70
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VanOudenhove J, Anderson E, Kreuger S, Cole JL. Analysis of PKR structure by small-angle scattering. J Mol Biol 2009; 387:910-20. [PMID: 19232355 PMCID: PMC2663012 DOI: 10.1016/j.jmb.2009.02.019] [Citation(s) in RCA: 38] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/06/2009] [Revised: 02/05/2009] [Accepted: 02/10/2009] [Indexed: 11/20/2022]
Abstract
Protein kinase R (PKR) is a key component of the interferon antiviral defense pathway. Upon binding double-stranded RNA, PKR undergoes autophosphorylation reactions that activate the kinase. PKR contains an N-terminal double-stranded RNA binding domain, which consists of two tandem double-stranded RNA binding motifs, and a C-terminal kinase domain. We have used small-angle X-ray scattering and small-angle neutron scattering to define the conformation of latent PKR in solution. Guinier analysis indicates a radius of gyration of about 35 A. The p(r) distance distribution function exhibits a peak near 30 A, with a broad shoulder extending to longer distances. Good fits to the scattering data require models that incorporate multiple compact and extended conformations of the two interdomain linker regions. Thus, PKR belongs to the growing family of proteins that contain intrinsically unstructured regions. We propose that the flexible linkers may allow PKR to productively dimerize upon interaction with RNA activators that have diverse structures.
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Affiliation(s)
- Jennifer VanOudenhove
- Department of Molecular and Cell Biology, University of Connecticut Storrs, Connecticut 06269, USA
| | - Eric Anderson
- Department of Molecular and Cell Biology, University of Connecticut Storrs, Connecticut 06269, USA
| | - Susan Kreuger
- NIST Center for Neutron Research National Institutes of Standards and Technology Gaithersburg, MD 21702-1201, USA
| | - James L. Cole
- Department of Molecular and Cell Biology, University of Connecticut Storrs, Connecticut 06269, USA
- Deparment of Chemistry University of Connecticut Storrs, Connecticut 06269, USA
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71
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Singh M, Fowlkes V, Handy I, Patel CV, Patel RC. Essential role of PACT-mediated PKR activation in tunicamycin-induced apoptosis. J Mol Biol 2008; 385:457-68. [PMID: 19007793 DOI: 10.1016/j.jmb.2008.10.068] [Citation(s) in RCA: 38] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2008] [Revised: 10/08/2008] [Accepted: 10/22/2008] [Indexed: 10/21/2022]
Abstract
Cellular stresses such as disruption of calcium homeostasis, inhibition of protein glycosylation, and reduction of disulfide bonds result in accumulation of misfolded proteins in the endoplasmic reticulum (ER) and lead to cell death by apoptosis. Tunicamycin, which is an inhibitor of protein glycosylation, induces ER stress and apoptosis. In this study, we examined the involvement of double-stranded RNA (dsRNA)-activated protein kinase (PKR) and its protein activator PACT in tunicamycin-induced apoptosis. We demonstrate for the first time that PACT is phosphorylated in response to tunicamycin and is responsible for PKR activation by direct interaction. Furthermore, PACT-induced PKR activation is essential for tunicamycin-induced apoptosis, since PACT as well as PKR null cells are markedly resistant to tunicamycin and show defective eIF2alpha phosphorylation and C/EBP homologous protein (CHOP, also known as GADD153) induction especially at low concentrations of tunicamycin. Reconstitution of PKR and PACT expression in the null cells renders them sensitive to tunicamycin, thus demonstrating that PACT-induced PKR activation plays an essential function in induction of apoptosis.
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Affiliation(s)
- Madhurima Singh
- Department of Biological Sciences, University of South Carolina, 700 Sumter Street, Columbia, SC 29208, USA
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72
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Abstract
Avian reovirus, an important avian pathogen, expresses eight structural and four nonstructural proteins. The structural sigmaA protein is a major component of the inner capsid, clamping together lambdaA building blocks. sigmaA has also been implicated in the resistance of avian reovirus to the antiviral action of interferon by strongly binding double-stranded RNA in the host cell cytoplasm and thus inhibiting activation of the double-stranded RNA-dependent protein kinase. We have solved the structure of bacterially expressed sigmaA by molecular replacement and refined it using data to 2.3-A resolution. Twelve sigmaA molecules are present in the P1 unit cell, arranged as two short double helical hexamers. A positively charged patch is apparent on the surface of sigmaA on the inside of this helix and mutation of either of two key arginine residues (Arg155 and Arg273) within this patch abolishes double-stranded RNA binding. The structural data, together with gel shift assay, electron microscopy, and sedimentation velocity centrifugation results, provide evidence for cooperative binding of sigmaA to double-stranded RNA. The minimal length of double-stranded RNA required for sigmaA binding was observed to be 14 to 18 bp.
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73
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Abstract
Since the discovery of interferons (IFNs), considerable progress has been made in describing the nature of the cytokines themselves, the signalling components that direct the cell response and their antiviral activities. Gene targeting studies have distinguished four main effector pathways of the IFN-mediated antiviral response: the Mx GTPase pathway, the 2',5'-oligoadenylate-synthetase-directed ribonuclease L pathway, the protein kinase R pathway and the ISG15 ubiquitin-like pathway. As discussed in this Review, these effector pathways individually block viral transcription, degrade viral RNA, inhibit translation and modify protein function to control all steps of viral replication. Ongoing research continues to expose additional activities for these effector proteins and has revealed unanticipated functions of the antiviral response.
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Affiliation(s)
- Anthony J. Sadler
- Monash Institute of Medical Research, Monash University, Clayton, 3168 Victoria Australia
| | - Bryan R. G. Williams
- Monash Institute of Medical Research, Monash University, Clayton, 3168 Victoria Australia
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74
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Mechanism of PKR Activation by dsRNA. J Mol Biol 2008; 381:351-60. [PMID: 18599071 DOI: 10.1016/j.jmb.2008.05.056] [Citation(s) in RCA: 142] [Impact Index Per Article: 8.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2008] [Revised: 05/20/2008] [Accepted: 05/23/2008] [Indexed: 01/20/2023]
Abstract
Protein kinase R (PKR) is a central component of the interferon antiviral defense pathway. Upon binding double-stranded RNA (dsRNA), PKR undergoes autophosphorylation reactions that activate the kinase. PKR then phosphorylates eukaryotic initiation factor 2alpha, thus inhibiting protein synthesis in virally infected cells. Using a series of dsRNAs of increasing length, we define the mechanism of PKR activation. A minimal dsRNA of 30 bp is required to bind two PKR monomers and 30 bp is the smallest dsRNA that elicits autophosphorylation activity. Thus, the ability of dsRNAs to function as PKR activators is correlated with binding of two or more PKR monomers. Sedimentation velocity data fit a model where PKR monomers sequentially attach to a single dsRNA. These results support an activation mechanism where the role of the dsRNA is to bring two or more PKR monomers in close proximity to enhance dimerization via the kinase domain. This model explains the inhibition observed at high dsRNA concentrations and the strong dependence of maximum activation on dsRNA binding affinity. Binding affinities increase dramatically upon reducing the salt concentration from 200 to 75 mM NaCl and we observe that a second PKR can bind to the 20-bp dsRNA. Nonspecific assembly of PKR on dsRNA occurs stochastically without apparent cooperativity.
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75
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Functional domains and the antiviral effect of the double-stranded RNA-dependent protein kinase PKR from Paralichthys olivaceus. J Virol 2008; 82:6889-901. [PMID: 18448522 DOI: 10.1128/jvi.02385-07] [Citation(s) in RCA: 90] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
The double-stranded RNA (dsRNA)-dependent protein kinase PKR is thought to mediate a conserved antiviral pathway by inhibiting viral protein synthesis via the phosphorylation of the alpha subunit of eukaryotic initiation factor 2 (eIF2alpha). However, little is known about the data related to the lower vertebrates, including fish. Recently, the identification of PKR-like, or PKZ, has addressed the question of whether there is an orthologous PKR in fish. Here, we identify the first fish PKR gene from the Japanese flounder Paralichthys olivaceus (PoPKR). PoPKR encodes a protein that shows a conserved structure that is characteristic of mammalian PKRs, having both the N-terminal region for dsRNA binding and the C-terminal region for the inhibition of protein translation. The catalytic activity of PoPKR is further evidence that it is required for protein translation inhibition in vitro. PoPKR is constitutively transcribed at low levels and is highly induced after virus infection. Strikingly, PoPKR overexpression increases eIF2alpha phosphorylation and inhibits the replication of Scophthalmus maximus rhabdovirus (SMRV) in flounder embryonic cells, whereas phosphorylation and antiviral effects are impaired in transfected cells expressing the catalytically inactive PKR-K421R variant, indicating that PoPKR inhibits virus replication by phosphorylating substrate eIF2alpha. The interaction between PoPKR and eIF2alpha is demonstrated by coimmunoprecipitation assays, and the transfection of PoPKR-specific short interfering RNA further reveals that the enhanced eIF2alpha phosphorylation is catalyzed by PoPKR during SMRV infection. The current data provide significant evidence for the existence of a PKR-mediated antiviral pathway in fish and reveal considerable conservation in the functional domains and the antiviral effect of PKR proteins between fish and mammals.
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76
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Anderson E, Cole JL. Domain stabilities in protein kinase R (PKR): evidence for weak interdomain interactions. Biochemistry 2008; 47:4887-97. [PMID: 18393532 DOI: 10.1021/bi702211j] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]
Abstract
PKR (protein kinase R) is induced by interferon and is a key component of the innate immunity antiviral pathway. Upon binding dsRNA, PKR undergoes autophosphorylation reactions that activate the kinase, leading it to phosphorylate eIF2alpha, thus inhibiting protein synthesis in virally infected cells. PKR contains a dsRNA-binding domain (dsRBD) and a kinase domain. The dsRBD is composed of two tandem dsRNA-binding motifs. An autoinhibition model for PKR has been proposed, whereby dsRNA binding activates the enzyme by inducing a conformational change that relieves the latent enzyme of the inhibition that is mediated by the interaction of the dsRBD with the kinase. However, recent biophysical data support an open conformation for the latent enzyme, where activation is mediated by dimerization of PKR induced upon binding dsRNA. We have probed the importance of interdomain contacts by comparing the relative stabilities of isolated domains with the same domain in the context of the intact enzyme using equilibrium chemical denaturation experiments. The two dsRNA-binding motifs fold independently, with the C-terminal motif exhibiting greater stability. The kinase domain is stabilized by about 1.5 kcal/mol in the context of the holenzyme, and we detect low-affinity binding of the kinase and dsRBD constructs in solution, indicating that these domains interact weakly. Limited proteolysis measurements confirm the expected domain boundaries and reveal that the activation loop in the kinase is accessible to cleavage and unstructured. Autophosphorylation induces a conformation change that blocks proteolysis of the activation loop.
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Affiliation(s)
- Eric Anderson
- Department of Molecular and Cell Biology, University of Connecticut, Storrs, Connecticut 06269-3125, USA
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77
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Rothenburg S, Deigendesch N, Dey M, Dever TE, Tazi L. Double-stranded RNA-activated protein kinase PKR of fishes and amphibians: varying the number of double-stranded RNA binding domains and lineage-specific duplications. BMC Biol 2008; 6:12. [PMID: 18312693 PMCID: PMC2291453 DOI: 10.1186/1741-7007-6-12] [Citation(s) in RCA: 64] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2007] [Accepted: 03/03/2008] [Indexed: 02/04/2023] Open
Abstract
Background Double-stranded (ds) RNA, generated during viral infection, binds and activates the mammalian anti-viral protein kinase PKR, which phosphorylates the translation initiation factor eIF2α leading to the general inhibition of protein synthesis. Although PKR-like activity has been described in fish cells, the responsible enzymes eluded molecular characterization until the recent discovery of goldfish and zebrafish PKZ, which contain Z-DNA-binding domains instead of dsRNA-binding domains (dsRBDs). Fish and amphibian PKR genes have not been described so far. Results Here we report the cloning and identification of 13 PKR genes from 8 teleost fish and amphibian species, including zebrafish, demonstrating the coexistence of PKR and PKZ in this latter species. Analyses of their genomic organization revealed up to three tandemly arrayed PKR genes, which are arranged in head-to-tail orientation. At least five duplications occurred independently in fish and amphibian lineages. Phylogenetic analyses reveal that the kinase domains of fish PKR genes are more closely related to those of fish PKZ than to the PKR kinase domains of other vertebrate species. The duplication leading to fish PKR and PKZ genes occurred early during teleost fish evolution after the divergence of the tetrapod lineage. While two dsRBDs are found in mammalian and amphibian PKR, one, two or three dsRBDs are present in fish PKR. In zebrafish, both PKR and PKZ were strongly upregulated after immunostimulation with some tissue-specific expression differences. Using genetic and biochemical assays we demonstrate that both zebrafish PKR and PKZ can phosphorylate eIF2α in yeast. Conclusion Considering the important role for PKR in host defense against viruses, the independent duplication and fixation of PKR genes in different lineages probably provided selective advantages by leading to the recognition of an extended spectrum of viral nucleic acid structures, including both dsRNA and Z-DNA/RNA, and perhaps by altering sensitivity to viral PKR inhibitors. Further implications of our findings for the evolution of the PKR family and for studying PKR/PKZ interactions with viral gene products and their roles in viral infections are discussed.
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Affiliation(s)
- Stefan Rothenburg
- Laboratory of Gene Regulation and Development, National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, MD 20892, USA.
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78
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McKenna SA, Lindhout DA, Shimoike T, Puglisi JD. Biophysical and biochemical investigations of dsRNA-activated kinase PKR. Methods Enzymol 2008; 430:373-96. [PMID: 17913645 DOI: 10.1016/s0076-6879(07)30014-1] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/07/2023]
Abstract
Protein kinase RNA-activated (PKR) is a serine/threonine kinase that contains an N-terminal RNA-binding domain (dsRNA) and a C-terminal kinase domain. On binding viral dsRNA molecules, PKR can become activated and phosphorylate cellular targets, such as eukaryotic translation initiation factor 2alpha (eIF-2alpha). Phosphorylation of eIF-2alpha results in attenuation of protein translation initiation. Therefore, PKR plays an integral role in the antiviral response to cellular infection. Here we provide a methodological framework for probing PKR function by use of assays for phosphorylation, RNA-protein stability, PKR dimerization, and in vitro translation. These methods are complemented by nuclear magnetic resonance approaches for probing structural features of PKR activation. Considerations required for both PKR and dsRNA sample preparation are also discussed.
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Affiliation(s)
- Sean A McKenna
- Department of Structural Biology, Stanford University School of Medicine, Stanford, California, USA
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79
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Mittelstadt M, Frump A, Khuu T, Fowlkes V, Handy I, Patel CV, Patel RC. Interaction of human tRNA-dihydrouridine synthase-2 with interferon-induced protein kinase PKR. Nucleic Acids Res 2007; 36:998-1008. [PMID: 18096616 PMCID: PMC2241914 DOI: 10.1093/nar/gkm1129] [Citation(s) in RCA: 33] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023] Open
Abstract
PKR is an interferon (IFN)-induced protein kinase, which is involved in regulation of antiviral innate immunity, stress signaling, cell proliferation and programmed cell death. Although a low amount of PKR is expressed ubiquitously in all cell types in the absence of IFNs, PKR expression is induced at transcriptional level by IFN. PKR's enzymatic activity is activated by its binding to one of its activators. Double-stranded (ds) RNA, protein activator PACT and heparin are the three known activators of PKR. Activation of PKR in cells leads to a general block in protein synthesis due to phosphorylation of eIF2α on serine 51 by PKR. PKR activation is regulated very tightly in mammalian cells and a prolonged activation of PKR leads to apoptosis. Thus, positive and negative regulation of PKR activation is important for cell viability and function. The studies presented here describe human dihydrouridine synthase-2 (hDUS2) as a novel regulator of PKR. We originally identified hDUS2 as a protein interacting with PACT in a yeast two-hybrid screen. Further characterization revealed that hDUS2 also interacts with PKR through its dsRNA binding/dimerization domain and inhibits its kinase activity. Our results suggest that hDUS2 may act as a novel inhibitor of PKR in cells.
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Affiliation(s)
- Megan Mittelstadt
- Department of Biological Sciences, University of South Carolina Columbia, SC 29208, USA
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80
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Abstract
Virus-infection of mammalian cells causes transcriptional induction of many cellular genes, collectively called as "viral stress-inducible genes." The proteins encoded by these genes are essential to maintain cell-virus homeostasis, which is required for both virus replication and host survival. Many viral products, including RNA, DNA, and proteins, can induce these genes by using distinct, but partially overlapping, signaling pathways. Type I interferons, direct products of virus infection, can also induce many of these genes, thus providing a positive feedback loop. Double-stranded RNA, a common by-product of virus replication, can induce them by multiple signaling pathways initiated by Toll-like receptor 3 or RIG-I/Mda-5. Several viral stress-inducible proteins inhibit protein synthesis. Proteins of the P56 family bind to the translation initiation factor, eIF-3, and block translation initiation. PKR, a protein kinase, phosphorylates a different initiation factor, eIF-2, and inhibits translation initiation. However, unlike P56, PKR needs to be first activated by dsRNA or PACT, another cellular protein. Another family of enzymes, the 2'-5' oligoadenylate synthetases, synthesizes 2'-5' linked oligoadenylates [2-5(A)] in the presence of dsRNA; 2-5(A) activates the latent ribonuclease, RNase L, which degrades mRNA. Many viruses have evolved mechanisms to evade these genes by blocking their induction or actions; often more than one strategy is used by the same virus to achieve this goal. Thus, in an infected cell, equilibrium is reached between the virus and the cell with regards to the viral stress-inducible genes.
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Affiliation(s)
- Ganes C Sen
- Department of Molecular Genetics, The Lerner Research Institute, Cleveland Clinic Foundation, Cleveland, Ohio 44195, USA
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81
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Lunde BM, Moore C, Varani G. RNA-binding proteins: modular design for efficient function. Nat Rev Mol Cell Biol 2007; 8:479-90. [PMID: 17473849 PMCID: PMC5507177 DOI: 10.1038/nrm2178] [Citation(s) in RCA: 907] [Impact Index Per Article: 53.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
Many RNA-binding proteins have modular structures and are composed of multiple repeats of just a few basic domains that are arranged in various ways to satisfy their diverse functional requirements. Recent studies have investigated how different modules cooperate in regulating the RNA-binding specificity and the biological activity of these proteins. They have also investigated how multiple modules cooperate with enzymatic domains to regulate the catalytic activity of enzymes that act on RNA. These studies have shown how, for many RNA-binding proteins, multiple modules define the fundamental structural unit that is responsible for biological function.
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Affiliation(s)
- Bradley M Lunde
- Department of Biochemistry, University of Washington, Seattle, Washington 98195, USA
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82
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Kalai M, Suin V, Festjens N, Meeus A, Bernis A, Wang XM, Saelens X, Vandenabeele P. The caspase-generated fragments of PKR cooperate to activate full-length PKR and inhibit translation. Cell Death Differ 2007; 14:1050-9. [PMID: 17318221 DOI: 10.1038/sj.cdd.4402110] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022] Open
Abstract
We have studied the involvement of receptor interacting protein kinase-1 (RIP1) and dsRNA-activated protein kinase (PKR) in external dsRNA-induced apoptotic and necrotic cell death in Jurkat T cell lymphoma. Our results suggest that RIP1 plays an imported role in dsRNA-induced apoptosis and necrosis. We demonstrated that contrary to necrosis, protein synthesis is inhibited in apoptosis. Here, we show that phosphorylation of translation initiation factor 2-alpha (eukaryotic initiation factor 2-alpha (eIF2-alpha)) and its kinase, PKR, occur in dsRNA-induced apoptosis but not in necrosis. These events are caspase-dependent and coincide with the appearance of the caspase-mediated PKR fragments, N-terminal domain (ND) and kinase domain (KD). Our immunoprecipitation experiments demonstrated that both fragments could independently co-precipitate with full-length PKR. Expression of PKR-KD leads to PKR and eIF2-alpha phosphorylation and inhibits protein translation, whereas that of PKR-ND does not. Co-expression of PKR-ND and PKR-KD promotes their interaction with PKR, PKR and eIF2-alpha phosphorylation and suppresses protein translation better than PKR-KD alone. Our findings suggest a caspase-dependent mode of activation of PKR in apoptosis in which the PKR-KD fragment interacts with and activates intact PKR. PKR-ND facilitates the interaction of PKR-KD with full-length PKR and thus the activation of the kinase and amplifies the translation inhibitory signal.
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Affiliation(s)
- M Kalai
- Laboratory of Cellular Microbiology, Pasteur Institute, Rue Engeland, Brussels, Belgium.
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83
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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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84
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McKenna SA, Lindhout DA, Kim I, Liu CW, Gelev VM, Wagner G, Puglisi JD. Molecular framework for the activation of RNA-dependent protein kinase. J Biol Chem 2007; 282:11474-86. [PMID: 17284445 DOI: 10.1074/jbc.m700301200] [Citation(s) in RCA: 46] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
The RNA-dependent protein kinase (PKR) plays an integral role in the antiviral response to cellular infection. PKR contains three distinct domains consisting of two conserved N-terminal double-stranded RNA (dsRNA)-binding domains, a C-terminal Ser-Thr kinase domain, and a central 80-residue linker. Despite rich structural and biochemical data, a detailed mechanistic explanation of PKR activation remains unclear. Here we provide a framework for understanding dsRNA-dependent activation of PKR using nuclear magnetic resonance spectroscopy, dynamic light scattering, gel filtration, and autophosphorylation kinetics. In the latent state, PKR exists as an extended monomer, with an increase in self-affinity upon dsRNA association. Subsequent phosphorylation leads to efficient release of dsRNA followed by a greater increase in self-affinity. Activated PKR displays extensive conformational perturbations within the kinase domain. We propose an updated model for PKR activation in which the communication between RNA binding, central linker, and kinase domains is critical in the propagation of the activation signal and for PKR dimerization.
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Affiliation(s)
- Sean A McKenna
- Department of Structural Biology and Stanford Magnetic Resonance Laboratory, Stanford University School of Medicine, Stanford, California 94305-5126, USA
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85
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Cole JL. Activation of PKR: an open and shut case? Trends Biochem Sci 2006; 32:57-62. [PMID: 17196820 PMCID: PMC2703476 DOI: 10.1016/j.tibs.2006.12.003] [Citation(s) in RCA: 115] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2006] [Revised: 11/16/2006] [Accepted: 12/18/2006] [Indexed: 11/15/2022]
Abstract
The double-stranded (ds) RNA-activated protein kinase, PKR, has a key role in the innate immunity response to viral infection in higher eukaryotes. PKR contains an N-terminal dsRNA-binding domain and a C-terminal kinase domain. In the prevalent autoinhibition model for PKR activation, dsRNA binding induces a conformational change that leads to the release of the dsRNA-binding domain from the kinase, thus relieving the inhibition of the latent enzyme. Structural and biophysical data now favor a model whereby dsRNA principally functions to induce dimerization of PKR via the kinase domain. This dimerization model has implications for other PKR regulatory mechanisms and represents a new structural paradigm for control of protein kinase activity.
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Affiliation(s)
- James L Cole
- Department of Molecular and Cell Biology, 91 N. Eagleville Road, U-3125 University of Connecticut, Storrs, CT 06269, USA.
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86
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Swayze EE, Siwkowski AM, Wancewicz EV, Migawa MT, Wyrzykiewicz TK, Hung G, Monia BP, Bennett CF. Antisense oligonucleotides containing locked nucleic acid improve potency but cause significant hepatotoxicity in animals. Nucleic Acids Res 2006; 35:687-700. [PMID: 17182632 PMCID: PMC1802611 DOI: 10.1093/nar/gkl1071] [Citation(s) in RCA: 310] [Impact Index Per Article: 17.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022] Open
Abstract
A series of antisense oligonucleotides (ASOs) containing either 2′-O-methoxyethylribose (MOE) or locked nucleic acid (LNA) modifications were designed to investigate whether LNA antisense oligonucleotides (ASOs) have the potential to improve upon MOE based ASO therapeutics. Some, but not all, LNA containing oligonucleotides increased potency for reducing target mRNA in mouse liver up to 5-fold relative to the corresponding MOE containing ASOs. However, they also showed profound hepatotoxicity as measured by serum transaminases, organ weights and body weights. This toxicity was evident for multiple sequences targeting three different biological targets, as well as in mismatch control sequences having no known mRNA targets. Histopathological evaluation of tissues from LNA treated animals confirmed the hepatocellular involvement. Toxicity was observed as early as 4 days after a single administration. In contrast, the corresponding MOE ASOs showed no evidence for toxicity while maintaining the ability to reduce target mRNA. These studies suggest that while LNA ASOs have the potential to improve potency, they impose a significant risk of hepatotoxicity.
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Affiliation(s)
- Eric E Swayze
- Isis Pharmaceuticals, Inc., 1896 Rutherford Road, Carlsbad, CA 92008, USA.
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87
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Ucci JW, Kobayashi Y, Choi G, Alexandrescu AT, Cole JL. Mechanism of Interaction of the Double-Stranded RNA (dsRNA) Binding Domain of Protein Kinase R with Short dsRNA Sequences. Biochemistry 2006; 46:55-65. [PMID: 17198375 DOI: 10.1021/bi061531o] [Citation(s) in RCA: 39] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
The dsRNA-activated protein kinase (PKR) plays a major role in the cellular response to viral infection. PKR contains an N-terminal dsRNA binding domain (dsRBD) and a C-terminal kinase domain. The dsRBD consists of two tandem copies of a conserved double-stranded RNA binding motif, dsRBM1 and dsRBM2. dsRNA binding is believed to activate PKR by inducing dimerization and subsequent autophosphorylation reactions. We have characterized the function of the dsRBD by assessing the binding of dsRBM1 and dsRBD to a series of dsRNA sequences ranging from 15 to 45 bp. For dsRBM1, the binding stoichiometries agree with an overlapping ligand binding model where the motif binds to multiple faces of the dsRNA duplex and overlaps along the helical axis. Similar behavior is observed for a dsRBD containing both dsRBM1 and dsRBM2 for sequences up to 30 bp; however, the binding affinity is enhanced 30-fold. Longer dsRNA sequences exhibit lower-than-expected stoichiometries, indicating a change in binding mode. NMR spectroscopy was used to define the regions of the dsRBD that interact with dsRNA. dsRNA binding induces exchange broadening of cross-peaks in 1H-15N HSQC spectra. For a 20 bp dsRNA, the resonances most affected map to the known dsRNA binding regions of dsRBM1 as well as the N-terminus of dsRBM2. For a longer 40 bp sequence, additional regions of dsRBM2 exhibit enhanced broadening. These data support a model in which dsRBM1 plays the dominant role in binding short dsRNA sequences and dsRBM2 makes additional interactions with the longer sequences capable of activating PKR.
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Affiliation(s)
- Jason W Ucci
- Department of Molecular and Cell Biology and National Analytical Ultracentrifugation Facility, University of Connecticut, Storrs, Connecticut 06269-3125, USA
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88
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Edwards MR, Hewson CA, Laza-Stanca V, Lau HTH, Mukaida N, Hershenson MB, Johnston SL. Protein kinase R, IkappaB kinase-beta and NF-kappaB are required for human rhinovirus induced pro-inflammatory cytokine production in bronchial epithelial cells. Mol Immunol 2006; 44:1587-97. [PMID: 16989899 DOI: 10.1016/j.molimm.2006.08.014] [Citation(s) in RCA: 29] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2006] [Accepted: 08/11/2006] [Indexed: 10/24/2022]
Abstract
Rhinovirus infections cause the majority of acute exacerbations of airway diseases such as asthma and chronic obstructive pulmonary disease, with increased pro-inflammatory cytokine production by infected bronchial epithelial cells contributing to disease pathogenesis. Theses diseases are a huge cause of morbidity worldwide, and contribute a major economic burden to healthcare costs. Current steroid based treatments are only partially efficient at controlling virus induced inflammation, which remains an unmet therapeutic goal. Although NF-kappaB has been implicated, the precise mechanisms of rhinovirus induction of pro-inflammatory gene expression in bronchial epithelial cells are unclear. We hypothesised that rhinovirus replication and generation of dsRNA was an important process of pro-inflammatory cytokine induction. Using pharmalogical (2-aminopurine and a new small molecule inhibitor) and genetic inhibition of the dsRNA binding kinase protein kinase R, striking inhibition of dsRNA (polyrIC) and rhinovirus induced CCL5, CXCL8 and IL-6 protein was observed. Using confocal microscopy, rhinovirus induced protein kinase R phosphorylation co-located with NF-kappaB p65 nuclear translocation. Focusing on CXCL8, both rhinovirus infection and dsRNA treatment required IkappaB kinase-beta for induction of CXCL8. Analysis of cis-acting sites in the CXCL8 promoter revealed that both rhinovirus infection and dsRNA treatment upregulated CXCL8 promoter activation via NF-kappaB and NF-IL6 binding sites. Together, the results demonstrate the importance of dsRNA in induction of pro-inflammatory cytokines by rhinoviruses, and suggest that protein kinase R is involved in NF-kappaB mediated gene transcription of pro-inflammatory cytokines via IkappaB kinase-beta. These molecules regulating rhinovirus induction of inflammation represent therapeutic targets.
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Affiliation(s)
- Michael R Edwards
- Department of Respiratory Medicine, National Heart Lung Institute and Wright Fleming Institute of Infection and Immunity, Imperial College London, Norfolk Place, London W2 1PG, UK.
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89
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Puthenveetil S, Whitby L, Ren J, Kelnar K, Krebs JF, Beal PA. Controlling activation of the RNA-dependent protein kinase by siRNAs using site-specific chemical modification. Nucleic Acids Res 2006; 34:4900-11. [PMID: 16982647 PMCID: PMC1635244 DOI: 10.1093/nar/gkl464] [Citation(s) in RCA: 59] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022] Open
Abstract
The RNA-dependent protein kinase (PKR) is activated by binding to double-stranded RNA (dsRNA). Activation of PKR by short-interfering RNAs (siRNAs) and stimulation of the innate immune response has been suggested to explain certain off-target effects in some RNA interference experiments. Here we show that PKR's kinase activity is stimulated in vitro 3- to 5-fold by siRNA duplexes with 19 bp and 2 nt 3′-overhangs, whereas the maximum activation observed for poly(I)•poly(C) was 17-fold over background under the same conditions. Directed hydroxyl radical cleavage experiments indicated that siRNA duplexes have at least four different binding sites for PKR's dsRNA binding motifs (dsRBMs). The location of these binding sites suggested specific nucleotide positions in the siRNA sense strand that could be modified with a corresponding loss of PKR binding. Modification at these sites with N2-benzyl-2′-deoxyguanosine (BndG) blocked interaction with PKR's dsRBMs and inhibited activation of PKR by the siRNA. Importantly, modification of an siRNA duplex that greatly reduced PKR activation did not prevent the duplex from lowering mRNA levels of a targeted message by RNA interference in HeLa cells. Thus, these studies demonstrate that specific positions in an siRNA can be rationally modified to prevent interaction with components of cellular dsRNA-regulated pathways.
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Affiliation(s)
| | | | | | - Kevin Kelnar
- Ambion, Inc.2130 Woodward, Austin, TX 78744, USA
| | | | - Peter A. Beal
- To whom correspondence should be addressed. Fax: +1 801 581 8433;
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90
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Lemaire PA, Tessmer I, Craig R, Erie DA, Cole JL. Unactivated PKR exists in an open conformation capable of binding nucleotides. Biochemistry 2006; 45:9074-84. [PMID: 16866353 PMCID: PMC2913708 DOI: 10.1021/bi060567d] [Citation(s) in RCA: 35] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/01/2023]
Abstract
The dsRNA-activated protein kinase, PKR, plays a pivotal role in the cellular antiviral response. PKR contains an N-terminal dsRNA binding domain (dsRBD) and a C-terminal kinase domain. An autoinhibition model has been proposed in which latent PKR exists in a closed conformation where the substrate binding cleft of the kinase is blocked by the dsRBD. Binding to dsRNA activates the enzyme by inducing an open conformation and enhancing dimerization. We have tested this model by characterizing the affinity and kinetics of binding of a nucleotide substrate to PKR. The fluorescent nucleotide mant-AMPPNP binds to unactivated PKR with a Kd of approximately 30 microM, and the affinity is not strongly affected by autophosphorylation or binding to dsRNA. We observe biphasic binding kinetics in which the fast phase depends on ligand concentration but the slow phase is ligand-independent. The kinetic data fit to a two-step model of ligand binding followed by a slow conformation change. The kinetics are also not strongly affected by phosphorylation state or dsRNA binding. Thus, the equilibrium and kinetic data indicate that the substrate accessibility of the kinase is not modulated by PKR activation state as predicted by the autoinhibition model. In atomic force microscopy images, monomers of the latent protein are resolved with three separate regions linked by flexible, bridgelike structures. The resolution of the individual domains in the images supports a model in which unactivated PKR exists in an open conformation where the kinase domain is accessible and capable of binding substrate.
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Affiliation(s)
- Peter A. Lemaire
- Department of Molecular and Cell Biology, University of Connecticut, Storrs, Connecticut 06269-3125
| | - Ingrid Tessmer
- Department of Chemistry and Curriculum in Materials and Applied Sciences, University of North Carolina, Chapel Hill, North Carolina 27599-3290
| | - Ranyelle Craig
- Department of Molecular and Cell Biology, University of Connecticut, Storrs, Connecticut 06269-3125
| | - Dorothy A. Erie
- Department of Chemistry and Curriculum in Materials and Applied Sciences, University of North Carolina, Chapel Hill, North Carolina 27599-3290
| | - James L. Cole
- Department of Molecular and Cell Biology, University of Connecticut, Storrs, Connecticut 06269-3125
- National Analytical Ultracentrifugation Facility, University of Connecticut, Storrs, Connecticut 06269-3125
- To whom correspondence may be addressed: (860) 486-4333 (telephone),
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91
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Gelev V, Aktas H, Marintchev A, Ito T, Frueh D, Hemond M, Rovnyak D, Debus M, Hyberts S, Usheva A, Halperin J, Wagner G. Mapping of the auto-inhibitory interactions of protein kinase R by nuclear magnetic resonance. J Mol Biol 2006; 364:352-63. [PMID: 17011579 PMCID: PMC3622519 DOI: 10.1016/j.jmb.2006.08.077] [Citation(s) in RCA: 29] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2006] [Revised: 08/24/2006] [Accepted: 08/28/2006] [Indexed: 11/23/2022]
Abstract
The dsRNA-dependent protein kinase (PKR) is a key mediator of the anti-viral and anti-proliferative effects of interferon. Unphosphorylated PKR is characterized by inhibitory interactions between the kinase and RNA binding domains (RBDs), but the structural details of the latent state and its unraveling during activation are not well understood. To study PKR regulation by NMR we assigned a large portion of the backbone resonances of the catalytically inactive K296R kinase domain, and performed (15)N-heteronuclear single quantum coherence (HSQC) titrations of this kinase domain with the RBDs. Chemical shift perturbations in the kinase indicate that RBD2 binds to the substrate eIF2alpha docking site in the kinase C-lobe. Consistent with these results, a mutation in the eIF2alpha docking site, F495A, displays weaker interactions with the RBD. The full-length RBD1+2 binds more strongly to the kinase domain than RBD2 alone. The observed chemical shift changes extend from the eIF2alpha binding site into the kinase N-lobe and inside the active site, consistent with weak interactions between the N-terminal part of the RBD and the kinase.
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Affiliation(s)
- Vladimir Gelev
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, 240 Longwood Ave, Boston, MA 02115
| | - Husseyin Aktas
- Laboratory for Membrane Transport, Harvard Medical School, 1 Kendall Square, Cambridge, MA 02139
| | - Assen Marintchev
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, 240 Longwood Ave, Boston, MA 02115
| | - Takuhiro Ito
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, 240 Longwood Ave, Boston, MA 02115
| | - Dominique Frueh
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, 240 Longwood Ave, Boston, MA 02115
| | - Michael Hemond
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, 240 Longwood Ave, Boston, MA 02115
| | - David Rovnyak
- Chemistry Department, Bucknell University, Lewisburg, PA 17837
| | - Miriam Debus
- Laboratory for Membrane Transport, Harvard Medical School, 1 Kendall Square, Cambridge, MA 02139
| | - Sven Hyberts
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, 240 Longwood Ave, Boston, MA 02115
| | - Anny Usheva
- Department of Medicine, Beth Israel Deaconnes Medical Center, 99 Brookline Ave, Boston, MA 02215
| | - Jose Halperin
- Laboratory for Membrane Transport, Harvard Medical School, 1 Kendall Square, Cambridge, MA 02139
| | - Gerhard Wagner
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, 240 Longwood Ave, Boston, MA 02115
- *Address correspondence to
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92
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Poulsen H, Jorgensen R, Heding A, Nielsen FC, Bonven B, Egebjerg J. Dimerization of ADAR2 is mediated by the double-stranded RNA binding domain. RNA (NEW YORK, N.Y.) 2006; 12:1350-60. [PMID: 16682559 PMCID: PMC1484439 DOI: 10.1261/rna.2314406] [Citation(s) in RCA: 49] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/09/2023]
Abstract
Members of the family of adenosine deaminases acting on RNA (ADARs) can catalyze the hydrolytic deamination of adenosine to inosine and thereby change the sequence of specific mRNAs with highly double-stranded structures. The ADARs all contain one or more repeats of the double-stranded RNA binding motif (DRBM). By both in vitro and in vivo assays, we show that the DRBMs of rat ADAR2 are necessary and sufficient for dimerization of the enzyme. Bioluminescence resonance energy transfer (BRET) demonstrates that ADAR2 also exists as dimers in living mammalian cells and that mutation of DRBM1 lowers the dimerization affinity while mutation of DRBM2 does not. Nonetheless, the editing efficiency of the GluR2 Q/R site depends on a functional DRBM2. The ADAR2 DRBMs thus serve differential roles in RNA dimerization and GluR2 Q/R editing, and we propose a model for RNA editing that incorporates the new findings.
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Affiliation(s)
- Hanne Poulsen
- Department of Molecular Biology, University of Aarhus, Denmark.
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93
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Li S, Peters GA, Ding K, Zhang X, Qin J, Sen GC. Molecular basis for PKR activation by PACT or dsRNA. Proc Natl Acad Sci U S A 2006; 103:10005-10. [PMID: 16785445 PMCID: PMC1502496 DOI: 10.1073/pnas.0602317103] [Citation(s) in RCA: 95] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/12/2023] Open
Abstract
The mammalian protein kinase PKR is a critical component of the innate immune response against virus infection. Its cellular actions are mediated by modulating cell signaling and translational regulation. To be enzymatically active, latent PKR needs to be activated by binding to one of its activators, dsRNA or PACT protein. Although the structures of the N-terminal dsRNA-binding domain and the C-terminal kinase domain of PKR have been separately determined, the mode of activation of the enzyme remains unknown. To address this problem, we used biochemical, genetic, and NMR analyses to identify the PACT-binding motif (PBM) located in the kinase domain and demonstrated an intramolecular interaction between PBM and dsRNA-binding domain. This interaction is responsible for keeping PKR in an inactive conformation, because its disruption by point mutations of appropriate residues produced constitutively active PKR. Furthermore, a short decoy peptide, representing PBM, was able to activate PKR by interfering with the intramolecular interaction. These observations suggest a model for PKR activation upon binding of dsRNA or PACT.
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Affiliation(s)
- Shoudong Li
- *Department of Molecular Genetics and
- Graduate Program in Molecular Virology, School of Medicine, Case Western Reserve University, Cleveland, OH 44106
| | | | - Keyang Ding
- Structural Biology Program and Department of Molecular Cardiology, Lerner Research Institute, Cleveland Clinic Foundation, Cleveland, OH 44195; and
| | - Xiaolun Zhang
- Structural Biology Program and Department of Molecular Cardiology, Lerner Research Institute, Cleveland Clinic Foundation, Cleveland, OH 44195; and
| | - Jun Qin
- Structural Biology Program and Department of Molecular Cardiology, Lerner Research Institute, Cleveland Clinic Foundation, Cleveland, OH 44195; and
| | - Ganes C. Sen
- *Department of Molecular Genetics and
- Graduate Program in Molecular Virology, School of Medicine, Case Western Reserve University, Cleveland, OH 44106
- To whom correspondence should be addressed at:
Department of Molecular Genetics/NE20, Lerner Research Institute, Cleveland Clinic Foundation, 9500 Euclid Avenue, Cleveland, OH 44195. E-mail:
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94
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Langland JO, Cameron JM, Heck MC, Jancovich JK, Jacobs BL. Inhibition of PKR by RNA and DNA viruses. Virus Res 2006; 119:100-10. [PMID: 16704884 DOI: 10.1016/j.virusres.2005.10.014] [Citation(s) in RCA: 164] [Impact Index Per Article: 9.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2005] [Revised: 09/28/2005] [Accepted: 10/20/2005] [Indexed: 11/28/2022]
Abstract
Interferons were the first of the anti-viral innate immune modulators to be characterized, initially characterized solely as anti-viral proteins [reviewed in Le Page, C., Genin, P., Baines, M.G., Hiscott, J., 2000. Inteferon activation and innate immunity. Rev. Immunogenet. 2, 374-386]. As we have progressed in our understanding of the interferons they have taken a more central role in our understanding of innate immunity and its interplay with the adaptive immune response. One of the key players in function of interferon is the interferon-inducible enzyme, protein kinase (PKR, activatable by RNA). The key role played by PKR in the innate response to virus infection is emphasized by the large number of viruses, DNA viruses as well as RNA viruses, whose hosts range from insects to humans, that code for PKR inhibitors. In this review we will first describe activation of PKR and then describe the myriad of ways that viruses inhibit function of PKR.
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Affiliation(s)
- Jeffrey O Langland
- Center for Infectious Disease and Vaccinology, The Biodesign Institute, Arizona State University, Tempe, AZ 85287-5401, USA
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95
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McKenna SA, Kim I, Liu CW, Puglisi JD. Uncoupling of RNA binding and PKR kinase activation by viral inhibitor RNAs. J Mol Biol 2006; 358:1270-85. [PMID: 16580685 DOI: 10.1016/j.jmb.2006.03.003] [Citation(s) in RCA: 54] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2006] [Revised: 03/01/2006] [Accepted: 03/01/2006] [Indexed: 11/23/2022]
Abstract
Protein kinase RNA-activated (PKR) is a serine/threonine kinase that contains an N-terminal RNA-binding domain and a C-terminal kinase domain. Upon binding double-stranded RNA (dsRNA), PKR can become activated and phosphorylate cellular targets, such as eukaryotic translation initiation factor 2alpha (eIF-2alpha). Phosphorylation of eIF-2alpha results in attenuation of protein translation by the ribosome in either a general or an mRNA-specific manner. Therefore, the interaction between PKR and dsRNAs represents a crucial host cell defense mechanism against viral infection. Viruses can circumvent PKR function by transcription of virus-encoded dsRNA inhibitors that bind to and inactivate PKR. We present here a biophysical characterization of the interactions between human PKR and two viral inhibitor RNAs, EBER(I) (from Epstein-Barr virus) and VA(I) (from human adenovirus). Autophosphorylation assays confirmed that both EBER(I) and VA(I) are inhibitors of PKR activation, and profiled the kinetics of the inhibition. Binding affinities of dsRNAs to PKR double-stranded RNA-binding domains (dsRBDs) were determined by isothermal titration calorimetry and gel electrophoresis. A single stem-loop domain from each inhibitory RNA mediates the interaction with both dsRBDs of PKR. The binding sites on inhibitor RNAs and the dsRBDs of PKR have been mapped by NMR chemical shift perturbation experiments, which indicate that inhibitors of PKR employ similar surfaces of interaction as activators. Finally, we show that dsRNA binding and inactivation are non-equivalent; regions other than the dsRBD stem-loops of inhibitory RNA are required for inhibition.
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MESH Headings
- Adenoviruses, Human/genetics
- Adenoviruses, Human/metabolism
- Base Sequence
- Binding Sites
- Biophysical Phenomena
- Biophysics
- Enzyme Activation
- Herpesvirus 4, Human/genetics
- Herpesvirus 4, Human/metabolism
- Humans
- In Vitro Techniques
- Models, Molecular
- Molecular Sequence Data
- Nuclear Magnetic Resonance, Biomolecular
- Nucleic Acid Conformation
- RNA, Catalytic/chemistry
- RNA, Catalytic/genetics
- RNA, Catalytic/metabolism
- RNA, Double-Stranded/chemistry
- RNA, Double-Stranded/genetics
- RNA, Double-Stranded/metabolism
- RNA, Viral/chemistry
- RNA, Viral/genetics
- RNA, Viral/metabolism
- Recombinant Proteins/antagonists & inhibitors
- Recombinant Proteins/chemistry
- Recombinant Proteins/genetics
- Recombinant Proteins/metabolism
- eIF-2 Kinase/antagonists & inhibitors
- eIF-2 Kinase/chemistry
- eIF-2 Kinase/genetics
- eIF-2 Kinase/metabolism
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Affiliation(s)
- Sean A McKenna
- Department of Structural Biology, Stanford University School of Medicine, Stanford, CA 94305-5126, USA
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96
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Li S, Min JY, Krug RM, Sen GC. Binding of the influenza A virus NS1 protein to PKR mediates the inhibition of its activation by either PACT or double-stranded RNA. Virology 2006; 349:13-21. [PMID: 16466763 DOI: 10.1016/j.virol.2006.01.005] [Citation(s) in RCA: 265] [Impact Index Per Article: 14.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2005] [Revised: 10/07/2005] [Accepted: 01/04/2006] [Indexed: 10/25/2022]
Abstract
A major component of the cellular antiviral system is the latent protein kinase PKR, which is activated by binding to either double-stranded RNA (dsRNA) or the cellular PACT protein. Activated PKR phosphorylates the translation initiation factor eIF2, thereby inhibiting viral and cellular protein synthesis and virus replication. To evade the antiviral effects of PKR, many viruses, including influenza A virus, have evolved multiple mechanisms. For influenza A virus, the non-structural (NS1A) protein plays a major role in blocking activation of PKR during virus infection. The mechanism by which the NS1A protein inhibits PKR activation in infected cells has not been established. In the present study, we first carried out a series of in vitro experiments to determine whether the NS1A protein could utilize a common mechanism to inhibit PKR activation by both PACT and dsRNA, despite their different modes of activation. We demonstrated that the direct binding of the NS1A protein to the N-terminal 230 amino acid region of PKR can serve as such a common mechanism and that this binding does not require the RNA-binding activity of the NS1A protein. The lack of requirement for NS1A RNA-binding activity for the inhibition of PKR activation in vivo was established by two approaches. First, we showed that an NS1A protein lacking RNA-binding activity, like the wild-type (wt) protein, blocked PKR activation by PACT in vivo, as well as the downstream effects of PKR activation in cells, namely, eIF2 phosphorylation and apoptosis. In addition, we demonstrated that PKR activation is inhibited in cells infected with a recombinant influenza A virus expressing NS1A mutant protein that cannot bind RNA, as is the case in cells infected with wild-type influenza A virus.
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Affiliation(s)
- Shoudong Li
- Department of Molecular Genetics, Lerner Research Institute, Cleveland Clinic Foundation, Cleveland, OH 44195, USA
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97
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Su Q, Wang S, Baltzis D, Qu LK, Wong AHT, Koromilas AE. Tyrosine phosphorylation acts as a molecular switch to full-scale activation of the eIF2alpha RNA-dependent protein kinase. Proc Natl Acad Sci U S A 2005; 103:63-8. [PMID: 16373505 PMCID: PMC1324992 DOI: 10.1073/pnas.0508207103] [Citation(s) in RCA: 60] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022] Open
Abstract
Phosphorylation of the alpha-subunit of translation eukaryotic initiation factor-2 (eIF2) leads to the inhibition of protein synthesis in response to diverse conditions of stress. Serine/threonine RNA-dependent protein kinase (PKR) is an eIF2alpha kinase family member induced by type I IFN and activated in response to dsRNA or virus infection. Herein, we demonstrate that human PKR is a dual specificity kinase phosphorylated at Y101, Y162 and Y293 in vitro and in vivo. Site-specific tyrosine phosphorylation is essential for efficient dsRNA-binding, dimerization, kinase activation and eIF2alpha phosphorylation of PKR. Biologically, tyrosine phosphorylation of PKR mediates the antiviral and antiproliferative properties of the kinase through its ability to control translation. Our data demonstrate an important role of tyrosine phosphorylation in biochemical and biological processes caused or mediated by the activation of the eIF2alpha kinase PKR.
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Affiliation(s)
- Qiaozhu Su
- Lady Davis Institute for Medical Research, McGiIl University, Sir Mortimer B. Davis Jewish General Hospital, Montreal, QC, Canada H3T 1E2
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98
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Dar AC, Dever TE, Sicheri F. Higher-order substrate recognition of eIF2alpha by the RNA-dependent protein kinase PKR. Cell 2005; 122:887-900. [PMID: 16179258 DOI: 10.1016/j.cell.2005.06.044] [Citation(s) in RCA: 292] [Impact Index Per Article: 15.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2005] [Revised: 05/03/2005] [Accepted: 06/28/2005] [Indexed: 11/18/2022]
Abstract
In response to binding viral double-stranded RNA byproducts within a cell, the RNA-dependent protein kinase PKR phosphorylates the alpha subunit of the translation initiation factor eIF2 on a regulatory site, Ser51. This triggers the general shutdown of protein synthesis and inhibition of viral propagation. To understand the basis for substrate recognition by and the regulation of PKR, we determined X-ray crystal structures of the catalytic domain of PKR in complex with eIF2alpha. The structures reveal that eIF2alpha binds to the C-terminal catalytic lobe while catalytic-domain dimerization is mediated by the N-terminal lobe. In addition to inducing a local unfolding of the Ser51 acceptor site in eIF2alpha, its mode of binding to PKR affords the Ser51 site full access to the catalytic cleft of PKR. The generality and implications of the structural mechanisms uncovered for PKR to the larger family of four human eIF2alpha protein kinases are discussed.
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Affiliation(s)
- Arvin C Dar
- Program in Molecular Biology and Cancer, Samuel Lunenfeld Research Institute, Mount Sinai Hospital, 600 University Avenue, Toronto, Ontario M5G 1X5, Canada
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99
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Dey M, Cao C, Dar AC, Tamura T, Ozato K, Sicheri F, Dever TE. Mechanistic link between PKR dimerization, autophosphorylation, and eIF2alpha substrate recognition. Cell 2005; 122:901-13. [PMID: 16179259 DOI: 10.1016/j.cell.2005.06.041] [Citation(s) in RCA: 270] [Impact Index Per Article: 14.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2005] [Revised: 05/05/2005] [Accepted: 06/29/2005] [Indexed: 01/27/2023]
Abstract
The antiviral protein kinase PKR inhibits protein synthesis by phosphorylating the translation initiation factor eIF2alpha on Ser51. Binding of double-stranded RNA to the regulatory domains of PKR promotes dimerization, autophosphorylation, and the functional activation of the kinase. Herein, we identify mutations that activate PKR in the absence of its regulatory domains and map the mutations to a recently identified dimerization surface on the kinase catalytic domain. Mutations of other residues on this surface block PKR autophosphorylation and eIF2alpha phosphorylation, while mutating Thr446, an autophosphorylation site within the catalytic-domain activation segment, impairs eIF2alpha phosphorylation and viral pseudosubstrate binding. Mutational analysis of catalytic-domain residues preferentially conserved in the eIF2alpha kinase family identifies helix alphaG as critical for the specific recognition of eIF2alpha. We propose an ordered mechanism of PKR activation in which catalytic-domain dimerization triggers Thr446 autophosphorylation and specific eIF2alpha substrate recognition.
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Affiliation(s)
- Madhusudan Dey
- Laboratory of Gene Regulation and Development, National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, Maryland 20892, USA
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100
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Barnwal RP, Chaudhuri TR, Nanduri S, Qin J, Chary KVR. Methyl dynamics for understanding hydrophobic core packing of dynamically different motifs of double-stranded RNA binding domain of protein kinase R. Proteins 2005; 62:501-8. [PMID: 16299777 DOI: 10.1002/prot.20793] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
Abstract
Double-stranded RNA binding domains of human protein kinase R (dsRBD-PKR) regulate distinct cellular functions and the fate of an RNA molecule in the cell. This highly homologous domains present in multiple copies in a number of species, exhibit individual and specific functional specificity. Number of NMR and X-ray crystallographic structural studies reveals that such domains take a common alpha-beta-beta-beta-alpha tertiary fold. However, the functional specificities of these domains could be due to the dynamics of the individual amino acid residues, as has been shown earlier in the case of backbone dynamics of 15N-1H of dsRNA binding motifs (dsRBMs) of human protein kinase R (PKR) (Nanduri S, Rahman F, Williams BRG, Qin J. EMBO J 2000;19:5567-5574). To further investigate if the differences in dynamics of the two dsRBMs are restricted to only backbone, or if the side-chain motions are also different to the extent of influencing their packing of the two hydrophobic cores, we have investigated the methyl group dynamics using 13C-methyl relaxation measurements. The results show that the hydrophobic core of dsRBM1 is more tightly packed than dsRBM2, and it seems to undergo less fast scale motions in the subnanosecond regime.
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Affiliation(s)
- Ravi P Barnwal
- Department of Chemical Sciences, Tata Institute of Fundamental Research, Colaba, Mumbai, India.
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