[en] Eukaryotic translation initiation factor 2 alpha kinase 2 (EIF2AK2), known as PKR, is a key antiviral kinase activated by double-stranded RNA (dsRNA) typically produced during viral replication. Upon activation, PKR phosphorylates eIF2α, leading to the inhibition of translation and viral replication. However, many viruses have evolved mechanisms to counteract PKR activity. In Cardioviruses, the leader protein (L), a short peptide cleaved from the N-terminus of the viral polyprotein, not only inhibits PKR but also blocks interferon production and disrupts nucleocytoplasmic trafficking (NCT). L disrupts NCT by recruiting host RSK kinases to the nuclear pore complex (NPC), where RSK phosphorylates FG-nucleoporins, thereby impairing NCT. L mutations that affect NCT disruption also impact PKR inhibition, suggesting a mechanistic link between NCT and PKR activity. Recombinant TMEV and EMCV viruses designed to disrupt NCT through different mechanisms exhibited some extent of PKR inhibition, supporting the link between NCT disruption and PKR inhibition. Immunostaining and live-cell imaging revealed that, during mitosis and after L-induced NCT disruption, a fraction of PKR maps to the nucleoli, where PKR remains inactive despite its recruitment by dsRNA-like structures. This suggests that nucleolar sequestration contributes to PKR inhibition. Additionally, L-mediated NCT disruption leads to the release of nuclear RNA-binding proteins (nRBPs) into the cytosol, which may bind or modify viral dsRNA, further preventing PKR activation. Collectively, these results highlight nucleocytoplasmic trafficking as a critical regulatory mechanism governing PKR activation. Thus, beyond the specific action of cardiovirus L protein, our study reveals that interference with host nucleocytoplasmic transport can significantly impact the subcellular localization and functional regulation of immune effectors such as PKR.
Disciplines :
Biochemistry, biophysics & molecular biology
Author, co-author :
Milcamps, Romane; Université catholique de Louvain, de Duve Institute, Brussels, Belgium
Lizcano-Perret, Belén; Université catholique de Louvain, de Duve Institute, Brussels, Belgium
Wavreil, Fanny; Université catholique de Louvain, de Duve Institute, Brussels, Belgium
Lebrun, Marielle ; Université de Liège - ULiège > Département des sciences de la vie > Virologie - Immunologie
Aloise, Chiara; Utrecht University, Section of Virology, Division of Infectious Diseases and Immunology, Department of Biomolecular Health Sciences, Faculty of Veterinary Medicine, Utrecht, the Netherlands
Vertommen, Didier; MASSPROT platform, de Duve Institute, Université Catholique de Louvain, Brussels, Belgium
Herinckx, Gaëtan; MASSPROT platform, de Duve Institute, Université Catholique de Louvain, Brussels, Belgium
van Kuppeveld, Frank J M; Utrecht University, Section of Virology, Division of Infectious Diseases and Immunology, Department of Biomolecular Health Sciences, Faculty of Veterinary Medicine, Utrecht, the Netherlands
Sadzot, Catherine ; Université de Liège - ULiège > GIGA > GIGA Immunobiology - Virology and Immunology
Michiels, Thomas ; Université catholique de Louvain, de Duve Institute, Brussels, Belgium
Language :
English
Title :
Cardiovirus-Mediated PKR inhibition results from nucleocytoplasmic trafficking disruption.
F.R.S.-FNRS - Fonds de la Recherche Scientifique FRIA - Fonds pour la Formation à la Recherche dans l'Industrie et dans l'Agriculture Loterie Nationale
Funding text :
RM was the recipient of an Aspirant fellowship from the Fonds de la recherche scientifique-FNRS and BLP was the recient of a FRIA fellowship. Work was supported by FNRS (PDR T.0154.23), EOS (EOS ID: 30981113 and 40007527), and Loterie Nationale through support to the de Duve Institute. The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript. We are grateful to Patrick Van Der Smissen for his long-standing help in confocal microscopy and Nicolas Dauguet for his expert assistance with cell sorting.Funding: RM was the recipient of an Aspirant fellowship from the Fonds de la recherche scientifique-FNRS and BLP was the recient of a FRIA fellowship. Work was supported by FNRS (PDR T.0154.23), EOS (EOS ID: 30981113 and 40007527), and Loterie Nationale through support to the de Duve Institute. The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript.
Pakos-Zebrucka K, Koryga I, Mnich K, Ljujic M, Samali A, Gorman AM. The integrated stress response. EMBO Rep. 2016;17(10):1374–95. https://doi.org/10.15252/embr.201642195 PMID: 27629041
Donnelly N, Gorman AM, Gupta S, Samali A. The eIF2α kinases: their structures and functions. Cell Mol Life Sci. 2013;70(19):3493–511. https://doi.org/10.1007/s00018-012-1252-6 PMID: 23354059
Wek RC, Jiang H-Y, Anthony TG. Coping with stress: eIF2 kinases and translational control. Biochem Soc Trans. 2006;34(Pt 1):7–11. https://doi.org/10.1042/BST20060007 PMID: 16246168
Cesaro T, Hayashi Y, Borghese F, Vertommen D, Wavreil F, Michiels T. PKR activity modulation by phosphomimetic mutations of serine residues located three aminoacids upstream of double-stranded RNA binding motifs. Sci Rep. 2021;11(1):9188. https://doi.org/10.1038/s41598-021-88610-z PMID: 33911136
García MA, Meurs EF, Esteban M. The dsRNA protein kinase PKR: virus and cell control. Biochimie. 2007;89(6–7):799–811. https://doi.org/10.1016/j.biochi.2007.03.001 PMID: 17451862
Dey M, Mann BR, Anshu A, Mannan MA. Activation of protein kinase PKR requires dimerization-induced cis-phosphorylation within the activation loop. J Biol Chem. 2014;289(9):5747–57. https://doi.org/10.1074/jbc.M113.527796 PMID: 24338483
Hoang H-D, Graber TE, Alain T. Battling for Ribosomes: Translational Control at the Forefront of the Antiviral Response. J Mol Biol. 2018;430(14):1965–92. https://doi.org/10.1016/j.jmb.2018.04.040 PMID: 29746850
Cesaro T, Michiels T. Inhibition of PKR by Viruses. Front Microbiol. 2021;12:757238. https://doi.org/10.3389/fmicb.2021.757238 PMID: 34759908
Rabouw HH, Langereis MA, Knaap RCM, Dalebout TJ, Canton J, Sola I, et al. Middle East Respiratory Coronavirus Accessory Protein 4a Inhibits PKR-Mediated Antiviral Stress Responses. PLoS Pathog. 2016;12(10):e1005982. https://doi.org/10.1371/journal.ppat.1005982 PMID: 27783669
Kitajewski J, Schneider RJ, Safer B, Munemitsu SM, Samuel CE, Thimmappaya B, et al. Adenovirus VAI RNA antagonizes the antiviral action of interferon by preventing activation of the interferon-induced eIF-2 alpha kinase. Cell. 1986;45(2):195–200. https://doi.org/10.1016/0092-8674 86 90383-1 PMID: 3698097
Nanbo A, Inoue K, Adachi-Takasawa K, Takada K. Epstein-Barr virus RNA confers resistance to interferon-alpha-induced apoptosis in Burkitt’s lymphoma. EMBO J. 2002;21(5):954–65. https://doi.org/10.1093/emboj/21.5.954 PMID: 11867523
Ziehr B, Vincent HA, Moorman NJ. Human Cytomegalovirus pTRS1 and pIRS1 Antagonize Protein Kinase R To Facilitate Virus Replication. J Virol. 2016;90(8):3839–48. https://doi.org/10.1128/JVI.02714-15 PMID: 26819306
Habjan M, Pichlmair A, Elliott RM, Overby AK, Glatter T, Gstaiger M, et al. NSs protein of rift valley fever virus induces the specific degradation of the double-stranded RNA-dependent protein kinase. J Virol. 2009;83(9):4365–75. https://doi.org/10.1128/JVI.02148-08 PMID: 19211744
Davies MV, Elroy-Stein O, Jagus R, Moss B, Kaufman RJ. The vaccinia virus K3L gene product potentiates translation by inhibiting double-stranded-RNA-activated protein kinase and phosphorylation of the alpha subunit of eukaryotic initiation factor 2. J Virol. 1992;66(4):1943–50. https://doi.org/10.1128/JVI.66.4.1943-1950.1992 PMID: 1347793
Carocci M, Bakkali-Kassimi L. The encephalomyocarditis virus. Virulence. 2012;3(4):351–67. https://doi.org/10.4161/viru.20573 PMID: 22722247
Jones MS, Lukashov VV, Ganac RD, Schnurr DP. Discovery of a novel human picornavirus in a stool sample from a pediatric patient presenting with fever of unknown origin. J Clin Microbiol. 2007;45(7):2144–50. https://doi.org/10.1128/JCM.00174-07 PMID: 17460053
Tan SZK, Tan MZY, Prabakaran M. Saffold virus, an emerging human cardiovirus. Rev Med Virol. 2017;27(1):e1908. https://doi.org/10.1002/rmv.1908 PMID: 27723176
Michiels T, Roos RP. Theiler’s Virus Central Nervous System Infection. The Picornaviruses. American Society of Microbiology. 411–28. https://doi.org/10.1128/9781555816537.ch26
Sorgeloos F, Lardinois C, Jacobs S, van Kuppeveld FJM, Kaspers B, Michiels T. Neurotropism of Saffold virus in a mouse model. J Gen Virol. 2016;97(6):1350–5. https://doi.org/10.1099/jgv.0.000452 PMID: 26959376
Strauss JH, Strauss EG. Plus-strand RNA viruses. Viruses and human disease. 2012.63.
van Pesch V, van Eyll O, Michiels T. The leader protein of Theiler’s virus inhibits immediate-early alpha/beta interferon production. J Virol. 2001;75(17):7811–7. https://doi.org/10.1128/jvi.75.17.7811-7817.2001 PMID: 11483724
Stavrou S, Feng Z, Lemon SM, Roos RP. Different strains of Theiler’s murine encephalomyelitis virus antagonize different sites in the type I interferon pathway. J Virol. 2010;84(18):9181–9. https://doi.org/10.1128/JVI.00603-10 PMID: 20610716
Borghese F, Michiels T. The leader protein of cardioviruses inhibits stress granule assembly. J Virol. 2011;85(18):9614–22. https://doi.org/10.1128/JVI.00480-11 PMID: 21752908
Borghese F, Sorgeloos F, Cesaro T, Michiels T. The Leader Protein of Theiler’s Virus Prevents the Activation of PKR. J Virol. 2019;93(19):e01010-19. https://doi.org/10.1128/JVI.01010-19 PMID: 31292248
Delhaye S, van Pesch V, Michiels T. The leader protein of Theiler’s virus interferes with nucleocytoplasmic trafficking of cellular proteins. J Virol. 2004;78(8):4357–62. https://doi.org/10.1128/jvi.78.8.4357-4362.2004 PMID: 15047849
Porter FW, Palmenberg AC. Leader-induced phosphorylation of nucleoporins correlates with nuclear trafficking inhibition by cardioviruses. J Virol. 2009;83(4):1941–51 https://doi org/10 1128/JVI 01752-08 PMID: 19073724
Sorgeloos F, Peeters M, Hayashi Y, Borghese F, Capelli N, Drappier M, et al. A case of convergent evolution: Several viral and bacterial pathogens hijack RSK kinases through a common linear motif. Proc Natl Acad Sci U S A. 2022;119(5):e2114647119. https://doi.org/10.1073/pnas.2114647119 PMID: 35091472
Veinstein M, Stroobant V, Wavreil F, Michiels T, Sorgeloos F. The “DDVF” motif used by viral and bacterial proteins to hijack RSK kinases mimics a short linear motif (SLiM) found in proteins related to the RAS-ERK MAP kinase pathway. PLoS Pathog. 2025;21(3):e1013016. https://doi.org/10.1371/journal.ppat.1013016 PMID: 40153681
Lizcano-Perret B, Wavreil F, Veinstein M, Duflos C, Milcamps R, Sorgeloos F. The leader proteins of Theiler’s virus and Boone cardiovirus use a combination of Short Linear Motifs (SLiMs) to target RSK kinases to the nuclear pore complex. bioRxiv. 2025. https://doi.org/20250409647954
Hato SV, Ricour C, Schulte BM, Lanke KHW, de Bruijni M, Zoll J, et al. The mengovirus leader protein blocks interferon-alpha/beta gene transcription and inhibits activation of interferon regulatory factor 3. Cell Microbiol. 2007;9(12):2921–30. https://doi.org/10.1111/j.1462-5822.2007.01006.x PMID: 17991048
Ricour C, Delhaye S, Hato SV, Olenyik TD, Michel B, van Kuppeveld FJM, et al. Inhibition of mRNA export and dimerization of interferon regulatory factor 3 by Theiler’s virus leader protein. J Gen Virol. 2009;90(Pt 1):177–86. https://doi.org/10.1099/vir.0.005678-0 PMID: 19088287
Lizcano-Perret B, Michiels T. Nucleocytoplasmic Trafficking Perturbation Induced by Picornaviruses. Viruses. 2021;13(7):1210. https://doi.org/10.3390/v13071210 PMID: 34201715
McBride AE, Schlegel A, Kirkegaard K. Human protein Sam68 relocalization and interaction with poliovirus RNA polymerase in infected cells. Proc Natl Acad Sci U S A. 1996;93(6):2296–301. https://doi.org/10.1073/pnas.93.6.2296 PMID: 8637866
Meerovitch K, Svitkin YV, Lee HS, Lejbkowicz F, Kenan DJ, Chan EK, et al. La autoantigen enhances and corrects aberrant translation of poliovirus RNA in reticulocyte lysate. J Virol. 1993;67(7):3798–807. https://doi.org/10.1128/JVI.67.7.3798-3807.1993 PMID: 8389906
Hellen CU, Witherell GW, Schmid M, Shin SH, Pestova TV, Gil A, et al. A cytoplasmic 57-kDa protein that is required for translation of picornavirus RNA by internal ribosomal entry is identical to the nuclear pyrimidine tract-binding protein. Proc Natl Acad Sci U S A. 1993;90(16):7642–6. https:// doi or /10 1073/ nas 90 16 7642 PMID: 8395052
Park N, Schweers NJ, Gustin KE. Selective Removal of FG Repeat Domains from the Nuclear Pore Complex by Enterovirus 2A(pro). J Virol. 2015;89(21):11069–79. https://doi.org/10.1128/JVI.00956-15 PMID: 26311873
Yang X, Aloise C, van Vliet ALW, Zwaagstra M, Lyoo H, Cheng A, et al. Proteolytic Activities of Enterovirus 2A Do Not Depend on Its Interaction with SETD3. Viruses. 2022;14(7):1360. https://doi.org/10.3390/v14071360 PMID: 35891342
Addetia A, Lieberman NAP, Phung Q, Hsiang T-Y, Xie H, Roychoudhury P, et al. SARS-CoV-2 ORF6 Disrupts Bidirectional Nucleocytoplasmic Transport through Interactions with Rae1 and Nup98. mBio. 2021;12(2):e00065-21. https://doi.org/10.1128/mBio.00065-21 PMID: 33849972
Jnaoui K, Michiels T. Adaptation of Theiler’s virus to L929 cells: mutations in the putative receptor binding site on the capsid map to neutralization sites and modulate viral persistence. Virology. 1998;244(2):397–404. https://doi.org/10.1006/viro.1998.9134 PMID: 9601508
Reineke LC, Kedersha N, Langereis MA, van Kuppeveld FJM, Lloyd RE. Stress granules regulate double-stranded RNA-dependent protein kinase activation through a complex containing G3BP1 and Caprin1. mBio. 2015;6(2):e02486. https://doi.org/10.1128/mBio.02486-14 PMID: 25784705
Reineke LC, Lloyd RE. The stress granule protein G3BP1 recruits protein kinase R to promote multiple innate immune antiviral responses. J Virol. 2015;89(5):2575–89. https://doi.org/10.1128/JVI.02791-14 PMID: 25520508
Gustin KE, Sarnow P. Inhibition of nuclear import and alteration of nuclear pore complex composition by rhinovirus. J Virol. 2002;76(17):8787–96. https://doi.org/10.1128/jvi.76.17.8787-8796.2002 PMID: 12163599
Borman A, Howell MT, Patton JG, Jackson RJ. The involvement of a spliceosome component in internal initiation of human rhinovirus RNA translation. J Gen Virol. 1993;74 (Pt 9):1775–88. https://doi.org/10.1099/0022-1317-74-9-1775 PMID: 8397279
Tan B, Peng S, Yatim SMJM, Gunaratne J, Hunziker W, Ludwig A. An Optimized Protocol for Proximity Biotinylation in Confluent Epithelial Cell Cultures Using the Peroxidase APEX2. STAR Protoc. 2020;1(2):100074. https://doi.org/10.1016/j.xpro.2020.100074 PMID: 33111110
Takizawa T, Tatematsu C, Watanabe M, Yoshida M, Nakajima K. Three leucine-rich sequences and the N-terminal region of double-stranded RNA-activated protein kinase (PKR) are responsible for its cytoplasmic localization. J Biochem. 2000;128(3):471–6. https://doi.org/10.1093/oxfordjournals.jbchem.a022776 PMID: 10965047
Jeffrey IW, Kadereit S, Meurs EF, Metzger T, Bachmann M, Schwemmle M, et al. Nuclear localization of the interferon-inducible protein kinase PKR in human cells and transfected mouse cells. Exp Cell Res. 1995;218(1):17–27. https://doi.org/10.1006/excr.1995.1126 PMID: 7737357
Hakki M, Marshall EE, De Niro KL, Geballe AP. Binding and nuclear relocalization of protein kinase R by human cytomegalovirus TRS1. J Virol. 2006;80(23):11817–26. https://doi.org/10.1128/JVI.00957-06 PMID: 16987971
Kim Y, Lee JH, Park J-E, Cho J, Yi H, Kim VN. PKR is activated by cellular dsRNAs during mitosis and acts as a mitotic regulator. Genes Dev. 2014;28(12):1310–22. https://doi.org/10.1101/gad.242644.114 PMID: 24939934
Lemaire PA, Anderson E, Lary J, Cole JL. Mechanism of PKR Activation by dsRNA. J Mol Biol. 2008;381(2):351–60. https://doi.org/10.1016/j.jmb.2008.05.056 PMID: 18599071
Mathews MB, Shenk T. Adenovirus virus-associated RNA and translation control. J Virol. 1991;65(11):5657–62. https://doi.org/10.1128/JVI.65.11.5657-5662.1991 PMID: 1920611
Sharp TV, Schwemmle M, Jeffrey I, Laing K, Mellor H, Proud CG, et al. Comparative analysis of the regulation of the interferon-inducible protein kinase PKR by Epstein-Barr virus RNAs EBER-1 and EBER-2 and adenovirus VAI RNA. Nucleic Acids Res. 1993;21(19):4483–90. https://doi.org/10.1093/nar/21.19.4483 PMID: 7901835
Jeon SH, Lee K, Lee KS, Kunkeaw N, Johnson BH, Holthauzen LMF, et al. Characterization of the direct physical interaction of nc886, a cellular non-coding RNA, and PKR. FEBS Lett. 2012;586(19):3477–84. https://doi.org/10.1016/j.febslet.2012.07.076 PMID: 22986343
Calderon BM, Conn GL. Human noncoding RNA 886 (nc886) adopts two structurally distinct conformers that are functionally opposing regulators of PKR. RNA. 2017;23(4):557–66. https://doi.org/10.1261/rna.060269.116 PMID: 28069888
Watkins JM, Burke JM. A closer look at mammalian antiviral condensates. Biochem Soc Trans. 2024;52(3):1393–404. https://doi.org/10.1042/ BST20231296 PMID: 38778761
Corbet GA, Burke JM, Bublitz GR, Tay JW, Parker R. dsRNA-induced condensation of antiviral proteins modulates PKR activity. Proc Natl Acad Sci U S A. 2022;119(33):e2204235119. https://doi.org/10.1073/pnas.2204235119 PMID: 35939694
Dong B, Niwa M, Walter P, Silverman RH. Basis for regulated RNA cleavage by functional analysis of RNase L and Ire1p. RNA. 2001;7(3):361–73. https://doi.org/10.1017/s1355838201002230 PMID: 11333017
DuBridge RB, Tang P, Hsia HC, Leong PM, Miller JH, Calos MP. Analysis of mutation in human cells by using an Epstein-Barr virus shuttle system. Mol Cell Biol. 1987;7(1):379–87. https://doi.org/10.1128/mcb.7.1.379-387.1987 PMID: 3031469
Follenzi A, Ailles LE, Bakovic S, Geuna M, Naldini L. Gene transfer by lentiviral vectors is limited by nuclear translocation and rescued by HIV-1 pol sequences. Nat Genet. 2000;25(2):217–22. https://doi.org/10.1038/76095 PMID: 10835641
Ricour C, Borghese F, Sorgeloos F, Hato SV, van Kuppeveld FJM, Michiels T. Random mutagenesis defines a domain of Theiler’s virus leader protein that is essential for antagonism of nucleocytoplasmic trafficking and cytokine gene expression. J Virol. 2009;83(21):11223–32. https://doi.org/10.1128/JVI.00829-09 PMID: 19710133
Duke GM, Palmenberg AC. Cloning and synthesis of infectious cardiovirus RNAs containing short, discrete poly(C) tracts. J Virol. 1989;63(4):1822–6. https://doi.org/10.1128/JVI.63.4.1822-1826.1989 PMID: 2538661