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Yang F, Dai Z, Xue MY, Chen XY, Liu J, Wang L, Xu LL, Di B. Identification and Validation of PKR as a Direct Target for the Novel Sulfonamide-Substituted Tetrahydroquinoline Nonselective Inhibitor of the NLRP3 Inflammasome. J Med Chem 2024; 67:10168-10189. [PMID: 38855903 DOI: 10.1021/acs.jmedchem.4c00343] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/11/2024]
Abstract
The NLRP3 inflammasome is a critical component of the innate immune system. The persistent abnormal activation of the NLRP3 inflammasome is implicated in numerous human diseases. Herein, sulfonamide-substituted tetrahydroquinoline derivative S-9 was identified as the most promising NLRP3 inhibitor, without obvious cytotoxicity. In vitro, S-9 inhibited the priming and activation stages of the NLRP3 inflammasome. Incidentally, we also observed that S-9 had inhibitory effects on the NLRC4 and AIM2 inflammasomes. To elucidate the multiple anti-inflammatory activities of S-9, photoaffinity probe P-2, which contained a photoaffinity label and a functional handle, was developed for target identification by chemical proteomics. We identified PKR as a novel target of S-9 in addition to NLRP3 by target fishing. Furthermore, S-9 exhibited a significant anti-neuroinflammatory effect in vivo. In summary, our findings show that S-9 is a promising lead compound targeting both PKR and NLRP3 that could emerge as a molecular tool for treating inflammasome-related diseases.
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Affiliation(s)
- Fan Yang
- Jiangsu Key Laboratory of Drug Design and Optimization, China Pharmaceutical University, Nanjing 210009, China
- Key Laboratory of Drug Quality Control and Pharmacovigilance, Ministry of Education, China Pharmaceutical University, Nanjing 210009, China
| | - Zhen Dai
- Jiangsu Key Laboratory of Drug Design and Optimization, China Pharmaceutical University, Nanjing 210009, China
- Key Laboratory of Drug Quality Control and Pharmacovigilance, Ministry of Education, China Pharmaceutical University, Nanjing 210009, China
- Sichuan Industrial Institute of Antibiotics, School of Pharmacy, Chengdu University, Chengdu 610106, China
| | - Ming-Yue Xue
- Jiangsu Key Laboratory of Drug Design and Optimization, China Pharmaceutical University, Nanjing 210009, China
- Key Laboratory of Drug Quality Control and Pharmacovigilance, Ministry of Education, China Pharmaceutical University, Nanjing 210009, China
| | - Xiao-Yi Chen
- Jiangsu Key Laboratory of Drug Design and Optimization, China Pharmaceutical University, Nanjing 210009, China
- Key Laboratory of Drug Quality Control and Pharmacovigilance, Ministry of Education, China Pharmaceutical University, Nanjing 210009, China
| | - Juan Liu
- Jiangsu Key Laboratory of Drug Design and Optimization, China Pharmaceutical University, Nanjing 210009, China
- Key Laboratory of Drug Quality Control and Pharmacovigilance, Ministry of Education, China Pharmaceutical University, Nanjing 210009, China
| | - Li Wang
- Jiangsu Key Laboratory of Drug Design and Optimization, China Pharmaceutical University, Nanjing 210009, China
- Key Laboratory of Drug Quality Control and Pharmacovigilance, Ministry of Education, China Pharmaceutical University, Nanjing 210009, China
| | - Li-Li Xu
- Jiangsu Key Laboratory of Drug Design and Optimization, China Pharmaceutical University, Nanjing 210009, China
- Key Laboratory of Drug Quality Control and Pharmacovigilance, Ministry of Education, China Pharmaceutical University, Nanjing 210009, China
| | - Bin Di
- Jiangsu Key Laboratory of Drug Design and Optimization, China Pharmaceutical University, Nanjing 210009, China
- Key Laboratory of Drug Quality Control and Pharmacovigilance, Ministry of Education, China Pharmaceutical University, Nanjing 210009, China
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Sarkar S, Ganguly S, Ganguly NK, Sarkar DP, Sharma NR. Chandipura Virus Forms Cytoplasmic Inclusion Bodies through Phase Separation and Proviral Association of Cellular Protein Kinase R and Stress Granule Protein TIA-1. Viruses 2024; 16:1027. [PMID: 39066190 PMCID: PMC11281494 DOI: 10.3390/v16071027] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2024] [Revised: 06/01/2024] [Accepted: 06/07/2024] [Indexed: 07/28/2024] Open
Abstract
Negative-strand RNA viruses form cytoplasmic inclusion bodies (IBs) representing virus replication foci through phase separation or biomolecular condensation of viral and cellular proteins, as a hallmark of their infection. Alternatively, mammalian cells form stalled mRNA containing antiviral stress granules (SGs), as a consequence of phosphorylation of eukaryotic initiation factor 2α (eIF2α) through condensation of several RNA-binding proteins including TIA-1. Whether and how Chandipura virus (CHPV), an emerging human pathogen causing influenza-like illness, coma and death, forms IBs and evades antiviral SGs remain unknown. By confocal imaging on CHPV-infected Vero-E6 cells, we found that CHPV infection does not induce formation of distinct canonical SGs. Instead, CHPV proteins condense and co-localize together with SG proteins to form heterogeneous IBs, which ensued independent of the activation of eIF2α and eIF2α kinase, protein kinase R (PKR). Interestingly, siRNA-mediated depletion of PKR or TIA-1 significantly decreased viral transcription and virion production. Moreover, CHPV infection also caused condensation and recruitment of PKR to IBs. Compared to SGs, IBs exhibited significant rapidity in disassembly dynamics. Altogether, our study demonstrating that CHPV replication co-optimizes with SG proteins and revealing an unprecedented proviral role of TIA-1/PKR may have implications in understanding the mechanisms regulating CHPV-IB formation and designing antiviral therapeutics. Importance: CHPV is an emerging tropical pathogen reported to cause acute influenza-like illness and encephalitis in children with a very high mortality rate of ~70%. Lack of vaccines and an effective therapy against CHPV makes it a potent pathogen for causing an epidemic in tropical parts of globe. Given these forewarnings, it is of paramount importance that CHPV biology must be understood comprehensively. Targeting of host factors offers several advantages over targeting the viral components due to the generally higher mutation rate in the viral genome. In this study, we aimed at understanding the role of SGs forming cellular RNA-binding proteins in CHPV replication. Our study helps understand participation of cellular factors in CHPV replication and could help develop effective therapeutics against the virus.
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Affiliation(s)
- Sharmistha Sarkar
- Department of Molecular Medicine, School of Interdisciplinary Studies, Jamia Hamdard University, Hamdard Nagar, New Delhi 110062, India; (S.S.); (S.G.)
| | - Surajit Ganguly
- Department of Molecular Medicine, School of Interdisciplinary Studies, Jamia Hamdard University, Hamdard Nagar, New Delhi 110062, India; (S.S.); (S.G.)
| | - Nirmal K. Ganguly
- Department of Education and Research, AERF, Artemis Hospitals, Gurugram 122001, India;
| | - Debi P. Sarkar
- Department of Biochemistry, University of Delhi South Campus, New Delhi 110021, India
| | - Nishi Raj Sharma
- Department of Molecular Medicine, School of Interdisciplinary Studies, Jamia Hamdard University, Hamdard Nagar, New Delhi 110062, India; (S.S.); (S.G.)
- Department of Education and Research, AERF, Artemis Hospitals, Gurugram 122001, India;
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Zaid A, Ariel A. Harnessing anti-inflammatory pathways and macrophage nano delivery to treat inflammatory and fibrotic disorders. Adv Drug Deliv Rev 2024; 207:115204. [PMID: 38342241 DOI: 10.1016/j.addr.2024.115204] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2023] [Revised: 12/08/2023] [Accepted: 02/05/2024] [Indexed: 02/13/2024]
Abstract
Targeting specific organs and cell types using nanotechnology and sophisticated delivery methods has been at the forefront of applicative biomedical sciences lately. Macrophages are an appealing target for immunomodulation by nanodelivery as they are heavily involved in various aspects of many diseases and are highly plastic in their nature. Their continuum of functional "polarization" states has been a research focus for many years yielding a profound understanding of various aspects of these cells. The ability of monocyte-derived macrophages to metamorphose from pro-inflammatory to reparative and consequently to pro-resolving effectors has raised significant interest in its therapeutic potential. Here, we briefly survey macrophages' ontogeny and various polarization phenotypes, highlighting their function in the inflammation-resolution shift. We review their inducing mediators, signaling pathways, and biological programs with emphasis on the nucleic acid sensing-IFN-I axis. We also portray the polarization spectrum of macrophages and the characteristics of their transition between different subtypes. Finally, we highlighted different current drug delivery methods for targeting macrophages with emphasis on nanotargeting that might lead to breakthroughs in the treatment of wound healing, bone regeneration, autoimmune, and fibrotic diseases.
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Affiliation(s)
- Ahmad Zaid
- Department of Biology and Human Biology, University of Haifa, Haifa, 3498838 Israel
| | - Amiram Ariel
- Department of Biology and Human Biology, University of Haifa, Haifa, 3498838 Israel.
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Luan X, Wang L, Song G, Zhou W. Innate immune responses to RNA: sensing and signaling. Front Immunol 2024; 15:1287940. [PMID: 38343534 PMCID: PMC10854198 DOI: 10.3389/fimmu.2024.1287940] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/04/2023] [Accepted: 01/11/2024] [Indexed: 02/15/2024] Open
Abstract
Nucleic acids are among the most essential PAMPs (pathogen-associated molecular patterns). Animals have evolved numerous sensors to recognize nucleic acids and trigger immune signaling against pathogen replication, cellular stress and cancer. Many sensor proteins (e.g., cGAS, AIM2, and TLR9) recognize the molecular signature of infection or stress and are responsible for the innate immune response to DNA. Remarkably, recent evidence demonstrates that cGAS-like receptors acquire the ability to sense RNA in some forms of life. Compared with the nucleic-acid sensing by cGAS, innate immune responses to RNA are based on various RNA sensors, including RIG-I, MDA5, ADAR1, TLR3/7/8, OAS1, PKR, NLRP1/6, and ZBP1, via a broad-spectrum signaling axis. Importantly, new advances have brought to light the potential clinical application of targeting these signaling pathways. Here, we highlight the latest discoveries in the field. We also summarize the activation and regulatory mechanisms of RNA-sensing signaling. In addition, we discuss how RNA sensing is tightly controlled in cells and why the disruption of immune homeostasis is linked to disease.
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Affiliation(s)
- Xiaohan Luan
- Shenzhen Key Laboratory of Biomolecular Assembling and Regulation, Southern University of Science and Technology, Shenzhen, Guangdong, China
- Department of Immunology and Microbiology, School of Life Sciences, Southern University of Science and Technology, Shenzhen, Guangdong, China
| | - Lei Wang
- Department of Systems Biology, School of Life Sciences, Southern University of Science and Technology, Shenzhen, Guangdong, China
| | - Guangji Song
- Department of Immunology and Microbiology, School of Life Sciences, Southern University of Science and Technology, Shenzhen, Guangdong, China
| | - Wen Zhou
- Shenzhen Key Laboratory of Biomolecular Assembling and Regulation, Southern University of Science and Technology, Shenzhen, Guangdong, China
- Department of Immunology and Microbiology, School of Life Sciences, Southern University of Science and Technology, Shenzhen, Guangdong, China
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Kaempfer R. RNA Activators of Stress Kinase PKR within Human Genes That Control Splicing or Translation Create Novel Targets for Hereditary Diseases. Int J Mol Sci 2024; 25:1323. [PMID: 38279321 PMCID: PMC10816128 DOI: 10.3390/ijms25021323] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/24/2023] [Revised: 01/14/2024] [Accepted: 01/20/2024] [Indexed: 01/28/2024] Open
Abstract
Specific sequences within RNA encoded by human genes essential for survival possess the ability to activate the RNA-dependent stress kinase PKR, resulting in phosphorylation of its substrate, eukaryotic translation initiation factor-2α (eIF2α), either to curb their mRNA translation or to enhance mRNA splicing. Thus, interferon-γ (IFNG) mRNA activates PKR through a 5'-terminal 203-nucleotide pseudoknot structure, thereby strongly downregulating its own translation and preventing a harmful hyper-inflammatory response. Tumor necrosis factor-α (TNF) pre-mRNA encodes within the 3'-untranslated region (3'-UTR) a 104-nucleotide RNA pseudoknot that activates PKR to enhance its splicing by an order of magnitude while leaving mRNA translation intact, thereby promoting effective TNF protein expression. Adult and fetal globin genes encode pre-mRNA structures that strongly activate PKR, leading to eIF2α phosphorylation that greatly enhances spliceosome assembly and splicing, yet also structures that silence PKR activation upon splicing to allow for unabated globin mRNA translation essential for life. Regulatory circuits resulting in each case from PKR activation were reviewed previously. Here, we analyze mutations within these genes created to delineate the RNA structures that activate PKR and to deconvolute their folding. Given the critical role of intragenic RNA activators of PKR in gene regulation, such mutations reveal novel potential RNA targets for human disease.
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Affiliation(s)
- Raymond Kaempfer
- Department of Biochemistry and Molecular Biology, Institute of Medical Research Israel-Canada, Faculty of Medicine, The Hebrew University, Jerusalem 9112102, Israel
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Kong LZ, Kim SM, Wang C, Lee SY, Oh SC, Lee S, Jo S, Kim TD. Understanding nucleic acid sensing and its therapeutic applications. Exp Mol Med 2023; 55:2320-2331. [PMID: 37945923 PMCID: PMC10689850 DOI: 10.1038/s12276-023-01118-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2023] [Revised: 08/16/2023] [Accepted: 08/20/2023] [Indexed: 11/12/2023] Open
Abstract
Nucleic acid sensing is involved in viral infections, immune response-related diseases, and therapeutics. Based on the composition of nucleic acids, nucleic acid sensors are defined as DNA or RNA sensors. Pathogen-associated nucleic acids are recognized by membrane-bound and intracellular receptors, known as pattern recognition receptors (PRRs), which induce innate immune-mediated antiviral responses. PRR activation is tightly regulated to eliminate infections and prevent abnormal or excessive immune responses. Nucleic acid sensing is an essential mechanism in tumor immunotherapy and gene therapies that target cancer and infectious diseases through genetically engineered immune cells or therapeutic nucleic acids. Nucleic acid sensing supports immune cells in priming desirable immune responses during tumor treatment. Recent studies have shown that nucleic acid sensing affects the efficiency of gene therapy by inhibiting translation. Suppression of innate immunity induced by nucleic acid sensing through small-molecule inhibitors, virus-derived proteins, and chemical modifications offers a potential therapeutic strategy. Herein, we review the mechanisms and regulation of nucleic acid sensing, specifically covering recent advances. Furthermore, we summarize and discuss recent research progress regarding the different effects of nucleic acid sensing on therapeutic efficacy. This study provides insights for the application of nucleic acid sensing in therapy.
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Affiliation(s)
- Ling-Zu Kong
- Immunotherapy Research Center, Korea Research Institute of Bioscience and Biotechnology, Daejeon, 34141, Republic of Korea
- Department of Biochemistry, College of Natural Sciences, Chungnam National University, Daejeon, 34134, Republic of Korea
| | - Seok-Min Kim
- Immunotherapy Research Center, Korea Research Institute of Bioscience and Biotechnology, Daejeon, 34141, Republic of Korea
| | - Chunli Wang
- Immunotherapy Research Center, Korea Research Institute of Bioscience and Biotechnology, Daejeon, 34141, Republic of Korea
| | - Soo Yun Lee
- Immunotherapy Research Center, Korea Research Institute of Bioscience and Biotechnology, Daejeon, 34141, Republic of Korea
| | - Se-Chan Oh
- Immunotherapy Research Center, Korea Research Institute of Bioscience and Biotechnology, Daejeon, 34141, Republic of Korea
| | - Sunyoung Lee
- Immunotherapy Research Center, Korea Research Institute of Bioscience and Biotechnology, Daejeon, 34141, Republic of Korea
- Department of Life Sciences, Korea University, Seoul, 02841, Korea
| | - Seona Jo
- Immunotherapy Research Center, Korea Research Institute of Bioscience and Biotechnology, Daejeon, 34141, Republic of Korea
- Department of Functional Genomics, KRIBB School of Bioscience, Korea University of Science and Technology (UST), Daejeon, 34113, Korea
| | - Tae-Don Kim
- Immunotherapy Research Center, Korea Research Institute of Bioscience and Biotechnology, Daejeon, 34141, Republic of Korea.
- Department of Functional Genomics, KRIBB School of Bioscience, Korea University of Science and Technology (UST), Daejeon, 34113, Korea.
- Biomedical Mathematics Group, Institute for Basic Science (IBS), Daejeon, Republic of Korea.
- Department of Biopharmaceutical Convergence, School of Pharmacy, Sungkyunkwan University, Suwon, Republic of Korea.
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Burke JM. Regulation of ribonucleoprotein condensates by RNase L during viral infection. WILEY INTERDISCIPLINARY REVIEWS. RNA 2023; 14:e1770. [PMID: 36479619 PMCID: PMC10244490 DOI: 10.1002/wrna.1770] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/08/2022] [Revised: 11/10/2022] [Accepted: 11/22/2022] [Indexed: 12/12/2022]
Abstract
In response to viral infection, mammalian cells activate several innate immune pathways to antagonize viral gene expression. Upon recognition of viral double-stranded RNA, protein kinase R (PKR) phosphorylates the alpha subunit of eukaryotic initiation factor 2 (eIF2α) on serine 51. This inhibits canonical translation initiation, which broadly antagonizes viral protein synthesis. It also promotes the assembly of cytoplasmic ribonucleoprotein complexes termed stress granules (SGs). SGs are widely thought to promote cell survival and antiviral signaling. However, co-activation of the OAS/RNase L antiviral pathway inhibits the assembly of SGs and promotes the assembly of an alternative ribonucleoprotein complex termed an RNase L-dependent body (RLB). The formation of RLBs has been observed in response to double-stranded RNA, dengue virus infection, or SARS-CoV-2 infection. Herein, we review the distinct biogenesis pathways and properties of SGs and RLBs, and we provide perspective on their potential functions during the antiviral response. This article is categorized under: RNA Interactions with Proteins and Other Molecules > RNA-Protein Complexes RNA Turnover and Surveillance > Regulation of RNA Stability RNA Export and Localization > RNA Localization.
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Affiliation(s)
- James M. Burke
- Department of Molecular Medicine, University of Florida Scripps Biomedical Research, Jupiter, Florida 33458, USA
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Kaempfer R. Positive Regulation of Splicing of Cellular and Viral mRNA by Intragenic RNA Elements That Activate the Stress Kinase PKR, an Antiviral Mechanism. Genes (Basel) 2023; 14:genes14050974. [PMID: 37239334 DOI: 10.3390/genes14050974] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2023] [Revised: 04/03/2023] [Accepted: 04/25/2023] [Indexed: 05/28/2023] Open
Abstract
The transient activation of the cellular stress kinase, protein kinase RNA-activated (PKR), by double-helical RNA, especially by viral double-stranded RNA generated during replication, results in the inhibition of translation via the phosphorylation of eukaryotic initiation factor 2 α-chain (eIF2α). Exceptionally, short intragenic elements within primary transcripts of the human tumor necrosis factor (TNF-α) and globin genes, genes essential for survival, can form RNA structures that strongly activate PKR and thereby render the splicing of their mRNAs highly efficient. These intragenic RNA activators of PKR promote early spliceosome assembly and splicing by inducing phosphorylation of nuclear eIF2α, without impairing the translation of the mature spliced mRNA. Unexpectedly, excision of the large human immunodeficiency virus (HIV) rev/tat intron was shown to require activation of PKR by the viral RNA and eIF2α phosphorylation. The splicing of rev/tat mRNA is abrogated by viral antagonists of PKR and by trans-dominant negative mutant PKR, yet enhanced by the overexpression of PKR. The TNFα and HIV RNA activators of PKR fold into compact pseudoknots that are highly conserved within the phylogeny, supporting their essential role in the upregulation of splicing. HIV provides the first example of a virus co-opting a major cellular antiviral mechanism, the activation of PKR by its RNA, to promote splicing.
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Affiliation(s)
- Raymond Kaempfer
- Department of Biochemistry and Molecular Biology, Institute of Medical Research Israel-Canada, The Hebrew University-Hadassah Medical School, Jerusalem 9112102, Israel
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Gan Z, Xu X, Tang S, Wen Q, Jin Y, Lu Y. Identification and functional characterization of protein kinase R (PKR) in amphibian Xenopus tropicalis. DEVELOPMENTAL AND COMPARATIVE IMMUNOLOGY 2023; 141:104648. [PMID: 36708793 DOI: 10.1016/j.dci.2023.104648] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/27/2022] [Revised: 01/09/2023] [Accepted: 01/24/2023] [Indexed: 06/18/2023]
Abstract
As one of interferon-induced serine/threonine kinases, the protein kinase R (PKR) plays vital roles in antiviral defense, and functional features of PKR remain largely unknown in amphibians, which suffer from ranaviral diseases in the last few decades. In this study, a PKR gene named Xt-PKR was characterized in the Western clawed frog (Xenopus tropicalis). Xt-PKR gene was widely expressed in different organs/tissues, and was rapidly induced by poly(I:C) in spleen, kidney, and liver. Intriguingly, Xt-PKR could be up-rugulated by the treatment of type I and type III interferons, and the transcript level of Xt-PKR induced by type I interferon was much higher than that of type III interferon. Moreover, overexpression of Xt-PKR can suppress the protein synthesis and ranavirus replication in vitro, and the residue lysine required for the translation inhibition activity in mammalian PKR is conserved in Xt-PKR. The present study represents the first characterization on the functions of amphibian PKR, and reveals considerable functional conservation of PKR in early tetrapods.
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Affiliation(s)
- Zhen Gan
- Guangdong Provincial Engineering Research Center for Aquatic Animal Health Assessment, Shenzhen Public Service Platform for Evaluation of Marine Economic Animal Seedings, Shenzhen Institute of Guangdong Ocean University, Shenzhen, 518120, China; Guangdong Provincial Key Laboratory of Aquatic Animal Disease Control and Healthy Culture, Key Laboratory of Control for Disease of Aquatic Animals of Guangdong Higher Education Institute, College of Fishery, Guangdong Ocean University, Zhanjiang, 524088, China.
| | - Xinlan Xu
- Guangdong Provincial Engineering Research Center for Aquatic Animal Health Assessment, Shenzhen Public Service Platform for Evaluation of Marine Economic Animal Seedings, Shenzhen Institute of Guangdong Ocean University, Shenzhen, 518120, China; Guangdong Provincial Key Laboratory of Aquatic Animal Disease Control and Healthy Culture, Key Laboratory of Control for Disease of Aquatic Animals of Guangdong Higher Education Institute, College of Fishery, Guangdong Ocean University, Zhanjiang, 524088, China
| | - Shaoshuai Tang
- Guangdong Provincial Engineering Research Center for Aquatic Animal Health Assessment, Shenzhen Public Service Platform for Evaluation of Marine Economic Animal Seedings, Shenzhen Institute of Guangdong Ocean University, Shenzhen, 518120, China
| | - Qingqing Wen
- Guangdong Provincial Engineering Research Center for Aquatic Animal Health Assessment, Shenzhen Public Service Platform for Evaluation of Marine Economic Animal Seedings, Shenzhen Institute of Guangdong Ocean University, Shenzhen, 518120, China; Guangdong Provincial Key Laboratory of Aquatic Animal Disease Control and Healthy Culture, Key Laboratory of Control for Disease of Aquatic Animals of Guangdong Higher Education Institute, College of Fishery, Guangdong Ocean University, Zhanjiang, 524088, China
| | - Yong Jin
- Guangdong Provincial Engineering Research Center for Aquatic Animal Health Assessment, Shenzhen Public Service Platform for Evaluation of Marine Economic Animal Seedings, Shenzhen Institute of Guangdong Ocean University, Shenzhen, 518120, China
| | - Yishan Lu
- Guangdong Provincial Engineering Research Center for Aquatic Animal Health Assessment, Shenzhen Public Service Platform for Evaluation of Marine Economic Animal Seedings, Shenzhen Institute of Guangdong Ocean University, Shenzhen, 518120, China; Guangdong Provincial Key Laboratory of Aquatic Animal Disease Control and Healthy Culture, Key Laboratory of Control for Disease of Aquatic Animals of Guangdong Higher Education Institute, College of Fishery, Guangdong Ocean University, Zhanjiang, 524088, China.
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Targeting Human Proteins for Antiviral Drug Discovery and Repurposing Efforts: A Focus on Protein Kinases. Viruses 2023; 15:v15020568. [PMID: 36851782 PMCID: PMC9966946 DOI: 10.3390/v15020568] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2023] [Revised: 02/07/2023] [Accepted: 02/09/2023] [Indexed: 02/22/2023] Open
Abstract
Despite the great technological and medical advances in fighting viral diseases, new therapies for most of them are still lacking, and existing antivirals suffer from major limitations regarding drug resistance and a limited spectrum of activity. In fact, most approved antivirals are directly acting antiviral (DAA) drugs, which interfere with viral proteins and confer great selectivity towards their viral targets but suffer from resistance and limited spectrum. Nowadays, host-targeted antivirals (HTAs) are on the rise, in the drug discovery and development pipelines, in academia and in the pharmaceutical industry. These drugs target host proteins involved in the virus life cycle and are considered promising alternatives to DAAs due to their broader spectrum and lower potential for resistance. Herein, we discuss an important class of HTAs that modulate signal transduction pathways by targeting host kinases. Kinases are considered key enzymes that control virus-host interactions. We also provide a synopsis of the antiviral drug discovery and development pipeline detailing antiviral kinase targets, drug types, therapeutic classes for repurposed drugs, and top developing organizations. Furthermore, we detail the drug design and repurposing considerations, as well as the limitations and challenges, for kinase-targeted antivirals, including the choice of the binding sites, physicochemical properties, and drug combinations.
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Namer LS, Harwig A, Heynen SP, Das AT, Berkhout B, Kaempfer R. HIV co-opts a cellular antiviral mechanism, activation of stress kinase PKR by its RNA, to enable splicing of rev/tat mRNA. Cell Biosci 2023; 13:28. [PMID: 36774495 PMCID: PMC9922466 DOI: 10.1186/s13578-023-00972-1] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2022] [Accepted: 01/24/2023] [Indexed: 02/13/2023] Open
Abstract
BACKGROUND Activation of RNA-dependent stress kinase PKR, especially by viral double-stranded RNA, induces eukaryotic initiation factor 2 α-chain (eIF2α) phosphorylation, attenuating thereby translation. We report that this RNA-mediated negative control mechanism, considered a cornerstone of the cell's antiviral response, positively regulates splicing of a viral mRNA. RESULTS Excision of the large human immunodeficiency virus (HIV) rev/tat intron depends strictly on activation of PKR by the viral RNA and on eIF2α phosphorylation. Rev/tat mRNA splicing was blocked by viral PKR antagonists Vaccinia E3L and Ebola VP35, as well as by a trans-dominant negative mutant of PKR, yet enhanced by overexpressing PKR. Expression of non-phosphorylatable mutant eIF2αS51A, but not of wild type eIF2α, abrogated efficient splicing of rev/tat mRNA. By contrast, expression of eIF2αS51D, a phosphomimetic mutant of eIF2α, left rev/tat mRNA splicing intact. Unlike eIF2αS51A, eIF2αS51D does not inhibit eIF2α phosphorylation by activated PKR. All HIV mRNA species contain terminal trans-activation response (TAR) stem-loop sequences that potentially could activate PKR, yet even upon TAR deletion, HIV mRNA production remained sensitive to inhibitors of PKR activation. Bioinformatic and mutational analyses revealed a compact RNA pseudoknot upstream of 3'-terminal TAR that promotes splicing by activating PKR. Supporting its essential role in control of splicing, this pseudoknot is conserved among diverse HIV and nonhuman primate SIVcpz isolates. The pseudoknot and 3'-terminal TAR collaborate in mediating PKR-regulated splicing of rev/tat intron, the pseudoknot being dominant. CONCLUSIONS Our results on HIV provide the first example of a virus co-opting activation of PKR by its RNA, a cellular antiviral mechanism, to promote splicing. They raise the question whether other viruses may use local activation of host kinase PKR through RNA elements within their genome to achieve efficient splicing of their mRNA. Our experiments reveal an indispensable role for eIF2α phosphorylation in HIV rev/tat mRNA splicing that accounts for the need for PKR activation.
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Affiliation(s)
- Lise Sarah Namer
- grid.9619.70000 0004 1937 0538Department of Biochemistry and Molecular Biology, Institute of Medical Research Israel-Canada, The Hebrew University-Hadassah Medical School, 9112102 Jerusalem, Israel
| | - Alex Harwig
- grid.509540.d0000 0004 6880 3010Laboratory of Experimental Virology, Department of Medical Microbiology, Amsterdam UMC, 1105 AZ Amsterdam, The Netherlands
| | - Stephan P. Heynen
- grid.509540.d0000 0004 6880 3010Laboratory of Experimental Virology, Department of Medical Microbiology, Amsterdam UMC, 1105 AZ Amsterdam, The Netherlands
| | - Atze T. Das
- grid.509540.d0000 0004 6880 3010Laboratory of Experimental Virology, Department of Medical Microbiology, Amsterdam UMC, 1105 AZ Amsterdam, The Netherlands
| | - Ben Berkhout
- grid.509540.d0000 0004 6880 3010Laboratory of Experimental Virology, Department of Medical Microbiology, Amsterdam UMC, 1105 AZ Amsterdam, The Netherlands
| | - Raymond Kaempfer
- Department of Biochemistry and Molecular Biology, Institute of Medical Research Israel-Canada, The Hebrew University-Hadassah Medical School, 9112102, Jerusalem, Israel.
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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:e2204235119. [PMID: 35939694 PMCID: PMC9388085 DOI: 10.1073/pnas.2204235119] [Citation(s) in RCA: 13] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2022] [Accepted: 07/01/2022] [Indexed: 12/21/2022] Open
Abstract
Mammalian cells respond to dsRNA in multiple manners. One key response to dsRNA is the activation of PKR, an eIF2α kinase, which triggers translational arrest and the formation of stress granules. However, the process of PKR activation in cells is not fully understood. In response to increased endogenous or exogenous dsRNA, we observed that PKR forms novel cytosolic condensates, referred to as dsRNA-induced foci (dRIFs). dRIFs contain dsRNA, form in proportion to dsRNA, and are enhanced by longer dsRNAs. dRIFs enrich several other dsRNA-binding proteins, including ADAR1, Stau1, NLRP1, and PACT. Strikingly, dRIFs correlate with and form before translation repression by PKR and localize to regions of cells where PKR activation is initiated. We hypothesize that dRIF formation is a mechanism that cells use to enhance the sensitivity of PKR activation in response to low levels of dsRNA or to overcome viral inhibitors of PKR activation.
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Affiliation(s)
- Giulia A. Corbet
- Department of Biochemistry, University of Colorado, Boulder, CO 80309
| | - James M. Burke
- Department of Biochemistry, University of Colorado, Boulder, CO 80309
| | - Gaia R. Bublitz
- Department of Biochemistry, University of Colorado, Boulder, CO 80309
| | | | - Roy Parker
- Department of Biochemistry, University of Colorado, Boulder, CO 80309
- BioFrontiers Institute, Boulder, CO 80309
- Howard Hughes Medical Institute, Chevy Chase, MD 20815-6789
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13
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Breuer J, Barth P, Noe Y, Shalamova L, Goesmann A, Weber F, Rossbach O. What goes around comes around: Artificial circular RNAs bypass cellular antiviral responses. MOLECULAR THERAPY - NUCLEIC ACIDS 2022; 28:623-635. [PMID: 35497503 PMCID: PMC9042720 DOI: 10.1016/j.omtn.2022.04.017] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 01/04/2022] [Accepted: 04/21/2022] [Indexed: 12/14/2022]
Abstract
Natural circular RNAs have been found to sequester microRNAs and suppress their function. We have used this principle as a molecular tool and produced artificial circular RNA sponges in a cell-free system by in vitro transcription and ligation. Formerly, we were able to inhibit hepatitis C virus propagation by applying a circular RNA decoy strategy against microRNA-122, which is essential for the viral life cycle. In another proof-of-principle study, we used circular RNAs to sequester microRNA-21, an oncogenic and pro-proliferative microRNA. This strategy slowed tumor growth in a 3D cell culture model system, as well as in xenograft mice upon systemic delivery. In the wake of the global use of an in vitro transcribed RNA in coronavirus disease 2019 (COVID-19) vaccines, the question arose whether therapeutic circular RNAs trigger cellular antiviral defense mechanisms when delivered systemically. In this study, we present data on the cellular innate immune response as a consequence of liposome-based transfection of the circular RNA sponges we previously used to inhibit microRNA function. We find that circular RNAs produced by the presented methodology do not trigger the antiviral response and do not activate innate immune-signaling pathways.
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14
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Krzyzosiak A, Pitera AP, Bertolotti A. An Overview of Methods for Detecting eIF2α Phosphorylation and the Integrated Stress Response. Methods Mol Biol 2022; 2428:3-18. [PMID: 35171470 DOI: 10.1007/978-1-0716-1975-9_1] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/14/2023]
Abstract
Phosphorylation of the translation initiation factor eIF2α is an adaptive signaling event that is essential for cell and organismal survival from yeast to humans. It is central to the integrated stress response (ISR) that maintains cellular homeostasis in the face of threats ranging from viral infection, amino acid, oxygen, and heme deprivation to the accumulation of misfolded proteins in the endoplasmic reticulum. Phosphorylation of eIF2α has broad physiological, pathological, and therapeutic relevance. However, despite more than two decades of research and growing pharmacological interest, phosphorylation of eIF2α remains difficult to detect and quantify, because of its transient nature and because substoichiometric amounts of this modification are sufficient to profoundly reshape cellular physiology. This review aims to provide a roadmap for facilitating a robust evaluation of eIF2α phosphorylation and its downstream consequences in cells and organisms.
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15
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Smyth R, Sun J. Protein Kinase R in Bacterial Infections: Friend or Foe? Front Immunol 2021; 12:702142. [PMID: 34305942 PMCID: PMC8297547 DOI: 10.3389/fimmu.2021.702142] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2021] [Accepted: 06/28/2021] [Indexed: 12/28/2022] Open
Abstract
The global antimicrobial resistance crisis poses a significant threat to humankind in the coming decades. Challenges associated with the development of novel antibiotics underscore the urgent need to develop alternative treatment strategies to combat bacterial infections. Host-directed therapy is a promising new therapeutic strategy that aims to boost the host immune response to bacteria rather than target the pathogen itself, thereby circumventing the development of antibiotic resistance. However, host-directed therapy depends on the identification of druggable host targets or proteins with key functions in antibacterial defense. Protein Kinase R (PKR) is a well-characterized human kinase with established roles in cancer, metabolic disorders, neurodegeneration, and antiviral defense. However, its role in antibacterial defense has been surprisingly underappreciated. Although the canonical role of PKR is to inhibit protein translation during viral infection, this kinase senses and responds to multiple types of cellular stress by regulating cell-signaling pathways involved in inflammation, cell death, and autophagy - mechanisms that are all critical for a protective host response against bacterial pathogens. Indeed, there is accumulating evidence to demonstrate that PKR contributes significantly to the immune response to a variety of bacterial pathogens. Importantly, there are existing pharmacological modulators of PKR that are well-tolerated in animals, indicating that PKR is a feasible target for host-directed therapy. In this review, we provide an overview of immune cell functions regulated by PKR and summarize the current knowledge on the role and functions of PKR in bacterial infections. We also review the non-canonical activators of PKR and speculate on the potential mechanisms that trigger activation of PKR during bacterial infection. Finally, we provide an overview of existing pharmacological modulators of PKR that could be explored as novel treatment strategies for bacterial infections.
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Affiliation(s)
- Robin Smyth
- Department of Biochemistry, Microbiology and Immunology, University of Ottawa, Ottawa, ON, Canada
| | - Jim Sun
- Department of Biochemistry, Microbiology and Immunology, University of Ottawa, Ottawa, ON, Canada
- Centre for Infection, Immunity and Inflammation, University of Ottawa, Ottawa, ON, Canada
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16
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Lee EJ, Neppl RL. Influence of Age on Skeletal Muscle Hypertrophy and Atrophy Signaling: Established Paradigms and Unexpected Links. Genes (Basel) 2021; 12:genes12050688. [PMID: 34063658 PMCID: PMC8147613 DOI: 10.3390/genes12050688] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2021] [Revised: 04/26/2021] [Accepted: 04/27/2021] [Indexed: 12/16/2022] Open
Abstract
Skeletal muscle atrophy in an inevitable occurrence with advancing age, and a consequence of disease including cancer. Muscle atrophy in the elderly is managed by a regimen of resistance exercise and increased protein intake. Understanding the signaling that regulates muscle mass may identify potential therapeutic targets for the prevention and reversal of muscle atrophy in metabolic and neuromuscular diseases. This review covers the major anabolic and catabolic pathways that regulate skeletal muscle mass, with a focus on recent progress and potential new players.
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17
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Gan Z, Cheng J, Hou J, Chen S, Xia H, Xia L, Kwok KWH, Lu Y, Nie P. Tilapia dsRNA-activated protein kinase R (PKR): An interferon-induced antiviral effector with translation inhibition activity. FISH & SHELLFISH IMMUNOLOGY 2021; 112:74-80. [PMID: 33667675 DOI: 10.1016/j.fsi.2021.02.016] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/20/2020] [Revised: 02/21/2021] [Accepted: 02/24/2021] [Indexed: 06/12/2023]
Abstract
The dsRNA-activated protein kinase R (PKR) is one of key antiviral effectors induced by interferons (IFNs), and its functions are largely unknown in tilapia, an important commercial fish species suffering from several viral infectious diseases. In the present study, a PKR gene named On-PKR was identified and cloned from Nile tilapia, Oreochromis niloticus. On-PKR gene was constitutively expressed in all tissues examined, with the highest expression level observed in head kidney and liver, and was rapidly induced in all organs/tissues tested following the stimulation of poly(I:C). Importantly, the expression of On-PKR is induced by group I and group II IFNs with distinct induction kinetics in vivo: group I IFN elicits a relative delayed but sustained induction of On-PKR, whereas group II IFN triggers a rapid and transient expression of On-PKR. Moreover, the overexpression of On-PKR has been proven to inhibit the protein translation and virus replication in fish cells. The present study thus contributes to a better understanding of the functions of antiviral effectors in tilapia, and may provide clues for the prevention and therapy of viral diseases in fish.
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Affiliation(s)
- Zhen Gan
- Shenzhen Institute of Guangdong Ocean University, Shenzhen, 518120, China; State Key Laboratory of Freshwater Ecology and Biotechnology, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, 430072, China; College of Fishery, Guangdong Ocean University, Zhanjiang, 524025, China; Guangdong Provincial Engineering Research Center for Aquatic Animal Health Assessment, And Shenzhen Public Service Platform for Evaluation of Marine Economic Animal Seedings, Shenzhen, 518120, China
| | - Jun Cheng
- Shenzhen Institute of Guangdong Ocean University, Shenzhen, 518120, China; College of Fishery, Guangdong Ocean University, Zhanjiang, 524025, China; Guangdong Provincial Engineering Research Center for Aquatic Animal Health Assessment, And Shenzhen Public Service Platform for Evaluation of Marine Economic Animal Seedings, Shenzhen, 518120, China
| | - Jing Hou
- Shenzhen Institute of Guangdong Ocean University, Shenzhen, 518120, China
| | - Shannan Chen
- State Key Laboratory of Freshwater Ecology and Biotechnology, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, 430072, China
| | - Hongli Xia
- Shenzhen Institute of Guangdong Ocean University, Shenzhen, 518120, China
| | - Liqun Xia
- Shenzhen Institute of Guangdong Ocean University, Shenzhen, 518120, China; College of Fishery, Guangdong Ocean University, Zhanjiang, 524025, China; Guangdong Provincial Engineering Research Center for Aquatic Animal Health Assessment, And Shenzhen Public Service Platform for Evaluation of Marine Economic Animal Seedings, Shenzhen, 518120, China
| | - Kevin W H Kwok
- Department of Applied Biology and Chemical Technology, Hong Kong Polytechnic University, Hong Kong, China
| | - Yishan Lu
- Shenzhen Institute of Guangdong Ocean University, Shenzhen, 518120, China; College of Fishery, Guangdong Ocean University, Zhanjiang, 524025, China; Guangdong Provincial Engineering Research Center for Aquatic Animal Health Assessment, And Shenzhen Public Service Platform for Evaluation of Marine Economic Animal Seedings, Shenzhen, 518120, China.
| | - Pin Nie
- State Key Laboratory of Freshwater Ecology and Biotechnology, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, 430072, China.
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18
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Smyth R, Berton S, Rajabalee N, Chan T, Sun J. Protein Kinase R Restricts the Intracellular Survival of Mycobacterium tuberculosis by Promoting Selective Autophagy. Front Microbiol 2021; 11:613963. [PMID: 33552025 PMCID: PMC7862720 DOI: 10.3389/fmicb.2020.613963] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2020] [Accepted: 12/30/2020] [Indexed: 12/18/2022] Open
Abstract
Tuberculosis (TB) is a deadly infectious lung disease caused by the pathogenic bacterium Mycobacterium tuberculosis (Mtb). The identification of macrophage signaling proteins exploited by Mtb during infection will enable the development of alternative host-directed therapies (HDT) for TB. HDT strategies will boost host immunity to restrict the intracellular replication of Mtb and therefore hold promise to overcome antimicrobial resistance, a growing crisis in TB therapy. Protein Kinase R (PKR) is a key host sensor that functions in the cellular antiviral response. However, its role in defense against intracellular bacterial pathogens is not clearly defined. Herein, we demonstrate that expression and activation of PKR is upregulated in macrophages infected with Mtb. Immunological profiling of human THP-1 macrophages that overexpress PKR (THP-PKR) showed increased production of IP-10 and reduced production of IL-6, two cytokines that are reported to activate and inhibit IFNγ-dependent autophagy, respectively. Indeed, sustained expression and activation of PKR reduced the intracellular survival of Mtb, an effect that could be enhanced by IFNγ treatment. We further demonstrate that the enhanced anti-mycobacterial activity of THP-PKR macrophages is mediated by a mechanism dependent on selective autophagy, as indicated by increased levels of LC3B-II that colocalize with intracellular Mtb. Consistent with this mechanism, inhibition of autophagolysosome maturation with bafilomycin A1 abrogated the ability of THP-PKR macrophages to limit replication of Mtb, whereas pharmacological activation of autophagy enhanced the anti-mycobacterial effect of PKR overexpression. As such, PKR represents a novel and attractive host target for development of HDT for TB, and our data suggest value in the design of more specific and potent activators of PKR.
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Affiliation(s)
- Robin Smyth
- Department of Biochemistry, Microbiology and Immunology, University of Ottawa, Ottawa, ON, Canada
| | - Stefania Berton
- Department of Biochemistry, Microbiology and Immunology, University of Ottawa, Ottawa, ON, Canada
| | - Nusrah Rajabalee
- Department of Biochemistry, Microbiology and Immunology, University of Ottawa, Ottawa, ON, Canada
| | - Therese Chan
- Department of Biochemistry, Microbiology and Immunology, University of Ottawa, Ottawa, ON, Canada
| | - Jim Sun
- Department of Biochemistry, Microbiology and Immunology, University of Ottawa, Ottawa, ON, Canada.,Centre for Infection, Immunity and Inflammation, University of Ottawa, Ottawa, ON, Canada
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19
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Abstract
The innate immune receptors in higher organisms have evolved to detect molecular signatures associated with pathogenic infection and trigger appropriate immune response. One common class of molecules utilized by the innate immune system for self vs. nonself discrimination is RNA, which is ironically present in all forms of life. To avoid self-RNA recognition, the innate immune sensors have evolved sophisticated discriminatory mechanisms that involve cellular RNA metabolic machineries. Posttranscriptional RNA modification and editing represent one such mechanism that allows cells to chemically tag the host RNAs as "self" and thus tolerate the abundant self-RNA molecules. In this chapter, we discuss recent advances in our understanding of the role of RNA editing/modification in the modulation of immune signaling pathways, and application of RNA editing/modification in RNA-based therapeutics and cancer immunotherapies.
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20
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Ding J, Zhao J, Huan L, Liu Y, Qiao Y, Wang Z, Chen Z, Huang S, Zhao Y, He X. Inflammation-Induced Long Intergenic Noncoding RNA (LINC00665) Increases Malignancy Through Activating the Double-Stranded RNA-Activated Protein Kinase/Nuclear Factor Kappa B Pathway in Hepatocellular Carcinoma. Hepatology 2020; 72:1666-1681. [PMID: 32083756 DOI: 10.1002/hep.31195] [Citation(s) in RCA: 48] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/28/2019] [Revised: 01/09/2020] [Accepted: 01/26/2020] [Indexed: 12/20/2022]
Abstract
BACKGROUND AND AIMS The nuclear factor kappa B (NF-κB) signaling pathway is important for linking inflammation and tumorigenesis. Here, we characterized an NF-κB signaling activation-induced long intergenic noncoding (LINC) RNA in hepatocellular carcinoma (HCC), LINC00665, that contributes to the enhanced cell proliferation of HCC cells both in vitro and in vivo. APPROACH AND RESULTS LINC00665 physically interacts with the double-stranded RNA (dsRNA)-activated protein kinase (PKR), enhances its activation, and maintains its protein stability by blocking ubiquitin/proteasome-dependent degradation, resulting in a positive feedback regulation of NF-κB signaling in HCC cells. Notably, patients with HCC and higher LINC00665 have poorer outcomes in the clinic. CONCLUSIONS Our findings indicate that LINC00665 is involved in the NF-κB signaling activation in HCC cells and that the inflammatory LINC00665/PKR/NF-κB loop plays important oncogenic roles in hepatic cancer progression and may be a potential therapeutic target.
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Affiliation(s)
- Jie Ding
- Fudan University Shanghai Cancer Center and Institutes of Biomedical Sciences, Department of Oncology, Shanghai Medical College, Fudan University, Shanghai, China
| | - Jingjing Zhao
- Fudan University Shanghai Cancer Center and Institutes of Biomedical Sciences, Department of Oncology, Shanghai Medical College, Fudan University, Shanghai, China
| | - Lin Huan
- Fudan University Shanghai Cancer Center and Institutes of Biomedical Sciences, Department of Oncology, Shanghai Medical College, Fudan University, Shanghai, China
| | - Yizhe Liu
- Fudan University Shanghai Cancer Center and Institutes of Biomedical Sciences, Department of Oncology, Shanghai Medical College, Fudan University, Shanghai, China
| | - Yejun Qiao
- Fudan University Shanghai Cancer Center and Institutes of Biomedical Sciences, Department of Oncology, Shanghai Medical College, Fudan University, Shanghai, China
| | - Zhen Wang
- Fudan University Shanghai Cancer Center and Institutes of Biomedical Sciences, Department of Oncology, Shanghai Medical College, Fudan University, Shanghai, China
| | - Zhiao Chen
- Fudan University Shanghai Cancer Center and Institutes of Biomedical Sciences, Department of Oncology, Shanghai Medical College, Fudan University, Shanghai, China
| | - Shenglin Huang
- Fudan University Shanghai Cancer Center and Institutes of Biomedical Sciences, Department of Oncology, Shanghai Medical College, Fudan University, Shanghai, China.,Key Laboratory of Breast Cancer in Shanghai, Fudan University Shanghai Cancer Center, Fudan University, Shanghai, China
| | - Yingjun Zhao
- Fudan University Shanghai Cancer Center and Institutes of Biomedical Sciences, Department of Oncology, Shanghai Medical College, Fudan University, Shanghai, China.,Key Laboratory of Breast Cancer in Shanghai, Fudan University Shanghai Cancer Center, Fudan University, Shanghai, China
| | - Xianghuo He
- Fudan University Shanghai Cancer Center and Institutes of Biomedical Sciences, Department of Oncology, Shanghai Medical College, Fudan University, Shanghai, China.,Key Laboratory of Breast Cancer in Shanghai, Fudan University Shanghai Cancer Center, Fudan University, Shanghai, China
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21
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Riad S, Xiang Y, AlDaif B, Mercer AA, Fleming SB. Rescue of a Vaccinia Virus Mutant Lacking IFN Resistance Genes K1L and C7L by the Parapoxvirus Orf Virus. Front Microbiol 2020; 11:1797. [PMID: 32903701 PMCID: PMC7438785 DOI: 10.3389/fmicb.2020.01797] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2020] [Accepted: 07/09/2020] [Indexed: 12/17/2022] Open
Abstract
Type 1 interferons induce the upregulation of hundreds of interferon-stimulated genes (ISGs) that combat viral replication. The parapoxvirus orf virus (ORFV) induces acute pustular skin lesions in sheep and goats and can reinfect its host, however, little is known of its ability to resist IFN. Vaccinia virus (VACV) encodes a number of factors that modulate the IFN response including the host-range genes C7L and K1L. A recombinant VACV-Western Reserve (WR) strain in which the K1L and C7L genes have been deleted does not replicate in cells treated with IFN-β nor in HeLa cells in which the IFN response is constitutive and is inhibited at the level of intermediate gene expression. Furthermore C7L is conserved in almost all poxviruses. We provide evidence that shows that although ORFV is more sensitive to IFN-β compared with VACV, and lacks homologues of KIL and C7L, it nevertheless has the ability to rescue a VACV KIL- C7L- gfp+ mutant in which gfp is expressed from a late promoter. Co-infection of HeLa cells with the mutant and ORFV demonstrated that ORFV was able to overcome the block in translation of intermediate transcripts in the mutant virus, allowing it to progress to late gene expression and new viral particles. Our findings strongly suggest that ORFV encodes a factor(s) that, although different in structure to C7L or KIL, targets an anti-viral cellular mechanism that is a highly potent at killing poxviruses.
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Affiliation(s)
- Sherief Riad
- Virus Research Unit, Department of Microbiology and Immunology, University of Otago, Dunedin, New Zealand
| | - Yan Xiang
- Department of Microbiology, Immunology and Molecular Genetics, University of Texas Health Science Center at San Antonio, San Antonio, TX, United States
| | - Basheer AlDaif
- Virus Research Unit, Department of Microbiology and Immunology, University of Otago, Dunedin, New Zealand
| | - Andrew A Mercer
- Virus Research Unit, Department of Microbiology and Immunology, University of Otago, Dunedin, New Zealand
| | - Stephen B Fleming
- Virus Research Unit, Department of Microbiology and Immunology, University of Otago, Dunedin, New Zealand
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22
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Cell fate determined by the activation balance between PKR and SPHK1. Cell Death Differ 2020; 28:401-418. [PMID: 32801355 PMCID: PMC7852545 DOI: 10.1038/s41418-020-00608-8] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2020] [Revised: 07/29/2020] [Accepted: 08/06/2020] [Indexed: 11/25/2022] Open
Abstract
Double-stranded RNA (dsRNA)-dependent protein kinase R (PKR) activation via autophosphorylation is the central cellular response to stress that promotes cell death or apoptosis. However, the key factors and mechanisms behind the simultaneous activation of pro-survival signaling pathways remain unknown. We have discovered a novel regulatory mechanism for the maintenance of cellular homeostasis that relies on the phosphorylation interplay between sphingosine kinase 1 (SPHK1) and PKR during exogenous stress. We identified SPHK1 as a previously unrecognized PKR substrate. Phosphorylated SPHK1, a central kinase, mediates the activation of PKR-induced pro-survival pathways by the S1P/S1PR1/MAPKs/IKKα signal axis, and antagonizes PKR-mediated endoplasmic reticulum (ER) stress signal transduction under stress conditions. Otherwise, phosphorylated SPHK1 also acts as the negative feedback factor, preferentially binding to the latent form of PKR at the C-terminal kinase motif, inhibiting the homodimerization of PKR, suppressing PKR autophosphorylation, and reducing the signaling strength for cell death and apoptosis. Our results suggest that the balance of the activation levels between PKR and SPHK1, a probable hallmark of homeostasis maintenance, determines cell fate during cellular stress response.
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23
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Jaud M, Philippe C, Di Bella D, Tang W, Pyronnet S, Laurell H, Mazzolini L, Rouault-Pierre K, Touriol C. Translational Regulations in Response to Endoplasmic Reticulum Stress in Cancers. Cells 2020; 9:cells9030540. [PMID: 32111004 PMCID: PMC7140484 DOI: 10.3390/cells9030540] [Citation(s) in RCA: 34] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2019] [Revised: 02/18/2020] [Accepted: 02/24/2020] [Indexed: 12/20/2022] Open
Abstract
During carcinogenesis, almost all the biological processes are modified in one way or another. Among these biological processes affected, anomalies in protein synthesis are common in cancers. Indeed, cancer cells are subjected to a wide range of stresses, which include physical injuries, hypoxia, nutrient starvation, as well as mitotic, oxidative or genotoxic stresses. All of these stresses will cause the accumulation of unfolded proteins in the Endoplasmic Reticulum (ER), which is a major organelle that is involved in protein synthesis, preservation of cellular homeostasis, and adaptation to unfavourable environment. The accumulation of unfolded proteins in the endoplasmic reticulum causes stress triggering an unfolded protein response in order to promote cell survival or to induce apoptosis in case of chronic stress. Transcription and also translational reprogramming are tightly controlled during the unfolded protein response to ensure selective gene expression. The majority of stresses, including ER stress, induce firstly a decrease in global protein synthesis accompanied by the induction of alternative mechanisms for initiating the translation of mRNA, later followed by a translational recovery. After a presentation of ER stress and the UPR response, we will briefly present the different modes of translation initiation, then address the specific translational regulatory mechanisms acting during reticulum stress in cancers and highlight the importance of translational control by ER stress in tumours.
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Affiliation(s)
- Manon Jaud
- Inserm UMR1037, CRCT (Cancer Research Center of Toulouse), F-31037 Toulouse, France; (M.J.); (S.P.); (L.M.)
- Université Toulouse III Paul-Sabatier, F-31000 Toulouse, France;
| | - Céline Philippe
- Barts Cancer Institute, Queen Mary University of London, London E1 4NS, UK; (C.P.); (D.D.B.); (W.T.); (K.R.-P.)
| | - Doriana Di Bella
- Barts Cancer Institute, Queen Mary University of London, London E1 4NS, UK; (C.P.); (D.D.B.); (W.T.); (K.R.-P.)
| | - Weiwei Tang
- Barts Cancer Institute, Queen Mary University of London, London E1 4NS, UK; (C.P.); (D.D.B.); (W.T.); (K.R.-P.)
| | - Stéphane Pyronnet
- Inserm UMR1037, CRCT (Cancer Research Center of Toulouse), F-31037 Toulouse, France; (M.J.); (S.P.); (L.M.)
- Université Toulouse III Paul-Sabatier, F-31000 Toulouse, France;
| | - Henrik Laurell
- Université Toulouse III Paul-Sabatier, F-31000 Toulouse, France;
- Inserm UMR1048, I2MC (Institut des Maladies Métaboliques et Cardiovasculaires), BP 84225, CEDEX 04, 31 432 Toulouse, France
| | - Laurent Mazzolini
- Inserm UMR1037, CRCT (Cancer Research Center of Toulouse), F-31037 Toulouse, France; (M.J.); (S.P.); (L.M.)
- CNRS ERL5294, CRCT, F-31037 Toulouse, France
| | - Kevin Rouault-Pierre
- Barts Cancer Institute, Queen Mary University of London, London E1 4NS, UK; (C.P.); (D.D.B.); (W.T.); (K.R.-P.)
| | - Christian Touriol
- Inserm UMR1037, CRCT (Cancer Research Center of Toulouse), F-31037 Toulouse, France; (M.J.); (S.P.); (L.M.)
- Université Toulouse III Paul-Sabatier, F-31000 Toulouse, France;
- Correspondence:
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24
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Zharkov MI, Zenkova MA, Vlassov VV, Chernolovskaya EL. Molecular Mechanism of the Antiproliferative Activity of Short Immunostimulating dsRNA. Front Oncol 2020; 9:1454. [PMID: 31921696 PMCID: PMC6933605 DOI: 10.3389/fonc.2019.01454] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2019] [Accepted: 12/05/2019] [Indexed: 12/23/2022] Open
Abstract
Small double-stranded RNAs with certain sequence motifs are able to interact with pattern-recognition receptors and activate the innate immune system. Recently, we identified a set of short double-stranded 19-bp RNA molecules with 3-nucleotide 3′-overhangs that exhibited pronounced antiproliferative activity against cancer cells in vitro, and antitumor and antimetastatic activities in mouse models in vivo. The main objectives of this study were to identify the pattern recognition receptors that mediate the antiproliferative action of immunostimulating RNA (isRNA). Two cell lines, epidermoid carcinoma KB-3-1 cells and lung cancer A549 cells, were used in the study. These lines respond to the action of isRNA by a decrease in the growth rate, and in the case of A549 cells, also by a secretion of IL-6. Two sets of cell lines with selectively silenced genes encoding potential sensors and signal transducers of isRNA action were obtained on the basis of KB-3-1 and A549 cells. It was found that the selective silencing of PKR and RIG-I genes blocked the antiproliferative effect of isRNA, both in KB-3-1 and A549 cells, whereas the expression of MDA5 and IRF3 was not required for the antiproliferative action of isRNA. It was shown that, along with PKR and RIG-I genes, the expression of IRF3 also plays a role in isRNA mediated IL-6 synthesis in A549 cells. Thus, PKR and RIG-I sensors play a major role in the anti-proliferative signaling triggered by isRNA.
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Affiliation(s)
- Mikhail I Zharkov
- Laboratory of Nucleic Acids Biochemistry, Institute of Chemical Biology and Fundamental Medicine SB RAS, Novosibirsk, Russia
| | - Marina A Zenkova
- Laboratory of Nucleic Acids Biochemistry, Institute of Chemical Biology and Fundamental Medicine SB RAS, Novosibirsk, Russia
| | - Valentin V Vlassov
- Laboratory of Nucleic Acids Biochemistry, Institute of Chemical Biology and Fundamental Medicine SB RAS, Novosibirsk, Russia
| | - Elena L Chernolovskaya
- Laboratory of Nucleic Acids Biochemistry, Institute of Chemical Biology and Fundamental Medicine SB RAS, Novosibirsk, Russia
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25
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Hippocampal PKR/NLRP1 Inflammasome Pathway Is Required for the Depression-Like Behaviors in Rats with Neuropathic Pain. Neuroscience 2019; 412:16-28. [DOI: 10.1016/j.neuroscience.2019.05.025] [Citation(s) in RCA: 25] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2018] [Revised: 03/28/2019] [Accepted: 05/13/2019] [Indexed: 01/08/2023]
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26
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Lamers MM, van den Hoogen BG, Haagmans BL. ADAR1: "Editor-in-Chief" of Cytoplasmic Innate Immunity. Front Immunol 2019; 10:1763. [PMID: 31404141 PMCID: PMC6669771 DOI: 10.3389/fimmu.2019.01763] [Citation(s) in RCA: 123] [Impact Index Per Article: 24.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2019] [Accepted: 07/11/2019] [Indexed: 12/12/2022] Open
Abstract
Specialized receptors that recognize molecular patterns such as double stranded RNA duplexes-indicative of viral replication-are potent triggers of the innate immune system. Although their activation is beneficial during viral infection, RNA transcribed from endogenous mobile genetic elements may also act as ligands potentially causing autoimmunity. Recent advances indicate that the adenosine deaminase ADAR1 through RNA editing is involved in dampening the canonical antiviral RIG-I-like receptor-, PKR-, and OAS-RNAse L pathways to prevent autoimmunity. However, this inhibitory effect must be overcome during viral infections. In this review we discuss ADAR1's critical role in balancing immune activation and self-tolerance.
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Klepsch O, Namer LS, Köhler N, Kaempfer R, Dittrich A, Schaper F. Intragenic regulation of SOCS3 isoforms. Cell Commun Signal 2019; 17:70. [PMID: 31238931 PMCID: PMC6593527 DOI: 10.1186/s12964-019-0379-6] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2018] [Accepted: 05/01/2019] [Indexed: 11/13/2022] Open
Abstract
Background Inflammatory reactions are commonly affected by stress responses. Interleukin-6 signalling is part of the inflammatory response and is stringently regulated by the feedback inhibitor SOCS3 expressed in a short and long isoform. Here, we studied the inhibitory potential of the two SOCS3 isoforms. Furthermore, we analysed the regulation of SOCS3 isoform expression and the role of PKR stress kinase signalling in SOCS3 protein expression. Methods We performed Western blotting, reporter assays, genetic analyses and manipulations for studying SOCS3 isoform expression and activation of signalling components involved in interleukin-6-induced and PKR-dependent signalling. Results Interleukin-6-induced endogenous expression of both SOCS3 isoforms was found in distinct cell types. Forced expression of either the long or short SOCS3 isoform demonstrated equal inhibitory activity of each isoform and confirmed longer half-life of the short isoform. Study of intragenic regulation of SOCS3 isoform expression revealed that (i) the 5′-UTR of SOCS3 mRNA restrains specifically expression of the long SOCS3 isoform, (ii) expression of the long isoform restrains expression of the short isoform, and (iii) signalling through the stress kinase PKR does not impact on SOCS3 isoform ratio. Conclusions Both SOCS3 isoforms show a similar potential for inhibiting interleukin-6 signalling but differ in their half-lives. Relative expression of the isoforms depends on intragenic elements yet is independent of PKR signalling. Graphic abstract ![]()
Electronic supplementary material The online version of this article (10.1186/s12964-019-0379-6) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Oliver Klepsch
- Department of Systems Biology, Institute of Biology, Otto-von-Guericke University Magdeburg, Universitätsplatz 2, 39106, Magdeburg, Germany
| | - Lise Sarah Namer
- Department of Biochemistry and Molecular Biology, Institute of Medical Research Israel-Canada, The Hebrew University-Hadassah Medical School, 9112102, Jerusalem, Israel
| | - Nadine Köhler
- Department of Systems Biology, Institute of Biology, Otto-von-Guericke University Magdeburg, Universitätsplatz 2, 39106, Magdeburg, Germany
| | - Raymond Kaempfer
- Department of Biochemistry and Molecular Biology, Institute of Medical Research Israel-Canada, The Hebrew University-Hadassah Medical School, 9112102, Jerusalem, Israel
| | - Anna Dittrich
- Department of Systems Biology, Institute of Biology, Otto-von-Guericke University Magdeburg, Universitätsplatz 2, 39106, Magdeburg, Germany.
| | - Fred Schaper
- Department of Systems Biology, Institute of Biology, Otto-von-Guericke University Magdeburg, Universitätsplatz 2, 39106, Magdeburg, Germany.
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28
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Guix FX, Sartório CL, Ill-Raga G. BACE1 Translation: At the Crossroads Between Alzheimer's Disease Neurodegeneration and Memory Consolidation. J Alzheimers Dis Rep 2019; 3:113-148. [PMID: 31259308 PMCID: PMC6597968 DOI: 10.3233/adr-180089] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022] Open
Abstract
Human life unfolds not only in time and space, but also in the recollection and interweaving of memories. Therefore, individual human identity depends fully on a proper access to the autobiographical memory. Such access is hindered under pathological conditions such as Alzheimer’s disease, which affects millions of people worldwide. Unfortunately, no effective cure exists to prevent this disorder, the impact of which will rise alarmingly within the next decades. While Alzheimer’s disease is largely considered to be the outcome of amyloid-β (Aβ) peptide accumulation in the brain, conceiving this complex disorder strictly as the result of Aβ-neurotoxicity is perhaps a too straight-line simplification. Instead, complementary to this view, the tableau of molecular disarrangements in the Alzheimer’s disease brain may be reflecting, at least in part, a loss of function phenotype in memory processing. Here we take BACE1 translation and degradation as a gateway to study molecular mechanisms putatively involved in the transition between memory and neurodegeneration. BACE1 participates in the excision of Aβ-peptide from its precursor holoprotein, but plays a role in synaptic plasticity too. Its translation is governed by eIF2α phosphorylation: a hub integrating cellular responses to stress, but also a critical switch in memory consolidation. Paralleling these dualities, the eIF2α-kinase HRI has been shown to be a nitric oxide-dependent physiological activator of hippocampal BACE1 translation. Finally, beholding BACE1 as a representative protease active in the CNS, we venture a new perspective on the cellular basis of memory, which may incorporate neurodegeneration in itself as a drift in memory consolidating systems.
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Affiliation(s)
- Francesc X Guix
- Department of Molecular Neuropathology, Centro de Biología Molecular Severo Ochoa-CSIC, Madrid, Spain
| | - Carmem L Sartório
- Division of Physiological Sciences, Federal University of Espírito Santo, Vitória, Espírito Santo, Brazil
| | - Gerard Ill-Raga
- Division of Physiological Sciences, Federal University of Espírito Santo, Vitória, Espírito Santo, Brazil
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29
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Kaempfer R, Ilan L, Cohen-Chalamish S, Turgeman O, Namer LS, Osman F. Control of mRNA Splicing by Intragenic RNA Activators of Stress Signaling: Potential Implications for Human Disease. Front Genet 2019; 10:464. [PMID: 31139209 PMCID: PMC6527590 DOI: 10.3389/fgene.2019.00464] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2019] [Accepted: 04/30/2019] [Indexed: 11/13/2022] Open
Abstract
A critical step in the cellular stress response is transient activation of the RNA-dependent protein kinase PKR by double-helical RNA, resulting in down-regulation of protein synthesis through phosphorylation of the α chain of translation initiation factor eIF2, a major PKR substrate. However, intragenic elements of 100–200 nucleotides in length within primary transcripts of cellular genes, exemplified by the tumor necrosis factor (TNF)-α gene and fetal and adult globin genes, are capable of forming RNA structures that potently activate PKR and thereby strongly enhance mRNA splicing efficiency. By inducing nuclear eIF2α phosphorylation, these PKR activator elements enable highly efficient early spliceosome assembly yet do not impair translation of the mature spliced mRNA. The TNF-α RNA activator of PKR folds into a compact pseudoknot that is highly conserved within the phylogeny. Upon excision of β-globin first intron, the RNA activator of PKR, located in exon 1, is silenced through strand displacement by a short sequence within exon 2, restricting thereby the ability to activate PKR to the splicing process without impeding subsequent synthesis of β-globin essential for survival. This activator/silencer mechanism likewise controls splicing of α-globin pre-mRNA, but the exonic locations of PKR activator and silencer sequences are reversed, demonstrating evolutionary flexibility. Impaired splicing efficiency may underlie numerous human β-thalassemia mutations that map to the β-globin RNA activator of PKR or its silencer. Even where such mutations change the encoded amino acid sequence during subsequent translation, they carry the potential of first impairing PKR-dependent mRNA splicing or shutoff of PKR activation needed for optimal translation.
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Affiliation(s)
- Raymond Kaempfer
- Department of Biochemistry and Molecular Biology, The Institute for Medical Research Israel-Canada, The Hebrew University-Hadassah Medical School, Jerusalem, Israel
| | - Lena Ilan
- Department of Biochemistry and Molecular Biology, The Institute for Medical Research Israel-Canada, The Hebrew University-Hadassah Medical School, Jerusalem, Israel
| | - Smadar Cohen-Chalamish
- Department of Biochemistry and Molecular Biology, The Institute for Medical Research Israel-Canada, The Hebrew University-Hadassah Medical School, Jerusalem, Israel
| | - Orli Turgeman
- Department of Biochemistry and Molecular Biology, The Institute for Medical Research Israel-Canada, The Hebrew University-Hadassah Medical School, Jerusalem, Israel
| | - Lise Sarah Namer
- Department of Biochemistry and Molecular Biology, The Institute for Medical Research Israel-Canada, The Hebrew University-Hadassah Medical School, Jerusalem, Israel
| | - Farhat Osman
- Department of Biochemistry and Molecular Biology, The Institute for Medical Research Israel-Canada, The Hebrew University-Hadassah Medical School, Jerusalem, Israel
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30
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Bou-Nader C, Gordon JM, Henderson FE, Zhang J. The search for a PKR code-differential regulation of protein kinase R activity by diverse RNA and protein regulators. RNA (NEW YORK, N.Y.) 2019; 25:539-556. [PMID: 30770398 PMCID: PMC6467004 DOI: 10.1261/rna.070169.118] [Citation(s) in RCA: 41] [Impact Index Per Article: 8.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/06/2023]
Abstract
The interferon-inducible protein kinase R (PKR) is a key component of host innate immunity that restricts viral replication and propagation. As one of the four eIF2α kinases that sense diverse stresses and direct the integrated stress response (ISR) crucial for cell survival and proliferation, PKR's versatile roles extend well beyond antiviral defense. Targeted by numerous host and viral regulators made of RNA and proteins, PKR is subject to multiple layers of endogenous control and external manipulation, driving its rapid evolution. These versatile regulators include not only the canonical double-stranded RNA (dsRNA) that activates the kinase activity of PKR, but also highly structured viral, host, and artificial RNAs that exert a full spectrum of effects. In this review, we discuss our deepening understanding of the allosteric mechanism that connects the regulatory and effector domains of PKR, with an emphasis on diverse structured RNA regulators in comparison to their protein counterparts. Through this analysis, we conclude that much of the mechanistic details that underlie this RNA-regulated kinase await structural and functional elucidation, upon which we can then describe a "PKR code," a set of structural and chemical features of RNA that are both descriptive and predictive for their effects on PKR.
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Affiliation(s)
- Charles Bou-Nader
- Laboratory of Molecular Biology, National Institute of Diabetes and Digestive and Kidney Diseases, Bethesda, Maryland 20892, USA
| | - Jackson M Gordon
- Laboratory of Molecular Biology, National Institute of Diabetes and Digestive and Kidney Diseases, Bethesda, Maryland 20892, USA
| | - Frances E Henderson
- Laboratory of Molecular Biology, National Institute of Diabetes and Digestive and Kidney Diseases, Bethesda, Maryland 20892, USA
| | - Jinwei Zhang
- Laboratory of Molecular Biology, National Institute of Diabetes and Digestive and Kidney Diseases, Bethesda, Maryland 20892, USA
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31
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Golec E, Lind L, Qayyum M, Blom AM, King BC. The Noncoding RNA nc886 Regulates PKR Signaling and Cytokine Production in Human Cells. THE JOURNAL OF IMMUNOLOGY 2018; 202:131-141. [PMID: 30518569 DOI: 10.4049/jimmunol.1701234] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/28/2017] [Accepted: 10/29/2018] [Indexed: 12/17/2022]
Abstract
Protein kinase RNA-activated (PKR) is a cytoplasmic receptor for dsRNA, and as such is involved in detection of viral infection. On binding dsRNA, PKR dimerizes, autophosphorylates, and then phosphorylates its substrate, eukaryotic translation initiation factor 2 subunit α (eIF2α), causing inhibition of mRNA translation and shutdown of viral protein production. However, active PKR has also been found to be involved in the NF-κB signaling pathway by inducing phosphorylation of IκBα. PKR is regulated by the noncoding RNA nc886, which has altered expression in cancer. We have found that expression of nc886 is highly upregulated during activation of human CD4+ T cells. As has been described in other cell types, nc886 bound to PKR in human T cell lysates, preventing PKR phosphorylation by polyinosinic:polycytidylic acid or HIV trans-activation response element RNA in lysates of T cell lines or primary human CD4+ T cells. Using clonal human T cell lines, we found that nc886 expression was strictly required for IFN-γ and IL-2 expression and secretion after T cell activation but did not affect proliferation or activation-induced cell death. In stimulated human PBMCs, nc886 expression strongly correlated with IFN-γ expression. Although nc886 inhibited PKR activation by dsRNA, it was required for PKR phosphorylation during T cell stimulation, with subsequent NF-κB signaling and CREB phosphorylation. nc886 also regulated PKR phosphorylation during human monocyte-derived macrophage activation. We have therefore identified nc886 as a noncoding RNA marker of T cell activation and regulator of PKR-dependent signaling.
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Affiliation(s)
- Ewelina Golec
- Division of Medical Protein Chemistry, Department of Translational Medicine, Lund University, 21428 Malmö, Sweden
| | - Liza Lind
- Division of Medical Protein Chemistry, Department of Translational Medicine, Lund University, 21428 Malmö, Sweden
| | - Munazza Qayyum
- Division of Medical Protein Chemistry, Department of Translational Medicine, Lund University, 21428 Malmö, Sweden
| | - Anna M Blom
- Division of Medical Protein Chemistry, Department of Translational Medicine, Lund University, 21428 Malmö, Sweden
| | - Ben C King
- Division of Medical Protein Chemistry, Department of Translational Medicine, Lund University, 21428 Malmö, Sweden
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32
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Kawasaki T, Kawai T. Discrimination Between Self and Non-Self-Nucleic Acids by the Innate Immune System. INTERNATIONAL REVIEW OF CELL AND MOLECULAR BIOLOGY 2018; 344:1-30. [PMID: 30798985 PMCID: PMC7105031 DOI: 10.1016/bs.ircmb.2018.08.004] [Citation(s) in RCA: 35] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
During viral and bacterial infections, the innate immune system recognizes various types of pathogen-associated molecular patterns (PAMPs), such as nucleic acids, via a series of membrane-bound or cytosolic pattern-recognition receptors. These include Toll-like receptors (TLRs), RIG-I-like receptors (RLRs), AIM2-like receptors (ALRs), and cytosolic DNA sensors. The binding of PAMPs to these receptors triggers the production of type I interferon (IFN) and inflammatory cytokines. Type I IFN induces the expression of interferon stimulated genes (ISGs), which protect surrounding cells from infection. Some ISGs are nucleic acids-binding proteins that bind viral nucleic acids and suppress their replication. As nucleic acids are essential components that store and transmit genetic information in every species, infectious pathogens have developed systems to escape from the host nucleic acid recognition system. Host cells also have their own nucleic acids that are frequently released to the extracellular milieu or the cytoplasm during cell death or stress responses, which, if able to bind pattern-recognition receptors, would induce autoimmunity and inflammation. Therefore, host cells have acquired mechanisms to protect themselves from contact with their own nucleic acids. In this review, we describe recent research progress into the nucleic acid recognition mechanism and the molecular bases of discrimination between self and non-self-nucleic acids.
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Affiliation(s)
- Takumi Kawasaki
- Laboratory of Molecular Immunobiology, Division of Biological Science, Graduate School of Science and Technology, Nara Institute of Science and Technology, Ikoma, Japan.
| | - Taro Kawai
- Laboratory of Molecular Immunobiology, Division of Biological Science, Graduate School of Science and Technology, Nara Institute of Science and Technology, Ikoma, Japan.
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33
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Kaempfer R, Namer LS, Osman F, Ilan L. Control of mRNA splicing by noncoding intragenic RNA elements that evoke a cellular stress response. Int J Biochem Cell Biol 2018; 105:20-23. [PMID: 30282053 DOI: 10.1016/j.biocel.2018.09.021] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2018] [Revised: 09/25/2018] [Accepted: 09/27/2018] [Indexed: 11/15/2022]
Abstract
Once activated by double-helical RNA, mammalian RNA-dependent stress protein kinase, PKR, phosphorylates its substrate, translation initiation factor eIF2α, to inhibit translation. eIF2α phosphorylation is critical for mounting a cellular stress response. We describe short, 100-200 nucleotide elements within cellular genes that, once transcribed, form RNA structures that potently activate PKR in the vicinity of the RNA and thereby tightly regulate gene expression in cis. Intragenic RNA activators of PKR can (a) attenuate translation of the encoded mRNA by activating PKR and inducing eIF2α phosphorylation, exemplified by the IFN-γ gene, or (b) greatly enhance mRNA splicing efficiency by activating PKR and inducing nuclear eIF2α phosphorylation, thus enabling efficient early spliceosome assembly, exemplified by the adult and fetal globin genes and the TNF-α gene that activates PKR through an RNA pseudoknot conserved from fish to humans. These opposite outcomes considerably extend the potential scope of gene regulation by these novel RNA elements.
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Affiliation(s)
- Raymond Kaempfer
- Department of Biochemistry and Molecular Biology, Faculty of Medicine, The Hebrew University, Jerusalem, Israel.
| | - Lise Sarah Namer
- Department of Biochemistry and Molecular Biology, Faculty of Medicine, The Hebrew University, Jerusalem, Israel
| | - Farhat Osman
- Department of Biochemistry and Molecular Biology, Faculty of Medicine, The Hebrew University, Jerusalem, Israel
| | - Lena Ilan
- Department of Biochemistry and Molecular Biology, Faculty of Medicine, The Hebrew University, Jerusalem, Israel
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34
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White MC, Schroeder RD, Zhu K, Xiong K, McConkey DJ. HRI-mediated translational repression reduces proteotoxicity and sensitivity to bortezomib in human pancreatic cancer cells. Oncogene 2018; 37:4413-4427. [PMID: 29720726 PMCID: PMC6138554 DOI: 10.1038/s41388-018-0227-y] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2013] [Revised: 10/26/2017] [Accepted: 11/03/2017] [Indexed: 12/31/2022]
Abstract
Human cancer cells display extensive heterogeneity in their sensitivities to the proteasome inhibitor bortezomib (Velcade). The molecular mechanisms underlying this heterogeneity remain unclear, and strategies to overcome resistance are limited. Here, we discover that inherent differences in eIF2α phosphorylation among a panel of ten human pancreatic cancer cell lines significantly impacts bortezomib sensitivity, and implicate the HRI (heme-regulated inhibitor) eIF2α kinase as a novel therapeutic target. Within our panel, we identified a subset of cell lines with defective induction of eIF2α phosphorylation, conferring a high degree of sensitivity to bortezomib. These bortezomib-sensitive cells exhibited impaired translation attenuation followed by toxic accumulation of protein aggregates and reactive oxygen species (ROS), whereas the bortezomib-resistant cell lines displayed increased phosphorylation of eIF2α, decreased translation, few protein aggregates, and minimal ROS production. Importantly, we identified HRI as the primary bortezomib-activated eIF2α kinase, and demonstrated that HRI knockdown promoted cell death in the bortezomib-resistant cells. Overall, our data implicate inducible HRI-mediated phosphorylation of eIF2α as a central cytoprotective mechanism following exposure to bortezomib and provide proof-of-concept for the development of HRI inhibitors to overcome proteasome inhibitor resistance.
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Affiliation(s)
- Matthew C White
- Departments of Urology, The University of Texas MD Anderson Cancer Center, Houston, TX, 77030, USA.,Department of Cancer Biology, The University of Texas MD Anderson Cancer Center, Houston, TX, 77030, USA.,The Program in Experimental Therapeutics, The University of Texas Graduate School of Biomedical Sciences, Houston, TX, 77030, USA
| | - Rebecca D Schroeder
- The Program in Experimental Therapeutics, The University of Texas Graduate School of Biomedical Sciences, Houston, TX, 77030, USA
| | - Keyi Zhu
- Departments of Urology, The University of Texas MD Anderson Cancer Center, Houston, TX, 77030, USA.,Department of Cancer Biology, The University of Texas MD Anderson Cancer Center, Houston, TX, 77030, USA
| | - Katherine Xiong
- Departments of Urology, The University of Texas MD Anderson Cancer Center, Houston, TX, 77030, USA.,Department of Cancer Biology, The University of Texas MD Anderson Cancer Center, Houston, TX, 77030, USA
| | - David J McConkey
- Departments of Urology, The University of Texas MD Anderson Cancer Center, Houston, TX, 77030, USA. .,Department of Cancer Biology, The University of Texas MD Anderson Cancer Center, Houston, TX, 77030, USA. .,The Program in Experimental Therapeutics, The University of Texas Graduate School of Biomedical Sciences, Houston, TX, 77030, USA. .,Johns Hopkins Greenberg Bladder Cancer Institute, Baltimore, MD, 21287, USA.
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35
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Radetskyy R, Daher A, Gatignol A. ADAR1 and PKR, interferon stimulated genes with clashing effects on HIV-1 replication. Cytokine Growth Factor Rev 2018; 40:48-58. [PMID: 29625900 DOI: 10.1016/j.cytogfr.2018.03.007] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2018] [Revised: 03/19/2018] [Accepted: 03/19/2018] [Indexed: 12/15/2022]
Abstract
The induction of hundreds of Interferon Stimulated Genes (ISGs) subsequent to virus infection generates an antiviral state that functions to restrict virus growth at multiple steps of their replication cycles. In the context of Human Immunodeficiency Virus-1 (HIV-1), ISGs also possess antiviral functions, but some ISGs show proapoptotic or proviral activity. One of the most studied ISGs, the RNA activated Protein Kinase (PKR), shuts down the viral protein synthesis upon activation. HIV-1 has evolved to evade its inhibition by PKR through viral and cellular mechanisms. One of the cellular mechanisms is the induction of another ISG, the Adenosine Deaminase acting on RNA 1 (ADAR1). ADAR1 promotes viral replication by acting as an RNA sensing inhibitor, by editing viral RNA and by inhibiting PKR. This review challenges the orthodox dogma of ISGs as antiviral proteins, by demonstrating that two ISGs have opposing and clashing effects on viral replication.
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Affiliation(s)
- Roman Radetskyy
- Laboratory of Virus-Cell Interactions, Lady Davis Institute for Medical Research, Canada; Department of Medicine, Division of Experimental Medicine, Canada
| | - Aïcha Daher
- Laboratory of Virus-Cell Interactions, Lady Davis Institute for Medical Research, Canada
| | - Anne Gatignol
- Laboratory of Virus-Cell Interactions, Lady Davis Institute for Medical Research, Canada; Department of Medicine, Division of Experimental Medicine, Canada; Department of Medicine, Division of Infectious Diseases, Canada; Department of Microbiology-Immunology, McGill University, Montréal, Québec, Canada.
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36
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Namer LS, Osman F, Banai Y, Masquida B, Jung R, Kaempfer R. An Ancient Pseudoknot in TNF-α Pre-mRNA Activates PKR, Inducing eIF2α Phosphorylation that Potently Enhances Splicing. Cell Rep 2018; 20:188-200. [PMID: 28683312 DOI: 10.1016/j.celrep.2017.06.035] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2017] [Revised: 05/15/2017] [Accepted: 06/12/2017] [Indexed: 12/22/2022] Open
Abstract
Tumor necrosis factor alpha (TNF-α) is expressed promptly during inflammatory responses. Efficient TNF-α mRNA splicing is achieved through a 3' UTR element that activates RNA-dependent eIF2α protein kinase (PKR). The TNF-α RNA activator, we show, folds into a pseudoknot conserved from teleost fish to humans, critical for PKR activation and mRNA splicing. The pseudoknot constrains the RNA into two double-helical stacks having parallel axes, permitting facile PKR dimerization and trans-autophosphorylation needed for kinase activation. Mutations show that the PKR activator potently enhances splicing without inhibiting translation. eIF2α phosphorylation represses translation and is essential for coping with cellular stress, yet PKR-enabled TNF mRNA splicing depends strictly on eIF2α phosphorylation. Indeed, eIF2α phosphorylation at Serine51 is necessary and sufficient to achieve highly efficient splicing, extending its role from negative control of translation to positive control of splicing. This mechanism, operational in human peripheral blood mononuclear cells (PBMCs), links stress signaling to protective immunity through TNF mRNA splicing rendered efficient upon eIF2α phosphorylation.
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Affiliation(s)
- Lise Sarah Namer
- Department of Biochemistry and Molecular Biology, Institute of Medical Research Israel-Canada, The Hebrew University-Hadassah Medical School, Jerusalem 9112102, Israel
| | - Farhat Osman
- Department of Biochemistry and Molecular Biology, Institute of Medical Research Israel-Canada, The Hebrew University-Hadassah Medical School, Jerusalem 9112102, Israel
| | - Yona Banai
- Department of Biochemistry and Molecular Biology, Institute of Medical Research Israel-Canada, The Hebrew University-Hadassah Medical School, Jerusalem 9112102, Israel
| | - Benoît Masquida
- Génétique Moléculaire Génomique Microbiologie, CNRS-University of Strasbourg, Strasbourg 67084, France
| | - Rodrigo Jung
- Department of Biochemistry and Molecular Biology, Institute of Medical Research Israel-Canada, The Hebrew University-Hadassah Medical School, Jerusalem 9112102, Israel
| | - Raymond Kaempfer
- Department of Biochemistry and Molecular Biology, Institute of Medical Research Israel-Canada, The Hebrew University-Hadassah Medical School, Jerusalem 9112102, Israel.
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37
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Watanabe T, Imamura T, Hiasa Y. Roles of protein kinase R in cancer: Potential as a therapeutic target. Cancer Sci 2018; 109:919-925. [PMID: 29478262 PMCID: PMC5891186 DOI: 10.1111/cas.13551] [Citation(s) in RCA: 37] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2018] [Revised: 02/15/2018] [Accepted: 02/17/2018] [Indexed: 01/13/2023] Open
Abstract
Double‐stranded (ds) RNA‐dependent protein kinase (PKR) is a ubiquitously expressed serine/threonine protein kinase. It was initially identified as an innate immune antiviral protein induced by interferon (IFN) and activated by dsRNA. PKR is recognized as a key executor of antiviral host defense. Moreover, it contributes to inflammation and immune regulation through several signaling pathways. In addition to IFN and dsRNA, PKR is activated by multiple stimuli and regulates various signaling pathways including the mitogen‐activated protein kinase (MAPK) and nuclear factor kappa‐light‐chain‐enhancer of activated B cells pathways. PKR was initially thought to be a tumor suppressor as a result of its ability to suppress cell growth and interact with major tumor suppressor genes. However, in several types of malignant disease, such as colon and breast cancers, its role remains controversial. In hepatocellular carcinoma, hepatitis C virus (HCV) is the main cause of liver cancer, and PKR inhibits HCV replication, indicating its role as a tumor suppressor. However, PKR is overexpressed in cirrhotic patients, and acts as a tumor promoter through enhancement of cancer cell growth by mediating MAPK or signal transducer and activator of transcription pathways. Moreover, PKR is reportedly required for the activation of inflammasomes and influences metabolic disorders. In the present review, we introduce the multifaceted roles of PKR such as antiviral function, tumor cell growth, regulation of inflammatory immune responses, and maintaining metabolic homeostasis; and discuss future perspectives on PKR biology including its potential as a therapeutic target for liver cancer.
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Affiliation(s)
- Takao Watanabe
- Department of Gastroenterology and Metabology, Ehime University Graduate School of Medicine, Toon, Japan
| | - Takeshi Imamura
- Department of Molecular Medicine for Pathogenesis, Ehime University Graduate School of Medicine, Toon, Ehime, Japan.,Translational Research Center, Ehime University Hospital, Toon, Japan
| | - Yoichi Hiasa
- Department of Gastroenterology and Metabology, Ehime University Graduate School of Medicine, Toon, Japan
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38
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Czerkies M, Korwek Z, Prus W, Kochańczyk M, Jaruszewicz-Błońska J, Tudelska K, Błoński S, Kimmel M, Brasier AR, Lipniacki T. Cell fate in antiviral response arises in the crosstalk of IRF, NF-κB and JAK/STAT pathways. Nat Commun 2018; 9:493. [PMID: 29402958 PMCID: PMC5799375 DOI: 10.1038/s41467-017-02640-8] [Citation(s) in RCA: 62] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/29/2016] [Accepted: 12/14/2017] [Indexed: 12/24/2022] Open
Abstract
The innate immune system processes pathogen-induced signals into cell fate decisions. How information is turned to decision remains unknown. By combining stochastic mathematical modelling and experimentation, we demonstrate that feedback interactions between the IRF3, NF-κB and STAT pathways lead to switch-like responses to a viral analogue, poly(I:C), in contrast to pulse-like responses to bacterial LPS. Poly(I:C) activates both IRF3 and NF-κB, a requirement for induction of IFNβ expression. Autocrine IFNβ initiates a JAK/STAT-mediated positive-feedback stabilising nuclear IRF3 and NF-κB in first responder cells. Paracrine IFNβ, in turn, sensitises second responder cells through a JAK/STAT-mediated positive feedforward pathway that upregulates the positive-feedback components: RIG-I, PKR and OAS1A. In these sensitised cells, the 'live-or-die' decision phase following poly(I:C) exposure is shorter-they rapidly produce antiviral responses and commit to apoptosis. The interlinked positive feedback and feedforward signalling is key for coordinating cell fate decisions in cellular populations restricting pathogen spread.
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Affiliation(s)
- Maciej Czerkies
- Institute of Fundamental Technological Research, Polish Academy of Sciences, Warsaw, 02-106, Poland
| | - Zbigniew Korwek
- Institute of Fundamental Technological Research, Polish Academy of Sciences, Warsaw, 02-106, Poland
| | - Wiktor Prus
- Institute of Fundamental Technological Research, Polish Academy of Sciences, Warsaw, 02-106, Poland
| | - Marek Kochańczyk
- Institute of Fundamental Technological Research, Polish Academy of Sciences, Warsaw, 02-106, Poland
| | | | - Karolina Tudelska
- Institute of Fundamental Technological Research, Polish Academy of Sciences, Warsaw, 02-106, Poland
| | - Sławomir Błoński
- Institute of Fundamental Technological Research, Polish Academy of Sciences, Warsaw, 02-106, Poland
| | - Marek Kimmel
- Departments of Statistics and Bioengineering, and Program in Systems, Synthetic, and Physical Biology, Rice University, Houston, TX, 77005, USA
- Systems Engineering Group, Silesian University of Technology, Gliwice, 44-100, Poland
| | - Allan R Brasier
- Institute for Translational Sciences, University of Texas Medical Branch, Galveston, TX, 77555-1060, USA
| | - Tomasz Lipniacki
- Institute of Fundamental Technological Research, Polish Academy of Sciences, Warsaw, 02-106, Poland.
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39
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Chukwurah E, Willingham V, Singh M, Castillo-Azofeifa D, Patel RC. Contribution of the two dsRBM motifs to the double-stranded RNA binding and protein interactions of PACT. J Cell Biochem 2018; 119:3598-3607. [PMID: 29231267 DOI: 10.1002/jcb.26561] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2017] [Accepted: 12/01/2017] [Indexed: 11/12/2022]
Abstract
PACT is a stress-modulated activator of protein kinase PKR (protein kinase, RNA activated), which is involved in antiviral innate immune responses and stress-induced apoptosis. Stress-induced phosphorylation of PACT is essential for PACT's increased association with PKR leading to PKR activation, phosphorylation of translation initiation factor eIF2α, inhibition of protein synthesis, and apoptosis. PACT-induced PKR activation is negatively regulated by TRBP (transactivation response element RNA-binding protein), which dissociates from PACT after PACT phosphorylation in response to stress signals. The conserved double-stranded RNA binding motifs (dsRBMs) in PKR, PACT, and TRBP mediate protein-protein interactions, and the stress-dependent phosphorylation of PACT changes the relative strengths of PKR-PACT, PACT-TRBP, and PACT-PACT interactions to bring about a timely and transient PKR activation. This regulates the general kinetics as well as level of eIF2α phosphorylation, thereby influencing the cellular response to stress either as recovery and survival or elimination by apoptosis. In the present study, we evaluated the effect of specific mutations within PACT's two evolutionarily conserved dsRBMs on dsRNA-binding, and protein-protein interactions between PKR, PACT, and TRBP. Our data show that the two motifs contribute to varying extents in dsRNA binding, and protein interactions. These findings indicate that although the dsRBM motifs have high sequence conservation, their functional contribution in the context of the whole proteins needs to be determined by mutational analysis. Furthermore, using a PACT mutant that is deficient in PACT-PACT interaction but competent for PACT-PKR interaction, we demonstrate that PACT-PACT interaction is essential for efficient PKR activation.
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Affiliation(s)
- Evelyn Chukwurah
- Department of Biological Sciences, University of South Carolina, Columbia, South Carolina
| | - Victoria Willingham
- Department of Biological Sciences, University of South Carolina, Columbia, South Carolina
| | - Madhurima Singh
- Department of Biological Sciences, University of South Carolina, Columbia, South Carolina
| | | | - Rekha C Patel
- Department of Biological Sciences, University of South Carolina, Columbia, South Carolina
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40
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Hwang KD, Bak MS, Kim SJ, Rhee S, Lee YS. Restoring synaptic plasticity and memory in mouse models of Alzheimer's disease by PKR inhibition. Mol Brain 2017; 10:57. [PMID: 29233183 PMCID: PMC5727890 DOI: 10.1186/s13041-017-0338-3] [Citation(s) in RCA: 33] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2017] [Accepted: 11/19/2017] [Indexed: 01/27/2023] Open
Abstract
Alzheimer’s disease (AD) is a neurodegenerative disorder associated with deficits in cognition and synaptic plasticity. While accumulation of amyloid β (Aβ) and hyper-phosphorylation of tau are parts of the etiology, AD can be caused by a large number of different genetic mutations and other unknown factors. Considering such a heterogeneous nature of AD, it would be desirable to develop treatment strategies that can improve memory irrespective of the individual causes. Reducing the phosphorylation of eukaryotic translation initiation factor 2α (eIF2α) was shown to enhance long-term memory and synaptic plasticity in naïve mice. Moreover, hyper-phosphorylation of eIF2α is observed in the brains of postmortem AD patients. Therefore, regulating eIF2α phosphorylation can be a plausible candidate for restoring memory in AD by targeting memory-enhancing mechanism. In this study, we examined whether PKR inhibition can rescue synaptic and learning deficits in two different AD mouse models; 5XFAD transgenic and Aβ1–42-injected mice. We found that the acute treatment of PKR inhibitor (PKRi) can restore the deficits in long-term memory and long-term potentiation (LTP) in both mouse models without affecting the Aβ load in the hippocampus. Our results prove the principle that targeting memory enhancing mechanisms can be a valid candidate for developing AD treatment.
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Affiliation(s)
- Kyoung-Doo Hwang
- Department of Life Science, College of Natural Science, Chung-Ang University, Seoul, 06974, Republic of Korea
| | - Myeong Seong Bak
- Department of Physiology, Seoul National University College of Medicine, Seoul, 03080, Republic of Korea.,Department of Biomedical Sciences, Seoul National University College of Medicine, Seoul, 03080, Republic of Korea
| | - Sang Jeong Kim
- Department of Physiology, Seoul National University College of Medicine, Seoul, 03080, Republic of Korea.,Department of Biomedical Sciences, Seoul National University College of Medicine, Seoul, 03080, Republic of Korea.,Neuroscience Research Institute, Seoul National University College of Medicine, Seoul, 03080, Republic of Korea
| | - Sangmyung Rhee
- Department of Life Science, College of Natural Science, Chung-Ang University, Seoul, 06974, Republic of Korea.
| | - Yong-Seok Lee
- Department of Physiology, Seoul National University College of Medicine, Seoul, 03080, Republic of Korea. .,Department of Biomedical Sciences, Seoul National University College of Medicine, Seoul, 03080, Republic of Korea. .,Neuroscience Research Institute, Seoul National University College of Medicine, Seoul, 03080, Republic of Korea.
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41
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KSHV inhibits stress granule formation by viral ORF57 blocking PKR activation. PLoS Pathog 2017; 13:e1006677. [PMID: 29084250 PMCID: PMC5679657 DOI: 10.1371/journal.ppat.1006677] [Citation(s) in RCA: 49] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2017] [Revised: 11/09/2017] [Accepted: 10/03/2017] [Indexed: 11/18/2022] Open
Abstract
TIA-1 positive stress granules (SG) represent the storage sites of stalled mRNAs and are often associated with the cellular antiviral response. In this report, we provide evidence that Kaposi's sarcoma-associated herpesvirus (KSHV) overcomes the host antiviral response by inhibition of SG formation via a viral lytic protein ORF57. By immunofluorescence analysis, we found that B lymphocytes with KSHV lytic infection are refractory to SG induction. KSHV ORF57, an essential post-transcriptional regulator of viral gene expression and the production of new viral progeny, inhibits SG formation induced experimentally by arsenite and poly I:C, but not by heat stress. KSHV ORF37 (vSOX) bearing intrinsic endoribonuclease activity also inhibits arsenite-induced SG formation, but KSHV RTA, vIRF-2, ORF45, ORF59 and LANA exert no such function. ORF57 binds both PKR-activating protein (PACT) and protein kinase R (PKR) through their RNA-binding motifs and prevents PACT-PKR interaction in the PKR pathway which inhibits KSHV production. Consistently, knocking down PKR expression significantly promotes KSHV virion production. ORF57 interacts with PKR to inhibit PKR binding dsRNA and its autophosphorylation, leading to inhibition of eIF2α phosphorylation and SG formation. Homologous protein HSV-1 ICP27, but not EBV EB2, resembles KSHV ORF57 in the ability to block the PKR/eIF2α/SG pathway. In addition, KSHV ORF57 inhibits poly I:C-induced TLR3 phosphorylation. Altogether, our data provide the first evidence that KSHV ORF57 plays a role in modulating PKR/eIF2α/SG axis and enhances virus production during virus lytic infection.
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42
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A Map of the Arenavirus Nucleoprotein-Host Protein Interactome Reveals that Junín Virus Selectively Impairs the Antiviral Activity of Double-Stranded RNA-Activated Protein Kinase (PKR). J Virol 2017; 91:JVI.00763-17. [PMID: 28539447 DOI: 10.1128/jvi.00763-17] [Citation(s) in RCA: 33] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2017] [Accepted: 05/12/2017] [Indexed: 11/20/2022] Open
Abstract
Arenaviruses are enveloped negative-strand RNA viruses that cause significant human disease. These viruses encode only four proteins to accomplish the viral life cycle, so each arenavirus protein likely plays unappreciated accessory roles during infection. Here we used immunoprecipitation and mass spectrometry to identify human proteins that interact with the nucleoproteins (NPs) of the Old World arenavirus lymphocytic choriomeningitis virus (LCMV) and the New World arenavirus Junín virus (JUNV) strain Candid #1. Bioinformatic analysis of the identified protein partners of NP revealed that host translation appears to be a key biological process engaged during infection. In particular, NP associates with the double-stranded RNA (dsRNA)-activated protein kinase (PKR), a well-characterized antiviral protein that inhibits cap-dependent protein translation initiation via phosphorylation of eIF2α. JUNV infection leads to increased expression of PKR as well as its redistribution to viral replication and transcription factories. Further, phosphorylation of PKR, which is a prerequisite for its ability to phosphorylate eIF2α, is readily induced by JUNV. However, JUNV prevents this pool of activated PKR from phosphorylating eIF2α, even following exposure to the synthetic dsRNA poly(I·C), a potent PKR agonist. This blockade of PKR function is highly specific, as LCMV is unable to similarly inhibit eIF2α phosphorylation. JUNV's ability to antagonize the antiviral activity of PKR appears to be complete, as silencing of PKR expression has no impact on viral propagation. In summary, we provide a detailed map of the host machinery engaged by arenavirus NPs and identify an antiviral pathway that is subverted by JUNV.IMPORTANCE Arenaviruses are important human pathogens for which FDA-approved vaccines do not exist and effective antiviral therapeutics are needed. Design of antiviral treatment options and elucidation of the mechanistic basis of disease pathogenesis will depend on an increased basic understanding of these viruses and, in particular, their interactions with the host cell machinery. Identifying host proteins critical for the viral life cycle and/or pathogenesis represents a useful strategy to uncover new drug targets. This study reveals, for the first time, the extensive human protein interactome of arenavirus nucleoproteins and uncovers a potent antiviral host protein that is neutralized during Junín virus infection. In so doing, it shows further insight into the interplay between the virus and the host innate immune response and provides an important data set for the field.
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43
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Cobbaut M, Derua R, Döppler H, Lou HJ, Vandoninck S, Storz P, Turk BE, Seufferlein T, Waelkens E, Janssens V, Van Lint J. Differential regulation of PKD isoforms in oxidative stress conditions through phosphorylation of a conserved Tyr in the P+1 loop. Sci Rep 2017; 7:887. [PMID: 28428613 PMCID: PMC5430542 DOI: 10.1038/s41598-017-00800-w] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2016] [Accepted: 03/13/2017] [Indexed: 01/06/2023] Open
Abstract
Protein kinases are essential molecules in life and their crucial function requires tight regulation. Many kinases are regulated via phosphorylation within their activation loop. This loop is embedded in the activation segment, which additionally contains the Mg2+ binding loop and a P + 1 loop that is important in substrate binding. In this report, we identify Abl-mediated phosphorylation of a highly conserved Tyr residue in the P + 1 loop of protein kinase D2 (PKD2) during oxidative stress. Remarkably, we observed that the three human PKD isoforms display very different degrees of P + 1 loop Tyr phosphorylation and we identify one of the molecular determinants for this divergence. This is paralleled by a different activation mechanism of PKD1 and PKD2 during oxidative stress. Tyr phosphorylation in the P + 1 loop of PKD2 increases turnover for Syntide-2, while substrate specificity and the role of PKD2 in NF-κB signaling remain unaffected. Importantly, Tyr to Phe substitution renders the kinase inactive, jeopardizing its use as a non-phosphorylatable mutant. Since large-scale proteomics studies identified P + 1 loop Tyr phosphorylation in more than 70 Ser/Thr kinases in multiple conditions, our results do not only demonstrate differential regulation/function of PKD isoforms under oxidative stress, but also have implications for kinase regulation in general.
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Affiliation(s)
- Mathias Cobbaut
- Department of Cellular and Molecular Medicine, Faculty of Medicine, KU Leuven, Leuven, Belgium.,Leuven Cancer Institute (LKI), KU Leuven, Leuven, Belgium
| | - Rita Derua
- Department of Cellular and Molecular Medicine, Faculty of Medicine, KU Leuven, Leuven, Belgium
| | - Heike Döppler
- Department of Cancer Biology, Mayo Clinic, Jacksonville, FL, USA
| | - Hua Jane Lou
- Department of Pharmacology, Yale School of Medicine, New Haven, Connecticut, USA
| | - Sandy Vandoninck
- Department of Cellular and Molecular Medicine, Faculty of Medicine, KU Leuven, Leuven, Belgium
| | - Peter Storz
- Department of Cancer Biology, Mayo Clinic, Jacksonville, FL, USA
| | - Benjamin E Turk
- Department of Pharmacology, Yale School of Medicine, New Haven, Connecticut, USA
| | | | - Etienne Waelkens
- Department of Cellular and Molecular Medicine, Faculty of Medicine, KU Leuven, Leuven, Belgium
| | - Veerle Janssens
- Department of Cellular and Molecular Medicine, Faculty of Medicine, KU Leuven, Leuven, Belgium.,Leuven Cancer Institute (LKI), KU Leuven, Leuven, Belgium
| | - Johan Van Lint
- Department of Cellular and Molecular Medicine, Faculty of Medicine, KU Leuven, Leuven, Belgium. .,Leuven Cancer Institute (LKI), KU Leuven, Leuven, Belgium.
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44
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PKR activation and eIF2α phosphorylation mediate human globin mRNA splicing at spliceosome assembly. Cell Res 2017; 27:688-704. [PMID: 28374749 DOI: 10.1038/cr.2017.39] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2016] [Revised: 11/20/2016] [Accepted: 12/30/2016] [Indexed: 02/01/2023] Open
Abstract
Short elements in mammalian mRNA can control gene expression by activating the RNA-dependent protein kinase PKR that attenuates translation by phosphorylating cytoplasmic eukaryotic initiation factor 2α (eIF2α). We demonstrate a novel, positive role for PKR activation and eIF2α phosphorylation in human globin mRNA splicing. PKR localizes in splicing complexes and associates with splicing factor SC35. Splicing and early-stage spliceosome assembly on β-globin pre-mRNA depend strictly on activation of PKR by a codon-containing RNA fragment within exon 1 and on phosphorylation of nuclear eIF2α on Serine 51. Nonphosphorylatable mutant eIF2αS51A blocked β-globin mRNA splicing in cells and nuclear extract. Mutations of the β-globin RNA activator abrogated PKR activation and profoundly affected mRNA splicing efficiency. PKR depletion abrogated splicing and spliceosome assembly; recombinant PKR effectively restored splicing. Excision of the first intron of β-globin induces strand displacement within the RNA activator of PKR by a sequence from exon 2, a structural rearrangement that silences the ability of spliced β-globin mRNA to activate PKR. Thus, the ability to activate PKR is transient, serving solely to enable splicing. α-Globin pre-mRNA splicing is controlled likewise but positions of PKR activator and silencer are reversed, demonstrating evolutionary flexibility in how PKR activation regulates globin mRNA splicing through eIF2α phosphorylation.
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45
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ADAR1 and PACT contribute to efficient translation of transcripts containing HIV-1 trans-activating response (TAR) element. Biochem J 2017; 474:1241-1257. [PMID: 28167698 PMCID: PMC5363390 DOI: 10.1042/bcj20160964] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2016] [Revised: 01/30/2017] [Accepted: 02/06/2017] [Indexed: 12/15/2022]
Abstract
Human immunodeficiency virus type 1 (HIV-1) has evolved various measures to counter the host cell's innate antiviral response during the course of infection. Interferon (IFN)-stimulated gene products are produced following HIV-1 infection to limit viral replication, but viral proteins and RNAs counteract their effect. One such mechanism is specifically directed against the IFN-induced Protein Kinase PKR, which is centrally important to the cellular antiviral response. In the presence of viral RNAs, PKR is activated and phosphorylates the translation initiation factor eIF2α. This shuts down the synthesis of both host and viral proteins, allowing the cell to mount an effective antiviral response. PACT (protein activator of PKR) is a cellular protein activator of PKR, primarily functioning to activate PKR in response to cellular stress. Recent studies have indicated that during HIV-1 infection, PACT's normal cellular function is compromised and that PACT is unable to activate PKR. Using various reporter systems and in vitro kinase assays, we establish in this report that interactions between PACT, ADAR1 and HIV-1-encoded Tat protein diminish the activation of PKR in response to HIV-1 infection. Our results highlight an important pathway by which HIV-1 transcripts subvert the host cell's antiviral activities to enhance their translation.
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46
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Smad7 knockdown activates protein kinase RNA-associated eIF2α pathway leading to colon cancer cell death. Cell Death Dis 2017; 8:e2681. [PMID: 28300830 PMCID: PMC5386514 DOI: 10.1038/cddis.2017.103] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2016] [Revised: 02/10/2017] [Accepted: 02/13/2017] [Indexed: 02/06/2023]
Abstract
Upregulation of Smad7, an inhibitor of transforming growth factor-β1 (TGF-β1), occurs in sporadic colorectal cancer (CRC) and knockdown of Smad7 inhibits CRC cell growth, a phenomenon that associates with decreased expression of cell division cycle 25 homolog A and arrest of cells in the S phase of the cell cycle. These findings occur in CRC cells unresponsive to TGF-β1, thus suggesting the existence of a Smad7-mediated TGF-β1-independent mechanism that controls CRC cell behavior. Here we show that Smad7 inhibition with a specific Smad7 antisense oligonucleotide upregulates eukaryotic translation initiation factor 2α (eIF2α) phosphorylation, a transcription factor involved in the regulation of cell cycle arrest and induction of cell death, and induces activating transcription factor 4 (ATF4) and CCAAT/enhancer binding protein homology protein (CHOP), two downstream targets of eIF2α. Among the upstream kinases that control eIF2α phosphorylation, the serine-threonine protein kinase RNA (PKR), but not general control non-derepressible 2 (GCN2) and protein kinase RNA-like endoplasmic reticulum kinase (PERK), is activated by Smad7 knockdown. PKR silencing abolishes Smad7 antisense-induced eIF2α phosphorylation and ATF4/CHOP induction, thereby preventing Smad7 antisense-driven cell death. Smad7 inhibition diminishes interaction of PKR with protein kinase inhibitor p58 (p58IPK), a cellular inhibitor of PKR, but does not change the expression and/or activity of other factors involved in the control of PKR activation. These findings delineate a novel mechanism by which Smad7 knockdown promotes CRC cell death.
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47
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DUX4-induced dsRNA and MYC mRNA stabilization activate apoptotic pathways in human cell models of facioscapulohumeral dystrophy. PLoS Genet 2017; 13:e1006658. [PMID: 28273136 PMCID: PMC5362247 DOI: 10.1371/journal.pgen.1006658] [Citation(s) in RCA: 65] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2016] [Revised: 03/22/2017] [Accepted: 02/26/2017] [Indexed: 12/19/2022] Open
Abstract
Facioscapulohumeral dystrophy (FSHD) is caused by the mis-expression of DUX4 in skeletal muscle cells. DUX4 is a transcription factor that activates genes normally associated with stem cell biology and its mis-expression in FSHD cells results in apoptosis. To identify genes and pathways necessary for DUX4-mediated apoptosis, we performed an siRNA screen in an RD rhabdomyosarcoma cell line with an inducible DUX4 transgene. Our screen identified components of the MYC-mediated apoptotic pathway and the double-stranded RNA (dsRNA) innate immune response pathway as mediators of DUX4-induced apoptosis. Further investigation revealed that DUX4 expression led to increased MYC mRNA, accumulation of nuclear dsRNA foci, and activation of the dsRNA response pathway in both RD cells and human myoblasts. Nuclear dsRNA foci were associated with aggregation of the exon junction complex component EIF4A3. The elevation of MYC mRNA, dsRNA accumulation, and EIF4A3 nuclear aggregates in FSHD muscle cells suggest that these processes might contribute to FSHD pathophysiology. Facioscapulohumeral dystrophy (FSHD) is a common form of muscular dystrophy which is currently untreatable. It is caused by the inappropriate expression in skeletal muscle of the gene DUX4 that encodes a transcription factor normally expressed in some stem cells. When DUX4 is expressed in cultured human or mouse skeletal muscle cells, it activates a program of cell death. Knowing the molecular basis for the cell death induced by DUX4 is important to determine the mechanism of muscle damage in FSHD. We used a molecular screening approach to identify genes and pathways necessary for DUX4 to induce the cell death program. We found that DUX4 activated a known MYC-induced cell death pathway, at least in part through stabilization of MYC mRNA. We also found that DUX4 expression led to an accumulation of double stranded RNAs (dsRNAs) that induced a cell death pathway evolved to protect against viral infections. This dsRNA accumulation was accompanied by aggregation of the EIF4A3 protein, a factor involved in mRNA surveillance and decay, which may provide a partial mechanism for how DUX4 can inhibit RNA quality control pathways in cells. Because FSHD muscle cells have increased MYC mRNA, dsRNA accumulation, and EIF4A3 nuclear aggregates, we conclude that these processes might contribute to FSHD pathophysiology.
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48
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Abstract
During viral and bacterial infections, pathogen-derived cytosolic nucleic acids are recognized by the intracellular RNA sensors retinoic acid-inducible gene I and melanoma-differentiated gene 5 and intracellular DNA sensors, including cyclic-di-GMP-AMP synthase, absent in melanoma 2, interferon (IFN)-gamma inducible protein 16, polymerase III, and so on. Binding of intracellular nucleic acids to these sensors activates downstream signaling cascades, resulting in the production of type I IFNs and pro-inflammatory cytokines to induce appropriate systematic immune responses. While these sensors also recognize endogenous nucleic acids and activate immune responses, they can discriminate between self- and non-self-nucleic acids. However, dysfunction of these sensors or failure of regulatory mechanisms causes aberrant activation of immune response and autoimmune disorders. In this review, we focus on how intracellular immune sensors recognize exogenous nucleic acids and activate the innate immune system, and furthermore, how autoimmune diseases result from dysfunction of these sensors.
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Affiliation(s)
- Daisuke Ori
- a Laboratory of Molecular Immunobiology , Graduate School of Biological Sciences, Nara Institute of Science and Technology (NAIST), Takayama-cho , Ikoma , Nara , Japan
| | - Motoya Murase
- a Laboratory of Molecular Immunobiology , Graduate School of Biological Sciences, Nara Institute of Science and Technology (NAIST), Takayama-cho , Ikoma , Nara , Japan
| | - Taro Kawai
- a Laboratory of Molecular Immunobiology , Graduate School of Biological Sciences, Nara Institute of Science and Technology (NAIST), Takayama-cho , Ikoma , Nara , Japan
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49
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Mechanism of Protein Kinase R Inhibition by Human Cytomegalovirus pTRS1. J Virol 2017; 91:JVI.01574-16. [PMID: 27974558 DOI: 10.1128/jvi.01574-16] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2016] [Accepted: 12/06/2016] [Indexed: 01/20/2023] Open
Abstract
Double-stranded RNAs (dsRNA) produced during human cytomegalovirus (HCMV) infection activate the antiviral kinase protein kinase R (PKR), which potently inhibits virus replication. The HCMV pTRS1 and pIRS1 proteins antagonize PKR to promote HCMV protein synthesis and replication; however, the mechanism by which pTRS1 inhibits PKR is unclear. PKR activation occurs in a three-step cascade. First, binding to dsRNA triggers PKR homodimerizaton. PKR dimers then autophosphorylate, leading to a conformational shift that exposes the binding site for the PKR substrate eIF2α. Consistent with previous in vitro studies, we found that pTRS1 bound and inhibited PKR. pTRS1 binding to PKR was not mediated by an RNA intermediate, and mutations in the pTRS1 RNA binding domain did not affect PKR binding or inhibition. Rather, mutations that disrupted the pTRS1 interaction with PKR ablated the ability of pTRS1 to antagonize PKR activation by dsRNA. pTRS1 did not block PKR dimerization and could bind and inhibit a constitutively dimerized PKR kinase domain. In addition, pTRS1 binding to PKR inhibited PKR kinase activity. Single amino acid point mutations in the conserved eIF2α binding domain of PKR disrupted pTRS1 binding and rendered PKR resistant to inhibition by pTRS1. Consistent with a critical role for the conserved eIF2α contact site in PKR binding, pTRS1 bound an additional eIF2α kinase, heme-regulated inhibitor (HRI), and inhibited eIF2α phosphorylation in response to an HRI agonist. Together our data suggest that pTRS1 inhibits PKR by binding to conserved amino acids in the PKR eIF2α binding site and blocking PKR kinase activity.IMPORTANCE The antiviral kinase PKR plays a critical role in controlling HCMV replication. This study furthered our understanding of how HCMV evades inhibition by PKR and identified new strategies for how PKR activity might be restored during infection to limit HCMV disease.
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50
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Pakos-Zebrucka K, Koryga I, Mnich K, Ljujic M, Samali A, Gorman AM. The integrated stress response. EMBO Rep 2016; 17:1374-1395. [PMID: 27629041 DOI: 10.15252/embr.201642195] [Citation(s) in RCA: 1500] [Impact Index Per Article: 187.5] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2016] [Accepted: 08/23/2016] [Indexed: 02/06/2023] Open
Abstract
In response to diverse stress stimuli, eukaryotic cells activate a common adaptive pathway, termed the integrated stress response (ISR), to restore cellular homeostasis. The core event in this pathway is the phosphorylation of eukaryotic translation initiation factor 2 alpha (eIF2α) by one of four members of the eIF2α kinase family, which leads to a decrease in global protein synthesis and the induction of selected genes, including the transcription factor ATF4, that together promote cellular recovery. The gene expression program activated by the ISR optimizes the cellular response to stress and is dependent on the cellular context, as well as on the nature and intensity of the stress stimuli. Although the ISR is primarily a pro-survival, homeostatic program, exposure to severe stress can drive signaling toward cell death. Here, we review current understanding of the ISR signaling and how it regulates cell fate under diverse types of stress.
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Affiliation(s)
- Karolina Pakos-Zebrucka
- Apoptosis Research Centre, National University of Ireland Galway, Galway, Ireland School of Natural Sciences, National University of Ireland Galway, Galway, Ireland
| | - Izabela Koryga
- Apoptosis Research Centre, National University of Ireland Galway, Galway, Ireland School of Natural Sciences, National University of Ireland Galway, Galway, Ireland
| | - Katarzyna Mnich
- Apoptosis Research Centre, National University of Ireland Galway, Galway, Ireland School of Natural Sciences, National University of Ireland Galway, Galway, Ireland
| | - Mila Ljujic
- Apoptosis Research Centre, National University of Ireland Galway, Galway, Ireland School of Natural Sciences, National University of Ireland Galway, Galway, Ireland
| | - Afshin Samali
- Apoptosis Research Centre, National University of Ireland Galway, Galway, Ireland School of Natural Sciences, National University of Ireland Galway, Galway, Ireland
| | - Adrienne M Gorman
- Apoptosis Research Centre, National University of Ireland Galway, Galway, Ireland School of Natural Sciences, National University of Ireland Galway, Galway, Ireland
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