1
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Chambers MJ, Scobell SB, Sadhu MJ. Systematic genetic characterization of the human PKR kinase domain highlights its functional malleability to escape a viral substrate mimic. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.05.29.596416. [PMID: 38903081 PMCID: PMC11188142 DOI: 10.1101/2024.05.29.596416] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/22/2024]
Abstract
Evolutionary arms races can arise at the contact surfaces between host and viral proteins, producing dynamic spaces in which genetic variants are continually pursued. However, the sampling of genetic variation must be balanced with the need to maintain protein function. A striking case is given by protein kinase R (PKR), a member of the mammalian innate immune system. PKR detects viral replication within the host cell and halts protein synthesis to prevent viral replication by phosphorylating eIF2α, a component of the translation initiation machinery. PKR is targeted by many viral antagonists, including poxvirus pseudosubstrate antagonists that inhibit PKR by interacting with the same binding surface as eIF2α. Remarkably, PKR has several rapidly evolving residues at this interface, suggesting it is engaging in an evolutionary arms race, despite the surface's critical role in phosphorylating eIF2α. To systematically explore the evolutionary opportunities available at this dynamic interface, we generated and characterized a library of 426 SNP-accessible nonsynonymous variants of human PKR for their ability to escape inhibition by the model pseudosubstrate inhibitor K3 from vaccinia virus. We identified key sites in the PKR kinase domain that harbor K3-resistant variants, as well as critical sites where variation leads to loss of function. We find K3-resistant variants are readily available throughout the interface and are enriched at sites under positive selection. Moreover, variants beneficial against K3 were also beneficial against an enhanced variant of K3, indicating resilience to viral adaptation. Overall, we find that the eIF2α-binding surface of PKR is highly malleable, potentiating its evolutionary ability to combat viral inhibition.
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Affiliation(s)
- Michael J Chambers
- Center for Genomics and Data Science Research, National Human Genome Research Institute, National Institutes of Health, Bethesda, Maryland, USA
- Department of Microbiology & Immunology, Georgetown University, Washington DC, USA
| | - Sophia B Scobell
- Center for Genomics and Data Science Research, National Human Genome Research Institute, National Institutes of Health, Bethesda, Maryland, USA
| | - Meru J Sadhu
- Center for Genomics and Data Science Research, National Human Genome Research Institute, National Institutes of Health, Bethesda, Maryland, USA
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2
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Wang X, Zhu B. SARS-CoV-2 nsp15 preferentially degrades AU-rich dsRNA via its dsRNA nickase activity. Nucleic Acids Res 2024; 52:5257-5272. [PMID: 38634805 PMCID: PMC11109939 DOI: 10.1093/nar/gkae290] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2023] [Revised: 04/02/2024] [Accepted: 04/05/2024] [Indexed: 04/19/2024] Open
Abstract
It has been proposed that coronavirus nsp15 mediates evasion of host cell double-stranded (ds) RNA sensors via its uracil-specific endoribonuclease activity. However, how nsp15 processes viral dsRNA, commonly considered as a genome replication intermediate, remains elusive. Previous research has mainly focused on short single-stranded RNA as substrates, and whether nsp15 prefers single-stranded or double-stranded RNA for cleavage is controversial. In the present work, we prepared numerous RNA substrates, including both long substrates mimicking the viral genome and short defined RNA, to clarify the substrate preference and cleavage pattern of SARS-CoV-2 nsp15. We demonstrated that SARS-CoV-2 nsp15 preferentially cleaved pyrimidine nucleotides located in less thermodynamically stable areas in dsRNA, such as AU-rich areas and mismatch-containing areas, in a nicking manner. Because coronavirus genomes generally have a high AU content, our work supported the mechanism that coronaviruses evade the antiviral response mediated by host cell dsRNA sensors by using nsp15 dsRNA nickase to directly cleave dsRNA intermediates formed during genome replication and transcription.
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Affiliation(s)
- Xionglue Wang
- Key Laboratory of Molecular Biophysics, the Ministry of Education, College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan, Hubei 430074, China
| | - Bin Zhu
- Key Laboratory of Molecular Biophysics, the Ministry of Education, College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan, Hubei 430074, China
- Shenzhen Huazhong University of Science and Technology Research Institute, Shenzhen 518063, China
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3
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Saw PE, Song E. Advancements in clinical RNA therapeutics: Present developments and prospective outlooks. Cell Rep Med 2024; 5:101555. [PMID: 38744276 PMCID: PMC11148805 DOI: 10.1016/j.xcrm.2024.101555] [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: 01/16/2024] [Revised: 03/05/2024] [Accepted: 04/15/2024] [Indexed: 05/16/2024]
Abstract
RNA molecules have emerged as promising clinical therapeutics due to their ability to target "undruggable" proteins or molecules with high precision and minimal side effects. Nevertheless, the primary challenge in RNA therapeutics lies in rapid degradation and clearance from systemic circulation, the inability to traverse cell membranes, and the efficient intracellular delivery of bioactive RNA molecules. In this review, we explore the implications of RNAs in diseases and provide a chronological overview of the development of RNA therapeutics. Additionally, we summarize the technological advances in RNA-screening design, encompassing various RNA databases and design platforms. The paper then presents an update on FDA-approved RNA therapeutics and those currently undergoing clinical trials for various diseases, with a specific emphasis on RNA medicine and RNA vaccines.
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Affiliation(s)
- Phei Er Saw
- Guangdong Provincial Key Laboratory of Malignant Tumor Epigenetics and Gene Regulation, Guangdong-Hong Kong Joint Laboratory for RNA Medicine, Sun Yat-sen Memorial Hospital, Sun Yat-sen University, Guangzhou 510120, China; Nanhai Clinical Translational Center, Sun Yat-sen Memorial Hospital, Foshan 528200, China
| | - Erwei Song
- Guangdong Provincial Key Laboratory of Malignant Tumor Epigenetics and Gene Regulation, Guangdong-Hong Kong Joint Laboratory for RNA Medicine, Sun Yat-sen Memorial Hospital, Sun Yat-sen University, Guangzhou 510120, China; Nanhai Clinical Translational Center, Sun Yat-sen Memorial Hospital, Foshan 528200, China; Breast Tumor Center, Sun Yat-sen Memorial Hospital, Sun Yat-sen University, Guangzhou 510120, China.
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4
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Guo SK, Liu CX, Xu YF, Wang X, Nan F, Huang Y, Li S, Nan S, Li L, Kon E, Li C, Wei MY, Su R, Wei J, Peng S, Ad-El N, Liu J, Peer D, Chen T, Yang L, Chen LL. Therapeutic application of circular RNA aptamers in a mouse model of psoriasis. Nat Biotechnol 2024:10.1038/s41587-024-02204-4. [PMID: 38653797 DOI: 10.1038/s41587-024-02204-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2023] [Accepted: 03/12/2024] [Indexed: 04/25/2024]
Abstract
Efforts to advance RNA aptamers as a new therapeutic modality have been limited by their susceptibility to degradation and immunogenicity. In a previous study, we demonstrated synthesized short double-stranded region-containing circular RNAs (ds-cRNAs) with minimal immunogenicity targeted to dsRNA-activated protein kinase R (PKR). Here we test the therapeutic potential of ds-cRNAs in a mouse model of imiquimod-induced psoriasis. We find that genetic supplementation of ds-cRNAs leads to inhibition of PKR, resulting in alleviation of downstream interferon-α and dsRNA signals and attenuation of psoriasis phenotypes. Delivery of ds-cRNAs by lipid nanoparticles to the spleen attenuates PKR activity in examined splenocytes, resulting in reduced epidermal thickness. These findings suggest that ds-cRNAs represent a promising approach to mitigate excessive PKR activation for therapeutic purposes.
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Affiliation(s)
- Si-Kun Guo
- Key Laboratory of RNA Innovation, Science and Engineering, CAS Center for Excellence in Molecular Cell Science, Shanghai Institute of Biochemistry and Cell Biology, University of Chinese Academy of Sciences, Chinese Academy of Sciences, Shanghai, China
| | - Chu-Xiao Liu
- Key Laboratory of RNA Innovation, Science and Engineering, CAS Center for Excellence in Molecular Cell Science, Shanghai Institute of Biochemistry and Cell Biology, University of Chinese Academy of Sciences, Chinese Academy of Sciences, Shanghai, China
| | - Yi-Feng Xu
- Key Laboratory of RNA Innovation, Science and Engineering, CAS Center for Excellence in Molecular Cell Science, Shanghai Institute of Biochemistry and Cell Biology, University of Chinese Academy of Sciences, Chinese Academy of Sciences, Shanghai, China
| | - Xiao Wang
- Key Laboratory of RNA Innovation, Science and Engineering, CAS Center for Excellence in Molecular Cell Science, Shanghai Institute of Biochemistry and Cell Biology, University of Chinese Academy of Sciences, Chinese Academy of Sciences, Shanghai, China
| | - Fang Nan
- Center for Molecular Medicine, Children's Hospital of Fudan University and Shanghai Key Laboratory of Medical Epigenetics, International Laboratory of Medical Epigenetics and Metabolism, Ministry of Science and Technology, Institutes of Biomedical Sciences, Fudan University, Shanghai, China
| | - Youkui Huang
- Key Laboratory of RNA Innovation, Science and Engineering, CAS Center for Excellence in Molecular Cell Science, Shanghai Institute of Biochemistry and Cell Biology, University of Chinese Academy of Sciences, Chinese Academy of Sciences, Shanghai, China
| | - Siqi Li
- Key Laboratory of RNA Innovation, Science and Engineering, CAS Center for Excellence in Molecular Cell Science, Shanghai Institute of Biochemistry and Cell Biology, University of Chinese Academy of Sciences, Chinese Academy of Sciences, Shanghai, China
| | - Shan Nan
- Key Laboratory of RNA Innovation, Science and Engineering, CAS Center for Excellence in Molecular Cell Science, Shanghai Institute of Biochemistry and Cell Biology, University of Chinese Academy of Sciences, Chinese Academy of Sciences, Shanghai, China
| | - Ling Li
- Key Laboratory of RNA Innovation, Science and Engineering, CAS Center for Excellence in Molecular Cell Science, Shanghai Institute of Biochemistry and Cell Biology, University of Chinese Academy of Sciences, Chinese Academy of Sciences, Shanghai, China
- School of Life Science and Technology, ShanghaiTech University, Shanghai, China
| | - Edo Kon
- Laboratory of Precision Nanomedicine, Shmunis School of Biomedicine and Cancer Research, George S. Wise Faculty of Life Sciences, Department of Materials Sciences and Engineering, Iby and Aladar Fleischman Faculty of Engineering, Center for Nanoscience and Nanotechnology, Cancer Biology Research Center, Tel Aviv University, Tel Aviv, Israel
| | - Chen Li
- Key Laboratory of RNA Innovation, Science and Engineering, CAS Center for Excellence in Molecular Cell Science, Shanghai Institute of Biochemistry and Cell Biology, University of Chinese Academy of Sciences, Chinese Academy of Sciences, Shanghai, China
| | - Meng-Yuan Wei
- Key Laboratory of RNA Innovation, Science and Engineering, CAS Center for Excellence in Molecular Cell Science, Shanghai Institute of Biochemistry and Cell Biology, University of Chinese Academy of Sciences, Chinese Academy of Sciences, Shanghai, China
| | - Rina Su
- Department of Dermatology, Beijing Chao-yang Hospital, Capital Medical University, Beijing, China
| | - Jia Wei
- Center for Molecular Medicine, Children's Hospital of Fudan University and Shanghai Key Laboratory of Medical Epigenetics, International Laboratory of Medical Epigenetics and Metabolism, Ministry of Science and Technology, Institutes of Biomedical Sciences, Fudan University, Shanghai, China
| | - Shiguang Peng
- Department of Dermatology, Beijing Chao-yang Hospital, Capital Medical University, Beijing, China
| | - Nitay Ad-El
- Laboratory of Precision Nanomedicine, Shmunis School of Biomedicine and Cancer Research, George S. Wise Faculty of Life Sciences, Department of Materials Sciences and Engineering, Iby and Aladar Fleischman Faculty of Engineering, Center for Nanoscience and Nanotechnology, Cancer Biology Research Center, Tel Aviv University, Tel Aviv, Israel
| | - Jiaquan Liu
- Key Laboratory of RNA Innovation, Science and Engineering, CAS Center for Excellence in Molecular Cell Science, Shanghai Institute of Biochemistry and Cell Biology, University of Chinese Academy of Sciences, Chinese Academy of Sciences, Shanghai, China
| | - Dan Peer
- Laboratory of Precision Nanomedicine, Shmunis School of Biomedicine and Cancer Research, George S. Wise Faculty of Life Sciences, Department of Materials Sciences and Engineering, Iby and Aladar Fleischman Faculty of Engineering, Center for Nanoscience and Nanotechnology, Cancer Biology Research Center, Tel Aviv University, Tel Aviv, Israel
| | - Ting Chen
- National Institute of Biological Sciences, Tsinghua Institute of Multidisciplinary Biomedical Research, Tsinghua University, Beijing, China
| | - Li Yang
- Center for Molecular Medicine, Children's Hospital of Fudan University and Shanghai Key Laboratory of Medical Epigenetics, International Laboratory of Medical Epigenetics and Metabolism, Ministry of Science and Technology, Institutes of Biomedical Sciences, Fudan University, Shanghai, China
| | - Ling-Ling Chen
- Key Laboratory of RNA Innovation, Science and Engineering, CAS Center for Excellence in Molecular Cell Science, Shanghai Institute of Biochemistry and Cell Biology, University of Chinese Academy of Sciences, Chinese Academy of Sciences, Shanghai, China.
- School of Life Science and Technology, ShanghaiTech University, Shanghai, China.
- New Cornerstone Science Laboratory, Shenzhen, China.
- Key Laboratory of Systems Health Science of Zhejiang Province, School of Life Science, Hangzhou Institute for Advanced Study, University of Chinese Academy of Sciences, Hangzhou, China.
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5
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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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6
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Aleksashin NA, Chang STL, Cate JHD. A highly efficient human cell-free translation system. RNA (NEW YORK, N.Y.) 2023; 29:1960-1972. [PMID: 37793791 PMCID: PMC10653386 DOI: 10.1261/rna.079825.123] [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: 09/05/2023] [Accepted: 09/21/2023] [Indexed: 10/06/2023]
Abstract
Cell-free protein synthesis (CFPS) systems enable easy in vitro expression of proteins with many scientific, industrial, and therapeutic applications. Here we present an optimized, highly efficient human cell-free translation system that bypasses many limitations of currently used in vitro systems. This CFPS system is based on extracts from human HEK293T cells engineered to endogenously express GADD34 and K3L proteins, which suppress phosphorylation of translation initiation factor eIF2α. Overexpression of GADD34 and K3L proteins in human cells before cell lysate preparation significantly simplifies lysate preparation. We find that expression of the GADD34 and K3L accessory proteins before cell lysis maintains low levels of phosphorylation of eIF2α in the extracts. During in vitro translation reactions, eIF2α phosphorylation increases moderately in a GCN2-dependent fashion that can be inhibited by GCN2 kinase inhibitors. This new CFPS system should be useful for exploring human translation mechanisms in more physiological conditions outside the cell.
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Affiliation(s)
- Nikolay A Aleksashin
- Innovative Genomics Institute, University of California-Berkeley, Berkeley, California 94720, USA
- Department of Molecular and Cell Biology, University of California-Berkeley, Berkeley, California 94720, USA
| | - Stacey Tsai-Lan Chang
- Innovative Genomics Institute, University of California-Berkeley, Berkeley, California 94720, USA
- Department of Molecular and Cell Biology, University of California-Berkeley, Berkeley, California 94720, USA
| | - Jamie H D Cate
- Innovative Genomics Institute, University of California-Berkeley, Berkeley, California 94720, USA
- Department of Molecular and Cell Biology, University of California-Berkeley, Berkeley, California 94720, USA
- Department of Chemistry, University of California-Berkeley, Berkeley, California 94720, USA
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7
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Niu D, Wu Y, Lian J. Circular RNA vaccine in disease prevention and treatment. Signal Transduct Target Ther 2023; 8:341. [PMID: 37691066 PMCID: PMC10493228 DOI: 10.1038/s41392-023-01561-x] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2023] [Revised: 06/02/2023] [Accepted: 07/09/2023] [Indexed: 09/12/2023] Open
Abstract
CircRNAs are a class of single-stranded RNAs with covalently linked head-to-tail topology. In the decades since its initial discovery, their biogenesis, regulation, and function have rapidly disclosed, permitting a better understanding and adoption of them as new tools for medical applications. With the development of biotechnology and molecular medicine, artificial circRNAs have been engineered as a novel class of vaccines for disease treatment and prevention. Unlike the linear mRNA vaccine which applications were limited by its instability, inefficiency, and innate immunogenicity, circRNA vaccine which incorporate internal ribosome entry sites (IRESs) and open reading frame (ORF) provides an improved approach to RNA-based vaccination with safety, stability, simplicity of manufacture, and scalability. However, circRNA vaccines are at an early stage, and their optimization, delivery and applications require further development and evaluation. In this review, we comprehensively describe circRNA vaccine, including their history and superiority. We also summarize and discuss the current methodological research for circRNA vaccine preparation, including their design, synthesis, and purification. Finally, we highlight the delivery options of circRNA vaccine and its potential applications in diseases treatment and prevention. Considering their unique high stability, low immunogenicity, protein/peptide-coding capacity and special closed-loop construction, circRNA vaccine, and circRNA-based therapeutic platforms may have superior application prospects in a broad range of diseases.
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Affiliation(s)
- Dun Niu
- Department of Clinical Laboratory Medicine, Southwest Hospital, Army Medical University (Third Military Medical University), 400038, Chongqing, China
- Department of Clinical Biochemistry, Army Medical University (Third Military Medical University), 400038, Chongqing, China
| | - Yaran Wu
- Department of Clinical Laboratory Medicine, Southwest Hospital, Army Medical University (Third Military Medical University), 400038, Chongqing, China
- Department of Clinical Biochemistry, Army Medical University (Third Military Medical University), 400038, Chongqing, China
| | - Jiqin Lian
- Department of Clinical Laboratory Medicine, Southwest Hospital, Army Medical University (Third Military Medical University), 400038, Chongqing, China.
- Department of Clinical Biochemistry, Army Medical University (Third Military Medical University), 400038, Chongqing, China.
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8
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Aleksashin NA, Chang STL, Cate JHD. A highly efficient human cell-free translation system. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.02.09.527910. [PMID: 36798401 PMCID: PMC9934684 DOI: 10.1101/2023.02.09.527910] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Indexed: 02/12/2023]
Abstract
Cell-free protein synthesis (CFPS) systems enable easy in vitro expression of proteins with many scientific, industrial, and therapeutic applications. Here we present an optimized, highly efficient human cell-free translation system that bypasses many limitations of currently used in vitro systems. This CFPS system is based on extracts from human HEK293T cells engineered to endogenously express GADD34 and K3L proteins, which suppress phosphorylation of translation initiation factor eIF2α. Overexpression of GADD34 and K3L proteins in human cells significantly simplifies cell lysate preparation. The new CFPS system improves the translation of 5' cap-dependent mRNAs as well as those that use internal ribosome entry site (IRES) mediated translation initiation. We find that expression of the GADD34 and K3L accessory proteins before cell lysis maintains low levels of phosphorylation of eIF2α in the extracts. During in vitro translation reactions, eIF2α phosphorylation increases moderately in a GCN2-dependent fashion that can be inhibited by GCN2 kinase inhibitors. We also find evidence for activation of regulatory pathways related to eukaryotic elongation factor 2 (eEF2) phosphorylation and ribosome quality control in the extracts. This new CFPS system should be useful for exploring human translation mechanisms in more physiological conditions outside the cell.
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Affiliation(s)
- Nikolay A. Aleksashin
- Innovative Genomics Institute, University of California-Berkeley, Berkeley, CA, USA
- Department of Molecular & Cell Biology, University of California-Berkeley, Berkeley, CA, USA
| | - Stacey Tsai-Lan Chang
- Innovative Genomics Institute, University of California-Berkeley, Berkeley, CA, USA
- Department of Molecular & Cell Biology, University of California-Berkeley, Berkeley, CA, USA
| | - Jamie H. D. Cate
- Innovative Genomics Institute, University of California-Berkeley, Berkeley, CA, USA
- Department of Molecular & Cell Biology, University of California-Berkeley, Berkeley, CA, USA
- Department of Chemistry, University of California-Berkeley, Berkeley, CA, USA
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9
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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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10
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Li Q, Zhao Y, Xu C, Liang Y, Zhao Y, He Q, Li J, Chen K, Qiao H, Liu N, Ma J, Chen L, Li Y. Chemotherapy-Induced Senescence Reprogramming Promotes Nasopharyngeal Carcinoma Metastasis by circRNA-Mediated PKR Activation. ADVANCED SCIENCE (WEINHEIM, BADEN-WURTTEMBERG, GERMANY) 2023; 10:e2205668. [PMID: 36683218 PMCID: PMC10015868 DOI: 10.1002/advs.202205668] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/29/2022] [Revised: 12/23/2022] [Indexed: 05/13/2023]
Abstract
Senescence is associated with tumor metastasis and chemotherapy resistance, yet the mechanisms remain elusive. Here, it is identified that nasopharyngeal carcinoma (NPC) patients who developed distant metastasis are characterized by senescence phenotypes, in which circWDR37 is a key regulator. CircWDR37 deficiency limits cisplatin or gemcitabine-induced senescent NPC cells from proliferation, migration, and invasion. Mechanistically, circWDR37 binds to and dimerizes double-stranded RNA-activated protein kinase R (PKR) to initiate PKR autophosphorylation and activation. Independent of its kinase activity, phosphorylated PKR induces I-kappaB kinase beta (IKKβ) phosphorylation, binds to and releases RELA from NF-κB inhibitor alpha (IκBα) to trigger nuclear factor kappa B (NF-κB) activation, thereby stimulating cyclin D1 (CCND1) and senescence-associated secretory phenotype component gene transcription in a circWDR37-dependent manner. Low circWDR37 levels correlate with chemotherapy response and favorable survival in NPC patients treated with gemcitabine or cisplatin induction chemotherapy. This study uncovers a new mechanism of circWDR37 activated PKR in senescence-driven metastasis and provides appealing therapeutic targets in NPC.
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Affiliation(s)
- Qian Li
- Sun Yat‐sen University Cancer Centerthe State Key Laboratory of Oncology in South ChinaCollaborative Innovation Center for Cancer MedicineGuangdong Key Laboratory of Nasopharyngeal Carcinoma Diagnosis and TherapyCenter for Precision Medicine of Sun Yat‐sen UniversityGuangzhou510060P. R. China
- Department of Radiation OncologySun Yat‐sen University Cancer CenterGuangzhou510060P. R. China
| | - Yu‐Heng Zhao
- Sun Yat‐sen University Cancer Centerthe State Key Laboratory of Oncology in South ChinaCollaborative Innovation Center for Cancer MedicineGuangdong Key Laboratory of Nasopharyngeal Carcinoma Diagnosis and TherapyCenter for Precision Medicine of Sun Yat‐sen UniversityGuangzhou510060P. R. China
- Department of Experimental ResearchSun Yat‐sen University Cancer CenterGuangzhou510060P. R. China
| | - Cheng Xu
- Sun Yat‐sen University Cancer Centerthe State Key Laboratory of Oncology in South ChinaCollaborative Innovation Center for Cancer MedicineGuangdong Key Laboratory of Nasopharyngeal Carcinoma Diagnosis and TherapyCenter for Precision Medicine of Sun Yat‐sen UniversityGuangzhou510060P. R. China
- Department of Radiation OncologySun Yat‐sen University Cancer CenterGuangzhou510060P. R. China
| | - Ye‐Lin Liang
- Sun Yat‐sen University Cancer Centerthe State Key Laboratory of Oncology in South ChinaCollaborative Innovation Center for Cancer MedicineGuangdong Key Laboratory of Nasopharyngeal Carcinoma Diagnosis and TherapyCenter for Precision Medicine of Sun Yat‐sen UniversityGuangzhou510060P. R. China
- Department of Radiation OncologySun Yat‐sen University Cancer CenterGuangzhou510060P. R. China
| | - Yin Zhao
- Sun Yat‐sen University Cancer Centerthe State Key Laboratory of Oncology in South ChinaCollaborative Innovation Center for Cancer MedicineGuangdong Key Laboratory of Nasopharyngeal Carcinoma Diagnosis and TherapyCenter for Precision Medicine of Sun Yat‐sen UniversityGuangzhou510060P. R. China
- Department of Experimental ResearchSun Yat‐sen University Cancer CenterGuangzhou510060P. R. China
| | - Qing‐Mei He
- Sun Yat‐sen University Cancer Centerthe State Key Laboratory of Oncology in South ChinaCollaborative Innovation Center for Cancer MedicineGuangdong Key Laboratory of Nasopharyngeal Carcinoma Diagnosis and TherapyCenter for Precision Medicine of Sun Yat‐sen UniversityGuangzhou510060P. R. China
- Department of Experimental ResearchSun Yat‐sen University Cancer CenterGuangzhou510060P. R. China
| | - Jun‐Yan Li
- Sun Yat‐sen University Cancer Centerthe State Key Laboratory of Oncology in South ChinaCollaborative Innovation Center for Cancer MedicineGuangdong Key Laboratory of Nasopharyngeal Carcinoma Diagnosis and TherapyCenter for Precision Medicine of Sun Yat‐sen UniversityGuangzhou510060P. R. China
- Department of Radiation OncologySun Yat‐sen University Cancer CenterGuangzhou510060P. R. China
| | - Kai‐Lin Chen
- Sun Yat‐sen University Cancer Centerthe State Key Laboratory of Oncology in South ChinaCollaborative Innovation Center for Cancer MedicineGuangdong Key Laboratory of Nasopharyngeal Carcinoma Diagnosis and TherapyCenter for Precision Medicine of Sun Yat‐sen UniversityGuangzhou510060P. R. China
- Department of Radiation OncologySun Yat‐sen University Cancer CenterGuangzhou510060P. R. China
| | - Han Qiao
- Sun Yat‐sen University Cancer Centerthe State Key Laboratory of Oncology in South ChinaCollaborative Innovation Center for Cancer MedicineGuangdong Key Laboratory of Nasopharyngeal Carcinoma Diagnosis and TherapyCenter for Precision Medicine of Sun Yat‐sen UniversityGuangzhou510060P. R. China
- Department of Experimental ResearchSun Yat‐sen University Cancer CenterGuangzhou510060P. R. China
| | - Na Liu
- Sun Yat‐sen University Cancer Centerthe State Key Laboratory of Oncology in South ChinaCollaborative Innovation Center for Cancer MedicineGuangdong Key Laboratory of Nasopharyngeal Carcinoma Diagnosis and TherapyCenter for Precision Medicine of Sun Yat‐sen UniversityGuangzhou510060P. R. China
- Department of Experimental ResearchSun Yat‐sen University Cancer CenterGuangzhou510060P. R. China
| | - Jun Ma
- Sun Yat‐sen University Cancer Centerthe State Key Laboratory of Oncology in South ChinaCollaborative Innovation Center for Cancer MedicineGuangdong Key Laboratory of Nasopharyngeal Carcinoma Diagnosis and TherapyCenter for Precision Medicine of Sun Yat‐sen UniversityGuangzhou510060P. R. China
- Department of Radiation OncologySun Yat‐sen University Cancer CenterGuangzhou510060P. R. China
| | - Lei Chen
- Sun Yat‐sen University Cancer Centerthe State Key Laboratory of Oncology in South ChinaCollaborative Innovation Center for Cancer MedicineGuangdong Key Laboratory of Nasopharyngeal Carcinoma Diagnosis and TherapyCenter for Precision Medicine of Sun Yat‐sen UniversityGuangzhou510060P. R. China
- Department of Radiation OncologySun Yat‐sen University Cancer CenterGuangzhou510060P. R. China
| | - Ying‐Qin Li
- Sun Yat‐sen University Cancer Centerthe State Key Laboratory of Oncology in South ChinaCollaborative Innovation Center for Cancer MedicineGuangdong Key Laboratory of Nasopharyngeal Carcinoma Diagnosis and TherapyCenter for Precision Medicine of Sun Yat‐sen UniversityGuangzhou510060P. R. China
- Department of Experimental ResearchSun Yat‐sen University Cancer CenterGuangzhou510060P. R. China
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11
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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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12
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Takeshita D. Protein expression and purification, molecular interaction, and X-ray crystallographic analysis of baculovirus protein PK2. Protein Expr Purif 2023; 202:106188. [PMID: 36229000 DOI: 10.1016/j.pep.2022.106188] [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: 07/04/2022] [Revised: 10/06/2022] [Accepted: 10/06/2022] [Indexed: 11/05/2022]
Abstract
Phosphorylation of the α subunit of eukaryotic translation initiation factor 2 (eIF2α) by eIF2α kinases is a common mechanism to regulate the initiation of translation under stress conditions. The PK2 protein from baculovirus Autographica californica multiple nucleopolyhedrovirus (AcMNPV) binds and inhibits eIF2α kinases to ensure efficient virus propagation. The C-terminal region of PK2 shares a homology with the C-lobe of eIF2α kinases, but the N-terminal region of PK2 is unique to the orthologous proteins. In order to understand the detailed structure and function of PK2, both the full-length PK2 and its N-terminal truncated protein (PK2Δ22) were expressed as a His-tag fusion protein in Escherichia coli and purified by three steps of chromatography. Notably, the cysteine mutant, PK2 C181S/C211S, promotes the solubility and stability of the PK2 protein. The results of the size-exclusion chromatography showed that the full-length PK2 exists in both multimeric and monomeric forms, and the molecular interaction of PK2 and the eIF2α kinase domain. The purified proteins were used further to screen various conditions to obtain these crystals. Crystals of the full-length PK2 and PK2Δ22 were obtained by a sitting-drop vapour-diffusion method using lithium sulfate and PEG3350 as the precipitant, respectively. The crystal of PK2 belonged to space group P41212, and diffracted X-rays to 2.7 Å resolution. The asymmetric unit contained four molecules of the protein, and the solvent content was 67.4%. Whereas, the crystal of the PK2Δ22 belonged to space group P212121, diffracted X-rays to 2.8 Å resolution. The asymmetric unit contained three molecules of the protein, and the solvent content was 48.1%. The crystallographic study of the PK2 protein will provide mechanistic insights into the inhibition of eIF2α kinase by the PK2 protein, and also pave the way for the improvement of the baculovirus-based protein expression system.
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Affiliation(s)
- Daijiro Takeshita
- Biomedical Research Institute, National Institute of Advanced Industrial Science and Technology (AIST), 1-1-1, Higashi, Tsukuba, Ibaraki, 305-8566, Japan
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13
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3dRNA: 3D structure prediction from linear to circular RNAs. J Mol Biol 2022; 434:167452. [DOI: 10.1016/j.jmb.2022.167452] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2021] [Revised: 01/07/2022] [Accepted: 01/07/2022] [Indexed: 12/30/2022]
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14
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Svitkin YV, Gingras AC, Sonenberg N. Membrane-dependent relief of translation elongation arrest on pseudouridine- and N1-methyl-pseudouridine-modified mRNAs. Nucleic Acids Res 2021; 50:7202-7215. [PMID: 34933339 PMCID: PMC9303281 DOI: 10.1093/nar/gkab1241] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2021] [Revised: 11/12/2021] [Accepted: 12/03/2021] [Indexed: 11/13/2022] Open
Abstract
Expression of therapeutically important proteins has benefited dramatically from the advent of chemically modified mRNAs that feature decreased lability and immunogenicity. This had a momentous effect on the rapid development of COVID-19 mRNA vaccines. Incorporation of the naturally occurring pseudouridine (Ψ) or N1-methyl-pseudouridine (N1mΨ) into in vitro transcribed mRNAs prevents the activation of unwanted immune responses by blocking eIF2α phosphorylation, which inhibits translation. Here, we report that Ψs in luciferase (Luc) mRNA exacerbate translation pausing in nuclease-untreated rabbit reticulocyte lysate (uRRL) and promote the formation of high-order-ribosome structures. The major deceleration of elongation occurs at the Ψ-rich nucleotides 1294-1326 of Ψ-Luc mRNA and results in premature termination of translation. The impairment of translation is mainly due to the shortage of membranous components. Supplementing uRRL with canine microsomal membranes (CMMs) relaxes the impediments to ribosome movement, resolves collided ribosomes, and greatly enhances full-size luciferase production. CMMs also strongly stimulated an extremely inefficient translation of N1mΨ-Luc mRNA in uRRL. Evidence is presented that translational pausing can promote membrane recruitment of polysomes with nascent polypeptides that lack a signal sequence. Our results highlight an underappreciated role of membrane binding to polysomes in the prevention of ribosome collision and premature release of nascent polypeptides.
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Affiliation(s)
- Yuri V Svitkin
- Department of Biochemistry, McGill University, Montréal, Québec H3A 1A3, Canada.,Rosalind and Morris Goodman Cancer Institute, Montréal, Québec H3A 1A3, Canada
| | - Anne-Claude Gingras
- Lunenfeld-Tanenbaum Research Institute, Sinai Health System, and Department of Molecular Genetics, University of Toronto, Toronto, Ontario, M5G 1×5, Canada
| | - Nahum Sonenberg
- Department of Biochemistry, McGill University, Montréal, Québec H3A 1A3, Canada.,Rosalind and Morris Goodman Cancer Institute, Montréal, Québec H3A 1A3, Canada
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15
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Liu CX, Guo SK, Nan F, Xu YF, Yang L, Chen LL. RNA circles with minimized immunogenicity as potent PKR inhibitors. Mol Cell 2021; 82:420-434.e6. [PMID: 34951963 DOI: 10.1016/j.molcel.2021.11.019] [Citation(s) in RCA: 52] [Impact Index Per Article: 17.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2021] [Revised: 08/31/2021] [Accepted: 11/17/2021] [Indexed: 12/16/2022]
Abstract
Exon back-splicing-generated circular RNAs, as a group, can suppress double-stranded RNA (dsRNA)-activated protein kinase R (PKR) in cells. We have sought to synthesize immunogenicity-free, short dsRNA-containing RNA circles as PKR inhibitors. Here, we report that RNA circles synthesized by permuted self-splicing thymidylate synthase (td) introns from T4 bacteriophage or by Anabaena pre-tRNA group I intron could induce an immune response. Autocatalytic splicing introduces ∼74 nt td or ∼186 nt Anabaena extraneous fragments that can distort the folding status of original circular RNAs or form structures themselves to provoke innate immune responses. In contrast, synthesized RNA circles produced by T4 RNA ligase without extraneous fragments exhibit minimized immunogenicity. Importantly, directly ligated circular RNAs that form short dsRNA regions efficiently suppress PKR activation 103- to 106-fold higher than reported chemical compounds C16 and 2-AP, highlighting the future use of circular RNAs as potent inhibitors for diseases related to PKR overreaction.
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Affiliation(s)
- Chu-Xiao Liu
- State Key Laboratory of Molecular Biology, Shanghai Key Laboratory of Molecular Andrology, CAS Center for Excellence in Molecular Cell Science, Shanghai Institute of Biochemistry and Cell Biology, University of Chinese Academy of Sciences, Chinese Academy of Sciences, 320 Yueyang Road, Shanghai 200031, China
| | - Si-Kun Guo
- State Key Laboratory of Molecular Biology, Shanghai Key Laboratory of Molecular Andrology, CAS Center for Excellence in Molecular Cell Science, Shanghai Institute of Biochemistry and Cell Biology, University of Chinese Academy of Sciences, Chinese Academy of Sciences, 320 Yueyang Road, Shanghai 200031, China
| | - Fang Nan
- CAS Key Laboratory of Computational Biology, Shanghai Institute of Nutrition and Health, Shanghai Institutes for Biological Sciences, University of Chinese Academy of Sciences, Chinese Academy of Sciences, 320 Yueyang Road, Shanghai 200031, China
| | - Yi-Feng Xu
- State Key Laboratory of Molecular Biology, Shanghai Key Laboratory of Molecular Andrology, CAS Center for Excellence in Molecular Cell Science, Shanghai Institute of Biochemistry and Cell Biology, University of Chinese Academy of Sciences, Chinese Academy of Sciences, 320 Yueyang Road, Shanghai 200031, China
| | - Li Yang
- CAS Key Laboratory of Computational Biology, Shanghai Institute of Nutrition and Health, Shanghai Institutes for Biological Sciences, University of Chinese Academy of Sciences, Chinese Academy of Sciences, 320 Yueyang Road, Shanghai 200031, China; School of Life Science and Technology, ShanghaiTech University, 100 Haike Road, Shanghai 201210, China
| | - Ling-Ling Chen
- State Key Laboratory of Molecular Biology, Shanghai Key Laboratory of Molecular Andrology, CAS Center for Excellence in Molecular Cell Science, Shanghai Institute of Biochemistry and Cell Biology, University of Chinese Academy of Sciences, Chinese Academy of Sciences, 320 Yueyang Road, Shanghai 200031, China; School of Life Science and Technology, ShanghaiTech University, 100 Haike Road, Shanghai 201210, China; School of Life Science, Hangzhou Institute for Advanced Study, University of Chinese Academy of Sciences, Hangzhou, China.
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16
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Rodriguez S, Sahin A, Schrank BR, Al-Lawati H, Costantino I, Benz E, Fard D, Albers AD, Cao L, Gomez AC, Evans K, Ratti E, Cudkowicz M, Frosch MP, Talkowski M, Sorger PK, Hyman BT, Albers MW. Genome-encoded cytoplasmic double-stranded RNAs, found in C9ORF72 ALS-FTD brain, propagate neuronal loss. Sci Transl Med 2021; 13:eaaz4699. [PMID: 34233951 PMCID: PMC8779652 DOI: 10.1126/scitranslmed.aaz4699] [Citation(s) in RCA: 20] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2019] [Revised: 06/29/2020] [Accepted: 03/15/2021] [Indexed: 12/12/2022]
Abstract
Triggers of innate immune signaling in the CNS of patients with amyotrophic lateral sclerosis and frontotemporal degeneration (ALS/FTD) remain elusive. We report the presence of cytoplasmic double-stranded RNA (cdsRNA), an established trigger of innate immunity, in ALS-FTD brains carrying C9ORF72 intronic hexanucleotide expansions that included genomically encoded expansions of the G4C2 repeat sequences. The presence of cdsRNA in human brains was coincident with cytoplasmic TAR DNA binding protein 43 (TDP-43) inclusions, a pathologic hallmark of ALS/FTD. Introducing cdsRNA into cultured human neural cells induced type I interferon (IFN-I) signaling and death that was rescued by FDA-approved JAK inhibitors. In mice, genomically encoded dsRNAs expressed exclusively in a neuronal class induced IFN-I and death in connected neurons non-cell-autonomously. Our findings establish that genomically encoded cdsRNAs trigger sterile, viral-mimetic IFN-I induction and propagated death within neural circuits and may drive neuroinflammation and neurodegeneration in patients with ALS/FTD.
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Affiliation(s)
- Steven Rodriguez
- Department of Neurology, Massachusetts General Hospital, Boston, MA 02129, USA
- Laboratory of Systems Pharmacology, Department of Systems Biology, Harvard Program in Therapeutic Science, Harvard Medical School, Boston, MA 02115, USA
| | - Asli Sahin
- Department of Neurology, Massachusetts General Hospital, Boston, MA 02129, USA
| | - Benjamin R Schrank
- Department of Neurology, Massachusetts General Hospital, Boston, MA 02129, USA
| | - Hawra Al-Lawati
- Department of Neurology, Massachusetts General Hospital, Boston, MA 02129, USA
| | - Isabel Costantino
- Department of Neurology, Massachusetts General Hospital, Boston, MA 02129, USA
| | - Eric Benz
- Department of Neurology, Massachusetts General Hospital, Boston, MA 02129, USA
| | - Darian Fard
- Department of Neurology, Massachusetts General Hospital, Boston, MA 02129, USA
| | - Alefiya D Albers
- Department of Neurology, Massachusetts General Hospital, Boston, MA 02129, USA
- Department of Psychology, Endicott College, Beverly, MA 01915, USA
| | - Luxiang Cao
- Department of Neurology, Massachusetts General Hospital, Boston, MA 02129, USA
| | - Alexis C Gomez
- Department of Neurology, Massachusetts General Hospital, Boston, MA 02129, USA
| | - Kyle Evans
- Department of Neurology, Massachusetts General Hospital, Boston, MA 02129, USA
- Laboratory of Systems Pharmacology, Department of Systems Biology, Harvard Program in Therapeutic Science, Harvard Medical School, Boston, MA 02115, USA
| | - Elena Ratti
- Department of Neurology, Massachusetts General Hospital, Boston, MA 02129, USA
| | - Merit Cudkowicz
- Department of Neurology, Massachusetts General Hospital, Boston, MA 02129, USA
| | - Matthew P Frosch
- Department of Pathology, Massachusetts General Hospital, Boston, MA 02114, USA
| | - Michael Talkowski
- Department of Neurology, Massachusetts General Hospital, Boston, MA 02129, USA
- Center for Genomic Medicine, Massachusetts General Hospital, Boston, MA 02114, USA
| | - Peter K Sorger
- Laboratory of Systems Pharmacology, Department of Systems Biology, Harvard Program in Therapeutic Science, Harvard Medical School, Boston, MA 02115, USA
| | - Bradley T Hyman
- Department of Neurology, Massachusetts General Hospital, Boston, MA 02129, USA
| | - Mark W Albers
- Department of Neurology, Massachusetts General Hospital, Boston, MA 02129, USA.
- Laboratory of Systems Pharmacology, Department of Systems Biology, Harvard Program in Therapeutic Science, Harvard Medical School, Boston, MA 02115, USA
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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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Zhang W, Liu Y, Min Chin J, Phua KKL. Sustained release of PKR inhibitor C16 from mesoporous silica nanoparticles significantly enhances mRNA translation and anti-tumor vaccination. Eur J Pharm Biopharm 2021; 163:179-187. [PMID: 33771622 DOI: 10.1016/j.ejpb.2021.03.011] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2020] [Revised: 02/14/2021] [Accepted: 03/17/2021] [Indexed: 12/28/2022]
Abstract
In this study, we developed a mesoporous silica nanoparticles - mRNA (MSN-mRNA) subcutaneous delivery system composed of naked mRNA and a subcutaneous depot of imidazolo-oxindole RNA-activated protein kinase (PKR) inhibitor C16. We show that C16 treatment during mRNA transfection is a potent immune evasion approach that non-linearly enhances translation of unmodified mRNA in both mouse fibroblasts and dendritic cells in vitro exceeding that of nucleoside-modified mRNA. Notably, C16 further enhances translation of nucleoside-modified mRNA and HPLC purified mRNA. However, translation enhancement is dependent on and potentiated by C16's continuous presence. C16 mediated translation enhancement is extended in vivo by employing MSN as an interface to sustain-release C16. Subcutaneously administered MSN-mRNA significantly enhanced in vivo translation and expression kinetics of naked mRNA in unmodified, nucleoside-modified, and HPLC purified formats. We applied a MSN-mRNA vaccine formulation composed of naked mRNA encoding ovalbumin and granulocyte macrophage colony stimulating factor, and C16@MSNs on a xenograft E.G7-OVA prophylactic tumor model, resulting in very potent tumor inhibition. The MSN-mRNA delivery system bears great translational potential in mRNA therapeutics.
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Affiliation(s)
- Wei Zhang
- Department of Chemical and Biomolecular Engineering, Faculty of Engineering, National University of Singapore, 4 Engineering Drive 4, Singapore 117585, Singapore
| | - Yi Liu
- Department of Chemical and Biomolecular Engineering, Faculty of Engineering, National University of Singapore, 4 Engineering Drive 4, Singapore 117585, Singapore
| | - Jas Min Chin
- Department of Chemical and Biomolecular Engineering, Faculty of Engineering, National University of Singapore, 4 Engineering Drive 4, Singapore 117585, Singapore
| | - Kyle K L Phua
- Department of Chemical and Biomolecular Engineering, Faculty of Engineering, National University of Singapore, 4 Engineering Drive 4, Singapore 117585, Singapore.
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19
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Thrown for a (stem) loop: How RNA structure impacts circular RNA regulation and function. Methods 2021; 196:56-67. [PMID: 33662561 DOI: 10.1016/j.ymeth.2021.02.019] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2020] [Revised: 02/09/2021] [Accepted: 02/26/2021] [Indexed: 12/26/2022] Open
Abstract
Exonic circular RNAs (circRNAs) are RNA molecules that are covalently closed by back-splicing via canonical splicing machinery. Despite overlapping sequences, exon circularization generates RNA secondary structures through intramolecular base-pairing that are different from the linear transcript. Here we review factors that may affect circRNA structure and how structure affects circRNA function and regulation. We highlight considerations for RNA sequencing and expression measurement to ensure highly structured circRNAs are accurately represented by the data and discuss issues that need to be addressed in generating circRNAs to recapitulate their endogenous structures. We conclude our review by discussing experimental strategies on revealing the varied roles of RNA structure in circRNA biogenesis, function and decay.
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20
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Girardi E, Pfeffer S, Baumert TF, Majzoub K. Roadblocks and fast tracks: How RNA binding proteins affect the viral RNA journey in the cell. Semin Cell Dev Biol 2021; 111:86-100. [PMID: 32847707 PMCID: PMC7443355 DOI: 10.1016/j.semcdb.2020.08.006] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2020] [Revised: 08/14/2020] [Accepted: 08/14/2020] [Indexed: 12/12/2022]
Abstract
As obligate intracellular parasites with limited coding capacity, RNA viruses rely on host cells to complete their multiplication cycle. Viral RNAs (vRNAs) are central to infection. They carry all the necessary information for a virus to synthesize its proteins, replicate and spread and could also play essential non-coding roles. Regardless of its origin or tropism, vRNA has by definition evolved in the presence of host RNA Binding Proteins (RBPs), which resulted in intricate and complicated interactions with these factors. While on one hand some host RBPs recognize vRNA as non-self and mobilize host antiviral defenses, vRNA must also co-opt other host RBPs to promote viral infection. Focusing on pathogenic RNA viruses, we will review important scenarios of RBP-vRNA interactions during which host RBPs recognize, modify or degrade vRNAs. We will then focus on how vRNA hijacks the largest ribonucleoprotein complex (RNP) in the cell, the ribosome, to selectively promote the synthesis of its proteins. We will finally reflect on how novel technologies are helping in deepening our understanding of vRNA-host RBPs interactions, which can be ultimately leveraged to combat everlasting viral threats.
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Affiliation(s)
- Erika Girardi
- Architecture et Réactivité de l'ARN, Université de Strasbourg, Institut de Biologie Moléculaire et Cellulaire du CNRS, Strasbourg, France
| | - Sebastien Pfeffer
- Architecture et Réactivité de l'ARN, Université de Strasbourg, Institut de Biologie Moléculaire et Cellulaire du CNRS, Strasbourg, France
| | - Thomas F Baumert
- Inserm, U1110, Institut de Recherche sur les Maladies Virales et Hépatiques, Université de Strasbourg, 67000, Strasbourg, France; Pole Hépatodigestif, Institut Hopitalo-universitaire, Hopitaux Universitaires de Strasbourg, 67000 Strasbourg, France
| | - Karim Majzoub
- Inserm, U1110, Institut de Recherche sur les Maladies Virales et Hépatiques, Université de Strasbourg, 67000, Strasbourg, France.
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21
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Gurung C, Fendereski M, Sapkota K, Guo J, Huang F, Guo YL. Dicer represses the interferon response and the double-stranded RNA-activated protein kinase pathway in mouse embryonic stem cells. J Biol Chem 2021; 296:100264. [PMID: 33837743 PMCID: PMC7948645 DOI: 10.1016/j.jbc.2021.100264] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2020] [Revised: 01/04/2021] [Accepted: 01/05/2021] [Indexed: 02/07/2023] Open
Abstract
Recent studies have demonstrated that embryonic stem cells (ESCs) are deficient in expressing type I interferons (IFN), the cytokines that play key roles in antiviral responses. However, the underlying molecular mechanisms and biological implications of this finding are poorly understood. In this study, we developed a synthetic RNA-based assay that can simultaneously assess multiple forms of antiviral responses. Dicer is an enzyme essential for RNA interference (RNAi), which is used as a major antiviral mechanism in invertebrates. RNAi activity is detected in wild-type ESCs but is abolished in Dicer knockout ESCs (D-/-ESCs) as expected. Surprisingly, D-/-ESCs have gained the ability to express IFN, which is otherwise deficient in wild-type ESCs. Furthermore, D-/-ESCs have constitutively active double-stranded RNA (dsRNA)-activated protein kinase (PKR), an enzyme that is also involved in antiviral response. D-/-ESCs show increased sensitivity to the cytotoxicity resulting from RNA transfection. The effects of dsRNA can be partly replicated with a synthetic B2RNA corresponding to the retrotransposon B2 short interspersed nuclear element. B2RNA has secondary structure features of dsRNA and accumulates in D-/-ESCs, suggesting that B2RNA could be a cellular RNA that activates PKR and contributes to the decreased cell proliferation and viability of D-/-ESCs. Treatment of D-/-ESCs with a PKR inhibitor and IFNβ-neutralizing antibodies increased cell proliferation rate and cell viability. Based on these findings, we propose that, in ESCs, Dicer acts as a repressor of antiviral responses and plays a key role in the maintenance of proliferation, viability, and pluripotency of ESCs.
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Affiliation(s)
- Chandan Gurung
- Department of Cell and Molecular Biology, The University of Southern Mississippi, Hattiesburg, Mississippi, USA
| | - Mona Fendereski
- Department of Cell and Molecular Biology, The University of Southern Mississippi, Hattiesburg, Mississippi, USA
| | - Krishna Sapkota
- Department of Chemistry and Biochemistry, The University of Southern Mississippi, Hattiesburg, Mississippi, USA
| | - Jason Guo
- Department of Cell and Molecular Biology, The University of Southern Mississippi, Hattiesburg, Mississippi, USA
| | - Faqing Huang
- Department of Chemistry and Biochemistry, The University of Southern Mississippi, Hattiesburg, Mississippi, USA
| | - Yan-Lin Guo
- Department of Cell and Molecular Biology, The University of Southern Mississippi, Hattiesburg, Mississippi, USA.
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22
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Yan L, Chen YG. Circular RNAs in Immune Response and Viral Infection. Trends Biochem Sci 2020; 45:1022-1034. [PMID: 32900574 PMCID: PMC7642119 DOI: 10.1016/j.tibs.2020.08.006] [Citation(s) in RCA: 62] [Impact Index Per Article: 15.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2020] [Revised: 07/28/2020] [Accepted: 08/07/2020] [Indexed: 12/11/2022]
Abstract
Circular RNAs (circRNAs) are a diverse class of RNAs with varying sizes, cellular abundance, and biological functions. Investigations from the past decade have revealed that circRNAs are ubiquitously found in eukaryotes and have defined the different biological roles of circRNAs to illuminate this previously unrecognized class of molecules. In the context of the immune system, immune responses and immune-related diseases alter circRNA expression. More recently, several oncogenic double-stranded DNA viruses have been found to encode circRNAs. In this review, we summarize the current understanding of circRNAs and their emerging functions in immune regulation and autoimmune disorders, and discuss the identification and potential roles of viral circRNAs during infections. Finally, we present promising areas for future investigations in the nascent field of circRNAs.
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Affiliation(s)
- Lichong Yan
- Department of Immunobiology, Yale University School of Medicine, New Haven, CT, USA
| | - Y Grace Chen
- Department of Immunobiology, Yale University School of Medicine, New Haven, CT, USA..
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23
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Gupta P, Taiyab A, Hassan MI. Emerging role of protein kinases in diabetes mellitus: From mechanism to therapy. ADVANCES IN PROTEIN CHEMISTRY AND STRUCTURAL BIOLOGY 2020; 124:47-85. [PMID: 33632470 DOI: 10.1016/bs.apcsb.2020.11.001] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 03/29/2023]
Abstract
Diabetes mellitus has emerged as a severe burden on the medical health system across the globe. Presently, around 422 million people are suffering from diabetes which is speculated to be expanded to about 600 million by 2035. Patients with type 2 diabetes are at increased risk of developing detrimental metabolic and cardiovascular complications. The scientific understanding of this chronic disease and its underlying root cause is not yet fully unraveled. Protein kinases are well known to regulate almost every cellular process through phosphorylation of target protein in diverse signaling pathways. The important role of several protein kinases including AMP-activated protein kinase, IκB kinase and protein kinase C have been well demonstrated in various animal models. They modulate glucose tolerance, inflammation and insulin resistance in the cells via acting on diverse downstream targets and signaling pathways. Thus, modulating the activity of potential human kinases which are significantly involved in diabetes by targeting with small molecule inhibitors could be an attractive therapeutic strategy to tackle diabetes. In this chapter, we have discussed the potential role of protein kinases in glucose metabolism and insulin sensitivity, and in the pathogenesis of diabetes mellitus. Furthermore, the small molecules reported in the literature that can be potentially used for the treatment of diabetes have been discussed in detail.
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Affiliation(s)
- Preeti Gupta
- Centre for Interdisciplinary Research in Basic Sciences, Jamia Millia Islamia, New Delhi, India
| | - Aaliya Taiyab
- Centre for Interdisciplinary Research in Basic Sciences, Jamia Millia Islamia, New Delhi, India
| | - Md Imtaiyaz Hassan
- Centre for Interdisciplinary Research in Basic Sciences, Jamia Millia Islamia, New Delhi, India.
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24
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Generation of Human iPSCs by Reprogramming with the Unmodified Synthetic mRNA. Methods Mol Biol 2020. [PMID: 33226619 DOI: 10.1007/978-1-0716-1084-8_11] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/03/2023]
Abstract
Human-induced pluripotent stem cells (iPSCs) are showing great promise for both disease modeling and regenerative medicine. The choice of reprogramming methods have a significant effect on the outcomes of the experiments. Standard methods, such as Sendai viruses, episomes, and the base-modified mRNA have limitations. Here, I describe a method to reprogram human fibroblasts using a cocktail of mRNAs without any base modification that increases reprogramming efficiency, reduces the RNA-associated toxicity, and yields iPSCs ready for expansion and characterization in as short as 10-14 days.
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25
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Yang B, Zhang X, Zhang D, Hou J, Xu G, Sheng C, Choudhury SM, Zhu Z, Li D, Zhang K, Zheng H, Liu X. Molecular Mechanisms of Immune Escape for Foot-and-Mouth Disease Virus. Pathogens 2020; 9:pathogens9090729. [PMID: 32899635 PMCID: PMC7558374 DOI: 10.3390/pathogens9090729] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2020] [Revised: 08/19/2020] [Accepted: 09/01/2020] [Indexed: 12/25/2022] Open
Abstract
Foot-and-mouth disease virus (FMDV) causes a highly contagious vesicular disease in cloven-hoofed livestock that results in severe consequences for international trade, posing a great economic threat to agriculture. The FMDV infection antagonizes the host immune responses via different signaling pathways to achieve immune escape. Strategies to escape the cell immune system are key to effective infection and pathogenesis. This review is focused on summarizing the recent advances to understand how the proteins encoded by FMDV antagonize the host innate and adaptive immune responses.
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Affiliation(s)
| | | | | | | | | | | | | | | | | | - Keshan Zhang
- Correspondence: (K.Z.); (H.Z.); Tel.: +86-15214078335 (K.Z.)
| | - Haixue Zheng
- Correspondence: (K.Z.); (H.Z.); Tel.: +86-15214078335 (K.Z.)
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26
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Hu Z, Du H, Lin G, Han K, Cheng X, Feng Z, Mao H, Hu C. Grass carp (Ctenopharyngodon idella) PACT induces cell apoptosis and activates NF-кB via PKR. FISH & SHELLFISH IMMUNOLOGY 2020; 103:377-384. [PMID: 32454210 DOI: 10.1016/j.fsi.2020.05.036] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/13/2020] [Revised: 04/17/2020] [Accepted: 05/12/2020] [Indexed: 06/11/2023]
Abstract
As a dsRNA-dependent and interferon-induced protein kinase, PKR is involved in antiviral immune response and apoptosis mediated by various cytokines. In mammalian cells, PKR can also be activated in the absence of dsRNA. A PKR activator, PACT (PKR activating protein), also referred to as RAX (PKR-associated protein X) plays an important role. In recent years, with the increasing recognition of fish interferon system, PKR and PACT have been gradually revealed in fish. However, the function of fish PACT is unclear. In our previous work, we suggested that grass carp (Ctenopharyngodon idella) PACT must be involved in IRF2 and ATF4-mediated stress response pathways. In the present study, we found that the expression of C. idella PACT (CiPACT) and CiPKR were significantly up-regulated under the stimulation of LPS. It indicated that CiPACT and CiPKR may play an important role in response to LPS stimulation. In addition, the response time of CiPACT to LPS is earlier than that of CiPKR. It has also shown that overexpression of CiPACT in CIK cells can significantly enhance the level of p-eIF2α, induces apoptosis and translocation of Cip65 to nucleus from cytoplasm. To further understand the mechanism, we carried out the co-immunoprecipitation assay. It proved that the interaction of CiPACT and CiPKR made the phosphorylation of CiPKR. Overexpression of CiPACT induced the down-regulation of intracellular expression of bcl-2 and up-regulation of bax. However, in CiPKR knocked-down cells the expression of bcl-2 and bax were just the opposite. Therefore, the mechanism of fish PACT induces apoptosis and activates NF-кB is dependent on PKR.
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Affiliation(s)
- Zhizhen Hu
- School of Life Science, Nanchang University, Nanchang, 330031, China
| | - Hailing Du
- School of Life Science, Nanchang University, Nanchang, 330031, China
| | - Gang Lin
- School of Life Science, Nanchang University, Nanchang, 330031, China
| | - Kun Han
- School of Life Science, Nanchang University, Nanchang, 330031, China
| | - Xining Cheng
- School of Life Science, Nanchang University, Nanchang, 330031, China
| | - Zhiqing Feng
- School of Life Science, Nanchang University, Nanchang, 330031, China
| | - Huiling Mao
- School of Life Science, Nanchang University, Nanchang, 330031, China
| | - Chengyu Hu
- School of Life Science, Nanchang University, Nanchang, 330031, China.
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27
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Peer E, Moshitch-Moshkovitz S, Rechavi G, Dominissini D. The Epitranscriptome in Translation Regulation. Cold Spring Harb Perspect Biol 2019; 11:cshperspect.a032623. [PMID: 30037968 DOI: 10.1101/cshperspect.a032623] [Citation(s) in RCA: 30] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
The cellular proteome reflects the total outcome of many regulatory mechanisms that affect the metabolism of messenger RNA (mRNA) along its pathway from synthesis to degradation. Accumulating evidence in recent years has uncovered the roles of a growing number of mRNA modifications in every step along this pathway, shaping translational output. mRNA modifications affect the translation machinery directly, by influencing translation initiation, elongation and termination, or by altering mRNA levels and subcellular localization. Features of modification-related translational control are described, charting a new and complex layer of translational regulation.
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Affiliation(s)
- Eyal Peer
- Sackler School of Medicine, Tel Aviv University, Tel Aviv 6997801, Israel; Cancer Research Center and Wohl Centre for Translational Medicine, Chaim Sheba Medical Center, Tel-Hashomer 5262160, Israel
| | - Sharon Moshitch-Moshkovitz
- Sackler School of Medicine, Tel Aviv University, Tel Aviv 6997801, Israel; Cancer Research Center and Wohl Centre for Translational Medicine, Chaim Sheba Medical Center, Tel-Hashomer 5262160, Israel
| | - Gideon Rechavi
- Sackler School of Medicine, Tel Aviv University, Tel Aviv 6997801, Israel; Cancer Research Center and Wohl Centre for Translational Medicine, Chaim Sheba Medical Center, Tel-Hashomer 5262160, Israel
| | - Dan Dominissini
- Sackler School of Medicine, Tel Aviv University, Tel Aviv 6997801, Israel; Cancer Research Center and Wohl Centre for Translational Medicine, Chaim Sheba Medical Center, Tel-Hashomer 5262160, Israel
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28
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Hood IV, Gordon JM, Bou-Nader C, Henderson FE, Bahmanjah S, Zhang J. Crystal structure of an adenovirus virus-associated RNA. Nat Commun 2019; 10:2871. [PMID: 31253805 PMCID: PMC6599070 DOI: 10.1038/s41467-019-10752-6] [Citation(s) in RCA: 33] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2019] [Accepted: 05/27/2019] [Indexed: 12/20/2022] Open
Abstract
Adenovirus Virus-Associated (VA) RNAs are the first discovered viral noncoding RNAs. By mimicking double-stranded RNAs (dsRNAs), the exceptionally abundant, multifunctional VA RNAs sabotage host machineries that sense, transport, process, or edit dsRNAs. How VA-I suppresses PKR activation despite its strong dsRNA character, and inhibits the crucial antiviral kinase to promote viral translation, remains largely unknown. Here, we report a 2.7 Å crystal structure of VA-I RNA. The acutely bent VA-I features an unusually structured apical loop, a wobble-enriched, coaxially stacked apical and tetra-stems necessary and sufficient for PKR inhibition, and a central domain pseudoknot that resembles codon-anticodon interactions and prevents PKR activation by VA-I. These global and local structural features collectively define VA-I as an archetypal PKR inhibitor made of RNA. The study provides molecular insights into how viruses circumnavigate cellular rules of self vs non-self RNAs to not only escape, but further compromise host innate immunity.
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Affiliation(s)
- Iris V Hood
- Laboratory of Molecular Biology, National Institute of Diabetes and Digestive and Kidney Diseases, 50 South Drive, Room 4503, Bethesda, MD, 20892, USA
| | - Jackson M Gordon
- Laboratory of Molecular Biology, National Institute of Diabetes and Digestive and Kidney Diseases, 50 South Drive, Room 4503, Bethesda, MD, 20892, USA
| | - Charles Bou-Nader
- Laboratory of Molecular Biology, National Institute of Diabetes and Digestive and Kidney Diseases, 50 South Drive, Room 4503, Bethesda, MD, 20892, USA
| | - Frances E Henderson
- Laboratory of Molecular Biology, National Institute of Diabetes and Digestive and Kidney Diseases, 50 South Drive, Room 4503, Bethesda, MD, 20892, USA
| | - Soheila Bahmanjah
- Laboratory of Molecular Biology, National Institute of Diabetes and Digestive and Kidney Diseases, 50 South Drive, Room 4503, Bethesda, MD, 20892, USA
| | - Jinwei Zhang
- Laboratory of Molecular Biology, National Institute of Diabetes and Digestive and Kidney Diseases, 50 South Drive, Room 4503, Bethesda, MD, 20892, USA.
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29
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Mayo CB, Erlandsen H, Mouser DJ, Feinstein AG, Robinson VL, May ER, Cole JL. Structural Basis of Protein Kinase R Autophosphorylation. Biochemistry 2019; 58:2967-2977. [PMID: 31246429 DOI: 10.1021/acs.biochem.9b00161] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
The RNA-activated protein kinase, PKR, is a key mediator of the innate immunity response to viral infection. Viral double-stranded RNAs induce PKR dimerization and autophosphorylation. The PKR kinase domain forms a back-to-back dimer. However, intermolecular ( trans) autophosphorylation is not feasible in this arrangement. We have obtained PKR kinase structures that resolves this dilemma. The kinase protomers interact via the known back-to-back interface as well as a front-to-front interface that is formed by exchange of activation segments. Mutational analysis of the front-to-front interface support a functional role in PKR activation. Molecular dynamics simulations reveal that the activation segment is highly dynamic in the front-to-front dimer and can adopt conformations conducive to phosphoryl transfer. We propose a mechanism where back-to-back dimerization induces a conformational change that activates PKR to phosphorylate a "substrate" kinase docked in a front-to-front geometry. This mechanism may be relevant to related kinases that phosphorylate the eukaryotic initiation factor eIF2α.
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30
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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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31
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TDP-43 knockdown causes innate immune activation via protein kinase R in astrocytes. Neurobiol Dis 2019; 132:104514. [PMID: 31229690 DOI: 10.1016/j.nbd.2019.104514] [Citation(s) in RCA: 32] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2019] [Revised: 04/26/2019] [Accepted: 06/19/2019] [Indexed: 12/13/2022] Open
Abstract
TAR-DNA binding protein 43 (TDP-43) is a multifunctional RNA binding protein directly implicated in the etiology of amyotrophic lateral sclerosis (ALS). Previous studies have demonstrated that loss of TDP-43 function leads to intracellular accumulation of non-coding repetitive element transcripts and double-stranded RNA (dsRNA). These events could cause immune activation and contribute to the neuroinflammation observed in ALS, but this possibility has not been investigated. Here, we knock down TDP-43 in primary rat astrocytes via siRNA, and we use RNA-seq, immunofluorescence, and immunoblotting to show that this results in: 1) accumulation of repetitive element transcripts and dsRNA; and 2) pro-inflammatory gene and protein expression consistent with innate immune signaling and astrocyte activation. We also show that both chemical inhibition and siRNA knockdown of protein kinase R (PKR), a dsRNA-activated kinase implicated in the innate immune response, block the expression of all activation markers assayed. Based on these findings, we suggest that intracellular accumulation of endogenous dsRNA may be a novel and important mechanism underlying the pathogenesis of ALS (and perhaps other neurodegenerative diseases), and that PKR inhibitors may have the potential to prevent reactive astrocytosis in ALS.
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32
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Watanabe T, Yamazaki S, Yoneda N, Shinohara H, Tomioka I, Higuchi Y, Yagoto M, Ema M, Suemizu H, Kawai K, Sasaki E. Highly efficient induction of primate iPS cells by combining RNA transfection and chemical compounds. Genes Cells 2019; 24:473-484. [PMID: 31099158 PMCID: PMC6852476 DOI: 10.1111/gtc.12702] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2019] [Revised: 05/13/2019] [Accepted: 05/13/2019] [Indexed: 12/30/2022]
Abstract
Induced pluripotent stem (iPS) cells hold great promise for regenerative medicine and the treatment of various diseases. Before proceeding to clinical trials, it is important to test the efficacy and safety of iPS cell‐based treatments using experimental animals. The common marmoset is a new world monkey widely used in biomedical studies. However, efficient methods that could generate iPS cells from a variety of cells have not been established. Here, we report that marmoset cells are efficiently reprogrammed into iPS cells by combining RNA transfection and chemical compounds. Using this novel combination, we generate transgene integration‐free marmoset iPS cells from a variety of cells that are difficult to reprogram using conventional RNA transfection method. Furthermore, we show this is similarly effective for human and cynomolgus monkey iPS cell generation. Thus, the addition of chemical compounds during RNA transfection greatly facilitates reprogramming and efficient generation of completely integration‐free safe iPS cells in primates, particularly from difficult‐to‐reprogram cells.
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Affiliation(s)
| | - Shun Yamazaki
- Central Institute for Experimental Animals, Kawasaki, Japan
| | - Nao Yoneda
- Central Institute for Experimental Animals, Kawasaki, Japan
| | | | - Ikuo Tomioka
- Laboratory of Applied Reproductive Science, Faculty of Agriculture, Shinshu University, Matsumoto, Japan
| | | | - Mika Yagoto
- Central Institute for Experimental Animals, Kawasaki, Japan
| | - Masatsugu Ema
- Department of Stem Cells and Human Disease Models, Research Center for Animal Life Science, Shiga University of Medical Science, Shiga, Japan.,Institute for the Advanced Study of Human Biology (ASHBi), Kyoto University Institute for Advanced Study, Kyoto, Japan
| | | | - Kenji Kawai
- Central Institute for Experimental Animals, Kawasaki, Japan
| | - Erika Sasaki
- Central Institute for Experimental Animals, Kawasaki, Japan
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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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34
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Structure and Degradation of Circular RNAs Regulate PKR Activation in Innate Immunity. Cell 2019; 177:865-880.e21. [DOI: 10.1016/j.cell.2019.03.046] [Citation(s) in RCA: 365] [Impact Index Per Article: 73.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2018] [Revised: 01/29/2019] [Accepted: 03/25/2019] [Indexed: 11/19/2022]
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35
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Schwartz SL, Conn GL. RNA regulation of the antiviral protein 2'-5'-oligoadenylate synthetase. WILEY INTERDISCIPLINARY REVIEWS-RNA 2019; 10:e1534. [PMID: 30989826 DOI: 10.1002/wrna.1534] [Citation(s) in RCA: 51] [Impact Index Per Article: 10.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/05/2019] [Revised: 03/12/2019] [Accepted: 03/14/2019] [Indexed: 12/25/2022]
Abstract
The innate immune system is a broad collection of critical intra- and extra-cellular processes that limit the infectivity of diverse pathogens. The 2'-5'-oligoadenylate synthetase (OAS) family of enzymes are important sensors of cytosolic double-stranded RNA (dsRNA) that play a critical role in limiting viral infection by activating the latent ribonuclease (RNase L) to halt viral replication and establish an antiviral state. Attesting to the importance of the OAS/RNase L pathway, diverse viruses have developed numerous distinct strategies to evade the effects of OAS activation. How OAS proteins are regulated by viral or cellular RNAs is not fully understood but several recent studies have provided important new insights into the molecular mechanisms of OAS activation by dsRNA. Other studies have revealed unanticipated features of RNA sequence and structure that strongly enhance activation of at least one OAS family member. While these discoveries represent important advances, they also underscore the fact that much remains to be learned about RNA-mediated regulation of the OAS/RNase L pathway. In particular, defining the full complement of RNA molecular signatures that activate OAS is essential to our understanding of how these proteins maximize their protective role against pathogens while still accurately discriminating host molecules to avoid inadvertent activation by cellular RNAs. A more complete knowledge of OAS regulation may also serve as a foundation for the development of novel antiviral therapeutic strategies and lead the way to a deeper understanding of currently unappreciated cellular functions of the OAS/RNase L pathway in the absence of infection. This article is categorized under: RNA in Disease and Development > RNA in Disease RNA Interactions with Proteins and Other Molecules > Protein-RNA Interactions: Functional Implications Translation > Translation Regulation.
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Affiliation(s)
- Samantha L Schwartz
- Department of Biochemistry, Emory University School of Medicine and Graduate Program in Biochemistry, Cell and Developmental Biology (BCDB), Atlanta, Georgia
| | - Graeme L Conn
- Department of Biochemistry, Emory University School of Medicine and Graduate Program in Biochemistry, Cell and Developmental Biology (BCDB), Atlanta, Georgia
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Bevilacqua PC, Assmann SM. Technique Development for Probing RNA Structure In Vivo and Genome-Wide. Cold Spring Harb Perspect Biol 2018; 10:a032250. [PMID: 30275275 PMCID: PMC6169808 DOI: 10.1101/cshperspect.a032250] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/30/2023]
Abstract
How organisms perceive and respond to their surroundings is one of the great questions in biology. It is clear that RNA plays key roles in sensing. Cellular and environmental cues that RNA responds to include temperature, ions, metabolites, and biopolymers. Recent advances in next-generation sequencing and in vivo chemical probing have provided unprecedented insights into RNA folding in vivo and genome-wide. Patterns of chemical reactivity have implicated control of gene expression by RNA and aided prediction of RNA structure. Central to these advances has been development of molecular biological and chemical techniques. Key advances are improvements in the quality, cost, and throughput of library preparation; availability of a wider array of chemicals for probing RNA structure in vivo; and robustness and user friendliness of data analysis. Insights from probing transcriptomes and future directions are provided.
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Affiliation(s)
- Philip C Bevilacqua
- Departments of Chemistry and Biochemistry & Molecular Biology, Pennsylvania State University, University Park, Pennsylvania 16802
| | - Sarah M Assmann
- Department of Biology, Pennsylvania State University, University Park, Pennsylvania 16802
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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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38
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Leppek K, Das R, Barna M. Functional 5' UTR mRNA structures in eukaryotic translation regulation and how to find them. Nat Rev Mol Cell Biol 2018; 19:158-174. [PMID: 29165424 PMCID: PMC5820134 DOI: 10.1038/nrm.2017.103] [Citation(s) in RCA: 482] [Impact Index Per Article: 80.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
Abstract
RNA molecules can fold into intricate shapes that can provide an additional layer of control of gene expression beyond that of their sequence. In this Review, we discuss the current mechanistic understanding of structures in 5' untranslated regions (UTRs) of eukaryotic mRNAs and the emerging methodologies used to explore them. These structures may regulate cap-dependent translation initiation through helicase-mediated remodelling of RNA structures and higher-order RNA interactions, as well as cap-independent translation initiation through internal ribosome entry sites (IRESs), mRNA modifications and other specialized translation pathways. We discuss known 5' UTR RNA structures and how new structure probing technologies coupled with prospective validation, particularly compensatory mutagenesis, are likely to identify classes of structured RNA elements that shape post-transcriptional control of gene expression and the development of multicellular organisms.
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Affiliation(s)
- Kathrin Leppek
- Department of Developmental Biology, Stanford University, Stanford, California 94305, USA
- Department of Genetics, Stanford University, Stanford, California 94305, USA
| | - Rhiju Das
- Departments of Biochemistry and Physics, Stanford University, Stanford, California 94305, USA
| | - Maria Barna
- Department of Developmental Biology, Stanford University, Stanford, California 94305, USA
- Department of Genetics, Stanford University, Stanford, California 94305, USA
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39
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Svitkin YV, Cheng YM, Chakraborty T, Presnyak V, John M, Sonenberg N. N1-methyl-pseudouridine in mRNA enhances translation through eIF2α-dependent and independent mechanisms by increasing ribosome density. Nucleic Acids Res 2017; 45:6023-6036. [PMID: 28334758 PMCID: PMC5449617 DOI: 10.1093/nar/gkx135] [Citation(s) in RCA: 149] [Impact Index Per Article: 21.3] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2017] [Accepted: 02/20/2017] [Indexed: 12/21/2022] Open
Abstract
Certain chemical modifications confer increased stability and low immunogenicity to in vitro transcribed mRNAs, thereby facilitating expression of therapeutically important proteins. Here, we demonstrate that N1-methyl-pseudouridine (N1mΨ) outperforms several other nucleoside modifications and their combinations in terms of translation capacity. Through extensive analysis of various modified transcripts in cell-free translation systems, we deconvolute the different components of the effect on protein expression independent of mRNA stability mechanisms. We show that in addition to turning off the immune/eIF2α phosphorylation-dependent inhibition of translation, the incorporated N1mΨ nucleotides dramatically alter the dynamics of the translation process by increasing ribosome pausing and density on the mRNA. Our results indicate that the increased ribosome loading of modified mRNAs renders them more permissive for initiation by favoring either ribosome recycling on the same mRNA or de novo ribosome recruitment.
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Affiliation(s)
- Yuri V Svitkin
- Department of Biochemistry, McGill University, Montréal, Québec H3A 1A3, Canada.,Rosalind and Morris Goodman Cancer Research Centre, Montréal, Québec H3A 1A3, Canada
| | | | | | | | | | - Nahum Sonenberg
- Department of Biochemistry, McGill University, Montréal, Québec H3A 1A3, Canada.,Rosalind and Morris Goodman Cancer Research Centre, Montréal, Québec H3A 1A3, Canada
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40
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Li C, Zhu Z, Du X, Cao W, Yang F, Zhang X, Feng H, Li D, Zhang K, Liu X, Zheng H. Foot-and-mouth disease virus induces lysosomal degradation of host protein kinase PKR by 3C proteinase to facilitate virus replication. Virology 2017; 509:222-231. [PMID: 28662438 PMCID: PMC7126777 DOI: 10.1016/j.virol.2017.06.023] [Citation(s) in RCA: 35] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2017] [Accepted: 06/20/2017] [Indexed: 12/16/2022]
Abstract
The interferon-induced double-strand RNA activated protein kinase (PKR) plays important roles in host defense against viral infection. Here we demonstrate the significant antiviral role of PKR against foot-and-mouth disease virus (FMDV) and report that FMDV infection inhibits PKR expression and activation in porcine kidney (PK-15) cells. The viral nonstructural protein 3C proteinase (3Cpro) is identified to be responsible for this inhibition. However, it is independent of the well-known proteinase activity of 3Cpro or 3Cpro-induced shutoff of host protein synthesis. We show that 3Cpro induces PKR degradation by lysosomal pathway and no interaction is determined between 3Cpro and PKR. Together, our results indicate that PKR acts an important antiviral factor during FMDV infection, and FMDV has evolved a strategy to overcome PKR-mediated antiviral role by downregulation of PKR protein.
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Affiliation(s)
- Chuntian Li
- State Key Laboratory of Veterinary Etiological Biology, National Foot and Mouth Diseases Reference Laboratory, Key Laboratory of Animal Virology of Ministry of Agriculture, Lanzhou Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Lanzhou, Gansu, PR China
| | - Zixiang Zhu
- State Key Laboratory of Veterinary Etiological Biology, National Foot and Mouth Diseases Reference Laboratory, Key Laboratory of Animal Virology of Ministry of Agriculture, Lanzhou Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Lanzhou, Gansu, PR China.
| | - Xiaoli Du
- State Key Laboratory of Veterinary Etiological Biology, National Foot and Mouth Diseases Reference Laboratory, Key Laboratory of Animal Virology of Ministry of Agriculture, Lanzhou Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Lanzhou, Gansu, PR China
| | - Weijun Cao
- State Key Laboratory of Veterinary Etiological Biology, National Foot and Mouth Diseases Reference Laboratory, Key Laboratory of Animal Virology of Ministry of Agriculture, Lanzhou Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Lanzhou, Gansu, PR China
| | - Fan Yang
- State Key Laboratory of Veterinary Etiological Biology, National Foot and Mouth Diseases Reference Laboratory, Key Laboratory of Animal Virology of Ministry of Agriculture, Lanzhou Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Lanzhou, Gansu, PR China
| | - Xiangle Zhang
- State Key Laboratory of Veterinary Etiological Biology, National Foot and Mouth Diseases Reference Laboratory, Key Laboratory of Animal Virology of Ministry of Agriculture, Lanzhou Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Lanzhou, Gansu, PR China
| | - Huanhuan Feng
- State Key Laboratory of Veterinary Etiological Biology, National Foot and Mouth Diseases Reference Laboratory, Key Laboratory of Animal Virology of Ministry of Agriculture, Lanzhou Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Lanzhou, Gansu, PR China
| | - Dan Li
- State Key Laboratory of Veterinary Etiological Biology, National Foot and Mouth Diseases Reference Laboratory, Key Laboratory of Animal Virology of Ministry of Agriculture, Lanzhou Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Lanzhou, Gansu, PR China
| | - Keshan Zhang
- State Key Laboratory of Veterinary Etiological Biology, National Foot and Mouth Diseases Reference Laboratory, Key Laboratory of Animal Virology of Ministry of Agriculture, Lanzhou Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Lanzhou, Gansu, PR China
| | - Xiangtao Liu
- State Key Laboratory of Veterinary Etiological Biology, National Foot and Mouth Diseases Reference Laboratory, Key Laboratory of Animal Virology of Ministry of Agriculture, Lanzhou Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Lanzhou, Gansu, PR China
| | - Haixue Zheng
- State Key Laboratory of Veterinary Etiological Biology, National Foot and Mouth Diseases Reference Laboratory, Key Laboratory of Animal Virology of Ministry of Agriculture, Lanzhou Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Lanzhou, Gansu, PR China.
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41
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Abstract
Efficient viral gene expression is threatened by cellular stress response programmes that rapidly reprioritize the translation machinery in response to varied environmental assaults, including virus infection. This results in inhibition of bulk synthesis of housekeeping proteins and causes the aggregation of messenger ribonucleoprotein complexes into cytoplasmic foci that are known as stress granules, which can entrap viral mRNAs. There is accumulating evidence for the antiviral nature of stress granules, which is supported by the discovery of many viral factors that interfere with stress granule formation and/or function. This Review focuses on recent advances in our understanding of the role of translation inhibition and stress granules in antiviral immune responses.
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42
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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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43
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Calderon BM, Conn GL. Human noncoding RNA 886 (nc886) adopts two structurally distinct conformers that are functionally opposing regulators of PKR. RNA (NEW YORK, N.Y.) 2017; 23:557-566. [PMID: 28069888 PMCID: PMC5340918 DOI: 10.1261/rna.060269.116] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/08/2016] [Accepted: 01/03/2017] [Indexed: 05/22/2023]
Abstract
The double-stranded RNA (dsRNA)-activated protein kinase (PKR) senses dsRNA produced during viral infection and halts cellular protein synthesis to block viral replication. How basal PKR activity is controlled in the absence of infection was unclear until the recent identification of a potential endogenous regulator, the cellular noncoding RNA 886 (nc886). However, nc886 adopts two distinct conformations for which the structural details and potential functional differences remain unclear. Here, we isolated and separately dissected the function of each form of nc886 to more clearly define the molecular mechanism of nc886-mediated PKR inhibition. We show that nc886 adopts two stable, noninterconverting RNA conformers that are functionally nonequivalent using complementary RNA structure probing and mutational analyses combined with PKR binding and activity assays. One conformer acts as a potent inhibitor, while the other is a pseudoinhibitor capable of weakly activating the kinase. We mapped the nc886 region necessary for high affinity binding and potent inhibition of PKR to an apical stem-loop structure present in only one conformer of the RNA. This structural feature is not only critical for inhibiting PKR autophosphorylation, but also the phosphorylation of its cellular substrate, the eukaryotic translation initiation factor 2α subunit. The identification of different activities of the nc886 conformers suggests a potential mechanism for producing a gradient of PKR regulation within the cell and reveals a way by which a cellular noncoding RNA can mask or present a structural feature to PKR for inhibition.
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Affiliation(s)
- Brenda M Calderon
- Department of Biochemistry, Emory University School of Medicine, Atlanta, Georgia 30322, USA
- Graduate Program in Biochemistry, Cell and Developmental Biology (BCDB), Emory University, Atlanta, Georgia 30322 USA
| | - Graeme L Conn
- Department of Biochemistry, Emory University School of Medicine, Atlanta, Georgia 30322, USA
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44
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Kindler E, Gil-Cruz C, Spanier J, Li Y, Wilhelm J, Rabouw HH, Züst R, Hwang M, V’kovski P, Stalder H, Marti S, Habjan M, Cervantes-Barragan L, Elliot R, Karl N, Gaughan C, van Kuppeveld FJM, Silverman RH, Keller M, Ludewig B, Bergmann CC, Ziebuhr J, Weiss SR, Kalinke U, Thiel V. Early endonuclease-mediated evasion of RNA sensing ensures efficient coronavirus replication. PLoS Pathog 2017; 13:e1006195. [PMID: 28158275 PMCID: PMC5310923 DOI: 10.1371/journal.ppat.1006195] [Citation(s) in RCA: 165] [Impact Index Per Article: 23.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2016] [Revised: 02/15/2017] [Accepted: 01/20/2017] [Indexed: 12/11/2022] Open
Abstract
Coronaviruses are of veterinary and medical importance and include highly pathogenic zoonotic viruses, such as SARS-CoV and MERS-CoV. They are known to efficiently evade early innate immune responses, manifesting in almost negligible expression of type-I interferons (IFN-I). This evasion strategy suggests an evolutionary conserved viral function that has evolved to prevent RNA-based sensing of infection in vertebrate hosts. Here we show that the coronavirus endonuclease (EndoU) activity is key to prevent early induction of double-stranded RNA (dsRNA) host cell responses. Replication of EndoU-deficient coronaviruses is greatly attenuated in vivo and severely restricted in primary cells even during the early phase of the infection. In macrophages we found immediate induction of IFN-I expression and RNase L-mediated breakdown of ribosomal RNA. Accordingly, EndoU-deficient viruses can retain replication only in cells that are deficient in IFN-I expression or sensing, and in cells lacking both RNase L and PKR. Collectively our results demonstrate that the coronavirus EndoU efficiently prevents simultaneous activation of host cell dsRNA sensors, such as Mda5, OAS and PKR. The localization of the EndoU activity at the site of viral RNA synthesis-within the replicase complex-suggests that coronaviruses have evolved a viral RNA decay pathway to evade early innate and intrinsic antiviral host cell responses.
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Affiliation(s)
- Eveline Kindler
- Department of Infectious Diseases and Pathobiology, University of Bern, Bern, Switzerland
- Federal Department of Home Affairs, Institute of Virology and Immunology, Bern and Mittelhäusern, Switzerland
| | - Cristina Gil-Cruz
- Institute of Immunobiology, Kantonsspital St.Gallen, St.Gallen, Switzerland
| | - Julia Spanier
- Institute for Experimental Infection Research, TWINCORE, Centre for Experimental and Clinical Infection Research, a joint venture between the Helmholtz Centre for Infection Research and the Hannover Medical School, Hannover, Germany
| | - Yize Li
- Department of Microbiology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, United States of America
| | - Jochen Wilhelm
- Universities Giessen & Marburg Lung Center (UGMLC), Deutsches Zentrum für Lungenforschung (DZL), Giessen, Germany
| | - Huib H. Rabouw
- Virology Division, Department of Infectious Diseases and Immunology, Faculty of Veterinary Medicine, Utrecht University, Utrecht, The Netherlands
| | | | - Mihyun Hwang
- Department of Neurosciences, Lerner Research Institute, Cleveland Clinic Foundation, Cleveland, Ohio, United States of America
| | - Philip V’kovski
- Department of Infectious Diseases and Pathobiology, University of Bern, Bern, Switzerland
- Federal Department of Home Affairs, Institute of Virology and Immunology, Bern and Mittelhäusern, Switzerland
- Graduate School for Biomedical Science, University of Bern, Bern, Switzerland
| | - Hanspeter Stalder
- Department of Infectious Diseases and Pathobiology, University of Bern, Bern, Switzerland
- Federal Department of Home Affairs, Institute of Virology and Immunology, Bern and Mittelhäusern, Switzerland
| | - Sabrina Marti
- Department of Infectious Diseases and Pathobiology, University of Bern, Bern, Switzerland
- Federal Department of Home Affairs, Institute of Virology and Immunology, Bern and Mittelhäusern, Switzerland
| | | | | | - Ruth Elliot
- Department of Microbiology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, United States of America
| | - Nadja Karl
- Institute for Medical Virology, Justus-Liebig-University, Giessen, Germany
| | - Christina Gaughan
- Department of Cancer Biology, Lerner Research Institute, Cleveland, Ohio, United States of America
| | - Frank J. M. van Kuppeveld
- Virology Division, Department of Infectious Diseases and Immunology, Faculty of Veterinary Medicine, Utrecht University, Utrecht, The Netherlands
| | - Robert H. Silverman
- Department of Cancer Biology, Lerner Research Institute, Cleveland, Ohio, United States of America
| | - Markus Keller
- Institute of Novel and Emerging Infectious Diseases, Friedrich-Loeffler-Institut, Greifswald-Insel Riems, Germany
| | - Burkhard Ludewig
- Institute of Immunobiology, Kantonsspital St.Gallen, St.Gallen, Switzerland
| | - Cornelia C. Bergmann
- Department of Neurosciences, Lerner Research Institute, Cleveland Clinic Foundation, Cleveland, Ohio, United States of America
| | - John Ziebuhr
- Institute for Medical Virology, Justus-Liebig-University, Giessen, Germany
| | - Susan R. Weiss
- Department of Microbiology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, United States of America
| | - Ulrich Kalinke
- Institute for Experimental Infection Research, TWINCORE, Centre for Experimental and Clinical Infection Research, a joint venture between the Helmholtz Centre for Infection Research and the Hannover Medical School, Hannover, Germany
| | - Volker Thiel
- Department of Infectious Diseases and Pathobiology, University of Bern, Bern, Switzerland
- Federal Department of Home Affairs, Institute of Virology and Immunology, Bern and Mittelhäusern, Switzerland
- * E-mail:
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45
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Roles of PKR in differentiation and apoptosis of bone-related cells. Anat Sci Int 2016; 92:313-319. [DOI: 10.1007/s12565-016-0385-3] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2016] [Accepted: 11/25/2016] [Indexed: 12/13/2022]
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46
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Abstract
Severe Acute Respiratory Syndrome (SARS) and Middle East Respiratory Syndrome (MERS) are the most severe coronavirus (CoV)-associated diseases in humans. The causative agents, SARS-CoV and MERS-CoV, are of zoonotic origin but may be transmitted to humans, causing severe and often fatal respiratory disease in their new host. The two coronaviruses are thought to encode an unusually large number of factors that allow them to thrive and replicate in the presence of efficient host defense mechanisms, especially the antiviral interferon system. Here, we review the recent progress in our understanding of the strategies that highly pathogenic coronaviruses employ to escape, dampen, or block the antiviral interferon response in human cells.
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Affiliation(s)
- E Kindler
- University of Bern, Bern, Switzerland; Institute of Virology and Immunology, Bern and Mittelhäusern, Switzerland
| | - V Thiel
- University of Bern, Bern, Switzerland; Institute of Virology and Immunology, Bern and Mittelhäusern, Switzerland
| | - F Weber
- Institute of Virology, Faculty of Veterinary Medicine, Justus Liebig University Giessen, Giessen, Germany.
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47
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Mayo CB, Wong CJ, Lopez PE, Lary JW, Cole JL. Activation of PKR by short stem-loop RNAs containing single-stranded arms. RNA (NEW YORK, N.Y.) 2016; 22:1065-75. [PMID: 27208315 PMCID: PMC4911914 DOI: 10.1261/rna.053348.115] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/16/2015] [Accepted: 04/19/2016] [Indexed: 05/22/2023]
Abstract
Protein kinase R (PKR) is a central component of the innate immunity antiviral pathway and is activated by dsRNA. PKR contains a C-terminal kinase domain and two tandem dsRNA binding domains. In the canonical activation model, binding of multiple PKR monomers to dsRNA enhances dimerization of the kinase domain, leading to enzymatic activation. A minimal dsRNA of 30 bp is required for activation. However, short (∼15 bp) stem-loop RNAs containing flanking single-stranded tails (ss-dsRNAs) are capable of activating PKR. Activation was reported to require a 5'-triphosphate. Here, we characterize the structural features of ss-dsRNAs that contribute to activation. We have designed a model ss-dsRNA containing 15-nt single-stranded tails and a 15-bp stem and made systematic truncations of the tail and stem regions. Autophosphorylation assays and analytical ultracentrifugation experiments were used to correlate activation and binding affinity. PKR activation requires both 5'- and 3'-single-stranded tails but the triphosphate is dispensable. Activation potency and binding affinity decrease as the ssRNA tails are truncated and activation is abolished in cases where the binding affinity is strongly reduced. These results indicate that the single-stranded regions bind to PKR and support a model where ss-dsRNA induced dimerization is required but not sufficient to activate the kinase. The length of the duplex regions in several natural RNA activators of PKR is below the minimum of 30 bp required for activation and similar interactions with single-stranded regions may contribute to PKR activation in these cases.
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Affiliation(s)
- Christopher B Mayo
- Department of Molecular and Cell Biology, University of Connecticut, Storrs, Connecticut 06269, USA
| | - C Jason Wong
- Department of Molecular and Cell Biology, University of Connecticut, Storrs, Connecticut 06269, USA
| | - Prisma E Lopez
- Department of Molecular and Cell Biology, University of Connecticut, Storrs, Connecticut 06269, USA
| | - Jeffrey W Lary
- National Analytical Ultracentrifugation Facility, University of Connecticut, Storrs, Connecticut 06269, USA
| | - James L Cole
- Department of Molecular and Cell Biology, University of Connecticut, Storrs, Connecticut 06269, USA Department of Chemistry, University of Connecticut, Storrs, Connecticut 06269, USA National Analytical Ultracentrifugation Facility, University of Connecticut, Storrs, Connecticut 06269, USA
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48
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Machitani M, Sakurai F, Wakabayashi K, Tomita K, Tachibana M, Mizuguchi H. Dicer functions as an antiviral system against human adenoviruses via cleavage of adenovirus-encoded noncoding RNA. Sci Rep 2016; 6:27598. [PMID: 27273616 PMCID: PMC4895142 DOI: 10.1038/srep27598] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2016] [Accepted: 05/20/2016] [Indexed: 12/20/2022] Open
Abstract
In various organisms, including nematodes and plants, RNA interference (RNAi) is a defense system against virus infection; however, it is unclear whether RNAi functions as an antivirus system in mammalian cells. Rather, a number of DNA viruses, including herpesviruses, utilize post-transcriptional silencing systems for their survival. Here we show that Dicer efficiently suppresses the replication of adenovirus (Ad) via cleavage of Ad-encoding small RNAs (VA-RNAs), which efficiently promote Ad replication via the inhibition of eIF2α phosphorylation, to viral microRNAs (mivaRNAs). The Dicer knockdown significantly increases the copy numbers of VA-RNAs, leading to the efficient inhibition of eIF2α phosphorylation and the subsequent promotion of Ad replication. Conversely, overexpression of Dicer significantly inhibits Ad replication. Transfection with mivaRNA does not affect eIF2α phosphorylation or Ad replication. These results indicate that Dicer-mediated processing of VA-RNAs leads to loss of activity of VA-RNAs for enhancement of Ad replication and that Dicer functions as a defence system against Ad in mammalian cells.
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Affiliation(s)
- Mitsuhiro Machitani
- Laboratory of Biochemistry and Molecular Biology, Graduate School of Pharmaceutical Sciences, Osaka University, 1-6 Yamadaoka, Suita, Osaka 565-0871, Japan
| | - Fuminori Sakurai
- Laboratory of Biochemistry and Molecular Biology, Graduate School of Pharmaceutical Sciences, Osaka University, 1-6 Yamadaoka, Suita, Osaka 565-0871, Japan.,Laboratory of Regulatory Sciences for Oligonucleotide Therapeutics, Clinical Drug Development Unit, Graduate School of Pharmaceutical Sciences, Osaka University, 1-6 Yamadaoka, Suita, Osaka, 565-0871, Japan
| | - Keisaku Wakabayashi
- Laboratory of Biochemistry and Molecular Biology, Graduate School of Pharmaceutical Sciences, Osaka University, 1-6 Yamadaoka, Suita, Osaka 565-0871, Japan
| | - Kyoko Tomita
- Laboratory of Biochemistry and Molecular Biology, Graduate School of Pharmaceutical Sciences, Osaka University, 1-6 Yamadaoka, Suita, Osaka 565-0871, Japan
| | - Masashi Tachibana
- Laboratory of Biochemistry and Molecular Biology, Graduate School of Pharmaceutical Sciences, Osaka University, 1-6 Yamadaoka, Suita, Osaka 565-0871, Japan
| | - Hiroyuki Mizuguchi
- Laboratory of Biochemistry and Molecular Biology, Graduate School of Pharmaceutical Sciences, Osaka University, 1-6 Yamadaoka, Suita, Osaka 565-0871, Japan.,Laboratory of Hepatocyte Regulation, National Institute of Biomedical Innovation, Health and Nutrition, 7-6-8 Saito, Asagi, Ibaraki, Osaka 567-0085, Japan.,iPS Cell-Based Research Project on Hepatic Toxicity and Metabolism, Graduate School of Pharmaceutical Sciences, Osaka University, 1-6 Yamadaoka, Suita, Osaka 565-0871, Japan.,Global Center for Advanced Medical Engineering and Informatics, Osaka University, 2-2 Yamadaoka, Suita, Osaka 565-0871, Japan.,Graduate School of Medicine, Osaka University, 2-2 Yamadaoka, Suita, Osaka 565-0871, Japan
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Shinohara H, Teramachi J, Okamura H, Yang D, Nagata T, Haneji T. Double Stranded RNA-Dependent Protein Kinase is Necessary for TNF-α-Induced Osteoclast Formation In Vitro and In Vivo. J Cell Biochem 2016; 116:1957-67. [PMID: 25739386 DOI: 10.1002/jcb.25151] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2014] [Accepted: 02/27/2015] [Indexed: 12/12/2022]
Abstract
Double-stranded RNA-dependent protein kinase (PKR) is involved in cell cycle progression, cell proliferation, cell differentiation, tumorgenesis, and apoptosis. We previously reported that PKR is required for differentiation and calcification in osteoblasts. TNF-α plays a key role in osteoclast differentiation. However, it is unknown about the roles of PKR in the TNF-α-induced osteoclast differentiation. The expression of PKR in osteoclast precursor RAW264.7 cells increased during TNF-α-induced osteoclastogenesis. The TNF-α-induced osteoclast differentiation in bone marrow-derived macrophages and RAW264.7 cells was markedly suppressed by the pretreatment of PKR inhibitor, 2-aminopurine (2AP), as well as gene silencing of PKR. The expression of gene markers in the differentiated osteoclasts including TRAP, Calcitonin receptor, cathepsin K, and ATP6V0d2 was also suppressed by the 2AP treatment. Bone resorption activity of TNF-α-induced osteoclasts was also supressed by 2AP treatment. Inhibition of PKR supressed the TNF-α-induced activation of NF-κB and MAPK in RAW264.7 cells. 2AP inhibited both the nuclear translocation of NF-κB and its transcriptional activity in RAW264.7 cells. 2AP inhibited the TNF-α-induced expression of NFATc1 and c-fos, master transcription factors in osteoclastogenesis. TNF-α-induced nuclear translocation of NFATc1 in mature osteoclasts was clearly inhibited by the 2AP treatment. The PKR inhibitor C16 decreased the TNF-α-induced osteoclast formation and bone resorption in mouse calvaria. The present study indicates that PKR is necessary for the TNF-α-induced osteoclast differentiation in vitro and in vivo.
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Affiliation(s)
- Hiroki Shinohara
- Department of Histology and Oral Histology, Institute of Health Biosciences, The University of Tokushima Graduate School, Tokushima, Japan.,Department of Periodontology and Endodontology, Institute of Health Biosciences, The University of Tokushima Graduate School, Tokushima, Japan
| | - Jumpei Teramachi
- Department of Histology and Oral Histology, Institute of Health Biosciences, The University of Tokushima Graduate School, Tokushima, Japan
| | - Hirohiko Okamura
- Department of Histology and Oral Histology, Institute of Health Biosciences, The University of Tokushima Graduate School, Tokushima, Japan
| | - Di Yang
- Department of Histology and Oral Histology, Institute of Health Biosciences, The University of Tokushima Graduate School, Tokushima, Japan
| | - Toshihiko Nagata
- Department of Periodontology and Endodontology, Institute of Health Biosciences, The University of Tokushima Graduate School, Tokushima, Japan
| | - Tatsuji Haneji
- Department of Histology and Oral Histology, Institute of Health Biosciences, The University of Tokushima Graduate School, Tokushima, Japan
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Hull CM, Anmangandla A, Bevilacqua PC. Bacterial Riboswitches and Ribozymes Potently Activate the Human Innate Immune Sensor PKR. ACS Chem Biol 2016; 11:1118-27. [PMID: 27011290 DOI: 10.1021/acschembio.6b00081] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
Abstract
The innate immune system provides the first line of defense against pathogens through the recognition of nonspecific patterns in RNA to protect the cell in a generalized way. The human RNA-activated protein kinase, PKR, is a dsRNA binding protein and an essential sensor in the innate immune response, which recognizes viral and bacterial pathogens through their RNAs. Upon activation via RNA-dependent autophosphorylation, PKR phosphorylates the eukaryotic initiation factor eIF2α, leading to termination of translation. PKR has a well-characterized role in recognizing viral RNA, where it binds long stretches of double-stranded RNA nonsequence specifically to promote activation; however, the mechanism by which bacterial RNA activates PKR and the mode by which self RNA avoids activating PKR are unknown. We characterized activation of PKR by three functional bacterial RNAs with pseudoknots and extensive tertiary structure: the cyclic di-GMP riboswitch, the glmS riboswitch-ribozyme, and the twister ribozyme, two of which are ligand-activated. These RNAs were found to activate PKR with comparable potency to long dsRNA. Enzymatic structure mapping in the absence and presence of PKR reveals a clear PKR footprint and provides a structural basis for how these bacterial RNAs activate PKR. In the case of the cyclic di-GMP riboswitch and the glmS riboswitch-ribozyme, PKR appears to dimerize on the peripheral double-stranded regions of the native RNA tertiary structure. Overall, these results provide new insights into how PKR acts as an innate immune signaling protein for the presence of bacteria and suggest a reason for the apparent absence of protein-free riboswitches and ribozymes in the human genome.
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Affiliation(s)
- Chelsea M. Hull
- Department
of Chemistry, Center for RNA Molecular Biology, The Pennsylvania State University, University Park, Pennsylvania 16802, United States
| | - Ananya Anmangandla
- Department
of Chemistry, Center for RNA Molecular Biology, The Pennsylvania State University, University Park, Pennsylvania 16802, United States
| | - Philip C. Bevilacqua
- Department
of Chemistry, Center for RNA Molecular Biology, The Pennsylvania State University, University Park, Pennsylvania 16802, United States
- Department
of Biochemistry and Molecular Biology, The Pennsylvania State University, University Park, Pennsylvania 16802, United States
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