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Shi W, Xu G, Gao Y, Yang H, Liu T, Zhao J, Li H, Wei Z, Hou X, Chen Y, Wen J, Li C, Zhao J, Zhang P, Wang Z, Xiao X, Bai Z. Compound Danshen Dripping Pill effectively alleviates cGAS-STING-triggered diseases by disrupting STING-TBK1 interaction. PHYTOMEDICINE : INTERNATIONAL JOURNAL OF PHYTOTHERAPY AND PHYTOPHARMACOLOGY 2024; 128:155404. [PMID: 38507852 DOI: 10.1016/j.phymed.2024.155404] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/17/2023] [Revised: 01/13/2024] [Accepted: 01/31/2024] [Indexed: 03/22/2024]
Abstract
BACKGROUND The cyclic GMP-AMP synthase (cGAS)-stimulator of interferon (IFN) genes (STING) pathway is critical in the innate immune system and can be mobilized by cytosolic DNA. The various inflammatory and autoimmune diseases progression is highly correlated with aberrant cGAS-STING pathway activation. While some cGAS-STING pathway inhibitor were identified, there are no drugs that can be applied to the clinic. Compound Danshen Dripping Pill (CDDP) has been successfully used in clinic around the world, but the most common application is limited to cardiovascular disease. Therefore, the purpose of the present investigation was to examine whether CDDP inhibits the cGAS-STING pathway and could be used as a therapeutic agent for multiple cGAS-STING-triggered diseases. METHODS BMDMs, THP1 cells or Trex1-/- BMDMs were stimulated with various cGAS-STING-agonists after pretreatment with CDDP to detect the function of CDDP on IFN-β and ISGs productionn. Next, we detect the influence on IRF3 and P65 nuclear translocation, STING oligomerization and STING-TBK1-IRF3 complex formation of CDDP. Additionally, the DMXAA-mediated activation mice model of cGAS-STING pathway was used to study the effects of CDDP. Trex1-/- mice model and HFD-mediated obesity model were established to clarify the efficacy of CDDP on inflammatory and autoimmune diseases. RESULTS CDDP efficacy suppressed the IRF3 phosphorylation or the generation of IFN-β, ISGs, IL-6 and TNF-α. Mechanistically, CDDP did not influence the STING oligomerization and IRF3-TBK1 and STING-IRF3 interaction, but remarkably eliminated the STING-TBK1 interaction, ultimately blocking the downstream responses. In addition, we also clarified that CDDP could suppress cGAS-STING pathway activation triggered by DMXAA, in vivo. Consistently, CDDP could alleviate multi-organ inflammatory responses in Trex1-/- mice model and attenuate the inflammatory disorders, incleding obesity-induced insulin resistance. CONCLUSION CDDP is a specifically cGAS-STING pathway inhibitor. Furthermore, we provide novel mechanism for CDDP and discovered a clinical agent for the therapy of cGAS-STING-triggered inflammatory and autoimmune diseases.
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Affiliation(s)
- Wei Shi
- Department of Hepatology, Fifth Medical Center of Chinese PLA General Hospital, Beijing, China; School of Life Sciences, Beijing University of Chinese Medicine, Beijing, China
| | - Guang Xu
- School of Traditional Chinese Medicine, Capital Medical University, Beijing, China
| | - Yuan Gao
- School of Traditional Chinese Medicine, Capital Medical University, Beijing, China
| | - Huijie Yang
- Department of Hepatology, Fifth Medical Center of Chinese PLA General Hospital, Beijing, China; School of Life Sciences, Beijing University of Chinese Medicine, Beijing, China
| | - Tingting Liu
- Department of Hepatology, Fifth Medical Center of Chinese PLA General Hospital, Beijing, China
| | - Jia Zhao
- Department of Hepatology, Fifth Medical Center of Chinese PLA General Hospital, Beijing, China
| | - Hui Li
- Department of Hepatology, Fifth Medical Center of Chinese PLA General Hospital, Beijing, China; School of Life Sciences, Beijing University of Chinese Medicine, Beijing, China
| | - Ziying Wei
- Department of Hepatology, Fifth Medical Center of Chinese PLA General Hospital, Beijing, China
| | - Xiaorong Hou
- Department of Hepatology, Fifth Medical Center of Chinese PLA General Hospital, Beijing, China
| | - Yuanyuan Chen
- Department of Hepatology, Fifth Medical Center of Chinese PLA General Hospital, Beijing, China
| | - Jincai Wen
- Department of Hepatology, Fifth Medical Center of Chinese PLA General Hospital, Beijing, China
| | - Chengwei Li
- Department of Hepatology, Fifth Medical Center of Chinese PLA General Hospital, Beijing, China
| | - Jun Zhao
- Department of Hepatology, Fifth Medical Center of Chinese PLA General Hospital, Beijing, China
| | - Ping Zhang
- Department of Hepatology, Fifth Medical Center of Chinese PLA General Hospital, Beijing, China
| | - Zhongxia Wang
- Department of Hepatology, Fifth Medical Center of Chinese PLA General Hospital, Beijing, China
| | - Xiaohe Xiao
- Department of Hepatology, Fifth Medical Center of Chinese PLA General Hospital, Beijing, China; Military Institute of Chinese Materia, the Fifth Medical Centre, General Hospital of PLA, Beijing, China; National Key Laboratory of Kidney Diseases, China.
| | - Zhaofang Bai
- Department of Hepatology, Fifth Medical Center of Chinese PLA General Hospital, Beijing, China; Military Institute of Chinese Materia, the Fifth Medical Centre, General Hospital of PLA, Beijing, China; National Key Laboratory of Kidney Diseases, China.
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Yoshioka D, Nakamura T, Kubota Y, Takekawa M. Formation of the NLRP3 inflammasome inhibits stress granule assembly by multiple mechanisms. J Biochem 2024; 175:629-641. [PMID: 38299728 PMCID: PMC11155693 DOI: 10.1093/jb/mvae009] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2023] [Revised: 01/21/2024] [Accepted: 01/30/2024] [Indexed: 02/02/2024] Open
Abstract
Proper regulation of cellular response to environmental stress is crucial for maintaining biological homeostasis and is achieved by the balance between cell death processes, such as the formation of the pyroptosis-inducing NLRP3 inflammasome, and pro-survival processes, such as stress granule (SG) assembly. However, the functional interplay between these two stress-responsive organelles remains elusive. Here, we identified DHX33, a viral RNA sensor for the NLRP3 inflammasome, as a SG component, and the SG-nucleating protein G3BP as an NLRP3 inflammasome component. We also found that a decrease in intracellular potassium (K+) concentration, a key 'common' step in NLRP3 inflammasome activation, markedly inhibited SG assembly. Therefore, when macrophages are exposed to stress stimuli with the potential to induce both SGs and the NLRP3 inflammasome, such as cytoplasmic poly(I:C) stimulation, they preferentially form the NLRP3 inflammasome but avoid SG assembly by sequestering G3BP into the inflammasome and by inducing a reduction in intracellular K+ levels. Thus, under such conditions, DHX33 is primarily utilized as a viral RNA sensor for the inflammasome. Our data reveal the functional crosstalk between NLRP3 inflammasome-mediated pyroptosis and SG-mediated cell survival pathways and delineate a molecular mechanism that regulates cell-fate decisions and anti-viral innate immunity under stress.
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Affiliation(s)
- Daisuke Yoshioka
- Division of Cell Signaling and Molecular Medicine, Institute of Medical Science, The University of Tokyo, 4-6-1 Shirokanedai, Minato-ku, Tokyo 108-8639, Japan
- Department of Computational Biology and Medical Sciences, Graduate School of Frontier Sciences, The University of Tokyo, Chiba 277-8583, Japan
| | - Takanori Nakamura
- Division of Cell Signaling and Molecular Medicine, Institute of Medical Science, The University of Tokyo, 4-6-1 Shirokanedai, Minato-ku, Tokyo 108-8639, Japan
| | - Yuji Kubota
- Division of Cell Signaling and Molecular Medicine, Institute of Medical Science, The University of Tokyo, 4-6-1 Shirokanedai, Minato-ku, Tokyo 108-8639, Japan
| | - Mutsuhiro Takekawa
- Division of Cell Signaling and Molecular Medicine, Institute of Medical Science, The University of Tokyo, 4-6-1 Shirokanedai, Minato-ku, Tokyo 108-8639, Japan
- Department of Computational Biology and Medical Sciences, Graduate School of Frontier Sciences, The University of Tokyo, Chiba 277-8583, Japan
- Medical Proteomics Laboratory, Institute of Medical Science, The University of Tokyo, 4-6-1 Shirokanedai, Minato-ku, Tokyo 108-8639, Japan
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3
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Choi Y, Um B, Na Y, Kim J, Kim JS, Kim VN. Time-resolved profiling of RNA binding proteins throughout the mRNA life cycle. Mol Cell 2024; 84:1764-1782.e10. [PMID: 38593806 DOI: 10.1016/j.molcel.2024.03.012] [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: 01/23/2024] [Revised: 02/16/2024] [Accepted: 03/14/2024] [Indexed: 04/11/2024]
Abstract
mRNAs continually change their protein partners throughout their lifetimes, yet our understanding of mRNA-protein complex (mRNP) remodeling is limited by a lack of temporal data. Here, we present time-resolved mRNA interactome data by performing pulse metabolic labeling with photoactivatable ribonucleoside in human cells, UVA crosslinking, poly(A)+ RNA isolation, and mass spectrometry. This longitudinal approach allowed the quantification of over 700 RNA binding proteins (RBPs) across ten time points. Overall, the sequential order of mRNA binding aligns well with known functions, subcellular locations, and molecular interactions. However, we also observed RBPs with unexpected dynamics: the transcription-export (TREX) complex recruited posttranscriptionally after nuclear export factor 1 (NXF1) binding, challenging the current view of transcription-coupled mRNA export, and stress granule proteins prevalent in aged mRNPs, indicating roles in late stages of the mRNA life cycle. To systematically identify mRBPs with unknown functions, we employed machine learning to compare mRNA binding dynamics with Gene Ontology (GO) annotations. Our data can be explored at chronology.rna.snu.ac.kr.
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Affiliation(s)
- Yeon Choi
- Center for RNA Research, Institute for Basic Science, Seoul 08826, Republic of Korea; School of Biological Sciences, Seoul National University, Seoul 08826, Republic of Korea
| | - Buyeon Um
- Center for RNA Research, Institute for Basic Science, Seoul 08826, Republic of Korea; School of Biological Sciences, Seoul National University, Seoul 08826, Republic of Korea
| | - Yongwoo Na
- Center for RNA Research, Institute for Basic Science, Seoul 08826, Republic of Korea; School of Biological Sciences, Seoul National University, Seoul 08826, Republic of Korea
| | - Jeesoo Kim
- Center for RNA Research, Institute for Basic Science, Seoul 08826, Republic of Korea; School of Biological Sciences, Seoul National University, Seoul 08826, Republic of Korea
| | - Jong-Seo Kim
- Center for RNA Research, Institute for Basic Science, Seoul 08826, Republic of Korea; School of Biological Sciences, Seoul National University, Seoul 08826, Republic of Korea.
| | - V Narry Kim
- Center for RNA Research, Institute for Basic Science, Seoul 08826, Republic of Korea; School of Biological Sciences, Seoul National University, Seoul 08826, Republic of Korea.
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Liu N, Yang W, Luo L, Ma M, Cui J, Dong X, Li Y. Critical role of G3BP1 in bovine parainfluenza virus type 3 (BPIV3)-inhibition of stress granules formation and viral replication. Front Immunol 2024; 15:1358036. [PMID: 38690262 PMCID: PMC11058653 DOI: 10.3389/fimmu.2024.1358036] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2023] [Accepted: 04/05/2024] [Indexed: 05/02/2024] Open
Abstract
Background It remains unclear whether BPIV3 infection leads to stress granules formation and whether G3BP1 plays a role in this process and in viral replication. This study aims to clarify the association between BPIV3 and stress granules, explore the effect of G3BP1 on BPIV3 replication, and provide significant insights into the mechanisms by which BPIV3 evades the host's antiviral immunity to support its own survival. Methods Here, we use Immunofluorescence staining to observe the effect of BPIV3 infection on the assembly of stress granules. Meanwhile, the expression changes of eIF2α and G3BP1 were determined. Overexpression or siRNA silencing of intracellular G3BP1 levels was examined for its regulatory control of BPIV3 replication. Results We identify that the BPIV3 infection elicited phosphorylation of the eIF2α protein. However, it did not induce the assembly of stress granules; rather, it inhibited the formation of stress granules and downregulated the expression of G3BP1. G3BP1 overexpression facilitated the formation of stress granules within cells and hindered viral replication, while G3BP1 knockdown enhanced BPIV3 expression. Conclusion This study suggest that G3BP1 plays a crucial role in BPIV3 suppressing stress granule formation and viral replication.
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Affiliation(s)
- Nian Liu
- College of Veterinary Medicine, Northeast Agricultural University, Harbin, China
| | - Wei Yang
- College of Veterinary Medicine, Northeast Agricultural University, Harbin, China
- Heilongjiang Key Laboratory for Animal Disease Control and Pharmaceutical Development, Harbin, China
| | - Lingzhi Luo
- College of Veterinary Medicine, Northeast Agricultural University, Harbin, China
| | - Mingshuang Ma
- College of Veterinary Medicine, Northeast Agricultural University, Harbin, China
| | - Jin Cui
- College of Veterinary Medicine, Northeast Agricultural University, Harbin, China
- Heilongjiang Key Laboratory for Animal Disease Control and Pharmaceutical Development, Harbin, China
| | - Xiumei Dong
- College of Veterinary Medicine, Northeast Agricultural University, Harbin, China
- Heilongjiang Key Laboratory for Animal Disease Control and Pharmaceutical Development, Harbin, China
| | - Yijing Li
- College of Veterinary Medicine, Northeast Agricultural University, Harbin, China
- Heilongjiang Key Laboratory for Animal Disease Control and Pharmaceutical Development, Harbin, China
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5
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Yeo SK, Haas M, Manupati K, Hao M, Yang F, Chen S, Guan JL. AZI2 mediates TBK1 activation at unresolved selective autophagy cargo receptor complexes with implications for CD8 T-cell infiltration in breast cancer. Autophagy 2024; 20:525-540. [PMID: 37733921 PMCID: PMC10936636 DOI: 10.1080/15548627.2023.2259775] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2022] [Accepted: 09/12/2023] [Indexed: 09/23/2023] Open
Abstract
Most breast cancers do not respond to immune checkpoint inhibitors and there is an urgent need to identify novel sensitization strategies. Herein, we uncovered that activation of the TBK-IFN pathway that is mediated by the TBK1 adapter protein AZI2 is a potent strategy for this purpose. Our initial observations showed that RB1CC1 depletion leads to accumulation of AZI2, in puncta along with selective macroautophagy/autophagy cargo receptors, which are both required for TBK1 activation. Specifically, disrupting the selective autophagy function of RB1CC1 was sufficient to sustain AZI2 puncta accumulation and TBK1 activation. AZI2 then mediates downstream activation of DDX3X, increasing its interaction with IRF3 for transcription of pro-inflammatory chemokines. Consequently, we performed a screen to identify inhibitors that can induce the AZI2-TBK1 pathway, and this revealed Lys05 as a pharmacological agent that induced pro-inflammatory chemokine expression and CD8+ T cell infiltration into tumors. Overall, we have identified a distinct AZI2-TBK1-IFN signaling pathway that is responsive to selective autophagy blockade and can be activated to make breast cancers more immunogenic.Abbreviations: AZI2/NAP1: 5-azacytidine induced 2; CALCOCO2: calcium binding and coiled-coil domain 2; DDX3X: DEAD-box helicase 3 X-linked; FCCP: carbonyl cyanide p-triflouromethoxyphenylhydrazone; a protonophore that depolarizes the mitochondrial inner membrane; ICI: immune checkpoint inhibitor; IFN: interferon; NBR1: NBR1 autophagy cargo receptor; OPTN: optineurin; RB1CC1/FIP200: RB1 inducible coiled-coil 1; SQSTM1/p62: sequestosome 1; TAX1BP1: Tax1 binding protein 1; TBK1: TANK binding kinase 1.
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Affiliation(s)
- Syn Kok Yeo
- Department of Cancer Biology, University of Cincinnati College of Medicine, Cincinnati, OH, USA
| | - Michael Haas
- Department of Cancer Biology, University of Cincinnati College of Medicine, Cincinnati, OH, USA
| | - Kanakaraju Manupati
- Department of Cancer Biology, University of Cincinnati College of Medicine, Cincinnati, OH, USA
| | - Mingang Hao
- Department of Cancer Biology, University of Cincinnati College of Medicine, Cincinnati, OH, USA
| | - Fuchun Yang
- Department of Cancer Biology, University of Cincinnati College of Medicine, Cincinnati, OH, USA
| | - Song Chen
- Department of Cancer Biology, University of Cincinnati College of Medicine, Cincinnati, OH, USA
- Translational Research Institute, Henan Provincial People’s Hospital, Academy of Medical Science, Zhengzhou University, Zhengzhou, Henan Province, China
| | - Jun-Lin Guan
- Department of Cancer Biology, University of Cincinnati College of Medicine, Cincinnati, OH, USA
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6
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Zhang Q, Xian W, Li Z, Lu Q, Chen X, Ge J, Tang Z, Liu B, Chen Z, Gao X, Hottiger MO, Zhang P, Qiu J, Shao F, Liu X. Shigella induces stress granule formation by ADP-riboxanation of the eIF3 complex. Cell Rep 2024; 43:113789. [PMID: 38368608 DOI: 10.1016/j.celrep.2024.113789] [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: 04/20/2023] [Revised: 01/09/2024] [Accepted: 01/29/2024] [Indexed: 02/20/2024] Open
Abstract
Under stress conditions, translationally stalled mRNA and associated proteins undergo liquid-liquid phase separation and condense into cytoplasmic foci called stress granules (SGs). Many viruses hijack SGs for their pathogenesis; however, whether pathogenic bacteria also exploit this pathway remains unknown. Here, we report that members of the OspC family of Shigella flexneri induce SG formation in infected cells. Mechanistically, the OspC effectors target multiple subunits of the host translation initiation factor 3 complex by ADP-riboxanation. The modification of eIF3 leads to translational arrest and thus the formation of SGs. Furthermore, OspC-mediated SGs are beneficial for S. flexneri replication within infected host cells, and bacterial strains unable to induce SGs are attenuated for virulence in a murine model of infection. Our findings reveal a mechanism by which bacterial pathogens induce SG assembly by inactivating host translational machinery and promote bacterial proliferation in host cells.
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Affiliation(s)
- Qinxin Zhang
- Department of Microbiology and Infectious Disease Center, NHC Key Laboratory of Medical Immunology, School of Basic Medical Sciences, Peking University Health Science Center, Beijing 100191, China
| | - Wei Xian
- Department of Microbiology and Infectious Disease Center, NHC Key Laboratory of Medical Immunology, School of Basic Medical Sciences, Peking University Health Science Center, Beijing 100191, China
| | - Zilin Li
- National Institute of Biological Sciences, Beijing 102206, China
| | - Qian Lu
- State Key Laboratory for Diagnosis and Treatment of Severe Zoonotic Infectious Diseases, Key Laboratory for Zoonosis Research of the Ministry of Education, College of Veterinary Medicine, Jilin University, Changchun 130062, China
| | - Xindi Chen
- Department of Microbiology and Infectious Disease Center, NHC Key Laboratory of Medical Immunology, School of Basic Medical Sciences, Peking University Health Science Center, Beijing 100191, China
| | - Jinli Ge
- State Key Laboratory for Diagnosis and Treatment of Severe Zoonotic Infectious Diseases, Key Laboratory for Zoonosis Research of the Ministry of Education, College of Veterinary Medicine, Jilin University, Changchun 130062, China
| | - Zhiheng Tang
- Department of Microbiology and Infectious Disease Center, NHC Key Laboratory of Medical Immunology, School of Basic Medical Sciences, Peking University Health Science Center, Beijing 100191, China
| | - Bohao Liu
- Department of Microbiology and Infectious Disease Center, NHC Key Laboratory of Medical Immunology, School of Basic Medical Sciences, Peking University Health Science Center, Beijing 100191, China
| | - Zhe Chen
- State Key Laboratory of Microbial Technology, Microbial Technology Institute, School of Life Science, Shandong University, Qingdao 266000, China
| | - Xiang Gao
- State Key Laboratory of Microbial Technology, Microbial Technology Institute, School of Life Science, Shandong University, Qingdao 266000, China
| | - Michael O Hottiger
- Department of Molecular Mechanisms of Disease, University of Zurich, 8057 Zurich, Switzerland
| | - Peipei Zhang
- Key Laboratory for Neuroscience, Ministry of Education/National Health and Family Planning Commission, Department of Biochemistry, School of Basic Medical Sciences, Peking University Health Science Center, Beijing 100191, China.
| | - Jiazhang Qiu
- State Key Laboratory for Diagnosis and Treatment of Severe Zoonotic Infectious Diseases, Key Laboratory for Zoonosis Research of the Ministry of Education, College of Veterinary Medicine, Jilin University, Changchun 130062, China.
| | - Feng Shao
- National Institute of Biological Sciences, Beijing 102206, China
| | - Xiaoyun Liu
- Department of Microbiology and Infectious Disease Center, NHC Key Laboratory of Medical Immunology, School of Basic Medical Sciences, Peking University Health Science Center, Beijing 100191, China.
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7
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Burke JM, Ratnayake OC, Watkins JM, Perera R, Parker R. G3BP1-dependent condensation of translationally inactive viral RNAs antagonizes infection. SCIENCE ADVANCES 2024; 10:eadk8152. [PMID: 38295168 PMCID: PMC10830107 DOI: 10.1126/sciadv.adk8152] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/12/2023] [Accepted: 12/28/2023] [Indexed: 02/02/2024]
Abstract
G3BP1 is an RNA binding protein that condenses untranslating messenger RNAs into stress granules (SGs). G3BP1 is inactivated by multiple viruses and is thought to antagonize viral replication by SG-enhanced antiviral signaling. Here, we show that neither G3BP1 nor SGs generally alter the activation of innate immune pathways. Instead, we show that the RNAs encoded by West Nile virus, Zika virus, and severe acute respiratory syndrome coronavirus 2 are prone to G3BP1-dependent RNA condensation, which is enhanced by limiting translation initiation and correlates with the disruption of viral replication organelles and viral RNA replication. We show that these viruses counteract condensation of their RNA genomes by inhibiting the RNA condensing function of G3BP proteins, hijacking the RNA decondensing activity of eIF4A, and/or maintaining efficient translation. These findings argue that RNA condensation can function as an intrinsic antiviral mechanism, which explains why many viruses inactivate G3BP proteins and suggests that SGs may have arisen as a vestige of this antiviral mechanism.
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Affiliation(s)
- James M. Burke
- Department of Molecular Medicine, The Herbert Wertheim UF Scripps Institute for Biomedical Innovation & Technology, Jupiter, FL 33458, USA
- Department of Immunology and Microbiology, The Herbert Wertheim UF Scripps Institute for Biomedical Innovation & Technology, Jupiter, FL 33458, USA
| | - Oshani C. Ratnayake
- Center for Vector-Borne and Infectious Diseases, Department of Microbiology, Immunology and Pathology, Colorado State University, Fort Collins, CO 80523, USA
- Center for Metabolism of Infectious Diseases, Colorado State University, Fort Collins, CO 80523, USA
| | - J. Monty Watkins
- Department of Molecular Medicine, The Herbert Wertheim UF Scripps Institute for Biomedical Innovation & Technology, Jupiter, FL 33458, USA
- Department of Immunology and Microbiology, The Herbert Wertheim UF Scripps Institute for Biomedical Innovation & Technology, Jupiter, FL 33458, USA
- Skaggs Graduate School of Chemical and Biological Sciences, The Scripps Research Institute, Jupiter, FL 33438, USA
| | - Rushika Perera
- Center for Vector-Borne and Infectious Diseases, Department of Microbiology, Immunology and Pathology, Colorado State University, Fort Collins, CO 80523, USA
- Center for Metabolism of Infectious Diseases, Colorado State University, Fort Collins, CO 80523, USA
| | - Roy Parker
- Howard Hughes Medical Institute, University of Colorado Boulder, Boulder, CO 80303, USA
- BioFrontiers Institute, University of Colorado Boulder, Boulder, CO 80303, USA
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8
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Yoo JS. Cellular Stress Responses against Coronavirus Infection: A Means of the Innate Antiviral Defense. J Microbiol Biotechnol 2024; 34:1-9. [PMID: 37674398 PMCID: PMC10840489 DOI: 10.4014/jmb.2307.07038] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2023] [Revised: 08/20/2023] [Accepted: 09/06/2023] [Indexed: 09/08/2023]
Abstract
Cellular stress responses are crucial for maintaining cellular homeostasis. Stress granules (SGs), activated by eIF2α kinases in response to various stimuli, play a pivotal role in dealing with diverse stress conditions. Viral infection, as one kind of cellular stress, triggers specific cellular programs aimed at overcoming virus-induced stresses. Recent studies have revealed that virus-derived stress responses are tightly linked to the host's antiviral innate immunity. Virus infection-induced SGs act as platforms for antiviral sensors, facilitating the initiation of protective antiviral responses called "antiviral stress granules" (avSGs). However, many viruses, including coronaviruses, have evolved strategies to suppress avSG formation, thereby counteracting the host's immune responses. This review discusses the intricate relationship between cellular stress responses and antiviral innate immunity, with a specific focus on coronaviruses. Furthermore, the diverse mechanisms employed by viruses to counteract avSGs are described.
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Affiliation(s)
- Ji-Seung Yoo
- School of Life Sciences, BK21 FOUR KNU Creative BioResearch Group, Kyungpook National University, Daegu 41566, Republic of Korea
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Giambruno R, Zacco E, Ugolini C, Vandelli A, Mulroney L, D’Onghia M, Giuliani B, Criscuolo E, Castelli M, Clementi N, Clementi M, Mancini N, Bonaldi T, Gustincich S, Leonardi T, Tartaglia GG, Nicassio F. Unveiling the role of PUS7-mediated pseudouridylation in host protein interactions specific for the SARS-CoV-2 RNA genome. MOLECULAR THERAPY. NUCLEIC ACIDS 2023; 34:102052. [PMID: 38028201 PMCID: PMC10630655 DOI: 10.1016/j.omtn.2023.102052] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 09/08/2023] [Accepted: 10/05/2023] [Indexed: 12/01/2023]
Abstract
Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), a positive single-stranded RNA virus, engages in complex interactions with host cell proteins throughout its life cycle. While these interactions enable the host to recognize and inhibit viral replication, they also facilitate essential viral processes such as transcription, translation, and replication. Many aspects of these virus-host interactions remain poorly understood. Here, we employed the catRAPID algorithm and utilized the RNA-protein interaction detection coupled with mass spectrometry technology to predict and validate the host proteins that specifically bind to the highly structured 5' and 3' terminal regions of the SARS-CoV-2 RNA. Among the interactions identified, we prioritized pseudouridine synthase PUS7, which binds to both ends of the viral RNA. Using nanopore direct RNA sequencing, we discovered that the viral RNA undergoes extensive post-transcriptional modifications. Modified consensus regions for PUS7 were identified at both terminal regions of the SARS-CoV-2 RNA, including one in the viral transcription regulatory sequence leader. Collectively, our findings offer insights into host protein interactions with the SARS-CoV-2 UTRs and highlight the likely significance of pseudouridine synthases and other post-transcriptional modifications in the viral life cycle. This new knowledge enhances our understanding of virus-host dynamics and could inform the development of targeted therapeutic strategies.
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Affiliation(s)
- Roberto Giambruno
- Center for Genomic Science of IIT@SEMM, Fondazione Istituto Italiano di Tecnologia, 20139 Milano, Italy
- Institute of Biomedical Technologies, National Research Council, 20090 Segrate, Italy
| | - Elsa Zacco
- Central RNA and RNA Systems Biology Labs, Centre for Human Technologies (CHT), Istituto Italiano di Tecnologia (IIT), 16152 Genova, Italy
| | - Camilla Ugolini
- Center for Genomic Science of IIT@SEMM, Fondazione Istituto Italiano di Tecnologia, 20139 Milano, Italy
- Department of Oncology and Hematology-Oncology, University of Milan, 20122 Milano, Italy
| | - Andrea Vandelli
- Central RNA and RNA Systems Biology Labs, Centre for Human Technologies (CHT), Istituto Italiano di Tecnologia (IIT), 16152 Genova, Italy
- Department of Biochemistry and Molecular Biology, Universitat Autònoma de Barcelona, Bellaterra, Barcelona 08193, Spain
- Universitat Pompeu Fabra (UPF), 08003 Barcelona, Spain
| | - Logan Mulroney
- Center for Genomic Science of IIT@SEMM, Fondazione Istituto Italiano di Tecnologia, 20139 Milano, Italy
- European Molecular Biology Laboratory, European Bioinformatics Institute, Hinxton, Cambridgeshire CB10 1SD, UK
- Epigenetics and Neurobiology Unit, European Molecular Biology Laboratory (EMBL), Monterotondo, RM 00015, Italy
| | - Manfredi D’Onghia
- Center for Genomic Science of IIT@SEMM, Fondazione Istituto Italiano di Tecnologia, 20139 Milano, Italy
| | - Bianca Giuliani
- Center for Genomic Science of IIT@SEMM, Fondazione Istituto Italiano di Tecnologia, 20139 Milano, Italy
| | - Elena Criscuolo
- Laboratory of Microbiology and Virology, Vita-Salute San Raffaele University, 20132 Milan, Italy
| | - Matteo Castelli
- Laboratory of Microbiology and Virology, Vita-Salute San Raffaele University, 20132 Milan, Italy
| | - Nicola Clementi
- Laboratory of Microbiology and Virology, Vita-Salute San Raffaele University, 20132 Milan, Italy
- Laboratory of Medical Microbiology and Virology, IRCCS San Raffaele Scientific Institute, 20132 Milan, Italy
| | - Massimo Clementi
- Laboratory of Microbiology and Virology, Vita-Salute San Raffaele University, 20132 Milan, Italy
- Laboratory of Medical Microbiology and Virology, IRCCS San Raffaele Scientific Institute, 20132 Milan, Italy
| | - Nicasio Mancini
- Laboratory of Microbiology and Virology, Vita-Salute San Raffaele University, 20132 Milan, Italy
- Laboratory of Medical Microbiology and Virology, IRCCS San Raffaele Scientific Institute, 20132 Milan, Italy
| | - Tiziana Bonaldi
- Department of Experimental Oncology, European Institute of Oncology IRCCS, 20139 Milano, Italy
- Department of Oncology and Hematology-Oncology, University of Milan, 20122 Milano, Italy
| | - Stefano Gustincich
- Central RNA and RNA Systems Biology Labs, Centre for Human Technologies (CHT), Istituto Italiano di Tecnologia (IIT), 16152 Genova, Italy
| | - Tommaso Leonardi
- Center for Genomic Science of IIT@SEMM, Fondazione Istituto Italiano di Tecnologia, 20139 Milano, Italy
| | - Gian Gaetano Tartaglia
- Central RNA and RNA Systems Biology Labs, Centre for Human Technologies (CHT), Istituto Italiano di Tecnologia (IIT), 16152 Genova, Italy
- Catalan Institution for Research and Advanced Studies, ICREA, 08010 Barcelona, Spain
| | - Francesco Nicassio
- Center for Genomic Science of IIT@SEMM, Fondazione Istituto Italiano di Tecnologia, 20139 Milano, Italy
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10
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He S, Gou H, Zhou Y, Wu C, Ren X, Wu X, Guan G, Jin B, Huang J, Jin Z, Zhao T. The SARS-CoV-2 nucleocapsid protein suppresses innate immunity by remodeling stress granules to atypical foci. FASEB J 2023; 37:e23269. [PMID: 37889852 DOI: 10.1096/fj.202201973rr] [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: 11/25/2022] [Revised: 08/10/2023] [Accepted: 10/10/2023] [Indexed: 10/29/2023]
Abstract
Viruses deploy multiple strategies to suppress the host innate immune response to facilitate viral replication and pathogenesis. Typical G3BP1+ stress granules (SGs) are usually formed in host cells after virus infection to restrain viral translation and to stimulate innate immunity. Thus, viruses have evolved various mechanisms to inhibit SGs or to repurpose SG components such as G3BP1. Previous studies showed that severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infection inhibited host immunity during the early stage of COVID-19. However, the precise mechanism is not yet well understood. Here we showed that the SARS-CoV-2 nucleocapsid (SARS2-N) protein suppressed the double-stranded RNA (dsRNA)-induced innate immune response, concomitant with inhibition of SGs and the induction of atypical SARS2-N+ /G3BP1+ foci (N+ foci). The SARS2-N protein-induced formation of N+ foci was dependent on the ability of its ITFG motif to hijack G3BP1, which contributed to suppress the innate immune response. Importantly, SARS2-N protein facilitated viral replication by inducing the formation of N+ foci. Viral mutations within SARS2-N protein that impair the formation of N+ foci are associated with the inability of the SARS2-N protein to suppress the immune response. Taken together, our study has revealed a novel mechanism by which SARS-CoV-2 suppresses the innate immune response via induction of atypical N+ foci. We think that this is a critical strategy for viral pathogenesis and has potential therapeutic implications.
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Affiliation(s)
- Su He
- College of Life Sciences, Zhejiang Normal University, Jinhua, Zhejiang, China
| | - Hongwei Gou
- College of Life Sciences, Zhejiang Normal University, Jinhua, Zhejiang, China
- School of Medicine, Hangzhou City University, Hangzhou, Zhejiang, China
| | - Yulin Zhou
- College of Life Sciences, Zhejiang Normal University, Jinhua, Zhejiang, China
| | - Chunxiu Wu
- College of Life Sciences, Zhejiang Normal University, Jinhua, Zhejiang, China
| | - Xinxin Ren
- College of Life Sciences, Zhejiang Normal University, Jinhua, Zhejiang, China
- School of Medicine, Hangzhou City University, Hangzhou, Zhejiang, China
| | - Xiajunpeng Wu
- College of Life Sciences, Zhejiang Normal University, Jinhua, Zhejiang, China
- School of Medicine, Hangzhou City University, Hangzhou, Zhejiang, China
| | - Guanwen Guan
- College of Life Sciences, Zhejiang Normal University, Jinhua, Zhejiang, China
| | - Boxing Jin
- College of Life Sciences, Zhejiang Normal University, Jinhua, Zhejiang, China
| | - Jinhua Huang
- College of Life Sciences, Zhejiang Normal University, Jinhua, Zhejiang, China
- School of Medicine, Hangzhou City University, Hangzhou, Zhejiang, China
| | - Zhigang Jin
- College of Life Sciences, Zhejiang Normal University, Jinhua, Zhejiang, China
| | - Tiejun Zhao
- College of Life Sciences, Zhejiang Normal University, Jinhua, Zhejiang, China
- School of Medicine, Hangzhou City University, Hangzhou, Zhejiang, China
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11
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Chathuranga WAG, Nikapitiya C, Kim JH, Chathuranga K, Weerawardhana A, Dodantenna N, Kim DJ, Poo H, Jung JU, Lee CH, Lee JS. Gadd45β is critical for regulation of type I interferon signaling by facilitating G3BP-mediated stress granule formation. Cell Rep 2023; 42:113358. [PMID: 37917584 DOI: 10.1016/j.celrep.2023.113358] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2023] [Revised: 09/04/2023] [Accepted: 10/12/2023] [Indexed: 11/04/2023] Open
Abstract
Stress granules (SGs) constitute a signaling hub that plays a critical role in type I interferon responses. Here, we report that growth arrest and DNA damage-inducible beta (Gadd45β) act as a positive regulator of SG-mediated interferon signaling by targeting G3BP upon RNA virus infection. Gadd45β deficiency markedly impairs SG formation and SG-mediated activation of interferon signaling in vitro. Gadd45β knockout mice are highly susceptible to RNA virus infection, and their ability to produce interferon and cytokines is severely impaired. Specifically, Gadd45β interacts with the RNA-binding domain of G3BP, leading to conformational expansion of G3BP1 via dissolution of its autoinhibitory electrostatic intramolecular interaction. The acidic loop 1- and RNA-binding properties of Gadd45β markedly increase the conformational expansion and RNA-binding affinity of the G3BP1-Gadd45β complex, thereby promoting assembly of SGs. These findings suggest a role for Gadd45β as a component and critical regulator of G3BP1-mediated SG formation, which facilitates RLR-mediated interferon signaling.
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Affiliation(s)
- W A Gayan Chathuranga
- College of Veterinary Medicine, Chungnam National University, Daejeon 34314, Republic of Korea
| | - Chamilani Nikapitiya
- College of Veterinary Medicine, Chungnam National University, Daejeon 34314, Republic of Korea
| | - Jae-Hoon Kim
- College of Veterinary Medicine, Chungnam National University, Daejeon 34314, Republic of Korea; Livestock Products Analysis Division, Division of Animal Health, Daejeon Metropolitan City Institute of Health and Environment, Daejeon 34146, Republic of Korea
| | - Kiramage Chathuranga
- College of Veterinary Medicine, Chungnam National University, Daejeon 34314, Republic of Korea
| | - Asela Weerawardhana
- College of Veterinary Medicine, Chungnam National University, Daejeon 34314, Republic of Korea
| | - Niranjan Dodantenna
- College of Veterinary Medicine, Chungnam National University, Daejeon 34314, Republic of Korea
| | - Doo-Jin Kim
- Infectious Disease Research Center, Korea Research Institute of Bioscience and Biotechnology (KRIBB), Daejeon 34141, Republic of Korea
| | - Haryoung Poo
- Department of Biomedical Science and Engineering, Konkuk Institute of Technology, Konkuk University, Seoul 05029, Republic of Korea
| | - Jae U Jung
- Department of Cancer Biology, Infection Biology Program, and Global Center for Pathogen Research and Human Health, Lerner Research Institute, Cleveland Clinic, Cleveland, OH, USA
| | - Chul-Ho Lee
- Laboratory Animal Resource Center, Korea Research Institute of Bioscience and Biotechnology (KRRIB), Daejeon 34141, Republic of Korea.
| | - Jong-Soo Lee
- College of Veterinary Medicine, Chungnam National University, Daejeon 34314, Republic of Korea.
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12
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Wang Y, Li Z, Liang X, Zhou Y, Liang J. Nuclear Localization of G3BP6 Is Essential for the Flowering Transition in Arabidopsis. Biomolecules 2023; 13:1697. [PMID: 38136569 PMCID: PMC10742247 DOI: 10.3390/biom13121697] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2023] [Revised: 11/17/2023] [Accepted: 11/21/2023] [Indexed: 12/24/2023] Open
Abstract
The Ras GTPase-activating protein SH3 domain-binding protein (G3BP) belongs to the highly conserved family of RNA-binding proteins, which has been well-investigated in humans and animals. However, limited study of plant G3BP has been reported, and the precise biological function of the G3BP family has not been elucidated yet. In this study, the Arabidopsis G3BP family, comprising seven members, was comparatively analyzed. Transcriptome analysis showed that most G3BP genes are ubiquitously expressed in various tissues/organs. Transient expression analysis revealed that all G3BPs were presented in the cytoplasm, among which G3BP6 was additionally found in the nucleus. Further study revealed a conserved NLS motif required for the nuclear localization of G3BP6. Additionally, phenotypic analysis revealed that loss-of-function g3bp6 presented late-flowering phenotypes. RNA-sequencing analysis and qRT-PCR assays demonstrated that the expressions of abundant floral genes were significantly altered in g3bp6 plants. We also discovered that overexpression of G3BP6 in the nucleus, rather than in the cytoplasm, propelled bolting. Furthermore, we revealed that the scaffold protein Receptor for Activated C Kinase 1 (RACK1) interacted with and modulated the nuclear localization of G3BP6. Altogether, this study sheds new light on G3BP6 and its specific role in regulating the flowering transition in Arabidopsis.
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Affiliation(s)
- Yuzhu Wang
- Jiangsu Key Laboratory of Crop Genetics and Physiology/Co-Innovation Center for Modern Production Technology of Grain Crop, Yangzhou University, Yangzhou 225009, China
- Department of Biology, Southern University of Science and Technology, Shenzhen 518055, China
| | - Zhiyong Li
- Department of Biology, Southern University of Science and Technology, Shenzhen 518055, China
- Key Laboratory of Molecular Design for Plant Cell Factory of Guangdong Higher Education Institutes, Department of Biology, Southern University of Science and Technology, Shenzhen 518055, China
- Academy for Advanced Interdisciplinary Studies, Southern University of Science and Technology, Shenzhen 518055, China
| | - Xiaoju Liang
- Department of Biology, Southern University of Science and Technology, Shenzhen 518055, China
- College of Life Sciences, Fujian Agriculture and Forest University, Fuzhou 350002, China
| | - Yeling Zhou
- Department of Biology, Southern University of Science and Technology, Shenzhen 518055, China
- Key Laboratory of Molecular Design for Plant Cell Factory of Guangdong Higher Education Institutes, Department of Biology, Southern University of Science and Technology, Shenzhen 518055, China
| | - Jiansheng Liang
- Department of Biology, Southern University of Science and Technology, Shenzhen 518055, China
- Key Laboratory of Molecular Design for Plant Cell Factory of Guangdong Higher Education Institutes, Department of Biology, Southern University of Science and Technology, Shenzhen 518055, China
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13
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Sun H, Wu M, Zhang Z, Wang Y, Yang J, Liu Z, Guan G, Luo J, Yin H, Niu Q. OAS1 suppresses African swine fever virus replication by recruiting TRIM21 to degrade viral major capsid protein. J Virol 2023; 97:e0121723. [PMID: 37815352 PMCID: PMC10617512 DOI: 10.1128/jvi.01217-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2023] [Accepted: 08/28/2023] [Indexed: 10/11/2023] Open
Abstract
IMPORTANCE African swine fever virus (ASFV) completes the replication process by resisting host antiviral response via inhibiting interferon (IFN) secretion and interferon-stimulated genes (ISGs) function. 2', 5'-Oligoadenylate synthetase gene 1 (OAS1) has been reported to inhibit the replication of various RNA and some DNA viruses. However, the regulatory mechanisms involved in the ASFV-induced IFN-related pathway still need to be fully elucidated. Here, we found that OAS1, as a critical host factor, inhibits ASFV replication in an RNaseL-dependent manner. Furthermore, overexpression of OAS1 can promote the activation of the JAK-STAT pathway promoting innate immune responses. In addition, OAS1 plays a new function, which could interact with ASFV P72 protein to suppress ASFV infection. Mechanistically, OAS1 enhances the proteasomal degradation of P72 by promoting TRIM21-mediated ubiquitination. Meanwhile, P72 inhibits the production of avSG and affects the interaction between OAS1 and DDX6. Our findings demonstrated OAS1 as an important target against ASFV replication and revealed the mechanisms and intrinsic regulatory relationships during ASFV infection.
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Affiliation(s)
- Hualin Sun
- African Swine Fever Regional Laboratory, China (Lanzhou); State Key Laboratory for Animal Disease Control and Prevention, College of Veterinary Medicine, Lanzhou University; Lanzhou Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Lanzhou, China
| | - Mengli Wu
- African Swine Fever Regional Laboratory, China (Lanzhou); State Key Laboratory for Animal Disease Control and Prevention, College of Veterinary Medicine, Lanzhou University; Lanzhou Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Lanzhou, China
| | - Zhonghui Zhang
- African Swine Fever Regional Laboratory, China (Lanzhou); State Key Laboratory for Animal Disease Control and Prevention, College of Veterinary Medicine, Lanzhou University; Lanzhou Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Lanzhou, China
| | - Yiwang Wang
- African Swine Fever Regional Laboratory, China (Lanzhou); State Key Laboratory for Animal Disease Control and Prevention, College of Veterinary Medicine, Lanzhou University; Lanzhou Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Lanzhou, China
| | - Jifei Yang
- African Swine Fever Regional Laboratory, China (Lanzhou); State Key Laboratory for Animal Disease Control and Prevention, College of Veterinary Medicine, Lanzhou University; Lanzhou Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Lanzhou, China
| | - Zhijie Liu
- African Swine Fever Regional Laboratory, China (Lanzhou); State Key Laboratory for Animal Disease Control and Prevention, College of Veterinary Medicine, Lanzhou University; Lanzhou Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Lanzhou, China
| | - Guiquan Guan
- African Swine Fever Regional Laboratory, China (Lanzhou); State Key Laboratory for Animal Disease Control and Prevention, College of Veterinary Medicine, Lanzhou University; Lanzhou Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Lanzhou, China
| | - Jianxun Luo
- African Swine Fever Regional Laboratory, China (Lanzhou); State Key Laboratory for Animal Disease Control and Prevention, College of Veterinary Medicine, Lanzhou University; Lanzhou Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Lanzhou, China
| | - Hong Yin
- African Swine Fever Regional Laboratory, China (Lanzhou); State Key Laboratory for Animal Disease Control and Prevention, College of Veterinary Medicine, Lanzhou University; Lanzhou Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Lanzhou, China
- Jiangsu Co-Innovation Center for the Prevention and Control of Important Animal Infectious Disease and Zoonosis, Yangzhou University, Yangzhou, China
| | - Qingli Niu
- African Swine Fever Regional Laboratory, China (Lanzhou); State Key Laboratory for Animal Disease Control and Prevention, College of Veterinary Medicine, Lanzhou University; Lanzhou Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Lanzhou, China
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14
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Sadasivan J, Hyrina A, DaSilva R, Jan E. An Insect Viral Protein Disrupts Stress Granule Formation in Mammalian Cells. J Mol Biol 2023; 435:168042. [PMID: 36898623 DOI: 10.1016/j.jmb.2023.168042] [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: 08/29/2022] [Revised: 02/23/2023] [Accepted: 03/02/2023] [Indexed: 03/12/2023]
Abstract
Stress granules (SGs) are cytosolic RNA-protein aggregates assembled during stress-induced translation arrest. Virus infection, in general, modulates and blocks SG formation. We previously showed that the model dicistrovirus Cricket paralysis virus (CrPV) 1A protein blocks stress granule formation in insect cells, which is dependent on a specific arginine 146 residue. CrPV-1A also inhibits SG formation in mammalian cells suggesting that this insect viral protein may be acting on a fundamental process that regulates SG formation. The mechanism underlying this process is not fully understood. Here, we show that overexpression of wild-type CrPV-1A, but not the CrPV-1A(R146A) mutant protein, inhibits distinct SG assembly pathways in HeLa cells. CrPV-1A mediated SG inhibition is independent of the Argonaute-2 (Ago-2) binding domain and the E3 ubiquitin ligase recruitment domain. CrPV-1A expression leads to nuclear poly(A)+ RNA accumulation and is correlated with the localization of CrPV-1A to the nuclear periphery. Finally, we show that the overexpression of CrPV-1A blocks FUS and TDP-43 granules, which are pathological hallmarks of neurodegenerative diseases. We propose a model whereby CrPV-1A expression in mammalian cells blocks SG formation by depleting cytoplasmic mRNA scaffolds via mRNA export inhibition. CrPV-1A provides a new molecular tool to study RNA-protein aggregates and potentially uncouple SG functions.
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Affiliation(s)
- Jibin Sadasivan
- Department of Biochemistry and Molecular Biology, Life Sciences Institute, University of British Columbia, Vancouver, British Columbia, Canada. https://twitter.com/@jibin_sadasivan
| | - Anastasia Hyrina
- Department of Biochemistry and Molecular Biology, Life Sciences Institute, University of British Columbia, Vancouver, British Columbia, Canada
| | - Rachel DaSilva
- Department of Biochemistry and Molecular Biology, Life Sciences Institute, University of British Columbia, Vancouver, British Columbia, Canada
| | - Eric Jan
- Department of Biochemistry and Molecular Biology, Life Sciences Institute, University of British Columbia, Vancouver, British Columbia, Canada.
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15
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Boccaccio GL, Thomas MG, García CC. Membraneless Organelles and Condensates Orchestrate Innate Immunity Against Viruses. J Mol Biol 2023; 435:167976. [PMID: 36702393 DOI: 10.1016/j.jmb.2023.167976] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2022] [Revised: 01/10/2023] [Accepted: 01/17/2023] [Indexed: 01/24/2023]
Abstract
The cellular defense against viruses involves the assembly of oligomers, granules and membraneless organelles (MLOs) that govern the activation of several arms of the innate immune response. Upon interaction with specific pathogen-derived ligands, a number of pattern recognition receptors (PRRs) undergo phase-separation thus triggering downstream signaling pathways. Among other relevant condensates, inflammasomes, apoptosis-associated speck-like protein containing a caspase-recruitment domain (ASC) specks, cyclic GMP-AMP synthase (cGAS) foci, protein kinase R (PKR) clusters, ribonuclease L-induced bodies (RLBs), stress granules (SGs), processing bodies (PBs) and promyelocytic leukemia protein nuclear bodies (PML NBs) play different roles in the immune response. In turn, viruses have evolved diverse strategies to evade the host defense. Viral DNA or RNA, as well as viral proteases or proteins carrying intrinsically disordered regions may interfere with condensate formation and function in multiple ways. In this review we discuss current and hypothetical mechanisms of viral escape that involve the disassembly, repurposing, or inactivation of membraneless condensates that govern innate immunity. We summarize emerging interconnections between these diverse condensates that ultimately determine the cellular outcome.
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Affiliation(s)
- Graciela Lidia Boccaccio
- Laboratorio de Biología Celular del ARN, Instituto Leloir (FIL) and Instituto de Investigaciones Bioquímicas de Buenos Aires (IIBBA) - Consejo Nacional de Investigaciones Científicas y Tecnológicas (CONICET), Buenos Aires, Argentina; Departamento de Fisiología y Biología Molecular y Celular (FBMyC), Facultad de Ciencias Exactas y Naturales (FCEN), Universidad de Buenos Aires, Buenos Aires, Argentina.
| | - María Gabriela Thomas
- Laboratorio de Biología Celular del ARN, Instituto Leloir (FIL) and Instituto de Investigaciones Bioquímicas de Buenos Aires (IIBBA) - Consejo Nacional de Investigaciones Científicas y Tecnológicas (CONICET), Buenos Aires, Argentina. https://www.twitter.com/_gabithomas
| | - Cybele Carina García
- Departamento de Química Biológica (QB), Facultad de Ciencias Exactas y Naturales (FCEN), and IQUIBICEN, Consejo Nacional de Investigaciones Científicas y Tecnológicas (CONICET) and Universidad de Buenos Aires, Buenos Aires, Argentina
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16
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Liu Y, Yao Z, Lian G, Yang P. Biomolecular phase separation in stress granule assembly and virus infection. Acta Biochim Biophys Sin (Shanghai) 2023; 55:1099-1118. [PMID: 37401177 PMCID: PMC10415189 DOI: 10.3724/abbs.2023117] [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: 12/28/2022] [Accepted: 05/06/2023] [Indexed: 07/05/2023] Open
Abstract
Liquid-liquid phase separation (LLPS) has emerged as a crucial mechanism for cellular compartmentalization. One prominent example of this is the stress granule. Found in various types of cells, stress granule is a biomolecular condensate formed through phase separation. It comprises numerous RNA and RNA-binding proteins. Over the past decades, substantial knowledge has been gained about the composition and dynamics of stress granules. SGs can regulate various signaling pathways and have been associated with numerous human diseases, such as neurodegenerative diseases, cancer, and infectious diseases. The threat of viral infections continues to loom over society. Both DNA and RNA viruses depend on host cells for replication. Intriguingly, many stages of the viral life cycle are closely tied to RNA metabolism in human cells. The field of biomolecular condensates has rapidly advanced in recent times. In this context, we aim to summarize research on stress granules and their link to viral infections. Notably, stress granules triggered by viral infections behave differently from the canonical stress granules triggered by sodium arsenite (SA) and heat shock. Studying stress granules in the context of viral infections could offer a valuable platform to link viral replication processes and host anti-viral responses. A deeper understanding of these biological processes could pave the way for innovative interventions and treatments for viral infectious diseases. They could potentially bridge the gap between basic biological processes and interactions between viruses and their hosts.
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Affiliation(s)
- Yi Liu
- />Westlake Laboratory of Life Sciences and BiomedicineSchool of Life SciencesWestlake UniversityHangzhou310030China
| | - Zhiying Yao
- />Westlake Laboratory of Life Sciences and BiomedicineSchool of Life SciencesWestlake UniversityHangzhou310030China
| | - Guiwei Lian
- />Westlake Laboratory of Life Sciences and BiomedicineSchool of Life SciencesWestlake UniversityHangzhou310030China
| | - Peiguo Yang
- />Westlake Laboratory of Life Sciences and BiomedicineSchool of Life SciencesWestlake UniversityHangzhou310030China
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17
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Li T, Li X, Wang X, Chen X, Zhao G, Liu C, Bao M, Song J, Li J, Huang L, Rong J, Tian K, Deng J, Zhu J, Cai X, Bu Z, Zheng J, Weng C. African swine fever virus pS273R antagonizes stress granule formation by cleaving the nucleating protein G3BP1 to facilitate viral replication. J Biol Chem 2023; 299:104844. [PMID: 37209818 PMCID: PMC10404608 DOI: 10.1016/j.jbc.2023.104844] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2022] [Revised: 05/08/2023] [Accepted: 05/12/2023] [Indexed: 05/22/2023] Open
Abstract
Cytoplasmic stress granules (SGs) are generally triggered by stress-induced translation arrest for storing mRNAs. Recently, it has been shown that SGs are regulated by different stimulators including viral infection, which is involved in the antiviral activity of host cells to limit viral propagation. To survive, several viruses have been reported to execute various strategies, such as modulating SG formation, to create optimal surroundings for viral replication. African swine fever virus (ASFV) is one of the most notorious pathogens in the global pig industry. However, the interplay between ASFV infection and SG formation remains largely unknown. In this study, we found that ASFV infection inhibited SG formation. Through SG inhibitory screening, we found that several ASFV-encoded proteins are involved in inhibition of SG formation. Among them, an ASFV S273R protein (pS273R), the only cysteine protease encoded by the ASFV genome, significantly affected SG formation. ASFV pS273R interacted with G3BP1 (Ras-GTPase-activating protein [SH3 domain] binding protein 1), a vital nucleating protein of SG formation. Furthermore, we found that ASFV pS273R cleaved G3BP1 at the G140-F141 to produce two fragments (G3BP1-N1-140 and G3BP1-C141-456). Interestingly, both the pS273R-cleaved fragments of G3BP1 lost the ability to induce SG formation and antiviral activity. Taken together, our finding reveals that the proteolytic cleavage of G3BP1 by ASFV pS273R is a novel mechanism by which ASFV counteracts host stress and innate antiviral responses.
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Affiliation(s)
- Tingting Li
- Division of Fundamental Immunology, State Key Laboratory for Animal Disease Control and Prevention, Harbin Veterinary Research Institute of Chinese Academy of Agricultural Sciences, Harbin, China; Heilongjiang Provincial Key Laboratory of Veterinary Immunology, Harbin, China
| | - Xuewen Li
- Division of Fundamental Immunology, State Key Laboratory for Animal Disease Control and Prevention, Harbin Veterinary Research Institute of Chinese Academy of Agricultural Sciences, Harbin, China; Heilongjiang Provincial Key Laboratory of Veterinary Immunology, Harbin, China; College of Life Sciences, Yangtze University, Jingzhou, China
| | - Xiao Wang
- Division of Fundamental Immunology, State Key Laboratory for Animal Disease Control and Prevention, Harbin Veterinary Research Institute of Chinese Academy of Agricultural Sciences, Harbin, China; Heilongjiang Provincial Key Laboratory of Veterinary Immunology, Harbin, China
| | - Xin Chen
- Division of Fundamental Immunology, State Key Laboratory for Animal Disease Control and Prevention, Harbin Veterinary Research Institute of Chinese Academy of Agricultural Sciences, Harbin, China; Heilongjiang Provincial Key Laboratory of Veterinary Immunology, Harbin, China
| | - Gaihong Zhao
- Division of Fundamental Immunology, State Key Laboratory for Animal Disease Control and Prevention, Harbin Veterinary Research Institute of Chinese Academy of Agricultural Sciences, Harbin, China; Heilongjiang Provincial Key Laboratory of Veterinary Immunology, Harbin, China
| | - Chuanxia Liu
- Division of Fundamental Immunology, State Key Laboratory for Animal Disease Control and Prevention, Harbin Veterinary Research Institute of Chinese Academy of Agricultural Sciences, Harbin, China; Heilongjiang Provincial Key Laboratory of Veterinary Immunology, Harbin, China
| | - Miaofei Bao
- Division of Fundamental Immunology, State Key Laboratory for Animal Disease Control and Prevention, Harbin Veterinary Research Institute of Chinese Academy of Agricultural Sciences, Harbin, China; Heilongjiang Provincial Key Laboratory of Veterinary Immunology, Harbin, China
| | - Jie Song
- Division of Fundamental Immunology, State Key Laboratory for Animal Disease Control and Prevention, Harbin Veterinary Research Institute of Chinese Academy of Agricultural Sciences, Harbin, China; Heilongjiang Provincial Key Laboratory of Veterinary Immunology, Harbin, China
| | - Jiangnan Li
- Division of Fundamental Immunology, State Key Laboratory for Animal Disease Control and Prevention, Harbin Veterinary Research Institute of Chinese Academy of Agricultural Sciences, Harbin, China; Heilongjiang Provincial Key Laboratory of Veterinary Immunology, Harbin, China
| | - Li Huang
- Division of Fundamental Immunology, State Key Laboratory for Animal Disease Control and Prevention, Harbin Veterinary Research Institute of Chinese Academy of Agricultural Sciences, Harbin, China; Heilongjiang Provincial Key Laboratory of Veterinary Immunology, Harbin, China
| | - Jun Rong
- College of Life Sciences, Yangtze University, Jingzhou, China
| | - Kegong Tian
- National Research Center for Veterinary Medicine, Luoyang, China
| | - Junhua Deng
- Luoyang Putai Biotechnology Co, Ltd, Luoyang, China
| | - Jianzhong Zhu
- College of Veterinary Medicine, Yangzhou University, Yangzhou, China
| | - Xuehui Cai
- Division of Fundamental Immunology, State Key Laboratory for Animal Disease Control and Prevention, Harbin Veterinary Research Institute of Chinese Academy of Agricultural Sciences, Harbin, China
| | - Zhigao Bu
- Division of Fundamental Immunology, State Key Laboratory for Animal Disease Control and Prevention, Harbin Veterinary Research Institute of Chinese Academy of Agricultural Sciences, Harbin, China
| | - Jun Zheng
- Division of Fundamental Immunology, State Key Laboratory for Animal Disease Control and Prevention, Harbin Veterinary Research Institute of Chinese Academy of Agricultural Sciences, Harbin, China; Heilongjiang Provincial Key Laboratory of Veterinary Immunology, Harbin, China.
| | - Changjiang Weng
- Division of Fundamental Immunology, State Key Laboratory for Animal Disease Control and Prevention, Harbin Veterinary Research Institute of Chinese Academy of Agricultural Sciences, Harbin, China; Heilongjiang Provincial Key Laboratory of Veterinary Immunology, Harbin, China.
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18
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Hussain I, Sureshkumar HK, Bauer M, Rubio I. Starvation Protects Hepatocytes from Inflammatory Damage through Paradoxical mTORC1 Signaling. Cells 2023; 12:1668. [PMID: 37371138 DOI: 10.3390/cells12121668] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2023] [Revised: 06/12/2023] [Accepted: 06/16/2023] [Indexed: 06/29/2023] Open
Abstract
Background and aims: Sepsis-related liver failure is associated with a particularly unfavorable clinical outcome. Calorie restriction is a well-established factor that can increase tissue resilience, protect against liver failure and improve outcome in preclinical models of bacterial sepsis. However, the underlying molecular basis is difficult to investigate in animal studies and remains largely unknown. METHODS We have used an immortalized hepatocyte line as a model of the liver parenchyma to uncover the role of caloric restriction in the resilience of hepatocytes to inflammatory cell damage. In addition, we applied genetic and pharmacological approaches to investigate the contribution of the three major intracellular nutrient/energy sensor systems, AMPK, mTORC1 and mTORC2, in this context. RESULTS We demonstrate that starvation reliably protects hepatocytes from cellular damage caused by pro-inflammatory cytokines. While the major nutrient- and energy-related signaling pathways AMPK, mTORC2/Akt and mTORC1 responded to caloric restriction as expected, mTORC1 was paradoxically activated by inflammatory stress in starved, energy-deprived hepatocytes. Pharmacological inhibition of mTORC1 or genetic silencing of the mTORC1 scaffold Raptor, but not its mTORC2 counterpart Rictor, abrogated the protective effect of starvation and exacerbated inflammation-induced cell death. Remarkably, mTORC1 activation in starved hepatocytes was uncoupled from the regulation of autophagy, but crucial for sustained protein synthesis in starved resistant cells. CONCLUSIONS AMPK engagement and paradoxical mTORC1 activation and signaling mediate protection against pro-inflammatory stress exerted by caloric restriction in hepatocytes.
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Affiliation(s)
- Iqra Hussain
- Department for Anesthesiology & Intensive Care Medicine, Jena University Hospital, Member of the Leibniz Center for Photonics in Infection Research (LPI), 07747 Jena, Germany
| | - Harini K Sureshkumar
- Department for Anesthesiology & Intensive Care Medicine, Jena University Hospital, Member of the Leibniz Center for Photonics in Infection Research (LPI), 07747 Jena, Germany
| | - Michael Bauer
- Department for Anesthesiology & Intensive Care Medicine, Jena University Hospital, Member of the Leibniz Center for Photonics in Infection Research (LPI), 07747 Jena, Germany
- Integrated Research and Treatment Center, Center for Sepsis Control and Care, Jena University Hospital, 07747 Jena, Germany
| | - Ignacio Rubio
- Department for Anesthesiology & Intensive Care Medicine, Jena University Hospital, Member of the Leibniz Center for Photonics in Infection Research (LPI), 07747 Jena, Germany
- Integrated Research and Treatment Center, Center for Sepsis Control and Care, Jena University Hospital, 07747 Jena, Germany
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19
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Zheng L, Liu H, Tian Z, Kay M, Wang H, Cheng L, Xia W, Zhang J, Wang W, Cao H, Xu X, Gao Z, Geng R, Wu Z, Zhang H. Porcine epidemic diarrhea virus (PEDV) ORF3 protein inhibits cellular type I interferon signaling through down-regulating proteins expression in RLRs-mediated pathway. Res Vet Sci 2023; 159:146-159. [PMID: 37148734 DOI: 10.1016/j.rvsc.2023.03.022] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2022] [Revised: 01/13/2023] [Accepted: 03/22/2023] [Indexed: 04/03/2023]
Abstract
Porcine epidemic diarrhea virus (PEDV) is an entero-pathogenic coronavirus, which belongs to the genus Alphacoronavirus in the family Coronaviridae, causing lethal watery diarrhea in piglets. Previous studies have shown that PEDV has developed an antagonistic mechanism by which it evades the antiviral activities of interferon (IFN), such as the sole accessory protein open reading frame 3 (ORF3) being found to inhibit IFN-β promoter activities, but how this mechanism used by PEDV ORF3 inhibits activation of the type I signaling pathway remains not fully understood. Thus, in this present study, we showed that PEDV ORF3 inhibited both polyinosine-polycytidylic acid (poly(I:C))- and IFNα2b-stimulated transcription of IFN-β and interferon-stimulated genes (ISGs) mRNAs. The expression levels of antiviral proteins in the retinoic acid-inducible gene I (RIG-I)-like receptors (RLRs)-mediated pathway was down-regulated in cells with over-expression of PEDV ORF3 protein, but global protein translation remained unchanged and the association of ORF3 with RLRs-related antiviral proteins was not detected, implying that ORF3 only specifically suppressed the expression of these signaling molecules. At the same time, we also found that the PEDV ORF3 protein inhibited interferon regulatory factor 3 (IRF3) phosphorylation and poly(I:C)-induced nuclear translocation of IRF3, which further supported the evidence that type I IFN production was abrogated by PEDV ORF3 through interfering with RLRs signaling. Furthermore, PEDV ORF3 counteracted transcription of IFN-β and ISGs mRNAs, which were triggered by over-expression of signal proteins in the RLRs-mediated pathway. However, to our surprise, PEDV ORF3 initially induced, but subsequently reduced the transcription of IFN-β and ISGs mRNAs to normal levels. Additionally, mRNA transcriptional levels of signaling molecules located at IFN-β upstream were not inhibited, but elevated by PEDV ORF3 protein. Collectively, these results demonstrate that inhibition of type I interferon signaling by PEDV ORF3 can be realized through down-regulating the expression of signal molecules in the RLRs-mediated pathway, but not via inhibiting their mRNAs transcription. This study points to a new mechanism evolved by PEDV through blockage of the RLRs-mediated pathway by ORF3 protein to circumvent the host's antiviral immunity.
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20
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Ramnani B, Powell S, Shetty AG, Manivannan P, Hibbard BR, Leaman DW, Malathi K. Viral Hemorrhagic Septicemia Virus Activates Integrated Stress Response Pathway and Induces Stress Granules to Regulate Virus Replication. Viruses 2023; 15:466. [PMID: 36851680 PMCID: PMC9965902 DOI: 10.3390/v15020466] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2023] [Accepted: 01/30/2023] [Indexed: 02/10/2023] Open
Abstract
Virus infection activates integrated stress response (ISR) and stress granule (SG) formation and viruses counteract by interfering with SG assembly, suggesting an important role in antiviral defense. The infection of fish cells by Viral Hemorrhagic Septicemia Virus (VHSV), activates the innate immune recognition pathway and the production of type I interferon (IFN). However, the mechanisms by which VHSV interacts with ISR pathway regulating SG formation is poorly understood. Here, we demonstrate that fish cells respond to heat shock, oxidative stress and VHSV infection by forming SG that localized key SG marker, Ras GTPase-activating protein (SH3 domain)-binding protein 1 (G3BP1). We show that PKR-like endoplasmic reticulum kinase (PERK), but not (dsRNA)-dependent protein kinase (PKR), is required for VHSV-induced SG formation. Furthermore, in VHSV Ia infected cells, PERK activity is required for IFN production, antiviral signaling and viral replication. SG formation required active virus replication as individual VHSV Ia proteins or inactive virus did not induce SG. Cells lacking G3BP1 produced increased IFN, antiviral genes and viral mRNA, however viral protein synthesis and viral titers were reduced. We show a critical role of the activation of ISR pathway and SG formation highlighting a novel role of G3BP1 in regulating VHSV protein translation and replication.
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Affiliation(s)
- Barkha Ramnani
- Department of Biological Sciences, University of Toledo, 2801 West Bancroft Street, Toledo, OH 43606, USA
| | - Shelby Powell
- Department of Biological Sciences, University of Toledo, 2801 West Bancroft Street, Toledo, OH 43606, USA
| | - Adarsh G. Shetty
- Department of Biological Sciences, University of Toledo, 2801 West Bancroft Street, Toledo, OH 43606, USA
| | - Praveen Manivannan
- Department of Biological Sciences, University of Toledo, 2801 West Bancroft Street, Toledo, OH 43606, USA
| | - Brian R. Hibbard
- Department of Biological Sciences, University of Toledo, 2801 West Bancroft Street, Toledo, OH 43606, USA
| | - Douglas W. Leaman
- College of Sciences, Auburn University at Montgomery, 7400 East Dr., Montgomery, AL 36117, USA
| | - Krishnamurthy Malathi
- Department of Biological Sciences, University of Toledo, 2801 West Bancroft Street, Toledo, OH 43606, USA
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21
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Matsumiya T, Shiba Y, Ding J, Kawaguchi S, Seya K, Imaizumi T. The double-stranded RNA-dependent protein kinase PKR negatively regulates the protein expression of IFN-β induced by RIG-I signaling. FASEB J 2023; 37:e22780. [PMID: 36651716 DOI: 10.1096/fj.202201520rr] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2022] [Revised: 12/27/2022] [Accepted: 01/06/2023] [Indexed: 01/19/2023]
Abstract
Retinoic acid-inducible gene-I (RIG-I) is a cytoplasmic RNA sensor that plays an important role in innate immune responses to viral RNAs. Double-stranded RNA (dsRNA)-dependent protein kinase (PKR) is a eukaryotic initiation factor 2α (eIF2α) kinase that is initially involved in the responses of the translational machinery to dsRNA. PKR is also thought to play an essential role in antiviral innate immunity. However, the coordinated mechanisms of RIG-I and PKR that induce the expression of type I interferons (IFNs), essential cytokines involved in antiviral defense, are not completely understood. In this study, we show that PKR negatively participates in the RIG-I-mediated induction of IFN-β expression. Stress granule (SG) formation is crucial to sequester mRNA to prevent aberrant protein synthesis by various stresses. SG formation in response to dsRNA was triggered by a PKR-mediated antiviral stress response. However, IFN-β mRNA was not sequestered in the SGs of dsRNA-treated cells. dsRNA-induced translational silencing was thought to be PKR dependent. However, our results indicated that some proteins, including IFN-β, were clearly translated despite PKR-mediated translational silencing. This study suggests that RIG-I responds mainly to IFN-β expression in cells to which non-self dsRNA is introduced. In addition, PKR negatively regulates IFN-β protein expression induced by RIG-I signaling. This may explain the essential role of PKR in fine-tuning the expression of IFN-β in RIG-I-mediated antiviral immune responses.
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Affiliation(s)
- Tomoh Matsumiya
- Department of Bioscience and Laboratory Medicine, Hirosaki University Graduate School of Health Sciences, Hirosaki, Japan.,Department of Vascular Biology, Hirosaki University Graduate School of Medicine, Hirosaki, Japan
| | - Yuko Shiba
- Department of Bioscience and Laboratory Medicine, Hirosaki University Graduate School of Health Sciences, Hirosaki, Japan.,Department of Vascular Biology, Hirosaki University Graduate School of Medicine, Hirosaki, Japan
| | - Jiangli Ding
- Department of Vascular Biology, Hirosaki University Graduate School of Medicine, Hirosaki, Japan
| | - Shogo Kawaguchi
- Department of Vascular Biology, Hirosaki University Graduate School of Medicine, Hirosaki, Japan
| | - Kazuhiko Seya
- Department of Vascular Biology, Hirosaki University Graduate School of Medicine, Hirosaki, Japan
| | - Tadaatsu Imaizumi
- Department of Vascular Biology, Hirosaki University Graduate School of Medicine, Hirosaki, Japan
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22
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Castello A, Iselin L. Viral RNA Is a Hub for Critical Host-Virus Interactions. Subcell Biochem 2023; 106:365-385. [PMID: 38159234 DOI: 10.1007/978-3-031-40086-5_13] [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] [Indexed: 01/03/2024]
Abstract
RNA is a central molecule in the life cycle of viruses, acting not only as messenger (m)RNA but also as a genome. Given these critical roles, it is not surprising that viral RNA is a hub for host-virus interactions. However, the interactome of viral RNAs remains largely unknown. This chapter discusses the importance of cellular RNA-binding proteins in virus infection and the emergent approaches developed to uncover and characterise them.
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Affiliation(s)
- Alfredo Castello
- MRC University of Glasgow Centre for Virus Research, Glasgow, UK.
| | - Louisa Iselin
- MRC University of Glasgow Centre for Virus Research, Glasgow, UK
- Nuffield Department of Medicine, Peter Medawar Building for Pathogen Research, University of Oxford, Oxford, UK
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23
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Brownsword MJ, Locker N. A little less aggregation a little more replication: Viral manipulation of stress granules. WILEY INTERDISCIPLINARY REVIEWS. RNA 2023; 14:e1741. [PMID: 35709333 PMCID: PMC10078398 DOI: 10.1002/wrna.1741] [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: 03/02/2022] [Revised: 04/29/2022] [Accepted: 05/05/2022] [Indexed: 01/31/2023]
Abstract
Recent exciting studies have uncovered how membrane-less organelles, also known as biocondensates, are providing cells with rapid response pathways, allowing them to re-organize their cellular contents and adapt to stressful conditions. Their assembly is driven by the phase separation of their RNAs and intrinsically disordered protein components into condensed foci. Among these, stress granules (SGs) are dynamic cytoplasmic biocondensates that form in response to many stresses, including activation of the integrated stress response or viral infections. SGs sit at the crossroads between antiviral signaling and translation because they concentrate signaling proteins and components of the innate immune response, in addition to translation machinery and stalled mRNAs. Consequently, they have been proposed to contribute to antiviral activities, and therefore are targeted by viral countermeasures. Equally, SGs components can be commandeered by viruses for their own efficient replication. Phase separation processes are an important component of the viral life cycle, for example, driving the assembly of replication factories or inclusion bodies. Therefore, in this review, we will outline the recent understanding of this complex interplay and tug of war between viruses, SGs, and their components. This article is categorized under: RNA in Disease and Development > RNA in Disease Translation > Regulation RNA Interactions with Proteins and Other Molecules > RNA-Protein Complexes.
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Affiliation(s)
- Matthew J. Brownsword
- Faculty of Health and Medical Sciences, School of Biosciences and MedicineUniversity of SurreyGuildfordSurreyUK
| | - Nicolas Locker
- Faculty of Health and Medical Sciences, School of Biosciences and MedicineUniversity of SurreyGuildfordSurreyUK
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24
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Challenging Cellular Homeostasis: Spatial and Temporal Regulation of miRNAs. Int J Mol Sci 2022; 23:ijms232416152. [PMID: 36555797 PMCID: PMC9787707 DOI: 10.3390/ijms232416152] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2022] [Revised: 12/11/2022] [Accepted: 12/15/2022] [Indexed: 12/23/2022] Open
Abstract
Mature microRNAs (miRNAs) are single-stranded non-coding RNA (ncRNA) molecules that act in post-transcriptional regulation in animals and plants. A mature miRNA is the end product of consecutive, highly regulated processing steps of the primary miRNA transcript. Following base-paring of the mature miRNA with its mRNA target, translation is inhibited, and the targeted mRNA is degraded. There are hundreds of miRNAs in each cell that work together to regulate cellular key processes, including development, differentiation, cell cycle, apoptosis, inflammation, viral infection, and more. In this review, we present an overlooked layer of cellular regulation that addresses cell dynamics affecting miRNA accessibility. We discuss the regulation of miRNA local storage and translocation among cell compartments. The local amounts of the miRNAs and their targets dictate their actual availability, which determines the ability to fine-tune cell responses to abrupt or chronic changes. We emphasize that changes in miRNA storage and compactization occur under induced stress and changing conditions. Furthermore, we demonstrate shared principles on cell physiology, governed by miRNA under oxidative stress, tumorigenesis, viral infection, or synaptic plasticity. The evidence presented in this review article highlights the importance of spatial and temporal miRNA regulation for cell physiology. We argue that limiting the research to mature miRNAs within the cytosol undermines our understanding of the efficacy of miRNAs to regulate cell fate under stress conditions.
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25
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Kim T, Abraham R, Pieterse L, Yeh JX, Griffin DE. Cell-Type-Dependent Role for nsP3 Macrodomain ADP-Ribose Binding and Hydrolase Activity during Chikungunya Virus Infection. Viruses 2022; 14:v14122744. [PMID: 36560748 PMCID: PMC9787352 DOI: 10.3390/v14122744] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2022] [Revised: 11/18/2022] [Accepted: 12/05/2022] [Indexed: 12/14/2022] Open
Abstract
Chikungunya virus (CHIKV) causes outbreaks of rash, arthritis, and fever associated with neurologic complications, where astrocytes are preferentially infected. A determinant of virulence is the macrodomain (MD) of nonstructural protein 3 (nsP3), which binds and removes ADP-ribose (ADPr) from ADP-ribosylated substrates and regulates stress-granule disruption. We compared the replication of CHIKV 181/25 (WT) and MD mutants with decreased ADPr binding and hydrolase (G32S) or increased ADPr binding and decreased hydrolase (Y114A) activities in C8-D1A astrocytic cells and NSC-34 neuronal cells. WT CHIKV replication was initiated more rapidly with earlier nsP synthesis in C8-D1A than in NSC-34 cells. G32S established infection, amplified replication complexes, and induced host-protein synthesis shut-off less efficiently than WT and produced less infectious virus, while Y114A replication was close to WT. However, G32S mutation effects on structural protein synthesis were cell-type-dependent. In NSC-34 cells, E2 synthesis was decreased compared to WT, while in C8-D1A cells synthesis was increased. Excess E2 produced by G32S-infected C8-D1A cells was assembled into virus particles that were less infectious than those from WT or Y114A-infected cells. Because nsP3 recruits ADP-ribosylated RNA-binding proteins in stress granules away from translation-initiation factors into nsP3 granules where the MD hydrolase can remove ADPr, we postulate that suboptimal translation-factor release decreased structural protein synthesis in NSC-34 cells while failure to de-ADP-ribosylate regulatory RNA-binding proteins increased synthesis in C8-D1A cells.
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26
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Sadasivan J, Vlok M, Wang X, Nayak A, Andino R, Jan E. Targeting Nup358/RanBP2 by a viral protein disrupts stress granule formation. PLoS Pathog 2022; 18:e1010598. [PMID: 36455064 PMCID: PMC9746944 DOI: 10.1371/journal.ppat.1010598] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2022] [Revised: 12/13/2022] [Accepted: 11/17/2022] [Indexed: 12/03/2022] Open
Abstract
Viruses have evolved mechanisms to modulate cellular pathways to facilitate infection. One such pathway is the formation of stress granules (SG), which are ribonucleoprotein complexes that assemble during translation inhibition following cellular stress. Inhibition of SG assembly has been observed under numerous virus infections across species, suggesting a conserved fundamental viral strategy. However, the significance of SG modulation during virus infection is not fully understood. The 1A protein encoded by the model dicistrovirus, Cricket paralysis virus (CrPV), is a multifunctional protein that can bind to and degrade Ago-2 in an E3 ubiquitin ligase-dependent manner to block the antiviral RNA interference pathway and inhibit SG formation. Moreover, the R146 residue of 1A is necessary for SG inhibition and CrPV infection in both Drosophila S2 cells and adult flies. Here, we uncoupled CrPV-1A's functions and provide insight into its underlying mechanism for SG inhibition. CrPV-1A mediated inhibition of SGs requires the E3 ubiquitin-ligase binding domain and the R146 residue, but not the Ago-2 binding domain. Wild-type but not mutant CrPV-1A R146A localizes to the nuclear membrane which correlates with nuclear enrichment of poly(A)+ RNA. Transcriptome changes in CrPV-infected cells are dependent on the R146 residue. Finally, Nup358/RanBP2 is targeted and degraded in CrPV-infected cells in an R146-dependent manner and the depletion of Nup358 blocks SG formation. We propose that CrPV utilizes a multiprong strategy whereby the CrPV-1A protein interferes with a nuclear event that contributes to SG inhibition in order to promote infection.
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Affiliation(s)
- Jibin Sadasivan
- Department of Biochemistry and Molecular Biology, Life Sciences Institute, University of British Columbia, Vancouver, British Columbia, Canada
| | - Marli Vlok
- Department of Biochemistry and Molecular Biology, Life Sciences Institute, University of British Columbia, Vancouver, British Columbia, Canada
| | - Xinying Wang
- Department of Biochemistry and Molecular Biology, Life Sciences Institute, University of British Columbia, Vancouver, British Columbia, Canada
| | - Arabinda Nayak
- Department of Microbiology and Immunology, University of California San Francisco, San Francisco, California, United States of America
| | - Raul Andino
- Department of Microbiology and Immunology, University of California San Francisco, San Francisco, California, United States of America
| | - Eric Jan
- Department of Biochemistry and Molecular Biology, Life Sciences Institute, University of British Columbia, Vancouver, British Columbia, Canada
- * E-mail:
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27
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Zhao JZ, Xu LM, Ren GM, Shao YZ, Lu TY. Identification and characterization of DEAD-box RNA helicase DDX3 in rainbow trout (Oncorhynchus mykiss) and its relationship with infectious hematopoietic necrosis virus infection. DEVELOPMENTAL AND COMPARATIVE IMMUNOLOGY 2022; 135:104493. [PMID: 35840014 DOI: 10.1016/j.dci.2022.104493] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/02/2022] [Revised: 07/05/2022] [Accepted: 07/10/2022] [Indexed: 06/15/2023]
Abstract
DDX3, a member of the DEAD-box RNA helicase family and has highly conserved ATP-dependent RNA helicase activity, has important roles in RNA metabolism and innate anti-viral immune responses. In this study, five transcript variants of the DDX3 gene were cloned and characterized from rainbow trout (Oncorhynchus mykiss). These five transcript variants of DDX3 encoded proteins were 74.2 kDa (686 aa), 76.4 kDa (709 aa), 77.8 kDa (711 aa), 78.0 kDa (718 aa), and 78.8 kDa (729 aa) and the predicted isoelectric points were 6.91, 7.63, 7.63, 7.18, and 7.23, respectively. All rainbow trout DDX3 proteins contained two conserved RecA-like domains that were similar to the DDX3 protein reported in mammals. Phylogenetic analysis showed that the five cloned rainbow trout DDX3 were separate from mammals but clustered with fish, especially Northern pike (Esox lucius) and Nile tilapia (Oreochromis niloticus). RT-qPCR analysis showed that the DDX3 gene was broadly expressed in all tissues studied. The expression of DDX3 after infectious hematopoietic necrosis virus (IHNV) infection increased gradually after the early stage of IHNV infection, decreased gradually with the proliferation of IHNV in vivo (liver, spleen, and kidney), and was significantly decreased after the in vitro infection of epithelioma papulosum cyprini (EPC) and rainbow trout gonad cell line-2 (RTG-2) cell lines. We also found that rainbow trout DDX3 was significantly increased by a time-dependent mechanism after the poly I:C treatment of EPC and RTG cells; however no significant changes were observed with lipopolysaccharide (LPS) treatment. Knockdown of DDX3 by siRNA showed significantly increased IHNV replication in infected RTG cells. This study suggests that DDX3 has an important role in host defense against IHNV infection and these results may provide new insights into IHNV pathogenesis and antiviral drug research.
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Affiliation(s)
- Jing-Zhuang Zhao
- Heilongjiang River Fishery Research Institute of Chinese Academy of Fishery Sciences, Harbin, 150070, PR China; Key Laboratory of Aquatic Animal Diseases and Immune Technology of Heilongjiang Province, Harbin, 150070, PR China.
| | - Li-Ming Xu
- Heilongjiang River Fishery Research Institute of Chinese Academy of Fishery Sciences, Harbin, 150070, PR China.
| | - Guang-Ming Ren
- Heilongjiang River Fishery Research Institute of Chinese Academy of Fishery Sciences, Harbin, 150070, PR China.
| | - Yi-Zhi Shao
- Heilongjiang River Fishery Research Institute of Chinese Academy of Fishery Sciences, Harbin, 150070, PR China.
| | - Tong-Yan Lu
- Heilongjiang River Fishery Research Institute of Chinese Academy of Fishery Sciences, Harbin, 150070, PR China.
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28
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The Amino Acid at Position 95 in the Matrix Protein of Rabies Virus Is Involved in Antiviral Stress Granule Formation in Infected Cells. J Virol 2022; 96:e0081022. [PMID: 36069552 PMCID: PMC9517722 DOI: 10.1128/jvi.00810-22] [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: 11/20/2022] Open
Abstract
Stress granules (SGs) are dynamic structures that store cytosolic messenger ribonucleoproteins. SGs have recently been shown to serve as a platform for activating antiviral innate immunity; however, several pathogenic viruses suppress SG formation to evade innate immunity. In this study, we investigated the relationship between rabies virus (RABV) virulence and SG formation, using viral strains with different levels of virulence. We found that the virulent Nishigahara strain did not induce SG formation, but its avirulent offshoot, the Ni-CE strain, strongly induced SG formation. Furthermore, we demonstrated that the amino acid at position 95 in the RABV matrix protein (M95), a pathogenic determinant for the Nishigahara strain, plays a key role in inhibiting SG formation, followed by protein kinase R (PKR)-dependent phosphorylation of the α subunit of eukaryotic initiation factor 2α (eIF2α). M95 was also implicated in the accumulation of RIG-I, a viral RNA sensor protein, in SGs and in the subsequent acceleration of interferon induction. Taken together, our findings strongly suggest that M95-related inhibition of SG formation contributes to the pathogenesis of RABV by allowing the virus to evade the innate immune responses of the host. IMPORTANCE Rabies virus (RABV) is a neglected zoonotic pathogen that causes lethal infections in almost all mammalian hosts, including humans. Recently, RABV has been reported to induce intracellular formation of stress granules (SGs), also known as platforms that activate innate immune responses. However, the relationship between SG formation capacity and pathogenicity of RABV has remained unclear. In this study, by comparing two RABV strains with completely different levels of virulence, we found that the amino acid mutation from valine to alanine at position 95 of matrix protein (M95), which is known to be one of the amino acid mutations that determine the difference in virulence between the strains, plays a major role in SG formation. Importantly, M95 was involved in the accumulation of RIG-I in SGs and in promoting interferon induction. These findings are the first report of the effect of a single amino acid substitution associated with SGs on viral virulence.
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Abstract
Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), the causative agent of coronavirus disease 2019 (COVID-19), has caused millions of deaths in the past two years. Although initially little was understood about this virus, recent research has significantly advanced and landed interferons (IFNs) in the spotlight. While Type I and III IFN have long been known as central to antiviral immunity, in the case of COVID-19 their role was initially controversial. However, the protective function of IFN is now well supported by the identification of human deficiencies in IFN responses as a predictor of disease severity. Here, we will review the cell types and pathways that lead to IFN production as well as the importance of IFN timing and location for disease outcome. We will further discuss the mechanisms that SARS-CoV-2 uses to evade IFN responses, and the current efforts to implement IFNs as therapeutics in the treatment of COVID-19. It is essential to understand the relationships between SARS-CoV-2 and IFN to better inform treatments that exploit IFN functions to alleviate COVID-19.
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Affiliation(s)
- Carolina Chiale
- Division of Biological SciencesUniversity of California San DiegoLa JollaCaliforniaUSA
| | - Trever T. Greene
- Division of Biological SciencesUniversity of California San DiegoLa JollaCaliforniaUSA
| | - Elina I. Zuniga
- Division of Biological SciencesUniversity of California San DiegoLa JollaCaliforniaUSA
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30
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Loh D, Reiter RJ. Melatonin: Regulation of Viral Phase Separation and Epitranscriptomics in Post-Acute Sequelae of COVID-19. Int J Mol Sci 2022; 23:8122. [PMID: 35897696 PMCID: PMC9368024 DOI: 10.3390/ijms23158122] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2022] [Revised: 07/09/2022] [Accepted: 07/20/2022] [Indexed: 01/27/2023] Open
Abstract
The relentless, protracted evolution of the SARS-CoV-2 virus imposes tremendous pressure on herd immunity and demands versatile adaptations by the human host genome to counter transcriptomic and epitranscriptomic alterations associated with a wide range of short- and long-term manifestations during acute infection and post-acute recovery, respectively. To promote viral replication during active infection and viral persistence, the SARS-CoV-2 envelope protein regulates host cell microenvironment including pH and ion concentrations to maintain a high oxidative environment that supports template switching, causing extensive mitochondrial damage and activation of pro-inflammatory cytokine signaling cascades. Oxidative stress and mitochondrial distress induce dynamic changes to both the host and viral RNA m6A methylome, and can trigger the derepression of long interspersed nuclear element 1 (LINE1), resulting in global hypomethylation, epigenetic changes, and genomic instability. The timely application of melatonin during early infection enhances host innate antiviral immune responses by preventing the formation of "viral factories" by nucleocapsid liquid-liquid phase separation that effectively blockades viral genome transcription and packaging, the disassembly of stress granules, and the sequestration of DEAD-box RNA helicases, including DDX3X, vital to immune signaling. Melatonin prevents membrane depolarization and protects cristae morphology to suppress glycolysis via antioxidant-dependent and -independent mechanisms. By restraining the derepression of LINE1 via multifaceted strategies, and maintaining the balance in m6A RNA modifications, melatonin could be the quintessential ancient molecule that significantly influences the outcome of the constant struggle between virus and host to gain transcriptomic and epitranscriptomic dominance over the host genome during acute infection and PASC.
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Affiliation(s)
- Doris Loh
- Independent Researcher, Marble Falls, TX 78654, USA;
| | - Russel J. Reiter
- Department of Cell Systems and Anatomy, UT Health San Antonio, San Antonio, TX 78229, USA
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31
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Guo X, Yu K, Xin Z, Liu L, Gao Y, Hu F, Ma X, Yu K, Li Y, Huang B, Yan Z, Wu J. Porcine Epidemic Diarrhea Virus Infection Subverts Arsenite-Induced Stress Granules Formation. Front Microbiol 2022; 13:931922. [PMID: 35859736 PMCID: PMC9289563 DOI: 10.3389/fmicb.2022.931922] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2022] [Accepted: 06/09/2022] [Indexed: 11/13/2022] Open
Abstract
Stress granules (SGs) are dynamic cytoplasmic protein-RNA structures that form in response to various stress conditions, including viral infection. Porcine epidemic diarrhea virus (PEDV) variant-related diarrhea has caused devastating economic losses to the swine industry worldwide. In this study, we found that the percentage of PEDV-infected cells containing SGs is nearly 20%; meanwhile, PEDV-infected cells were resistant to sodium arsenite (SA)-induced SGs formation, as demonstrated by the recruitment of SGs marker proteins, including G3BP1 and TIA1. Moreover, the formation of SGs induced by SA treatment was suppressed by PEDV papain-like protease confirmed by confocal microscopy. Further study showed that PEDV infection disrupted SGs formation by downregulating G3BP1 expression. Additionally, PEDV replication was significantly enhanced when SGs' assembly was impaired by silencing G3BP1. Taken together, our findings attempt to illuminate the specific interaction mechanism between SGs and PEDV, which will help us to elucidate the pathogenesis of PEDV infection in the near future.
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Affiliation(s)
- Xiaozhen Guo
- Shandong Key Laboratory of Immunity and Diagnosis of Poultry Diseases, Institute of Poultry Science, Shandong Academy of Agricultural Sciences, Jinan, China
| | - Kejian Yu
- Shandong Provincial Key Laboratory of Animal Biotechnology and Disease Control and Prevention, College of Animal Science and Technology, Shandong Agricultural University, Taian, China
| | - Zhonghao Xin
- Shandong Provincial Key Laboratory of Animal Biotechnology and Disease Control and Prevention, College of Animal Science and Technology, Shandong Agricultural University, Taian, China
| | - Liping Liu
- Shandong Key Laboratory of Immunity and Diagnosis of Poultry Diseases, Institute of Poultry Science, Shandong Academy of Agricultural Sciences, Jinan, China
| | - Yuehua Gao
- Shandong Key Laboratory of Immunity and Diagnosis of Poultry Diseases, Institute of Poultry Science, Shandong Academy of Agricultural Sciences, Jinan, China
| | - Feng Hu
- Shandong Key Laboratory of Immunity and Diagnosis of Poultry Diseases, Institute of Poultry Science, Shandong Academy of Agricultural Sciences, Jinan, China
| | - Xiuli Ma
- Shandong Key Laboratory of Immunity and Diagnosis of Poultry Diseases, Institute of Poultry Science, Shandong Academy of Agricultural Sciences, Jinan, China
| | - Kexiang Yu
- Shandong Key Laboratory of Immunity and Diagnosis of Poultry Diseases, Institute of Poultry Science, Shandong Academy of Agricultural Sciences, Jinan, China
| | - Yufeng Li
- Shandong Key Laboratory of Immunity and Diagnosis of Poultry Diseases, Institute of Poultry Science, Shandong Academy of Agricultural Sciences, Jinan, China
| | - Bing Huang
- Shandong Key Laboratory of Immunity and Diagnosis of Poultry Diseases, Institute of Poultry Science, Shandong Academy of Agricultural Sciences, Jinan, China
| | - Zhengui Yan
- Shandong Provincial Key Laboratory of Animal Biotechnology and Disease Control and Prevention, College of Animal Science and Technology, Shandong Agricultural University, Taian, China
- *Correspondence: Zhengui Yan
| | - Jiaqiang Wu
- Shandong Provincial Key Laboratory of Animal Biotechnology and Disease Control and Prevention, College of Animal Science and Technology, Shandong Agricultural University, Taian, China
- Shandong Key Laboratory of Disease Control and Breeding, Institute of Animal Science and Veterinary Medicine, Shandong Academy of Agricultural Science, Jinan, China
- Shandong Key Laboratory of Animal Resistant Biology, College of Life Sciences, Shandong Normal University, Jinan, China
- Jiaqiang Wu
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32
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Role of Stress Granules in Suppressing Viral Replication by the Infectious Bronchitis Virus Endoribonuclease. J Virol 2022; 96:e0068622. [PMID: 35638780 DOI: 10.1128/jvi.00686-22] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Infectious bronchitis virus (IBV), a γ-coronavirus, causes the economically important poultry disease infectious bronchitis. Cellular stress response is an effective antiviral strategy that leads to stress granule (SG) formation. Previous studies suggested that SGs were involved in the antiviral activity of host cells to limit viral propagation. Here, we aimed to delineate the molecular mechanisms regulating the SG response to pathogenic IBV strain infection. We found that most chicken embryo kidney (CEK) cells formed no SGs during IBV infection and IBV replication inhibited arsenite-induced SG formation. This inhibition was not caused by changes in the integrity or abundance of SG proteins during infection. IBV nonstructural protein 15 (Nsp15) endoribonuclease activity suppressed SG formation. Regardless of whether Nsp15 was expressed alone, with recombinant viral infection with Newcastle disease virus as a vector, or with EndoU-deficient IBV, the Nsp15 endoribonuclease activity was the main factor inhibiting SG formation. Importantly, uridine-specific endoribonuclease (EndoU)-deficient IBV infection induced colocalization of IBV N protein/dsRNA and SG-associated protein TIA1 in infected cells. Additionally, overexpressing TIA1 in CEK cells suppressed IBV replication and may be a potential antiviral factor for impairing viral replication. These data provide a novel foundation for future investigations of the mechanisms by which coronavirus endoribonuclease activity affects viral replication. IMPORTANCE Endoribonuclease is conserved in coronaviruses and affects viral replication and pathogenicity. Infectious bronchitis virus (IBV), a γ-coronavirus, infects respiratory, renal, and reproductive systems, causing millions of dollars in lost revenue to the poultry industry worldwide annually. Mutating the viral endoribonuclease poly(U) resulted in SG formation, and TIA1 protein colocalized with the viral N protein and dsRNA, thus damaging IBV replication. These results suggest a new antiviral target design strategy for coronaviruses.
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Koliński M, Kałużna E, Piwecka M. RNA–protein interactomes as invaluable resources to study RNA viruses: Insights from SARS CoV‐2 studies. WIRES RNA 2022; 13:e1727. [PMID: 35343064 PMCID: PMC9111084 DOI: 10.1002/wrna.1727] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 11/27/2021] [Revised: 03/03/2022] [Accepted: 03/07/2022] [Indexed: 12/27/2022]
Abstract
Understanding the molecular mechanisms of severe respiratory syndrome coronavirus 2 (SARS‐CoV‐2) infection is essential for the successful development of therapeutic strategies against the COVID‐19 pandemic. Numerous studies have focused on the identification of host factors and cellular pathways involved in the viral replication cycle. The speed and magnitude of hijacking the translation machinery of host mRNA, and shutting down host transcription are still not well understood. Since SARS‐CoV‐2 relies on host RNA‐binding proteins for the infection progression, several efforts have been made to define the SARS‐CoV‐2 RNA‐bound proteomes (RNA–protein interactomes). Methodologies that enable the systemic capture of protein interactors of given RNA in vivo have been adapted for the identification of the SARS‐CoV‐2 RNA interactome. The obtained proteomic data aided by genome‐wide and targeted CRISPR perturbation screens, revealed host factors with either pro‐ or anti‐viral activity and highlighted cellular processes and factors involved in host response. We focus here on the recent studies on SARS‐CoV‐2 RNA–protein interactomes, with regard to both the technological aspects of RNA interactome capture methods and the obtained results. We also summarize several related studies, which were used in the interpretation of the SARS‐CoV‐2 RNA–protein interactomes. These studies provided the selection of host factors that are potentially suitable candidates for antiviral therapy. Finally, we underscore the importance of RNA–protein interactome studies in regard to the effective development of antiviral strategies against current and future threats. This article is categorized under:RNA Interactions with Proteins and Other Molecules > Protein‐RNA Interactions: Functional Implications RNA in Disease and Development > RNA in Disease RNA Methods > RNA Analyses in Cells
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Affiliation(s)
- Marcin Koliński
- Department of Non‐Coding RNAs Institute of Bioorganic Chemistry, Polish Academy of Sciences Poznan Poland
| | - Ewelina Kałużna
- Department of Non‐Coding RNAs Institute of Bioorganic Chemistry, Polish Academy of Sciences Poznan Poland
| | - Monika Piwecka
- Department of Non‐Coding RNAs Institute of Bioorganic Chemistry, Polish Academy of Sciences Poznan Poland
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34
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Role of the Ubiquitin System in Stress Granule Metabolism. Int J Mol Sci 2022; 23:ijms23073624. [PMID: 35408984 PMCID: PMC8999021 DOI: 10.3390/ijms23073624] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2022] [Revised: 03/24/2022] [Accepted: 03/25/2022] [Indexed: 02/01/2023] Open
Abstract
Eukaryotic cells react to various stress conditions with the rapid formation of membrane-less organelles called stress granules (SGs). SGs form by multivalent interactions between RNAs and RNA-binding proteins and are believed to protect stalled translation initiation complexes from stress-induced degradation. SGs contain hundreds of different mRNAs and proteins, and their assembly and disassembly are tightly controlled by post-translational modifications. The ubiquitin system, which mediates the covalent modification of target proteins with the small protein ubiquitin (‘ubiquitylation’), has been implicated in different aspects of SG metabolism, but specific functions in SG turnover have only recently emerged. Here, we summarize the evidence for the presence of ubiquitylated proteins at SGs, review the functions of different components of the ubiquitin system in SG formation and clearance, and discuss the link between perturbed SG clearance and the pathogenesis of neurodegenerative disorders. We conclude that the ubiquitin system plays an important, medically relevant role in SG biology.
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35
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Xue W, Ding C, Qian K, Liao Y. The Interplay Between Coronavirus and Type I IFN Response. Front Microbiol 2022; 12:805472. [PMID: 35317429 PMCID: PMC8934427 DOI: 10.3389/fmicb.2021.805472] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2021] [Accepted: 12/24/2021] [Indexed: 12/14/2022] Open
Abstract
In the past few decades, newly evolved coronaviruses have posed a global threat to public health and animal breeding. To control and prevent the coronavirus-related diseases, understanding the interaction of the coronavirus and the host immune system is the top priority. Coronaviruses have evolved multiple mechanisms to evade or antagonize the host immune response to ensure their replication. As the first line and main component of innate immune response, type I IFN response is able to restrict virus in the initial infection stage; it is thus not surprising that the primary aim of the virus is to evade or antagonize the IFN response. Gaining a profound understanding of the interaction between coronaviruses and type I IFN response will shed light on vaccine development and therapeutics. In this review, we provide an update on the current knowledge on strategies employed by coronaviruses to evade type I IFN response.
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Affiliation(s)
- Wenxiang Xue
- Department of Avian Diseases, Shanghai Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Shanghai, China
| | - Chan Ding
- Department of Avian Diseases, Shanghai Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Shanghai, China
- Jiangsu Co-innovation Center for Prevention and Control of Important Animal Infectious Diseases and Zoonoses, Yangzhou University, Yangzhou, China
| | - Kun Qian
- Jiangsu Co-innovation Center for Prevention and Control of Important Animal Infectious Diseases and Zoonoses, Yangzhou University, Yangzhou, China
| | - Ying Liao
- Department of Avian Diseases, Shanghai Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Shanghai, China
- *Correspondence: Ying Liao,
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36
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Wang J, Gan Y, Cao J, Dong X, Ouyang W. Pathophysiology of stress granules: An emerging link to diseases (Review). Int J Mol Med 2022; 49:44. [PMID: 35137915 PMCID: PMC8846937 DOI: 10.3892/ijmm.2022.5099] [Citation(s) in RCA: 14] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2021] [Accepted: 01/21/2022] [Indexed: 11/19/2022] Open
Abstract
Under unfavorable environmental conditions, eukaryotic cells may form stress granules (SGs) in the cytosol to protect against injury and promote cell survival. The initiation, mRNA and protein composition, distribution and degradation of SGs are subject to multiple intracellular post-translational modifications and signaling pathways to cope with stress damage. Despite accumulated comprehensive knowledge of their composition and dynamics, the function of SGs remains poorly understood. When the stress persists, aberrant and/or persistent intracellular SGs and aggregation of SGs-related proteins may lead to various diseases. In the present article, the research progress regarding the generation, modification and function of SGs was reviewed. The regulatory effects and influencing factors of SGs in the development of tumors, cardiovascular diseases, viral infections and neurodegenerative diseases were also summarized, which may provide novel insight for preventing and treating SG-related diseases.
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Affiliation(s)
- Jihui Wang
- Department of Kinesiology and Human Sciences, College of Physical Education and Health Sciences, Zhejiang Normal University, Jinhua, Zhejiang 321004, P.R. China
| | - Yixia Gan
- Department of Kinesiology and Human Sciences, College of Physical Education and Health Sciences, Zhejiang Normal University, Jinhua, Zhejiang 321004, P.R. China
| | - Jian Cao
- Department of Kinesiology and Human Sciences, College of Physical Education and Health Sciences, Zhejiang Normal University, Jinhua, Zhejiang 321004, P.R. China
| | - Xuefen Dong
- Department of Kinesiology and Human Sciences, College of Physical Education and Health Sciences, Zhejiang Normal University, Jinhua, Zhejiang 321004, P.R. China
| | - Wei Ouyang
- Department of Kinesiology and Human Sciences, College of Physical Education and Health Sciences, Zhejiang Normal University, Jinhua, Zhejiang 321004, P.R. China
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37
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Xue G, Braczyk K, Gonçalves-Carneiro D, Dawidziak DM, Sanchez K, Ong H, Wan Y, Zadrozny KK, Ganser-Pornillos BK, Bieniasz PD, Pornillos O. Poly(ADP-ribose) potentiates ZAP antiviral activity. PLoS Pathog 2022; 18:e1009202. [PMID: 35130321 PMCID: PMC8853533 DOI: 10.1371/journal.ppat.1009202] [Citation(s) in RCA: 19] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2020] [Revised: 02/17/2022] [Accepted: 01/12/2022] [Indexed: 12/13/2022] Open
Abstract
Zinc-finger antiviral protein (ZAP), also known as poly(ADP-ribose) polymerase 13 (PARP13), is an antiviral factor that selectively targets viral RNA for degradation. ZAP is active against both DNA and RNA viruses, including important human pathogens such as hepatitis B virus and type 1 human immunodeficiency virus (HIV-1). ZAP selectively binds CpG dinucleotides through its N-terminal RNA-binding domain, which consists of four zinc fingers. ZAP also contains a central region that consists of a fifth zinc finger and two WWE domains. Through structural and biochemical studies, we found that the fifth zinc finger and tandem WWEs of ZAP combine into a single integrated domain that binds to poly(ADP-ribose) (PAR), a cellular polynucleotide. PAR binding is mediated by the second WWE module of ZAP and likely involves specific recognition of an adenosine diphosphate-containing unit of PAR. Mutation of the PAR binding site in ZAP abrogates the interaction in vitro and diminishes ZAP activity against a CpG-rich HIV-1 reporter virus and murine leukemia virus. In cells, PAR facilitates formation of non-membranous sub-cellular compartments such as DNA repair foci, spindle poles and cytosolic RNA stress granules. Our results suggest that ZAP-mediated viral mRNA degradation is facilitated by PAR, and provides a biophysical rationale for the reported association of ZAP with RNA stress granules.
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Affiliation(s)
- Guangai Xue
- Department of Molecular Physiology and Biological Physics, University of Virginia, Charlottesville, Virginia, United States of America
| | - Klaudia Braczyk
- Department of Molecular Physiology and Biological Physics, University of Virginia, Charlottesville, Virginia, United States of America
| | - Daniel Gonçalves-Carneiro
- Laboratory of Retrovirology, Howard Hughes Medical Institute, The Rockefeller University, New York, New York, United States of America
| | - Daria M. Dawidziak
- Department of Molecular Physiology and Biological Physics, University of Virginia, Charlottesville, Virginia, United States of America
| | - Katarzyna Sanchez
- Department of Molecular Physiology and Biological Physics, University of Virginia, Charlottesville, Virginia, United States of America
| | - Heley Ong
- Laboratory of Retrovirology, Howard Hughes Medical Institute, The Rockefeller University, New York, New York, United States of America
| | - Yueping Wan
- Department of Molecular Physiology and Biological Physics, University of Virginia, Charlottesville, Virginia, United States of America
| | - Kaneil K. Zadrozny
- Department of Molecular Physiology and Biological Physics, University of Virginia, Charlottesville, Virginia, United States of America
| | - Barbie K. Ganser-Pornillos
- Department of Molecular Physiology and Biological Physics, University of Virginia, Charlottesville, Virginia, United States of America
| | - Paul D. Bieniasz
- Laboratory of Retrovirology, Howard Hughes Medical Institute, The Rockefeller University, New York, New York, United States of America
| | - Owen Pornillos
- Department of Molecular Physiology and Biological Physics, University of Virginia, Charlottesville, Virginia, United States of America
- * E-mail:
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38
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Sharma NR, Zheng ZM. RNA Granules in Antiviral Innate Immunity: A Kaposi's Sarcoma-Associated Herpesvirus Journey. Front Microbiol 2022; 12:794431. [PMID: 35069491 PMCID: PMC8767106 DOI: 10.3389/fmicb.2021.794431] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2021] [Accepted: 12/02/2021] [Indexed: 11/18/2022] Open
Abstract
RNA granules are cytoplasmic, non-membranous ribonucleoprotein compartments that form ubiquitously and are often referred to as foci for post-transcriptional gene regulation. Recent research on RNA processing bodies (PB) and stress granules (SG) has shown wide implications of these cytoplasmic RNA granules and their components in suppression of RNA translation as host intracellular innate immunity against infecting viruses. Many RNA viruses either counteract or co-opt these RNA granules; however, many fundamental questions about DNA viruses with respect to their interaction with these two RNA granules remain elusive. Kaposi’s sarcoma-associated herpesvirus (KSHV), a tumor-causing DNA virus, exhibits two distinct phases of infection and encodes ∼90 viral gene products during the lytic phase of infection compared to only a few (∼5) during the latent phase. Thus, productive KSHV infection relies heavily on the host cell translational machinery, which often links to the formation of PB and SG. One major question is how KSHV counteracts the hostile environment of RNA granules for its productive infection. Recent studies demonstrated that KSHV copes with the translational suppression by cellular RNA granules, PB and SG, by expressing ORF57, a viral RNA-binding protein, during KSHV lytic infection. ORF57 interacts with Ago2 and GW182, two major components of PB, and prevents the scaffolding activity of GW182 at the initial stage of PB formation in the infected cells. ORF57 also interacts with protein kinase R (PKR) and PKR-activating protein (PACT) to block PKR dimerization and kinase activation, and thus inhibits eIF2α phosphorylation and SG formation. The homologous immediate-early regulatory protein ICP27 of herpes simplex virus type 1 (HSV-1), but not the EB2 protein of Epstein-Barr virus (EBV), shares this conserved inhibitory function with KSHV ORF57 on PB and SG. Through KSHV ORF57 studies, we have learned much about how a DNA virus in the infected cells is equipped to evade host antiviral immunity for its replication and productive infection. KSHV ORF57 would be an excellent viral target for development of anti-KSHV-specific therapy.
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Affiliation(s)
- Nishi R Sharma
- Department of Molecular Medicine, School of Interdisciplinary Studies, Jamia Hamdard University, New Delhi, India
| | - Zhi-Ming Zheng
- Tumor Virus RNA Biology Section, HIV Dynamics and Replication Program, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Frederick, MD, United States
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39
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Zhao M, Xia T, Xing J, Yin L, Li X, Pan J, Liu J, Sun L, Wang M, Li T, Mao J, Han Q, Xue W, Cai H, Wang K, Xu X, Li T, He K, Wang N, Li A, Zhou T, Zhang X, Li W, Li T. The stress granule protein G3BP1 promotes pre-condensation of cGAS to allow rapid responses to DNA. EMBO Rep 2022; 23:e53166. [PMID: 34779554 PMCID: PMC8728604 DOI: 10.15252/embr.202153166] [Citation(s) in RCA: 21] [Impact Index Per Article: 10.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2021] [Revised: 10/11/2021] [Accepted: 10/15/2021] [Indexed: 01/07/2023] Open
Abstract
Cyclic GMP-AMP synthase (cGAS) functions as a key sensor for microbial invasion and cellular damage by detecting emerging cytosolic DNA. Here, we report that GTPase-activating protein-(SH3 domain)-binding protein 1 (G3BP1) primes cGAS for its prompt activation by engaging cGAS in a primary liquid-phase condensation state. Using high-resolution microscopy, we show that in resting cells, cGAS exhibits particle-like morphological characteristics, which are markedly weakened when G3BP1 is deleted. Upon DNA challenge, the pre-condensed cGAS undergoes liquid-liquid phase separation (LLPS) more efficiently. Importantly, G3BP1 deficiency or its inhibition dramatically diminishes DNA-induced LLPS and the subsequent activation of cGAS. Interestingly, RNA, previously reported to form condensates with cGAS, does not activate cGAS. Accordingly, we find that DNA - but not RNA - treatment leads to the dissociation of G3BP1 from cGAS. Taken together, our study shows that the primary condensation state of cGAS is critical for its rapid response to DNA.
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Affiliation(s)
- Ming Zhao
- State Key Laboratory of ProteomicsNational Center of Biomedical AnalysisBeijingChina
| | - Tian Xia
- State Key Laboratory of ProteomicsNational Center of Biomedical AnalysisBeijingChina
| | - Jia‐Qing Xing
- State Key Laboratory of ProteomicsNational Center of Biomedical AnalysisBeijingChina
| | - Le‐Hua Yin
- State Key Laboratory of ProteomicsNational Center of Biomedical AnalysisBeijingChina
| | - Xiao‐Wei Li
- State Key Laboratory of ProteomicsNational Center of Biomedical AnalysisBeijingChina
| | - Jie Pan
- State Key Laboratory of ProteomicsNational Center of Biomedical AnalysisBeijingChina
| | - Jia‐Yu Liu
- State Key Laboratory of ProteomicsNational Center of Biomedical AnalysisBeijingChina
| | - Li‐Ming Sun
- State Key Laboratory of ProteomicsNational Center of Biomedical AnalysisBeijingChina
| | - Miao Wang
- State Key Laboratory of ProteomicsNational Center of Biomedical AnalysisBeijingChina
| | - Tingting Li
- State Key Laboratory of ProteomicsNational Center of Biomedical AnalysisBeijingChina
- Nanhu LaboratoryJiaxingChina
| | - Jie Mao
- State Key Laboratory of ProteomicsNational Center of Biomedical AnalysisBeijingChina
| | - Qiu‐Ying Han
- State Key Laboratory of ProteomicsNational Center of Biomedical AnalysisBeijingChina
- Nanhu LaboratoryJiaxingChina
| | - Wen Xue
- State Key Laboratory of ProteomicsNational Center of Biomedical AnalysisBeijingChina
- Nanhu LaboratoryJiaxingChina
| | - Hong Cai
- State Key Laboratory of ProteomicsNational Center of Biomedical AnalysisBeijingChina
| | - Kai Wang
- State Key Laboratory of ProteomicsNational Center of Biomedical AnalysisBeijingChina
| | - Xin Xu
- State Key Laboratory of ProteomicsNational Center of Biomedical AnalysisBeijingChina
| | - Teng Li
- State Key Laboratory of ProteomicsNational Center of Biomedical AnalysisBeijingChina
| | - Kun He
- State Key Laboratory of ProteomicsNational Center of Biomedical AnalysisBeijingChina
| | - Na Wang
- State Key Laboratory of ProteomicsNational Center of Biomedical AnalysisBeijingChina
| | - Ai‐Ling Li
- State Key Laboratory of ProteomicsNational Center of Biomedical AnalysisBeijingChina
- Nanhu LaboratoryJiaxingChina
| | - Tao Zhou
- State Key Laboratory of ProteomicsNational Center of Biomedical AnalysisBeijingChina
- Nanhu LaboratoryJiaxingChina
| | - Xue‐Min Zhang
- State Key Laboratory of ProteomicsNational Center of Biomedical AnalysisBeijingChina
- Nanhu LaboratoryJiaxingChina
- School of Basic Medical SciencesFudan UniversityShanghaiChina
| | - Wei‐Hua Li
- State Key Laboratory of ProteomicsNational Center of Biomedical AnalysisBeijingChina
| | - Tao Li
- State Key Laboratory of ProteomicsNational Center of Biomedical AnalysisBeijingChina
- Nanhu LaboratoryJiaxingChina
- School of Basic Medical SciencesFudan UniversityShanghaiChina
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40
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Iselin L, Palmalux N, Kamel W, Simmonds P, Mohammed S, Castello A. Uncovering viral RNA-host cell interactions on a proteome-wide scale. Trends Biochem Sci 2022; 47:23-38. [PMID: 34509361 PMCID: PMC9187521 DOI: 10.1016/j.tibs.2021.08.002] [Citation(s) in RCA: 13] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2021] [Revised: 07/12/2021] [Accepted: 08/06/2021] [Indexed: 01/14/2023]
Abstract
RNA viruses interact with a wide range of cellular RNA-binding proteins (RBPs) during their life cycle. The prevalence of these host-virus interactions has been highlighted by new methods that elucidate the composition of viral ribonucleoproteins (vRNPs). Applied to 11 viruses so far, these approaches have revealed hundreds of cellular RBPs that interact with viral (v)RNA in infected cells. However, consistency across methods is limited, raising questions about methodological considerations when designing and interpreting these studies. Here, we discuss these caveats and, through comparing available vRNA interactomes, describe RBPs that are consistently identified as vRNP components and outline their potential roles in infection. In summary, these novel approaches have uncovered a new universe of host-virus interactions holding great therapeutic potential.
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Affiliation(s)
- Louisa Iselin
- Nuffield Department of Medicine, Peter Medawar Building for Pathogen Research, University of Oxford, Oxford, OX1 3SY, UK,Department of Biochemistry, University of Oxford, South Parks Road, OX1 3QU, Oxford, UK
| | - Natasha Palmalux
- MRC-University of Glasgow Centre for Virus Research, 464 Bearsden Road, Glasgow G61 1QH, Scotland, (UK)
| | - Wael Kamel
- Department of Biochemistry, University of Oxford, South Parks Road, OX1 3QU, Oxford, UK,MRC-University of Glasgow Centre for Virus Research, 464 Bearsden Road, Glasgow G61 1QH, Scotland, (UK)
| | - Peter Simmonds
- Nuffield Department of Medicine, Peter Medawar Building for Pathogen Research, University of Oxford, Oxford, OX1 3SY, UK
| | - Shabaz Mohammed
- Department of Biochemistry, University of Oxford, South Parks Road, OX1 3QU, Oxford, UK,Chemistry Research Laboratory, University of Oxford, Mansfield Road, Oxford, OX1 3TA, UK,The Rosalind Franklin Institute, Oxfordshire, OX11 0FA, UK
| | - Alfredo Castello
- Department of Biochemistry, University of Oxford, South Parks Road, OX1 3QU, Oxford, UK,MRC-University of Glasgow Centre for Virus Research, 464 Bearsden Road, Glasgow G61 1QH, Scotland, (UK),Correspondence:
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41
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Li J, Boix E. Host Defence RNases as Antiviral Agents against Enveloped Single Stranded RNA Viruses. Virulence 2021; 12:444-469. [PMID: 33660566 PMCID: PMC7939569 DOI: 10.1080/21505594.2021.1871823] [Citation(s) in RCA: 21] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2020] [Revised: 12/26/2020] [Accepted: 12/30/2020] [Indexed: 02/06/2023] Open
Abstract
Owing to the recent outbreak of Coronavirus Disease of 2019 (COVID-19), it is urgent to develop effective and safe drugs to treat the present pandemic and prevent other viral infections that might come in the future. Proteins from our own innate immune system can serve as ideal sources of novel drug candidates thanks to their safety and immune regulation versatility. Some host defense RNases equipped with antiviral activity have been reported over time. Here, we try to summarize the currently available information on human RNases that can target viral pathogens, with special focus on enveloped single-stranded RNA (ssRNA) viruses. Overall, host RNases can fight viruses by a combined multifaceted strategy, including the enzymatic target of the viral genome, recognition of virus unique patterns, immune modulation, control of stress granule formation, and induction of autophagy/apoptosis pathways. The review also includes a detailed description of representative enveloped ssRNA viruses and their strategies to interact with the host and evade immune recognition. For comparative purposes, we also provide an exhaustive revision of the currently approved or experimental antiviral drugs. Finally, we sum up the current perspectives of drug development to achieve successful eradication of viral infections.
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Affiliation(s)
- Jiarui Li
- Dpt. Of Biochemistry and Molecular Biology, Faculty of Biosciences, Universitat Autònoma De Barcelona, Spain
| | - Ester Boix
- Dpt. Of Biochemistry and Molecular Biology, Faculty of Biosciences, Universitat Autònoma De Barcelona, Spain
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42
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Somasekharan SP, Gleave M. SARS-CoV-2 nucleocapsid protein interacts with immunoregulators and stress granules and phase separates to form liquid droplets. FEBS Lett 2021; 595:2872-2896. [PMID: 34780058 PMCID: PMC8652540 DOI: 10.1002/1873-3468.14229] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2021] [Revised: 11/02/2021] [Accepted: 11/04/2021] [Indexed: 12/16/2022]
Abstract
The current work investigated SARS‐CoV‐2 Nucleocapsid (NCAP or N protein) interactors in A549 human lung cancer cells using a SILAC‐based mass spectrometry approach. NCAP interactors included proteins of the stress granule (SG) machinery and immunoregulators. NCAP showed specific interaction with the SG proteins G3BP1, G3BP2, YTHDF3, USP10 and PKR, and translocated to SGs following oxidative stress and heat shock. Treatment of recombinant NCAP with RNA isolated from A549 cells exposed to oxidative stress‐stimulated NCAP to undergo liquid–liquid phase separation (LLPS). RNA degradation using RNase A treatment completely blocked the LLPS property of NCAP as well as its SG association. The RNA intercalator mitoxantrone also disrupted NCAP assembly in vitro and in cells. This study provides insight into the biological processes and biophysical properties of the SARS‐CoV‐2 NCAP.
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Affiliation(s)
- Syam Prakash Somasekharan
- Department of Urologic Sciences, Faculty of Medicine, Vancouver Prostate Centre, University of British Columbia, Vancouver, BC, Canada
| | - Martin Gleave
- Department of Urologic Sciences, Faculty of Medicine, Vancouver Prostate Centre, University of British Columbia, Vancouver, BC, Canada
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43
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Abstract
Cells respond to viral infections through sensors that detect non-self-molecules, and through effectors, which can have direct antiviral activities or adapt cell physiology to limit viral infection and propagation. Eukaryotic translation initiation factor 2 alpha kinase 2, better known as PKR, acts as both a sensor and an effector in the response to viral infections. After sensing double-stranded RNA molecules in infected cells, PKR self-activates and majorly exerts its antiviral function by blocking the translation machinery and inducing apoptosis. The antiviral potency of PKR is emphasized by the number of strategies developed by viruses to antagonize the PKR pathway. In this review, we present an update on the diversity of such strategies, which range from preventing double-stranded RNA recognition upstream from PKR activation, to activating eIF2B downstream from PKR targets.
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Affiliation(s)
- Teresa Cesaro
- de Duve Institute, Université catholique de Louvain, Brussels, Belgium
| | - Thomas Michiels
- de Duve Institute, Université catholique de Louvain, Brussels, Belgium
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44
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Insights into the SARS-CoV-2-Mediated Alteration in the Stress Granule Protein Regulatory Networks in Humans. Pathogens 2021; 10:pathogens10111459. [PMID: 34832615 PMCID: PMC8624858 DOI: 10.3390/pathogens10111459] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2021] [Revised: 11/01/2021] [Accepted: 11/06/2021] [Indexed: 12/15/2022] Open
Abstract
The rapidly and constantly evolving coronavirus, SARS-CoV-2, imposes a great threat to human health causing severe lung disease and significant mortality. Cytoplasmic stress granules (SGs) exert anti-viral activities due to their involvement in translation inhibition and innate immune signaling. SARS-CoV-2 sequesters important SG nucleator proteins and impairs SG formation, thus evading the host response for efficient viral replication. However, the significance of SGs in COVID-19 infection remains elusive. In this study, we utilize a protein-protein interaction network approach to systematically dissect the crosstalk of human post-translational regulatory networks governed by SG proteins due to SARS-CoV-2 infection. We uncovered that 116 human SG proteins directly interact with SARS-CoV-2 proteins and are involved in 430 different brain disorders including COVID-19. Further, we performed gene set enrichment analysis to identify the drugs against three important key SG proteins (DYNC1H1, DCTN1, and LMNA) and also looked for potential microRNAs (miRNAs) targeting these proteins. We identified bexarotene as a potential drug molecule and miRNAs, hsa-miR-615-3p, hsa-miR-221-3p, and hsa-miR-124-3p as potential candidates for the treatment of COVID-19 and associated manifestations.
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45
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He X, Yuan J, Wang Y. G3BP1 binds to guanine quadruplexes in mRNAs to modulate their stabilities. Nucleic Acids Res 2021; 49:11323-11336. [PMID: 34614161 PMCID: PMC8565330 DOI: 10.1093/nar/gkab873] [Citation(s) in RCA: 23] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2021] [Revised: 09/12/2021] [Accepted: 10/04/2021] [Indexed: 12/21/2022] Open
Abstract
RNA guanine quadruplexes (rG4) assume important roles in post-transcriptional regulations of gene expression, which are often modulated by rG4-binding proteins. Hence, understanding the biological functions of rG4s requires the identification and functional characterizations of rG4-recognition proteins. By employing a bioinformatic approach based on the analysis of overlap between peaks obtained from rG4-seq analysis and those detected in >230 eCLIP-seq datasets for RNA-binding proteins generated from the ENCODE project, we identified a large number of candidate rG4-binding proteins. We showed that one of these proteins, G3BP1, is able to bind directly to rG4 structures with high affinity and selectivity, where the binding entails its C-terminal RGG domain and is further enhanced by its RRM domain. Additionally, our seCLIP-Seq data revealed that pyridostatin, a small-molecule rG4 ligand, could displace G3BP1 from mRNA in cells, with the most pronounced effects being observed for the 3′-untranslated regions (3′-UTR) of mRNAs. Moreover, luciferase reporter assay results showed that G3BP1 positively regulates mRNA stability through its binding with rG4 structures. Together, we identified a number of candidate rG4-binding proteins and validated that G3BP1 can bind directly with rG4 structures and regulate the stabilities of mRNAs.
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Affiliation(s)
- Xiaomei He
- Department of Chemistry, University of California, Riverside, CA 92521-0403, USA
| | - Jun Yuan
- Department of Chemistry, University of California, Riverside, CA 92521-0403, USA
| | - Yinsheng Wang
- Department of Chemistry, University of California, Riverside, CA 92521-0403, USA
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46
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Nakahama T, Kawahara Y. Deciphering the Biological Significance of ADAR1-Z-RNA Interactions. Int J Mol Sci 2021; 22:ijms222111435. [PMID: 34768866 PMCID: PMC8584189 DOI: 10.3390/ijms222111435] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2021] [Revised: 10/19/2021] [Accepted: 10/21/2021] [Indexed: 12/24/2022] Open
Abstract
Adenosine deaminase acting on RNA 1 (ADAR1) is an enzyme responsible for double-stranded RNA (dsRNA)-specific adenosine-to-inosine RNA editing, which is estimated to occur at over 100 million sites in humans. ADAR1 is composed of two isoforms transcribed from different promoters: p150 and N-terminal truncated p110. Deletion of ADAR1 p150 in mice activates melanoma differentiation-associated protein 5 (MDA5)-sensing pathway, which recognizes endogenous unedited RNA as non-self. In contrast, we have recently demonstrated that ADAR1 p110-mediated RNA editing does not contribute to this function, implying that a unique Z-DNA/RNA-binding domain α (Zα) in the N terminus of ADAR1 p150 provides specific RNA editing, which is critical for preventing MDA5 activation. In addition, a mutation in the Zα domain is identified in patients with Aicardi–Goutières syndrome (AGS), an inherited encephalopathy characterized by overproduction of type I interferon. Accordingly, we and other groups have recently demonstrated that Adar1 Zα-mutated mice show MDA5-dependent type I interferon responses. Furthermore, one such mutant mouse carrying a W197A point mutation in the Zα domain, which inhibits Z-RNA binding, manifests AGS-like encephalopathy. These findings collectively suggest that Z-RNA binding by ADAR1 p150 is essential for proper RNA editing at certain sites, preventing aberrant MDA5 activation.
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Affiliation(s)
- Taisuke Nakahama
- Department of RNA Biology and Neuroscience, Graduate School of Medicine, Osaka University, Osaka 565-0871, Japan;
| | - Yukio Kawahara
- Department of RNA Biology and Neuroscience, Graduate School of Medicine, Osaka University, Osaka 565-0871, Japan;
- Integrated Frontier Research for Medical Science Division, Institute for Open and Transdisciplinary Research Initiatives (OTRI), Osaka University, Osaka 565-0871, Japan
- Correspondence: ; Tel.: +81-6-6879-3827
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47
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The PERK/PKR-eIF2α pathway negatively regulates porcine hemagglutinating encephalomyelitis virus replication by attenuating global protein translation and facilitating stress granule formation. J Virol 2021; 96:e0169521. [PMID: 34643429 PMCID: PMC8754228 DOI: 10.1128/jvi.01695-21] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/29/2023] Open
Abstract
The replication of coronaviruses, including severe acute respiratory syndrome coronavirus (SARS-CoV), Middle East respiratory syndrome coronavirus (MERS-CoV), and the recently emerged severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), is closely associated with the endoplasmic reticulum (ER) of infected cells. The unfolded protein response (UPR), which is mediated by ER stress (ERS), is a typical outcome in coronavirus-infected cells and is closely associated with the characteristics of coronaviruses. However, the interaction between virus-induced ERS and coronavirus replication is poorly understood. Here, we demonstrate that infection with the betacoronavirus porcine hemagglutinating encephalomyelitis virus (PHEV) induced ERS and triggered all three branches of the UPR signaling pathway both in vitro and in vivo. In addition, ERS suppressed PHEV replication in mouse neuro-2a (N2a) cells primarily by activating the protein kinase R-like ER kinase (PERK)–eukaryotic initiation factor 2α (eIF2α) axis of the UPR. Moreover, another eIF2α phosphorylation kinase, interferon (IFN)-induced double-stranded RNA-dependent protein kinase (PKR), was also activated and acted cooperatively with PERK to decrease PHEV replication. Furthermore, we demonstrate that the PERK/PKR-eIF2α pathways negatively regulated PHEV replication by attenuating global protein translation. Phosphorylated eIF2α also promoted the formation of stress granules (SGs), which in turn repressed PHEV replication. In summary, our study presents a vital aspect of the host innate response to invading pathogens and reveals attractive host targets (e.g., PERK, PKR, and eIF2α) for antiviral drugs. IMPORTANCE Coronavirus diseases are caused by different coronaviruses of importance in humans and animals, and specific treatments are extremely limited. ERS, which can activate the UPR to modulate viral replication and the host innate response, is a frequent occurrence in coronavirus-infected cells. PHEV, a neurotropic betacoronavirus, causes nerve cell damage, which accounts for the high mortality rates in suckling piglets. However, it remains incompletely understood whether the highly developed ER in nerve cells plays an antiviral role in ERS and how ERS regulates viral proliferation. In this study, we found that PHEV infection induced ERS and activated the UPR both in vitro and in vivo and that the activated PERK/PKR-eIF2α axis inhibited PHEV replication through attenuating global protein translation and promoting SG formation. A better understanding of coronavirus-induced ERS and UPR activation may reveal the pathogenic mechanism of coronavirus and facilitate the development of new treatment strategies for these diseases.
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48
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Liquid-liquid phase separation in human health and diseases. Signal Transduct Target Ther 2021; 6:290. [PMID: 34334791 PMCID: PMC8326283 DOI: 10.1038/s41392-021-00678-1] [Citation(s) in RCA: 165] [Impact Index Per Article: 55.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2021] [Revised: 05/26/2021] [Accepted: 06/10/2021] [Indexed: 02/07/2023] Open
Abstract
Emerging evidence suggests that liquid-liquid phase separation (LLPS) represents a vital and ubiquitous phenomenon underlying the formation of membraneless organelles in eukaryotic cells (also known as biomolecular condensates or droplets). Recent studies have revealed evidences that indicate that LLPS plays a vital role in human health and diseases. In this review, we describe our current understanding of LLPS and summarize its physiological functions. We further describe the role of LLPS in the development of human diseases. Additionally, we review the recently developed methods for studying LLPS. Although LLPS research is in its infancy-but is fast-growing-it is clear that LLPS plays an essential role in the development of pathophysiological conditions. This highlights the need for an overview of the recent advances in the field to translate our current knowledge regarding LLPS into therapeutic discoveries.
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49
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Exploring peptide studies related to SARS-CoV to accelerate the development of novel therapeutic and prophylactic solutions against COVID-19. J Infect Public Health 2021; 14:1106-1119. [PMID: 34280732 PMCID: PMC8253661 DOI: 10.1016/j.jiph.2021.06.017] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2021] [Revised: 06/18/2021] [Accepted: 06/27/2021] [Indexed: 01/18/2023] Open
Abstract
Recent advances in peptide research revolutionized therapeutic discoveries for various infectious diseases. In view of the ongoing threat of the COVID-19 pandemic, there is an urgent need to develop potential therapeutic options. Intense and accomplishing research is being carried out to develop broad-spectrum vaccines and treatment options for corona viruses, due to the risk of recurrent infection by the existing strains or pandemic outbreaks by new mutant strains. Developing a novel medicine is costly and time consuming, which increases the value of repurposing existing therapies. Since, SARS-CoV-2 shares significant genomic homology with SARS-CoV, we have summarized various peptides identified against SARS-CoV using in silico and molecular studies and also the peptides effective against SARS-CoV-2. Dissecting the molecular mechanisms underlying viral infection could yield fundamental insights in the discovery of new antiviral agents, targeting viral proteins or host factors. We postulate that these peptides can serve as effective components for therapeutic options against SARS-CoV-2, supporting clinical scientists globally in selectively identifying and testing the therapeutic and prophylactic agents for COVID-19 treatment. In addition, we also summarized the latest updates on peptide therapeutics against SARS-CoV-2.
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50
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He A, Dean JM, Lodhi IJ. Peroxisomes as cellular adaptors to metabolic and environmental stress. Trends Cell Biol 2021; 31:656-670. [PMID: 33674166 PMCID: PMC8566112 DOI: 10.1016/j.tcb.2021.02.005] [Citation(s) in RCA: 38] [Impact Index Per Article: 12.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2020] [Revised: 02/02/2021] [Accepted: 02/04/2021] [Indexed: 02/06/2023]
Abstract
Peroxisomes are involved in multiple metabolic processes, including fatty acid oxidation, ether lipid synthesis, and reactive oxygen species (ROS) metabolism. Recent studies suggest that peroxisomes are critical mediators of cellular responses to various forms of stress, including oxidative stress, hypoxia, starvation, cold exposure, and noise. As dynamic organelles, peroxisomes can modulate their proliferation, morphology, and movement within cells, and engage in crosstalk with other organelles in response to external cues. Although peroxisome-derived hydrogen peroxide has a key role in cellular signaling related to stress, emerging studies suggest that other products of peroxisomal metabolism, such as acetyl-CoA and ether lipids, are also important for metabolic adaptation to stress. Here, we review molecular mechanisms through which peroxisomes regulate metabolic and environmental stress.
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Affiliation(s)
- Anyuan He
- Division of Endocrinology, Metabolism and Lipid Research, Department of Medicine, Washington University School of Medicine, St Louis, MO 63110, USA.
| | - John M Dean
- Division of Endocrinology, Metabolism and Lipid Research, Department of Medicine, Washington University School of Medicine, St Louis, MO 63110, USA
| | - Irfan J Lodhi
- Division of Endocrinology, Metabolism and Lipid Research, Department of Medicine, Washington University School of Medicine, St Louis, MO 63110, USA.
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