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Buchynskyi M, Oksenych V, Kamyshna I, Budarna O, Halabitska I, Petakh P, Kamyshnyi O. Genomic insight into COVID-19 severity in MAFLD patients: a single-center prospective cohort study. Front Genet 2024; 15:1460318. [PMID: 39296547 PMCID: PMC11408174 DOI: 10.3389/fgene.2024.1460318] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2024] [Accepted: 08/23/2024] [Indexed: 09/21/2024] Open
Abstract
This study investigated the influence of single nucleotide polymorphisms (SNPs) in genes associated with the interferon pathway (IFNAR2 rs2236757), antiviral response (OAS1 rs10774671, OAS3 rs10735079), and viral entry (ACE2 rs2074192) on COVID-19 severity and their association with nonalcoholic fatty liver disease (MAFLD). We did not observe a significant association between the investigated SNPs and COVID-19 severity. While the IFNAR2 rs2236757 A allele was correlated with higher creatinine levels upon admission and the G allele was correlated with lower band neutrophils upon discharge, these findings require further investigation. The distribution of OAS gene polymorphisms (rs10774671 and rs10735079) did not differ between MAFLD patients and non-MAFLD patients. Our study population's distribution of ACE2 rs2074192 genotypes and alleles differed from that of the European reference population. Overall, our findings suggest that these specific SNPs may not be major contributors to COVID-19 severity in our patient population, highlighting the potential role of other genetic factors and environmental influences.
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Affiliation(s)
- Mykhailo Buchynskyi
- Department of Microbiology, Virology, and Immunology, I. Horbachevsky Ternopil National Medical University, Ternopil, Ukraine
| | - Valentyn Oksenych
- Broegelmann Research Laboratory, Department of Clinical Science, University of Bergen, Bergen, Norway
| | - Iryna Kamyshna
- Department of Medical Rehabilitation, I. Horbachevsky Ternopil National Medical University, Ternopil, Ukraine
| | - Olena Budarna
- Department of Neurology, I. Horbachevsky Ternopil National Medical University, Ternopil, Ukraine
| | - Iryna Halabitska
- Department of Therapy and Family Medicine, I. Horbachevsky Ternopil National Medical University, Ternopil, Ukraine
| | - Pavlo Petakh
- Department of Microbiology, Virology, and Immunology, I. Horbachevsky Ternopil National Medical University, Ternopil, Ukraine
- Department of Biochemistry and Pharmacology, Uzhhorod National University, Uzhhorod, Ukraine
| | - Oleksandr Kamyshnyi
- Department of Microbiology, Virology, and Immunology, I. Horbachevsky Ternopil National Medical University, Ternopil, Ukraine
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Chen X, Guo Y, Wang R. Detecting 2'-5'-adenosine linked nucleic acids via acylation of secondary hydroxy functionality. Bioorg Med Chem Lett 2024; 109:129847. [PMID: 38857849 DOI: 10.1016/j.bmcl.2024.129847] [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: 04/07/2024] [Revised: 05/22/2024] [Accepted: 06/07/2024] [Indexed: 06/12/2024]
Abstract
2'-5'-Adenosine linked nucleic acids are crucial components in living cells that play significant roles, including participating in antiviral defense mechanisms by facilitating the breakdown of viral genetic material. In this report, we present a chemical derivatization method employing 5-fluoro-2-pyridinoyl-imidazole as the acylation agent, a strategy that can be effectively combined with advanced analytical tools, including Nuclear Magnetic Resonance spectroscopy and Liquid Chromatography-Mass Spectrometry, to enhance the characterization and detection capabilities. This marks the first instance of a simple method designed to detect 2'-5'-adenosine linked nucleic acids. The new method is characterized by its time-saving nature, simplicity, and relative accuracy compared to previous methods.
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Affiliation(s)
- Xiaoqian Chen
- Hubei Key Laboratory of Natural Medicinal Chemistry and Resource Evaluation, School of Pharmacy, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Hubei 430030, China
| | - Yuyang Guo
- Hubei Key Laboratory of Natural Medicinal Chemistry and Resource Evaluation, School of Pharmacy, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Hubei 430030, China
| | - Rui Wang
- Hubei Key Laboratory of Natural Medicinal Chemistry and Resource Evaluation, School of Pharmacy, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Hubei 430030, China; Shenzhen Huazhong University of Science and Technology Research Institute, Shenzhen, Guangdong 518057, China.
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3
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Govande AA, Babnis AW, Urban C, Habjan M, Hartmann R, Kranzusch PJ, Pichlmair A. RNase L-activating 2'-5' oligoadenylates bind ABCF1, ABCF3 and Decr-1. J Gen Virol 2023; 104. [PMID: 37676257 DOI: 10.1099/jgv.0.001890] [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: 09/08/2023] Open
Abstract
A notable signalling mechanism employed by mammalian innate immune signalling pathways uses nucleotide-based second messengers such as 2'3'-cGAMP and 2'-5'-oligoadenylates (OAs), which bind and activate STING and RNase L, respectively. Interestingly, the involvement of nucleotide second messengers to activate antiviral responses is evolutionarily conserved, as evidenced by the identification of an antiviral cGAMP-dependent pathway in Drosophila. Using a mass spectrometry approach, we identified several members of the ABCF family in human, mouse and Drosophila cell lysates as 2'-5' OA-binding proteins, suggesting an evolutionarily conserved function. Biochemical characterization of these interactions demonstrates high-affinity binding of 2'-5' OA to ABCF1, dependent on phosphorylated 2'-5' OA and an intact Walker A/B motif of the ABC cassette of ABCF1. As further support for species-specific interactions with 2'-5' OA, we additionally identified that the metabolic enzyme Decr1 from mouse, but not human or Drosophila cells, forms a high-affinity complex with 2'-5' OA. A 1.4 Å co-crystal structure of the mouse Decr1-2'-5' OA complex explains high-affinity recognition of 2'-5' OA and the mechanism of species specificity. Despite clear evidence of physical interactions, we could not identify profound antiviral functions of ABCF1, ABCF3 or Decr1 or 2'-5' OA-dependent regulation of cellular translation rates, as suggested by the engagement of ABCF proteins. Thus, although the biological consequences of the here identified interactions need to be further studied, our data suggest that 2'-5' OA can serve as a signalling hub to distribute a signal to different recipient proteins.
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Affiliation(s)
- Apurva A Govande
- Department of Microbiology, Harvard Medical School, Boston, MA 02115, USA
- Department of Cancer Immunology and Virology, Dana-Farber Cancer Institute, Boston, MA 02115, USA
| | | | - Christian Urban
- Institute of Virology, Technical University of Munich, Munich, Germany
| | - Matthias Habjan
- Institute of Virology, Technical University of Munich, Munich, Germany
| | - Rune Hartmann
- Department of Molecular Biology and Genetics, Aarhus University, Aarhus, Denmark
| | - Philip J Kranzusch
- Department of Microbiology, Harvard Medical School, Boston, MA 02115, USA
- Department of Cancer Immunology and Virology, Dana-Farber Cancer Institute, Boston, MA 02115, USA
- Parker Institute for Cancer Immunotherapy at Dana-Farber Cancer Institute, Boston, MA 02115, USA
| | - Andreas Pichlmair
- Institute of Virology, Technical University of Munich, Munich, Germany
- German Center for Infection Research (DZIF), Munich partner site, Munich, Germany
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Buchynskyi M, Oksenych V, Kamyshna I, Vari SG, Kamyshnyi A. Genetic Predictors of Comorbid Course of COVID-19 and MAFLD: A Comprehensive Analysis. Viruses 2023; 15:1724. [PMID: 37632067 PMCID: PMC10459448 DOI: 10.3390/v15081724] [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: 07/06/2023] [Revised: 07/26/2023] [Accepted: 08/10/2023] [Indexed: 08/27/2023] Open
Abstract
Metabolic-associated fatty liver disease (MAFLD) and its potential impact on the severity of COVID-19 have gained significant attention during the pandemic. This review aimed to explore the genetic determinants associated with MAFLD, previously recognized as non-alcoholic fatty liver disease (NAFLD), and their potential influence on COVID-19 outcomes. Various genetic polymorphisms, including PNPLA3 (rs738409), GCKR (rs780094), TM6SF2 (rs58542926), and LYPLAL1 (rs12137855), have been investigated in relation to MAFLD susceptibility and progression. Genome-wide association studies and meta-analyses have revealed associations between these genetic variants and MAFLD risk, as well as their effects on lipid metabolism, glucose regulation, and liver function. Furthermore, emerging evidence suggests a possible connection between these MAFLD-associated polymorphisms and the severity of COVID-19. Studies exploring the association between indicated genetic variants and COVID-19 outcomes have shown conflicting results. Some studies observed a potential protective effect of certain variants against severe COVID-19, while others reported no significant associations. This review highlights the importance of understanding the genetic determinants of MAFLD and its potential implications for COVID-19 outcomes. Further research is needed to elucidate the precise mechanisms linking these genetic variants to disease severity and to develop gene profiling tools for the early prediction of COVID-19 outcomes. If confirmed as determinants of disease severity, these genetic polymorphisms could aid in the identification of high-risk individuals and in improving the management of COVID-19.
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Affiliation(s)
- Mykhailo Buchynskyi
- Department of Microbiology, Virology, and Immunology, I. Horbachevsky Ternopil National Medical University, 46001 Ternopil, Ukraine
| | - Valentyn Oksenych
- Broegelmann Research Laboratory, Department of Clinical Science, University of Bergen, 5020 Bergen, Norway
| | - Iryna Kamyshna
- Department of Medical Rehabilitation, I. Horbachevsky Ternopil National Medical University, 46001 Ternopil, Ukraine
| | - Sandor G. Vari
- International Research and Innovation in Medicine Program, Cedars–Sinai Medical Center, Los Angeles, CA 90048, USA
| | - Aleksandr Kamyshnyi
- Department of Microbiology, Virology, and Immunology, I. Horbachevsky Ternopil National Medical University, 46001 Ternopil, Ukraine
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Abstract
Poxviruses have been long regarded as potent inhibitors of apoptotic cell death. More recently, they have been shown to inhibit necroptotic cell death through two distinct strategies. These strategies involve either blocking virus sensing by the host pattern recognition receptor, ZBP1 (also called DAI) or by influencing receptor interacting protein kinase (RIPK)3 signal transduction by inhibition of activation of the executioner of necroptosis, mixed lineage kinase-like protein (MLKL). Vaccinia virus E3 specifically blocks ZBP1 → RIPK3 → MLKL necroptosis, leaving virus-infected cells susceptible to the TNF death-receptor signaling (e.g., TNFR1 → FADD → RIPK1 → RIPK3 → MLKL), and, potentially, TLR3 → TRIF → RIPK3 → MLKL necroptosis. While E3 restriction of necroptosis appears to be common to many poxviruses that infect vertebrate hosts, another modulatory strategy not observed in vaccinia or variola virus manifests through subversion of MLKL activation. Recently described viral mimics of MLKL in other chordopoxviruses inhibit all three modes of necroptotic cell death. As with inhibition of apoptosis, the evolution of potentially redundant viral mechanisms to inhibit programmed necroptotic cell death emphasizes the importance of this pathway in the arms race between pathogens and their hosts.
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Affiliation(s)
- Heather S Koehler
- Department of Microbiology and Immunology, Emory University School of Medicine, Emory Vaccine Center, Atlanta, GA, 30322, USA
| | - Bertram L Jacobs
- Arizona State University, Center for Immunotherapy, Vaccines and Virotherapy, Biodesign Institute, Tempe, AZ, 85287, USA.
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Banday AR, Stanifer ML, Florez-Vargas O, Onabajo OO, Papenberg BW, Zahoor MA, Mirabello L, Ring TJ, Lee CH, Albert PS, Andreakos E, Arons E, Barsh G, Biesecker LG, Boyle DL, Brahier MS, Burnett-Hartman A, Carrington M, Chang E, Choe PG, Chisholm RL, Colli LM, Dalgard CL, Dude CM, Edberg J, Erdmann N, Feigelson HS, Fonseca BA, Firestein GS, Gehring AJ, Guo C, Ho M, Holland S, Hutchinson AA, Im H, Irby L, Ison MG, Joseph NT, Kim HB, Kreitman RJ, Korf BR, Lipkin SM, Mahgoub SM, Mohammed I, Paschoalini GL, Pacheco JA, Peluso MJ, Rader DJ, Redden DT, Ritchie MD, Rosenblum B, Ross ME, Anna HPS, Savage SA, Sharma S, Siouti E, Smith AK, Triantafyllia V, Vargas JM, Vargas JD, Verma A, Vij V, Wesemann DR, Yeager M, Yu X, Zhang Y, Boulant S, Chanock SJ, Feld JJ, Prokunina-Olsson L. Genetic regulation of OAS1 nonsense-mediated decay underlies association with COVID-19 hospitalization in patients of European and African ancestries. Nat Genet 2022; 54:1103-1116. [PMID: 35835913 PMCID: PMC9355882 DOI: 10.1038/s41588-022-01113-z] [Citation(s) in RCA: 65] [Impact Index Per Article: 32.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2021] [Accepted: 05/26/2022] [Indexed: 12/22/2022]
Abstract
The chr12q24.13 locus encoding OAS1-OAS3 antiviral proteins has been associated with coronavirus disease 2019 (COVID-19) susceptibility. Here, we report genetic, functional and clinical insights into this locus in relation to COVID-19 severity. In our analysis of patients of European (n = 2,249) and African (n = 835) ancestries with hospitalized versus nonhospitalized COVID-19, the risk of hospitalized disease was associated with a common OAS1 haplotype, which was also associated with reduced severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) clearance in a clinical trial with pegIFN-λ1. Bioinformatic analyses and in vitro studies reveal the functional contribution of two associated OAS1 exonic variants comprising the risk haplotype. Derived human-specific alleles rs10774671-A and rs1131454 -A decrease OAS1 protein abundance through allele-specific regulation of splicing and nonsense-mediated decay (NMD). We conclude that decreased OAS1 expression due to a common haplotype contributes to COVID-19 severity. Our results provide insight into molecular mechanisms through which early treatment with interferons could accelerate SARS-CoV-2 clearance and mitigate against severe COVID-19.
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Affiliation(s)
- A Rouf Banday
- Laboratory of Translational Genomics, Division of Cancer Epidemiology and Genetics, National Cancer Institute, Rockville, MD, USA
| | - Megan L Stanifer
- Department of Infectious Diseases, Molecular Virology, University Hospital Heidelberg, Heidelberg, Germany
- Department of Molecular Genetics and Microbiology, College of Medicine, University of Florida, Gainesville, FL, USA
| | - Oscar Florez-Vargas
- Laboratory of Translational Genomics, Division of Cancer Epidemiology and Genetics, National Cancer Institute, Rockville, MD, USA
| | - Olusegun O Onabajo
- Laboratory of Translational Genomics, Division of Cancer Epidemiology and Genetics, National Cancer Institute, Rockville, MD, USA
| | - Brenen W Papenberg
- Laboratory of Translational Genomics, Division of Cancer Epidemiology and Genetics, National Cancer Institute, Rockville, MD, USA
| | - Muhammad A Zahoor
- Toronto Centre for Liver Disease, Toronto General Hospital Research Institute, University Health Network, Toronto, Ontario, Canada
| | - Lisa Mirabello
- Clinical Genetics Branch, Division of Cancer Epidemiology and Genetics, National Cancer Institute, Rockville, MD, USA
| | - Timothy J Ring
- Laboratory of Translational Genomics, Division of Cancer Epidemiology and Genetics, National Cancer Institute, Rockville, MD, USA
| | - Chia-Han Lee
- Laboratory of Translational Genomics, Division of Cancer Epidemiology and Genetics, National Cancer Institute, Rockville, MD, USA
| | - Paul S Albert
- Biostatistics Branch, Division of Cancer Epidemiology and Genetics, National Cancer Institute, Rockville, MD, USA
| | - Evangelos Andreakos
- Laboratory of Immunobiology, Center for Clinical, Experimental Surgery and Translational Research, Biomedical Research Foundation of the Academy of Athens, Athens, Greece
| | - Evgeny Arons
- Laboratory of Molecular Biology, Center for Cancer Research, National Cancer Institute, Bethesda, MD, USA
| | - Greg Barsh
- HudsonAlpha Institute for Biotechnology, Huntsville, AL, USA
| | - Leslie G Biesecker
- Center for Precision Health Research, National Human Genome Research Institute, Bethesda, MD, USA
| | - David L Boyle
- Altman Clinical & Translational Research Institute, UC San Diego Health Sciences, San Diego, CA, USA
| | - Mark S Brahier
- Georgetown University School of Medicine, Washington, DC, USA
| | | | - Mary Carrington
- Basic Science Program, Frederick National Laboratory for Cancer Research, National Cancer Institute, Frederick, MD, USA
- Laboratory of Integrative Cancer Immunology, Center for Cancer Research, National Cancer Institute, Bethesda, MD, USA
- Ragon Institute of MGH, MIT and Harvard, Cambridge, MA, USA
| | - Euijin Chang
- Department of Internal Medicine, Seoul National University College of Medicine, Seoul, Republic of Korea
| | - Pyoeng Gyun Choe
- Department of Internal Medicine, Seoul National University College of Medicine, Seoul, Republic of Korea
| | - Rex L Chisholm
- Center for Genetic Medicine, Northwestern University Feinberg School of Medicine, Chicago, IL, USA
| | - Leandro M Colli
- Department of Medical Imaging, Hematology, and Oncology, Ribeirão Preto Medical School, University of São Paulo, Ribeirão Preto, Brazil
| | - Clifton L Dalgard
- Uniformed Services University of the Health Sciences, Bethesda, MD, USA
| | - Carolynn M Dude
- Department of Gynecology and Obstetrics, Emory University School of Medicine, Atlanta, GA, USA
| | - Jeff Edberg
- Department of Medicine, Division of Clinical Immunology and Rheumatology, University of Alabama at Birmingham, Birmingham, AL, USA
| | - Nathan Erdmann
- Department of Medicine, Division of Infectious Diseases, University of Alabama at Birmingham, Birmingham, AL, USA
| | | | - Benedito A Fonseca
- Department of Internal Medicine, Ribeirão Preto Medical School, University of São Paulo, Ribeirão Preto, Brazil
| | - Gary S Firestein
- Altman Clinical & Translational Research Institute, UC San Diego Health Sciences, San Diego, CA, USA
| | - Adam J Gehring
- Toronto Centre for Liver Disease, Toronto General Hospital Research Institute, University Health Network, Toronto, Ontario, Canada
- Department of Immunology, University of Toronto, Toronto, Ontario, Canada
| | - Cuncai Guo
- Division of Cellular Polarity and Viral Infection, German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Michelle Ho
- Laboratory of Translational Genomics, Division of Cancer Epidemiology and Genetics, National Cancer Institute, Rockville, MD, USA
| | - Steven Holland
- Laboratory of Clinical Immunology and Microbiology, National Institute of Allergy and Infectious Diseases, Bethesda, MD, USA
| | - Amy A Hutchinson
- Cancer Genomics Research Laboratory, Frederick National Laboratory for Cancer Research, Frederick, MD, USA
| | - Hogune Im
- Genome Opinion, Inc., Seoul, Republic of Korea
| | - Les'Shon Irby
- Department of Gynecology and Obstetrics, Emory University School of Medicine, Atlanta, GA, USA
| | - Michael G Ison
- Divisions of Infectious Diseases and Organ Transplantation, Northwestern University Feinberg School of Medicine, Chicago, IL, USA
| | - Naima T Joseph
- Department of Obstetrics & Gynecology, Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, MA, USA
| | - Hong Bin Kim
- Department of Internal Medicine, Seoul National University College of Medicine, Seoul, Republic of Korea
- Department of Internal Medicine, Seoul National University Bundang Hospital, Seongnam, Republic of Korea
| | - Robert J Kreitman
- Laboratory of Molecular Biology, Center for Cancer Research, National Cancer Institute, Bethesda, MD, USA
| | - Bruce R Korf
- Department of Genetics, University of Alabama at Birmingham, Birmingham, AL, USA
| | - Steven M Lipkin
- Department of Medicine and Program in Mendelian Genetics, Weill Cornell Medicine, New York, NY, USA
| | - Siham M Mahgoub
- Department of Medicine, Infectious Diseases Division, Howard University Hospital, Howard University College of Medicine, Washington, DC, USA
| | - Iman Mohammed
- Feil Family Brain and Mind Research Institute, Weill Cornell Medicine, New York, NY, USA
| | - Guilherme L Paschoalini
- Department of Medical Imaging, Hematology, and Oncology, Ribeirão Preto Medical School, University of São Paulo, Ribeirão Preto, Brazil
| | - Jennifer A Pacheco
- Center for Genetic Medicine, Northwestern University Feinberg School of Medicine, Chicago, IL, USA
| | - Michael J Peluso
- Division of HIV, Infectious Diseases and Global Medicine, University of California, San Francisco, CA, USA
| | - Daniel J Rader
- Department of Genetics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - David T Redden
- Department of Biostatistics, University of Alabama at Birmingham, Birmingham, AL, USA
| | - Marylyn D Ritchie
- Department of Genetics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Brooke Rosenblum
- Center for Precision Health Research, National Human Genome Research Institute, Bethesda, MD, USA
| | - M Elizabeth Ross
- Feil Family Brain and Mind Research Institute, Weill Cornell Medicine, New York, NY, USA
| | - Hanaisa P Sant Anna
- Laboratory of Genetic Susceptibility, Division of Cancer Epidemiology and Genetics, National Cancer Institute, Rockville, MD, USA
| | - Sharon A Savage
- Clinical Genetics Branch, Division of Cancer Epidemiology and Genetics, National Cancer Institute, Rockville, MD, USA
| | - Sudha Sharma
- Department of Biochemistry and Molecular Biology, National Human Genome Center, Howard University College of Medicine, Washington, DC, USA
| | - Eleni Siouti
- Laboratory of Immunobiology, Center for Clinical, Experimental Surgery and Translational Research, Biomedical Research Foundation of the Academy of Athens, Athens, Greece
| | - Alicia K Smith
- Department of Gynecology and Obstetrics, Emory University School of Medicine, Atlanta, GA, USA
| | - Vasiliki Triantafyllia
- Laboratory of Immunobiology, Center for Clinical, Experimental Surgery and Translational Research, Biomedical Research Foundation of the Academy of Athens, Athens, Greece
| | - Joselin M Vargas
- Laboratory of Translational Genomics, Division of Cancer Epidemiology and Genetics, National Cancer Institute, Rockville, MD, USA
| | - Jose D Vargas
- Veterans Affairs Medical Center, Washington, DC, USA
| | - Anurag Verma
- Department of Genetics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Vibha Vij
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, Rockville, MD, USA
| | - Duane R Wesemann
- Department of Medicine, Division of Allergy and Immunology, Division of Genetics, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA
| | - Meredith Yeager
- Cancer Genomics Research Laboratory, Frederick National Laboratory for Cancer Research, Frederick, MD, USA
| | - Xu Yu
- Ragon Institute of MGH, MIT and Harvard, Cambridge, MA, USA
| | - Yu Zhang
- Laboratory of Clinical Immunology and Microbiology, National Institute of Allergy and Infectious Diseases, Bethesda, MD, USA
| | - Steeve Boulant
- Department of Molecular Genetics and Microbiology, College of Medicine, University of Florida, Gainesville, FL, USA
- Division of Cellular Polarity and Viral Infection, German Cancer Research Center (DKFZ), Heidelberg, Germany
- Department of Infectious Diseases, Virology, University Hospital Heidelberg, Heidelberg, Germany
| | - Stephen J Chanock
- Laboratory of Genetic Susceptibility, Division of Cancer Epidemiology and Genetics, National Cancer Institute, Rockville, MD, USA
| | - Jordan J Feld
- Toronto Centre for Liver Disease, Toronto General Hospital Research Institute, University Health Network, Toronto, Ontario, Canada
- Department of Immunology, University of Toronto, Toronto, Ontario, Canada
| | - Ludmila Prokunina-Olsson
- Laboratory of Translational Genomics, Division of Cancer Epidemiology and Genetics, National Cancer Institute, Rockville, MD, USA.
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Crocodilepox Virus Protein 157 Is an Independently Evolved Inhibitor of Protein Kinase R. Viruses 2022; 14:v14071564. [PMID: 35891544 PMCID: PMC9318007 DOI: 10.3390/v14071564] [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: 05/25/2022] [Revised: 07/14/2022] [Accepted: 07/16/2022] [Indexed: 02/05/2023] Open
Abstract
Crocodilepox virus (CRV) belongs to the Poxviridae family and mainly infects hatchling and juvenile Nile crocodiles. Most poxviruses encode inhibitors of the host antiviral protein kinase R (PKR), which is activated by viral double-stranded (ds) RNA formed during virus replication, resulting in the phosphorylation of eIF2α and the subsequent shutdown of general mRNA translation. Because CRV lacks orthologs of known poxviral PKR inhibitors, we experimentally characterized one candidate (CRV157), which contains a predicted dsRNA-binding domain. Bioinformatic analyses indicated that CRV157 evolved independently from other poxvirus PKR inhibitors. CRV157 bound to dsRNA, co-localized with PKR in the cytosol, and inhibited PKR from various species. To analyze whether CRV157 could inhibit PKR in the context of a poxvirus infection, we constructed recombinant vaccinia virus strains that contain either CRV157, or a mutant CRV157 deficient in dsRNA binding in a strain that lacks PKR inhibitors. The presence of wild-type CRV157 rescued vaccinia virus replication, while the CRV157 mutant did not. The ability of CRV157 to inhibit PKR correlated with virus replication and eIF2α phosphorylation. The independent evolution of CRV157 demonstrates that poxvirus PKR inhibitors evolved from a diverse set of ancestral genes in an example of convergent evolution.
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Szczerba M, Subramanian S, Trainor K, McCaughan M, Kibler KV, Jacobs BL. Small Hero with Great Powers: Vaccinia Virus E3 Protein and Evasion of the Type I IFN Response. Biomedicines 2022; 10:biomedicines10020235. [PMID: 35203445 PMCID: PMC8869630 DOI: 10.3390/biomedicines10020235] [Citation(s) in RCA: 16] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2021] [Revised: 01/12/2022] [Accepted: 01/15/2022] [Indexed: 12/14/2022] Open
Abstract
Poxviridae have developed a plethora of strategies to evade innate and adaptive immunity. In this review, we focused on the vaccinia virus E3 protein, encoded by the E3L gene. E3 is present within the Chordopoxvirinae subfamily (with the exception of the avipoxviruses and molluscum contagiosum virus) and displays pleiotropic effects on the innate immune system. Initial studies identified E3 as a double-stranded RNA (dsRNA)-binding protein (through its C terminus), able to inhibit the activation of protein kinase dependent on RNA (PKR) and the 2′5′-oligoadenylate synthetase (OAS)/RNase L pathway, rendering E3 a protein counteracting the type I interferon (IFN) system. In recent years, N-terminal mutants of E3 unable to bind to Z-form nucleic acids have been shown to induce the cellular death pathway necroptosis. This pathway was dependent on host IFN-inducible Z-DNA-binding protein 1 (ZBP1); full-length E3 is able to inhibit ZBP1-mediated necroptosis. Binding to what was identified as Z-RNA has emerged as a novel mechanism of counteracting the type I IFN system and has broadened our understanding of innate immunity against viral infections. This article gives an overview of the studies leading to our understanding of the vaccinia virus E3 protein function and its involvement in viral pathogenesis. Furthermore, a short summary of other viral systems is provided.
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Affiliation(s)
- Mateusz Szczerba
- Biodesign Center for Immunotherapy, Vaccines and Virotherapy, Arizona State University, Tempe, AZ 85281, USA; (M.S.); (S.S.); (K.T.); (M.M.); (K.V.K.)
| | - Sambhavi Subramanian
- Biodesign Center for Immunotherapy, Vaccines and Virotherapy, Arizona State University, Tempe, AZ 85281, USA; (M.S.); (S.S.); (K.T.); (M.M.); (K.V.K.)
- School of Life Sciences, Arizona State University, Tempe, AZ 85281, USA
- Vir Biotechnology, San Francisco, CA 94158, USA
| | - Kelly Trainor
- Biodesign Center for Immunotherapy, Vaccines and Virotherapy, Arizona State University, Tempe, AZ 85281, USA; (M.S.); (S.S.); (K.T.); (M.M.); (K.V.K.)
- Faculty of Biology, Coconino Community College, Flagstaff, AZ 86005, USA
| | - Megan McCaughan
- Biodesign Center for Immunotherapy, Vaccines and Virotherapy, Arizona State University, Tempe, AZ 85281, USA; (M.S.); (S.S.); (K.T.); (M.M.); (K.V.K.)
- School of Life Sciences, Arizona State University, Tempe, AZ 85281, USA
| | - Karen V. Kibler
- Biodesign Center for Immunotherapy, Vaccines and Virotherapy, Arizona State University, Tempe, AZ 85281, USA; (M.S.); (S.S.); (K.T.); (M.M.); (K.V.K.)
| | - Bertram L. Jacobs
- Biodesign Center for Immunotherapy, Vaccines and Virotherapy, Arizona State University, Tempe, AZ 85281, USA; (M.S.); (S.S.); (K.T.); (M.M.); (K.V.K.)
- School of Life Sciences, Arizona State University, Tempe, AZ 85281, USA
- Correspondence:
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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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10
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Banday AR, Stanifer ML, Florez-Vargas O, Onabajo OO, Zahoor MA, Papenberg BW, Ring TJ, Lee CH, Andreakos E, Arons E, Barsh G, Biesecker LG, Boyle DL, Burnett-Hartman A, Carrington M, Chang E, Choe PG, Chrisholm RL, Dalgard C, Edberg J, Erdmann N, Feigelson HS, Firestein GS, Gehring AJ, Ho M, Holland S, Hutchinson AA, Im H, Ison MG, Kim HB, Kreitman RJ, Korf BR, Mirabello L, Pacheco JA, Peluso MJ, Rader DJ, Redden DT, Ritchie MD, Rosenbloom B, Sant Anna HP, Savage S, Siouti E, Triantafyllia V, Vargas JM, Verma A, Vij V, Wesemann DR, Yeager M, Yu X, Zhang Y, Boulant S, Chanock SJ, Feld JJ, Prokunina-Olsson L. Genetic regulation of OAS1 nonsense-mediated decay underlies association with risk of severe COVID-19. MEDRXIV : THE PREPRINT SERVER FOR HEALTH SCIENCES 2021:2021.07.09.21260221. [PMID: 34282422 PMCID: PMC8288155 DOI: 10.1101/2021.07.09.21260221] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
Genomic regions have been associated with COVID-19 susceptibility and outcomes, including the chr12q24.13 locus encoding antiviral proteins OAS1-3. Here, we report genetic, functional, and clinical insights into genetic associations within this locus. In Europeans, the risk of hospitalized vs. non-hospitalized COVID-19 was associated with a single 19Kb-haplotype comprised of 76 OAS1 variants included in a 95% credible set within a large genomic fragment introgressed from Neandertals. The risk haplotype was also associated with impaired spontaneous but not treatment-induced SARS-CoV-2 clearance in a clinical trial with pegIFN-λ1. We demonstrate that two exonic variants, rs10774671 and rs1131454, affect splicing and nonsense-mediated decay of OAS1 . We suggest that genetically-regulated loss of OAS1 expression contributes to impaired spontaneous clearance of SARS-CoV-2 and elevated risk of hospitalization for COVID-19. Our results provide the rationale for further clinical studies using interferons to compensate for impaired spontaneous SARS-CoV-2 clearance, particularly in carriers of the OAS1 risk haplotypes.
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Affiliation(s)
- A Rouf Banday
- Laboratory of Translational Genomics, Division of Cancer Epidemiology and Genetics, National Cancer Institute, Rockville, MD, USA
| | - Megan L Stanifer
- Department of Infectious Diseases, Molecular Virology, University Hospital Heidelberg, Heidelberg, Germany
| | - Oscar Florez-Vargas
- Laboratory of Translational Genomics, Division of Cancer Epidemiology and Genetics, National Cancer Institute, Rockville, MD, USA
| | - Olusegun O Onabajo
- Laboratory of Translational Genomics, Division of Cancer Epidemiology and Genetics, National Cancer Institute, Rockville, MD, USA
| | - Muhammad A Zahoor
- Toronto Centre for Liver Disease, Toronto General Hospital Research Institute, University Health Network, Toronto, ON, Canada
- Department of Immunology, University of Toronto, Toronto, ON, Canada
| | - Brenen W Papenberg
- Laboratory of Translational Genomics, Division of Cancer Epidemiology and Genetics, National Cancer Institute, Rockville, MD, USA
| | - Timothy J Ring
- Laboratory of Translational Genomics, Division of Cancer Epidemiology and Genetics, National Cancer Institute, Rockville, MD, USA
| | - Chia-Han Lee
- Laboratory of Translational Genomics, Division of Cancer Epidemiology and Genetics, National Cancer Institute, Rockville, MD, USA
| | - Evangelos Andreakos
- Laboratory of Immunobiology, Center for Clinical, Experimental Surgery and Translational Research, Biomedical Research Foundation of the Academy of Athens, Athens, Greece
| | - Evgeny Arons
- Laboratory of Molecular Biology, Center for Cancer Research, National Cancer Institute, Bethesda, MD, USA
| | - Greg Barsh
- HudsonAlpha Institute for Biotechnology, Huntsville, AL, USA
| | - Leslie G Biesecker
- Center for Precision Health Research, National Human Genome Research Institute, Bethesda, MD, USA
| | - David L Boyle
- Altman Clinical & Translational Research Institute, University of California San Diego Health Sciences, San Diego, CA, USA
| | | | - Mary Carrington
- Basic Science Program, Frederick National Laboratory for Cancer Research, National Cancer Institute, Frederick, MD, USA
- Laboratory of Integrative Cancer Immunology, Center for Cancer Research, National Cancer Institute, Bethesda, MD, USA
- Ragon Institute of MGH, MIT and Harvard, Cambridge, MA, USA
| | - Euijin Chang
- Department of Internal Medicine, Seoul National University College of Medicine, Seoul, Republic of Korea
| | - Pyoeng Gyun Choe
- Department of Internal Medicine, Seoul National University College of Medicine, Seoul, Republic of Korea
| | - Rex L Chrisholm
- Center for Genetic Medicine, Northwestern University Feinberg School of Medicine, Chicago, IL, USA
| | - Clifton Dalgard
- Uniformed Services University of the Health Sciences, Bethesda, MD, USA
| | - Jeff Edberg
- Department of Medicine, Division of Clinical Immunology and Rheumatology, University of Alabama at Birmingham, Birmingham, AL, USA
| | - Nathan Erdmann
- Department of Medicine, Division of Infectious Diseases, University of Alabama at Birmingham, Birmingham, AL, USA
| | | | - Gary S Firestein
- Altman Clinical & Translational Research Institute, University of California San Diego Health Sciences, San Diego, CA, USA
| | - Adam J Gehring
- Toronto Centre for Liver Disease, Toronto General Hospital Research Institute, University Health Network, Toronto, ON, Canada
- Department of Immunology, University of Toronto, Toronto, ON, Canada
| | - Michelle Ho
- Laboratory of Translational Genomics, Division of Cancer Epidemiology and Genetics, National Cancer Institute, Rockville, MD, USA
| | - Steven Holland
- Laboratory of Clinical Immunology and Microbiology, National Institute of Allergy and Infectious Diseases, Bethesda, MD, USA
| | - Amy A Hutchinson
- Cancer Genomics Research Laboratory, Frederick National Laboratory for Cancer Research, Frederick, MD, USA
| | - Hogune Im
- Genome Opinion Inc, Seoul, Republic of Korea
| | - Michael G Ison
- Divisions of Infectious Diseases and Organ Transplantation, Northwestern University Feinberg School of Medicine, Chicago, IL, USA
| | - Hong Bin Kim
- Department of Internal Medicine, Seoul National University College of Medicine, Seoul, Republic of Korea
- Department of Internal Medicine, Seoul National University Bundang Hospital, Seongnam, Republic of Korea
| | - Robert J Kreitman
- Laboratory of Molecular Biology, Center for Cancer Research, National Cancer Institute, Bethesda, MD, USA
| | - Bruce R Korf
- Department of Genetics, University of Alabama at Birmingham, Birmingham, AL, USA
| | - Lisa Mirabello
- Clinical Genetics Branch, Division of Cancer Epidemiology and Genetics, National Cancer Institute, Rockville, MD, USA
| | - Jennifer A Pacheco
- Center for Genetic Medicine, Northwestern University Feinberg School of Medicine, Chicago, IL, USA
| | - Michael J Peluso
- Division of HIV, Infectious Diseases and Global Medicine, University of California, San Francisco, CA, USA
| | - Daniel J Rader
- Department of Genetics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - David T Redden
- Department of Biostatistics, University of Alabama at Birmingham, Birmingham, AL, USA
| | - Marylyn D Ritchie
- Department of Genetics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Brooke Rosenbloom
- Center for Precision Health Research, National Human Genome Research Institute, Bethesda, MD, USA
| | - Hanaisa P Sant Anna
- Laboratory of Genetic Susceptibility, Division of Cancer Epidemiology and Genetics, National Cancer Institute, Rockville, MD, USA
| | - Sharon Savage
- Clinical Genetics Branch, Division of Cancer Epidemiology and Genetics, National Cancer Institute, Rockville, MD, USA
| | - Eleni Siouti
- Laboratory of Immunobiology, Center for Clinical, Experimental Surgery and Translational Research, Biomedical Research Foundation of the Academy of Athens, Athens, Greece
| | - Vasiliki Triantafyllia
- Laboratory of Immunobiology, Center for Clinical, Experimental Surgery and Translational Research, Biomedical Research Foundation of the Academy of Athens, Athens
| | - Joselin M Vargas
- Laboratory of Translational Genomics, Division of Cancer Epidemiology and Genetics, National Cancer Institute, Rockville, MD, USA
| | - Anurag Verma
- Department of Genetics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Vibha Vij
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, Rockville, MD, USA
| | - Duane R Wesemann
- Department of Medicine, Division of Allergy and Immunology, Division of Genetics, Brigham and Women’s Hospital, Harvard Medical School, Boston, MA, USA
| | - Meredith Yeager
- Cancer Genomics Research Laboratory, Frederick National Laboratory for Cancer Research, Frederick, MD, USA
| | - Xu Yu
- Ragon Institute of MGH, MIT and Harvard, Cambridge, MA, USA
| | - Yu Zhang
- Laboratory of Clinical Immunology and Microbiology, National Institute of Allergy and Infectious Diseases, Bethesda, MD, USA
| | - Steeve Boulant
- Division of Cellular Polarity and Viral Infection, German Cancer Research Center (DKFZ), Heidelberg, Germany
- Department of Infectious Diseases, Virology, University Hospital Heidelberg, Heidelberg, Germany
| | - Stephen J Chanock
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, Rockville, MD, USA
| | - Jordan J Feld
- Toronto Centre for Liver Disease, Toronto General Hospital Research Institute, University Health Network, Toronto, ON, Canada
- Department of Immunology, University of Toronto, Toronto, ON, Canada
| | - Ludmila Prokunina-Olsson
- Laboratory of Translational Genomics, Division of Cancer Epidemiology and Genetics, National Cancer Institute, Rockville, MD, USA
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11
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Yu H, Bruneau RC, Brennan G, Rothenburg S. Battle Royale: Innate Recognition of Poxviruses and Viral Immune Evasion. Biomedicines 2021; 9:biomedicines9070765. [PMID: 34356829 PMCID: PMC8301327 DOI: 10.3390/biomedicines9070765] [Citation(s) in RCA: 46] [Impact Index Per Article: 15.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/21/2021] [Revised: 06/25/2021] [Accepted: 06/26/2021] [Indexed: 12/17/2022] Open
Abstract
Host pattern recognition receptors (PRRs) sense pathogen-associated molecular patterns (PAMPs), which are molecular signatures shared by different pathogens. Recognition of PAMPs by PRRs initiate innate immune responses via diverse signaling pathways. Over recent decades, advances in our knowledge of innate immune sensing have enhanced our understanding of the host immune response to poxviruses. Multiple PRR families have been implicated in poxvirus detection, mediating the initiation of signaling cascades, activation of transcription factors, and, ultimately, the expression of antiviral effectors. To counteract the host immune defense, poxviruses have evolved a variety of immunomodulators that have diverse strategies to disrupt or circumvent host antiviral responses triggered by PRRs. These interactions influence the outcomes of poxvirus infections. This review focuses on our current knowledge of the roles of PRRs in the recognition of poxviruses, their elicited antiviral effector functions, and how poxviral immunomodulators antagonize PRR-mediated host immune responses.
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12
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Tallmadge RL, Antczak DF, Felippe MJB. Genetics of Immune Disease in the Horse. Vet Clin North Am Equine Pract 2020; 36:273-288. [PMID: 32654783 DOI: 10.1016/j.cveq.2020.03.007] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/22/2023] Open
Abstract
Host defenses against infection by viruses, bacteria, fungi, and parasites are critical to survival. It has been estimated that upwards of 7% of the coding genes of mammals function in immunity and inflammation. This high level of genomic investment in defense has resulted in an immune system characterized by extraordinary complexity and many levels of redundancy. Because so many genes are involved with immunity, there are many opportunities for mutations to arise that have negative effects. However, redundancy in the mammalian defense system and the adaptive nature of key immune mechanisms buffer the untoward outcomes of many such deleterious mutations.
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Affiliation(s)
- Rebecca L Tallmadge
- Animal Health Diagnostic Center, College of Veterinary Medicine, Cornell University, 240 Farrier Road, Ithaca, NY 14853, USA
| | - Douglas F Antczak
- Baker Institute for Animal Health, College of Veterinary Medicine, Cornell University, 235 Hungerford Hill Road, Ithaca, NY 14853, USA.
| | - Maria Julia Bevilaqua Felippe
- Department of Clinical Sciences, College of Veterinary Medicine, Cornell University, 930 Campus Road, Ithaca, NY 14853, USA
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13
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Guo CJ, He J, He JG. The immune evasion strategies of fish viruses. FISH & SHELLFISH IMMUNOLOGY 2019; 86:772-784. [PMID: 30543936 DOI: 10.1016/j.fsi.2018.12.013] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/28/2018] [Revised: 12/07/2018] [Accepted: 12/09/2018] [Indexed: 06/09/2023]
Abstract
Viral infection of a host rapidly triggers intracellular signaling events that induce interferon production and a cellular antiviral state. Viral diseases are important concerns in fish aquaculture. The major mechanisms of the fish antiviral immune response are suggested to be similar to those of mammals, although the specific details of the process require further studies. Throughout the process of pathogen-host coevolution, fish viruses have developed a battery of distinct strategies to overcome the biochemical and immunological defenses of the host. Such strategies include signaling interference, effector modulation, and manipulation of host apoptosis. This review provide an overview of the different mechanisms that fish viruses use to evade host immune responses. The basic mechanisms of immune evasion of fish virus are discussed, and some examples are provided to illustrate particular points.
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Affiliation(s)
- C J Guo
- Guangdong Provincial Key Laboratory of Marine Resources and Coastal Engineering / State Key Laboratory for Biocontrol, School of Marine, Sun Yat-sen University, 135 Xingang Road West, Guangzhou 510275, PR China; Institute of Aquatic Economic Animals and Guangdong Province Key Laboratory for Aquatic Economic Animals, School of Life Sciences, Sun Yat-sen University, 135 Xingang Road West, Guangzhou 510275, PR China
| | - J He
- Guangdong Provincial Key Laboratory of Marine Resources and Coastal Engineering / State Key Laboratory for Biocontrol, School of Marine, Sun Yat-sen University, 135 Xingang Road West, Guangzhou 510275, PR China; Institute of Aquatic Economic Animals and Guangdong Province Key Laboratory for Aquatic Economic Animals, School of Life Sciences, Sun Yat-sen University, 135 Xingang Road West, Guangzhou 510275, PR China
| | - J G He
- Guangdong Provincial Key Laboratory of Marine Resources and Coastal Engineering / State Key Laboratory for Biocontrol, School of Marine, Sun Yat-sen University, 135 Xingang Road West, Guangzhou 510275, PR China; Institute of Aquatic Economic Animals and Guangdong Province Key Laboratory for Aquatic Economic Animals, School of Life Sciences, Sun Yat-sen University, 135 Xingang Road West, Guangzhou 510275, PR China.
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14
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Nuclear import sequence identification in hOAS3 protein. Inflamm Res 2016; 65:895-904. [PMID: 27379722 DOI: 10.1007/s00011-016-0972-8] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2016] [Revised: 06/14/2016] [Accepted: 06/28/2016] [Indexed: 10/21/2022] Open
Abstract
OBJECTIVE The OAS proteins are characterized by their capacity to synthesize 2',5'-linked phosphodiester bonds to polymerize ATP into oligomers of adenosine. OAS3, belonging to OASs gene family, synthesizes dimeric 2-5A that binds to RNase L with low affinity and produces 2-5A oligomers shorter than the tri-tetramer 2-5As produced by other family members. METHODS For these studies, we used the open source tools cNLS Mapper, PredictProtein and COMPARTMENTS for the nuclear localization signal prediction, UCSF Chimera for molecular graphics and analyses, The Human Protein Atlas to confirm with the IF the OAS3 cell localization and Ensembl Variation Table to identify the presence of putative single nucleotide polymorphisms in the NLS sequence identification. RESULTS The analysis of OAS3 protein sequence (NP_006178.2) displayed a putative nuclear localization signal (cNLS Mapper score 8 and PP 100 %), identified by 11 and 5 amino acids (LQRQL KRPRP V) located in the outer portion ready to interact with the importin α/β. Furthermore, we showed that in all cells lines available in the Human Protein Atlas subcell section, the OAS3 was mainly localized in the cytoplasm and nucleus, but not in the nucleoli. We identify six known variant SNPs mapping in the nuclear import sequence, but only three were associated with a missense variation (rs781335794, rs750458641, rs550465943) and were able to strongly reduce the cNLS score. CONCLUSIONS The catalytically inactive domain of human OAS3 has a potential nuclear import function, susceptible to SNPs, which could determine their roles in the viral infection and IFNs response.
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15
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Zhang J, Shao J, Wu X, Mao Q, Wang Y, Gao F, Kong W, Liang Z. Type I interferon related genes are common genes on the early stage after vaccination by meta-analysis of microarray data. Hum Vaccin Immunother 2015; 11:739-45. [PMID: 25839220 DOI: 10.1080/21645515.2015.1008884] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022] Open
Abstract
The objective of this study was to find common immune mechanism across different kinds of vaccines. A meta-analysis of microarray datasets was performed using publicly available microarray Gene Expression Omnibus (GEO) and Array Express data sets of vaccination records. Seven studies (out of 35) were selected for this meta-analysis. A total of 447 chips (145 pre-vaccination and 302 post-vaccination) were included. Significance analysis of microarrays (SAM) program was used for screening differentially expressed genes (DEGs). Functional pathway enrichment for the DEGs was conducted in DAVID Gene Ontology (GO) database. Twenty DEGs were identified, of which 10 up-regulated genes involved immune response. Six of which were type I interferon (IFN) related genes, including LY6E, MX1, OAS3, IFI44L, IFI6 and IFITM3. Ten down-regulated genes mainly mediated negative regulation of cell proliferation and cell motion. Results of a subgroup analysis showed that although the kinds of genes varied widely between days 3 and 7 post vaccination, the pathways between them are basically the same, such as immune response and response to viruses, etc. For an independent verification of these 6 type I IFN related genes, peripheral blood mononuclear cells (PBMCs) were collected at baseline and day 3 after the vaccination from 8 Enterovirus 71(EV71) vaccinees and were assayed by RT-PCR. Results showed that the 6 DEGs were also upregulated in EV71 vaccinees. In summary, meta-analysis methods were used to explore the immune mechanism of vaccines and results indicated that the type I IFN related genes and corresponding pathways were common in early immune responses for different kinds of vaccines.
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Key Words
- CPE, cytopathogenic effect
- DCs, dendritic cells
- DEGs, differentially expressed genes
- EV71, enterovirus 71
- GEO, Gene Expression Omnibus
- GO, gene ontology
- IFN, interferon
- PBMCs, peripheral blood mononuclear cells
- PRRs, pattern recognition receptors
- SAM, significance analysis of microarrays
- TLRs, Toll-like receptors
- immune mechanism
- meta-analysis
- microarray
- type I interferon
- vaccine
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Affiliation(s)
- Junnan Zhang
- a National Institutes for Food and Drug Control ; Beijing , P.R. China
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16
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Zheng S, Zhu D, Lian X, Liu W, Cao R, Chen P. Porcine 2′, 5′-oligoadenylate synthetases inhibit Japanese encephalitis virus replication in vitro. J Med Virol 2015; 88:760-8. [DOI: 10.1002/jmv.24397] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 09/29/2015] [Indexed: 12/15/2022]
Affiliation(s)
- Sheng Zheng
- Key Laboratory of Animal Diseases Diagnosis and Immunology, Ministry of Agriculture, College of Veterinary Medicine; Nanjing Agricultural University; Nanjing China
| | - Dan Zhu
- Key Laboratory of Animal Diseases Diagnosis and Immunology, Ministry of Agriculture, College of Veterinary Medicine; Nanjing Agricultural University; Nanjing China
| | - Xue Lian
- Key Laboratory of Animal Diseases Diagnosis and Immunology, Ministry of Agriculture, College of Veterinary Medicine; Nanjing Agricultural University; Nanjing China
| | - Weiting Liu
- Key Laboratory of Animal Diseases Diagnosis and Immunology, Ministry of Agriculture, College of Veterinary Medicine; Nanjing Agricultural University; Nanjing China
| | - Ruibing Cao
- Key Laboratory of Animal Diseases Diagnosis and Immunology, Ministry of Agriculture, College of Veterinary Medicine; Nanjing Agricultural University; Nanjing China
| | - Puyan Chen
- Key Laboratory of Animal Diseases Diagnosis and Immunology, Ministry of Agriculture, College of Veterinary Medicine; Nanjing Agricultural University; Nanjing China
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17
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Drappier M, Michiels T. Inhibition of the OAS/RNase L pathway by viruses. Curr Opin Virol 2015; 15:19-26. [PMID: 26231767 PMCID: PMC7185432 DOI: 10.1016/j.coviro.2015.07.002] [Citation(s) in RCA: 76] [Impact Index Per Article: 8.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2015] [Revised: 07/03/2015] [Accepted: 07/11/2015] [Indexed: 02/02/2023]
Abstract
The OAS/RNase L pathway was one of the first characterized IFN effector pathways. 2–5A molecules link ankyrin domains of two RNase L protomers to activate the enzyme. Viruses evolved a variety of strategies to escape the OAS/RNase L host response. Antagonism by viruses highlights the importance of RNase L as an antiviral defense. Why do some viruses act upstream and others downstream of the pathway?
The OAS/RNase L system was one of the first characterized interferon effector pathways. It relies on the synthesis, by oligoadenylate synthetases (OAS), of short oligonucleotides that act as second messengers to activate the latent cellular RNase L. Viruses have developed diverse strategies to escape its antiviral effects. This underscores the importance of the OAS/RNase L pathway in antiviral defenses. Viral proteins such as the NS1 protein of Influenza virus A act upstream of the pathway while other viral proteins such as Theiler's virus L* protein act downstream. The diversity of escape strategies used by viruses likely stems from their relative susceptibility to OAS/RNase L and other antiviral pathways, which may depend on their host and cellular tropism.
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Affiliation(s)
- Melissa Drappier
- Université catholique de Louvain, de Duve Institute, Brussels, Belgium
| | - Thomas Michiels
- Université catholique de Louvain, de Duve Institute, Brussels, Belgium.
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18
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Vachon VK, Conn GL. Adenovirus VA RNA: An essential pro-viral non-coding RNA. Virus Res 2015; 212:39-52. [PMID: 26116898 DOI: 10.1016/j.virusres.2015.06.018] [Citation(s) in RCA: 43] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2015] [Revised: 06/15/2015] [Accepted: 06/17/2015] [Indexed: 12/25/2022]
Abstract
Adenovirus (AdV) 'virus-associated' RNAs (VA RNAs) are exceptionally abundant (up to 10(8)copies/cell), heterogeneous, non-coding RNA transcripts (∼ 150-200 nucleotides). The predominant species, VA RNAI, is best recognized for its essential function in relieving the cellular anti-viral blockade of protein synthesis through inhibition of the double-stranded RNA-activated protein kinase (PKR). More recent evidence has revealed that VA RNAs also interfere with several other host cell processes, in part by virtue of the high level to which they accumulate. Following transcription by cellular RNA polymerase III, VA RNAs saturate the nuclear export protein Exportin 5 (Exp5) and the cellular endoribonculease Dicer, interfering with pre-micro (mi)RNA export and miRNA biogenesis, respectively. Dicer-processed VA RNA fragments are incorporated into the RNA-induced silencing complex (RISC) as 'mivaRNAs', where they may specifically target cellular genes. VA RNAI also interacts with other innate immune proteins, including OAS1. While intact VA RNAI has the paradoxical effect of activating OAS1, a non-natural VA RNAI construct lacking the entire Terminal Stem has been reported to be a pseudoinhibitor of OAS1. Here, we show that a VA RNAI construct corresponding to an authentic product of Dicer processing similarly fails to activate OAS1 but also retains only a modest level of inhibitory activity against PKR in contrast to the non-natural deletion construct. These findings underscore the complexity of the arms race between virus and host, and highlight the need for further exploration of the impact of VA RNAI interactions with host defenses on the outcome of AdV infection beyond that of well-established PKR inhibition. Additional contributions of VA RNAI heterogeneity resulting from variations in transcription initiation and termination to each of these functions remain open questions that are discussed here.
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Affiliation(s)
- Virginia K Vachon
- Department of Biochemistry, Emory University School of Medicine, Atlanta, GA 30322, USA; Microbiology and Molecular Genetics (MMG) Program, Graduate Division of Biological and Biomedical Sciences, Emory University School of Medicine, Atlanta, GA 30322, USA
| | - Graeme L Conn
- Department of Biochemistry, Emory University School of Medicine, Atlanta, GA 30322, USA.
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19
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Li MMH, MacDonald MR, Rice CM. To translate, or not to translate: viral and host mRNA regulation by interferon-stimulated genes. Trends Cell Biol 2015; 25:320-9. [PMID: 25748385 PMCID: PMC4441850 DOI: 10.1016/j.tcb.2015.02.001] [Citation(s) in RCA: 61] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2014] [Revised: 01/28/2015] [Accepted: 02/05/2015] [Indexed: 01/08/2023]
Abstract
Translational regulation of viral and host mRNA is an important function of a subset of interferon-stimulated genes (ISGs). These ISGs repress translation through binding to viral RNA, direct interaction with, or perturbation of the translation machinery components. Several ISGs localize to cytoplasmic granules such as stress granules (SGs) and processing bodies (PBs), and interfere with the processing or function of microRNAs (miRNAs).
Type I interferon (IFN) is one of the first lines of cellular defense against viral pathogens. As a result of IFN signaling, a wide array of IFN-stimulated gene (ISG) products is upregulated to target different stages of the viral life cycle. We review recent findings implicating a subset of ISGs in translational regulation of viral and host mRNAs. Translation inhibition is mediated either by binding to viral RNA or by disrupting physiological interactions or levels of the translation complex components. In addition, many of these ISGs localize to translationally silent cytoplasmic granules, such as stress granules and processing bodies, and intersect with the microRNA (miRNA)-mediated silencing pathway to regulate translation of cellular mRNAs.
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Affiliation(s)
- Melody M H Li
- Laboratory of Virology and Infectious Disease, The Rockefeller University, New York, NY, USA.
| | - Margaret R MacDonald
- Laboratory of Virology and Infectious Disease, The Rockefeller University, New York, NY, USA
| | - Charles M Rice
- Laboratory of Virology and Infectious Disease, The Rockefeller University, New York, NY, USA
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Abstract
My Ph.D. thesis in the laboratory of Severo Ochoa at New York University School of Medicine in 1962 included the determination of the nucleotide compositions of codons specifying amino acids. The experiments were based on the use of random copolyribonucleotides (synthesized by polynucleotide phosphorylase) as messenger RNA in a cell-free protein-synthesizing system. At Yale University, where I joined the faculty, my co-workers and I first studied the mechanisms of protein synthesis. Thereafter, we explored the interferons (IFNs), which were discovered as antiviral defense agents but were revealed to be components of a highly complex multifunctional system. We isolated pure IFNs and characterized IFN-activated genes, the proteins they encode, and their functions. We concentrated on a cluster of IFN-activated genes, the p200 cluster, which arose by repeated gene duplications and which encodes a large family of highly multifunctional proteins. For example, the murine protein p204 can be activated in numerous tissues by distinct transcription factors. It modulates cell proliferation and the differentiation of a variety of tissues by binding to many proteins. p204 also inhibits the activities of wild-type Ras proteins and Ras oncoproteins.
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Affiliation(s)
- Peter Lengyel
- From the Department of Molecular Biophysics and Biochemistry, Yale University School of Medicine, New Haven, Connecticut 06520
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21
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Murine AKAP7 has a 2',5'-phosphodiesterase domain that can complement an inactive murine coronavirus ns2 gene. mBio 2014; 5:e01312-14. [PMID: 24987090 PMCID: PMC4161237 DOI: 10.1128/mbio.01312-14] [Citation(s) in RCA: 35] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022] Open
Abstract
Viral 2′,5′-phosphodiesterases (2′,5′-PDEs) help disparate RNA viruses evade the antiviral activity of interferon (IFN) by degrading 2′,5′-oligoadenylate (2-5A) activators of RNase L. A kinase anchoring proteins (AKAPs) bind the regulatory subunits of protein kinase A (PKA) to localize and organize cyclic AMP (cAMP) signaling during diverse physiological processes. Among more than 43 AKAP isoforms, AKAP7 appears to be unique in its homology to viral 2′,5′-PDEs. Here we show that mouse AKAP7 rapidly degrades 2-5A with kinetics similar to that of murine coronavirus (mouse hepatitis virus [MHV]) strain A59 ns2 and human rotavirus strain WA VP3 proteins. To determine whether AKAP7 could substitute for a viral 2′,5′-PDE, we inserted AKAP7 cDNA into an MHV genome with an inactivated ns2 gene. The AKAP7 PDE domain or N-terminally truncated AKAP7 (both lacking a nuclear localization motif), but not full-length AKAP7 or a mutant, AKAP7H185R, PDE domain restored the infectivity of ns2 mutant MHV in bone marrow macrophages and in livers of infected mice. Interestingly, the AKAP7 PDE domain and N-terminally deleted AKAP7 were present in the cytoplasm (the site of MHV replication), whereas full-length AKAP7 was observed only in nuclei. We suggest the possibility that viral acquisition of the host AKAP7 PDE domain might have occurred during evolution, allowing diverse RNA viruses to antagonize the RNase L pathway. Early virus-host interactions determine whether an infection is established, highlighting the need to understand fundamental mechanisms regulating viral pathogenesis. Recently, our laboratories reported a novel mode of regulation of the IFN antiviral response. We showed that the coronavirus MHV accessory protein ns2 antagonizes the type I IFN response, promoting viral replication and hepatitis. ns2 confers virulence by cleaving 2′,5′-oligoadenylate (2-5A) activators of RNase L in macrophages. We also reported that the rotavirus VP3 C-terminal domain (VP3-CTD) cleaves 2-5A and that it may rescue ns2 mutant MHV. Here we report that a cellular protein, AKAP7, has an analogous 2′,5′-phosphodiesterase (2′,5′-PDE) domain that is able to restore the growth of chimeric MHV expressing inactive ns2. The proviral effect requires cytoplasmic localization of the AKAP7 PDE domain. We speculate that AKAP7 is the ancestral precursor of viral proteins, such as ns2 and VP3, that degrade 2-5A to evade the antiviral activity of RNase L.
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Boasso A. Type I Interferon at the Interface of Antiviral Immunity and Immune Regulation: The Curious Case of HIV-1. SCIENTIFICA 2013; 2013:580968. [PMID: 24455433 PMCID: PMC3885208 DOI: 10.1155/2013/580968] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/12/2013] [Accepted: 12/10/2013] [Indexed: 06/03/2023]
Abstract
Type I interferon (IFN-I) play a critical role in the innate immune response against viral infections. They actively participate in antiviral immunity by inducing molecular mechanisms of viral restriction and by limiting the spread of the infection, but they also orchestrate the initial phases of the adaptive immune response and influence the quality of T cell immunity. During infection with the human immunodeficiency virus type 1 (HIV-1), the production of and response to IFN-I may be severely altered by the lymphotropic nature of the virus. In this review I consider the different aspects of virus sensing, IFN-I production, signalling, and effects on target cells, with a particular focus on the alterations observed following HIV-1 infection.
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Affiliation(s)
- Adriano Boasso
- Immunology Section, Chelsea and Westminster Hospital, 369 Fulham Road, London SW10 9NH, UK
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Learning from the messengers: innate sensing of viruses and cytokine regulation of immunity - clues for treatments and vaccines. Viruses 2013; 5:470-527. [PMID: 23435233 PMCID: PMC3640511 DOI: 10.3390/v5020470] [Citation(s) in RCA: 37] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/28/2012] [Revised: 01/22/2013] [Accepted: 01/23/2013] [Indexed: 12/14/2022] Open
Abstract
Virus infections are a major global public health concern, and only via substantial knowledge of virus pathogenesis and antiviral immune responses can we develop and improve medical treatments, and preventive and therapeutic vaccines. Innate immunity and the shaping of efficient early immune responses are essential for control of viral infections. In order to trigger an efficient antiviral defense, the host senses the invading microbe via pattern recognition receptors (PRRs), recognizing distinct conserved pathogen-associated molecular patterns (PAMPs). The innate sensing of the invading virus results in intracellular signal transduction and subsequent production of interferons (IFNs) and proinflammatory cytokines. Cytokines, including IFNs and chemokines, are vital molecules of antiviral defense regulating cell activation, differentiation of cells, and, not least, exerting direct antiviral effects. Cytokines shape and modulate the immune response and IFNs are principle antiviral mediators initiating antiviral response through induction of antiviral proteins. In the present review, I describe and discuss the current knowledge on early virus–host interactions, focusing on early recognition of virus infection and the resulting expression of type I and type III IFNs, proinflammatory cytokines, and intracellular antiviral mediators. In addition, the review elucidates how targeted stimulation of innate sensors, such as toll-like receptors (TLRs) and intracellular RNA and DNA sensors, may be used therapeutically. Moreover, I present and discuss data showing how current antimicrobial therapies, including antibiotics and antiviral medication, may interfere with, or improve, immune response.
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Grayfer L, Andino FDJ, Chen G, Chinchar GV, Robert J. Immune evasion strategies of ranaviruses and innate immune responses to these emerging pathogens. Viruses 2012; 4:1075-92. [PMID: 22852041 PMCID: PMC3407895 DOI: 10.3390/v4071075] [Citation(s) in RCA: 47] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2012] [Revised: 06/19/2012] [Accepted: 06/20/2012] [Indexed: 12/29/2022] Open
Abstract
Ranaviruses (RV, Iridoviridae) are large double-stranded DNA viruses that infect fish, amphibians and reptiles. For ecological and commercial reasons, considerable attention has been drawn to the increasing prevalence of ranaviral infections of wild populations and in aquacultural settings. Importantly, RVs appear to be capable of crossing species barriers of numerous poikilotherms, suggesting that these pathogens possess a broad host range and potent immune evasion mechanisms. Indeed, while some of the 95–100 predicted ranavirus genes encode putative evasion proteins (e.g., vIFα, vCARD), roughly two-thirds of them do not share significant sequence identity with known viral or eukaryotic genes. Accordingly, the investigation of ranaviral virulence and immune evasion strategies is promising for elucidating potential antiviral targets. In this regard, recombination-based technologies are being employed to knock out gene candidates in the best-characterized RV member, Frog Virus (FV3). Concurrently, by using animal infection models with extensively characterized immune systems, such as the African clawed frog, Xenopus laevis, it is becoming evident that components of innate immunity are at the forefront of virus-host interactions. For example, cells of the macrophage lineage represent important combatants of RV infections while themselves serving as targets for viral infection, maintenance and possibly dissemination. This review focuses on the recent advances in the understanding of the RV immune evasion strategies with emphasis on the roles of the innate immune system in ranaviral infections.
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Affiliation(s)
- Leon Grayfer
- Department of Microbiology and Immunology, University of Rochester Medical Center, Rochester, NY 14642, USA; (L.G.); (F.D.J.A.); (G.C.)
| | - Francisco De Jesús Andino
- Department of Microbiology and Immunology, University of Rochester Medical Center, Rochester, NY 14642, USA; (L.G.); (F.D.J.A.); (G.C.)
| | - Guangchun Chen
- Department of Microbiology and Immunology, University of Rochester Medical Center, Rochester, NY 14642, USA; (L.G.); (F.D.J.A.); (G.C.)
| | - Gregory V. Chinchar
- Department of Microbiology, University of Mississippi Medical Center, Jackson, MS 39216, USA;
| | - Jacques Robert
- Department of Microbiology and Immunology, University of Rochester Medical Center, Rochester, NY 14642, USA; (L.G.); (F.D.J.A.); (G.C.)
- Author to whom correspondence should be addressed; ; Tel.: +1-585-275-1722; Fax: +1-585-473-9573
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Abstract
We look back on the discoveries that the tyrosine kinases TYK2 and JAK1 and the transcription factors STAT1, STAT2, and IRF9 are required for the cellular response to type I interferons. This initial description of the JAK-STAT pathway led quickly to additional discoveries that type II interferons and many other cytokines signal through similar mechanisms. This well-understood pathway now serves as a paradigm showing how information from protein-protein contacts at the cell surface can be conveyed directly to genes in the nucleus. We also review recent work on the STAT proteins showing the importance of several different posttranslational modifications, including serine phosphorylation, acetylation, methylation, and sumoylation. These remarkably proficient proteins also provide noncanonical functions in transcriptional regulation and they also function in mitochondrial respiration and chromatin organization in ways that may not involve transcription at all.
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Affiliation(s)
- George R. Stark
- Department of Molecular Genetics, Lerner Research Institute, Cleveland Clinic, Cleveland, OH 44195, USA
| | - James E. Darnell
- Laboratory of Molecular Cell Biology, The Rockefeller University, New York, NY 10065-6399, USA
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Differential impact of interferon regulatory factor 7 in initiation of the type I interferon response in the lymphocytic choriomeningitis virus-infected central nervous system versus the periphery. J Virol 2012; 86:7384-92. [PMID: 22514347 DOI: 10.1128/jvi.07090-11] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/27/2023] Open
Abstract
Interferon (IFN) regulatory factors (IRFs) are a family of transcription factors involved in regulating type I IFN genes and other genes participating in the early antiviral host response. To better understand the mechanisms involved in virus-induced central nervous system (CNS) inflammation, we studied the influence of IRF1, -3, -7, and -9 on the transcriptional activity of key genes encoding antiviral host factors in the CNS of mice infected with lymphocytic choriomeningitis virus (LCMV). A key finding is that neither IRF3 nor IRF7 is absolutely required for induction of a type I IFN response in the LCMV-infected CNS, whereas concurrent elimination of both factors markedly reduces the virus-induced host response. This is unlike the situation in the periphery, where deficiency of IRF7 almost eliminates the LCMV-induced production of the type I IFNs. This difference is seemingly related to the local environment, as peripheral production of type I IFNs is severely reduced in intracerebrally (i.c.) infected IRF7-deficient mice, which undergo a combined infection of the CNS and peripheral organs, such as spleen and lymph nodes. Interestingly, despite the redundancy of IRF7 in initiating the type I IFN response in the CNS, the response is not abolished in IFN-β-deficient mice, as might have been expected. Collectively, these data demonstrate that the early type I IFN response to LCMV infection in the CNS is controlled by a concerted action of IRF3 and -7. Consequently this work provides strong evidence for differential regulation of the type I IFN response in the CNS versus the periphery during viral infection.
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Poulsen JB, Andersen KR, Kjær KH, Durand F, Faou P, Vestergaard AL, Talbo GH, Hoogenraad N, Brodersen DE, Justesen J, Martensen PM. Human 2'-phosphodiesterase localizes to the mitochondrial matrix with a putative function in mitochondrial RNA turnover. Nucleic Acids Res 2011; 39:3754-70. [PMID: 21245038 PMCID: PMC3089451 DOI: 10.1093/nar/gkq1282] [Citation(s) in RCA: 37] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
The vertebrate 2-5A system is part of the innate immune system and central to cellular antiviral defense. Upon activation by viral double-stranded RNA, 5'-triphosphorylated, 2'-5'-linked oligoadenylate polyribonucleotides (2-5As) are synthesized by one of several 2'-5'-oligoadenylate synthetases. These unusual oligonucleotides activate RNase L, an unspecific endoribonuclease that mediates viral and cellular RNA breakdown. Subsequently, the 2-5As are removed by a 2'-phosphodiesterase (2'-PDE), an enzyme that apart from breaking 2'-5' bonds also degrades regular, 3'-5'-linked oligoadenylates. Interestingly, 2'-PDE shares both functionally and structurally characteristics with the CCR4-type exonuclease-endonuclease-phosphatase family of deadenylases. Here we show that 2'-PDE locates to the mitochondrial matrix of human cells, and comprise an active 3'-5' exoribonuclease exhibiting a preference for oligo-adenosine RNA like canonical cytoplasmic deadenylases. Furthermore, we document a marked negative association between 2'-PDE and mitochondrial mRNA levels following siRNA-directed knockdown and plasmid-mediated overexpression, respectively. The results indicate that 2'-PDE, apart from playing a role in the cellular immune system, may also function in mitochondrial RNA turnover.
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Kristiansen H, Gad HH, Eskildsen-Larsen S, Despres P, Hartmann R. The oligoadenylate synthetase family: an ancient protein family with multiple antiviral activities. J Interferon Cytokine Res 2010; 31:41-7. [PMID: 21142819 DOI: 10.1089/jir.2010.0107] [Citation(s) in RCA: 221] [Impact Index Per Article: 15.8] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
The 2'-5' oligoadenylate synthetases (OAS) are interferon-induced antiviral enzymes that recognize virally produced dsRNA and initiate RNA destabilization through activation of RNase L within infected cells. However, recent evidence points toward several RNase L-independent pathways, through which members of the OAS family can exert antiviral activity. The crystal structure of OAS led to a novel insight into the catalytic mechanism, and revealed a remarkable similarity between OAS, Polyadenosine polymerase, and the class I CCA-adding enzyme from Archeoglobus fulgidus. This, combined with a variety of bioinformatic data, leads to the definition of a superfamily of template independent polymerases and proved that the OAS family are ancient proteins, which probably arose as early as the beginning of metazoan evolution.
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Affiliation(s)
- Helle Kristiansen
- Centre for Structural Biology, Department of Molecular Biology, Aarhus University, Aarhus, Denmark
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29
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Rios JJ, Fleming JGW, Bryant UK, Carter CN, Huber JC, Long MT, Spencer TE, Adelson DL. OAS1 polymorphisms are associated with susceptibility to West Nile encephalitis in horses. PLoS One 2010; 5:e10537. [PMID: 20479874 PMCID: PMC2866329 DOI: 10.1371/journal.pone.0010537] [Citation(s) in RCA: 41] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2009] [Accepted: 04/18/2010] [Indexed: 12/13/2022] Open
Abstract
West Nile virus, first identified within the United States in 1999, has since spread across the continental states and infected birds, humans and domestic animals, resulting in numerous deaths. Previous studies in mice identified the Oas1b gene, a member of the OAS/RNASEL innate immune system, as a determining factor for resistance to West Nile virus (WNV) infection. A recent case-control association study described mutations of human OAS1 associated with clinical susceptibility to WNV infection. Similar studies in horses, a particularly susceptible species, have been lacking, in part, because of the difficulty in collecting populations sufficiently homogenous in their infection and disease states. The equine OAS gene cluster most closely resembles the human cluster, with single copies of OAS1, OAS3 and OAS2 in the same orientation. With naturally occurring susceptible and resistant sub-populations to lethal West Nile encephalitis, we undertook a case-control association study to investigate whether, similar to humans (OAS1) and mice (Oas1b), equine OAS1 plays a role in resistance to severe WNV infection. We identified naturally occurring single nucleotide mutations in equine (Equus caballus) OAS1 and RNASEL genes and, using Fisher's Exact test, we provide evidence that mutations in equine OAS1 contribute to host susceptibility. Virtually all of the associated OAS1 polymorphisms were located within the interferon-inducible promoter, suggesting that differences in OAS1 gene expression may determine the host's ability to resist clinical manifestations associated with WNV infection.
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Affiliation(s)
- Jonathan J. Rios
- McDermott Center for Human Growth and Development, University of Texas Southwestern Medical Center, Dallas, Texas, United States of America
| | - JoAnn G. W. Fleming
- Department of Animal Science, Texas A&M University, College Station, Texas, United States of America
| | - Uneeda K. Bryant
- Livestock Disease Diagnostic Center, University of Kentucky, Lexington, Kentucky, United States of America
| | - Craig N. Carter
- Livestock Disease Diagnostic Center, University of Kentucky, Lexington, Kentucky, United States of America
| | - John C. Huber
- School of Rural Public Health, Texas A&M University, College Station, Texas, United States of America
| | - Maureen T. Long
- College of Veterinary Medicine, University of Florida, Gainesville, Florida, United States of America
| | - Thomas E. Spencer
- Department of Animal Science, Texas A&M University, College Station, Texas, United States of America
| | - David L. Adelson
- School of Molecular and Biomedical Science, The University of Adelaide, Adelaide, South Australia, Australia
- * E-mail:
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30
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Yoon CH, Miah MA, Kim KP, Bae YS. New Cdc2 Tyr 4 phosphorylation by dsRNA-activated protein kinase triggers Cdc2 polyubiquitination and G2 arrest under genotoxic stresses. EMBO Rep 2010; 11:393-9. [PMID: 20395957 DOI: 10.1038/embor.2010.45] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2009] [Revised: 03/03/2010] [Accepted: 03/04/2010] [Indexed: 02/03/2023] Open
Abstract
Cell division cycle 2 (Cdc2) protein is an essential subunit of M-phase kinase (MPK), which has a key role in G2/M transition. Even though the control of MPK activity has been well established with regard to the phosphorylation of Cdc2 at Thr 14 and/or Tyr 15 and Thr 161, little is known about the proteolytic control of Cdc2. In this study, we observed that Cdc2 was downregulated under genotoxic stresses and that double-stranded RNA-activated protein kinase (PKR) was involved in the process. The PKR-mediated Tyr4 phosphorylation triggered Cdc2 ubiquitination. Phospho-mimic mutations at the Tyr 4 residue (Y4D or Y4E) caused significant ubiquitination of Cdc2 even in the absence of PKR. Our findings demonstrate that (i) PKR, Ser/Thr kinase, phosphorylates its new substrate Cdc2 at the Tyr 4 residue, (ii) PKR-mediated Tyr 4-phosphorylation facilitates Cdc2 ubiquitination and proteosomal degradation, (iii) unphosphorylated Tyr 4 prevents Cdc2 ubiquitination, and (iv) downstream from p53, PKR has a crucial role in G2 arrest and triggers Cdc2 downregulation under genotoxic conditions.
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Affiliation(s)
- Cheol-Hee Yoon
- Department of Biological Sciences, Sungkyunkwan University, Suwon, Gyeonggi-Do, South Korea
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31
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APOBEC3 proteins mediate the clearance of foreign DNA from human cells. Nat Struct Mol Biol 2010; 17:222-9. [PMID: 20062055 PMCID: PMC2921484 DOI: 10.1038/nsmb.1744] [Citation(s) in RCA: 263] [Impact Index Per Article: 18.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2009] [Accepted: 11/09/2009] [Indexed: 12/11/2022]
Abstract
Bacteria evolved restriction endonucleases to prevent interspecies DNA transmission and bacteriophage infection. Here, we show that human cells possess an analogous mechanism. APOBEC3A is induced by interferon following DNA detection, and it deaminates foreign double-stranded DNA cytidines to uridines. These atypical DNA nucleosides are converted by the uracil DNA glycosylase UNG2 to abasic lesions, which lead to foreign DNA degradation. This mechanism is evident in cell lines and primary monocytes, where up to 97% of cytidines in foreign DNA are deaminated. In contrast, cellular genomic DNA appears unaffected. Several other APOBEC3s also restrict foreign gene transfer. Related proteins exist in all vertebrates, indicating that foreign DNA restriction may be a conserved innate immune defense mechanism. The efficiency and fidelity of genetic engineering, gene therapy, and DNA vaccination are likely to be influenced by this anti-DNA defense system.
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Abstract
Since the discovery of interferons (IFNs), considerable progress has been made in describing the nature of the cytokines themselves, the signalling components that direct the cell response and their antiviral activities. Gene targeting studies have distinguished four main effector pathways of the IFN-mediated antiviral response: the Mx GTPase pathway, the 2',5'-oligoadenylate-synthetase-directed ribonuclease L pathway, the protein kinase R pathway and the ISG15 ubiquitin-like pathway. As discussed in this Review, these effector pathways individually block viral transcription, degrade viral RNA, inhibit translation and modify protein function to control all steps of viral replication. Ongoing research continues to expose additional activities for these effector proteins and has revealed unanticipated functions of the antiviral response.
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Affiliation(s)
- Anthony J. Sadler
- Monash Institute of Medical Research, Monash University, Clayton, 3168 Victoria Australia
| | - Bryan R. G. Williams
- Monash Institute of Medical Research, Monash University, Clayton, 3168 Victoria Australia
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Lengyel P. From RNase L to the Multitalented p200 Family Proteins: An Exploration of the Modes of Interferon Action. J Interferon Cytokine Res 2008; 28:273-81. [DOI: 10.1089/jir.2008.3993.hp] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022] Open
Affiliation(s)
- Peter Lengyel
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT 06520
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Rios JJ, Perelygin AA, Long MT, Lear TL, Zharkikh AA, Brinton MA, Adelson DL. Characterization of the equine 2'-5' oligoadenylate synthetase 1 (OAS1) and ribonuclease L (RNASEL) innate immunity genes. BMC Genomics 2007; 8:313. [PMID: 17822564 PMCID: PMC2048516 DOI: 10.1186/1471-2164-8-313] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2007] [Accepted: 09/07/2007] [Indexed: 11/13/2022] Open
Abstract
Background The mammalian OAS/RNASEL pathway plays an important role in antiviral host defense. A premature stop-codon within the murine Oas1b gene results in the increased susceptibility of mice to a number of flaviviruses, including West Nile virus (WNV). Mutations in either the OAS1 or RNASEL genes may also modulate the outcome of WNV-induced disease or other viral infections in horses. Polymorphisms in the human OAS gene cluster have been previously utilized for case-control analysis of virus-induced disease in humans. No polymorphisms have yet been identified in either the equine OAS1 or RNASEL genes for use in similar case-control studies. Results Genomic sequence for equine OAS1 was obtained from a contig assembly generated from a shotgun subclone library of CHORI-241 BAC 100I10. Specific amplification of regions of the OAS1 gene from 13 horses of various breeds identified 33 single nucleotide polymorphisms (SNP) and two microsatellites. RNASEL cDNA sequences were determined for 8 mammals and utilized in a phylogenetic analysis. The chromosomal location of the RNASEL gene was assigned by FISH to ECA5p17-p16 using two selected CHORI-241 BAC clones. The horse genomic RNASEL sequence was assembled. Specific amplification of regions of the RNASEL gene from 13 horses identified 31 SNPs. Conclusion In this report, two dinucleotide microsatellites and 64 single nucleotide polymorphisms within the equine OAS1 and RNASEL genes were identified. These polymorphisms are the first to be reported for these genes and will facilitate future case-control studies of horse susceptibility to infectious diseases.
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Affiliation(s)
- Jonathan J Rios
- Department of Animal Science, Texas A&M University, 2471 TAMU, College Station, Texas 77843, USA
| | - Andrey A Perelygin
- Biology Department, Georgia State University, 24 Peachtree Center Ave., Atlanta, Georgia 30302, USA
| | - Maureen T Long
- College of Veterinary Medicine, University of Florida, 2015 SW 16th Ave., Gainesville, Florida 32608, USA
| | - Teri L Lear
- Department of Veterinary Science, University of Kentucky, 108 Maxwell H. Gluck Equine Research Center, Lexington, Kentucky, 40546, USA
| | - Andrey A Zharkikh
- Bioinformatics Department, Myriad Genetics, Inc., 320 Wakara Way, Salt Lake City, UT, 84108, USA
| | - Margo A Brinton
- Biology Department, Georgia State University, 24 Peachtree Center Ave., Atlanta, Georgia 30302, USA
| | - David L Adelson
- School of Molecular and Biomedical Science, University of Adelaide, SA 5005, Australia
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Hovanessian AG. On the discovery of interferon-inducible, double-stranded RNA activated enzymes: the 2'-5'oligoadenylate synthetases and the protein kinase PKR. Cytokine Growth Factor Rev 2007; 18:351-61. [PMID: 17681872 DOI: 10.1016/j.cytogfr.2007.06.003] [Citation(s) in RCA: 97] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
Abstract
The demonstration that double-stranded (ds) RNA inhibits protein synthesis in cell-free systems prepared from interferon-treated cells, lead to the discovery of the two interferon-induced, dsRNA-dependent enzymes: the serine/threonine protein kinase that is referred to as PKR and the 2',5'-oligoadenylate synthetase (2',5'-OAS), which converts ATP to 2',5'-linked oligoadenylates with the unusual 2'-5' instead of 3'-5' phosphodiesterase bond. We raised monoclonal and polyclonal antibodies against human PKR and the two larger forms of the 2',5'-OAS. Such specific antibodies proved to be indispensable for the detailed characterization of these enzyme and the cloning of cDNAs corresponding to the human PKR and the 69-71 and 100 kDa forms of the 2',5'-OAS. When activated by dsRNA, PKR becomes autophosphorylated and catalyzes phosphorylation of the protein synthesis initiation factor eIF2, whereas the 2'-5'OAS forms 2',5'-oligoadenylates that activate the latent endoribonuclease, the RNAse L. By inhibiting initiation of protein synthesis or by degrading RNA, these enzymes play key roles in two independent pathways that regulate overall protein synthesis and the mechanism of the antiviral action of interferon. In addition, these enzymes are now shown to regulate other cellular events, such as gene induction, normal control of cell growth, differentiation and apoptosis.
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Affiliation(s)
- Ara G Hovanessian
- UPR 2228 CNRS, UFR Biomédicale - Université René Descartes, 45 rue des Saints Pères, 75270 Paris Cedex 06, France.
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Bisbal C, Silverman RH. Diverse functions of RNase L and implications in pathology. Biochimie 2007; 89:789-98. [PMID: 17400356 PMCID: PMC2706398 DOI: 10.1016/j.biochi.2007.02.006] [Citation(s) in RCA: 73] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2006] [Accepted: 02/06/2007] [Indexed: 01/16/2023]
Abstract
The endoribonuclease L (RNase L) is the effector of the 2-5A system, a major enzymatic pathway involved in the molecular mechanism of interferons (IFNs). RNase L is a very unusual nuclease with a complex mechanism of regulation. It is a latent enzyme, expressed in nearly every mammalian cell type. Its activation requires its binding to a small oligonucleotide, 2-5A. 2-5A is a series of unique 5'-triphosphorylated oligoadenylates with 2'-5' phosphodiester bonds. By regulating viral and cellular RNA expression, RNase L plays an important role in the antiviral and antiproliferative activities of IFN and contributes to innate immunity and cell metabolism. The 2-5A/RNase L pathway is implicated in mediating apoptosis in response to viral infections and to several types of external stimuli. Several recent studies have suggested that RNase L could have a role in cancer biology and evidence of a tumor suppressor function of RNase L has emerged from studies on the genetics of hereditary prostate cancer.
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Affiliation(s)
- Catherine Bisbal
- IGH UPR CNRS 1142. 141 rue de la Cardonille. 34396. Montpellier France. E-mail address: , Phone: 33 (0)4 99 61 99 73, Fax: 33 (0)4 99 61 99 01
| | - Robert H. Silverman
- Department of Cancer Biology, Lerner Research Institute, 9500 Euclid Avenue NB40, Cleveland Clinic, Cleveland OH 44195 USA, E-mail address: , Phone: (1) 216 445 9650, Fax: (1) 216 445 6269
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37
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Hovanessian AG, Justesen J. The human 2'-5'oligoadenylate synthetase family: unique interferon-inducible enzymes catalyzing 2'-5' instead of 3'-5' phosphodiester bond formation. Biochimie 2007; 89:779-88. [PMID: 17408844 DOI: 10.1016/j.biochi.2007.02.003] [Citation(s) in RCA: 137] [Impact Index Per Article: 8.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2006] [Accepted: 02/06/2007] [Indexed: 01/13/2023]
Abstract
The demonstration by Kerr and colleagues that double-stranded (ds) RNA inhibits drastically protein synthesis in cell-free systems prepared from interferon-treated cells, suggested the existence of an interferon-induced enzyme, which is dependent on dsRNA. Consequently, two distinct dsRNA-dependent enzymes were discovered: a serine/threonine protein kinase that nowadays is referred to as PKR and a 2'-5'oligoadenylate synthetase (2'-5'OAS) that polymerizes ATP to 2'-5'-linked oligomers of adenosine with the general formula pppA(2'p5'A)(n), n>or=1. The product is pppG2'p5'G when GTP is used as a substrate. Three distinct forms of 2'-5'OAS exist in human cells, small, medium, and large, which contain one, two, and three OAS units, respectively, and are encoded by distinct genes clustered on the 2'-5'OAS locus on human chromosome 12. OASL is an OAS like IFN-induced protein encoded by a gene located about 8 Mb telomeric from the 2'-5'OAS locus. OASL is composed of one OAS unit fused at its C-terminus with two ubiquitin-like repeats. The human OASL is devoid of the typical 2'-5'OAS catalytic activity. In addition to these structural differences between the various OAS proteins, the three forms of 2'-5'OAS are characterized by different subcellular locations and enzymatic parameters. These findings illustrate the apparent structural and functional complexity of the human 2'-5'OAS family, and suggest that these proteins may have distinct roles in the cell.
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Affiliation(s)
- Ara G Hovanessian
- UPR 2228 CNRS, UFR Biomédicale, Université René Descartes, 45 rue des Saints Pères, 75270 Paris Cedex 06, France.
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38
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Abstract
This historical account covers 50 years of seminal research work on interferon done since its discovery in 1957. Topics related to molecular structure, production and action of interferons are considered from the viewpoint of how our insights have expanded and deepened within the context of evolving tools and general knowledge in cellular and molecular biology. Lines of thought that linked each discovery to the next are expounded.
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Affiliation(s)
- Alfons Billiau
- Rega Institute, University of Leuven, Minderbroedersstraat 10, 3000 Leuven, Belgium.
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39
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Charubala R, Uhlmann E, Pfleiderer W. Nucleotide, XVI. Synthese und Eigenschaften von Adenylyl-adenylyl-adenosinen. ACTA ACUST UNITED AC 2006. [DOI: 10.1002/jlac.198119811223] [Citation(s) in RCA: 16] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
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40
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Kubota K, Nakahara K, Ohtsuka T, Yoshida S, Kawaguchi J, Fujita Y, Ozeki Y, Hara A, Yoshimura C, Furukawa H, Haruyama H, Ichikawa K, Yamashita M, Matsuoka T, Iijima Y. Identification of 2'-phosphodiesterase, which plays a role in the 2-5A system regulated by interferon. J Biol Chem 2004; 279:37832-41. [PMID: 15231837 DOI: 10.1074/jbc.m400089200] [Citation(s) in RCA: 64] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
The 2-5A system is one of the major pathways for antiviral and antitumor functions that can be induced by interferons (IFNs). The 2-5A system is modulated by 5'-triphosphorylated, 2',5'-phosphodiester-linked oligoadenylates (2-5A), which are synthesized by 2',5'-oligoadenylate synthetases (2',5'-OASs), inactivated by 5'-phosphatase and completely degraded by 2'-phosphodiesterase (2'-PDE). Generated 2-5A activates 2-5A-dependent endoribonuclease, RNase L, which induces RNA degradation in cells and finally apoptosis. Although 2',5'-OASs and RNase L have been molecularly cloned and studied well, the identification of 2'-PDE has remained elusive. Here, we describe the first identification of 2'-PDE, the third key enzyme of the 2-5A system. We found a putative 2'-PDE band on SDS-PAGE by successive six-step chromatographies from ammonium sulfate precipitates of bovine liver and identified a partial amino acid sequence of the human 2'-PDE by mass spectrometry. Based on the full-length sequence of the human 2'-PDE obtained by in silico expressed sequence tag assembly, the gene was cloned by reverse transcription-PCR. The recombinant human 2'-PDE expressed in mammalian cells certainly cleaved the 2',5'-phosphodiester bond of 2-5A trimer and 2-5A analogs. Because no sequences with high homology to this human 2'-PDE were found, the human 2'-PDE was considered to be a unique enzyme without isoform. Suppression of 2'-PDE by a small interfering RNA and a 2'-PDE inhibitor resulted in significant reduction of viral replication, whereas overexpression of 2'-PDE protected cells from IFN-induced antiproliferative activity. These observations identify 2'-PDE as a key regulator of the 2-5A system and as a potential novel target for antiviral and antitumor treatments.
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Affiliation(s)
- Kazuishi Kubota
- Biomedical Research Laboratories, Sankyo Co., Ltd., 1-2-58, Hiromachi, Shinagawa-ku, Tokyo 140-8710, Japan.
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41
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Ikuta K, Yamada T, Shimomura T, Kuratsune H, Kawahara R, Ikawa S, Ohnishi E, Sokawa Y, Fukushi H, Hirai K, Watanabe Y, Kurata T, Kitani T, Sairenji T. Diagnostic evaluation of 2′, 5′-oligoadenylate synthetase activities and antibodies against Epstein–Barr virus and Coxiella burnetii in patients with chronic fatigue syndrome in Japan. Microbes Infect 2003; 5:1096-102. [PMID: 14554250 DOI: 10.1016/j.micinf.2003.07.002] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/27/2022]
Abstract
To investigate the association of viral infections with chronic fatigue syndrome (CFS), we assayed 2', 5'-oligoadenylate synthetase (2-5AS) activities in peripheral blood mononuclear cells from CFS patients in Japan. These patients were diagnosed in two hospitals, H1 and H2, located in different areas of the country. The activities were detected in 19 (86%) and 7 (32%) of each of the 22 patients in H1 and H2, respectively, while they were detected in only four (11%) out of the 38 healthy controls. IFN-alpha was similarly detected in a few CFS patients and healthy controls. We also assayed the antibody titers against Epstein-Barr virus (EBV) and Coxiella burnetii in these patients. The EBV anti-EA-IgG antibodies were detected in two (9%) and seven (32%) of each of the 22 patients in H1 and H2, respectively. Anti-C. burnetii IgG antibodies were detected in six (27%) out of 22 patients in H1 but not in 22 patients in H2, while they were detected in one (11%) of the nine healthy controls. Some CFS patients may be associated with EBV or C. burnetii infection. There were some statistical correlations between the 2-5AS activities and antibody titers of EA-IgG (P < 0.05, Student's t-test) but not to the antibody titers of C. burnetii. The up-regulation of 2-5AS activities suggests immunological dysfunctions with some virus infections in the CFS patients. Our results indicate that 2-5AS activities are useful for a diagnostic marker of CFS and for exploring the complicated pathogenesis of CFS.
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Affiliation(s)
- Kazufumi Ikuta
- Division of Biosignaling, Department of Biomedical Sciences, Faculty of Medicine, School of Life Science, Tottori University, Yonago 683-8503, Japan
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42
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Lopp A, Kuusksalu A, Reintamm T, Müller WEG, Kelve M. 2',5'-oligoadenylate synthetase from a lower invertebrate, the marine sponge Geodia cydonium, does not need dsRNA for its enzymatic activity. BIOCHIMICA ET BIOPHYSICA ACTA 2002; 1590:140-9. [PMID: 12063177 DOI: 10.1016/s0167-4889(02)00207-0] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/19/2022]
Abstract
Recently, the presence of 2',5'-linked oligoadenylates and a high 2',5'-oligoadenylate synthetase activity were discovered in a lower invertebrate, the marine sponge Geodia cydonium. It has been demonstrated that mammalian 2-5A synthetase isozymes require a dsRNA cofactor for their enzymatic activity. Our results show that, unlike mammalian 2-5A synthetases, the 2-5A synthetase from the sponge acts in a dsRNA-independent manner in vitro. A prolonged incubation of the G. cydonium extract with a high concentration of a micrococcal nuclease had no effect on the activity of the 2-5A synthetase. At the same time, the micrococcal nuclease was effective within 30 min in degrading dsRNA needed for the enzymatic activity in IFN-induced PC12 cells. These results indicate that the 2-5A synthetase from G. cydonium may be active per se or is activated by some other mechanism. The sponge enzyme is capable of synthesizing a series of 2-5A oligomers ranging from dimers to octamers. The accumulation of a dimer in the predominant proportion during the first stage of the reaction was observed, followed by a gradual increase in longer oligoadenylates. By its product profile and kinetics of formation, the sponge 2-5A synthetase behaves like a specific isoform of enzymes of the 2-5A synthetase family.
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Affiliation(s)
- Annika Lopp
- Laboratory of Molecular Genetics, National Institute of Chemical Physics and Biophysics, Akadeemia tee 23, 12618, Tallinn, Estonia
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43
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Dagon Y, Dovrat S, Vilchik S, Hacohen D, Shlomo G, Sredni B, Salzberg S, Nir U. Double-stranded RNA-dependent protein kinase, PKR, down-regulates CDC2/cyclin B1 and induces apoptosis in non-transformed but not in v-mos transformed cells. Oncogene 2001; 20:8045-56. [PMID: 11781817 DOI: 10.1038/sj.onc.1204945] [Citation(s) in RCA: 20] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2001] [Revised: 08/28/2001] [Accepted: 09/04/2001] [Indexed: 01/19/2023]
Abstract
The interferon (IFN)-induced, double stranded RNA (dsRNA)-activated serine/threonine kinase, PKR, is a potent negative regulator of cell growth when overexpressed in yeast or mammalian cells. Paradoxically, while it can function as a tumor suppressor and inducer of apoptosis, it is overexpressed in a variety of human cancers. To resolve this enigma, we established cell-lines that overexpress PKR in non-transformed and in v-mos transformed CHO cells. Overexpression of PKR suppressed the proliferation of CHO cells by inducing a transient G0/G1 arrest, followed by a delayed G2/M arrest, which attenuated cell cycle progression. These effects were accompanied by early induction of p21/WAF-1 and delayed downregulation of CDC2 and cyclin B1. Induction of proapoptotic activity of the ectopic PKR paralleled the onset of G2/M arrest in CHO cells. However, while transiently inducing p21/WAF-1, PKR did not impose G2/M arrest or apoptosis in v-mos-transformed cells, nor was CDC2 or cyclin B1 down-regulated in those cells. These findings link the proapoptotic activity of PKR to the arrest of cell cycle at the G2/M phase. Consequently, the apoptotic activity of PKR could be counter-acted by an oncogene-like v-mos that overrides the G2/M arrest induced by PKR.
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Affiliation(s)
- Y Dagon
- Faculty of Life Sciences, Bar-Ilan University, Ramat-Gan 52900, Israel
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44
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Yamamoto N, Takizawa T, Iwanaga Y, Shimizu N, Yamamoto N. Malignant transformation of B lymphoma cell line BJAB by Epstein-Barr virus-encoded small RNAs. FEBS Lett 2000; 484:153-8. [PMID: 11068051 DOI: 10.1016/s0014-5793(00)02145-1] [Citation(s) in RCA: 67] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Abstract
EBV-encoded small RNAs (EBERs) are non-polyadenylated and abundantly transcribed RNAs, whose functions have not yet been fully elucidated. Here, we report that the EBV-negative B lymphoma cell line, BJAB, was rendered more malignant and resistant to apoptosis by EBERs. EBER-transfected cells exhibited enhanced growth potential in SCID mice as well as in soft agar, and showed resistance to apoptotic stimuli in comparison with the vector control. EBERs inhibited the activity of the double-stranded RNA-dependent protein kinase, PKR, which is reputed to act as a tumor-suppressor. These results suggest that EBERs play an important role in the pathogenesis of EBV-associated malignancies through the inhibition of PKR.
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Affiliation(s)
- N Yamamoto
- Department of Microbiology and Molecular Virology, School of Medicine, Tokyo Medical and Dental University, Tokyo, Japan
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45
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Bandyopadhyay SK, de La Motte CA, Williams BR. Induction of E-selectin expression by double-stranded RNA and TNF-alpha is attenuated in murine aortic endothelial cells derived from double-stranded RNA-activated kinase (PKR)-null mice. JOURNAL OF IMMUNOLOGY (BALTIMORE, MD. : 1950) 2000; 164:2077-83. [PMID: 10657661 DOI: 10.4049/jimmunol.164.4.2077] [Citation(s) in RCA: 21] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
Abstract
The adherence of leukocytes on the endothelium is mediated in part by the transient expression of the E-selectin adhesion molecule. Because we have previously shown that the dsRNA-activated kinase PKR mediates dsRNA induction of NF-kappaB, we used murine aortic endothelial (MuAE) cells isolated from wild-type and PKR-null mice to investigate the role of PKR in the induction of E-selectin expression by dsRNA (pIC) and TNF-alpha. E-selectin mRNA and protein expression was inducible by both pIC and TNF-alpha in wild-type MuAE cells, whereas induction of E-selectin expression by these agents was defective in PKR-null MuAE cells. Induction of E-selectin promoter activity and NF-kappaB DNA binding activity were substantially reduced in pIC- or TNF-alpha-treated PKR-null cells, indicating a role for PKR in both pIC and TNF-alpha induction of E-selectin via an NF-kappaB-dependent pathway. In PKR-null cells, pIC-mediated degradation of IkappaBbeta is deficient. Activation of this pathway requires the PKR-dependent degradation of the IkappaBbeta protein. Moreover, both phosphorylated and unphosphorylated activating transcription factor 2 DNA-binding activities were reduced in PKR-null aortic endothelial cells. These results indicate that the PKR is required for full activation of E-selectin expression by pIC and TNF-alpha in primary mouse aortic endothelial cells identifying activating transcription factor 2 as a new target for PKR-dependent regulation and suggest a role for PKR in leukocyte adhesion.
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MESH Headings
- Animals
- Aorta
- Cells, Cultured
- Cyclic AMP Response Element-Binding Protein/antagonists & inhibitors
- Cyclic AMP Response Element-Binding Protein/genetics
- Cyclic AMP Response Element-Binding Protein/metabolism
- E-Selectin/biosynthesis
- E-Selectin/genetics
- E-Selectin/metabolism
- Endothelium, Vascular/cytology
- Endothelium, Vascular/enzymology
- Endothelium, Vascular/metabolism
- Enzyme Activation/immunology
- Enzyme Induction/drug effects
- Enzyme Induction/genetics
- Enzyme Induction/immunology
- Gene Expression Regulation/drug effects
- Gene Expression Regulation/immunology
- Luciferases/biosynthesis
- Luciferases/genetics
- Macromolecular Substances
- Mice
- Mice, Knockout
- Promoter Regions, Genetic/drug effects
- Promoter Regions, Genetic/immunology
- Protein Binding/drug effects
- Protein Binding/immunology
- RNA, Double-Stranded/pharmacology
- RNA, Messenger/antagonists & inhibitors
- RNA, Messenger/biosynthesis
- Tumor Necrosis Factor-alpha/pharmacology
- eIF-2 Kinase/deficiency
- eIF-2 Kinase/genetics
- eIF-2 Kinase/physiology
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Affiliation(s)
- S K Bandyopadhyay
- Department of Cancer Biology, Lerner Research Institute, Cleveland Clinic Foundation, Cleveland, OH 44195, USA.
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46
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Zamanian-Daryoush M, Mogensen TH, DiDonato JA, Williams BR. NF-kappaB activation by double-stranded-RNA-activated protein kinase (PKR) is mediated through NF-kappaB-inducing kinase and IkappaB kinase. Mol Cell Biol 2000; 20:1278-90. [PMID: 10648614 PMCID: PMC85265 DOI: 10.1128/mcb.20.4.1278-1290.2000] [Citation(s) in RCA: 288] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/1999] [Accepted: 11/18/1999] [Indexed: 11/20/2022] Open
Abstract
The interferon (IFN)-inducible double-stranded-RNA (dsRNA)-activated serine-threonine protein kinase (PKR) is a major mediator of the antiviral and antiproliferative activities of IFNs. PKR has been implicated in different stress-induced signaling pathways including dsRNA signaling to nuclear factor kappa B (NF-kappaB). The mechanism by which PKR mediates activation of NF-kappaB is unknown. Here we show that in response to poly(rI). poly(rC) (pIC), PKR activates IkappaB kinase (IKK), leading to the degradation of the inhibitors IkappaBalpha and IkappaBbeta and the concomitant release of NF-kappaB. The results of kinetic studies revealed that pIC induced a slow and prolonged activation of IKK, which was preceded by PKR activation. In PKR null cell lines, pIC failed to stimulate IKK activity compared to cells from an isogenic background wild type for PKR in accord with the inability of PKR null cells to induce NF-kappaB in response to pIC. Moreover, PKR was required to establish a sustained response to tumor necrosis factor alpha (TNF-alpha) and to potentiate activation of NF-kappaB by cotreatment with TNF-alpha and IFN-gamma. By coimmunoprecipitation, PKR was shown to be physically associated with the IKK complex. Transient expression of a dominant negative mutant of IKKbeta or the NF-kappaB-inducing kinase (NIK) inhibited pIC-induced gene expression from an NF-kappaB-dependent reporter construct. Taken together, these results demonstrate that PKR-dependent dsRNA induction of NF-kappaB is mediated by NIK and IKK activation.
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Affiliation(s)
- M Zamanian-Daryoush
- Department of Cancer Biology, The Lerner Research Institute, The Cleveland Clinic Foundation, Cleveland, Ohio 44195, USA
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47
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Rebouillat D, Hovanessian AG. The human 2',5'-oligoadenylate synthetase family: interferon-induced proteins with unique enzymatic properties. J Interferon Cytokine Res 1999; 19:295-308. [PMID: 10334380 DOI: 10.1089/107999099313992] [Citation(s) in RCA: 179] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/13/2023] Open
Abstract
2',5'-Oligoadenylate synthetase (2',5'-OAS) was discovered and characterized as an interferon (IFN)-induced enzyme that in the presence of double-stranded (ds) RNA converts ATP into 2',5'-linked oligomers of adenosine with the general formula pppA(2'p'A)n, n > or = 1. The product is pppG2'p5'G when GTP is used as a substrate. Now, 20 years later, this activity is attributed to several well-characterized, homologous, and IFN-induced proteins in human cells. Three distinct forms of 2',5'-OAS exist, small, medium, and large, which contain 1, 2, and 3 OAS units, respectively, and are encoded by distinct genes clustered on the 2',5'-OAS locus on human chromosome 12. Recently, other IFN-induced proteins homologous to the OAS unit but devoid of the typical 2',5'-OAS catalytic activity have been described. These OAS-related proteins are encoded by a gene located at the proximity of the 2',5'-OAS locus. These findings illustrate the apparent structural and functional complexity of the human 2',5'-OAS family.
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Affiliation(s)
- D Rebouillat
- Institut Pasteur, Unité de Virologie et Immunologie Cellulaire, URA CNRS 1930, Paris, France
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48
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Zamanian-Daryoush M, Der SD, Williams BR. Cell cycle regulation of the double stranded RNA activated protein kinase, PKR. Oncogene 1999; 18:315-26. [PMID: 9927188 DOI: 10.1038/sj.onc.1202293] [Citation(s) in RCA: 55] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/17/2023]
Abstract
The interferon (IFN)-induced, double stranded RNA (dsRNA)-activated serine/threonine kinase, PKR, is a potent negative regulator of cell growth when overexpressed in yeast or mammalian cells. To determine whether endogenous PKR plays a role in cell growth control, we have investigated the regulation of PKR levels and activity during the cell cycle in human glioblastoma T98G cells. The steady-state level of PKR mRNA in T98G cells was highest in growth arrested cells, dropped sharply within 3 h of serum stimulation then gradually increased as cells progressed through G1, reaching a plateau in early S phase. PKR protein level increased following serum stimulation reaching a peak at the G2+M boundary and declining thereafter. In contrast, PKR kinase activity exhibited two peaks, in early G1 and at the G1/S boundary, declining sharply in early S phase. Thus, the activity profile did not follow the protein profile indicating a tight regulation of PKR at the level of activity. In T98G cells expressing the catalytically inactive PKRK296R the dsRNA-induced activation of NF-kappaB and IRF-1 was suppressed and the mutant cells exhibited resistance to stress induced apoptosis. Cell cycle distribution analysis showed that the mutant expressing cells exhibited longer G1 phase and fewer cells engaged in S phase. Furthermore, early passage mouse embryo fibroblasts derived from PKR knockout mice grew more slowly compared with the control cells. Taken together these results suggest that PKR may play a role in cell cycle progression.
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Affiliation(s)
- M Zamanian-Daryoush
- Department of Cancer Biology, Lerner Research Institute, The Cleveland Clinic Foundation, Ohio 44195, USA
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49
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Hartmann R, Olsen HS, Widder S, Jorgensen R, Justesen J. p59OASL, a 2'-5' oligoadenylate synthetase like protein: a novel human gene related to the 2'-5' oligoadenylate synthetase family. Nucleic Acids Res 1998; 26:4121-8. [PMID: 9722630 PMCID: PMC147837 DOI: 10.1093/nar/26.18.4121] [Citation(s) in RCA: 84] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
The 2'-5' oligoadenylate synthetases form a well conserved family of interferon induced proteins, presumably present throughout the mammalian class. Using the Expressed Sequence Tag databases, we have identified a novel member of this family. This protein, which we named p59 2'-5' oligoadenylate synthetase-like protein (p59OASL), shares a highly conserved N-terminal domain with the known forms of 2'-5' oligoadenylate synthetases, but differs completely in its C-terminal part. The C-terminus of p59OASL is formed of two domains of ubiquitin-like sequences. Here we present the characterisation of a full-length cDNA clone, the genomic sequence and the expression pattern of this gene. We have addressed the evolution of the 2'-5' oligoadenylate synthetase gene family, in the light of both this new member and new 2'-5' oligoadenylate synthetase sequence data from other species, which have recently appeared in the databases.
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Affiliation(s)
- R Hartmann
- Department of Molecular and Structural Biology, University of Aarhus, C. F. Mollers allé Building 130, DK-8000 Aarhus C, Denmark and Human Genome Sciences Inc., 9410 Key West Avenue, Rockville, MD 20850, USA
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50
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Player MR, Torrence PF. The 2-5A system: modulation of viral and cellular processes through acceleration of RNA degradation. Pharmacol Ther 1998; 78:55-113. [PMID: 9623881 PMCID: PMC7157933 DOI: 10.1016/s0163-7258(97)00167-8] [Citation(s) in RCA: 227] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
The 2-5A system is an RNA degradation pathway that can be induced by the interferons (IFNs). Treatment of cells with IFN activates genes encoding several double-stranded RNA (dsRNA)-dependent synthetases. These enzymes generate 5'-triphosphorylated, 2',5'-phosphodiester-linked oligoadenylates (2-5A) from ATP. The effects of 2-5A in cells are transient since 2-5A is unstable in cells due to the activities of phosphodiesterase and phosphatase. 2-5A activates the endoribonuclease 2-5A-dependent RNase L, causing degradation of single-stranded RNA with moderate specificity. The human 2-5A-dependent RNase is an 83.5 kDa polypeptide that has little, if any, RNase activity, unless 2-5A is present. 2-5A binding to RNase L switches the enzyme from its off-state to its on-state. At least three 2',5'-linked oligoadenylates and a single 5'-phosphoryl group are required for maximal activation of the RNase. Even though the constitutive presence of 2-5A-dependent RNase is observed in nearly all mammalian cell types, cellular amounts of 2-5A-dependent mRNA and activity can increase after IFN treatment. One well-established role of the 2-5A system is as a host defense against some types of viruses. Since virus infection of cells results in the production and secretion of IFNs, and since dsRNA is both a frequent product of virus infection and an activator of 2-5A synthesis, the replication of encephalomyocarditis virus, which produces dsRNA during its life cycle, is greatly suppressed in IFN-treated cells as a direct result of RNA decay by the activated 2-5A-dependent RNase. This review covers the organic chemistry, enzymology, and molecular biology of 2-5A and its associated enzymes. Additional possible biological roles of the 2-5A system, such as in cell growth and differentiation, human immunodeficiency virus replication, heat shock, atherosclerotic plaque, pathogenesis of Type I diabetes, and apoptosis, are presented.
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Affiliation(s)
- M R Player
- Section on Biomedical Chemistry, Laboratory of Medicinal Chemistry, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, MD 20892-0805, USA
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