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Gan Z, Xu X, Tang S, Wen Q, Jin Y, Lu Y. Identification and functional characterization of protein kinase R (PKR) in amphibian Xenopus tropicalis. DEVELOPMENTAL AND COMPARATIVE IMMUNOLOGY 2023; 141:104648. [PMID: 36708793 DOI: 10.1016/j.dci.2023.104648] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/27/2022] [Revised: 01/09/2023] [Accepted: 01/24/2023] [Indexed: 06/18/2023]
Abstract
As one of interferon-induced serine/threonine kinases, the protein kinase R (PKR) plays vital roles in antiviral defense, and functional features of PKR remain largely unknown in amphibians, which suffer from ranaviral diseases in the last few decades. In this study, a PKR gene named Xt-PKR was characterized in the Western clawed frog (Xenopus tropicalis). Xt-PKR gene was widely expressed in different organs/tissues, and was rapidly induced by poly(I:C) in spleen, kidney, and liver. Intriguingly, Xt-PKR could be up-rugulated by the treatment of type I and type III interferons, and the transcript level of Xt-PKR induced by type I interferon was much higher than that of type III interferon. Moreover, overexpression of Xt-PKR can suppress the protein synthesis and ranavirus replication in vitro, and the residue lysine required for the translation inhibition activity in mammalian PKR is conserved in Xt-PKR. The present study represents the first characterization on the functions of amphibian PKR, and reveals considerable functional conservation of PKR in early tetrapods.
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Affiliation(s)
- Zhen Gan
- Guangdong Provincial Engineering Research Center for Aquatic Animal Health Assessment, Shenzhen Public Service Platform for Evaluation of Marine Economic Animal Seedings, Shenzhen Institute of Guangdong Ocean University, Shenzhen, 518120, China; Guangdong Provincial Key Laboratory of Aquatic Animal Disease Control and Healthy Culture, Key Laboratory of Control for Disease of Aquatic Animals of Guangdong Higher Education Institute, College of Fishery, Guangdong Ocean University, Zhanjiang, 524088, China.
| | - Xinlan Xu
- Guangdong Provincial Engineering Research Center for Aquatic Animal Health Assessment, Shenzhen Public Service Platform for Evaluation of Marine Economic Animal Seedings, Shenzhen Institute of Guangdong Ocean University, Shenzhen, 518120, China; Guangdong Provincial Key Laboratory of Aquatic Animal Disease Control and Healthy Culture, Key Laboratory of Control for Disease of Aquatic Animals of Guangdong Higher Education Institute, College of Fishery, Guangdong Ocean University, Zhanjiang, 524088, China
| | - Shaoshuai Tang
- Guangdong Provincial Engineering Research Center for Aquatic Animal Health Assessment, Shenzhen Public Service Platform for Evaluation of Marine Economic Animal Seedings, Shenzhen Institute of Guangdong Ocean University, Shenzhen, 518120, China
| | - Qingqing Wen
- Guangdong Provincial Engineering Research Center for Aquatic Animal Health Assessment, Shenzhen Public Service Platform for Evaluation of Marine Economic Animal Seedings, Shenzhen Institute of Guangdong Ocean University, Shenzhen, 518120, China; Guangdong Provincial Key Laboratory of Aquatic Animal Disease Control and Healthy Culture, Key Laboratory of Control for Disease of Aquatic Animals of Guangdong Higher Education Institute, College of Fishery, Guangdong Ocean University, Zhanjiang, 524088, China
| | - Yong Jin
- Guangdong Provincial Engineering Research Center for Aquatic Animal Health Assessment, Shenzhen Public Service Platform for Evaluation of Marine Economic Animal Seedings, Shenzhen Institute of Guangdong Ocean University, Shenzhen, 518120, China
| | - Yishan Lu
- Guangdong Provincial Engineering Research Center for Aquatic Animal Health Assessment, Shenzhen Public Service Platform for Evaluation of Marine Economic Animal Seedings, Shenzhen Institute of Guangdong Ocean University, Shenzhen, 518120, China; Guangdong Provincial Key Laboratory of Aquatic Animal Disease Control and Healthy Culture, Key Laboratory of Control for Disease of Aquatic Animals of Guangdong Higher Education Institute, College of Fishery, Guangdong Ocean University, Zhanjiang, 524088, China.
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Teekas L, Sharma S, Vijay N. Lineage-specific protein repeat expansions and contractions reveal malleable regions of immune genes. Genes Immun 2022; 23:218-234. [PMID: 36203090 DOI: 10.1038/s41435-022-00186-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2022] [Revised: 09/21/2022] [Accepted: 09/22/2022] [Indexed: 01/07/2023]
Abstract
Functional diversification, a higher evolutionary rate, and intense positive selection help a limited number of immune genes interact with many pathogens. Repeats in protein-coding regions are a well-known source of functional diversification, adaptive variation, and evolutionary novelty in a short time. Repeats play a crucial role in biochemical functions like functional diversification of transcription regulation, protein kinases, cell adhesion, signaling pathways, morphogenesis, DNA repair, recombination, and RNA processing. Repeat length variation can change the associated protein's interaction, efficacy, and overall protein network. Repeats have an intrinsic unstable nature and can potentially evolve rapidly and expedite the acquisition of complex phenotypic traits and functions. Because of their ability to generate rapid, adaptive variations over short evolutionary distances, repeats are considered "tuning knobs." Repeat length variation in specific genes, like RUNX2 and ALX4, is associated with morphological and physiological changes across vertebrates. Here we study repeat length variation as a potent source of species-specific immune diversification across several clades of tetrapods. Moreover, we provide a clade-wise comprehensive list of immune genes with repeat types for future studies of morphological/evolutionary changes within species groups. We observe significant repeat length variation of FASLG and C1QC in Rodentia and Primates' contrasting species groups, respectively.
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Affiliation(s)
- Lokdeep Teekas
- Department of Biological Sciences, Computational Evolutionary Genomics Lab, IISER Bhopal, Bhauri, Madhya Pradesh, India
| | - Sandhya Sharma
- Department of Biological Sciences, Computational Evolutionary Genomics Lab, IISER Bhopal, Bhauri, Madhya Pradesh, India
| | - Nagarjun Vijay
- Department of Biological Sciences, Computational Evolutionary Genomics Lab, IISER Bhopal, Bhauri, Madhya Pradesh, India.
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Price AM, Steinbock RT, Di C, Hayer KE, Li Y, Herrmann C, Parenti NA, Whelan JN, Weiss SR, Weitzman MD. Adenovirus prevents dsRNA formation by promoting efficient splicing of viral RNA. Nucleic Acids Res 2021; 50:1201-1220. [PMID: 34671803 PMCID: PMC8860579 DOI: 10.1093/nar/gkab896] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2021] [Revised: 09/10/2021] [Accepted: 10/08/2021] [Indexed: 12/14/2022] Open
Abstract
Eukaryotic cells recognize intracellular pathogens through pattern recognition receptors, including sensors of aberrant nucleic acid structures. Sensors of double-stranded RNA (dsRNA) are known to detect replication intermediates of RNA viruses. It has long been suggested that annealing of mRNA from symmetrical transcription of both top and bottom strands of DNA virus genomes can produce dsRNA during infection. Supporting this hypothesis, nearly all DNA viruses encode inhibitors of dsRNA-recognition pathways. However, direct evidence that DNA viruses produce dsRNA is lacking. Contrary to dogma, we show that the nuclear-replicating DNA virus adenovirus (AdV) does not produce detectable levels of dsRNA during infection. In contrast, abundant dsRNA is detected within the nucleus of cells infected with AdV mutants defective for viral RNA processing. In the presence of nuclear dsRNA, the cytoplasmic dsRNA sensor PKR is relocalized and activated within the nucleus. Accumulation of viral dsRNA occurs in the late phase of infection, when unspliced viral transcripts form intron/exon base pairs between top and bottom strand transcripts. We propose that DNA viruses actively limit dsRNA formation by promoting efficient splicing and mRNA processing, thus avoiding detection and restriction by host innate immune sensors of pathogenic nucleic acids.
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Affiliation(s)
- Alexander M Price
- Division of Protective Immunity, Department of Pathology and Laboratory Medicine, The Children's Hospital of Philadelphia, Philadelphia, PA, USA
| | - Robert T Steinbock
- Division of Protective Immunity, Department of Pathology and Laboratory Medicine, The Children's Hospital of Philadelphia, Philadelphia, PA, USA.,Cell & Molecular Biology Graduate Group, University of Pennsylvania, Philadelphia, PA, USA
| | - Chao Di
- Department of Biomedical and Health Informatics, The Children's Hospital of Philadelphia, Philadelphia, PA, USA
| | - Katharina E Hayer
- Department of Biomedical and Health Informatics, The Children's Hospital of Philadelphia, Philadelphia, PA, USA
| | - Yize Li
- Department of Microbiology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Christin Herrmann
- Division of Protective Immunity, Department of Pathology and Laboratory Medicine, The Children's Hospital of Philadelphia, Philadelphia, PA, USA.,Cell & Molecular Biology Graduate Group, University of Pennsylvania, Philadelphia, PA, USA
| | - Nicholas A Parenti
- Department of Microbiology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Jillian N Whelan
- Department of Microbiology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Susan R Weiss
- Department of Microbiology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Matthew D Weitzman
- Division of Protective Immunity, Department of Pathology and Laboratory Medicine, The Children's Hospital of Philadelphia, Philadelphia, PA, USA.,Department of Pathology and Laboratory Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
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Lin YT, Chau LF, Coutts H, Mahmoudi M, Drampa V, Lee CH, Brown A, Hughes DJ, Grey F. Does the Zinc Finger Antiviral Protein (ZAP) Shape the Evolution of Herpesvirus Genomes? Viruses 2021; 13:1857. [PMID: 34578438 PMCID: PMC8473364 DOI: 10.3390/v13091857] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2021] [Revised: 09/12/2021] [Accepted: 09/13/2021] [Indexed: 01/02/2023] Open
Abstract
An evolutionary arms race occurs between viruses and hosts. Hosts have developed an array of antiviral mechanisms aimed at inhibiting replication and spread of viruses, reducing their fitness, and ultimately minimising pathogenic effects. In turn, viruses have evolved sophisticated counter-measures that mediate evasion of host defence mechanisms. A key aspect of host defences is the ability to differentiate between self and non-self. Previous studies have demonstrated significant suppression of CpG and UpA dinucleotide frequencies in the coding regions of RNA and small DNA viruses. Artificially increasing these dinucleotide frequencies results in a substantial attenuation of virus replication, suggesting dinucleotide bias could facilitate recognition of non-self RNA. The interferon-inducible gene, zinc finger antiviral protein (ZAP) is the host factor responsible for sensing CpG dinucleotides in viral RNA and restricting RNA viruses through direct binding and degradation of the target RNA. Herpesviruses are large DNA viruses that comprise three subfamilies, alpha, beta and gamma, which display divergent CpG dinucleotide patterns within their genomes. ZAP has recently been shown to act as a host restriction factor against human cytomegalovirus (HCMV), a beta-herpesvirus, which in turn evades ZAP detection by suppressing CpG levels in the major immediate-early transcript IE1, one of the first genes expressed by the virus. While suppression of CpG dinucleotides allows evasion of ZAP targeting, synonymous changes in nucleotide composition that cause genome biases, such as low GC content, can cause inefficient gene expression, especially in unspliced transcripts. To maintain compact genomes, the majority of herpesvirus transcripts are unspliced. Here we discuss how the conflicting pressures of ZAP evasion, the need to maintain compact genomes through the use of unspliced transcripts and maintaining efficient gene expression may have shaped the evolution of herpesvirus genomes, leading to characteristic CpG dinucleotide patterns.
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Affiliation(s)
- Yao-Tang Lin
- Division of Infection and Immunity, The Roslin Institute, University of Edinburgh, Easter Bush, Edinburgh EH25 9RG, UK; (Y.-T.L.); (L.-F.C.); (H.C.); (M.M.); (V.D.); (C.-H.L.); (A.B.)
| | - Long-Fung Chau
- Division of Infection and Immunity, The Roslin Institute, University of Edinburgh, Easter Bush, Edinburgh EH25 9RG, UK; (Y.-T.L.); (L.-F.C.); (H.C.); (M.M.); (V.D.); (C.-H.L.); (A.B.)
| | - Hannah Coutts
- Division of Infection and Immunity, The Roslin Institute, University of Edinburgh, Easter Bush, Edinburgh EH25 9RG, UK; (Y.-T.L.); (L.-F.C.); (H.C.); (M.M.); (V.D.); (C.-H.L.); (A.B.)
| | - Matin Mahmoudi
- Division of Infection and Immunity, The Roslin Institute, University of Edinburgh, Easter Bush, Edinburgh EH25 9RG, UK; (Y.-T.L.); (L.-F.C.); (H.C.); (M.M.); (V.D.); (C.-H.L.); (A.B.)
| | - Vayalena Drampa
- Division of Infection and Immunity, The Roslin Institute, University of Edinburgh, Easter Bush, Edinburgh EH25 9RG, UK; (Y.-T.L.); (L.-F.C.); (H.C.); (M.M.); (V.D.); (C.-H.L.); (A.B.)
| | - Chen-Hsuin Lee
- Division of Infection and Immunity, The Roslin Institute, University of Edinburgh, Easter Bush, Edinburgh EH25 9RG, UK; (Y.-T.L.); (L.-F.C.); (H.C.); (M.M.); (V.D.); (C.-H.L.); (A.B.)
| | - Alex Brown
- Division of Infection and Immunity, The Roslin Institute, University of Edinburgh, Easter Bush, Edinburgh EH25 9RG, UK; (Y.-T.L.); (L.-F.C.); (H.C.); (M.M.); (V.D.); (C.-H.L.); (A.B.)
| | - David J. Hughes
- Biomedical Sciences Research Complex, School of Biology, University of St Andrews, St Andrews KY16 9ST, UK;
| | - Finn Grey
- Division of Infection and Immunity, The Roslin Institute, University of Edinburgh, Easter Bush, Edinburgh EH25 9RG, UK; (Y.-T.L.); (L.-F.C.); (H.C.); (M.M.); (V.D.); (C.-H.L.); (A.B.)
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Species-Specific Host-Virus Interactions: Implications for Viral Host Range and Virulence. Trends Microbiol 2019; 28:46-56. [PMID: 31597598 DOI: 10.1016/j.tim.2019.08.007] [Citation(s) in RCA: 56] [Impact Index Per Article: 11.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2019] [Revised: 08/11/2019] [Accepted: 08/19/2019] [Indexed: 01/09/2023]
Abstract
A growing number of studies indicate that host species-specific and virus strain-specific interactions of viral molecules with the host innate immune system play a pivotal role in determining virus host range and virulence. Because interacting proteins are likely constrained in their evolution, mutations that are selected to improve virus replication in one species may, by chance, alter the ability of a viral antagonist to inhibit immune responses in hosts the virus has not yet encountered. Based on recent findings of host-species interactions of poxvirus, herpesvirus, and influenza virus proteins, we propose a model for viral fitness and host range which considers the full interactome between a specific host species and a virus, resulting from the combination of all interactions, positive and negative, that influence whether a virus can productively infect a cell and cause disease in different hosts.
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