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Choonnasard A, Shofa M, Okabayashi T, Saito A. Conserved Functions of Orthohepadnavirus X Proteins to Inhibit Type-I Interferon Signaling. Int J Mol Sci 2024; 25:3753. [PMID: 38612565 PMCID: PMC11011558 DOI: 10.3390/ijms25073753] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2024] [Revised: 03/19/2024] [Accepted: 03/25/2024] [Indexed: 04/14/2024] Open
Abstract
Orthohepadnavirus causes chronic hepatitis in a broad range of mammals, including primates, cats, woodchucks, and bats. Hepatitis B virus (HBV) X protein inhibits type-I interferon (IFN) signaling, thereby promoting HBV escape from the human innate immune system and establishing persistent infection. However, whether X proteins of Orthohepadnavirus viruses in other species display a similar inhibitory activity remains unknown. Here, we investigated the anti-IFN activity of 17 Orthohepadnavirus X proteins derived from various hosts. We observed conserved activity of Orthohepadnavirus X proteins in inhibiting TIR-domain-containing adaptor protein inducing IFN-β (TRIF)-mediated IFN-β signaling pathway through TRIF degradation. X proteins from domestic cat hepadnavirus (DCH), a novel member of Orthohepadnavirus, inhibited mitochondrial antiviral signaling protein (MAVS)-mediated IFNβ signaling pathway comparable with HBV X. These results indicate that inhibition of IFN signaling is conserved in Orthohepadnavirus X proteins.
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Affiliation(s)
- Amonrat Choonnasard
- Department of Veterinary Science, Faculty of Agriculture, University of Miyazaki, Miyazaki 889-2192, Japan; (A.C.); (M.S.); (T.O.)
- Graduate School of Medicine and Veterinary Medicine, University of Miyazaki, Miyazaki 889-1692, Japan
| | - Maya Shofa
- Department of Veterinary Science, Faculty of Agriculture, University of Miyazaki, Miyazaki 889-2192, Japan; (A.C.); (M.S.); (T.O.)
- Graduate School of Medicine and Veterinary Medicine, University of Miyazaki, Miyazaki 889-1692, Japan
| | - Tamaki Okabayashi
- Department of Veterinary Science, Faculty of Agriculture, University of Miyazaki, Miyazaki 889-2192, Japan; (A.C.); (M.S.); (T.O.)
- Graduate School of Medicine and Veterinary Medicine, University of Miyazaki, Miyazaki 889-1692, Japan
- Center for Animal Disease Control, University of Miyazaki, Miyazaki 889-2192, Japan
| | - Akatsuki Saito
- Department of Veterinary Science, Faculty of Agriculture, University of Miyazaki, Miyazaki 889-2192, Japan; (A.C.); (M.S.); (T.O.)
- Graduate School of Medicine and Veterinary Medicine, University of Miyazaki, Miyazaki 889-1692, Japan
- Center for Animal Disease Control, University of Miyazaki, Miyazaki 889-2192, Japan
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2
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Dudka D, Akins RB, Lampson MA. FREEDA: An automated computational pipeline guides experimental testing of protein innovation. J Cell Biol 2023; 222:e202212084. [PMID: 37358475 PMCID: PMC10292211 DOI: 10.1083/jcb.202212084] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2022] [Revised: 04/22/2023] [Accepted: 06/07/2023] [Indexed: 06/27/2023] Open
Abstract
Cell biologists typically focus on conserved regions of a protein, overlooking innovations that can shape its function over evolutionary time. Computational analyses can reveal potential innovations by detecting statistical signatures of positive selection that lead to rapid accumulation of beneficial mutations. However, these approaches are not easily accessible to non-specialists, limiting their use in cell biology. Here, we present an automated computational pipeline FREEDA that provides a simple graphical user interface requiring only a gene name; integrates widely used molecular evolution tools to detect positive selection in rodents, primates, carnivores, birds, and flies; and maps results onto protein structures predicted by AlphaFold. Applying FREEDA to >100 centromere proteins, we find statistical evidence of positive selection within loops and turns of ancient domains, suggesting innovation of essential functions. As a proof-of-principle experiment, we show innovation in centromere binding of mouse CENP-O. Overall, we provide an accessible computational tool to guide cell biology research and apply it to experimentally demonstrate functional innovation.
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Affiliation(s)
- Damian Dudka
- Department of Biology, School of Arts and Sciences, University of Pennsylvania, Philadelphia, PA, USA
| | - R. Brian Akins
- Department of Biology, School of Arts and Sciences, University of Pennsylvania, Philadelphia, PA, USA
| | - Michael A. Lampson
- Department of Biology, School of Arts and Sciences, University of Pennsylvania, Philadelphia, PA, USA
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3
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Dudka D, Akins RB, Lampson MA. FREEDA: an automated computational pipeline guides experimental testing of protein innovation by detecting positive selection. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.02.27.530329. [PMID: 36909479 PMCID: PMC10002610 DOI: 10.1101/2023.02.27.530329] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 03/06/2023]
Abstract
Cell biologists typically focus on conserved regions of a protein, overlooking innovations that can shape its function over evolutionary time. Computational analyses can reveal potential innovations by detecting statistical signatures of positive selection that leads to rapid accumulation of beneficial mutations. However, these approaches are not easily accessible to non-specialists, limiting their use in cell biology. Here, we present an automated computational pipeline FREEDA (Finder of Rapidly Evolving Exons in De novo Assemblies) that provides a simple graphical user interface requiring only a gene name, integrates widely used molecular evolution tools to detect positive selection, and maps results onto protein structures predicted by AlphaFold. Applying FREEDA to >100 mouse centromere proteins, we find evidence of positive selection in intrinsically disordered regions of ancient domains, suggesting innovation of essential functions. As a proof-of-principle experiment, we show innovation in centromere binding of CENP-O. Overall, we provide an accessible computational tool to guide cell biology research and apply it to experimentally demonstrate functional innovation.
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4
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Villamayor L, Rivero V, López-García D, Topham DJ, Martínez-Sobrido L, Nogales A, DeDiego ML. Interferon alpha inducible protein 6 is a negative regulator of innate immune responses by modulating RIG-I activation. Front Immunol 2023; 14:1105309. [PMID: 36793726 PMCID: PMC9923010 DOI: 10.3389/fimmu.2023.1105309] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2022] [Accepted: 01/05/2023] [Indexed: 01/31/2023] Open
Abstract
Interferons (IFNs), IFN-stimulated genes (ISGs), and inflammatory cytokines mediate innate immune responses, and are essential to establish an antiviral response. Within the innate immune responses, retinoic acid-inducible gene I (RIG-I) is a key sensor of virus infections, mediating the transcriptional induction of IFNs and inflammatory proteins. Nevertheless, since excessive responses could be detrimental to the host, these responses need to be tightly regulated. In this work, we describe, for the first time, how knocking-down or knocking-out the expression of IFN alpha-inducible protein 6 (IFI6) increases IFN, ISG, and pro-inflammatory cytokine expression after the infections with Influenza A Virus (IAV), Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2), and Sendai Virus (SeV), or poly(I:C) transfection. We also show how overexpression of IFI6 produces the opposite effect, in vitro and in vivo, indicating that IFI6 negatively modulates the induction of innate immune responses. Knocking-out or knocking-down the expression of IFI6 diminishes the production of infectious IAV and SARS-CoV-2, most likely because of its effect on antiviral responses. Importantly, we report a novel interaction of IFI6 with RIG-I, most likely mediated through binding to RNA, that affects RIG-I activation, providing a molecular mechanism for the effect of IFI6 on negatively regulating innate immunity. Remarkably, these new functions of IFI6 could be targeted to treat diseases associated with an exacerbated induction of innate immune responses and to combat viral infections, such as IAV and SARS-CoV-2.
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Affiliation(s)
- Laura Villamayor
- Department of Molecular and Cell Biology. Centro Nacional de Biotecnología (CNB-CSIC), Madrid, Spain
| | - Vanessa Rivero
- Department of Molecular and Cell Biology. Centro Nacional de Biotecnología (CNB-CSIC), Madrid, Spain
| | - Darío López-García
- Department of Molecular and Cell Biology. Centro Nacional de Biotecnología (CNB-CSIC), Madrid, Spain
| | - David J. Topham
- David H. Smith Center for Vaccine Biology and Immunology, Department of Microbiology and Immunology, University of Rochester Medical Center, Rochester, NY, United States
| | - Luis Martínez-Sobrido
- Disease Intervention and Prevention and Population Health Programs, Texas Biomedical Research Institute, San Antonio, TX, United States
| | - Aitor Nogales
- Center for Animal Health Research, CISA-INIA-CSIC, Valdeolmos, Madrid, Spain
| | - Marta L. DeDiego
- Department of Molecular and Cell Biology. Centro Nacional de Biotecnología (CNB-CSIC), Madrid, Spain,*Correspondence: Marta L. DeDiego,
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5
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Villamayor L, López-García D, Rivero V, Martínez-Sobrido L, Nogales A, DeDiego ML. The IFN-stimulated gene IFI27 counteracts innate immune responses after viral infections by interfering with RIG-I signaling. Front Microbiol 2023; 14:1176177. [PMID: 37187533 PMCID: PMC10175689 DOI: 10.3389/fmicb.2023.1176177] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2023] [Accepted: 04/13/2023] [Indexed: 05/17/2023] Open
Abstract
The recognition of viral nucleic acids by host pattern recognition receptors (PRRs) is critical for initiating innate immune responses against viral infections. These innate immune responses are mediated by the induction of interferons (IFNs), IFN-stimulated genes (ISGs) and pro-inflammatory cytokines. However, regulatory mechanisms are critical to avoid excessive or long-lasting innate immune responses that may cause detrimental hyperinflammation. Here, we identified a novel regulatory function of the ISG, IFN alpha inducible protein 27 (IFI27) in counteracting the innate immune responses triggered by cytoplasmic RNA recognition and binding. Our model systems included three unrelated viral infections caused by Influenza A virus (IAV), Severe Acute Respiratory Syndrome coronavirus 2 (SARS-CoV-2), and Sendai virus (SeV), and transfection with an analog of double-stranded (ds) RNA. Furthermore, we found that IFI27 has a positive effect on IAV and SARS-CoV-2 replication, most likely due to its ability to counteract host-induced antiviral responses, including in vivo. We also show that IFI27 interacts with nucleic acids and PRR retinoic acid-inducible gene I (RIG-I), being the interaction of IFI27 with RIG-I most likely mediated through RNA binding. Interestingly, our results indicate that interaction of IFI27 with RIG-I impairs RIG-I activation, providing a molecular mechanism for the effect of IFI27 on modulating innate immune responses. Our study identifies a molecular mechanism that may explain the effect of IFI27 in counterbalancing innate immune responses to RNA viral infections and preventing excessive innate immune responses. Therefore, this study will have important implications in drug design to control viral infections and viral-induced pathology.
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Affiliation(s)
- Laura Villamayor
- Department of Molecular and Cell Biology, Centro Nacional de Biotecnología (CNB-CSIC), Madrid, Spain
| | - Darío López-García
- Department of Molecular and Cell Biology, Centro Nacional de Biotecnología (CNB-CSIC), Madrid, Spain
| | - Vanessa Rivero
- Department of Molecular and Cell Biology, Centro Nacional de Biotecnología (CNB-CSIC), Madrid, Spain
| | | | - Aitor Nogales
- Center for Animal Health Research, CISA-INIA-CSIC, Madrid, Spain
| | - Marta L. DeDiego
- Department of Molecular and Cell Biology, Centro Nacional de Biotecnología (CNB-CSIC), Madrid, Spain
- *Correspondence: Marta L. DeDiego,
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6
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Evolution of SLiM-mediated hijack functions in intrinsically disordered viral proteins. Essays Biochem 2022; 66:945-958. [DOI: 10.1042/ebc20220059] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2022] [Revised: 11/07/2022] [Accepted: 11/08/2022] [Indexed: 12/07/2022]
Abstract
Abstract
Viruses and their hosts are involved in an ‘arms race’ where they continually evolve mechanisms to overcome each other. It has long been proposed that intrinsic disorder provides a substrate for the evolution of viral hijack functions and that short linear motifs (SLiMs) are important players in this process. Here, we review evidence in support of this tenet from two model systems: the papillomavirus E7 protein and the adenovirus E1A protein. Phylogenetic reconstructions reveal that SLiMs appear and disappear multiple times across evolution, providing evidence of convergent evolution within individual viral phylogenies. Multiple functionally related SLiMs show strong coevolution signals that persist across long distances in the primary sequence and occur in unrelated viral proteins. Moreover, changes in SLiMs are associated with changes in phenotypic traits such as host range and tropism. Tracking viral evolutionary events reveals that host switch events are associated with the loss of several SLiMs, suggesting that SLiMs are under functional selection and that changes in SLiMs support viral adaptation. Fine-tuning of viral SLiM sequences can improve affinity, allowing them to outcompete host counterparts. However, viral SLiMs are not always competitive by themselves, and tethering of two suboptimal SLiMs by a disordered linker may instead enable viral hijack. Coevolution between the SLiMs and the linker indicates that the evolution of disordered regions may be more constrained than previously thought. In summary, experimental and computational studies support a role for SLiMs and intrinsic disorder in viral hijack functions and in viral adaptive evolution.
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7
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Enterovirus 3C Protease Cleaves TRIM7 To Dampen Its Antiviral Activity. J Virol 2022; 96:e0133222. [PMID: 36106874 PMCID: PMC9555159 DOI: 10.1128/jvi.01332-22] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Mammalian TRIM7 is an antiviral protein that inhibits multiple human enteroviruses by degrading the viral 2BC protein. Whether TRIM7 is reciprocally targeted by enteroviruses is not known. Here, we report that the 3C protease (3Cpro) from two enteroviruses, coxsackievirus B3 (CVB3) and poliovirus, targets TRIM7 for cleavage. CVB3 3Cpro cleaves TRIM7 at glutamine 24 (Q24), resulting in a truncated TRIM7 that fails to inhibit CVB3 due to dampened E3 ubiquitin ligase activity. TRIM7 Q24 is highly conserved across mammals, except in marsupials, which instead have a naturally occurring histidine (H24) that is not subject to 3Cpro cleavage. Marsupials also express two isoforms of TRIM7, and the two proteins from koalas have distinct antiviral activities. The longer isoform contains an additional exon due to alternate splice site usage. This additional exon contains a unique 3Cpro cleavage site, suggesting that certain enteroviruses may have evolved to target marsupial TRIM7 even if the canonical Q24 is missing. Combined with computational analyses indicating that TRIM7 is rapidly evolving, our data raise the possibility that TRIM7 may be targeted by enterovirus evasion strategies and that evolution of TRIM7 across mammals may have conferred unique antiviral properties. IMPORTANCE Enteroviruses are significant human pathogens that cause viral myocarditis, pancreatitis, and meningitis. Knowing how the host controls these viruses and how the viruses may evade host restriction is important for understanding fundamental concepts in antiviral immunity and for informing potential therapeutic interventions. In this study, we demonstrate that coxsackievirus B3 uses its virally encoded protease to target the host antiviral protein TRIM7 for cleavage, suggesting a potential mechanism of viral immune evasion. We additionally show that TRIM7 has evolved in certain mammalian lineages to express protein variants with distinct antiviral activities and susceptibilities to viral protease-mediated cleavage.
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8
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Pajic P, Shen S, Qu J, May AJ, Knox S, Ruhl S, Gokcumen O. A mechanism of gene evolution generating mucin function. SCIENCE ADVANCES 2022; 8:eabm8757. [PMID: 36026444 PMCID: PMC9417175 DOI: 10.1126/sciadv.abm8757] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/18/2021] [Accepted: 07/12/2022] [Indexed: 05/12/2023]
Abstract
How novel gene functions evolve is a fundamental question in biology. Mucin proteins, a functionally but not evolutionarily defined group of proteins, allow the study of convergent evolution of gene function. By analyzing the genomic variation of mucins across a wide range of mammalian genomes, we propose that exonic repeats and their copy number variation contribute substantially to the de novo evolution of new gene functions. By integrating bioinformatic, phylogenetic, proteomic, and immunohistochemical approaches, we identified 15 undescribed instances of evolutionary convergence, where novel mucins originated by gaining densely O-glycosylated exonic repeat domains. Our results suggest that secreted proteins rich in proline are natural precursors for acquiring mucin function. Our findings have broad implications for understanding the role of exonic repeats in the parallel evolution of new gene functions, especially those involving protein glycosylation.
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Affiliation(s)
- Petar Pajic
- Department of Biological Sciences, University at Buffalo, The State University of New York, Buffalo, NY 14260, USA
- Department of Oral Biology, School of Dental Medicine, University at Buffalo, The State University of New York, Buffalo, NY 14214, USA
| | - Shichen Shen
- Department of Pharmaceutical Sciences, University at Buffalo, The State University of New York, Buffalo, NY 14214, USA
- Center of Excellence in Bioinformatics and Life Science, Buffalo, NY 14203, USA
| | - Jun Qu
- Department of Pharmaceutical Sciences, University at Buffalo, The State University of New York, Buffalo, NY 14214, USA
- Center of Excellence in Bioinformatics and Life Science, Buffalo, NY 14203, USA
| | - Alison J. May
- Program in Craniofacial Biology, Department of Cell and Tissue Biology, School of Dentistry, University of California, San Francisco, San Francisco, CA 94143, USA
| | - Sarah Knox
- Program in Craniofacial Biology, Department of Cell and Tissue Biology, School of Dentistry, University of California, San Francisco, San Francisco, CA 94143, USA
| | - Stefan Ruhl
- Department of Oral Biology, School of Dental Medicine, University at Buffalo, The State University of New York, Buffalo, NY 14214, USA
| | - Omer Gokcumen
- Department of Biological Sciences, University at Buffalo, The State University of New York, Buffalo, NY 14260, USA
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9
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Abstract
Mitochondria are dynamic organelles vital for energy production with now appreciated roles in immune defense. During microbial infection, mitochondria serve as signaling hubs to induce immune responses to counteract invading pathogens like viruses. Mitochondrial functions are central to a variety of antiviral responses including apoptosis and type I interferon signaling (IFN-I). While apoptosis and IFN-I mediated by mitochondrial antiviral signaling (MAVS) are well-established defenses, new dimensions of mitochondrial biology are emerging as battlefronts during viral infection. Increasingly, it has become apparent that mitochondria serve as reservoirs for distinct cues that trigger immune responses and that alterations in mitochondrial morphology may also tip infection outcomes. Furthermore, new data are foreshadowing pivotal roles for classic, homeostatic facets of this organelle as host-virus interfaces, namely, the tricarboxylic acid (TCA) cycle and electron transport chain (ETC) complexes like respiratory supercomplexes. Underscoring the importance of "housekeeping" mitochondrial activities in viral infection is the growing list of viral-encoded inhibitors including mimics derived from cellular genes that antagonize these functions. For example, virologs for ETC factors and several enzymes from the TCA cycle have been recently identified in DNA virus genomes and serve to pinpoint new vulnerabilities during infection. Here, we highlight recent advances for known antiviral functions associated with mitochondria as well as where the next battlegrounds may be based on viral effectors. Collectively, new methodology and mechanistic insights over the coming years will strengthen our understanding of how an ancient molecular truce continues to defend cells against viruses.
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Affiliation(s)
- Mahsa Sorouri
- Department of Immunology, University of Texas Southwestern Medical Center, Dallas, Texas, USA
| | - Tyron Chang
- Department of Immunology, University of Texas Southwestern Medical Center, Dallas, Texas, USA
- Genetics, Disease, and Development Graduate Program, University of Texas Southwestern Medical Center, Dallas, Texas, USA
| | - Dustin C Hancks
- Department of Immunology, University of Texas Southwestern Medical Center, Dallas, Texas, USA
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10
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Ahmad HI, Afzal G, Iqbal MN, Iqbal MA, Shokrollahi B, Mansoor MK, Chen J. Positive Selection Drives the Adaptive Evolution of Mitochondrial Antiviral Signaling (MAVS) Proteins-Mediating Innate Immunity in Mammals. Front Vet Sci 2022; 8:814765. [PMID: 35174241 PMCID: PMC8841730 DOI: 10.3389/fvets.2021.814765] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2021] [Accepted: 12/24/2021] [Indexed: 12/17/2022] Open
Abstract
The regulated production of filamentous protein complexes is essential in many biological processes and provides a new paradigm in signal transmission. The mitochondrial antiviral signaling protein (MAVS) is a critical signaling hub in innate immunity that is activated when a receptor induces a shift in the globular caspase activation and recruitment domain of MAVS into helical superstructures (filaments). It is of interest whether adaptive evolution affects the proteins involved in innate immunity. Here, we explore and confer the role of selection and diversification on mitochondrial antiviral signaling protein in mammalian species. We obtined the MAVS proteins of mammalian species and examined their differences in evolutionary patterns. We discovered evidence for these proteins being subjected to substantial positive selection. We demonstrate that immune system proteins, particularly those encoding recognition proteins, develop under positive selection using codon-based probability methods. Positively chosen regions within recognition proteins cluster in domains involved in microorganism recognition, implying that molecular interactions between hosts and pathogens may promote adaptive evolution in the mammalian immune systems. These significant variations in MAVS development in mammalian species highlights the involvement of MAVS in innate immunity. Our findings highlight the significance of accounting for how non-synonymous alterations affect structure and function when employing sequence-level studies to determine and quantify positive selection.
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Affiliation(s)
- Hafiz Ishfaq Ahmad
- Department of Animal Breeding and Genetics, University of Veterinary and Animal Sciences, Lahore, Pakistan
| | - Gulnaz Afzal
- Department of Zoology, The Islamia University of Bahawalpur, Bahawalpur, Pakistan
| | | | | | - Borhan Shokrollahi
- Department of Animal Science, Sanandaj Branch, Islamic Azad University, Sanandaj, Iran
| | - Muhammad Khalid Mansoor
- Department of Microbiology, Faculty of Veterinary and Animal Science, The Islamia University of Bahawalpur, Bahawalpur, Pakistan
| | - Jinping Chen
- Guangdong Key Laboratory of Animal Conservation and Resource Utilization, Guangdong Public Laboratory of Wild Animal Conservation and Utilization, Institute of Zoology, Guangdong Academy of Sciences, Guangzhou, China
- *Correspondence: Jinping Chen
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11
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Tsu BV, Fay EJ, Nguyen KT, Corley MR, Hosuru B, Dominguez VA, Daugherty MD. Running With Scissors: Evolutionary Conflicts Between Viral Proteases and the Host Immune System. Front Immunol 2021; 12:769543. [PMID: 34790204 PMCID: PMC8591160 DOI: 10.3389/fimmu.2021.769543] [Citation(s) in RCA: 19] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2021] [Accepted: 10/08/2021] [Indexed: 12/28/2022] Open
Abstract
Many pathogens encode proteases that serve to antagonize the host immune system. In particular, viruses with a positive-sense single-stranded RNA genome [(+)ssRNA], including picornaviruses, flaviviruses, and coronaviruses, encode proteases that are not only required for processing viral polyproteins into functional units but also manipulate crucial host cellular processes through their proteolytic activity. Because these proteases must cleave numerous polyprotein sites as well as diverse host targets, evolution of these viral proteases is expected to be highly constrained. However, despite this strong evolutionary constraint, mounting evidence suggests that viral proteases such as picornavirus 3C, flavivirus NS3, and coronavirus 3CL, are engaged in molecular ‘arms races’ with their targeted host factors, resulting in host- and virus-specific determinants of protease cleavage. In cases where protease-mediated cleavage results in host immune inactivation, recurrent host gene evolution can result in avoidance of cleavage by viral proteases. In other cases, such as recently described examples in NLRP1 and CARD8, hosts have evolved ‘tripwire’ sequences that mimic protease cleavage sites and activate an immune response upon cleavage. In both cases, host evolution may be responsible for driving viral protease evolution, helping explain why viral proteases and polyprotein sites are divergent among related viruses despite such strong evolutionary constraint. Importantly, these evolutionary conflicts result in diverse protease-host interactions even within closely related host and viral species, thereby contributing to host range, zoonotic potential, and pathogenicity of viral infection. Such examples highlight the importance of examining viral protease-host interactions through an evolutionary lens.
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Affiliation(s)
- Brian V Tsu
- Division of Biological Sciences, University of California, San Diego, CA, United States
| | - Elizabeth J Fay
- Division of Biological Sciences, University of California, San Diego, CA, United States
| | - Katelyn T Nguyen
- Division of Biological Sciences, University of California, San Diego, CA, United States
| | - Miles R Corley
- Division of Biological Sciences, University of California, San Diego, CA, United States
| | - Bindhu Hosuru
- Division of Biological Sciences, University of California, San Diego, CA, United States
| | - Viviana A Dominguez
- Division of Biological Sciences, University of California, San Diego, CA, United States
| | - Matthew D Daugherty
- Division of Biological Sciences, University of California, San Diego, CA, United States
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12
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Palmer S, Chappidi S, Pinkham C, Hancks DC. Evolutionary profile for (host and viral) MLKL indicates its activities as a battlefront for extensive counteradaptation. Mol Biol Evol 2021; 38:5405-5422. [PMID: 34436583 PMCID: PMC8662602 DOI: 10.1093/molbev/msab256] [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] [Indexed: 01/11/2023] Open
Abstract
Pathogen infection triggers host innate defenses which may result in the activation of regulated cell death (RCD) pathways such as apoptosis. Given a vital role in immunity, apoptotic effectors are often counteracted by pathogen-encoded antagonists. Mounting evidence indicates that programmed necrosis, which is mediated by the RIPK3/MLKL axis and termed necroptosis, evolved as a countermeasure to pathogen-mediated inhibition of apoptosis. Yet, it is unclear whether components of this emerging RCD pathway display signatures associated with pathogen conflict that are rare in combination but common to key host defense factors, namely, rapid evolution, viral homolog (virolog), and cytokine induction. We leveraged evolutionary sequence analysis that examines rates of amino acid replacement, which revealed: 1) strong and recurrent signatures of positive selection for primate and bat RIPK3 and MLKL, and 2) elevated rates of amino acid substitution on multiple RIPK3/MLKL surfaces suggestive of past antagonism with multiple, distinct pathogen-encoded inhibitors. Furthermore, our phylogenomics analysis across poxvirus genomes illuminated volatile patterns of evolution for a recently described MLKL viral homolog. Specifically, poxviral MLKLs have undergone numerous gene replacements mediated by duplication and deletion events. In addition, MLKL protein expression is stimulated by interferons in human and mouse cells. Thus, MLKL displays all three hallmarks of pivotal immune factors of which only a handful of factors like OAS1 exhibit. These data support the hypothesis that over evolutionary time MLKL functions—which may include execution of necroptosis—have served as a major determinant of infection outcomes despite gene loss in some host genomes.
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Affiliation(s)
- Suzette Palmer
- Department of Immunology, University of Texas Southwestern Medical Center, Dallas, Texas, United States of America
| | - Sruthi Chappidi
- Department of Immunology, University of Texas Southwestern Medical Center, Dallas, Texas, United States of America
| | - Chelsea Pinkham
- Department of Immunology, University of Texas Southwestern Medical Center, Dallas, Texas, United States of America
| | - Dustin C Hancks
- Department of Immunology, University of Texas Southwestern Medical Center, Dallas, Texas, United States of America
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13
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Judd EN, Gilchrist AR, Meyerson NR, Sawyer SL. Positive natural selection in primate genes of the type I interferon response. BMC Ecol Evol 2021; 21:65. [PMID: 33902453 PMCID: PMC8074226 DOI: 10.1186/s12862-021-01783-z] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2020] [Accepted: 03/29/2021] [Indexed: 12/28/2022] Open
Abstract
Background The Type I interferon response is an important first-line defense against viruses. In turn, viruses antagonize (i.e., degrade, mis-localize, etc.) many proteins in interferon pathways. Thus, hosts and viruses are locked in an evolutionary arms race for dominance of the Type I interferon pathway. As a result, many genes in interferon pathways have experienced positive natural selection in favor of new allelic forms that can better recognize viruses or escape viral antagonists. Here, we performed a holistic analysis of selective pressures acting on genes in the Type I interferon family. We initially hypothesized that the genes responsible for inducing the production of interferon would be antagonized more heavily by viruses than genes that are turned on as a result of interferon. Our logic was that viruses would have greater effect if they worked upstream of the production of interferon molecules because, once interferon is produced, hundreds of interferon-stimulated proteins would activate and the virus would need to counteract them one-by-one.
Results We curated multiple sequence alignments of primate orthologs for 131 genes active in interferon production and signaling (herein, “induction” genes), 100 interferon-stimulated genes, and 100 randomly chosen genes. We analyzed each multiple sequence alignment for the signatures of recurrent positive selection. Counter to our hypothesis, we found the interferon-stimulated genes, and not interferon induction genes, are evolving significantly more rapidly than a random set of genes. Interferon induction genes evolve in a way that is indistinguishable from a matched set of random genes (22% and 18% of genes bear signatures of positive selection, respectively). In contrast, interferon-stimulated genes evolve differently, with 33% of genes evolving under positive selection and containing a significantly higher fraction of codons that have experienced selection for recurrent replacement of the encoded amino acid. Conclusion Viruses may antagonize individual products of the interferon response more often than trying to neutralize the system altogether.
Supplementary Information The online version contains supplementary material available at 10.1186/s12862-021-01783-z.
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Affiliation(s)
- Elena N Judd
- Department of Molecular, Cellular and Developmental Biology; BioFrontiers Institute, University of Colorado Boulder, Boulder, USA
| | - Alison R Gilchrist
- Department of Molecular, Cellular and Developmental Biology; BioFrontiers Institute, University of Colorado Boulder, Boulder, USA
| | - Nicholas R Meyerson
- Department of Molecular, Cellular and Developmental Biology; BioFrontiers Institute, University of Colorado Boulder, Boulder, USA
| | - Sara L Sawyer
- Department of Molecular, Cellular and Developmental Biology; BioFrontiers Institute, University of Colorado Boulder, Boulder, USA.
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14
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Modeling the complete kinetics of coxsackievirus B3 reveals human determinants of host-cell feedback. Cell Syst 2021; 12:304-323.e13. [PMID: 33740397 DOI: 10.1016/j.cels.2021.02.004] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2020] [Revised: 01/13/2021] [Accepted: 02/19/2021] [Indexed: 12/13/2022]
Abstract
Complete kinetic models are pervasive in chemistry but lacking in biological systems. We encoded the complete kinetics of infection for coxsackievirus B3 (CVB3), a compact and fast-acting RNA virus. The model consists of separable, detailed modules describing viral binding-delivery, translation-replication, and encapsidation. Specific module activities are dampened by the type I interferon response to viral double-stranded RNAs (dsRNAs), which is itself disrupted by viral proteinases. The experimentally validated kinetics uncovered that cleavability of the dsRNA transducer mitochondrial antiviral signaling protein (MAVS) becomes a stronger determinant of viral outcomes when cells receive supplemental interferon after infection. Cleavability is naturally altered in humans by a common MAVS polymorphism, which removes a proteinase-targeted site but paradoxically elevates CVB3 infectivity. These observations are reconciled with a simple nonlinear model of MAVS regulation. Modeling complete kinetics is an attainable goal for small, rapidly infecting viruses and perhaps viral pathogens more broadly. A record of this paper's transparent peer review process is included in the Supplemental information.
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15
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Tsu BV, Beierschmitt C, Ryan AP, Agarwal R, Mitchell PS, Daugherty MD. Diverse viral proteases activate the NLRP1 inflammasome. eLife 2021; 10:60609. [PMID: 33410748 PMCID: PMC7857732 DOI: 10.7554/elife.60609] [Citation(s) in RCA: 89] [Impact Index Per Article: 29.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2020] [Accepted: 01/06/2021] [Indexed: 12/29/2022] Open
Abstract
The NLRP1 inflammasome is a multiprotein complex that is a potent activator of inflammation. Mouse NLRP1B can be activated through proteolytic cleavage by the bacterial Lethal Toxin (LeTx) protease, resulting in degradation of the N-terminal domains of NLRP1B and liberation of the bioactive C-terminal domain, which includes the caspase activation and recruitment domain (CARD). However, natural pathogen-derived effectors that can activate human NLRP1 have remained unknown. Here, we use an evolutionary model to identify several proteases from diverse picornaviruses that cleave human NLRP1 within a rapidly evolving region of the protein, leading to host-specific and virus-specific activation of the NLRP1 inflammasome. Our work demonstrates that NLRP1 acts as a 'tripwire' to recognize the enzymatic function of a wide range of viral proteases and suggests that host mimicry of viral polyprotein cleavage sites can be an evolutionary strategy to activate a robust inflammatory immune response. The immune system recognizes disease-causing microbes, such as bacteria and viruses, and removes them from the body before they can cause harm. When the immune system first detects these foreign invaders, a multi-part structure known as the inflammasome launches an inflammatory response to help fight the microbes off. Several sensor proteins can activate the inflammasome, including one in mice called NLRP1B. This protein has evolved a specialized site that can be cut by a bacterial toxin. Once cleaved, this region acts like a biological tripwire and sparks NLRP1B into action, allowing the sensor to activate the inflammasome system. Humans have a similar protein called NLRP1, but it is unclear whether this protein has also evolved a tripwire region that can sense microbial proteins. To answer this question, Tsu, Beierschmitt et al. set out to find whether NLRP1 can be activated by viruses in the Picornaviridae family, which are responsible for diseases like polio, hepatitis A, and the common cold. This revealed that NLRP1 contains a cleavage site for enzymes produced by some, but not all, of the viruses in the picornavirus family. Further experiments confirmed that when a picornavirus enzyme cuts through this region during a viral infection, it triggers NLRP1 to activate the inflammasome and initiate an immune response. The enzymes from different viruses were also found to cleave human NLRP1 at different sites, and the protein’s susceptibility to cleavage varied between different animal species. For instance, Tsu, Beierschmitt et al. discovered that NLRP1B in mice is also able to sense picornaviruses, and that different enzymes activate and cleave NLRP1B and NLRP1 to varying degrees: this affected how well the two proteins are expected to be able to sense specific viral infections. This variation suggests that there is an ongoing evolutionary arms-race between viral proteins and the immune system: as viral proteins change and new ones emerge, NLRP1 rapidly evolves new tripwire sites that allow it to sense the infection and launch an inflammatory response. What happens when NLRP1B activates the inflammasome during a viral infection is still an open question. The discovery that mouse NLRP1B shares features with human NLRP1 could allow the development of animal models to study the role of the tripwire in antiviral defenses and the overactive inflammation associated with some viral infections. Understanding the types of viruses that activate the NLRP1 inflammasome, and the outcomes of the resulting immune response, may have implications for future treatments of viral infections.
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Affiliation(s)
- Brian V Tsu
- Division of Biological Sciences, University of California San Diego, San Diego, United States
| | | | - Andrew P Ryan
- Division of Biological Sciences, University of California San Diego, San Diego, United States
| | - Rimjhim Agarwal
- Division of Immunology & Pathogenesis, University of California Berkeley, Berkeley, United States
| | - Patrick S Mitchell
- Division of Immunology & Pathogenesis, University of California Berkeley, Berkeley, United States.,Department of Microbiology, University of Washington, Seattle, United States
| | - Matthew D Daugherty
- Division of Biological Sciences, University of California San Diego, San Diego, United States
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16
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Dultz G, Shimakami T, Schneider M, Murai K, Yamane D, Marion A, Zeitler TM, Stross C, Grimm C, Richter RM, Bäumer K, Yi M, Biondi RM, Zeuzem S, Tampé R, Antes I, Lange CM, Welsch C. Extended interaction networks with HCV protease NS3-4A substrates explain the lack of adaptive capability against protease inhibitors. J Biol Chem 2020; 295:13862-13874. [PMID: 32747444 PMCID: PMC7535904 DOI: 10.1074/jbc.ra120.013898] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2020] [Revised: 07/26/2020] [Indexed: 12/20/2022] Open
Abstract
Inhibitors against the NS3-4A protease of hepatitis C virus (HCV) have proven to be useful drugs in the treatment of HCV infection. Although variants have been identified with mutations that confer resistance to these inhibitors, the mutations do not restore replicative fitness and no secondary mutations that rescue fitness have been found. To gain insight into the molecular mechanisms underlying the lack of fitness compensation, we screened known resistance mutations in infectious HCV cell culture with different genomic backgrounds. We observed that the Q41R mutation of NS3-4A efficiently rescues the replicative fitness in cell culture for virus variants containing mutations at NS3-Asp168 To understand how the Q41R mutation rescues activity, we performed protease activity assays complemented by molecular dynamics simulations, which showed that protease-peptide interactions far outside the targeted peptide cleavage sites mediate substrate recognition by NS3-4A and support protease cleavage kinetics. These interactions shed new light on the mechanisms by which NS3-4A cleaves its substrates, viral polyproteins and a prime cellular antiviral adaptor protein, the mitochondrial antiviral signaling protein MAVS. Peptide binding is mediated by an extended hydrogen-bond network in NS3-4A that was effectively optimized for protease-MAVS binding in Asp168 variants with rescued replicative fitness from NS3-Q41R. In the protease harboring NS3-Q41R, the N-terminal cleavage products of MAVS retained high affinity to the active site, rendering the protease susceptible for potential product inhibition. Our findings reveal delicately balanced protease-peptide interactions in viral replication and immune escape that likely restrict the protease adaptive capability and narrow the virus evolutionary space.
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Affiliation(s)
- Georg Dultz
- Department of Internal Medicine 1, Goethe University Hospital Frankfurt, Frankfurt, Germany
| | - Tetsuro Shimakami
- Department of Gastroenterology, Kanazawa University Hospital, Kanazawa, Japan
| | - Markus Schneider
- Center for Integrated Protein Science Munich (CIPSM) at the Department of Life Sciences, Technical University Munich, Freising-Weihenstephan, Germany
| | - Kazuhisa Murai
- Department of Gastroenterology, Kanazawa University Hospital, Kanazawa, Japan
| | - Daisuke Yamane
- Tokyo Metropolitan Institute of Medical Science, Tokyo, Japan
| | - Antoine Marion
- Center for Integrated Protein Science Munich (CIPSM) at the Department of Life Sciences, Technical University Munich, Freising-Weihenstephan, Germany
| | - Tobias M Zeitler
- Center for Integrated Protein Science Munich (CIPSM) at the Department of Life Sciences, Technical University Munich, Freising-Weihenstephan, Germany
| | - Claudia Stross
- Department of Internal Medicine 1, Goethe University Hospital Frankfurt, Frankfurt, Germany
| | - Christian Grimm
- Department of Internal Medicine 1, Goethe University Hospital Frankfurt, Frankfurt, Germany
| | - Rebecca M Richter
- Department of Internal Medicine 1, Goethe University Hospital Frankfurt, Frankfurt, Germany
| | - Katrin Bäumer
- Department of Internal Medicine 1, Goethe University Hospital Frankfurt, Frankfurt, Germany
| | - MinKyung Yi
- Department of Microbiology and Immunology, University of Texas Medical Branch at Galveston, Galveston, Texas, USA
| | - Ricardo M Biondi
- Department of Internal Medicine 1, Goethe University Hospital Frankfurt, Frankfurt, Germany; Biomedicine Research Institute of Buenos Aires - CONICET - Partner Institute of the Max Planck Society, Buenos Aires, Argentina
| | - Stefan Zeuzem
- Department of Internal Medicine 1, Goethe University Hospital Frankfurt, Frankfurt, Germany; University Center for Infectious Diseases, Goethe University Hospital Frankfurt, Frankfurt, Germany
| | - Robert Tampé
- Institute of Biochemistry, Biocenter and Cluster of Excellence-Macromolecular Complexes, Goethe University Frankfurt, Frankfurt, Germany
| | - Iris Antes
- Center for Integrated Protein Science Munich (CIPSM) at the Department of Life Sciences, Technical University Munich, Freising-Weihenstephan, Germany
| | - Christian M Lange
- Department of Internal Medicine 1, Goethe University Hospital Frankfurt, Frankfurt, Germany
| | - Christoph Welsch
- Department of Internal Medicine 1, Goethe University Hospital Frankfurt, Frankfurt, Germany; University Center for Infectious Diseases, Goethe University Hospital Frankfurt, Frankfurt, Germany.
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17
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Xu L, Yu D, Yao YL, Gu T, Zheng X, Wu Y, Luo RH, Zheng YT, Zhong J, Yao YG. Tupaia MAVS Is a Dual Target during Hepatitis C Virus Infection for Innate Immune Evasion and Viral Replication via NF-κB. THE JOURNAL OF IMMUNOLOGY 2020; 205:2091-2099. [PMID: 32907995 DOI: 10.4049/jimmunol.2000376] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/06/2020] [Accepted: 08/07/2020] [Indexed: 01/02/2023]
Abstract
Hepatitis C virus (HCV) infection is the cause of severe liver disease in many people. The restricted species tropism of HCV hinders the research and development of drugs and vaccines. The Chinese tree shrew (Tupaia belangeri chinensis) is a close relative of primates and can be infected by HCV, but the underlying mechanisms are unknown. In this study, we have characterized the functions of tree shrew MAVS (tMAVS) in response to HCV infection and defined the capacity of HCV replication. HCV was shown to be colocalized with tMAVS in primary tree shrew hepatocytes and cleaved tMAVS at site Cys508 via its NS3/4A protease, with a modulating effect by site Glu506 of tMAVS. The tMAVS cleavage by HCV NS3/4A impaired the IRF3-mediated induction of IFN-β but maintained the activated NF-κB signaling in the tree shrew primary cells. Activation of the tMAVS-dependent NF-κB signaling inversely inhibited HCV replication and might limit the establishment of persistent infection. Overall, our study has revealed an elegant example of the balance between the host defenses and HCV infection via the MAVS-mediated antiviral signaling and has provided an insight into the mechanisms underpinning HCV infection in the Chinese tree shrew.
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Affiliation(s)
- Ling Xu
- Key Laboratory of Animal Models and Human Disease Mechanisms of the Chinese Academy of Sciences and Yunnan Province, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, Yunnan 650223, China.,Kunming Institute of Zoology - Chinese University of Hong Kong Joint Laboratory of Bioresources and Molecular Research in Common Diseases, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, Yunnan 650223, China
| | - Dandan Yu
- Key Laboratory of Animal Models and Human Disease Mechanisms of the Chinese Academy of Sciences and Yunnan Province, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, Yunnan 650223, China.,Kunming Institute of Zoology - Chinese University of Hong Kong Joint Laboratory of Bioresources and Molecular Research in Common Diseases, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, Yunnan 650223, China
| | - Yu-Lin Yao
- Key Laboratory of Animal Models and Human Disease Mechanisms of the Chinese Academy of Sciences and Yunnan Province, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, Yunnan 650223, China.,Kunming Institute of Zoology - Chinese University of Hong Kong Joint Laboratory of Bioresources and Molecular Research in Common Diseases, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, Yunnan 650223, China.,Kunming College of Life Science, University of Chinese Academy of Sciences, Kunming, Yunnan 650204, China
| | - Tianle Gu
- Key Laboratory of Animal Models and Human Disease Mechanisms of the Chinese Academy of Sciences and Yunnan Province, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, Yunnan 650223, China.,Kunming Institute of Zoology - Chinese University of Hong Kong Joint Laboratory of Bioresources and Molecular Research in Common Diseases, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, Yunnan 650223, China.,Kunming College of Life Science, University of Chinese Academy of Sciences, Kunming, Yunnan 650204, China
| | - Xiao Zheng
- Key Laboratory of Animal Models and Human Disease Mechanisms of the Chinese Academy of Sciences and Yunnan Province, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, Yunnan 650223, China.,Kunming Institute of Zoology - Chinese University of Hong Kong Joint Laboratory of Bioresources and Molecular Research in Common Diseases, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, Yunnan 650223, China.,School of Life Sciences, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei, Anhui, 230026, China
| | - Yong Wu
- Key Laboratory of Animal Models and Human Disease Mechanisms of the Chinese Academy of Sciences and Yunnan Province, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, Yunnan 650223, China.,Kunming Institute of Zoology - Chinese University of Hong Kong Joint Laboratory of Bioresources and Molecular Research in Common Diseases, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, Yunnan 650223, China
| | - Rong-Hua Luo
- Key Laboratory of Animal Models and Human Disease Mechanisms of the Chinese Academy of Sciences and Yunnan Province, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, Yunnan 650223, China.,Kunming Institute of Zoology - Chinese University of Hong Kong Joint Laboratory of Bioresources and Molecular Research in Common Diseases, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, Yunnan 650223, China
| | - Yong-Tang Zheng
- Key Laboratory of Animal Models and Human Disease Mechanisms of the Chinese Academy of Sciences and Yunnan Province, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, Yunnan 650223, China.,Kunming Institute of Zoology - Chinese University of Hong Kong Joint Laboratory of Bioresources and Molecular Research in Common Diseases, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, Yunnan 650223, China
| | - Jin Zhong
- Key Laboratory of Molecular Virology and Immunology, Institute Pasteur of Shanghai, Chinese Academy of Sciences, Shanghai 200031, China
| | - Yong-Gang Yao
- Key Laboratory of Animal Models and Human Disease Mechanisms of the Chinese Academy of Sciences and Yunnan Province, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, Yunnan 650223, China; .,Kunming Institute of Zoology - Chinese University of Hong Kong Joint Laboratory of Bioresources and Molecular Research in Common Diseases, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, Yunnan 650223, China.,Kunming College of Life Science, University of Chinese Academy of Sciences, Kunming, Yunnan 650204, China.,National Resource Center for Non-Human Primates, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, Yunnan 650107, China; and.,National Research Facility for Phenotypic and Genetic Analysis of Model Animals (Primate Facility), Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, Yunnan 650107, China
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18
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Affiliation(s)
- Omoshola Aleru
- Institute of Ecology & Evolution, University of Oregon, Eugene, Oregon, United States of America
- Department of Biology, University of Oregon, Eugene, Oregon, United States of America
| | - Matthew F. Barber
- Institute of Ecology & Evolution, University of Oregon, Eugene, Oregon, United States of America
- Department of Biology, University of Oregon, Eugene, Oregon, United States of America
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19
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Abstract
Cell-autonomous immunity relies on the rapid detection of invasive pathogens by host proteins. Guanylate binding proteins (GBPs) have emerged as key mediators of vertebrate immune defense through their ability to recognize a diverse array of intracellular pathogens and pathogen-containing cellular compartments. Human and mouse GBPs have been shown to target distinct groups of microbes, although the molecular determinants of pathogen specificity remain unclear. We show that rapid diversification of a C-terminal polybasic motif (PBM) in primate GBPs controls recognition of the model cytosolic bacterial pathogen Shigella flexneri By swapping this membrane-binding motif between primate GBP orthologs, we found that the ability to target S. flexneri has been enhanced and lost in specific lineages of New World primates. Single substitutions in rapidly evolving sites of the GBP1 PBM are sufficient to abolish or restore bacterial detection abilities, illustrating a role for epistasis in the evolution of pathogen recognition. We further demonstrate that the squirrel monkey GBP2 C-terminal domain recently gained the ability to target S. flexneri through a stepwise process of convergent evolution. These findings reveal a mechanism by which accelerated evolution of a PBM shifts GBP target specificity and aid in resolving the molecular basis of GBP function in cell-autonomous immune defense.IMPORTANCE Many infectious diseases are caused by microbes that enter and survive within host cells. Guanylate binding proteins (GBPs) are a group of immune proteins which recognize and inhibit a variety of intracellular pathogenic microbes. We discovered that a short sequence within GBPs required for the detection of bacteria, the polybasic motif (PBM), has been rapidly evolving between primate species. By swapping PBMs between primate GBP1 genes, we were able to show that specific sequences can both reduce and improve the ability of GBP1 to target intracellular bacteria. We also show that the ability to envelop bacteria has independently evolved in GBP2 of South American monkeys. Taking the results together, this report illustrates how primate GBPs have adapted to defend against infectious pathogens.
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20
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Key residues of the receptor binding motif in the spike protein of SARS-CoV-2 that interact with ACE2 and neutralizing antibodies. Cell Mol Immunol 2020; 17:621-630. [PMID: 32415260 PMCID: PMC7227451 DOI: 10.1038/s41423-020-0458-z] [Citation(s) in RCA: 319] [Impact Index Per Article: 79.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2020] [Accepted: 04/29/2020] [Indexed: 11/08/2022] Open
Abstract
Coronavirus disease 2019 (COVID-19), caused by the novel human coronavirus SARS-CoV-2, is currently a major threat to public health worldwide. The viral spike protein binds the host receptor angiotensin-converting enzyme 2 (ACE2) via the receptor-binding domain (RBD), and thus is believed to be a major target to block viral entry. Both SARS-CoV-2 and SARS-CoV share this mechanism. Here we functionally analyzed the key amino acid residues located within receptor binding motif of RBD that may interact with human ACE2 and available neutralizing antibodies. The in vivo experiments showed that immunization with either the SARS-CoV RBD or SARS-CoV-2 RBD was able to induce strong clade-specific neutralizing antibodies in mice; however, the cross-neutralizing activity was much weaker, indicating that there are distinct antigenic features in the RBDs of the two viruses. This finding was confirmed with the available neutralizing monoclonal antibodies against SARS-CoV or SARS-CoV-2. It is worth noting that a newly developed SARS-CoV-2 human antibody, HA001, was able to neutralize SARS-CoV-2, but failed to recognize SARS-CoV. Moreover, the potential epitope residues of HA001 were identified as A475 and F486 in the SARS-CoV-2 RBD, representing new binding sites for neutralizing antibodies. Overall, our study has revealed the presence of different key epitopes between SARS-CoV and SARS-CoV-2, which indicates the necessity to develop new prophylactic vaccine and antibody drugs for specific control of the COVID-19 pandemic although the available agents obtained from the SARS-CoV study are unneglectable.
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21
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Moreira-Soto A, Arroyo-Murillo F, Sander AL, Rasche A, Corman V, Tegtmeyer B, Steinmann E, Corrales-Aguilar E, Wieseke N, Avey-Arroyo J, Drexler JF. Cross-order host switches of hepatitis C-related viruses illustrated by a novel hepacivirus from sloths. Virus Evol 2020; 6:veaa033. [PMID: 32704383 PMCID: PMC7368370 DOI: 10.1093/ve/veaa033] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022] Open
Abstract
The genealogy of the hepatitis C virus (HCV) and the genus Hepacivirus remains elusive despite numerous recently discovered animal hepaciviruses (HVs). Viruses from evolutionarily ancient mammals might elucidate the HV macro-evolutionary patterns. Here, we investigated sixty-seven two-toed and nine three-toed sloths from Costa Rica for HVs using molecular and serological tools. A novel sloth HV was detected by reverse transcription polymerase chain reaction (RT-PCR) in three-toed sloths (2/9, 22.2%; 95% confidence interval (CI), 5.3-55.7). Genomic characterization revealed typical HV features including overall polyprotein gene structure, a type 4 internal ribosomal entry site in the viral 5'-genome terminus, an A-U-rich region and X-tail structure in the viral 3'-genome terminus. Different from other animal HVs, HV seropositivity in two-toed sloths was low at 4.5 per cent (3/67; CI, 1.0-12.9), whereas the RT-PCR-positive three-toed sloths were seronegative. Limited cross-reactivity of the serological assay implied exposure of seropositive two-toed sloths to HVs of unknown origin and recent infections in RT-PCR-positive animals preceding seroconversion. Recent infections were consistent with only 9 nucleotide exchanges between the two sloth HVs, located predominantly within the E1/E2 encoding regions. Translated sequence distances of NS3 and NS5 proteins and host comparisons suggested that the sloth HV represents a novel HV species. Event- and sequence distance-based reconciliations of phylogenies of HVs and of their hosts revealed complex macro-evolutionary patterns, including both long-term evolutionary associations and host switches, most strikingly from rodents into sloths. Ancestral state reconstructions corroborated rodents as predominant sources of HV host switches during the genealogy of extant HVs. Sequence distance comparisons, partial conservation of critical amino acid residues associated with HV entry and selection pressure signatures of host genes encoding entry and antiviral protein orthologs were consistent with HV host switches between genetically divergent mammals, including the projected host switch from rodents into sloths. Structural comparison of HCV and sloth HV E2 proteins suggested conserved modes of hepaciviral entry. Our data corroborate complex macro-evolutionary patterns shaping the genus Hepacivirus, highlight that host switches are possible across highly diverse host taxa, and elucidate a prominent role of rodent hosts during the Hepacivirus genealogy.
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Affiliation(s)
- Andres Moreira-Soto
- Charité-Universitätsmedizin Berlin, corporate member of Freie Universität Berlin, Humboldt-Universität zu Berlin, and Berlin Institute of Health, Institute of Virology, Berlin 10117, Germany.,Virology-CIET, Faculty of Microbiology, University of Costa Rica, San José, Costa Rica
| | | | - Anna-Lena Sander
- Charité-Universitätsmedizin Berlin, corporate member of Freie Universität Berlin, Humboldt-Universität zu Berlin, and Berlin Institute of Health, Institute of Virology, Berlin 10117, Germany
| | - Andrea Rasche
- Charité-Universitätsmedizin Berlin, corporate member of Freie Universität Berlin, Humboldt-Universität zu Berlin, and Berlin Institute of Health, Institute of Virology, Berlin 10117, Germany
| | - Victor Corman
- Charité-Universitätsmedizin Berlin, corporate member of Freie Universität Berlin, Humboldt-Universität zu Berlin, and Berlin Institute of Health, Institute of Virology, Berlin 10117, Germany
| | - Birthe Tegtmeyer
- Institute for Experimental Virology, TWINCORE Centre for Experimental and Clinical Infection Research, a Joint Venture Between the Medical School Hannover (MHH) and the Helmholtz Centre for Infection Research (HZI), Hannover 30625, Germany
| | - Eike Steinmann
- Department of Molecular and Medical Virology, Faculty of Medicine, Ruhr-University Bochum, Bochum 44801, Germany
| | | | - Nicolas Wieseke
- Swarm Intelligence and Complex Systems Group, Department of Computer Science, Leipzig University, Leipzig, Germany
| | | | - Jan Felix Drexler
- Charité-Universitätsmedizin Berlin, corporate member of Freie Universität Berlin, Humboldt-Universität zu Berlin, and Berlin Institute of Health, Institute of Virology, Berlin 10117, Germany.,German Centre for Infection Research (DZIF), Germany
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22
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Interferon Response in Hepatitis C Virus-Infected Hepatocytes: Issues to Consider in the Era of Direct-Acting Antivirals. Int J Mol Sci 2020; 21:ijms21072583. [PMID: 32276399 PMCID: PMC7177520 DOI: 10.3390/ijms21072583] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2020] [Revised: 04/04/2020] [Accepted: 04/07/2020] [Indexed: 12/16/2022] Open
Abstract
When interferons (IFNs) bind to their receptors, they upregulate numerous IFN-stimulated genes (ISGs) with antiviral and immune regulatory activities. Hepatitis C virus (HCV) is a single-stranded, positive-sense RNA virus that affects over 71 million people in the global population. Hepatocytes infected with HCV produce types I and III IFNs. These endogenous IFNs upregulate a set of ISGs that negatively impact the outcome of pegylated IFN-α and ribavirin treatments, which were previously used to treat HCV. In addition, the IFNL4 genotype was the primary polymorphism responsible for a suboptimal treatment response to pegylated IFN-α and ribavirin. However, recently developed direct-acting antivirals have demonstrated a high rate of sustained virological response without pegylated IFN-α. Herein, we review recent studies on types I and III IFN responses to in HCV-infected hepatocytes. In particular, we focused on open issues related to IFN responses in the direct-acting antiviral era.
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23
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Metabolic Control of Astrocyte Pathogenic Activity via cPLA2-MAVS. Cell 2019; 179:1483-1498.e22. [PMID: 31813625 DOI: 10.1016/j.cell.2019.11.016] [Citation(s) in RCA: 118] [Impact Index Per Article: 23.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2019] [Revised: 07/31/2019] [Accepted: 11/13/2019] [Indexed: 12/22/2022]
Abstract
Metabolism has been shown to control peripheral immunity, but little is known about its role in central nervous system (CNS) inflammation. Through a combination of proteomic, metabolomic, transcriptomic, and perturbation studies, we found that sphingolipid metabolism in astrocytes triggers the interaction of the C2 domain in cytosolic phospholipase A2 (cPLA2) with the CARD domain in mitochondrial antiviral signaling protein (MAVS), boosting NF-κB-driven transcriptional programs that promote CNS inflammation in experimental autoimmune encephalomyelitis (EAE) and, potentially, multiple sclerosis. cPLA2 recruitment to MAVS also disrupts MAVS-hexokinase 2 (HK2) interactions, decreasing HK enzymatic activity and the production of lactate involved in the metabolic support of neurons. Miglustat, a drug used to treat Gaucher and Niemann-Pick disease, suppresses astrocyte pathogenic activities and ameliorates EAE. Collectively, these findings define a novel immunometabolic mechanism that drives pro-inflammatory astrocyte activities, outlines a new role for MAVS in CNS inflammation, and identifies candidate targets for therapeutic intervention.
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24
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Feng H, Sander AL, Moreira-Soto A, Yamane D, Drexler JF, Lemon SM. Hepatovirus 3ABC proteases and evolution of mitochondrial antiviral signaling protein (MAVS). J Hepatol 2019; 71:25-34. [PMID: 30876947 PMCID: PMC6581616 DOI: 10.1016/j.jhep.2019.02.020] [Citation(s) in RCA: 20] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/24/2018] [Revised: 01/31/2019] [Accepted: 02/19/2019] [Indexed: 02/06/2023]
Abstract
BACKGROUND & AIMS Unlike other hepatitis viruses that have infected primates for millions of years, hepatitis A virus (HAV) likely entered human populations only 10-12 thousand years ago after jumping from a rodent host. The phylogeny of modern hepatoviruses that infect rodents and bats suggest that multiple similar host shifts have occurred in the past. The factors determining such shifts are unknown, but the capacity to overcome innate antiviral responses in a foreign species is likely key. METHODS We assessed the capacity of diverse hepatovirus 3ABC proteases to cleave mitochondrial antiviral signaling protein (MAVS) and disrupt antiviral signaling in HEK293 and human hepatocyte-derived cell lines. We also applied maximum-likelihood and Bayesian algorithms to identify sites of diversifying selection in MAVS orthologs from 75 chiropteran, rodent and primate species. RESULTS 3ABC proteases from bat, but not rodent hepatoviruses efficiently cleaved human MAVS at Glu463/Gly464, disrupting virus activation of the interferon-β promoter, whereas human HAV 3ABC cleaved at Gln427/Val428. In contrast, MAVS orthologs from rodents and bats were resistant to cleavage by 3ABC proteases of cognate hepatoviruses and in several cases human HAV. A search for diversifying selection among MAVS orthologs from all 3 orders revealed 90 of ∼540 residues to be under positive selection, including residues in chiropteran MAVS that align with the site of cleavage of human MAVS by bat 3ABC proteases. CONCLUSIONS 3ABC protease cleavage of MAVS is a conserved attribute of hepatoviruses, acting broadly across different mammalian species and associated with evidence of diversifying selection at cleavage sites in rodent and bat MAVS orthologs. The capacity of hepatoviruses to disrupt MAVS-mediated innate immune responses has shaped evolution of both hepatoviruses and their hosts, and facilitates cross-species transmission of hepatitis A. LAY SUMMARY Hepatitis A virus, a common cause of acute hepatitis globally, is likely to have evolved from a virus that jumped from a rodent species to humans within the last 10-12 thousand years. Here we show that distantly related hepatoviruses, that infect bats and rodents today, express proteases that disrupt innate antiviral responses in human cells. This conserved attribute of hepatoviruses may have contributed to that ancient host species shift.
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Affiliation(s)
- Hui Feng
- Lineberger Comprehensive Cancer Center, The University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, USA;,Department of Medicine, The University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, USA
| | - Anna-Lena Sander
- Charité-Universitätsmedizin Berlin, corporate member of Freie Universität Berlin, Humboldt-Universität zu Berlin, and Berlin Institute of Health, Institute of Virology, 10117 Berlin, Germany
| | - Andrés Moreira-Soto
- Charité-Universitätsmedizin Berlin, corporate member of Freie Universität Berlin, Humboldt-Universität zu Berlin, and Berlin Institute of Health, Institute of Virology, 10117 Berlin, Germany
| | - Daisuke Yamane
- Lineberger Comprehensive Cancer Center, The University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, USA;,Department of Medicine, The University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, USA
| | - Jan Felix Drexler
- Charité-Universitätsmedizin Berlin, corporate member of Freie Universität Berlin, Humboldt-Universität zu Berlin, and Berlin Institute of Health, Institute of Virology, 10117 Berlin, Germany;,German Centre for Infection Research (Deutsches Zentrum für Infektionsforschung), Berlin, Germany
| | - Stanley M. Lemon
- Lineberger Comprehensive Cancer Center, The University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, USA;,Department of Medicine, The University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, USA;,Department of Microbiology & Immunology, The University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, USA
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25
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Mesev EV, LeDesma RA, Ploss A. Decoding type I and III interferon signalling during viral infection. Nat Microbiol 2019; 4:914-924. [PMID: 30936491 PMCID: PMC6554024 DOI: 10.1038/s41564-019-0421-x] [Citation(s) in RCA: 308] [Impact Index Per Article: 61.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2018] [Accepted: 02/22/2019] [Indexed: 02/08/2023]
Abstract
Interferon (IFN)-mediated antiviral responses are central to host defence against viral infection. Despite the existence of at least 20 IFNs, there are only three known cell surface receptors. IFN signalling and viral evasion mechanisms form an immensely complex network that differs across species. In this Review, we begin by highlighting some of the advances that have been made towards understanding the complexity of differential IFN signalling inputs and outputs that contribute to antiviral defences. Next, we explore some of the ways viruses can interfere with, or circumvent, these defences. Lastly, we address the largely under-reviewed impact of IFN signalling on host tropism, and we offer perspectives on the future of research into IFN signalling complexity and viral evasion across species. This Review highlights some of the advances that have been made towards understanding the complexity of differential interferon (IFN) signalling inputs and outputs as well as some of the strategies viruses use to interfere with or circumvent IFN-induced antiviral responses.
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Affiliation(s)
- Emily V Mesev
- Lewis Thomas Laboratory, Department of Molecular Biology, Princeton University, Princeton, NJ, USA
| | - Robert A LeDesma
- Lewis Thomas Laboratory, Department of Molecular Biology, Princeton University, Princeton, NJ, USA
| | - Alexander Ploss
- Lewis Thomas Laboratory, Department of Molecular Biology, Princeton University, Princeton, NJ, USA.
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26
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Abstract
Viruses of wild and domestic animals can infect humans in a process called zoonosis, and these events can give rise to explosive epidemics such as those caused by the HIV and Ebola viruses. While humans are constantly exposed to animal viruses, those that can successfully infect and transmit between humans are exceedingly rare. The key event in zoonosis is when an animal virus begins to replicate (one virion making many) in the first human subject. Only at this point will the animal virus first experience the selective environment of the human body, rendering possible viral adaptation and refinement for humans. In addition, appreciable viral titers in this first human may enable infection of a second, thus initiating selection for viral variants with increased capacity for spread. We assert that host genetics plays a critical role in defining which animal viruses in nature will achieve this key event of replication in a first human host. This is because animal viruses that pose the greatest risk to humans will have few (or no) genetic barriers to replicating themselves in human cells, thus requiring minimal mutations to make this jump. Only experimental virology provides a path to identifying animal viruses with the potential to replicate themselves in humans because this information will not be evident from viral sequencing data alone.
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Affiliation(s)
- Cody J. Warren
- BioFrontiers Institute and Department of Molecular, Cellular, and Developmental Biology, University of Colorado Boulder, Boulder, Colorado, United States of America
| | - Sara L. Sawyer
- BioFrontiers Institute and Department of Molecular, Cellular, and Developmental Biology, University of Colorado Boulder, Boulder, Colorado, United States of America
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27
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Ding S, Zhu S, Ren L, Feng N, Song Y, Ge X, Li B, Flavell RA, Greenberg HB. Rotavirus VP3 targets MAVS for degradation to inhibit type III interferon expression in intestinal epithelial cells. eLife 2018; 7:39494. [PMID: 30460894 PMCID: PMC6289572 DOI: 10.7554/elife.39494] [Citation(s) in RCA: 51] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2018] [Accepted: 11/16/2018] [Indexed: 12/31/2022] Open
Abstract
Rotaviruses (RVs), a leading cause of severe diarrhea in young children and many mammalian species, have evolved multiple strategies to counteract the host innate immunity, specifically interferon (IFN) signaling through RV non-structural protein 1 (NSP1). However, whether RV structural components also subvert antiviral response remains under-studied. Here, we found that MAVS, critical for the host RNA sensing pathway upstream of IFN induction, is degraded by the RV RNA methyl- and guanylyl-transferase (VP3) in a host-range-restricted manner. Mechanistically, VP3 localizes to the mitochondria and mediates the phosphorylation of a previously unidentified SPLTSS motif within the MAVS proline-rich region, leading to its proteasomal degradation and blockade of IFN-λ production in RV-infected intestinal epithelial cells. Importantly, VP3 inhibition of MAVS activity contributes to enhanced RV replication and to viral pathogenesis in vivo. Collectively, our findings establish RV VP3 as a viral antagonist of MAVS function in mammals and uncover a novel pathogen-mediated inhibitory mechanism of MAVS signaling.
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Affiliation(s)
- Siyuan Ding
- Department of Medicine, Division of Gastroenterology and Hepatology, Stanford University, Stanford, United States.,Department of Microbiology and Immunology, Stanford University, Stanford, United States.,Palo Alto Veterans Institute of Research, VA Palo Alto Health Care System, Palo Alto, United States
| | - Shu Zhu
- Institute of Immunology, CAS Key Laboratory of Innate Immunity and Chronic Disease, School of Life Sciences and Medical Center, University of Science and Technology of China, Hefei, China
| | - Lili Ren
- Department of Medicine, Division of Gastroenterology and Hepatology, Stanford University, Stanford, United States.,Department of Microbiology and Immunology, Stanford University, Stanford, United States.,Palo Alto Veterans Institute of Research, VA Palo Alto Health Care System, Palo Alto, United States.,School of Pharmaceutical Sciences, Nanjing Tech University, Nanjing, China
| | - Ningguo Feng
- Department of Medicine, Division of Gastroenterology and Hepatology, Stanford University, Stanford, United States.,Department of Microbiology and Immunology, Stanford University, Stanford, United States.,Palo Alto Veterans Institute of Research, VA Palo Alto Health Care System, Palo Alto, United States
| | - Yanhua Song
- Department of Medicine, Division of Gastroenterology and Hepatology, Stanford University, Stanford, United States.,Department of Microbiology and Immunology, Stanford University, Stanford, United States.,Palo Alto Veterans Institute of Research, VA Palo Alto Health Care System, Palo Alto, United States.,Institute of Veterinary Medicine, Jiangsu Academy of Agricultural Sciences, Nanjing, China
| | - Xiaomei Ge
- Palo Alto Veterans Institute of Research, VA Palo Alto Health Care System, Palo Alto, United States.,Department of Medicine, Division of Hematology, Stanford University, Stanford, United States
| | - Bin Li
- Institute of Veterinary Medicine, Jiangsu Academy of Agricultural Sciences, Nanjing, China
| | - Richard A Flavell
- Department of Immunobiology, Yale University, New Haven, United States.,Howard Hughes Medical Institute, Chevy Chase, United States
| | - Harry B Greenberg
- Department of Medicine, Division of Gastroenterology and Hepatology, Stanford University, Stanford, United States.,Department of Microbiology and Immunology, Stanford University, Stanford, United States.,Palo Alto Veterans Institute of Research, VA Palo Alto Health Care System, Palo Alto, United States
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28
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Zhang J, Zhao J, Xu S, Li J, He S, Zeng Y, Xie L, Xie N, Liu T, Lee K, Seo GJ, Chen L, Stabell AC, Xia Z, Sawyer SL, Jung J, Huang C, Feng P. Species-Specific Deamidation of cGAS by Herpes Simplex Virus UL37 Protein Facilitates Viral Replication. Cell Host Microbe 2018; 24:234-248.e5. [PMID: 30092200 PMCID: PMC6094942 DOI: 10.1016/j.chom.2018.07.004] [Citation(s) in RCA: 131] [Impact Index Per Article: 21.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2018] [Revised: 05/26/2018] [Accepted: 06/26/2018] [Indexed: 02/05/2023]
Abstract
Herpes simplex virus 1 (HSV-1) establishes infections in humans and mice, but some non-human primates exhibit resistance via unknown mechanisms. Innate immune recognition pathways are highly conserved but are pivotal in determining susceptibility to DNA virus infections. We report that variation of a single amino acid residue in the innate immune sensor cGAS determines species-specific inactivation by HSV-1. The HSV-1 UL37 tegument protein deamidates human and mouse cGAS. Deamidation impairs the ability of cGAS to catalyze cGAMP synthesis, which activates innate immunity. HSV-1 with deamidase-deficient UL37 promotes robust antiviral responses and is attenuated in mice in a cGAS- and STING-dependent manner. Mutational analyses identified a single asparagine in human and mouse cGAS that is not conserved in many non-human primates. This residue underpins UL37-mediated cGAS deamidation and species permissiveness of HSV-1. Thus, HSV-1 mediates cGAS deamidation for immune evasion and exploits species sequence variation to disarm host defenses.
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Affiliation(s)
- Junjie Zhang
- Department of Molecular Microbiology and Immunology, Norris Comprehensive Cancer Center, Keck School of Medicine, University of Southern California, Los Angeles, CA 90033, USA
| | - Jun Zhao
- Department of Molecular Microbiology and Immunology, Norris Comprehensive Cancer Center, Keck School of Medicine, University of Southern California, Los Angeles, CA 90033, USA
| | - Simin Xu
- Department of Molecular Microbiology and Immunology, Norris Comprehensive Cancer Center, Keck School of Medicine, University of Southern California, Los Angeles, CA 90033, USA
| | - Junhua Li
- Department of Molecular Microbiology and Immunology, Norris Comprehensive Cancer Center, Keck School of Medicine, University of Southern California, Los Angeles, CA 90033, USA
| | - Shanping He
- Department of Molecular Microbiology and Immunology, Norris Comprehensive Cancer Center, Keck School of Medicine, University of Southern California, Los Angeles, CA 90033, USA; School of Life Sciences, Hunan Normal University, Changsha, Hunan, China
| | - Yi Zeng
- Youjiang Medical University for Nationalities, Baise, Guangxi, China
| | - Linshen Xie
- The Fourth West China Hospital, Sichuan University, Chengdu, China
| | - Na Xie
- Department of Molecular Microbiology and Immunology, Norris Comprehensive Cancer Center, Keck School of Medicine, University of Southern California, Los Angeles, CA 90033, USA; State Key Laboratory of Biotherapy and Cancer Center, West China Hospital, School of Basic Medical Sciences and Forensic Medicine, Sichuan University and Collaborative Innovation Center for Biotherapy, Chengdu, Sichuan 610041, China
| | - Ting Liu
- Department of Molecular Microbiology and Immunology, Norris Comprehensive Cancer Center, Keck School of Medicine, University of Southern California, Los Angeles, CA 90033, USA
| | - Katie Lee
- Department of Molecular Microbiology and Immunology, Norris Comprehensive Cancer Center, Keck School of Medicine, University of Southern California, Los Angeles, CA 90033, USA
| | - Gil Ju Seo
- Department of Molecular Microbiology and Immunology, Norris Comprehensive Cancer Center, Keck School of Medicine, University of Southern California, Los Angeles, CA 90033, USA
| | - Lin Chen
- Departments of Biological Sciences and Chemistry, University of Southern California, Los Angeles, CA 90089, USA
| | - Alex C Stabell
- BioFrontiers Institute and Department of Molecular, Cellular, and Developmental Biology, University of Colorado Boulder, Boulder, CO 80303, USA
| | - Zanxian Xia
- School of Life Sciences, Central South University, Changsha, Hunan 410008, China
| | - Sara L Sawyer
- BioFrontiers Institute and Department of Molecular, Cellular, and Developmental Biology, University of Colorado Boulder, Boulder, CO 80303, USA
| | - Jae Jung
- Department of Molecular Microbiology and Immunology, Norris Comprehensive Cancer Center, Keck School of Medicine, University of Southern California, Los Angeles, CA 90033, USA
| | - Canhua Huang
- State Key Laboratory of Biotherapy and Cancer Center, West China Hospital, School of Basic Medical Sciences and Forensic Medicine, Sichuan University and Collaborative Innovation Center for Biotherapy, Chengdu, Sichuan 610041, China
| | - Pinghui Feng
- Department of Molecular Microbiology and Immunology, Norris Comprehensive Cancer Center, Keck School of Medicine, University of Southern California, Los Angeles, CA 90033, USA.
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29
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Multinucleotide mutations cause false inferences of lineage-specific positive selection. Nat Ecol Evol 2018; 2:1280-1288. [PMID: 29967485 PMCID: PMC6093625 DOI: 10.1038/s41559-018-0584-5] [Citation(s) in RCA: 88] [Impact Index Per Article: 14.7] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2017] [Accepted: 05/18/2018] [Indexed: 11/08/2022]
Abstract
Phylogenetic tests of adaptive evolution, such as the widely used branch-site test, assume that nucleotide substitutions occur singly and independently. But recent research has shown that errors at adjacent sites often occur during DNA replication, and the resulting multinucleotide mutations (MNMs) are overwhelmingly likely to be nonsynonymous. We evaluated whether the branch-site test (BST) might misinterpret sequence patterns produced by MNMs as false support for positive selection. We analyzed two genome-scale datasets– one from mammals and one from flies – and found that codons with multiple differences account for virtually all the support for lineage-specific positive selection in the BST. Simulations under conditions derived from these alignments but without positive selection show that realistic rates of MNMs cause a strong and systematic bias towards false inferences of selection. This bias is sufficient under empirically derived conditions to produce false positive inferences as often as the branch-site test infers positive selection from the empirical data. Although some genes with BST-positive results may have evolved adaptively, the test cannot distinguish sequence patterns produced by authentic positive selection from those caused by neutral fixation of MNMs. Many published inferences of adaptive evolution using this technique may therefore be artifacts of model violation caused by unincorporated neutral mutational processes. We introduce a model that incorporates MNMs and may help to ameliorate this bias.
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30
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The Detection and Phylogenetic Analysis of Bovine Hepacivirus in China. BIOMED RESEARCH INTERNATIONAL 2018; 2018:6216853. [PMID: 29955606 PMCID: PMC6000834 DOI: 10.1155/2018/6216853] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/05/2018] [Accepted: 05/07/2018] [Indexed: 01/08/2023]
Abstract
Hepacivirus has been identified in cattle in Africa, Europe, and South America. In this survey of bovine hepacivirus (BovHepV) in 131 serum samples from Chinese cattle herds using RT-PCR, five of 131 sera were BovHepV positive, with the infection rate of 3.82%. Phylogenetic analysis based on the partial NS3 coding sequence showed that the BovHepV of the five positive samples clustered with other BovHepV but formed a separate branch. The results indicated that these new BovHepV represent emerging and novel strains. Further investigations are necessary to determine the epidemiology and viral pathogenesis of these BovHepV strains, as well as the potential threat to ruminant and livestock workers in China.
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31
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Stabell AC, Meyerson NR, Gullberg RC, Gilchrist AR, Webb KJ, Old WM, Perera R, Sawyer SL. Dengue viruses cleave STING in humans but not in nonhuman primates, their presumed natural reservoir. eLife 2018; 7:31919. [PMID: 29557779 PMCID: PMC5860865 DOI: 10.7554/elife.31919] [Citation(s) in RCA: 40] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2017] [Accepted: 02/08/2018] [Indexed: 12/25/2022] Open
Abstract
Human dengue viruses emerged from primate reservoirs, yet paradoxically dengue does not reach high titers in primate models. This presents a unique opportunity to examine the genetics of spillover versus reservoir hosts. The dengue virus 2 (DENV2) - encoded protease cleaves human STING, reducing type I interferon production and boosting viral titers in humans. We find that both human and sylvatic (reservoir) dengue viruses universally cleave human STING, but not the STING of primates implicated as reservoir species. The special ability of dengue to cleave STING is thus specific to humans and a few closely related ape species. Conversion of residues 78/79 to the human-encoded 'RG' renders all primate (and mouse) STINGs sensitive to viral cleavage. Dengue viruses may have evolved to increase viral titers in the dense and vast human population, while maintaining decreased titers and pathogenicity in the more rare animals that serve as their sustaining reservoir in nature.
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Affiliation(s)
- Alex C Stabell
- Department of Molecular, Cellular and Developmental Biology, University of Colorado Boulder, Boulder, United States
| | - Nicholas R Meyerson
- Department of Molecular, Cellular and Developmental Biology, University of Colorado Boulder, Boulder, United States
| | - Rebekah C Gullberg
- Arthropod-borne and Infectious Diseases Laboratory, Department of Microbiology, Immunology and Pathology, Colorado State University, Fort Collins, United States
| | - Alison R Gilchrist
- Department of Molecular, Cellular and Developmental Biology, University of Colorado Boulder, Boulder, United States
| | - Kristofor J Webb
- Department of Molecular, Cellular and Developmental Biology, University of Colorado Boulder, Boulder, United States
| | - William M Old
- Department of Molecular, Cellular and Developmental Biology, University of Colorado Boulder, Boulder, United States
| | - Rushika Perera
- Arthropod-borne and Infectious Diseases Laboratory, Department of Microbiology, Immunology and Pathology, Colorado State University, Fort Collins, United States
| | - Sara L Sawyer
- Department of Molecular, Cellular and Developmental Biology, University of Colorado Boulder, Boulder, United States
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32
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Castiglione GM, Schott RK, Hauser FE, Chang BSW. Convergent selection pressures drive the evolution of rhodopsin kinetics at high altitudes via nonparallel mechanisms. Evolution 2018; 72:170-186. [DOI: 10.1111/evo.13396] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2017] [Accepted: 11/02/2017] [Indexed: 01/01/2023]
Affiliation(s)
- Gianni M. Castiglione
- Department of Cell & Systems Biology; University of Toronto; Toronto Ontario M5S 3G5 Canada
- Department of Ecology & Evolutionary Biology; University of Toronto; Toronto Ontario M5S 3B2 Canada
| | - Ryan K. Schott
- Department of Ecology & Evolutionary Biology; University of Toronto; Toronto Ontario M5S 3B2 Canada
| | - Frances E. Hauser
- Department of Ecology & Evolutionary Biology; University of Toronto; Toronto Ontario M5S 3B2 Canada
| | - Belinda S. W. Chang
- Department of Cell & Systems Biology; University of Toronto; Toronto Ontario M5S 3G5 Canada
- Department of Ecology & Evolutionary Biology; University of Toronto; Toronto Ontario M5S 3B2 Canada
- Centre for the Analysis of Genome Evolution and Function; University of Toronto; Toronto Ontario M5S 3B2 Canada
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33
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Abstract
Hepaciviruses and pegiviruses constitute two closely related sister genera of the family Flaviviridae. In the past five years, the known phylogenetic diversity of the hepacivirus genera has absolutely exploded. What was once an isolated infection in humans (and possibly other primates) has now expanded to include horses, rodents, bats, colobus monkeys, cows, and, most recently, catsharks, shedding new light on the genetic diversity and host range of hepaciviruses. Interestingly, despite the identification of these many animal and primate hepaciviruses, the equine hepaciviruses remain the closest genetic relatives of the human hepaciviruses, providing an intriguing clue to the zoonotic source of hepatitis C virus. This review summarizes the significance of these studies and discusses current thinking about the origin and evolution of the animal hepaciviruses as well as their potential usage as surrogate models for the study of hepatitis C virus.
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Affiliation(s)
- Alex S Hartlage
- Center for Vaccines and Immunity, The Research Institute at Nationwide Children's Hospital, Columbus, Ohio 43205;
| | - John M Cullen
- North Carolina State University College of Veterinary Medicine, Raleigh, North Carolina 27606
| | - Amit Kapoor
- Center for Vaccines and Immunity, The Research Institute at Nationwide Children's Hospital, Columbus, Ohio 43205; .,Department of Pediatrics, College of Medicine and Public Health, Ohio State University, Columbus, Ohio 43210
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34
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van der Lee R, Wiel L, van Dam TJP, Huynen MA. Genome-scale detection of positive selection in nine primates predicts human-virus evolutionary conflicts. Nucleic Acids Res 2017; 45:10634-10648. [PMID: 28977405 PMCID: PMC5737536 DOI: 10.1093/nar/gkx704] [Citation(s) in RCA: 47] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2017] [Accepted: 08/02/2017] [Indexed: 12/17/2022] Open
Abstract
Hotspots of rapid genome evolution hold clues about human adaptation. We present a comparative analysis of nine whole-genome sequenced primates to identify high-confidence targets of positive selection. We find strong statistical evidence for positive selection in 331 protein-coding genes (3%), pinpointing 934 adaptively evolving codons (0.014%). Our new procedure is stringent and reveals substantial artefacts (20% of initial predictions) that have inflated previous estimates. The final 331 positively selected genes (PSG) are strongly enriched for innate and adaptive immunity, secreted and cell membrane proteins (e.g. pattern recognition, complement, cytokines, immune receptors, MHC, Siglecs). We also find evidence for positive selection in reproduction and chromosome segregation (e.g. centromere-associated CENPO, CENPT), apolipoproteins, smell/taste receptors and mitochondrial proteins. Focusing on the virus–host interaction, we retrieve most evolutionary conflicts known to influence antiviral activity (e.g. TRIM5, MAVS, SAMHD1, tetherin) and predict 70 novel cases through integration with virus–human interaction data. Protein structure analysis further identifies positive selection in the interaction interfaces between viruses and their cellular receptors (CD4-HIV; CD46-measles, adenoviruses; CD55-picornaviruses). Finally, primate PSG consistently show high sequence variation in human exomes, suggesting ongoing evolution. Our curated dataset of positive selection is a rich source for studying the genetics underlying human (antiviral) phenotypes. Procedures and data are available at https://github.com/robinvanderlee/positive-selection.
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Affiliation(s)
- Robin van der Lee
- Centre for Molecular and Biomolecular Informatics, Radboud Institute for Molecular Life Sciences, Radboud University Medical Center, Nijmegen, The Netherlands
| | - Laurens Wiel
- Centre for Molecular and Biomolecular Informatics, Radboud Institute for Molecular Life Sciences, Radboud University Medical Center, Nijmegen, The Netherlands.,Department of Human Genetics, Radboud Institute for Molecular Life Sciences, Radboud University Medical Center, Nijmegen, The Netherlands
| | - Teunis J P van Dam
- Centre for Molecular and Biomolecular Informatics, Radboud Institute for Molecular Life Sciences, Radboud University Medical Center, Nijmegen, The Netherlands
| | - Martijn A Huynen
- Centre for Molecular and Biomolecular Informatics, Radboud Institute for Molecular Life Sciences, Radboud University Medical Center, Nijmegen, The Netherlands
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35
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Vignuzzi M, Higgs S. The Bridges and Blockades to Evolutionary Convergence on the Road to Predicting Chikungunya Virus Evolution. Annu Rev Virol 2017; 4:181-200. [PMID: 28961411 DOI: 10.1146/annurev-virology-101416-041757] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
Chikungunya virus, first isolated in the 1950s, has since reemerged to cause several epidemics and millions of infections throughout the world. What was once blurred and confused with dengue virus in both diagnosis and name has since become one of the best-characterized arboviral diseases. In this review, we cover the history of this virus, its evolution into distinct genotypes and lineages, and, most notably, the convergent evolution observed in recent years. We highlight research that reveals to what extent convergent evolution, and its inherent predictability, may occur and what genetic or environmental factors may hinder it.
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Affiliation(s)
- Marco Vignuzzi
- Institut Pasteur, Viral Populations and Pathogenesis Unit, CNRS UMR 3569, 75724 Paris Cedex 15, France;
| | - Stephen Higgs
- Biosecurity Research Institute and Department of Diagnostic Medicine and Pathobiology, Kansas State University, Manhattan, Kansas 66506;
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36
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Abstract
Selfishness is pervasive and manifests at all scales of biology, from societies, to individuals, to genetic elements within a genome. The relentless struggle to seek evolutionary advantages drives perpetual cycles of adaptation and counter-adaptation, commonly referred to as Red Queen interactions. In this review, we explore insights gleaned from molecular and genetic studies of such genetic conflicts, both extrinsic (between genomes) and intrinsic (within genomes or cells). We argue that many different characteristics of selfish genetic elements can be distilled into two types of advantages: an over-replication advantage (e.g. mobile genetic elements in genomes) and a transmission distortion advantage (e.g. meiotic drivers in populations). These two general categories may help classify disparate types of selfish genetic elements.
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Affiliation(s)
- Richard N McLaughlin
- Division of Basic Sciences, Fred Hutchinson Cancer Research Center, Seattle, WA 98109, USA
| | - Harmit S Malik
- Division of Basic Sciences, Fred Hutchinson Cancer Research Center, Seattle, WA 98109, USA .,Howard Hughes Medical Institute, Fred Hutchinson Cancer Research Center, Seattle, WA 98109, USA
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37
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Abstract
High-altitude environments present a range of biochemical and physiological challenges for organisms through decreases in oxygen, pressure, and temperature relative to lowland habitats. Protein-level adaptations to hypoxic high-altitude conditions have been identified in multiple terrestrial endotherms; however, comparable adaptations in aquatic ectotherms, such as fishes, have not been as extensively characterized. In enzyme proteins, cold adaptation is attained through functional trade-offs between stability and activity, often mediated by substitutions outside the active site. Little is known whether signaling proteins [e.g., G protein-coupled receptors (GPCRs)] exhibit natural variation in response to cold temperatures. Rhodopsin (RH1), the temperature-sensitive visual pigment mediating dim-light vision, offers an opportunity to enhance our understanding of thermal adaptation in a model GPCR. Here, we investigate the evolution of rhodopsin function in an Andean mountain catfish system spanning a range of elevations. Using molecular evolutionary analyses and site-directed mutagenesis experiments, we provide evidence for cold adaptation in RH1. We find that unique amino acid substitutions occur at sites under positive selection in high-altitude catfishes, located at opposite ends of the RH1 intramolecular hydrogen-bonding network. Natural high-altitude variants introduced into these sites via mutagenesis have limited effects on spectral tuning, yet decrease the stability of dark-state and light-activated rhodopsin, accelerating the decay of ligand-bound forms. As found in cold-adapted enzymes, this phenotype likely compensates for a cold-induced decrease in kinetic rates-properties of rhodopsin that mediate rod sensitivity and visual performance. Our results support a role for natural variation in enhancing the performance of GPCRs in response to cold temperatures.
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Geoghegan JL, Duchêne S, Holmes EC. Comparative analysis estimates the relative frequencies of co-divergence and cross-species transmission within viral families. PLoS Pathog 2017; 13:e1006215. [PMID: 28178344 PMCID: PMC5319820 DOI: 10.1371/journal.ppat.1006215] [Citation(s) in RCA: 164] [Impact Index Per Article: 23.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2016] [Revised: 02/21/2017] [Accepted: 02/02/2017] [Indexed: 01/20/2023] Open
Abstract
The cross-species transmission of viruses from one host species to another is responsible for the majority of emerging infections. However, it is unclear whether some virus families have a greater propensity to jump host species than others. If related viruses have an evolutionary history of co-divergence with their hosts there should be evidence of topological similarities between the virus and host phylogenetic trees, whereas host jumping generates incongruent tree topologies. By analyzing co-phylogenetic processes in 19 virus families and their eukaryotic hosts we provide a quantitative and comparative estimate of the relative frequency of virus-host co-divergence versus cross-species transmission among virus families. Notably, our analysis reveals that cross-species transmission is a near universal feature of the viruses analyzed here, with virus-host co-divergence occurring less frequently and always on a subset of viruses. Despite the overall high topological incongruence among virus and host phylogenies, the Hepadnaviridae, Polyomaviridae, Poxviridae, Papillomaviridae and Adenoviridae, all of which possess double-stranded DNA genomes, exhibited more frequent co-divergence than the other virus families studied here. At the other extreme, the virus and host trees for all the RNA viruses studied here, particularly the Rhabdoviridae and the Picornaviridae, displayed high levels of topological incongruence, indicative of frequent host switching. Overall, we show that cross-species transmission plays a major role in virus evolution, with all the virus families studied here having the potential to jump host species, and that increased sampling will likely reveal more instances of host jumping.
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Affiliation(s)
- Jemma L. Geoghegan
- Marie Bashir Institute for Infectious Diseases and Biosecurity, Charles Perkins Centre, School of Life and Environmental Sciences and Sydney Medical School, The University of Sydney, Sydney, New South Wales, Australia
| | - Sebastián Duchêne
- Marie Bashir Institute for Infectious Diseases and Biosecurity, Charles Perkins Centre, School of Life and Environmental Sciences and Sydney Medical School, The University of Sydney, Sydney, New South Wales, Australia
- Centre for Systems Genomics, The University of Melbourne, Melbourne, Victoria, Australia
| | - Edward C. Holmes
- Marie Bashir Institute for Infectious Diseases and Biosecurity, Charles Perkins Centre, School of Life and Environmental Sciences and Sydney Medical School, The University of Sydney, Sydney, New South Wales, Australia
- * E-mail:
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Crowl JT, Gray EE, Pestal K, Volkman HE, Stetson DB. Intracellular Nucleic Acid Detection in Autoimmunity. Annu Rev Immunol 2017; 35:313-336. [PMID: 28142323 DOI: 10.1146/annurev-immunol-051116-052331] [Citation(s) in RCA: 152] [Impact Index Per Article: 21.7] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
Protective immune responses to viral infection are initiated by innate immune sensors that survey extracellular and intracellular space for foreign nucleic acids. The existence of these sensors raises fundamental questions about self/nonself discrimination because of the abundance of self-DNA and self-RNA that occupy these same compartments. Recent advances have revealed that enzymes that metabolize or modify endogenous nucleic acids are essential for preventing inappropriate activation of the innate antiviral response. In this review, we discuss rare human diseases caused by dysregulated nucleic acid sensing, focusing primarily on intracellular sensors of nucleic acids. We summarize lessons learned from these disorders, we rationalize the existence of these diseases in the context of evolution, and we propose that this framework may also apply to a number of more common autoimmune diseases for which the underlying genetics and mechanisms are not yet fully understood.
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Affiliation(s)
- John T Crowl
- Department of Immunology, University of Washington School of Medicine, Seattle, Washington 98109;
| | - Elizabeth E Gray
- Department of Immunology, University of Washington School of Medicine, Seattle, Washington 98109;
| | - Kathleen Pestal
- Department of Immunology, University of Washington School of Medicine, Seattle, Washington 98109;
| | - Hannah E Volkman
- Department of Immunology, University of Washington School of Medicine, Seattle, Washington 98109;
| | - Daniel B Stetson
- Department of Immunology, University of Washington School of Medicine, Seattle, Washington 98109;
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Hepacivirus NS3/4A Proteases Interfere with MAVS Signaling in both Their Cognate Animal Hosts and Humans: Implications for Zoonotic Transmission. J Virol 2016; 90:10670-10681. [PMID: 27654291 DOI: 10.1128/jvi.01634-16] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2016] [Accepted: 09/09/2016] [Indexed: 12/14/2022] Open
Abstract
Multiple novel members of the genus Hepacivirus have recently been discovered in diverse mammalian species. However, to date, their replication mechanisms and zoonotic potential have not been explored in detail. The NS3/4A serine protease of hepatitis C virus (HCV) is critical for cleavage of the viral polyprotein. It also cleaves the cellular innate immune adaptor MAVS, thus decreasing interferon (IFN) production and contributing to HCV persistence in the human host. To investigate the conservation of fundamental aspects of the hepaciviral life cycle, we explored if MAVS cleavage and suppression of innate immune signaling represent a common mechanism employed across different clades of the genus Hepacivirus to enhance viral replication. To estimate the zoonotic potential of these nonhuman hepaciviruses, we assessed if their NS3/4A proteases were capable of cleaving human MAVS. NS3/4A proteases of viruses infecting colobus monkeys, rodents, horses, and cows cleaved the MAVS proteins of their cognate hosts and interfered with the ability of MAVS to induce the IFN-β promoter. All NS3/4A proteases from nonhuman viruses readily cleaved human MAVS. Thus, NS3/4A-dependent cleavage of MAVS is a conserved replication strategy across multiple clades within the genus Hepacivirus Human MAVS is susceptible to cleavage by these nonhuman viral proteases, indicating that it does not pose a barrier for zoonotic transmission of these viruses to humans. IMPORTANCE Virus infection is recognized by cellular sensor proteins triggering innate immune signaling and antiviral defenses. While viruses have evolved strategies to thwart these antiviral programs in their cognate host species, these evasion mechanisms are often ineffective in a novel host, thus limiting viral transmission across species. HCV, the best-characterized member of the genus Hepacivirus within the family Flaviviridae, uses its NS3/4A protease to disrupt innate immune signaling by cleaving the cellular adaptor protein MAVS. Recently, a large number of HCV-related viruses have been discovered in various animal species, including wild, livestock, and companion animals. We show that the NS3/4A proteases of these hepaciviruses from different animals and representing various clades of the genus cleave their cognate host MAVS proteins in addition to human MAVS. Therefore, cleavage of MAVS is a common strategy of hepaciviruses, and human MAVS is likely unable to limit replication of these nonhuman viruses upon zoonotic exposure.
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41
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Li N, Hong T, Li R, Wang Y, Guo M, Cao Z, Cai Y, Liu S, Chai T, Wei L. Cherry Valley Ducks Mitochondrial Antiviral-Signaling Protein-Mediated Signaling Pathway and Antiviral Activity Research. Front Immunol 2016; 7:377. [PMID: 27708647 PMCID: PMC5030477 DOI: 10.3389/fimmu.2016.00377] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2016] [Accepted: 09/08/2016] [Indexed: 02/06/2023] Open
Abstract
Mitochondrial antiviral-signaling protein (MAVS), an adaptor protein of retinoic acid-inducible gene I (RIG-I)-like receptors (RLRs)-mediated signal pathway, is involved in innate immunity. In this study, Cherry Valley duck MAVS (duMAVS) was cloned from the spleen and analyzed. duMAVS was determined to have a caspase activation and recruitment domain at N-terminal, followed by a proline-rich domain and a transmembrane domain at C-terminal. Quantitative real-time PCR indicated that duMAVS was expressed in all tissues tested across a broad expression spectrum. The expression of duMAVS was significantly upregulated after infection with duck Tembusu virus (DTMUV). Overexpression of duMAVS could drive the activation of interferon (IFN)-β, nuclear factor-κB, interferon regulatory factor 7, and many downstream factors (such as Mx, PKR, OAS, and IL-8) in duck embryo fibroblast cells. What is more, RNA interference further confirmed that duMAVS was an important adaptor for IFN-β activation. The antiviral assay showed that duMAVS could suppress the various viral replications (DTMUV, novel reovirus, and duck plague virus) at early stages of infection. Overall, these results showed that the main signal pathway mediated by duMAVS and it had a broad-spectrum antiviral ability. This research will be helpful to better understanding the innate immune system of ducks.
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Affiliation(s)
- Ning Li
- Sino-German Cooperative Research Centre for Zoonosis of Animal Origin of Shandong Province, College of Veterinary Medicine, Shandong Agricultural University, Tai'an City, China; Collaborative Innovation Centre for the Origin and Control of Emerging Infectious Diseases of Taishan Medical College, Tai'an City, China
| | - Tianqi Hong
- Sino-German Cooperative Research Centre for Zoonosis of Animal Origin of Shandong Province, College of Veterinary Medicine, Shandong Agricultural University , Tai'an City , China
| | - Rong Li
- Sino-German Cooperative Research Centre for Zoonosis of Animal Origin of Shandong Province, College of Veterinary Medicine, Shandong Agricultural University , Tai'an City , China
| | - Yao Wang
- Sino-German Cooperative Research Centre for Zoonosis of Animal Origin of Shandong Province, College of Veterinary Medicine, Shandong Agricultural University , Tai'an City , China
| | - Mengjiao Guo
- Sino-German Cooperative Research Centre for Zoonosis of Animal Origin of Shandong Province, College of Veterinary Medicine, Shandong Agricultural University , Tai'an City , China
| | - Zongxi Cao
- Hainan Provincial Key Laboratory of Tropical Animal Reproduction and Breeding and Veterinary Medicine, Institute of Animal Husbandry and Veterinary Medicine, Hainan Academy of Agricultural Sciences , Haikou , China
| | - Yumei Cai
- Sino-German Cooperative Research Centre for Zoonosis of Animal Origin of Shandong Province, College of Veterinary Medicine, Shandong Agricultural University , Tai'an City , China
| | - Sidang Liu
- Sino-German Cooperative Research Centre for Zoonosis of Animal Origin of Shandong Province, College of Veterinary Medicine, Shandong Agricultural University , Tai'an City , China
| | - Tongjie Chai
- Sino-German Cooperative Research Centre for Zoonosis of Animal Origin of Shandong Province, College of Veterinary Medicine, Shandong Agricultural University, Tai'an City, China; Collaborative Innovation Centre for the Origin and Control of Emerging Infectious Diseases of Taishan Medical College, Tai'an City, China
| | - Liangmeng Wei
- Sino-German Cooperative Research Centre for Zoonosis of Animal Origin of Shandong Province, College of Veterinary Medicine, Shandong Agricultural University, Tai'an City, China; Collaborative Innovation Centre for the Origin and Control of Emerging Infectious Diseases of Taishan Medical College, Tai'an City, China
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Zhao J, He S, Minassian A, Li J, Feng P. Recent advances on viral manipulation of NF-κB signaling pathway. Curr Opin Virol 2015; 15:103-11. [PMID: 26385424 PMCID: PMC4688235 DOI: 10.1016/j.coviro.2015.08.013] [Citation(s) in RCA: 60] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2015] [Revised: 08/09/2015] [Accepted: 08/26/2015] [Indexed: 12/18/2022]
Abstract
NF-κB transcription factors regulate the expression of hundreds of genes primarily involved in immune responses. Signaling events leading to NF-κB activation constitute a major antiviral immune pathway. To replicate and persist within their hosts, viruses have evolved diverse strategies to evade and exploit cellular NF-κB immune signaling cascades for their benefit. We summarize recent studies concerning viral manipulation of the NF-κB signaling pathway downstream of pattern recognition receptors. Signal transduction mediated by pattern recognition receptors is a research frontier for both infectious disease and innate immunology.
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Affiliation(s)
- Jun Zhao
- Department of Molecular Microbiology and Immunology, Norris Comprehensive Cancer Center, Keck School of Medicine, University of Southern California, United States
| | - Shanping He
- Department of Molecular Microbiology and Immunology, Norris Comprehensive Cancer Center, Keck School of Medicine, University of Southern California, United States
| | - Arlet Minassian
- Department of Molecular Microbiology and Immunology, Norris Comprehensive Cancer Center, Keck School of Medicine, University of Southern California, United States
| | - Junhua Li
- Department of Molecular Microbiology and Immunology, Norris Comprehensive Cancer Center, Keck School of Medicine, University of Southern California, United States
| | - Pinghui Feng
- Department of Molecular Microbiology and Immunology, Norris Comprehensive Cancer Center, Keck School of Medicine, University of Southern California, United States.
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43
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Schweppe DK, Harding C, Chavez JD, Wu X, Ramage E, Singh PK, Manoil C, Bruce JE. Host-Microbe Protein Interactions during Bacterial Infection. ACTA ACUST UNITED AC 2015; 22:1521-1530. [PMID: 26548613 DOI: 10.1016/j.chembiol.2015.09.015] [Citation(s) in RCA: 94] [Impact Index Per Article: 10.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2015] [Revised: 09/11/2015] [Accepted: 09/24/2015] [Indexed: 12/24/2022]
Abstract
Interspecies protein-protein interactions are essential mediators of infection. While bacterial proteins required for host cell invasion and infection can be identified through bacterial mutant library screens, information about host target proteins and interspecies complex structures has been more difficult to acquire. Using an unbiased chemical crosslinking/mass spectrometry approach, we identified interspecies protein-protein interactions in human lung epithelial cells infected with Acinetobacter baumannii. These efforts resulted in identification of 3,076 crosslinked peptide pairs and 46 interspecies protein-protein interactions. Most notably, the key A. baumannii virulence factor, OmpA, was identified as crosslinked to host proteins involved in desmosomes, specialized structures that mediate host cell-to-cell adhesion. Co-immunoprecipitation and transposon mutant experiments were used to verify these interactions and demonstrate relevance for host cell invasion and acute murine lung infection. These results shed new light on A. baumannii-host protein interactions and their structural features, and the presented approach is generally applicable to other systems.
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Affiliation(s)
- Devin K Schweppe
- Department of Genome Sciences, University of Washington School of Medicine, Seattle, WA 98195, USA
| | - Christopher Harding
- Departments of Medicine and Microbiology, University of Washington School of Medicine, Seattle, WA 98195, USA
| | - Juan D Chavez
- Department of Genome Sciences, University of Washington School of Medicine, Seattle, WA 98195, USA
| | - Xia Wu
- Department of Genome Sciences, University of Washington School of Medicine, Seattle, WA 98195, USA
| | - Elizabeth Ramage
- Department of Genome Sciences, University of Washington School of Medicine, Seattle, WA 98195, USA
| | - Pradeep K Singh
- Departments of Medicine and Microbiology, University of Washington School of Medicine, Seattle, WA 98195, USA
| | - Colin Manoil
- Department of Genome Sciences, University of Washington School of Medicine, Seattle, WA 98195, USA
| | - James E Bruce
- Department of Genome Sciences, University of Washington School of Medicine, Seattle, WA 98195, USA; Departments of Medicine and Microbiology, University of Washington School of Medicine, Seattle, WA 98195, USA; Department of Genome Sciences, University of Washington School of Medicine, 850 Republican Street, Brotman Building, Room 154, Seattle, WA 98109, USA.
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44
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Thézé J, Lowes S, Parker J, Pybus OG. Evolutionary and Phylogenetic Analysis of the Hepaciviruses and Pegiviruses. Genome Biol Evol 2015; 7:2996-3008. [PMID: 26494702 PMCID: PMC5635594 DOI: 10.1093/gbe/evv202] [Citation(s) in RCA: 54] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023] Open
Abstract
The known genetic diversity of the hepaciviruses and pegiviruses has increased greatly in recent years through the discovery of viruses related to hepatitis C virus and human pegivirus in bats, bovines, equines, primates, and rodents. Analysis of these new species is important for research into animal models of hepatitis C virus infection and into the zoonotic origins of human viruses. Here, we provide the first systematic phylogenetic and evolutionary analysis of these two genera at the whole-genome level. Phylogenies confirmed that hepatitis C virus is most closely related to viruses from horses whereas human pegiviruses clustered with viruses from African primates. Within each genus, several well-supported lineages were identified and viral diversity was structured by both host species and location of sampling. Recombination analyses provided evidence of interspecific recombination in hepaciviruses, but none in the pegiviruses. Putative mosaic genome structures were identified in NS5B gene region and were supported by multiple tests. The identification of interspecific recombination in the hepaciviruses represents an important evolutionary event that could be clarified by future sampling of novel viruses. We also identified parallel amino acid changes shared by distantly related lineages that infect similar types of host. Notable parallel changes were clustered in the NS3 and NS4B genes and provide a useful starting point for experimental studies of the evolution of Hepacivirus host-virus interactions.
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Affiliation(s)
- Julien Thézé
- Department of Zoology, University of Oxford, United Kingdom
| | - Sophia Lowes
- Department of Zoology, University of Oxford, United Kingdom
| | - Joe Parker
- Biodiversity Informatics and Spatial Analysis, The Jodrell Laboratory, Royal Botanic Gardens, Kew, United Kingdom
| | - Oliver G Pybus
- Department of Zoology, University of Oxford, United Kingdom
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45
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van der Lee R, Feng Q, Langereis MA, ter Horst R, Szklarczyk R, Netea MG, Andeweg AC, van Kuppeveld FJM, Huynen MA. Integrative Genomics-Based Discovery of Novel Regulators of the Innate Antiviral Response. PLoS Comput Biol 2015; 11:e1004553. [PMID: 26485378 PMCID: PMC4618338 DOI: 10.1371/journal.pcbi.1004553] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/03/2015] [Accepted: 09/12/2015] [Indexed: 01/16/2023] Open
Abstract
The RIG-I-like receptor (RLR) pathway is essential for detecting cytosolic viral RNA to trigger the production of type I interferons (IFNα/β) that initiate an innate antiviral response. Through systematic assessment of a wide variety of genomics data, we discovered 10 molecular signatures of known RLR pathway components that collectively predict novel members. We demonstrate that RLR pathway genes, among others, tend to evolve rapidly, interact with viral proteins, contain a limited set of protein domains, are regulated by specific transcription factors, and form a tightly connected interaction network. Using a Bayesian approach to integrate these signatures, we propose likely novel RLR regulators. RNAi knockdown experiments revealed a high prediction accuracy, identifying 94 genes among 187 candidates tested (~50%) that affected viral RNA-induced production of IFNβ. The discovered antiviral regulators may participate in a wide range of processes that highlight the complexity of antiviral defense (e.g. MAP3K11, CDK11B, PSMA3, TRIM14, HSPA9B, CDC37, NUP98, G3BP1), and include uncharacterized factors (DDX17, C6orf58, C16orf57, PKN2, SNW1). Our validated RLR pathway list (http://rlr.cmbi.umcn.nl/), obtained using a combination of integrative genomics and experiments, is a new resource for innate antiviral immunity research.
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Affiliation(s)
- Robin van der Lee
- Centre for Molecular and Biomolecular Informatics, Radboud Institute for Molecular Life Sciences, Radboud university medical center, Nijmegen, The Netherlands
| | - Qian Feng
- Virology Division, Department of Infectious Diseases and Immunology, Faculty of Veterinary Medicine, University of Utrecht, Utrecht, The Netherlands
| | - Martijn A. Langereis
- Virology Division, Department of Infectious Diseases and Immunology, Faculty of Veterinary Medicine, University of Utrecht, Utrecht, The Netherlands
| | - Rob ter Horst
- Centre for Molecular and Biomolecular Informatics, Radboud Institute for Molecular Life Sciences, Radboud university medical center, Nijmegen, The Netherlands
| | - Radek Szklarczyk
- Centre for Molecular and Biomolecular Informatics, Radboud Institute for Molecular Life Sciences, Radboud university medical center, Nijmegen, The Netherlands
| | - Mihai G. Netea
- Department of Internal Medicine and Radboud Center for Infectious Diseases, Radboud university medical center, Nijmegen, The Netherlands
| | - Arno C. Andeweg
- Department of Viroscience, Erasmus Medical Center, Rotterdam, The Netherlands
| | - Frank J. M. van Kuppeveld
- Virology Division, Department of Infectious Diseases and Immunology, Faculty of Veterinary Medicine, University of Utrecht, Utrecht, The Netherlands
| | - Martijn A. Huynen
- Centre for Molecular and Biomolecular Informatics, Radboud Institute for Molecular Life Sciences, Radboud university medical center, Nijmegen, The Netherlands
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Barber MF, Elde NC. Buried Treasure: Evolutionary Perspectives on Microbial Iron Piracy. Trends Genet 2015; 31:627-636. [PMID: 26431675 PMCID: PMC4639441 DOI: 10.1016/j.tig.2015.09.001] [Citation(s) in RCA: 75] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2015] [Revised: 08/18/2015] [Accepted: 09/04/2015] [Indexed: 12/14/2022]
Abstract
Host–pathogen interactions provide valuable systems for the study of evolutionary genetics and natural selection. The sequestration of essential iron has emerged as a crucial innate defense system termed nutritional immunity, leading pathogens to evolve mechanisms of ‘iron piracy’ to scavenge this metal from host proteins. This battle for iron carries numerous consequences not only for host–pathogen evolution but also microbial community interactions. Here we highlight recent and potential future areas of investigation on the evolutionary implications of microbial iron piracy in relation to molecular arms races, host range, competition, and virulence. Applying evolutionary genetic approaches to the study of microbial iron acquisition could also provide new inroads for understanding and combating infectious disease. The battle between microbes and their hosts for nutrient iron is emerging as a new front of evolutionary genetic conflict. Molecular arms races can emerge between host iron-binding proteins and microbial ‘iron piracy’ factors that steal this nutrient for growth. Such rapid evolution may also contribute to the host range of pathogenic microbes. Iron acquisition plays an important role in evolutionary interactions between microbes, both in the environment and within the host. Competition for iron can prevent infection by pathogens, while genetic changes in iron acquisition systems can enhance microbial virulence. Evolutionary conflicts for nutrient iron are revealing potential new genetic mechanisms of disease resistance as well as avenues for therapeutic development.
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Affiliation(s)
- Matthew F Barber
- Department of Human Genetics, University of Utah School of Medicine, Salt Lake City, UT 84112, USA.
| | - Nels C Elde
- Department of Human Genetics, University of Utah School of Medicine, Salt Lake City, UT 84112, USA
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47
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Douam F, Gaska JM, Winer BY, Ding Q, von Schaewen M, Ploss A. Genetic Dissection of the Host Tropism of Human-Tropic Pathogens. Annu Rev Genet 2015; 49:21-45. [PMID: 26407032 DOI: 10.1146/annurev-genet-112414-054823] [Citation(s) in RCA: 28] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Abstract
Infectious diseases are the second leading cause of death worldwide. Although the host multitropism of some pathogens has rendered their manipulation possible in animal models, the human-restricted tropism of numerous viruses, bacteria, fungi, and parasites has seriously hampered our understanding of these pathogens. Hence, uncovering the genetic basis underlying the narrow tropism of such pathogens is critical for understanding their mechanisms of infection and pathogenesis. Moreover, such genetic dissection is essential for the generation of permissive animal models that can serve as critical tools for the development of therapeutics or vaccines against challenging human pathogens. In this review, we describe different experimental approaches utilized to uncover the genetic foundation regulating pathogen host tropism as well as their relevance for studying the tropism of several important human pathogens. Finally, we discuss the current and future uses of this knowledge for generating genetically modified animal models permissive for these pathogens.
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Affiliation(s)
- Florian Douam
- Department of Molecular Biology, Princeton University, Princeton, New Jersey 08544; , , , , ,
| | - Jenna M Gaska
- Department of Molecular Biology, Princeton University, Princeton, New Jersey 08544; , , , , ,
| | - Benjamin Y Winer
- Department of Molecular Biology, Princeton University, Princeton, New Jersey 08544; , , , , ,
| | - Qiang Ding
- Department of Molecular Biology, Princeton University, Princeton, New Jersey 08544; , , , , ,
| | - Markus von Schaewen
- Department of Molecular Biology, Princeton University, Princeton, New Jersey 08544; , , , , ,
| | - Alexander Ploss
- Department of Molecular Biology, Princeton University, Princeton, New Jersey 08544; , , , , ,
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48
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Scull MA, Shi C, de Jong YP, Gerold G, Ries M, von Schaewen M, Donovan BM, Labitt RN, Horwitz JA, Gaska JM, Hrebikova G, Xiao JW, Flatley B, Fung C, Chiriboga L, Walker CM, Evans DT, Rice CM, Ploss A. Hepatitis C virus infects rhesus macaque hepatocytes and simianized mice. Hepatology 2015; 62:57-67. [PMID: 25820364 PMCID: PMC4482775 DOI: 10.1002/hep.27773] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/02/2014] [Accepted: 03/01/2015] [Indexed: 12/31/2022]
Abstract
UNLABELLED At least 170 million people are chronically infected with hepatitis C virus (HCV). Owing to the narrow host range of HCV and restricted use of chimpanzees, there is currently no suitable animal model for HCV pathogenesis studies or the development of a HCV vaccine. To identify cellular determinants of interspecies transmission and establish a novel immunocompetent model system, we examined the ability of HCV to infect hepatocytes from a small nonhuman primate, the rhesus macaque (Macaca mulatta). We show that the rhesus orthologs of critical HCV entry factors support viral glycoprotein-dependent virion uptake. Primary hepatocytes from rhesus macaques are also permissive for HCV-RNA replication and particle production, which is enhanced when antiviral signaling is suppressed. We demonstrate that this may be owing to the diminished capacity of HCV to antagonize mitochondrial antiviral-signaling protein-dependent innate cellular defenses. To test the ability of HCV to establish persistent replication in vivo, we engrafted primary rhesus macaque hepatocytes into immunocompromised xenorecipients. Inoculation of resulting simian liver chimeric mice with either HCV genotype 1a or 2a resulted in HCV serum viremia for up to 10 weeks. CONCLUSION Together, these data indicate that rhesus macaques may be a viable model for HCV and implicate host immunity as a potential species-specific barrier to HCV infection. We conclude that suppression of host immunity or further viral adaptation may allow robust HCV infection in rhesus macaques and creation of a new animal model for studies of HCV pathogenesis, lentivirus coinfection, and vaccine development.
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Affiliation(s)
- Margaret A. Scull
- Center for the Study of Hepatitis C, Laboratory of Virology and Infectious Diseases, The Rockefeller University, New York, New York 10065, USA
| | - Chao Shi
- Center for the Study of Hepatitis C, Laboratory of Virology and Infectious Diseases, The Rockefeller University, New York, New York 10065, USA
| | - Ype P. de Jong
- Center for the Study of Hepatitis C, Laboratory of Virology and Infectious Diseases, The Rockefeller University, New York, New York 10065, USA,Division of Gastroenterology and Hepatology, Center for the Study of Hepatitis C, Weill Cornell Medical College, New York, New York 10065, USA
| | - Gisa Gerold
- Center for the Study of Hepatitis C, Laboratory of Virology and Infectious Diseases, The Rockefeller University, New York, New York 10065, USA
| | - Moritz Ries
- AIDS Vaccine Research Laboratory, Department of Pathology and Laboratory Medicine, University of Wisconsin School of Medicine and Public Health, Madison, WI 53711, USA
| | - Markus von Schaewen
- Department of Molecular Biology, Princeton University, Princeton, New Jersey 08544, USA
| | - Bridget M. Donovan
- Center for the Study of Hepatitis C, Laboratory of Virology and Infectious Diseases, The Rockefeller University, New York, New York 10065, USA
| | - Rachael N. Labitt
- Center for the Study of Hepatitis C, Laboratory of Virology and Infectious Diseases, The Rockefeller University, New York, New York 10065, USA
| | - Joshua A. Horwitz
- Center for the Study of Hepatitis C, Laboratory of Virology and Infectious Diseases, The Rockefeller University, New York, New York 10065, USA
| | - Jenna M. Gaska
- Department of Molecular Biology, Princeton University, Princeton, New Jersey 08544, USA
| | - Gabriela Hrebikova
- Department of Molecular Biology, Princeton University, Princeton, New Jersey 08544, USA
| | - Jing W. Xiao
- Center for the Study of Hepatitis C, Laboratory of Virology and Infectious Diseases, The Rockefeller University, New York, New York 10065, USA
| | - Brenna Flatley
- Center for the Study of Hepatitis C, Laboratory of Virology and Infectious Diseases, The Rockefeller University, New York, New York 10065, USA
| | - Canny Fung
- Center for the Study of Hepatitis C, Laboratory of Virology and Infectious Diseases, The Rockefeller University, New York, New York 10065, USA
| | - Luis Chiriboga
- Department of Pathology, New York University Medical Center, New York, New York, USA
| | | | - David T. Evans
- AIDS Vaccine Research Laboratory, Department of Pathology and Laboratory Medicine, University of Wisconsin School of Medicine and Public Health, Madison, WI 53711, USA
| | - Charles M. Rice
- Center for the Study of Hepatitis C, Laboratory of Virology and Infectious Diseases, The Rockefeller University, New York, New York 10065, USA
| | - Alexander Ploss
- Center for the Study of Hepatitis C, Laboratory of Virology and Infectious Diseases, The Rockefeller University, New York, New York 10065, USA,Department of Molecular Biology, Princeton University, Princeton, New Jersey 08544, USA,Correspondence to: Alexander Ploss, Ph.D., Department of Molecular Biology, Princeton University, Washington Road, LTL 110, Princeton, NJ 08544, Phone: (609) 258-7128, Fax: (609) 258-1701,
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Abstract
The world of primate genomics is expanding rapidly in new and exciting ways owing to lowered costs and new technologies in molecular methods and bioinformatics. The primate order is composed of 78 genera and 478 species, including human. Taxonomic inferences are complex and likely a consequence of ongoing hybridization, introgression, and reticulate evolution among closely related taxa. Recently, we applied large-scale sequencing methods and extensive taxon sampling to generate a highly resolved phylogeny that affirms, reforms, and extends previous depictions of primate speciation. The next stage of research uses this phylogeny as a foundation for investigating genome content, structure, and evolution across primates. Ongoing and future applications of a robust primate phylogeny are discussed, highlighting advancements in adaptive evolution of genes and genomes, taxonomy and conservation management of endangered species, next-generation genomic technologies, and biomedicine.
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Affiliation(s)
- Jill Pecon-Slattery
- Laboratory of Genomic Diversity, National Cancer Institute, Frederick, Maryland 21702; Current Affiliation: Smithsonian Conservation Biology Institute, National Zoological Park, Front Royal, Virginia 22630;
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50
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Convergent evolution and mimicry of protein linear motifs in host–pathogen interactions. Curr Opin Struct Biol 2015; 32:91-101. [DOI: 10.1016/j.sbi.2015.03.004] [Citation(s) in RCA: 36] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2014] [Revised: 03/09/2015] [Accepted: 03/15/2015] [Indexed: 12/21/2022]
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