Viroporin Activity of the JC Polyomavirus Is Regulated by Interactions with the Adaptor Protein Complex 3
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Multiple Origins of Viral Capsid Proteins from Cellular Ancestors
Multiple origins of viral capsid proteins from PNAS PLUS cellular ancestors Mart Krupovica,1 and Eugene V. Kooninb,1 aInstitut Pasteur, Department of Microbiology, Unité Biologie Moléculaire du Gène chez les Extrêmophiles, 75015 Paris, France; and bNational Center for Biotechnology Information, National Library of Medicine, Bethesda, MD 20894 Contributed by Eugene V. Koonin, February 3, 2017 (sent for review December 21, 2016; reviewed by C. Martin Lawrence and Kenneth Stedman) Viruses are the most abundant biological entities on earth and show genome replication. Understanding the origin of any virus group is remarkable diversity of genome sequences, replication and expres- possible only if the provenances of both components are elucidated sion strategies, and virion structures. Evolutionary genomics of (11). Given that viral replication proteins often have no closely viruses revealed many unexpected connections but the general related homologs in known cellular organisms (6, 12), it has been scenario(s) for the evolution of the virosphere remains a matter of suggested that many of these proteins evolved in the precellular intense debate among proponents of the cellular regression, escaped world (4, 6) or in primordial, now extinct, cellular lineages (5, 10, genes, and primordial virus world hypotheses. A comprehensive 13). The ability to transfer the genetic information encased within sequence and structure analysis of major virion proteins indicates capsids—the protective proteinaceous shells that comprise the that they evolved on about 20 independent occasions, and in some of cores of virus particles (virions)—is unique to bona fide viruses and these cases likely ancestors are identifiable among the proteins of distinguishes them from other types of selfish genetic elements cellular organisms. -
A Small Molecule Compound IMB-LA Inhibits HIV-1 Infection By
www.nature.com/scientificreports OPEN A small molecule compound IMB-LA inhibits HIV-1 infection by preventing viral Vpu from Received: 18 May 2015 Accepted: 19 November 2015 antagonizing the host restriction Published: 16 December 2015 factor BST-2 Zeyun Mi1,5,*, Jiwei Ding1,*, Quan Zhang1,*, Jianyuan Zhao2, Ling Ma1, Haisheng Yu6, Zhenlong Liu3, Guangzhi Shan1, Xiaoyu Li1, Jinming Zhou1, Tao Wei2, Liguo Zhang6, Fei Guo4, Chen Liang3 & Shan Cen1 Human BST-2 inhibits HIV-1 replication by tethering nascent virions to the cell surface. HIV-1 codes Vpu that counteracts BST-2 by down-regulating this restriction factor from the cell surface. This important function makes Vpu a potential therapeutic target. Yet, no agents have been reported to block Vpu from antagonizing BST-2. In this study, we report a small molecule compound IMB-LA that abrogates the function of Vpu and thereby strongly suppresses HIV-1 replication by sensitizing the virus to BST-2 restriction. Further studies revealed that IMB-LA specifically inhibits Vpu-mediated degradation of BST-2 and restores the expression of BST-2 at the cell surface. Although IMB-LA does not prevent Vpu from interacting with BST-2 or β-TrCP2-containing ubiquitin E3 ligase, sorting of BST-2 into lysosomes in Vpu-expressing cells is blocked by IMB-LA. Most importantly, HIV-1 release and infection is inhibited by IMB-LA only in BST-2-expressing cells. In summary, results herein demonstrated that IMB-LA could specifically inhibit the degradation of BST-2 induced by Vpu, and impair HIV-1 replication in a BST-2 dependent manner, suggesting the feasibility of utilizing small molecule compounds to disable the antagonist function of Vpu and thereby expose HIV-1 to the restriction by BST-2. -
A Family of Mammalian E3 Ubiquitin Ligases That Contain the UBR Box Motif and Recognize N-Degrons Takafumi Tasaki,1 Lubbertus C
MOLECULAR AND CELLULAR BIOLOGY, Aug. 2005, p. 7120–7136 Vol. 25, No. 16 0270-7306/05/$08.00ϩ0 doi:10.1128/MCB.25.16.7120–7136.2005 Copyright © 2005, American Society for Microbiology. All Rights Reserved. A Family of Mammalian E3 Ubiquitin Ligases That Contain the UBR Box Motif and Recognize N-Degrons Takafumi Tasaki,1 Lubbertus C. F. Mulder,2 Akihiro Iwamatsu,3 Min Jae Lee,1 Ilia V. Davydov,4† Alexander Varshavsky,4 Mark Muesing,2 and Yong Tae Kwon1* Center for Pharmacogenetics and Department of Pharmaceutical Sciences, School of Pharmacy, University of Pittsburgh, Pittsburgh, Pennsylvania 152611; Aaron Diamond AIDS Research Center, The Rockefeller University, New York, New York 100162; Protein Research Network, Inc., Yokohama, Kanagawa 236-0004, Japan3; and Division of Biology, California Institute of Technology, Pasadena, California 911254 Received 15 March 2005/Returned for modification 27 April 2005/Accepted 13 May 2005 A subset of proteins targeted by the N-end rule pathway bear degradation signals called N-degrons, whose determinants include destabilizing N-terminal residues. Our previous work identified mouse UBR1 and UBR2 as E3 ubiquitin ligases that recognize N-degrons. Such E3s are called N-recognins. We report here that while double-mutant UBR1؊/؊ UBR2؊/؊ mice die as early embryos, the rescued UBR1؊/؊ UBR2؊/؊ fibroblasts still retain the N-end rule pathway, albeit of lower activity than that of wild-type fibroblasts. An affinity assay for proteins that bind to destabilizing N-terminal residues has identified, in addition to UBR1 and UBR2, a huge (570 kDa) mouse protein, termed UBR4, and also the 300-kDa UBR5, a previously characterized mammalian E3 known as EDD/hHYD. -
Type of the Paper (Article
Viruses 2018 – Breakthroughs in Viral Replication Faculty of Biology University of Barcelona Spain 7 – 9 February 2018 Conference Chair Eric O. Freed Conference Co-Chair Albert Bosch Organised by Conference Secretariat Antonio Peteira Man Luo George Andrianou Nikoleta Kiapidou Kristjana Xhuxhi Pablo Velázquez Lucia Russo Sara Martínez Lynn Huang Sarai Rodríguez Viruses 2018 – Breakthroughs in Viral Replication 1 CONTENTS Abridged Programme 5 Conference Programme 6 Welcome 13 General Information 15 Abstracts – Session 1 25 General Topics in Virology Abstracts – Session 2 45 Structural Virology Abstracts – Session 3 67 Virus Replication Compartments Abstracts – Session 4 89 Replication and Pathogenesis of RNA viruses Abstracts – Session 5 105 Genome Packaging and Replication/Assembly Abstracts – Session 6 127 Antiviral Innate Immunity and Viral Pathogenesis Abstracts – Poster Exhibition 147 List of Participants 297 Viruses 2018 – Breakthroughs in Viral Replication 3 Viruses 2018 – Breakthroughs in Viral Replication 7 – 9 February 2018, Barcelona, Spain Wednesday Thursday Friday 7 February 2018 8 February 2018 9 February 2018 S3. Virus S5. Genome Check-in Replication Packaging and Compartments Replication/Assembly Opening Ceremony S1. General Topics in Virology Morning Coffee Break S1. General Topics S3. Virus S5. Genome in Virology Replication Packaging and Compartments Replication/Assembly Lunch S2. Structural S4. Replication and S6. Antiviral Innate Virology Pathogenesis of Immunity and Viral RNA Viruses Pathogenesis Coffee Break Apéro and Poster Coffee Break Session S2. Structural S6. Antiviral Innate Virology Immunity and Viral Afternoon Conference Group Pathogenesis Photograph Closing Remarks Conference Dinner Wednesday 7 February 2018: 08:00 - 12:30 / 14:00 - 18:00 / Conference Dinner: 20:30 Thursday 8 February 2018: 08:30 - 12:30 / 14:00 - 18:30 Friday 9 February 2018: 08:30 - 12:30 / 14:00 - 18:15 Viruses 2018 – Breakthroughs in Viral Replication 5 Conference Programme Wednesday 7 February 08:00 – 08:45 Check-in 08:45 – 09:00 Opening Ceremony by Eric O. -
Dissecting Negative Regulation of Toll-Like Receptor Signaling
Review Dissecting negative regulation of Toll-like receptor signaling 1,2 1,2 1,2 Takeshi Kondo , Taro Kawai and Shizuo Akira 1 Laboratory of Host Defense, WPI Immunology Frontier Research Center, Osaka University, 3-1 Yamada-oka, Suita, Osaka 565-0871, Japan 2 Research Institute for Microbial Diseases, Osaka University, 3-1 Yamada-oka, Suita, Osaka 565-0871, Japan Toll-like receptors (TLRs) sense invading microbial pathogens. MyD88 is recruited to all TLRs except for pathogens and play crucial roles in the activation of TLR3 and associates with IL-1R-associated kinases (IRAKs) innate and adaptive immunity. However, excessive and TNFR-associated factor 6 (TRAF6), resulting in activa- TLR activation can disrupt immune homeostasis, and tion of canonical inhibitor of kappa light polypeptide gene may be responsible for the development of autoimmune enhancer in B-cells, kinases (IKKs) (IKKa and IKKb) and and inflammatory diseases. As such, the molecules and nuclear factor (NF)-kBs (Figure 1). In contrast, TRIF is pathways that negatively control TLR signaling have recruited to TLR3 and TLR4, leading to activation of been intensively investigated. Here, we discuss recent NF-kB as well as noncanonical IKKs (TRAF-family- insights into the negative regulation of TLR signaling, member-associated NF-kB activator (TANK) binding kinase with focus on three major mechanisms: (i) dissociation 1 (TBK1) and IKKi) and interferon (IFN) regulatory factor of adaptor complexes; (ii) degradation of signal proteins; (IRF)3 via TRAF proteins (Figure 2). TIRAP functions as a and (iii) transcriptional regulation. We also highlight sorting adapter that recruits MyD88 to TLR2 and TLR4, how pathogens negatively target TLR signaling as a whereas TRAM functions as a bridge adapter between TLR4 strategy to evade the host immune response. -
A Picorna-Like Virus Suppresses the N-End Rule Pathway to Inhibit Apoptosis
RESEARCH ARTICLE A picorna-like virus suppresses the N-end rule pathway to inhibit apoptosis Zhaowei Wang1,2†, Xiaoling Xia1,2,3†, Xueli Yang1, Xueyi Zhang1,2, Yongxiang Liu1,2, Di Wu1,2, Yuan Fang1,2, Yujie Liu1,2, Jiuyue Xu2, Yang Qiu2, Xi Zhou1,2* 1State Key Laboratory of Virology, College of Life Sciences, Wuhan University, Wuhan, China; 2State Key Laboratory of Virology, Wuhan Institute of Virology, Chinese Academy of Sciences, Wuhan, China; 3Guangzhou Key Laboratory of Insect Development Regulation and Application Research, Institute of Insect Science and Technology & School of Life Sciences, South China Normal University, Guangzhou, China Abstract The N-end rule pathway is an evolutionarily conserved proteolytic system that degrades proteins containing N-terminal degradation signals called N-degrons, and has emerged as a key regulator of various processes. Viruses manipulate diverse host pathways to facilitate viral replication and evade antiviral defenses. However, it remains unclear if viral infection has any impact on the N-end rule pathway. Here, using a picorna-like virus as a model, we found that viral infection promoted the accumulation of caspase-cleaved Drosophila inhibitor of apoptosis 1 (DIAP1) by inducing the degradation of N-terminal amidohydrolase 1 (NTAN1), a key N-end rule component that identifies N-degron to initiate the process. The virus-induced NTAN1 degradation is independent of polyubiquitylation but dependent on proteasome. Furthermore, the virus- induced N-end rule pathway suppression inhibits apoptosis and benefits viral replication. Thus, our findings demonstrate that a virus can suppress the N-end rule pathway, and uncover a new *For correspondence: mechanism for virus to evade apoptosis. -
A SARS-Cov-2-Human Protein-Protein Interaction Map Reveals Drug Targets and Potential Drug-Repurposing
A SARS-CoV-2-Human Protein-Protein Interaction Map Reveals Drug Targets and Potential Drug-Repurposing Supplementary Information Supplementary Discussion All SARS-CoV-2 protein and gene functions described in the subnetwork appendices, including the text below and the text found in the individual bait subnetworks, are based on the functions of homologous genes from other coronavirus species. These are mainly from SARS-CoV and MERS-CoV, but when available and applicable other related viruses were used to provide insight into function. The SARS-CoV-2 proteins and genes listed here were designed and researched based on the gene alignments provided by Chan et. al. 1 2020 . Though we are reasonably sure the genes here are well annotated, we want to note that not every protein has been verified to be expressed or functional during SARS-CoV-2 infections, either in vitro or in vivo. In an effort to be as comprehensive and transparent as possible, we are reporting the sub-networks of these functionally unverified proteins along with the other SARS-CoV-2 proteins. In such cases, we have made notes within the text below, and on the corresponding subnetwork figures, and would advise that more caution be taken when examining these proteins and their molecular interactions. Due to practical limits in our sample preparation and data collection process, we were unable to generate data for proteins corresponding to Nsp3, Orf7b, and Nsp16. Therefore these three genes have been left out of the following literature review of the SARS-CoV-2 proteins and the protein-protein interactions (PPIs) identified in this study. -
Thiopurines Activate an Antiviral Unfolded Protein Response That
bioRxiv preprint doi: https://doi.org/10.1101/2020.09.30.319863; this version posted October 1, 2020. The copyright holder for this preprint (which was not certified by peer review) is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. It is made available under aCC-BY-NC-ND 4.0 International license. 1 Thiopurines activate an antiviral unfolded protein response that blocks viral glycoprotein 2 accumulation in cell culture infection model 3 Patrick Slaine1, Mariel Kleer 2, Brett Duguay 1, Eric S. Pringle 1, Eileigh Kadijk 1, Shan Ying 1, 4 Aruna D. Balgi 3, Michel Roberge 3, Craig McCormick 1, #, Denys A. Khaperskyy 1, # 5 6 1Department of Microbiology & Immunology, Dalhousie University, 5850 College Street, Halifax 7 NS, Canada B3H 4R2 8 2Department of Microbiology, Immunology and Infectious Diseases, University of Calgary, 3330 9 Hospital Drive NW, Calgary AB, Canada T2N 4N1 10 3Department of Biochemistry and Molecular Biology, 2350 Health Sciences Mall, University of 11 British Columbia, Vancouver BC, Canada V6T 1Z3 12 13 14 #Co-corresponding authors: C.M., [email protected], D.A.K., [email protected] 15 16 17 Running Title: Drug-induced antiviral unfolded protein response 18 Keywords: virus, influenza, coronavirus, SARS-CoV-2, thiopurine, 6-thioguanine, 6- 19 thioguanosine, unfolded protein response, hemagglutinin, neuraminidase, glycosylation, host- 20 targeted antiviral 21 22 23 ABSTRACT 24 Enveloped viruses, including influenza A viruses (IAVs) and coronaviruses (CoVs), utilize the 25 host cell secretory pathway to synthesize viral glycoproteins and direct them to sites of assembly. 26 Using an image-based high-content screen, we identified two thiopurines, 6-thioguanine (6-TG) 27 and 6-thioguanosine (6-TGo), that selectively disrupted the processing and accumulation of IAV 28 glycoproteins hemagglutinin (HA) and neuraminidase (NA). -
Viroporins: Structures and Functions Beyond Cell Membrane Permeabilization
Editorial Viroporins: Structures and Functions beyond Cell Membrane Permeabilization José Luis Nieva 1,* and Luis Carrasco 2,* Received: 17 September 2015 ; Accepted: 21 September 2015 ; Published: 29 September 2015 Academic Editor: Eric O. Freed 1 Biophysics Unit (CSIC, UPV/EHU) and Biochemistry and Molecular Biology Department, University of the Basque Country (UPV/EHU), P.O. Box 644, 48080 Bilbao, Spain 2 Centro de Biología Molecular Severo Ochoa (CSIC, UAM), c/Nicolás Cabrera, 1, Universidad Autónoma de Madrid, Cantoblanco, 28049 Madrid, Spain * Correspondence: [email protected] (J.L.N.); [email protected] (L.C.); Tel.: +34-94-601-3353 (J.L.N.); +34-91-497-8450 (L.C.) Viroporins represent an interesting group of viral proteins that exhibit two sets of functions. First, they participate in several viral processes that are necessary for efficient production of virus progeny. Besides, viroporins interfere with a number of cellular functions, thus contributing to viral cytopathogenicity. Twenty years have elapsed from the first review on viroporins [1]; since then several reviews have covered the advances on viroporin structure and functioning [2–8]. This Special Issue updates and revises new emerging roles of viroporins, highlighting their potential use as antiviral targets and in vaccine development. Viroporin structure. Viroporins are usually short proteins with at least one hydrophobic amphipathic helix. Homo-oligomerization is achieved by helix–helix interactions in membranes rendering higher order structures, forming aqueous pores. Progress in viroporin structures during the last 2–3 years has in some instances provided a detailed knowledge of their functional architecture, including the fine definition of binding sites for effective inhibitors. -
Opportunistic Intruders: How Viruses Orchestrate ER Functions to Infect Cells
REVIEWS Opportunistic intruders: how viruses orchestrate ER functions to infect cells Madhu Sudhan Ravindran*, Parikshit Bagchi*, Corey Nathaniel Cunningham and Billy Tsai Abstract | Viruses subvert the functions of their host cells to replicate and form new viral progeny. The endoplasmic reticulum (ER) has been identified as a central organelle that governs the intracellular interplay between viruses and hosts. In this Review, we analyse how viruses from vastly different families converge on this unique intracellular organelle during infection, co‑opting some of the endogenous functions of the ER to promote distinct steps of the viral life cycle from entry and replication to assembly and egress. The ER can act as the common denominator during infection for diverse virus families, thereby providing a shared principle that underlies the apparent complexity of relationships between viruses and host cells. As a plethora of information illuminating the molecular and cellular basis of virus–ER interactions has become available, these insights may lead to the development of crucial therapeutic agents. Morphogenesis Viruses have evolved sophisticated strategies to establish The ER is a membranous system consisting of the The process by which a virus infection. Some viruses bind to cellular receptors and outer nuclear envelope that is contiguous with an intri‑ particle changes its shape and initiate entry, whereas others hijack cellular factors that cate network of tubules and sheets1, which are shaped by structure. disassemble the virus particle to facilitate entry. After resident factors in the ER2–4. The morphology of the ER SEC61 translocation delivering the viral genetic material into the host cell and is highly dynamic and experiences constant structural channel the translation of the viral genes, the resulting proteins rearrangements, enabling the ER to carry out a myriad An endoplasmic reticulum either become part of a new virus particle (or particles) of functions5. -
NSP4)-Induced Intrinsic Apoptosis
viruses Article Viperin, an IFN-Stimulated Protein, Delays Rotavirus Release by Inhibiting Non-Structural Protein 4 (NSP4)-Induced Intrinsic Apoptosis Rakesh Sarkar †, Satabdi Nandi †, Mahadeb Lo, Animesh Gope and Mamta Chawla-Sarkar * Division of Virology, National Institute of Cholera and Enteric Diseases, P-33, C.I.T. Road Scheme-XM, Beliaghata, Kolkata 700010, India; [email protected] (R.S.); [email protected] (S.N.); [email protected] (M.L.); [email protected] (A.G.) * Correspondence: [email protected]; Tel.: +91-33-2353-7470; Fax: +91-33-2370-5066 † These authors contributed equally to this work. Abstract: Viral infections lead to expeditious activation of the host’s innate immune responses, most importantly the interferon (IFN) response, which manifests a network of interferon-stimulated genes (ISGs) that constrain escalating virus replication by fashioning an ill-disposed environment. Interestingly, most viruses, including rotavirus, have evolved numerous strategies to evade or subvert host immune responses to establish successful infection. Several studies have documented the induction of ISGs during rotavirus infection. In this study, we evaluated the induction and antiviral potential of viperin, an ISG, during rotavirus infection. We observed that rotavirus infection, in a stain independent manner, resulted in progressive upregulation of viperin at increasing time points post-infection. Knockdown of viperin had no significant consequence on the production of total Citation: Sarkar, R.; Nandi, S.; Lo, infectious virus particles. Interestingly, substantial escalation in progeny virus release was observed M.; Gope, A.; Chawla-Sarkar, M. upon viperin knockdown, suggesting the antagonistic role of viperin in rotavirus release. Subsequent Viperin, an IFN-Stimulated Protein, studies unveiled that RV-NSP4 triggered relocalization of viperin from the ER, the normal residence Delays Rotavirus Release by Inhibiting of viperin, to mitochondria during infection. -
Journal of Virology
JOURNAL OF VIROLOGY Volume 80 September 2006 No. 18 SPOTLIGHT Articles of Significant Interest Selected from This Issue by 8847 the Editors STRUCTURE AND ASSEMBLY Alphavirus Capsid Protein Helix I Controls a Checkpoint Eunmee M. Hong, Rushika Perera, 8848–8855 in Nucleocapsid Core Assembly and Richard J. Kuhn Mutation at Residue 523 Creates a Second Receptor Tatiana Bousse and Toru Takimoto 9009–9016 Binding Site on Human Parainfluenza Virus Type 1 Hemagglutinin-Neuraminidase Protein Proteomic and Biochemical Analysis of Purified Human Elena Chertova, Oleg Chertov, Lori 9039–9052 Immunodeficiency Virus Type 1 Produced from Infected V. Coren, James D. Roser, Charles Monocyte-Derived Macrophages M. Trubey, Julian W. Bess, Jr., Raymond C. Sowder II, Eugene Barsov, Brian L. Hood, Robert J. Fisher, Kunio Nagashima, Thomas P. Conrads, Timothy D. Veenstra, Jeffrey D. Lifson, and David E. Ott Oligomerization of Hantavirus Nucleocapsid Protein: Agne Alminaite, Vera Halttunen, 9073–9081 Analysis of the N-Terminal Coiled-Coil Domain Vibhor Kumar, Antti Vaheri, Liisa Holm, and Alexander Plyusnin Crystal Structure of the Receptor-Binding Protein Head Stefano Ricagno, Vale´rie 9331–9335 Domain from Lactococcus lactis Phage bIL170 Campanacci, Ste´phanie Blangy, Silvia Spinelli, Denise Tremblay, Sylvain Moineau, Mariella Tegoni, and Christian Cambillau GENOME REPLICATION AND REGULATION OF VIRAL GENE EXPRESSION High-Throughput, Library-Based Selection of a Murine Julie H. Yu and David V. Schaffer 8981–8988 Leukemia Virus Variant To Infect Nondividing Cells Temporal Transcription Program of Recombinant Shih Sheng Jiang, I-Shou Chang, 8989–8999 Autographa californica Multiple Nucleopolyhedrosis Virus Lin-Wei Huang, Po-Cheng Chen, Chi-Chung Wen, Shu-Chen Liu, Li- Chu Chien, Chung-Yen Lin, Chao A.