Structural Variability and Complexity of the Giant Pithovirus Sibericum
Total Page:16
File Type:pdf, Size:1020Kb
Load more
Recommended publications
-
Chapitre Quatre La Spécificité D'hôtes Des Virophages Sputnik
AIX-MARSEILLE UNIVERSITE FACULTE DE MEDECINE DE MARSEILLE ECOLE DOCTORALE DES SCIENCES DE LA VIE ET DE LA SANTE THESE DE DOCTORAT Présentée par Morgan GAÏA Né le 24 Octobre 1987 à Aubagne, France Pour obtenir le grade de DOCTEUR de l’UNIVERSITE AIX -MARSEILLE SPECIALITE : Pathologie Humaine, Maladies Infectieuses Les virophages de Mimiviridae The Mimiviridae virophages Présentée et publiquement soutenue devant la FACULTE DE MEDECINE de MARSEILLE le 10 décembre 2013 Membres du jury de la thèse : Pr. Bernard La Scola Directeur de thèse Pr. Jean -Marc Rolain Président du jury Pr. Bruno Pozzetto Rapporteur Dr. Hervé Lecoq Rapporteur Faculté de Médecine, 13385 Marseille Cedex 05, France URMITE, UM63, CNRS 7278, IRD 198, Inserm 1095 Directeur : Pr. Didier RAOULT Avant-propos Le format de présentation de cette thèse correspond à une recommandation de la spécialité Maladies Infectieuses et Microbiologie, à l’intérieur du Master des Sciences de la Vie et de la Santé qui dépend de l’Ecole Doctorale des Sciences de la Vie de Marseille. Le candidat est amené à respecter des règles qui lui sont imposées et qui comportent un format de thèse utilisé dans le Nord de l’Europe permettant un meilleur rangement que les thèses traditionnelles. Par ailleurs, la partie introduction et bibliographie est remplacée par une revue envoyée dans un journal afin de permettre une évaluation extérieure de la qualité de la revue et de permettre à l’étudiant de commencer le plus tôt possible une bibliographie exhaustive sur le domaine de cette thèse. Par ailleurs, la thèse est présentée sur article publié, accepté ou soumis associé d’un bref commentaire donnant le sens général du travail. -
Diversity and Evolution of the Emerging Pandoraviridae Family
bioRxiv preprint doi: https://doi.org/10.1101/230904; this version posted December 8, 2017. The copyright holder for this preprint (which was not certified by peer review) is the author/funder. All rights reserved. No reuse allowed without permission. PNAS formated 30/08/17 Pandoraviridae Title: Diversity and evolution of the emerging Pandoraviridae family Authors: Matthieu Legendre1, Elisabeth Fabre1, Olivier Poirot1, Sandra Jeudy1, Audrey Lartigue1, Jean- Marie Alempic1, Laure Beucher2, Nadège Philippe1, Lionel Bertaux1, Karine Labadie3, Yohann Couté2, Chantal Abergel1, Jean-Michel Claverie1 Adresses: 1Structural and Genomic Information Laboratory, UMR 7256 (IMM FR 3479) CNRS Aix- Marseille Université, 163 Avenue de Luminy, Case 934, 13288 Marseille cedex 9, France. 2CEA-Institut de Génomique, GENOSCOPE, Centre National de Séquençage, 2 rue Gaston Crémieux, CP5706, 91057 Evry Cedex, France. 3 Univ. Grenoble Alpes, CEA, Inserm, BIG-BGE, 38000 Grenoble, France. Corresponding author: Jean-Michel Claverie Structural and Genomic Information Laboratory, UMR 7256, 163 Avenue de Luminy, Case 934, 13288 Marseille cedex 9, France. Tel: +33 491825447 , Email: [email protected] Co-corresponding author: Chantal Abergel Structural and Genomic Information Laboratory, UMR 7256, 163 Avenue de Luminy, Case 934, 13288 Marseille cedex 9, France. Tel: +33 491825420 , Email: [email protected] Keywords: Nucleocytoplasmic large DNA virus; environmental isolates; comparative genomics; de novo gene creation. 1 bioRxiv preprint doi: -
Imaging, Tracking and Computational Analyses of Virus Entry and Egress
1 Review 2 Imaging, Tracking and Computational Analyses of 3 Virus Entry and Egress with the Cytoskeleton 4 I-Hsuan Wang 1,†, Christoph J. Burckhardt 2,†, A. Yakimovich 3 and Urs F. Greber 4,* 5 1 Division of Virology, Institute of Medical Science, tHe University of ToKyo, ToKyo 108-8639, Japan 6 2 UT SoutHwestern Medical Center, Lyda Hill Department of Bioinformatics, Dallas TX 75390, USA 7 3 MRC Laboratory for Molecular Cell Biology, University College London, London, United Kingdom 8 4 Department of Molecular Life Sciences, University of ZuricH, WintertHurerstrasse 190, CH-8057 ZuricH, 9 Switzerland 10 * Correspondence: [email protected], Telephone: +41 44 635 4841, Fax: +41 44 635 6817 11 † These autHors contributed equally to tHis work. 12 Received: date; Accepted: date; PublisHed: date 13 Abstract: Viruses Have a dual nature - particles are ‘passive substances’ lacKing chemical energy 14 transformation, wHereas infected cells are ‘active substances’ turning-over energy. How passive 15 viral substances convert to active substances, comprising viral replication and assembly 16 compartments Has been of intense interest to virologists, cell and molecular biologists and 17 immunologists. Infection starts witH virus entry into a susceptible cell and delivers tHe viral 18 genome to the replication site. THis is a multi-step process, and involves tHe cytosKeleton and 19 associated motor proteins. LiKewise, the egress of progeny virus particles from the replication site 20 to the extracellular space is enHanced by tHe cytosKeleton and associated motor proteins. THis 21 overcomes tHe limitation of tHermal diffusion, and transports virions and virion components, 22 often in association witH cellular organelles. -
Identification of Capsid/Coat Related Protein Folds and Their Utility for Virus Classification
ORIGINAL RESEARCH published: 10 March 2017 doi: 10.3389/fmicb.2017.00380 Identification of Capsid/Coat Related Protein Folds and Their Utility for Virus Classification Arshan Nasir 1, 2 and Gustavo Caetano-Anollés 1* 1 Department of Crop Sciences, Evolutionary Bioinformatics Laboratory, University of Illinois at Urbana-Champaign, Urbana, IL, USA, 2 Department of Biosciences, COMSATS Institute of Information Technology, Islamabad, Pakistan The viral supergroup includes the entire collection of known and unknown viruses that roam our planet and infect life forms. The supergroup is remarkably diverse both in its genetics and morphology and has historically remained difficult to study and classify. The accumulation of protein structure data in the past few years now provides an excellent opportunity to re-examine the classification and evolution of viruses. Here we scan completely sequenced viral proteomes from all genome types and identify protein folds involved in the formation of viral capsids and virion architectures. Viruses encoding similar capsid/coat related folds were pooled into lineages, after benchmarking against published literature. Remarkably, the in silico exercise reproduced all previously described members of known structure-based viral lineages, along with several proposals for new Edited by: additions, suggesting it could be a useful supplement to experimental approaches and Ricardo Flores, to aid qualitative assessment of viral diversity in metagenome samples. Polytechnic University of Valencia, Spain Keywords: capsid, virion, protein structure, virus taxonomy, SCOP, fold superfamily Reviewed by: Mario A. Fares, Consejo Superior de Investigaciones INTRODUCTION Científicas(CSIC), Spain Janne J. Ravantti, The last few years have dramatically increased our knowledge about viral systematics and University of Helsinki, Finland evolution. -
An Expanded View of Viruses
An Expanded View of Viruses Urs F. Greber 1) & Ralf Bartenschlager 2) 1) Department of Molecular Life Sciences, University of Zurich, Winterthurerstrasse 190, 8057 Zurich, Switzerland 2) Department of Infectious Diseases, Molecular Virology, Heidelberg University, Im Neuenheimer Feld 345, 69198 Heidelberg, Germany Correspondence to: [email protected] [email protected] 1 figure Keywords: Zoonosis; Pandemics; Dengue, Ebola; Influenza; Entry; Endocytosis; Uncoating; Transport; Filovirus; Comparative genomics; Computational analyses; Virus-host interactions; Filamentous virus; Bacterial biofilm; Phage; Bacteriophage; Glycan; Immunity; Infection; Disease; Evolution; Variability; Giant virus; Ferret; Guinea pig; Emerging disease; Pandemic; Host range; Enveloped virus; 1 Viruses are ubiquitous, and are important in medicine, biology, biotechnology and ecology. All kinds of cells can be infected with viruses, and sometimes, a particular cell is infected with different viruses at the same time. The virus particle, ‘virion’ is composed of the viral coat proteins sheltering the viral genome, and is often surrounded by a lipid “envelope”. A virion is small compared to cells, and when it enters cells gives rise to infection distinct from an intracellular bacterial pathogen (Lwoff, 1957). A virus-infected cell has a profoundly altered homeostasis due to numerous interactions between cellular and viral components. This leads to evolutionary pressure on both virus and host, and argues that viruses are a part of life (Ludmir & Enquist, 2009). Our cells can be infected by viruses causing acute disease, such as respiratory disease by Influenza virus or rhinoviruses, or chronic disease, such as hepatitis or immune deficiency. However, most viral attacks on cells are fend off, or the spread of viruses in an infected organism is restricted, and infection abrogated. -
A Persistent Giant Algal Virus, with a Unique Morphology, Encodes An
bioRxiv preprint doi: https://doi.org/10.1101/2020.07.30.228163; this version posted January 13, 2021. 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 A persistent giant algal virus, with a unique morphology, encodes an 2 unprecedented number of genes involved in energy metabolism 3 4 Romain Blanc-Mathieu1,2, Håkon Dahle3, Antje Hofgaard4, David Brandt5, Hiroki 5 Ban1, Jörn Kalinowski5, Hiroyuki Ogata1 and Ruth-Anne Sandaa6* 6 7 1: Institute for Chemical Research, Kyoto University, Gokasho, Uji, 611-0011, Japan 8 2: Laboratoire de Physiologie Cellulaire & Végétale, CEA, Univ. Grenoble Alpes, 9 CNRS, INRA, IRIG, Grenoble, France 10 3: Department of Biological Sciences and K.G. Jebsen Center for Deep Sea Research, 11 University of Bergen, Bergen, Norway 12 4: Department of Biosciences, University of Oslo, Norway 13 5: Center for Biotechnology, Universität Bielefeld, Bielefeld, 33615, Germany 14 6: Department of Biological Sciences, University of Bergen, Bergen, Norway 15 *Corresponding author: Ruth-Anne Sandaa, +47 55584646, [email protected] 1 bioRxiv preprint doi: https://doi.org/10.1101/2020.07.30.228163; this version posted January 13, 2021. 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. 16 Abstract 17 Viruses have long been viewed as entities possessing extremely limited metabolic 18 capacities. -
The LUCA and Its Complex Virome in Another Recent Synthesis, We Examined the Origins of the Replication and Structural Mart Krupovic , Valerian V
PERSPECTIVES archaea that form several distinct, seemingly unrelated groups16–18. The LUCA and its complex virome In another recent synthesis, we examined the origins of the replication and structural Mart Krupovic , Valerian V. Dolja and Eugene V. Koonin modules of viruses and posited a ‘chimeric’ scenario of virus evolution19. Under this Abstract | The last universal cellular ancestor (LUCA) is the most recent population model, the replication machineries of each of of organisms from which all cellular life on Earth descends. The reconstruction of the four realms derive from the primordial the genome and phenotype of the LUCA is a major challenge in evolutionary pool of genetic elements, whereas the major biology. Given that all life forms are associated with viruses and/or other mobile virion structural proteins were acquired genetic elements, there is no doubt that the LUCA was a host to viruses. Here, by from cellular hosts at different stages of evolution giving rise to bona fide viruses. projecting back in time using the extant distribution of viruses across the two In this Perspective article, we combine primary domains of life, bacteria and archaea, and tracing the evolutionary this recent work with observations on the histories of some key virus genes, we attempt a reconstruction of the LUCA virome. host ranges of viruses in each of the four Even a conservative version of this reconstruction suggests a remarkably complex realms, along with deeper reconstructions virome that already included the main groups of extant viruses of bacteria and of virus evolution, to tentatively infer archaea. We further present evidence of extensive virus evolution antedating the the composition of the virome of the last universal cellular ancestor (LUCA; also LUCA. -
The Mimivirus 1.2 Mb Dsdna Genome Is Elegantly Organized Into a Nuclear-Like Weapon
The Mimivirus 1.2 Mb dsDNA genome is elegantly organized into a nuclear-like weapon Chantal Abergel ( [email protected] ) French National Centre for Scientic Research https://orcid.org/0000-0003-1875-4049 Alejandro Villalta Casares French National Centre for Scientic Research https://orcid.org/0000-0002-7857-7067 Emmanuelle Quemin University of Hamburg Alain Schmitt French National Centre for Scientic Research Jean-Marie Alempic French National Centre for Scientic Research Audrey Lartigue French National Centre for Scientic Research Vojta Prazak University of Oxford Daven Vasishtan Oxford Agathe Colmant French National Centre for Scientic Research Flora Honore French National Centre for Scientic Research https://orcid.org/0000-0002-0390-8730 Yohann Coute University Grenoble Alpes, CEA https://orcid.org/0000-0003-3896-6196 Kay Gruenewald University of Oxford https://orcid.org/0000-0002-4788-2691 Lucid Belmudes Univ. Grenoble Alpes, CEA, INSERM, IRIG, BGE Biological Sciences - Article Keywords: Mimivirus 1.2 Mb dsDNA, viral genome, organization, RNA polymerase subunits Posted Date: February 16th, 2021 DOI: https://doi.org/10.21203/rs.3.rs-83682/v1 License: This work is licensed under a Creative Commons Attribution 4.0 International License. Read Full License Mimivirus 1.2 Mb genome is elegantly organized into a nuclear-like weapon Alejandro Villaltaa#, Emmanuelle R. J. Queminb#, Alain Schmitta#, Jean-Marie Alempica, Audrey Lartiguea, Vojtěch Pražákc, Lucid Belmudesd, Daven Vasishtanc, Agathe M. G. Colmanta, Flora A. Honoréa, Yohann Coutéd, Kay Grünewaldb,c, Chantal Abergela* aAix–Marseille University, Centre National de la Recherche Scientifique, Information Génomique & Structurale, Unité Mixte de Recherche 7256 (Institut de Microbiologie de la Méditerranée, FR3479), 13288 Marseille Cedex 9, France. -
Persistent Virus and Addiction Modules: an Engine of Symbiosis
UC Irvine UC Irvine Previously Published Works Title Persistent virus and addiction modules: an engine of symbiosis. Permalink https://escholarship.org/uc/item/5ck1g026 Journal Current opinion in microbiology, 31 ISSN 1369-5274 Author Villarreal, Luis P Publication Date 2016-06-01 DOI 10.1016/j.mib.2016.03.005 Peer reviewed eScholarship.org Powered by the California Digital Library University of California Available online at www.sciencedirect.com ScienceDirect Persistent virus and addiction modules: an engine of symbiosis Luis P Villarreal The giant DNA viruses are highly prevalent and have a particular host would occasionally survive but still retain a bit of affinity for the lytic infection of unicellular eukaryotic host. The the selfish virus DNA. Thus although parasitic selfish giant viruses can also be infected by inhibitory virophage which (virus-like) information is common in the genomes of all can provide lysis protection to their host. The combined life forms, its presence was explained as mostly defective protective and destructive action of such viruses can define a remnants of past plague sweeps that provides no func- general model (PD) of virus-mediated host survival. Here, I tional benefit to the host (e.g. junk). Until recently, this present a general model for role such viruses play in the explanation seemed satisfactory. In the last twenty years, evolution of host symbiosis. By considering how virus mixtures however, various observation-based developments have can participate in addiction modules, I provide a functional compelled us to re-evaluate this stance. Both comparative explanation for persistence of virus derived genetic ‘junk’ in genomics and metagenomics (sequencing habitats) has their host genomic habitats. -
The Analysis of Translation-Related Gene Set
The analysis of translation-related gene set boosts debates around origin and evolution of mimiviruses Jonatas Santos Abrahao, Rodrigo Araujo, Philippe Colson, Bernard La Scola To cite this version: Jonatas Santos Abrahao, Rodrigo Araujo, Philippe Colson, Bernard La Scola. The analysis of translation-related gene set boosts debates around origin and evolution of mimiviruses. PLoS Ge- netics, Public Library of Science, 2017, 13 (2), 10.1371/journal.pgen.1006532. hal-01496184 HAL Id: hal-01496184 https://hal.archives-ouvertes.fr/hal-01496184 Submitted on 7 May 2018 HAL is a multi-disciplinary open access L’archive ouverte pluridisciplinaire HAL, est archive for the deposit and dissemination of sci- destinée au dépôt et à la diffusion de documents entific research documents, whether they are pub- scientifiques de niveau recherche, publiés ou non, lished or not. The documents may come from émanant des établissements d’enseignement et de teaching and research institutions in France or recherche français ou étrangers, des laboratoires abroad, or from public or private research centers. publics ou privés. REVIEW The analysis of translation-related gene set boosts debates around origin and evolution of mimiviruses JoÃnatas Santos Abrahão1,2☯, Rodrigo Arau jo2☯, Philippe Colson1, Bernard La Scola1* 1 Unite de Recherche sur les Maladies Infectieuses et Tropicales Emergentes (URMITE) UM63 CNRS 7278 IRD 198 INSERM U1095, Aix-Marseille Univ., 27 boulevard Jean Moulin, Faculte de MeÂdecine, Marseille, France, 2 Instituto de Ciências BioloÂgicas, Departamento de Microbiologia, LaboratoÂrio de VõÂrus, Universidade Federal de Minas Gerais, Belo Horizonte, Brazil ☯ These authors contributed equally to this work. * [email protected] Abstract a1111111111 a1111111111 The giant mimiviruses challenged the well-established concept of viruses, blurring the roots a1111111111 of the tree of life, mainly due to their genetic content. -
Virus World As an Evolutionary Network of Viruses and Capsidless Selfish Elements
Virus World as an Evolutionary Network of Viruses and Capsidless Selfish Elements Koonin, E. V., & Dolja, V. V. (2014). Virus World as an Evolutionary Network of Viruses and Capsidless Selfish Elements. Microbiology and Molecular Biology Reviews, 78(2), 278-303. doi:10.1128/MMBR.00049-13 10.1128/MMBR.00049-13 American Society for Microbiology Version of Record http://cdss.library.oregonstate.edu/sa-termsofuse Virus World as an Evolutionary Network of Viruses and Capsidless Selfish Elements Eugene V. Koonin,a Valerian V. Doljab National Center for Biotechnology Information, National Library of Medicine, Bethesda, Maryland, USAa; Department of Botany and Plant Pathology and Center for Genome Research and Biocomputing, Oregon State University, Corvallis, Oregon, USAb Downloaded from SUMMARY ..................................................................................................................................................278 INTRODUCTION ............................................................................................................................................278 PREVALENCE OF REPLICATION SYSTEM COMPONENTS COMPARED TO CAPSID PROTEINS AMONG VIRUS HALLMARK GENES.......................279 CLASSIFICATION OF VIRUSES BY REPLICATION-EXPRESSION STRATEGY: TYPICAL VIRUSES AND CAPSIDLESS FORMS ................................279 EVOLUTIONARY RELATIONSHIPS BETWEEN VIRUSES AND CAPSIDLESS VIRUS-LIKE GENETIC ELEMENTS ..............................................280 Capsidless Derivatives of Positive-Strand RNA Viruses....................................................................................................280 -
Structural Variability and Complexity of the Giant Pithovirus Sibericum
Structural variability and complexity of the giant Pithovirus sibericum particle revealed by high-voltage electron cryo-tomography and energy-filtered electron cryo-microscopy Kenta Okamoto, Naoyuki Miyazaki, Chihong Song, Filipe Maia, Hemanth Reddy, Chantal Abergel, Jean-Michel Claverie, Janos Hajdu, Martin Svenda, Kazuyoshi Murata To cite this version: Kenta Okamoto, Naoyuki Miyazaki, Chihong Song, Filipe Maia, Hemanth Reddy, et al.. Structural variability and complexity of the giant Pithovirus sibericum particle revealed by high-voltage electron cryo-tomography and energy-filtered electron cryo-microscopy. Scientific Reports, Nature Publishing Group, 2017, 7 (1), pp.13291. 10.1038/s41598-017-13390-4. hal-01785112 HAL Id: hal-01785112 https://hal-amu.archives-ouvertes.fr/hal-01785112 Submitted on 4 May 2018 HAL is a multi-disciplinary open access L’archive ouverte pluridisciplinaire HAL, est archive for the deposit and dissemination of sci- destinée au dépôt et à la diffusion de documents entific research documents, whether they are pub- scientifiques de niveau recherche, publiés ou non, lished or not. The documents may come from émanant des établissements d’enseignement et de teaching and research institutions in France or recherche français ou étrangers, des laboratoires abroad, or from public or private research centers. publics ou privés. www.nature.com/scientificreports OPEN Structural variability and complexity of the giant Pithovirus sibericum particle revealed by high- Received: 29 March 2017 Accepted: 22 September 2017 voltage electron cryo-tomography Published: xx xx xxxx and energy-fltered electron cryo- microscopy Kenta Okamoto1, Naoyuki Miyazaki2, Chihong Song2, Filipe R. N. C. Maia1, Hemanth K. N. Reddy1, Chantal Abergel 3, Jean-Michel Claverie3,4, Janos Hajdu1,5, Martin Svenda1 & Kazuyoshi Murata2 The Pithoviridae giant virus family exhibits the largest viral particle known so far, a prolate spheroid up to 2.5 μm in length and 0.9 μm in diameter.