DOCSLIB.ORG

Complete Sections As Applicable

Total Page：16

File Type：pdf, Size：1020Kb

Download full-text PDF Read full-text
Complete Sections As Applicable This form should be used for all taxonomic proposals. Please complete all those modules that are applicable (and then delete the unwanted sections). For guidance, see the notes written in blue and the separate document “Help with completing a taxonomic proposal” Please try to keep related proposals within a single document; you can copy the modules to create more than one genus within a new family, for example. MODULE 1: TITLE, AUTHORS, etc (to be completed by ICTV Code assigned: 2015.001a-kF officers) Short title: A new family and two new genera for classification of virophages two new species (e.g. 6 new species in the genus Zetavirus) Modules attached 1 2 3 4 5 (modules 1 and 10 are required) 6 7 8 9 10 Author(s): Matthias Fischer – Max Planck Institute for Medical Research, Germany Mart Krupovic – Institut Pasteur, France Jens H. Kuhn – NIH/NIAID/IRF-Frederick, Maryland, USA Bernard La Scola – Aix Marseille Université, France Didier Raoult – Aix Marseille Université, France Corresponding author with e-mail address: Matthias Fischer, [email protected] Mart Krupovic, [email protected] List the ICTV study group(s) that have seen this proposal: A list of study groups and contacts is provided at http://www.ictvonline.org/subcommittees.asp . If in doubt, contact the appropriate subcommittee chair (fungal, invertebrate, plant, prokaryote or vertebrate viruses) ICTV Study Group comments (if any) and response of the proposer: Date first submitted to ICTV: June 11, 2015 Date of this revision (if different to above): ICTV-EC comments and response of the proposer: Fungal and Protist Viruses Subcommittee Chair: Proposal approved for submission. Page 1 of 14 MODULE 2a: NEW SPECIES creating and naming one or more new species. If more than one, they should be a group of related species belonging to the same genus. All new species must be placed in a higher taxon. This is usually a genus although it is also permissible for species to be “unassigned” within a subfamily or family. Wherever possible, provide sequence accession number(s) for one isolate of each new species proposed. Code 2015.001aF (assigned by ICTV officers) To create 2 new species within: Fill in all that apply. Genus: Sputnikvirus (new) If the higher taxon has yet to be created (in a later module, below) write Subfamily: “(new)” after its proposed name. Family: Lavidaviridae (new) If no genus is specified, enter Order: “unassigned” in the genus box. Name of new species: Representative isolate: (only 1 GenBank sequence per species please) accession number(s) Mimivirus-dependent virus Sputnik virus 1 EU606015 Sputnik Mimivirus-dependent virus Zamilon virus HG531932 Zamilon Reasons to justify the creation and assignment of the new species: Explain how the proposed species differ(s) from all existing species. o If species demarcation criteria (see module 3) have previously been defined for the genus, explain how the new species meet these criteria. o If criteria for demarcating species need to be defined (because there will now be more than one species in the genus), please state the proposed criteria. Further material in support of this proposal may be presented in the Appendix, Module 9 Both virus species represent satellite-like viruses of protists, also known as virophages, which depend for multiplication on members of the genus Mimivirus within the family Mimiviridae. Sputnik and Zamilon are able to replicate in Acanthamoeba polyphaga cells that are co-infected with Acanthamoeba polyphaga mimivirus (APMV) or Mont1 mimivirus, respectively [1, 2]. The latter virus is more closely related to “Megavirus chilensis” [3] than to APMV [4]. Both Sputnik and Zamilon have similarly-sized (17,276-18,342 base pairs), circular double-stranded DNA genomes that code for 20-21 proteins (Module 10; Figure 1) [1, 2, 5, 6]. The virions are icosahedral with a diameter of 60-75 nm, and are composed of at least two different proteins with jelly-roll folds, the minor and the major capsid protein (Module 10; Figure 2a) [7, 8]. The capsid proteins of viruses in the proposed genus are homologous and the major capsid protein can be used as a phylogenetic marker to demonstrate membership in the proposed genus (Module 10; Figure 3). In addition to the two capsid protein genes, both species encode a FtsK-HerA family DNA- packaging ATPase, a cysteine protease, a primase-superfamily 3 helicase, a lambda-type integrase, a transposase, a Zinc-ribbon domain protein, a collagen-like protein, and six proteins of unknown function [1, 2]. Page 2 of 14 MODULE 2b: NEW SPECIES creating and naming one or more new species. If more than one, they should be a group of related species belonging to the same genus. All new species must be placed in a higher taxon. This is usually a genus although it is also permissible for species to be “unassigned” within a subfamily or family. Wherever possible, provide sequence accession number(s) for one isolate of each new species proposed. Code 2015.001bF (assigned by ICTV officers) To create 1 new species within: Fill in all that apply. Genus: Mavirus (new) If the higher taxon has yet to be created (in a later module, below) write Subfamily: “(new)” after its proposed name. Family: Lavidaviridae (new) If no genus is specified, enter Order: “unassigned” in the genus box. Name of new species: Representative isolate: (only 1 GenBank sequence per species please) accession number(s) Cafeteriavirus-dependent Maverick-related virus HQ712116 mavirus (Mavirus), strain Spezl Reasons to justify the creation and assignment of the new species: Explain how the proposed species differ(s) from all existing species. o If species demarcation criteria (see module 3) have previously been defined for the genus, explain how the new species meet these criteria. o If criteria for demarcating species need to be defined (because there will now be more than one species in the genus), please state the proposed criteria. Further material in support of this proposal may be presented in the Appendix, Module 9 Mavirus replicates in the marine heterotrophic nanoflagellate Cafeteria roenbergensis in the presence of Cafeteria roenbergensis virus (CroV) [9, 10]. The circular, double-stranded DNA genome consists of 19,063 bp and encodes 20 proteins. The virions are icosahedral with a diameter of ~75 nm, and are composed of at least two different proteins with jelly-roll folds, the minor and the major capsid protein (Module 10; Figure 2b). The capsid proteins of viruses in the proposed genus are homologous and the major capsid protein can be used as a phylogenetic marker to demonstrate membership in the proposed genus (Module 10; Figure 3). In addition to the two capsid protein genes, Mavirus encodes a FtsK-HerA family DNA- packaging ATPase, a cysteine protease, a superfamily 3 helicase, a retroviral-type integrase, a lipase, and a FNIP repeat-containing protein [9]. Mavirus shares many features with the large, virus-like transposons of the Maverick/Polinton superfamily which are widespread in eukaryotes [11, 12]. Both types of elements encode 7 homologous proteins involved in virion morphogenesis (minor and major capsid proteins, FtsK-HerA-type genome packaging ATPase and cysteine protease homologous to adenoviral maturation proteases), genome replication (protein-primed family B DNA polymerase and superfamily 3 helicase) and integration (retrovirus-like integrase which belongs to a broad superfamily of DDE transposases) [9, 13]. Furthermore, the Mavirus genome contains long inverted repeats that resemble those found at the termini of Maverick/Polinton transposons. Page 3 of 14 MODULE 3a: NEW GENUS creating a new genus Ideally, a genus should be placed within a higher taxon. Code 2015.001cF (assigned by ICTV officers) To create a new genus within: Fill in all that apply. Subfamily: If the higher taxon has yet to be created (in a later module, below) write “(new)” Family: Lavidaviridae (new) after its proposed name. Order: If no family is specified, enter “unassigned” in the family box naming a new genus Code 2015.001dF (assigned by ICTV officers) To name the new genus: Sputnikvirus Assigning the type species and other species to a new genus Code 2015.001eF (assigned by ICTV officers) To designate the following as the type species of the new genus Every genus must have a type species. This should Mimivirus-dependent virus Sputnik be a well characterized species although not necessarily the first to be discovered The new genus will also contain any other new species created and assigned to it (Module 2) and any that are being moved from elsewhere (Module 7b). Please enter here the TOTAL number of species (including the type species) that the genus will contain: 2 Reasons to justify the creation of a new genus: Additional material in support of this proposal may be presented in the Appendix, Module 9 Viruses in this genus depend on members of the genus Mimivirus within the family Mimiviridae for multiplication and are able to replicate in Acanthamoeba polyphaga cells that are co-infected with their respective associated giant virus. All viruses in this genus contain similarly-sized (17,276-18,342 base pairs), circular double-stranded DNA genomes that code for 20-21 proteins. (Module 10; Figure 1) [1, 2, 5, 6]. The virions are icosahedral with a diameter of 60-75 nm, and are composed of at least two different proteins with jelly-roll folds, the minor and the major capsid protein (Module 10; Figure 2a) [7, 8]. In addition to the two capsid protein genes, both species encode a FtsK-HerA family DNA- packaging ATPase, a cysteine protease, a primase-superfamily 3 helicase, a lambda-type integrase, a transposase, a Zinc-ribbon domain protein, a collagen-like protein, and six proteins of unknown function [1, 2].
Load more

Recommended publications
  • A New Family of Hybrid Virophages from an Animal Gut Metagenome Natalya Yutin, Vladimir V Kapitonov and Eugene V Koonin*
    Yutin et al. Biology Direct (2015) 10:19 DOI 10.1186/s13062-015-0054-9 DISCOVERY NOTES Open Access A new family of hybrid virophages from an animal gut metagenome Natalya Yutin, Vladimir V Kapitonov and Eugene V Koonin* Abstract Search of metagenomics sequence databases for homologs of virophage capsid proteins resulted in the discovery of a new family of virophages in the sheep rumen metagenome. The genomes of the rumen virophages (RVP) encode a typical virophage major capsid protein, ATPase and protease combined with a Polinton-type, protein primed family B DNA polymerase. The RVP genomes appear to be linear molecules, with terminal inverted repeats. Thus, the RVP seem to represent virophage-Polinton hybrids that are likely capable of formation of infectious virions. Virion proteins of mimiviruses were detected in the same metagenomes as the RVP suggesting that the virophages of the new family parasitize on giant viruses that infect protist inhabitants of the rumen. This article was reviewed by Mart Krupovic and Kenneth Stedman; for complete reviews, see the Reviewers’ Reports section. Findings been isolated as infectious particles and shown to be associ- With the rapid increase of the quantity and quality of ated with different members of the family Mimiviridae available metagenomics sequences, metagenomes have [11-13], and 9 additional virophage genomes have been as- become a rich source for the discovery of novel viruses sembled from aquatic metagenomes [14-16]. The first vir- [1-3]. A prominent case in point is the recent discovery ophage, named Sputnik, was discovered as a parasite of of a novel, abundant and diversified group of viruses that Acanthamoeba castellani mimivirus [11], and reproduction are chimeras of genes from single-stranded DNA and of the related Zamilon virophage is supported by several positive-strand RNA viruses [4-7].
    [Show full text]
  • 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.
    [Show full text]
  • Characteristics of Virophages and Giant Viruses Beata Tokarz-Deptuła1*, Paulina Czupryńska2, Agata Poniewierska-Baran1 and Wiesław Deptuła2
    Vol. 65, No 4/2018 487–496 https://doi.org/10.18388/abp.2018_2631 Review Characteristics of virophages and giant viruses Beata Tokarz-Deptuła1*, Paulina Czupryńska2, Agata Poniewierska-Baran1 and Wiesław Deptuła2 1Department of Immunology, 2Department of Microbiology, Faculty of Biology, University of Szczecin, Szczecin, Poland Five years after being discovered in 2003, some giant genus, Mimiviridae family (Table 3). It was found in the viruses were demonstrated to play a role of the hosts protozoan A. polyphaga in a water-cooling tower in Brad- for virophages, their parasites, setting out a novel and ford (Table 1). Sputnik has a spherical dsDNA genome yet unknown regulatory mechanism of the giant virus- closed in a capsid with icosahedral symmetry, 50–74 nm es presence in an aqueous. So far, 20 virophages have in size, inside which there is a lipid membrane made of been registered and 13 of them have been described as phosphatidylserine, which probably protects the genetic a metagenomic material, which indirectly impacts the material of the virophage (Claverie et al., 2009; Desnues number of single- and multi-cell organisms, the environ- et al., 2012). Sputnik’s genome has 18343 base pairs with ment where giant viruses replicate. 21 ORFs that encode proteins of 88 to 779 amino ac- ids. They compose the capsids and are responsible for Key words: virophages, giant viruses, MIMIVIRE, Sputnik N-terminal acetylation of amino acids and transposases Received: 14 June, 2018; revised: 21 August, 2018; accepted: (Claverie et al., 2009; Desnues et al., 2012; Tokarz-Dep- 09 September, 2018; available on-line: 23 October, 2018 tula et al., 2015).
    [Show full text]
  • A Field Guide to Eukaryotic Transposable Elements
    GE54CH23_Feschotte ARjats.cls September 12, 2020 7:34 Annual Review of Genetics A Field Guide to Eukaryotic Transposable Elements Jonathan N. Wells and Cédric Feschotte Department of Molecular Biology and Genetics, Cornell University, Ithaca, New York 14850; email: [email protected], [email protected] Annu. Rev. Genet. 2020. 54:23.1–23.23 Keywords The Annual Review of Genetics is online at transposons, retrotransposons, transposition mechanisms, transposable genet.annualreviews.org element origins, genome evolution https://doi.org/10.1146/annurev-genet-040620- 022145 Abstract Annu. Rev. Genet. 2020.54. Downloaded from www.annualreviews.org Access provided by Cornell University on 09/26/20. For personal use only. Copyright © 2020 by Annual Reviews. Transposable elements (TEs) are mobile DNA sequences that propagate All rights reserved within genomes. Through diverse invasion strategies, TEs have come to oc- cupy a substantial fraction of nearly all eukaryotic genomes, and they rep- resent a major source of genetic variation and novelty. Here we review the defining features of each major group of eukaryotic TEs and explore their evolutionary origins and relationships. We discuss how the unique biology of different TEs influences their propagation and distribution within and across genomes. Environmental and genetic factors acting at the level of the host species further modulate the activity, diversification, and fate of TEs, producing the dramatic variation in TE content observed across eukaryotes. We argue that cataloging TE diversity and dissecting the idiosyncratic be- havior of individual elements are crucial to expanding our comprehension of their impact on the biology of genomes and the evolution of species. 23.1 Review in Advance first posted on , September 21, 2020.
    [Show full text]
  • Tiny Giants | Maxplanckresearch 3/2019
    BIOLOGY & MEDICINE_Viruses Tiny giants Viruses are usually incredibly small, but some deviate from the norm and reach sizes greater than that of a bacterial cell. Matthias Fischer from the Max Planck Institute for Medical Research in Heidelberg is one of a small number of scientists working on giant viruses of this kind. TEXT STEFANIE REINBERGER Photo: Wolfram Scheible 58 MaxPlanckResearch 3 | 19 n the laboratory of Matthias Fischer Although they look like nothing more As giant viruses are about at the Max Planck Institute in Hei- than vials of water to the naked eye, the the same size as bacteria, delberg, vials containing water samples are actually teeming with it is almost impossible to purify them by filtration samples are lined up against one life, which only becomes visible when only. However, as viruses another, each containing a whole viewed through a microscope: countless and bacteria have different I world of aquatic single-celled organ- tiny dots are scurrying back and forth. densities, they form layers isms and viruses. The labels reveal the “The smaller ones are bacteria, which when spun in an ultracen- trifuge. Scientists can then origins of the samples: Guenzburg, are devoured by larger cells that have a extract the viral band using Kiel, but also more exotic locations nucleus. These so-called protists are the a syringe and needle. such as Tallinn or the British Virgin reason we created the collection in the Islands. “The collection is the result of first place,” Fischer explains. Indeed, many years of work,” the microbiolo- these protists are susceptible to attack Photo: Wolfram Scheible gist explains.
    [Show full text]
  • Interactions Between Marine Picoeukaryotes and Their Viruses One Cell at a Time
    Interactions between marine picoeukaryotes and their viruses one cell at a time Interacciones entre picoeucariotas marinos y sus virus célula a célula Yaiza M. Castillo de la Peña Aquesta tesi doctoral està subjecta a la llicència Reconeixement 4.0. Espanya de Creative Commons . Esta tesis doctoral está sujeta a la licencia Reconocimiento 4.0. España de Creative Commons . This doctoral thesis is licensed under the Creative Commons Attribution 4.0. Spain License . Interactions between marine picoeukaryotes and their viruses one cell at a time (Interacciones entre picoeucariotas marinos y sus virus célula a célula) Yaiza M. Castillo de la Peña Tesis doctoral presentada por Dª Yaiza M. Castillo de la Peña para obtener el grado de Doctora por la Universitat de Barcelona y el Institut de Ciències del Mar, programa de doctorado en Biotecnología, Facultat de Farmàcia i Ciències de l’Alimentació . Directoras: Dra. Mª Dolors Vaqué Vidal y Dra. Marta Sebastián Caumel Tutora: Dra. Josefa Badía Palacín Universitat de Barcelona (UB) Institut de Ciències del Mar (ICM-CSIC) La doctoranda La directora La co -directora La tutora Yaiza M. Castillo Dolors Vaqué Marta Sebastián Josefa Badía En Barcelona, a 25 de noviembre de 2019 Cover design and images: © Yaiza M. Castillo. TEM images from Derelle et al ., 2008 This thesis has been funded by the Spanish Ministry of Economy and competitivity (MINECO) through a PhD fellowship to Yaiza M. Castillo de la Peña (BES-2014- 067849), under the program “Formación de Personal Investigador (FPI)”, and adscribed to the project: “Impact of viruses on marine microbial communities using virus-host models and metagenomic analyzes.” MEFISTO (Ref.
    [Show full text]
  • 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
    [Show full text]
  • The Origins of Giant Viruses, Virophages and Their Relatives in Host Genomes Aris Katzourakis* and Amr Aswad
    Katzourakis A and Aswad A BMC Biology 2014, 12:51 http://www.biomedcentral.com/1741-7007/12/51 COMMENTARY The origins of giant viruses, virophages and their relatives in host genomes Aris Katzourakis* and Amr Aswad Abstract including the discovery last month of Samba virus, a wild mimivirus from the Amazonian Rio Negro [4]. Al- Giant viruses have revealed a number of surprises that though slightly larger, Samba virus shares identity across challenge conventions on what constitutes a virus. the majority of its genome to the original Bradford The Samba virus newly isolated in Brazil expands the mimivirus, further expanding the widespread distribu- known distribution of giant mimiviruses to a near- tion of these giant viruses. The defining feature of giant global scale. These viruses, together with the viruses is that they are an extreme outlier in terms of transposon-related virophages that infect them, pose a genome size: Acanthamoeba polyphaga mimivirus has a number of questions about their evolutionary origins 1.2 Mb genome [1], which was double the size of the lar- that need to be considered in the light of the gest virus known at the time, and pandoravirus genomes complex entanglement between host, virus and reach up to 2.5 Mb [2]. Giant viruses are also extreme virophage genomes. outliers in terms of their physical size, being too large to pass through porcelain filters, a criterion historically See research article: used to define a virus. As a further challenge to the trad- http://www.virologyj.com/content/11/1/95. itional definition of viruses, giant viruses have several es- sential protein synthesis genes that have thus far been The discovery of giant viruses thought to be exclusive to cellular life [1].
    [Show full text]
  • Virophages Question the Existence of Satellites
    CORRESPONDENCE LINK TO ORIGINAL ARTICLE LINK TO AUTHOR’S REPLY located in front of 12 out of 21 Sputnik coding sequences and all 20 Cafeteria roenbergensis Virophages question the virus coding sequences (both promoters being associated with the late expression of genes) existence of satellites imply that virophage gene expression is gov- erned by the transcription machinery of the Christelle Desnues and Didier Raoult host virus during the late stages of infection. Another point concerns the effect of the virophage on the host virus. It has been argued In a recent Comment (Virophages or satel- genome sequences of other known viruses that the effect of Sputnik or Mavirus on the lite viruses? Nature Rev. Microbiol. 9, 762– indicates that the virophages probably belong host is similar to that observed for STNV and 763 (2011))1, Mart Krupovic and Virginija to a new viral family. This is further supported its helper virus1. However, in some cases the Cvirkaite-Krupovic argued that the recently by structural analysis of Sputnik, which infectivity of TNV is greater when inoculated described virophages, Sputnik and Mavirus, showed that MCP probably adopts a double- along with STNV (or its nucleic acid) than should be classified as satellite viruses. In a jelly-roll fold, although there is no sequence when inoculated alone, suggesting that STNV response2, to which Krupovic and Cvirkaite- similarity between the virophage MCPs and makes cells more susceptible to TNV11. Such Krupovic replied3, Matthias Fisher presented those of other members of the bacteriophage an effect has never been observed for Sputnik two points supporting the concept of the PRD1–adenovirus lineage9.
    [Show full text]
  • Exploration of the Propagation of Transpovirons Within Mimiviridae Reveals a Unique Example of Commensalism in the Viral World
    The ISME Journal (2020) 14:727–739 https://doi.org/10.1038/s41396-019-0565-y ARTICLE Exploration of the propagation of transpovirons within Mimiviridae reveals a unique example of commensalism in the viral world 1 1 1 1 1 Sandra Jeudy ● Lionel Bertaux ● Jean-Marie Alempic ● Audrey Lartigue ● Matthieu Legendre ● 2 1 1 2 3 4 Lucid Belmudes ● Sébastien Santini ● Nadège Philippe ● Laure Beucher ● Emanuele G. Biondi ● Sissel Juul ● 4 2 1 1 Daniel J. Turner ● Yohann Couté ● Jean-Michel Claverie ● Chantal Abergel Received: 9 September 2019 / Revised: 27 November 2019 / Accepted: 28 November 2019 / Published online: 10 December 2019 © The Author(s) 2019. This article is published with open access Abstract Acanthamoeba-infecting Mimiviridae are giant viruses with dsDNA genome up to 1.5 Mb. They build viral factories in the host cytoplasm in which the nuclear-like virus-encoded functions take place. They are themselves the target of infections by 20-kb-dsDNA virophages, replicating in the giant virus factories and can also be found associated with 7-kb-DNA episomes, dubbed transpovirons. Here we isolated a virophage (Zamilon vitis) and two transpovirons respectively associated to B- and C-clade mimiviruses. We found that the virophage could transfer each transpoviron provided the host viruses were devoid of 1234567890();,: 1234567890();,: a resident transpoviron (permissive effect). If not, only the resident transpoviron originally isolated from the corresponding virus was replicated and propagated within the virophage progeny (dominance effect). Although B- and C-clade viruses devoid of transpoviron could replicate each transpoviron, they did it with a lower efficiency across clades, suggesting an ongoing process of adaptive co-evolution.
    [Show full text]
  • Endogenous Virophages Populate the Genomes of a Marine Heterotrophic Flagellate
    bioRxiv preprint doi: https://doi.org/10.1101/2020.11.30.404863; this version posted November 30, 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. Endogenous virophages populate the genomes of a marine heterotrophic flagellate Thomas Hackl1, Sarah Duponchel1, Karina Barenhoff1, Alexa Weinmann1 & Matthias G. Fischer1* Affiliations 1. Max Planck Institute for Medical Research, Department of Biomolecular Mechanisms, 69120 Heidelberg, Germany *Corresponding author ([email protected]) Abstract Endogenous viral elements (EVEs) are frequently found in eukaryotic genomes, yet their integration dynamics and biological functions remain largely unknown. Unlike most other eukaryotic DNA viruses, the virophage mavirus integrates efficiently into the nuclear genome of its host, the marine heterotrophic flagellate Cafeteria burkhardae. Mavirus EVEs can reactivate upon superinfection with the lytic giant virus CroV and may act as an adaptive antiviral defense system, because mavirus increases host population survival during a coinfection with CroV. However, the prevalence of endogenous virophages in natural flagellate populations has not been explored. Here we report dozens of endogenous mavirus-like elements (EMALEs) in the nuclear genomes of four C. burkhardae strains. EMALEs were typically 20 kilobase pairs long and constituted 0.7% to 1.8% of each host genome. We analyzed 33 fully assembled EMALEs that fell into two main clusters and eight types based on GC-content, nucleotide similarity, and coding potential. Inter-strain comparison showed conservation of some EMALE insertion loci, whereas the majority of integration sites were unique to a given host strain.
    [Show full text]
  • Host Genome Integration and Giant Virus-Induced Reactivation of the Virophage Mavirus
    bioRxiv preprint doi: https://doi.org/10.1101/068312; this version posted October 14, 2016. 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. Host genome integration and giant virus-induced reactivation of the virophage mavirus Matthias G. Fischer1* and Thomas Hackl1† 1Department of Biomolecular Mechanisms, Max Planck Institute for Medical Research, 69120 Heidelberg, Germany †Present address: Massachusetts Institute of Technology, 15 Vassar Street, Cambridge, MA 02139, USA Endogenous viral elements (EVEs) are increasingly found in eukaryotic genomes1, yet little is known about their origins, dynamics, or function. Here, we provide a compelling example of a DNA virus that readily integrates into a eukaryotic genome where it acts as an inducible antiviral defense system. We found that the virophage mavirus2, a parasite of the giant Cafeteria roenbergensis virus (CroV)3, integrates at multiple sites within the nuclear genome of the marine protozoan Cafeteria roenbergensis4. The endogenous mavirus is structurally and genetically similar to eukaryotic DNA transposons and endogenous viruses of the Maverick/Polinton family5–7. Provirophage genes are not constitutively expressed, but are specifically activated by superinfection with CroV, which induces the production of infectious mavirus particles. Virophages can inhibit the replication of mimivirus-like giant viruses and an anti-viral protective effect of provirophages on their hosts has been hypothesized2,8. We found that provirophage- carrying cells are not directly protected from CroV; however, lysis of these cells releases infectious mavirus particles that are then able to suppress CroV replication and enhance host survival during subsequent rounds of infection.
    [Show full text]