Interspecific Interactions That Affect Ageing
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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 The copyright holder for this preprint (which was not certified by peer review) is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity.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 The copyright holder for this preprint (which was not certified by peer review) is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity.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. -
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. -
Giant Virus with a Remarkable Complement of Genes Infects Marine Zooplankton
Giant virus with a remarkable complement of genes infects marine zooplankton Matthias G. Fischera, Michael J. Allenb, William H. Wilsonc, and Curtis A. Suttlea,d,e,1 Departments of aMicrobiology and Immunology, dBotany, and eEarth and Ocean Sciences, University of British Columbia, Vancouver, BC, Canada V6T 1Z4; bPlymouth Marine Laboratory, Plymouth PL1 3DH, United Kingdom; and cBigelow Laboratory for Ocean Sciences, West Boothbay Harbor, ME 04575-0475 Edited* by James L. Van Etten, University of Nebraska, Lincoln, NE, and approved October 4, 2010 (received for review June 2, 2010) As major consumers of heterotrophic bacteria and phytoplankton, viruses (13), was originally misidentified as Bodo sp. (12). It is a 2- microzooplankton are a critical link in aquatic foodwebs. Here, we μm– to 6-μm–long bicosoecid heterokont phagotrophic flagellate show that a major marine microflagellate grazer is infected by (Stramenopiles) that is widespread in marine environments and is a giant virus, Cafeteria roenbergensis virus (CroV), which has the found in various habitats such as surface waters, deep sea sedi- largest genome of any described marine virus (≈730 kb of double- ments, and hydrothermal vents (14, 15). Populations of C. roen- stranded DNA). The central 618-kb coding part of this AT-rich ge- bergensis may be regulated by viruses in nature (16). nome contains 544 predicted protein-coding genes; putative early and late promoter motifs have been detected and assigned to 191 Results and Discussion and 72 of them, respectively, and at least 274 genes were expressed General Genome Features. The genome of CroV is a linear double- during infection. -
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 -
Discovery and Further Studies on Giant Viruses
Discovery and Further Studies on Giant Viruses at the IHU Mediterranee Infection That Modified the Perception of the Virosphere Clara Rolland, Julien Andreani, Amina Louazani, Sarah Aherfi, Rania Francis, Rodrigo Rodrigues, Ludmila Silva, Dehia Sahmi, Said Mougari, Nisrine Chelkha, et al. To cite this version: Clara Rolland, Julien Andreani, Amina Louazani, Sarah Aherfi, Rania Francis, et al.. Discovery and Further Studies on Giant Viruses at the IHU Mediterranee Infection That Modified the Perception of the Virosphere. Viruses, MDPI, 2019, 11 (4), pp.312. 10.3390/v11040312. hal-02094406 HAL Id: hal-02094406 https://hal.archives-ouvertes.fr/hal-02094406 Submitted on 19 Dec 2020 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. Distributed under a Creative Commons Attribution - NoDerivatives| 4.0 International License viruses Review Discovery and Further Studies on Giant Viruses at the IHU Mediterranee Infection That Modified the Perception of the Virosphere Clara Rolland 1, Julien Andreani 1, Amina Cherif Louazani 1, Sarah Aherfi 1,3, Rania Francis 1 -
Evolution of Double-Stranded DNA Viruses of Eukaryotes: from Bacteriophages to Transposons to Giant Viruses Eugene V
Evolution of double-stranded DNA viruses of eukaryotes: from bacteriophages to transposons to giant viruses Eugene V. Koonin, Mart Krupovic, Natalya Yutin To cite this version: Eugene V. Koonin, Mart Krupovic, Natalya Yutin. Evolution of double-stranded DNA viruses of eukaryotes: from bacteriophages to transposons to giant viruses. Annals of the New York Academy of Sciences, Wiley, 2015, DNA Habitats and Their RNA Inhabitants, 1341 (1), pp.10-24. 10.1111/nyas.12728. pasteur-01977390 HAL Id: pasteur-01977390 https://hal-pasteur.archives-ouvertes.fr/pasteur-01977390 Submitted on 10 Jan 2019 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. Distributed under a Creative Commons Attribution - NonCommercial| 4.0 International License Ann. N.Y. Acad. Sci. ISSN 0077-8923 ANNALS OF THE NEW YORK ACADEMY OF SCIENCES Issue: DNA Habitats and Their RNA Inhabitants Evolution of double-stranded DNA viruses of eukaryotes: from bacteriophages to transposons to giant viruses Eugene V. Koonin,1 Mart Krupovic,2 and Natalya Yutin1 1National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, Maryland. 2Institut Pasteur, Unite´ Biologie Moleculaire´ du Gene` chez les Extremophiles,ˆ Paris, France Address for correspondence: Eugene V. -
1 Boiling Acid Mimics Intracellular Giant Virus Genome Release Jason
bioRxiv preprint doi: https://doi.org/10.1101/777854; this version posted September 20, 2019. 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. Boiling Acid Mimics Intracellular Giant Virus Genome Release Jason R. Schrad1, Jônatas S. Abrahão2, Juliana R. Cortines3*, Kristin N. Parent1* Affiliations 1Department of Biochemistry and Molecular Biology, Michigan State University, East Lansing, Michigan, USA 48824 2Department of Microbiology, Federal University of Minas Gerais, Belo Horizonte, Brazil 31270-901 3Department of Virology, Institute of Microbiology Paulo de Goes, Federal University of Rio de Janeiro, Rio de Janeiro, Rio de Janeiro, Brazil 21941-902 *Correspondence: [email protected] Summary Since their discovery, giant viruses have expanded our understanding of the principles of virology. Due to their gargantuan size and complexity, little is known about the life cycles of these viruses. To answer outstanding questions regarding giant virus infection mechanisms, we set out to determine biomolecular conditions that promote giant virus genome release. We generated four metastable infection intermediates in Samba virus (lineage A Mimiviridae) as visualized by cryo-EM, cryo-ET, and SEM. Each of these four intermediates reflects a stage that occurs in vivo. We show that these genome release stages are conserved in other, diverse giant viruses. Finally, we identified proteins that are released from Samba and newly discovered Tupanvirus through differential mass spectrometry. Our work revealed the molecular forces that trigger infection are conserved amongst disparate giant viruses. -
In-Depth Study of Mollivirus Sibericum, a New 30000-Y-Old Giant
In-depth study of Mollivirus sibericum, a new 30,000-y- PNAS PLUS old giant virus infecting Acanthamoeba Matthieu Legendrea,1, Audrey Lartiguea,1, Lionel Bertauxa, Sandra Jeudya, Julia Bartolia,2, Magali Lescota, Jean-Marie Alempica, Claire Ramusb,c,d, Christophe Bruleyb,c,d, Karine Labadiee, Lyubov Shmakovaf, Elizaveta Rivkinaf, Yohann Coutéb,c,d, Chantal Abergela,3, and Jean-Michel Claveriea,g,3 aInformation Génomique and Structurale, Unité Mixte de Recherche 7256 (Institut de Microbiologie de la Méditerranée, FR3479) Centre National de la Recherche Scientifique, Aix-Marseille Université, 13288 Marseille Cedex 9, France; bUniversité Grenoble Alpes, Institut de Recherches en Technologies et Sciences pour le Vivant–Laboratoire Biologie à Grande Echelle, F-38000 Grenoble, France; cCommissariat à l’Energie Atomique, Centre National de la Recherche Scientifique, Institut de Recherches en Technologies et Sciences pour le Vivant–Laboratoire Biologie à Grande Echelle, F-38000 Grenoble, France; dINSERM, Laboratoire Biologie à Grande Echelle, F-38000 Grenoble, France; eCommissariat à l’Energie Atomique, Institut de Génomique, Centre National de Séquençage, 91057 Evry Cedex, France; fInstitute of Physicochemical and Biological Problems in Soil Science, Russian Academy of Sciences, Pushchino 142290, Russia; and gAssistance Publique–Hopitaux de Marseille, 13385 Marseille, France Edited by James L. Van Etten, University of Nebraska, Lincoln, NE, and approved August 12, 2015 (received for review June 2, 2015) Acanthamoeba species are infected by the largest known DNA genome was recently made available [Pandoravirus inopinatum (15)]. viruses. These include icosahedral Mimiviruses, amphora-shaped Pan- These genomes encode a number of predicted proteins comparable doraviruses, and Pithovirus sibericum, the latter one isolated from to that of the most reduced parasitic unicellular eukaryotes, such as 30,000-y-old permafrost. -
Downloaded from NCBI
viruses Article ViralRecall—A Flexible Command-Line Tool for the Detection of Giant Virus Signatures in ‘Omic Data Frank O. Aylward * and Mohammad Moniruzzaman Department of Biological Sciences, Virginia Tech, Blacksburg, VA 24061, USA; [email protected] * Correspondence: [email protected] Abstract: Giant viruses are widespread in the biosphere and play important roles in biogeochemical cycling and host genome evolution. Also known as nucleo-cytoplasmic large DNA viruses (NCLDVs), these eukaryotic viruses harbor the largest and most complex viral genomes known. Studies have shown that NCLDVs are frequently abundant in metagenomic datasets, and that sequences derived from these viruses can also be found endogenized in diverse eukaryotic genomes. The accurate detection of sequences derived from NCLDVs is therefore of great importance, but this task is challenging owing to both the high level of sequence divergence between NCLDV families and the extraordinarily high diversity of genes encoded in their genomes, including some encoding for metabolic or translation-related functions that are typically found only in cellular lineages. Here, we present ViralRecall, a bioinformatic tool for the identification of NCLDV signatures in ‘omic data. This tool leverages a library of giant virus orthologous groups (GVOGs) to identify sequences that bear signatures of NCLDVs. We demonstrate that this tool can effectively identify NCLDV sequences with high sensitivity and specificity. Moreover, we show that it can be useful both for removing contaminating sequences in metagenome-assembled viral genomes as well as the identification of eukaryotic genomic loci that derived from NCLDV. ViralRecall is written in Python 3.5 and is freely available on GitHub: https://github.com/faylward/viralrecall. -
Mimivirus and the Emerging Concept of « Giant » Virus
Mimivirus and the emerging concept of « giant » virus 1,2+ 1 1,2 Jean-Michel Claverie , Hiroyuki Ogata , Stéphane Audic , 1 1 1 Chantal Abergel , Pierre-Edouard Fournier , Karsten Suhre 1 Information Génomique et Structurale, CNRS UPR 2589, Institute of Microbiology and Structural Biology, 31 Chemin Joseph Aiguier, 13402 Marseille Cedex 20 2 Faculté de Médecine, Université de la Méditerranée, 27 Blvd Jean Moulin, 13385 Marseille Cedex 5, France Tel : (33) 491 16 45 48 Fax: (33) 491 16 45 49 + correspondance to: E-mail : [email protected] 1 Summary The recently discovered Acanthamoeba polyphaga Mimivirus is the largest known DNA virus. Its particle size (>400 nm), genome length (1.2 million bp) and large gene repertoire (911 protein coding genes) blur the established boundaries between viruses and parasitic cellular organisms. In addition, the analysis of its genome sequence identified new types of genes not expected to be seen in a virus, such as aminoacyl-tRNA synthetases and other central components of the translation machinery. In this article, we examine how the finding of a giant virus for the first time overlapping with the world of cellular organisms in terms of size and genome complexity might durably influence the way we look at microbial biodiversity, and force us to fundamentally revise our classification of life forms. We propose to introduce the word “girus” to recognize the intermediate status of these giant DNA viruses, the genome complexity of which make them closer to small parasitic prokaryotes than to regular viruses. 2 Introduction The discovery of Acanthamoeba polyphaga Mimivirus (La Scola et al., 2003) and the analysis of its complete genome sequence (Raoult et al. -
The Incredible Diversity of Viruses
Feature ACANTHAMOEBA ACANTHAMOEBA BOTTLE-SHAPED VIRUS; VIRUS; BOTTLE-SHAPED ACIDIANUS ; FREDERICK A. MURPHY/CDC GLOBAL ; FREDERICK A. MURPHY/CDC PLOS PATHOG. PLOS / ET AL. ; E. GHIGO J. VIROL. J. / ET AL. MIMIVIRUS. CENTRE ROW L–R: RABIES VIRUS; T4 BACTERIOPHAGE; ROTAVIRUS. BOTTOM ROW L–R: EBOLA VIRUS; TOBACCO RATTLE VIRUS; VIRUS; RATTLE TOBACCO EBOLA VIRUS; L–R: ROW BOTTOM ROTAVIRUS. T4 BACTERIOPHAGE; RABIES VIRUS; L–R: ROW CENTRE MIMIVIRUS. FALSE-COLOUR ELECTRON MICROGRAPHS (NOT TO SAME SCALE). TOP ROW L–R: SMALLPOX VIRUS; VIRUS; SMALLPOX L–R: ROW SCALE). TOP SAME TO (NOT MICROGRAPHS ELECTRON FALSE-COLOUR POLYPHAGA SPL; M. HÄRING HIV-2. Viruses come in all shapes and sizes, such as the giant mimivirus (top right) and the lunar-lander-shaped bacteriophage (centre). The incredible diversity of viruses They’re everywhere virologists look, and they’re not all bad. Scientists are beginning to identify and classify the nonillions of viruses on the planet and their contributions to global ecosystems. By Amber Dance 22 | Nature | Vol 595 | 1 July 2021 ©2021 Spri nger Nature Li mited. All rights reserved. ©2021 Spri nger Nature Li mited. All rights reserved. ya Breitbart has hunted novel time to be doing this kind of research, says part of a group whose members are large in viruses in African termite Breitbart. “I think, in many ways, now is the terms of both genome size and absolute size mounds, Antarctic seals and time of the virome.” (typically, 200 nanometres or more across). water from the Red Sea. But to In 2020 alone, the ICTV added 1,044 species These viruses infect amoebae, algae and other hit pay dirt, she has only to step to its official list, and thousands more await protists, putting them in a position to influ- into her back garden in Florida. -
A Novel 80-Nm Virus Infecting Acanthamoeba Castellanii
Yaravirus: A novel 80-nm virus infecting Acanthamoeba castellanii Paulo V. M. Borattoa,b,1, Graziele P. Oliveiraa,b,1, Talita B. Machadoa, Ana Cláudia S. P. Andradea, Jean-Pierre Baudoinb,c, Thomas Klosed, Frederik Schulze, Saïd Azzab,c, Philippe Decloquementb,c, Eric Chabrièreb,c, Philippe Colsonb,c, Anthony Levasseurb,c, Bernard La Scolab,c,2, and Jônatas S. Abrahãoa,2 aLaboratório de Vírus, Instituto de Ciências Biológicas, Departamento de Microbiologia, Universidade Federal de Minas Gerais, Belo Horizonte, MG 31270-901, Brazil; bMicrobes, Evolution, Phylogeny and Infection, Aix-Marseille Université UM63, Institut de Recherche pour le Développement 198, Assistance Publique–Hôpitaux de Marseille, 13005 Marseille, France; cInstitut Hospitalo-Universitaire Méditerranée Infection, Faculté de Médecine, 13005 Marseille, France; dDepartment of Biological Sciences, Purdue University, West Lafayette, IN 47907; and eDepartment of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA 94720 Edited by James L. Van Etten, University of Nebraska-Lincoln, Lincoln, NE, and approved June 2, 2020 (received for review January 29, 2020) Here we report the discovery of Yaravirus, a lineage of amoebal others. NCDLVs have dsDNA genomes and were proposed to virus with a puzzling origin and evolution. Yaravirus presents share a monophyletic origin based on criteria that include the 80-nm-sized particles and a 44,924-bp dsDNA genome encoding sharing of a set of ancestral vertically inherited genes (17, 18). for 74 predicted proteins. Yaravirus genome annotation showed From this handful set of genes, a core gene cluster is found to be that none of its genes matched with sequences of known organ- present in almost all members of the NCLDVs, being composed isms at the nucleotide level; at the amino acid level, six predicted by five distinct genes, namely a DNA polymerase family B, a proteins had distant matches in the nr database.