Viruses As Symbionts
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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. -
Mutational Load Causes Stochastic Evolutionary Outcomes In
View metadata, citation and similar papers at core.ac.uk brought to you by CORE provided by Apollo Virus Evolution, 2019, 5(1): vez008 doi: 10.1093/ve/vez008 Research article Mutational load causes stochastic evolutionary outcomes in acute RNA viral infection Downloaded from https://academic.oup.com/ve/article-abstract/5/1/vez008/5476199 by guest on 01 June 2020 Lei Zhao,1,† Ali B. Abbasi,1 and Christopher J. R. Illingworth1,2,*,‡ 1Department of Genetics, University of Cambridge, Cambridge, UK and 2Department of Applied Mathematics and Theoretical Physics, University of Cambridge, Cambridge, UK *Corresponding author: E-mail: [email protected] †http://orcid.org/0000-0002-6551-2707 ‡http://orcid.org/0000-0002-0030-2784 Abstract Mutational load is known to be of importance for the evolution of RNA viruses, the combination of a high mutation rate and large population size leading to an accumulation of deleterious mutations. However, while the effects of mutational load on global viral populations have been considered, its quantitative effects at the within-host scale of infection are less well un- derstood. We here show that even on the rapid timescale of acute disease, mutational load has an effect on within-host vi- ral adaptation, reducing the effective selection acting upon beneficial variants by 10 per cent. Furthermore, mutational load induces considerable stochasticity in the pattern of evolution, causing a more than five-fold uncertainty in the effective fitness of a transmitted beneficial variant. Our work aims to bridge the gap between classic models from population genetic theory and the biology of viral infection. -
Extreme Genome Reduction in Buchnera Spp.: Toward the Minimal Genome Needed for Symbiotic Life
Extreme genome reduction in Buchnera spp.: Toward the minimal genome needed for symbiotic life Rosario Gil, Beatriz Sabater-Mun˜ oz, Amparo Latorre, Francisco J. Silva, and Andre´ s Moya* Institut Cavanilles de Biodiversitat i Biologı´aEvolutiva, Universitat de Valencia, Apartat Oficial 2085, 46071 Vale`ncia, Spain Communicated by Francisco J. Ayala, University of California, Irvine, CA, February 5, 2002 (received for review November 27, 2001) Buchnera is a mutualistic intracellular symbiont of aphids. Their transmission (10). A recent study has demonstrated they may association began about 200 million years ago, with host and have positive effects in host fitness (14). It is conceivable that symbiont lineages evolving in parallel since that time. During this S-endosymbionts may interact and modify the established mu- coevolutionary process, Buchnera has experienced a dramatic de- tualism between the aphid and Buchnera. crease of genome size, retaining only essential genes for its Phylogenetic studies have proven that the symbiosis between specialized lifestyle. Previous studies reported that genome size in Buchnera and its host resulted from a single bacterial infection Buchnera spp. is very uniform, suggesting that genome shrinkage of the common ancestor to all extant aphids about 200 million occurred early in evolution, and that modern lineages retain the years ago (15), leading to the cospeciation of the host and their genome size of a common ancestor. Our physical mapping of symbionts. During this coevolutionary process, Buchnera suf- Buchnera genomes obtained from five aphid lineages shows that fered considerable genomic changes (i.e., a great reduction in the genome size is not conserved among them, but has been genome size, an increased AϩT bias, great accumulation of reduced down to 450 kb in some species. -
Metagenomic Analysis Indicates That Stressors Induce Production of Herpes-Like Viruses in the Coral Porites Compressa
Metagenomic analysis indicates that stressors induce production of herpes-like viruses in the coral Porites compressa Rebecca L. Vega Thurbera,b,1, Katie L. Barotta, Dana Halla, Hong Liua, Beltran Rodriguez-Muellera, Christelle Desnuesa,c, Robert A. Edwardsa,d,e,f, Matthew Haynesa, Florent E. Anglya, Linda Wegleya, and Forest L. Rohwera,e aDepartment of Biology, dComputational Sciences Research Center, and eCenter for Microbial Sciences, San Diego State University, San Diego, CA 92182; bDepartment of Biological Sciences, Florida International University, 3000 North East 151st, North Miami, FL 33181; cUnite´des Rickettsies, Unite Mixte de Recherche, Centre National de la Recherche Scientifique 6020. Faculte´deMe´ decine de la Timone, 13385 Marseille, France; and fMathematics and Computer Science Division, Argonne National Laboratory, Argonne, IL 60439 Communicated by Baruch S. Blumberg, Fox Chase Cancer Center, Philadelphia, PA, September 11, 2008 (received for review April 25, 2008) During the last several decades corals have been in decline and at least established, an increase in viral particles within dinoflagellates has one-third of all coral species are now threatened with extinction. been hypothesized to be responsible for symbiont loss during Coral disease has been a major contributor to this threat, but little is bleaching (25–27). VLPs also have been identified visually on known about the responsible pathogens. To date most research has several species of scleractinian corals, specifically: Acropora muri- focused on bacterial and fungal diseases; however, viruses may also cata, Porites lobata, Porites lutea, and Porites australiensis (28). Based be important for coral health. Using a combination of empirical viral on morphological characteristics, these VLPs belong to several viral metagenomics and real-time PCR, we show that Porites compressa families including: tailed phages, large filamentous, and small corals contain a suite of eukaryotic viruses, many related to the (30–80 nm) to large (Ͼ100 nm) polyhedral viruses (29). -
Profile of Nancy A. Moran ‘‘ Always Liked Insects,’’ Says Nancy A
Profile of Nancy A. Moran ‘‘ always liked insects,’’ says Nancy A. bination,’’ she says. ‘‘Why have males Moran, Regent’s Professor of Ecol- and females, and not just reproduce by ogy and Evolutionary Biology at parthenogenesis and have all females?’’ the University of Arizona (Tuc- One of her advisors, William Hamilton, son,I AZ). ‘‘As a little kid, I was known had proposed that sexual reproduction as the girl who collected insects and had was important to create genetic diversity them in jars and things like that.’’ Years to stay one step ahead of coevolving later, this youthful bug collector has be- natural enemies, especially parasites and come a renowned entomologist whose pathogens. ‘‘I became interested in that work crosses over into multiple disci- idea and began looking at it in aphids,’’ plines, including microbiology, ecology, she says, ‘‘which are very useful since and molecular evolution. Moran’s re- they are parthogenetic for part of their search primarily focuses on the ecology life cycle’’ (3). and evolution of aphids and, since 1990, After receiving her Ph.D. in zoology has especially focused on the interaction in 1982, Moran spent the next several and coevolution of these small insects years studying evolutionary ecology in and the symbiotic bacteria that live in- aphids. ‘‘It was less than completely side of them. satisfying in a lot of ways,’’ she admits. ‘‘The whole evolution of insects has ‘‘At that time you were so far from the been in tandem with these bacteria,’’ actual genetic basis of the variation you Moran says. ‘‘We would not see insects were looking at, so you had no handle feeding on plant sap if it weren’t for as to which genes were actually causing symbiosis.’’ Elected to the National Nancy A. -
Phylogenetics of Buchnera Aphidicola Munson Et Al., 1991
Türk. entomol. derg., 2019, 43 (2): 227-237 ISSN 1010-6960 DOI: http://dx.doi.org/10.16970/entoted.527118 E-ISSN 2536-491X Original article (Orijinal araştırma) Phylogenetics of Buchnera aphidicola Munson et al., 1991 (Enterobacteriales: Enterobacteriaceae) based on 16S rRNA amplified from seven aphid species1 Farklı yaprak biti türlerinden izole edilen Buchnera aphidicola Munson et al., 1991 (Enterobacteriales: Enterobacteriaceae)’nın 16S rRNA’ya göre filogenetiği Gül SATAR2* Abstract The obligate symbiont, Buchnera aphidicola Munson et al., 1991 (Enterobacteriales: Enterobacteriaceae) is important for the physiological processes of aphids. Buchnera aphidicola genes detected in seven aphid species, collected in 2017 from different plants and altitudes in Adana Province, Turkey were analyzed to reveal phylogenetic interactions between Buchnera and aphids. The 16S rRNA gene was amplified and sequenced for this purpose and a phylogenetic tree built up by the neighbor-joining method. A significant correlation between B. aphidicola genes and the aphid species was revealed by this phylogenetic tree and the haplotype network. Specimens collected in Feke from Solanum melongena L. was distinguished from the other B. aphidicola genes on Aphis gossypii Glover, 1877 (Hemiptera: Aphididae) with a high bootstrap value of 99. Buchnera aphidicola in Myzus spp. was differentiated from others, and the difference between Myzus cerasi (Fabricius, 1775) and Myzus persicae (Sulzer, 1776) was clear. Although, B. aphidicola is specific to its host aphid, certain nucleotide differences obtained within the species could enable specification to geographic region or host plant in the future. Keywords: Aphid, genetic similarity, phylogenetics, symbiotic bacterium Öz Obligat simbiyont, Buchnera aphidicola Munson et al., 1991 (Enterobacteriales: Enterobacteriaceae), yaprak bitlerinin fizyolojik olaylarının sürdürülmesinde önemli bir rol oynar. -
Changes in Population Dynamics in Mutualistic Versus Pathogenic Viruses
Viruses 2011, 3, 12-19; doi:10.3390/v3010012 OPEN ACCESS viruses ISSN 1999-4915 www.mdpi.com/journal/viruses Commentary Changes in Population Dynamics in Mutualistic versus Pathogenic Viruses Marilyn J. Roossinck Plant Biology Division, The Samuel Roberts Noble Foundation, Inc., P.O. Box 2180, Ardmore, OK 73402, USA; E-Mail: [email protected]; Tel.: +1 580 224 6600; Fax: +1 580 224 6692. Received: 17 December 2010; in revised form: 31 December 2010 / Accepted: 6 January 2011 / Published: 17 January 2011 Abstract: Although generally regarded as pathogens, viruses can also be mutualists. A number of examples of extreme mutualism (i.e., symbiogenesis) have been well studied. Other examples of mutualism are less common, but this is likely because viruses have rarely been thought of as having any beneficial effects on their hosts. The effect of mutualism on the population dynamics of viruses is a topic that has not been addressed experimentally. However, the potential for understanding mutualism and how a virus might become a mutualist may be elucidated by understanding these dynamics. Keywords: beneficial viruses; polymerase fidelity; quasispecies; symbiosis; symbiogenesis 1. Introduction Viruses have been studied predominantly as pathogens, beginning with the first virus ever described, Tobacco mosaic virus [1] that was causing spots on tobacco plants. However, a number of viruses in plants, animals, fungi and bacteria have been described that are not pathogens; many are commensals and some are mutualists. Traditionally, mutualistic symbioses are thought of as long-term stable relationships, but viruses can clearly switch lifestyles depending on conditions. What effect does mutualism have on the population dynamics of a virus? Do the population dynamics of conditional mutualists change depending on their lifestyle? This is the subject of this brief perspective. -
Serial Horizontal Transfer of Vitamin-Biosynthetic Genes Enables the Establishment of New Nutritional Symbionts in Aphids’ Di-Symbiotic Systems
The ISME Journal (2020) 14:259–273 https://doi.org/10.1038/s41396-019-0533-6 ARTICLE Serial horizontal transfer of vitamin-biosynthetic genes enables the establishment of new nutritional symbionts in aphids’ di-symbiotic systems 1 1 1 2 2 Alejandro Manzano-Marıń ● Armelle Coeur d’acier ● Anne-Laure Clamens ● Céline Orvain ● Corinne Cruaud ● 2 1 Valérie Barbe ● Emmanuelle Jousselin Received: 25 February 2019 / Revised: 24 August 2019 / Accepted: 7 September 2019 / Published online: 17 October 2019 © The Author(s) 2019. This article is published with open access Abstract Many insects depend on obligate mutualistic bacteria to provide essential nutrients lacking from their diet. Most aphids, whose diet consists of phloem, rely on the bacterial endosymbiont Buchnera aphidicola to supply essential amino acids and B vitamins. However, in some aphid species, provision of these nutrients is partitioned between Buchnera and a younger bacterial partner, whose identity varies across aphid lineages. Little is known about the origin and the evolutionary stability of these di-symbiotic systems. It is also unclear whether the novel symbionts merely compensate for losses in Buchnera or 1234567890();,: 1234567890();,: carry new nutritional functions. Using whole-genome endosymbiont sequences of nine Cinara aphids that harbour an Erwinia-related symbiont to complement Buchnera, we show that the Erwinia association arose from a single event of symbiont lifestyle shift, from a free-living to an obligate intracellular one. This event resulted in drastic genome reduction, long-term genome stasis, and co-divergence with aphids. Fluorescence in situ hybridisation reveals that Erwinia inhabits its own bacteriocytes near Buchnera’s. Altogether these results depict a scenario for the establishment of Erwinia as an obligate symbiont that mirrors Buchnera’s. -
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. -
Table S4. Phylogenetic Distribution of Bacterial and Archaea Genomes in Groups A, B, C, D, and X
Table S4. Phylogenetic distribution of bacterial and archaea genomes in groups A, B, C, D, and X. Group A a: Total number of genomes in the taxon b: Number of group A genomes in the taxon c: Percentage of group A genomes in the taxon a b c cellular organisms 5007 2974 59.4 |__ Bacteria 4769 2935 61.5 | |__ Proteobacteria 1854 1570 84.7 | | |__ Gammaproteobacteria 711 631 88.7 | | | |__ Enterobacterales 112 97 86.6 | | | | |__ Enterobacteriaceae 41 32 78.0 | | | | | |__ unclassified Enterobacteriaceae 13 7 53.8 | | | | |__ Erwiniaceae 30 28 93.3 | | | | | |__ Erwinia 10 10 100.0 | | | | | |__ Buchnera 8 8 100.0 | | | | | | |__ Buchnera aphidicola 8 8 100.0 | | | | | |__ Pantoea 8 8 100.0 | | | | |__ Yersiniaceae 14 14 100.0 | | | | | |__ Serratia 8 8 100.0 | | | | |__ Morganellaceae 13 10 76.9 | | | | |__ Pectobacteriaceae 8 8 100.0 | | | |__ Alteromonadales 94 94 100.0 | | | | |__ Alteromonadaceae 34 34 100.0 | | | | | |__ Marinobacter 12 12 100.0 | | | | |__ Shewanellaceae 17 17 100.0 | | | | | |__ Shewanella 17 17 100.0 | | | | |__ Pseudoalteromonadaceae 16 16 100.0 | | | | | |__ Pseudoalteromonas 15 15 100.0 | | | | |__ Idiomarinaceae 9 9 100.0 | | | | | |__ Idiomarina 9 9 100.0 | | | | |__ Colwelliaceae 6 6 100.0 | | | |__ Pseudomonadales 81 81 100.0 | | | | |__ Moraxellaceae 41 41 100.0 | | | | | |__ Acinetobacter 25 25 100.0 | | | | | |__ Psychrobacter 8 8 100.0 | | | | | |__ Moraxella 6 6 100.0 | | | | |__ Pseudomonadaceae 40 40 100.0 | | | | | |__ Pseudomonas 38 38 100.0 | | | |__ Oceanospirillales 73 72 98.6 | | | | |__ Oceanospirillaceae -
Genomic Exploration of Individual Giant Ocean Viruses
The ISME Journal (2017) 11, 1736–1745 © 2017 International Society for Microbial Ecology All rights reserved 1751-7362/17 www.nature.com/ismej ORIGINAL ARTICLE Genomic exploration of individual giant ocean viruses William H Wilson1,2, Ilana C Gilg1, Mohammad Moniruzzaman3, Erin K Field1,4, Sergey Koren5, Gary R LeCleir3, Joaquín Martínez Martínez1, Nicole J Poulton1, Brandon K Swan1,6, Ramunas Stepanauskas1 and Steven W Wilhelm3 1Bigelow Laboratory for Ocean Sciences, Boothbay, ME, USA; 2School of Marine Science and Engineering, Plymouth University, Plymouth, UK; 3Department of Microbiology, The University of Tennessee, Knoxville, TN, USA; 4Department of Biology, Howell Science Complex, East Carolina University, Greenville, NC, USA; 5Genome Informatics Section, Computational and Statistical Genomics Branch, National Human Genome Research Institute, National Institutes of Health, Bethesda, MD, USA and 6National Biodefense Analysis and Countermeasures Center, Frederick, MD, USA Viruses are major pathogens in all biological systems. Virus propagation and downstream analysis remains a challenge, particularly in the ocean where the majority of their microbial hosts remain recalcitrant to current culturing techniques. We used a cultivation-independent approach to isolate and sequence individual viruses. The protocol uses high-speed fluorescence-activated virus sorting flow cytometry, multiple displacement amplification (MDA), and downstream genomic sequencing. We focused on ‘giant viruses’ that are readily distinguishable by flow cytometry. From a single- milliliter sample of seawater collected from off the dock at Boothbay Harbor, ME, USA, we sorted almost 700 single virus particles, and subsequently focused on a detailed genome analysis of 12. A wide diversity of viruses was identified that included Iridoviridae, extended Mimiviridae and even a taxonomically novel (unresolved) giant virus. -
On the Biological Success of Viruses
MI67CH25-Turner ARI 19 June 2013 8:14 V I E E W R S Review in Advance first posted online on June 28, 2013. (Changes may still occur before final publication E online and in print.) I N C N A D V A On the Biological Success of Viruses Brian R. Wasik and Paul E. Turner Department of Ecology and Evolutionary Biology, Yale University, New Haven, Connecticut 06520-8106; email: [email protected], [email protected] Annu. Rev. Microbiol. 2013. 67:519–41 Keywords The Annual Review of Microbiology is online at adaptation, biodiversity, environmental change, evolvability, extinction, micro.annualreviews.org robustness This article’s doi: 10.1146/annurev-micro-090110-102833 Abstract Copyright c 2013 by Annual Reviews. Are viruses more biologically successful than cellular life? Here we exam- All rights reserved ine many ways of gauging biological success, including numerical abun- dance, environmental tolerance, type biodiversity, reproductive potential, and widespread impact on other organisms. We especially focus on suc- cessful ability to evolutionarily adapt in the face of environmental change. Viruses are often challenged by dynamic environments, such as host immune function and evolved resistance as well as abiotic fluctuations in temperature, moisture, and other stressors that reduce virion stability. Despite these chal- lenges, our experimental evolution studies show that viruses can often readily adapt, and novel virus emergence in humans and other hosts is increasingly problematic. We additionally consider whether viruses are advantaged in evolvability—the capacity to evolve—and in avoidance of extinction. On the basis of these different ways of gauging biological success, we conclude that viruses are the most successful inhabitants of the biosphere.