High-Level Diversity of Tailed Phages, Eukaryote-Associated Viruses, and Virophage-Like Elements in the Metaviromes of Antarctic Soils
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Chlorovirus PBCV-1 Multidomain Protein A111/114R Has Three Glycosyltransferase Functions Involved in the Synthesis of Atypical N-Glycans
viruses Article Chlorovirus PBCV-1 Multidomain Protein A111/114R Has Three Glycosyltransferase Functions Involved in the Synthesis of Atypical N-Glycans Eric Noel 1,2,† , Anna Notaro 3,4,† , Immacolata Speciale 3,5,† , Garry A. Duncan 1, Cristina De Castro 5,* and James L. Van Etten 1,6,* 1 Nebraska Center for Virology, University of Nebraska, Lincoln, NE 68583-0900, USA; [email protected] (E.N.); [email protected] (G.A.D.) 2 School of Biological Sciences, University of Nebraska, Lincoln, NE 68588-0118, USA 3 Department of Chemical Sciences, University of Napoli Federico II, Via Cintia 4, 80126 Napoli, Italy; [email protected] (A.N.); [email protected] (I.S.) 4 Information Génomique et Structurale, Centre National de la Recherche Scientifique, Aix-Marseille Université, UMR 7256, IMM FR3479, Institut de Microbiologie (FR3479), CEDEX 9, 13288 Marseille, France 5 Department of Agricultural Sciences, University of Napoli Federico II, Via Università 100, 80055 Portici, Italy 6 Department of Plant Pathology, University of Nebraska, Lincoln, NE 68583-0722, USA * Correspondence: [email protected] (C.D.C.); [email protected] (J.L.V.E.) † These authors contributed equally to this work. Abstract: The structures of the four N-linked glycans from the prototype chlorovirus PBCV-1 major capsid protein do not resemble any other glycans in the three domains of life. All known chloroviruses and antigenic variants (or mutants) share a unique conserved central glycan core consisting of five sugars, except for antigenic mutant virus P1L6, which has four of the five sugars. A combination of ge- netic and structural analyses indicates that the protein coded by PBCV-1 gene a111/114r, conserved in Citation: Noel, E.; Notaro, A.; all chloroviruses, is a glycosyltransferase with three putative domains of approximately 300 amino Speciale, I.; Duncan, G.A.; De Castro, C.; Van Etten, J.L. -
Chlorovirus: a Genus of Phycodnaviridae That Infects Certain Chlorella-Like Green Algae
University of Nebraska - Lincoln DigitalCommons@University of Nebraska - Lincoln Papers in Plant Pathology Plant Pathology Department 2005 Chlorovirus: A Genus of Phycodnaviridae that Infects Certain Chlorella-Like Green Algae Ming Kang University of Nebraska-Lincoln, [email protected] David Dunigan University of Nebraska-Lincoln, [email protected] James L. Van Etten University of Nebraska-Lincoln, [email protected] Follow this and additional works at: https://digitalcommons.unl.edu/plantpathpapers Part of the Plant Pathology Commons Kang, Ming; Dunigan, David; and Van Etten, James L., "Chlorovirus: A Genus of Phycodnaviridae that Infects Certain Chlorella-Like Green Algae" (2005). Papers in Plant Pathology. 130. https://digitalcommons.unl.edu/plantpathpapers/130 This Article is brought to you for free and open access by the Plant Pathology Department at DigitalCommons@University of Nebraska - Lincoln. It has been accepted for inclusion in Papers in Plant Pathology by an authorized administrator of DigitalCommons@University of Nebraska - Lincoln. Published in Molecular Plant Pathology 6:3 (2005), pp. 213–224; doi 10.1111/j.1364-3703.2005.00281.x Copyright © 2005 Black- well Publishing Ltd. Used by permission. http://www3.interscience.wiley.com/journal/118491680/ Published online May 23, 2005. Chlorovirus: a genus of Phycodnaviridae that infects certain chlorella-like green algae Ming Kang,1 David D. Dunigan,1,2 and James L. Van Etten 1,2 1 Department of Plant Pathology and 2 Nebraska Center for Virology, University of Nebraska-Lincoln, Lincoln, NE 68583-0722, USA Correspondence — M. Kang, [email protected] ; J. L. Van Etten, [email protected] Abstract INTRODUCTION Taxonomy: Chlorella viruses are assigned to the family Phy- The chlorella viruses are large, icosahedral, plaque-form- codnaviridae, genus Chlorovirus, and are divided into ing, dsDNA viruses that infect certain unicellular, chlorella- three species: Chlorella NC64A viruses, Chlorella Pbi vi- like green algae (Van Etten et al., 1991). -
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. -
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. -
Viruses in a 14Th-Century Coprolite
AEM Accepts, published online ahead of print on 7 February 2014 Appl. Environ. Microbiol. doi:10.1128/AEM.03242-13 Copyright © 2014, American Society for Microbiology. All Rights Reserved. 1 Title: Viruses in a 14th-century coprolite 2 Running title: Viruses in a 14th-century coprolite 3 4 Sandra Appelt1,*, Laura Fancello1,*, Matthieu Le Bailly2, Didier Raoult1, Michel Drancourt1, 5 Christelle Desnues†,1 6 7 1 Aix Marseille Université, URMITE, UM63, CNRS 7278, IRD 198, Inserm 1095, 13385 8 Marseille, France. 9 2 Franche-Comté University, CNRS UMR 6249 Chrono-Environment, 25 030 Besançon, France. 10 * These authors have contributed equally to this work 11 † Corresponding author: 12 Christelle Desnues, Unité de recherche sur les maladies infectieuses et tropicales émergentes 13 (URMITE), UM63, CNRS 7278, IRD 198, Inserm 1095, Faculté de médecine, Aix Marseille 14 Université, 27 Bd Jean Moulin, 13385 Marseille, France. Tel: (+33) 4 91 38 46 30, Fax: (+33) 4 15 91 38 77 72. 16 Email: [email protected] 17 Number of words in Abstract: 133 words 18 Number of words in Main Text: 2538 words 19 Number of words in Methods: 954 words 20 Figures: 4, Supplementary Figures: 3 21 Tables: 0, Supplementary Tables: 6 22 Keywords: coprolite, paleomicrobiology, metagenomics, bacteriophages, viruses, ancient DNA 1 23 Abstract 24 Coprolites are fossilized fecal material that can reveal information about ancient intestinal and 25 environmental microbiota. Viral metagenomics has allowed systematic characterization of viral 26 diversity in environmental and human-associated specimens, but little is known about the viral 27 diversity in fossil remains. Here, we analyzed the viral community of a 14th-century coprolite 28 from a closed barrel in a Middle Age site in Belgium using electron microscopy and 29 metagenomics. -
WO 2015/061752 Al 30 April 2015 (30.04.2015) P O P CT
(12) INTERNATIONAL APPLICATION PUBLISHED UNDER THE PATENT COOPERATION TREATY (PCT) (19) World Intellectual Property Organization International Bureau (10) International Publication Number (43) International Publication Date WO 2015/061752 Al 30 April 2015 (30.04.2015) P O P CT (51) International Patent Classification: Idit; 816 Fremont Street, Apt. D, Menlo Park, CA 94025 A61K 39/395 (2006.01) A61P 35/00 (2006.01) (US). A61K 31/519 (2006.01) (74) Agent: HOSTETLER, Michael, J.; Wilson Sonsini (21) International Application Number: Goodrich & Rosati, 650 Page Mill Road, Palo Alto, CA PCT/US20 14/062278 94304 (US). (22) International Filing Date: (81) Designated States (unless otherwise indicated, for every 24 October 2014 (24.10.2014) kind of national protection available): AE, AG, AL, AM, AO, AT, AU, AZ, BA, BB, BG, BH, BN, BR, BW, BY, (25) Filing Language: English BZ, CA, CH, CL, CN, CO, CR, CU, CZ, DE, DK, DM, (26) Publication Language: English DO, DZ, EC, EE, EG, ES, FI, GB, GD, GE, GH, GM, GT, HN, HR, HU, ID, IL, IN, IR, IS, JP, KE, KG, KN, KP, KR, (30) Priority Data: KZ, LA, LC, LK, LR, LS, LU, LY, MA, MD, ME, MG, 61/895,988 25 October 2013 (25. 10.2013) US MK, MN, MW, MX, MY, MZ, NA, NG, NI, NO, NZ, OM, 61/899,764 4 November 2013 (04. 11.2013) US PA, PE, PG, PH, PL, PT, QA, RO, RS, RU, RW, SA, SC, 61/91 1,953 4 December 2013 (04. 12.2013) us SD, SE, SG, SK, SL, SM, ST, SV, SY, TH, TJ, TM, TN, 61/937,392 7 February 2014 (07.02.2014) us TR, TT, TZ, UA, UG, US, UZ, VC, VN, ZA, ZM, ZW. -
Seasonal Determinations of Algal Virus Decay Rates Reveal Overwintering in a Temperate Freshwater Pond
The ISME Journal (2016) 10, 1602–1612 © 2016 International Society for Microbial Ecology All rights reserved 1751-7362/16 www.nature.com/ismej ORIGINAL ARTICLE Seasonal determinations of algal virus decay rates reveal overwintering in a temperate freshwater pond Andrew M Long1 and Steven M Short1,2 1Department of Ecology and Evolutionary Biology, University of Toronto, Toronto, Ontario, Canada and 2Department of Biology, University of Toronto Mississauga, Mississauga, Ontario, Canada To address questions about algal virus persistence (i.e., continued existence) in the environment, rates of decay of infectivity for two viruses that infect Chlorella-like algae, ATCV-1 and CVM-1, and a virus that infects the prymnesiophyte Chrysochromulina parva, CpV-BQ1, were estimated from in situ incubations in a temperate, seasonally frozen pond. A series of experiments were conducted to estimate rates of decay of infectivity in all four seasons with incubations lasting 21 days in spring, summer and autumn, and 126 days in winter. Decay rates observed across this study were relatively low compared with previous estimates obtained for other algal viruses, and ranged from 0.012 to 11% h− 1. Overall, the virus CpV-BQ1 decayed most rapidly whereas ATCV-1 decayed most slowly, but for all viruses the highest decay rates were observed during the summer and the lowest were observed during the winter. Furthermore, the winter incubations revealed the ability of each virus to overwinter under ice as ATCV-1, CVM-1 and CpV-BQ1 retained up to 48%, 19% and 9% of their infectivity after 126 days, respectively. The observed resilience of algal viruses in a seasonally frozen freshwater pond provides a mechanism that can support the maintenance of viral seed banks in nature. -
Extended Evaluation of Viral Diversity in Lake Baikal Through Metagenomics
microorganisms Article Extended Evaluation of Viral Diversity in Lake Baikal through Metagenomics Tatyana V. Butina 1,* , Yurij S. Bukin 1,*, Ivan S. Petrushin 1 , Alexey E. Tupikin 2, Marsel R. Kabilov 2 and Sergey I. Belikov 1 1 Limnological Institute, Siberian Branch of the Russian Academy of Sciences, Ulan-Batorskaya Str., 3, 664033 Irkutsk, Russia; [email protected] (I.S.P.); [email protected] (S.I.B.) 2 Institute of Chemical Biology and Fundamental Medicine, Siberian Branch of the Russian Academy of Sciences, Lavrentiev Ave., 8, 630090 Novosibirsk, Russia; [email protected] (A.E.T.); [email protected] (M.R.K.) * Correspondence: [email protected] (T.V.B.); [email protected] (Y.S.B.) Abstract: Lake Baikal is a unique oligotrophic freshwater lake with unusually cold conditions and amazing biological diversity. Studies of the lake’s viral communities have begun recently, and their full diversity is not elucidated yet. Here, we performed DNA viral metagenomic analysis on integral samples from four different deep-water and shallow stations of the southern and central basins of the lake. There was a strict distinction of viral communities in areas with different environmental conditions. Comparative analysis with other freshwater lakes revealed the highest similarity of Baikal viromes with those of the Asian lakes Soyang and Biwa. Analysis of new data, together with previ- ously published data allowed us to get a deeper insight into the diversity and functional potential of Baikal viruses; however, the true diversity of Baikal viruses in the lake ecosystem remains still un- Citation: Butina, T.V.; Bukin, Y.S.; Petrushin, I.S.; Tupikin, A.E.; Kabilov, known. -
ICTV Code Assigned: 2011.001Ag Officers)
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: 2011.001aG officers) Short title: Change existing virus species names to non-Latinized binomials (e.g. 6 new species in the genus Zetavirus) Modules attached 1 2 3 4 5 (modules 1 and 9 are required) 6 7 8 9 Author(s) with e-mail address(es) of the proposer: Van Regenmortel Marc, [email protected] Burke Donald, [email protected] Calisher Charles, [email protected] Dietzgen Ralf, [email protected] Fauquet Claude, [email protected] Ghabrial Said, [email protected] Jahrling Peter, [email protected] Johnson Karl, [email protected] Holbrook Michael, [email protected] Horzinek Marian, [email protected] Keil Guenther, [email protected] Kuhn Jens, [email protected] Mahy Brian, [email protected] Martelli Giovanni, [email protected] Pringle Craig, [email protected] Rybicki Ed, [email protected] Skern Tim, [email protected] Tesh Robert, [email protected] Wahl-Jensen Victoria, [email protected] Walker Peter, [email protected] Weaver Scott, [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 . -
DNA Viruses: the Really Big Ones (Giruses)
View metadata, citation and similar papers at core.ac.uk brought to you by CORE provided by DigitalCommons@University of Nebraska University of Nebraska - Lincoln DigitalCommons@University of Nebraska - Lincoln Papers in Plant Pathology Plant Pathology Department 5-2010 DNA Viruses: The Really Big Ones (Giruses) James L. Van Etten University of Nebraska-Lincoln, [email protected] Leslie C. Lane University of Nebraska-Lincoln, [email protected] David Dunigan University of Nebraska-Lincoln, [email protected] Follow this and additional works at: https://digitalcommons.unl.edu/plantpathpapers Part of the Plant Pathology Commons Van Etten, James L.; Lane, Leslie C.; and Dunigan, David, "DNA Viruses: The Really Big Ones (Giruses)" (2010). Papers in Plant Pathology. 203. https://digitalcommons.unl.edu/plantpathpapers/203 This Article is brought to you for free and open access by the Plant Pathology Department at DigitalCommons@University of Nebraska - Lincoln. It has been accepted for inclusion in Papers in Plant Pathology by an authorized administrator of DigitalCommons@University of Nebraska - Lincoln. Published in Annual Review of Microbiology 64 (2010), pp. 83–99; doi: 10.1146/annurev.micro.112408.134338 Copyright © 2010 by Annual Reviews. Used by permission. http://micro.annualreviews.org Published online May 12, 2010. DNA Viruses: The Really Big Ones (Giruses) James L. Van Etten,1,2 Leslie C. Lane,1 and David D. Dunigan 1,2 1. Department of Plant Pathology, University of Nebraska–Lincoln, Lincoln, Nebraska 68583 2. Nebraska Center for Virology, University of Nebraska–Lincoln, Lincoln, Nebraska 68583 Corresponding author — J. L. Van Etten, email [email protected] Abstract Viruses with genomes greater than 300 kb and up to 1200 kb are being discovered with increas- ing frequency. -
Spindle Shaped Virus (SSV) : Mutants and Their Infectivity
Portland State University PDXScholar University Honors Theses University Honors College 2014 Spindle Shaped Virus (SSV) : Mutants and Their Infectivity Thien Hoang Portland State University Follow this and additional works at: https://pdxscholar.library.pdx.edu/honorstheses Let us know how access to this document benefits ou.y Recommended Citation Hoang, Thien, "Spindle Shaped Virus (SSV) : Mutants and Their Infectivity" (2014). University Honors Theses. Paper 231. https://doi.org/10.15760/honors.56 This Thesis is brought to you for free and open access. It has been accepted for inclusion in University Honors Theses by an authorized administrator of PDXScholar. Please contact us if we can make this document more accessible: [email protected]. Spindle Shaped Virus (SSV): Mutants and Their Infectivity by Thien Hoang An undergraduate honors thesis submitted in partial fulfillment of the requirements for the degree of Bachelor of Science in University Honors and Biology: Micro/molecular biology Thesis Adviser Dr. Kenneth Stedman Portland State University 2014 Abstract: SSV1 is an archaeal virus that infects the thermoacidophile Sulfolobus residing in hot springs. The lemon shaped/spindle-shaped fuselloviruses (SSV) that infect Sulfolobus solfataricus is quite morphologically different from almost all other viruses. Because these archaeal viruses live in hot springs with high temperatures and low pH, their genomes and structures have adapted to withstand such harsh conditions. Little research has been done on these extreme viruses, and of the little research, SSV has been the most prominent. Not much is known about the genes that the genome encodes and so I have inserted transposons randomly into genome to determine functionality. -
Meta-Transcriptomic Detection of Diverse and Divergent RNA Viruses
bioRxiv preprint doi: https://doi.org/10.1101/2020.06.08.141184; this version posted June 8, 2020. The copyright holder for this preprint (which was not certified by peer review) is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. It is made available under aCC-BY-NC-ND 4.0 International license. 1 Meta-transcriptomic detection of diverse and divergent 2 RNA viruses in green and chlorarachniophyte algae 3 4 5 Justine Charon1, Vanessa Rossetto Marcelino1,2, Richard Wetherbee3, Heroen Verbruggen3, 6 Edward C. Holmes1* 7 8 9 1Marie Bashir Institute for Infectious Diseases and Biosecurity, School of Life and 10 Environmental Sciences and School of Medical Sciences, The University of Sydney, 11 Sydney, Australia. 12 2Centre for Infectious Diseases and Microbiology, Westmead Institute for Medical 13 Research, Westmead, NSW 2145, Australia. 14 3School of BioSciences, University of Melbourne, VIC 3010, Australia. 15 16 17 *Corresponding author: 18 Marie Bashir Institute for Infectious Diseases and Biosecurity, School of Life and 19 Environmental Sciences and School of Medical Sciences, 20 The University of Sydney, 21 Sydney, NSW 2006, Australia. 22 Tel: +61 2 9351 5591 23 Email: [email protected] 1 bioRxiv preprint doi: https://doi.org/10.1101/2020.06.08.141184; this version posted June 8, 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.