DOCSLIB.ORG

Secoviridae: a Proposed Family of Plant Viruses Within the Order

Total Page：16

File Type：pdf, Size：1020Kb

Download full-text PDF Read full-text
Secoviridae: a Proposed Family of Plant Viruses Within the Order Arch Virol (2009) 154:899–907 DOI 10.1007/s00705-009-0367-z VIROLOGY DIVISION NEWS Secoviridae: a proposed family of plant viruses within the order Picornavirales that combines the families Sequiviridae and Comoviridae, the unassigned genera Cheravirus and Sadwavirus, and the proposed genus Torradovirus He´le`ne Sanfac¸on Æ Joan Wellink Æ Olivier Le Gall Æ Alexander Karasev Æ Rene´ van der Vlugt Æ Thierry Wetzel Received: 21 November 2008 / Accepted: 16 March 2009 / Published online: 7 April 2009 Ó Her Majesty the Queen in Right of Canada 2009 Abstract The order Picornavirales includes several plant specialized proteins or protein domains to move through viruses that are currently classified into the families Com- their host. In phylogenetic analysis based on their repli- oviridae (genera Comovirus, Fabavirus and Nepovirus) and cation proteins, these viruses form a separate distinct Sequiviridae (genera Sequivirus and Waikavirus) and into lineage within the picornavirales branch. To recognize the unassigned genera Cheravirus and Sadwavirus. These these common properties at the taxonomic level, we pro- viruses share properties in common with other picornavi- pose to create a new family termed ‘‘Secoviridae’’ to rales (particle structure, positive-strand RNA genome with include the genera Comovirus, Fabavirus, Nepovirus, a polyprotein expression strategy, a common replication Cheravirus, Sadwavirus, Sequivirus and Waikavirus. Two block including type III helicase, a 3C-like cysteine pro- newly discovered plant viruses share common properties teinase and type I RNA-dependent RNA polymerase). with members of the proposed family Secoviridae but have However, they also share unique properties that distinguish distinct specific genomic organizations. In phylogenetic them from other picornavirales. They infect plants and use reconstructions, they form a separate sub-branch within the Secoviridae lineage. We propose to create a new genus termed Torradovirus (type species, Tomato torrado virus) Electronic supplementary material The online version of this and to assign this genus to the proposed family article (doi:10.1007/s00705-009-0367-z) contains supplementary Secoviridae. material, which is available to authorized users. H. Sanfac¸on (&) Pacific Agri-Food Research Centre, Agriculture and Agri-Food Canada, P. O. Box 5000, Introduction 4200 Highway 97, Summerland, BC V0H-1Z0, Canada e-mail: [email protected] The creation of the order Picornavirales has given a useful J. Wellink framework for the taxonomy of a large group of viruses, Wageningen University, Wageningen, The Netherlands previously referred to as ‘picorna-like viruses’ or ‘members of the picornavirus-like superfamily or supergroup’ [23]. O. Le Gall INRA Bordeaux-Aquitaine and Universite´ Victor Segalen, Members of the order Picornavirales share many common Villenave d’Ornon, France properties. They all have small icosahedral particles (25– 30 nm) with a pseudo-T = 3 symmetry. The coat pro- A. Karasev tein(s) structure is similar among picornavirales. It is made Department of PSES, University of Idaho, Moscow, ID, USA up of jelly rolls that can all be present in one large CP, or R. van der Vlugt divided among two or three smaller CPs [8, 23 and refer- Plant Research International, Wageningen, The Netherlands ences therein]. All picornavirales have a positive-strand RNA genome that may be monopartite or bipartite. Each T. Wetzel RLP Agroscience, AlPlanta, Neustadt an der Weinstrasse, genome segment encodes a large polyprotein. This poly- Germany protein is cleaved by cysteine proteinases (such as the 123 900 H. Sanfac¸on et al. picornavirus 3C proteinase) that are structurally related to Table 1 Proposed structure of the family Secoviridae chymotrypsin [1, 9, 13]. The genome organization is con- Subfamily Genus Type species served among picornavirales. The genome contains a typical ‘replication block’ that includes a type III helicase, Comovirinae Comovirus Cowpea mosaic virus (CPMV) the 3C-like proteinase and a type I RNA-dependent RNA- Comovirinae Fabavirus Broad bean wilt virus 2 (BBWV2) polymerase (Hel–Pro–Pol) [23]. The order Picornavirales Comovirinae Nepovirus Tobacco ringspot virus (TRSV) includes viruses that infect vertebrates, insects, arthropods, N/A Sequivirus Parsnip yellow fleck virus (PYFV) higher plants, fungi and algae. N/A Waikavirus Rice tungro spherical virus (RTSV) The family Comoviridae was for a long time the only N/A Sadwavirus Satsuma dwarf virus (SDV) known group of plant ‘‘picorna-like viruses’’ [12, 18]. N/A Cheravirus Cherry rasp leaf virus (CRLV) Members of the family Comoviridae have bipartite gen- N/A Torradovirus Tomato torrado virus (ToTV) omes and contain either a single coat protein (genus N/A not applicable Nepovirus) or two coat proteins (genera: Comovirus and Fabavirus that are mainly distinguished on the basis of their mode of transmission and hierarchical clustering of clusters with cheraviruses in phylogenetic analysis using amino acid sequences). The discovery of plant ‘‘picorna- the amino acid sequence of replication proteins and has like viruses’’ with a monopartite genome and three CP other characteristics typical of cheraviruses [22]. Recently, subunits resulted in the creation of a distinct family, the elucidation of the complete genomic sequence of Sequiviridae, which currently includes two genera tomato torrado virus (ToTV) and tomato marchitez virus (Sequivirus and Waikavirus, distinguished by their specific (ToMarV), two plant ‘‘picorna-like viruses’’ of a new type, genomic organization and mode of transmission) [19]. The also suggests that they do not belong to any of the existing molecular characterization of a number of new viruses as genera and that a new genus should be created within the well as viruses previously considered to be members of the order Picornavirales [44, 45]. The ‘‘plant picornavirales’’ genus Nepovirus revealed that they differ significantly ICTV study group reevaluated the taxonomy of this group from nepoviruses, comoviruses and fabaviruses [22]. These of viruses and proposed to create a new family that would new viruses have a bipartite genome and encode either two encompass all plant viruses that currently belong to the or three CP subunits, which distinguishes them from the order Picornavirales (these viruses will be referred to as nepoviruses. In phylogenetic studies based on their repli- plant picornavirales in the remainder of this paper). cation proteins, they were found to be related to members Because the proposed family is mainly an amalgamation of of the families Comoviridae or Sequiviridae, but branched the families Sequiviridae and Comoviridae (as well as the in separate clades. Two new genera were created [22]. The unassigned genera Cheravirus and Sadwavirus), the name genus Cheravirus includes viruses that have three CPs [20], ‘‘Secoviridae’’ was selected for the new family. The family and the genus Sadwavirus includes viruses that have two is proposed to include the genera Comovirus, Fabavirus, CPs [21]. Originally, various studies proposed that the new Nepovirus, Sequivirus, Waikavirus, Cheravirus and Sad- genera should be included in the families Comoviridae or wavirus (Table 1). In addition, the study group proposed to Sequiviridae or that a new family should be created [10, 14, create a new genus termed Torradovirus and to assign this 16, 17, 24, 40]. However, at the time of creation of these new genus to the proposed family Secoviridae. The ICTV genera, the executive committee from the International executive committee approved the proposals in 2008 and Committee for the Taxonomy of Viruses (ICTV) felt that a posted them for ratification by the ICTV membership. This reevaluation of the taxonomy of plant picorna-like viruses paper discusses the rationale for the creation of the family was necessary before the two new genera could be assigned Secoviridae and genus Torradovirus and outlines the to either existing families or to a new family. Thus, for the common characteristics of members of the new family as time being, the genera Cheravirus and Sadwavirus are well as criteria distinguishing genera within the family. included in the order Picornavirales but are not assigned to any family [20–23]. The current classification has limitations in that prop- Rationale for the creation of the proposed family erties shared by cheraviruses, sadwaviruses and other plant Secoviridae viruses classified in the order Picornavirales are not rec- ognized. In addition, some viruses are still difficult to Although the diversity in the genomic organization of plant assign to existing genera/families. For example, strawberry picornavirales is apparent (Fig. 1), these viruses share latent ringspot virus (SLRSV), a founder member of the many common features. In addition to having characteris- nepovirus ‘‘group’’ is currently considered a tentative tics in common with other picornavirales as discussed sadwavirus because it encodes two CP subunits, but it above (general capsid structure, polyprotein strategy for 123 The proposed plant virus family Secoviridae 901 RNA2 RNA1 COMOVIRINAE (proposed sub-family) AUG HelPro Pol An Comovirus (CPMV) MP An CPL CPS HelPro Pol An Fabavirus (BBWV2) MP An CPL CPS Nepovirus A Subgroup A (ArMV) MP CP n HelPro Pol An Subgroup B (TBRV) MP CP An HelPro Pol An Subgroup C (ToRSV) MP CP An HelPro Pol An ADDITIONAL GENERA Sadwavirus MP An HelPro Pol An (Type species: SDV) CPL CPS Tentative species MP? CP ? An HelPro Pol A SMoV and BRNV n Tentative species A MP n HelPro Pol An SLRSV CPL CPS CP2 Cheravirus (CRLV and ALSV) A MP n HelPro Pol An CP1 CP3 CP2 Proposed Torradovirus (ToTV) A MP? n HelPro Pol An CP1 CP3 CP2 Sequivirus (PYFV) Hel Pro Pol CP1 CP3 CP2 Waikavirus (RTSV) Hel Pro Pol An CP1 CP3 Fig. 1 Genome organization of plant picornavirales. Hel Helicase, polyproteins differing by their translation initiation site as indicated Pro 3C-like Proteinase, Pol RNA-dependent RNA polymerase, CP by the second AUG above the CPMV polyprotein. Dashed lines capsid protein, MP movement protein, An poly(A). Question marks below the 30 or 50 UTR represent areas of sequence identity (?) after MP or CP indicate that the position and/or function of the between RNA1 and RNA2.
Load more

Recommended publications
  • Genome Sequence and Phylogenetic Analysis of a Novel Comovirus from Tabasco Pepper (Capsicum Frutescens)
    Virus Genes (2019) 55:854–858 https://doi.org/10.1007/s11262-019-01707-6 SHORT REPORT Genome sequence and phylogenetic analysis of a novel comovirus from tabasco pepper (Capsicum frutescens) Ricardo Iván Alcalá‑Briseño1 · Pongtharin Lotrakul2 · Rodrigo A. Valverde3 Received: 12 June 2019 / Accepted: 28 September 2019 / Published online: 11 October 2019 © Springer Science+Business Media, LLC, part of Springer Nature 2019 Abstract A virus isolate from tabasco pepper (Capsicum frutescens) has been reported as a strain of the comovirus Andean potato mottle virus (APMoV). Using the replicative intermediate viral dsRNA, the pepper virus strain was sequenced by Illumina MiSeq. The viral genome was de novo assembled resulting in two RNAs with lengths of 6028 and 3646 nt. Nucleotide sequence analysis indicated that they corresponded to the RNA-1 and RNA-2 of a novel comovirus which we tentatively named pepper mild mosaic virus (PepMMV). Predictions of the open reading frame (ORF) of RNA-1 resulted in a single ORF of 5871 nt with fve cistrons typical of comoviruses, cofactor proteinase, helicase, viral protein genome-linked, 3C-like proteinase (Pro), and RNA-dependent RNA polymerase (RdRP). Similarly, sequence analysis of RNA-2 resulted in a single ORF of 3009 nt with two cistrons typical of comoviruses: movement protein and coat protein (large coat protein and small coat proteins). In pairwise amino acid sequence alignments using the Pro-Pol protein, PepMMV shared the closest identities with broad bean true mosaic virus and cowpea mosaic virus, 56% and 53.9% respectively. In contrast, in alignments of the amino acid sequence of the coat protein (small and large coat proteins) PepMMV shared the closest identities to APMoV and red clover mottle virus, 54% and 40.9% respectively.
    [Show full text]
  • Icvg 2009 Part I Pp 1-131.Pdf
    16th Meeting of the International Council for the Study of Virus and Virus-like Diseases of the Grapevine (ICVG XVI) 31 August - 4 September 2009 Dijon, France Extended Abstracts Le Progrès Agricole et Viticole - ISSN 0369-8173 Modifications in the layout of abstracts received from authors have been made to fit with the publication format of Le Progrès Agricole et Viticole. We apologize for errors that could have arisen during the editing process despite our careful vigilance. Acknowledgements Cover page : Olivier Jacquet Photos : Gérard Simonin Jean Le Maguet ICVG Steering Committee ICVG XVI Organising committee Giovanni, P. MARTELLI, chairman (I) Elisabeth BOUDON-PADIEU (INRA) Paul GUGERLI, secretary (CH) Silvio GIANINAZZI (INRA - CNRS) Giuseppe BELLI (I) Jocelyne PÉRARD (Chaire UNESCO Culture et Johan T. BURGER (RSA) Traditions du Vin, Univ Bourgogne) Marc FUCHS (F – USA) Olivier JACQUET (Chaire UNESCO Culture et Deborah A. GOLINO (USA) Traditions du Vin, Univ Bourgogne) Raymond JOHNSON (CA) Pascale SEDDAS (INRA) Michael MAIXNER (D) Sandrine ROUSSEAUX (Institut Jules Guyot, Univ Gustavo NOLASCO (P) Bourgogne) Denis CLAIR (INRA) Ali REZAIAN (USA) Dominique MILLOT (INRA) Iannis C. RUMBOS (G) Xavier DAIRE (INRA – CRECEP) Oscar A. De SEQUEIRA (P) Mary Jo FARMER (INRA) Edna TANNE (IL) Caroline CHATILLON (SEDIAG) Etienne HERRBACH (INRA Colmar) René BOVEY, Honorary secretary Jean Le MAGUET (INRA Colmar) Honorary committee members Session convenors A. CAUDWELL (F) D. GONSALVES (USA) Michael MAIXNER H.-H. KASSEMEYER (D) Olivier LEMAIRE G. KRIEL (RSA) Etienne HERRBACH D. STELLMACH, (D) Élisabeth BOUDON-PADIEU A. TELIZ, (Mex) Sandrine ROUSSEAUX A. VUITTENEZ (F) Pascale SEDDAS B. WALTER (F). Invited speakers to ICVG XVI Giovanni P.
    [Show full text]
  • Grapevine Virus Diseases: Economic Impact and Current Advances in Viral Prospection and Management1
    1/22 ISSN 0100-2945 http://dx.doi.org/10.1590/0100-29452017411 GRAPEVINE VIRUS DISEASES: ECONOMIC IMPACT AND CURRENT ADVANCES IN VIRAL PROSPECTION AND MANAGEMENT1 MARCOS FERNANDO BASSO2, THOR VINÍCIUS MArtins FAJARDO3, PASQUALE SALDARELLI4 ABSTRACT-Grapevine (Vitis spp.) is a major vegetative propagated fruit crop with high socioeconomic importance worldwide. It is susceptible to several graft-transmitted agents that cause several diseases and substantial crop losses, reducing fruit quality and plant vigor, and shorten the longevity of vines. The vegetative propagation and frequent exchanges of propagative material among countries contribute to spread these pathogens, favoring the emergence of complex diseases. Its perennial life cycle further accelerates the mixing and introduction of several viral agents into a single plant. Currently, approximately 65 viruses belonging to different families have been reported infecting grapevines, but not all cause economically relevant diseases. The grapevine leafroll, rugose wood complex, leaf degeneration and fleck diseases are the four main disorders having worldwide economic importance. In addition, new viral species and strains have been identified and associated with economically important constraints to grape production. In Brazilian vineyards, eighteen viruses, three viroids and two virus-like diseases had already their occurrence reported and were molecularly characterized. Here, we review the current knowledge of these viruses, report advances in their diagnosis and prospection of new species, and give indications about the management of the associated grapevine diseases. Index terms: Vegetative propagation, plant viruses, crop losses, berry quality, next-generation sequencing. VIROSES EM VIDEIRAS: IMPACTO ECONÔMICO E RECENTES AVANÇOS NA PROSPECÇÃO DE VÍRUS E MANEJO DAS DOENÇAS DE ORIGEM VIRAL RESUMO-A videira (Vitis spp.) é propagada vegetativamente e considerada uma das principais culturas frutíferas por sua importância socioeconômica mundial.
    [Show full text]
  • Vector Capability of Xiphinema Americanum Sensu Lato in California 1
    Journal of Nematology 21(4):517-523. 1989. © The Society of Nematologists 1989. Vector Capability of Xiphinema americanum sensu lato in California 1 JOHN A. GRIESBACH 2 AND ARMAND R. MAGGENTI s Abstract: Seven field populations of Xiphineraa americanum sensu lato from California's major agronomic areas were tested for their ability to transmit two nepoviruses, including the prune brownline, peach yellow bud, and grapevine yellow vein strains of" tomato ringspot virus and the bud blight strain of tobacco ringspot virus. Two field populations transmitted all isolates, one population transmitted all tomato ringspot virus isolates but failed to transmit bud blight strain of tobacco ringspot virus, and the remaining four populations failed to transmit any virus. Only one population, which transmitted all isolates, bad been associated with field spread of a nepovirus. As two California populations of Xiphinema americanum sensu lato were shown to have the ability to vector two different nepoviruses, a nematode taxonomy based on a parsimony of virus-vector re- lationship is not practical for these populations. Because two California populations ofX. americanum were able to vector tobacco ringspot virus, commonly vectored by X. americanum in the eastern United States, these western populations cannot be differentiated from eastern populations by vector capability tests using tobacco ringspot virus. Key words: dagger nematode, tobacco ringspot virus, tomato ringspot virus, nepovirus, Xiphinema americanum, Xiphinema californicum. Populations of Xiphinema americanum brownline (PBL), prunus stem pitting (PSP) Cobb, 1913 shown through rigorous test- and cherry leaf mottle (CLM) (8). Both PBL ing (23) to be nepovirus vectors include X. and PSP were transmitted with a high de- americanum sensu lato (s.1.) for tobacco gree of efficiency, whereas CLM was trans- ringspot virus (TobRSV) (5), tomato ring- mitted rarely.
    [Show full text]
  • Changes to Virus Taxonomy 2004
    Arch Virol (2005) 150: 189–198 DOI 10.1007/s00705-004-0429-1 Changes to virus taxonomy 2004 M. A. Mayo (ICTV Secretary) Scottish Crop Research Institute, Invergowrie, Dundee, U.K. Received July 30, 2004; accepted September 25, 2004 Published online November 10, 2004 c Springer-Verlag 2004 This note presents a compilation of recent changes to virus taxonomy decided by voting by the ICTV membership following recommendations from the ICTV Executive Committee. The changes are presented in the Table as decisions promoted by the Subcommittees of the EC and are grouped according to the major hosts of the viruses involved. These new taxa will be presented in more detail in the 8th ICTV Report scheduled to be published near the end of 2004 (Fauquet et al., 2004). Fauquet, C.M., Mayo, M.A., Maniloff, J., Desselberger, U., and Ball, L.A. (eds) (2004). Virus Taxonomy, VIIIth Report of the ICTV. Elsevier/Academic Press, London, pp. 1258. Recent changes to virus taxonomy Viruses of vertebrates Family Arenaviridae • Designate Cupixi virus as a species in the genus Arenavirus • Designate Bear Canyon virus as a species in the genus Arenavirus • Designate Allpahuayo virus as a species in the genus Arenavirus Family Birnaviridae • Assign Blotched snakehead virus as an unassigned species in family Birnaviridae Family Circoviridae • Create a new genus (Anellovirus) with Torque teno virus as type species Family Coronaviridae • Recognize a new species Severe acute respiratory syndrome coronavirus in the genus Coro- navirus, family Coronaviridae, order Nidovirales
    [Show full text]
  • Virology Journal Biomed Central
    Virology Journal BioMed Central Research Open Access The complete genomes of three viruses assembled from shotgun libraries of marine RNA virus communities Alexander I Culley1, Andrew S Lang2 and Curtis A Suttle*1,3 Address: 1University of British Columbia, Department of Botany, 3529-6270 University Blvd, Vancouver, B.C. V6T 1Z4, Canada, 2Department of Biology, Memorial University of Newfoundland, St. John's, NL A1B 3X9, Canada and 3University of British Columbia, Department of Earth and Ocean Sciences, Department of Microbiology and Immunology, 1461-6270 University Blvd, Vancouver, BC, V6T 1Z4, Canada Email: Alexander I Culley - [email protected]; Andrew S Lang - [email protected]; Curtis A Suttle* - [email protected] * Corresponding author Published: 6 July 2007 Received: 10 May 2007 Accepted: 6 July 2007 Virology Journal 2007, 4:69 doi:10.1186/1743-422X-4-69 This article is available from: http://www.virologyj.com/content/4/1/69 © 2007 Culley et al; licensee BioMed Central Ltd. This is an Open Access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/2.0), which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited. Abstract Background: RNA viruses have been isolated that infect marine organisms ranging from bacteria to whales, but little is known about the composition and population structure of the in situ marine RNA virus community. In a recent study, the majority of three genomes of previously unknown positive-sense single-stranded (ss) RNA viruses were assembled from reverse-transcribed whole- genome shotgun libraries.
    [Show full text]
  • Virus Particle Structures
    Virus Particle Structures Virus Particle Structures Palmenberg, A.C. and Sgro, J.-Y. COLOR PLATE LEGENDS These color plates depict the relative sizes and comparative virion structures of multiple types of viruses. The renderings are based on data from published atomic coordinates as determined by X-ray crystallography. The international online repository for 3D coordinates is the Protein Databank (www.rcsb.org/pdb/), maintained by the Research Collaboratory for Structural Bioinformatics (RCSB). The VIPER web site (mmtsb.scripps.edu/viper), maintains a parallel collection of PDB coordinates for icosahedral viruses and additionally offers a version of each data file permuted into the same relative 3D orientation (Reddy, V., Natarajan, P., Okerberg, B., Li, K., Damodaran, K., Morton, R., Brooks, C. and Johnson, J. (2001). J. Virol., 75, 11943-11947). VIPER also contains an excellent repository of instructional materials pertaining to icosahedral symmetry and viral structures. All images presented here, except for the filamentous viruses, used the standard VIPER orientation along the icosahedral 2-fold axis. With the exception of Plate 3 as described below, these images were generated from their atomic coordinates using a novel radial depth-cue colorization technique and the program Rasmol (Sayle, R.A., Milner-White, E.J. (1995). RASMOL: biomolecular graphics for all. Trends Biochem Sci., 20, 374-376). First, the Temperature Factor column for every atom in a PDB coordinate file was edited to record a measure of the radial distance from the virion center. The files were rendered using the Rasmol spacefill menu, with specular and shadow options according to the Van de Waals radius of each atom.
    [Show full text]
  • Coordinated Action of RTBV and RTSV Proteins Suppress Host RNA Silencing Machinery
    bioRxiv preprint doi: https://doi.org/10.1101/2021.01.19.427099; this version posted January 19, 2021. The copyright holder for this preprint (which was not certified by peer review) is the author/funder. All rights reserved. No reuse allowed without permission. Coordinated action of RTBV and RTSV proteins suppress host RNA silencing machinery Abhishek Anand1, Malathi Pinninti2, Anita Tripathi1, Satendra Kumar Mangrauthia2 and Neeti Sanan-Mishra1* 1 Plant RNAi Biology Group, International Center for Genetic Engineering and Biotechnology, New Delhi-110067 2 Biotechnology Section, ICAR-Indian Institute of Rice Research, Rajendranangar, Hyderabad- 500030 *Corresponding Author: Neeti Sanan-Mishra E-mail address: [email protected] Author e-mail: Abhishek Anand: [email protected] Malathi Pinninti: [email protected] Anita Tripathi: [email protected] Satendra K. Mangrauthia: [email protected] Abstract RNA silencing is as an adaptive immune response in plants that limits accumulation or spread of invading viruses. Successful virus infection entails countering the RNA silencing for efficient replication and systemic spread in the host. The viruses encode proteins having the ability to suppress or block the host silencing mechanism, resulting in severe pathogenic symptoms and diseases. Tungro virus disease caused by a complex of two viruses provides an excellent system to understand these host and virus interactions during infection. It is known that Rice tungro bacilliform virus (RTBV) is the major determinant of the disease while Rice tungro spherical virus (RTSV) accentuates the symptoms. This study brings to focus the important role of RTBV ORF-IV in Tungro disease manifestation, by acting as both the victim and silencer of the RNA silencing pathway.
    [Show full text]
  • Multiple Origins of Prokaryotic and Eukaryotic Single-Stranded DNA Viruses from Bacterial and Archaeal Plasmids
    ARTICLE https://doi.org/10.1038/s41467-019-11433-0 OPEN Multiple origins of prokaryotic and eukaryotic single-stranded DNA viruses from bacterial and archaeal plasmids Darius Kazlauskas 1, Arvind Varsani 2,3, Eugene V. Koonin 4 & Mart Krupovic 5 Single-stranded (ss) DNA viruses are a major component of the earth virome. In particular, the circular, Rep-encoding ssDNA (CRESS-DNA) viruses show high diversity and abundance 1234567890():,; in various habitats. By combining sequence similarity network and phylogenetic analyses of the replication proteins (Rep) belonging to the HUH endonuclease superfamily, we show that the replication machinery of the CRESS-DNA viruses evolved, on three independent occa- sions, from the Reps of bacterial rolling circle-replicating plasmids. The CRESS-DNA viruses emerged via recombination between such plasmids and cDNA copies of capsid genes of eukaryotic positive-sense RNA viruses. Similarly, the rep genes of prokaryotic DNA viruses appear to have evolved from HUH endonuclease genes of various bacterial and archaeal plasmids. Our findings also suggest that eukaryotic polyomaviruses and papillomaviruses with dsDNA genomes have evolved via parvoviruses from CRESS-DNA viruses. Collectively, our results shed light on the complex evolutionary history of a major class of viruses revealing its polyphyletic origins. 1 Institute of Biotechnology, Life Sciences Center, Vilnius University, Saulėtekio av. 7, Vilnius 10257, Lithuania. 2 The Biodesign Center for Fundamental and Applied Microbiomics, School of Life Sciences, Center for Evolution and Medicine, Arizona State University, Tempe, AZ 85287, USA. 3 Structural Biology Research Unit, Department of Integrative Biomedical Sciences, University of Cape Town, Rondebosch, 7700 Cape Town, South Africa.
    [Show full text]
  • Journal of Virological Methods 153 (2008) 16–21
    Journal of Virological Methods 153 (2008) 16–21 Contents lists available at ScienceDirect Journal of Virological Methods journal homepage: www.elsevier.com/locate/jviromet Use of primers with 5 non-complementary sequences in RT-PCR for the detection of nepovirus subgroups A and B Ting Wei, Gerard Clover ∗ Plant Health and Environment Laboratory, Investigation and Diagnostic Centre, MAF Biosecurity New Zealand, P.O. Box 2095, Auckland 1140, New Zealand abstract Article history: Two generic PCR protocols were developed to detect nepoviruses in subgroups A and B using degenerate Received 21 April 2008 primers designed to amplify part of the RNA-dependent RNA polymerase (RdRp) gene. It was observed that Received in revised form 17 June 2008 detection sensitivity and specificity could be improved by adding a 12-bp non-complementary sequence Accepted 19 June 2008 to the 5 termini of the forward, but not the reverse, primers. The optimized PCR protocols amplified a specific product (∼340 bp and ∼250 bp with subgroups A and B, respectively) from all 17 isolates of the 5 Keywords: virus species in subgroup A and 3 species in subgroup B tested. The primers detect conserved protein motifs Nepoviruses in the RdRp gene and it is anticipated that they have the potential to detect unreported or uncharacterised Primer flap Universal primers nepoviruses in subgroups A and B. RT-PCR © 2008 Elsevier B.V. All rights reserved. 1. Introduction together with nematode transmission make these viruses partic- ularly hard to eradicate or control (Harrison and Murant, 1977; The genus Nepovirus is classified in the family Comoviridae, Fauquet et al., 2005).
    [Show full text]
  • The Defective Rnas of Closteroviridae
    MINI REVIEW ARTICLE published: 23 May 2013 doi: 10.3389/fmicb.2013.00132 The defective RNAs of Closteroviridae Moshe Bar-Joseph* and Munir Mawassi The S. Tolkowsky Laboratory, Virology Department, Plant Protection Institute, Agricultural Research Organization, Beit Dagan, Israel Edited by: The family Closteroviridae consists of two genera, Closterovirus and Ampelovirus with Ricardo Flores, Instituto de Biología monopartite genomes transmitted respectively by aphids and mealybugs and the Crinivirus Molecular y Celular de Plantas (Universidad Politécnica with bipartite genomes transmitted by whiteflies. The Closteroviridae consists of more de Valencia-Consejo Superior than 30 virus species, which differ considerably in their phytopathological significance. de Investigaciones Científicas), Spain Some, like beet yellows virus and citrus tristeza virus (CTV) were associated for many Reviewed by: decades with their respective hosts, sugar beets and citrus. Others, like the grapevine Pedro Moreno, Instituto Valenciano leafroll-associated ampeloviruses 1, and 3 were also associated with their grapevine de Investigaciones Agrarias, Spain Jesus Navas-Castillo, Instituto hosts for long periods; however, difficulties in virus isolation hampered their molecular de Hortofruticultura Subtropical y characterization. The majority of the recently identified Closteroviridae were probably Mediterranea La Mayora (University associated with their vegetative propagated host plants for long periods and only detected of Málaga-Consejo Superior through the considerable
    [Show full text]
  • Symptom Recovery in Tomato Ringspot Virus Infected Nicotiana
    SYMPTOM RECOVERY IN TOMATO RINGSPOT VIRUS INFECTED NICOTIANA BENTHAMIANA PLANTS: INVESTIGATION INTO THE ROLE OF PLANT RNA SILENCING MECHANISMS by BASUDEV GHOSHAL B.Sc., Surendranath College, University of Calcutta, Kolkata, India, 2003 M. Sc., University of Calcutta, Kolkata, India, 2005 A THESIS SUBMITTED IN PARTIAL FULFILLMENT OF THE REQUIREMENTS FOR THE DEGREE OF DOCTOR OF PHILOSOPHY in THE FACULTY OF GRADUATE AND POSTDOCTORAL STUDIES (Botany) THE UNIVERSITY OF BRITISH COLUMBIA (Vancouver) August 2014 © Basudev Ghoshal, 2014 Abstract Symptom recovery in virus-infected plants is characterized by the emergence of asymptomatic leaves after a systemic symptomatic phase of infection and has been linked with the clearance of the viral RNA due to the induction of RNA silencing. However, the recovery of Tomato ringspot virus (ToRSV)-infected Nicotiana benthamiana plants is not associated with viral RNA clearance in spite of active RNA silencing triggered against viral sequences. ToRSV isolate Rasp1-infected plants recover from infection at 27°C but not at 21°C, indicating a temperature-dependent recovery. In contrast, plants infected with ToRSV isolate GYV recover from infection at both temperatures. In this thesis, I studied the molecular mechanisms leading to symptom recovery in ToRSV-infected plants. I provide evidence that recovery of Rasp1-infected N. benthamiana plants at 27°C is associated with a reduction of the steady-state levels of RNA2-encoded coat protein (CP) but not of RNA2. In vivo labelling experiments revealed efficient synthesis of CP early in infection, but reduced RNA2 translation later in infection. Silencing of Argonaute1-like (NbAgo1) genes prevented both symptom recovery and RNA2 translation repression at 27°C.
    [Show full text]