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Alisawi O, Richert-Pöggeler KR, Heslop-Harrison J(P, Schwarzacher T. The nature and organization of satellite DNAs in Petunia hybrida, related, and ancestral genomes. Front Plant Sci 2023; 14:1232588. [PMID: 37868307 PMCID: PMC10587573 DOI: 10.3389/fpls.2023.1232588] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 06/05/2023] [Accepted: 09/11/2023] [Indexed: 10/24/2023]
Abstract
Introduction The garden petunia, Petunia hybrida (Solanaceae) is a fertile, diploid, annual hybrid species (2n=14) originating from P. axillaris and P. inflata 200 years ago. To understand the recent evolution of the P. hybrida genome, we examined tandemly repeated or satellite sequences using bioinformatic and molecular cytogenetic analysis. Methods Raw reads from available genomic assemblies and survey sequences of P. axillaris N (PaxiN), P. inflata S6, (PinfS6), P. hybrida (PhybR27) and the here sequenced P. parodii S7 (PparS7) were used for graph and k-mer based cluster analysis of TAREAN and RepeatExplorer. Analysis of repeat specific monomer lengths and sequence heterogeneity of the major tandem repeat families with more than 0.01% genome proportion were complemented by fluorescent in situ hybridization (FISH) using consensus sequences as probes to chromosomes of all four species. Results Seven repeat families, PSAT1, PSAT3, PSAT4, PSAT5 PSAT6, PSAT7 and PSAT8, shared high consensus sequence similarity and organisation between the four genomes. Additionally, many degenerate copies were present. FISH in P. hybrida and in the three wild petunias confirmed the bioinformatics data and gave corresponding signals on all or some chromosomes. PSAT1 is located at the ends of all chromosomes except the 45S rDNA bearing short arms of chromosomes II and III, and we classify it as a telomere associated sequence (TAS). It is the most abundant satellite repeat with over 300,000 copies, 0.2% of the genomes. PSAT3 and the variant PSAT7 are located adjacent to the centromere or mid-arm of one to three chromosome pairs. PSAT5 has a strong signal at the end of the short arm of chromosome III in P. axillaris and P.inflata, while in P. hybrida additional interstitial sites were present. PSAT6 is located at the centromeres of chromosomes II and III. PSAT4 and PSAT8 were found with only short arrays. Discussion These results demonstrate that (i) repeat families occupy distinct niches within chromosomes, (ii) they differ in the copy number, cluster organization and homogenization events, and that (iii) the recent genome hybridization in breeding P. hybrida preserved the chromosomal position of repeats but affected the copy number of repetitive DNA.
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Affiliation(s)
- Osamah Alisawi
- Department of Plant Protection, Faculty of Agriculture, University of Kufa, Najaf, Iraq
- Department of Genetics and Genome Biology, Institute for Environmental Futures, University of Leicester, Leicester, United Kingdom
| | - Katja R. Richert-Pöggeler
- Julius Kühn-Institut, Federal Research Centre for Cultivated Plants, Institute for Epidemiology and Pathogen Diagnostics, Braunschweig, Germany
| | - J.S. (Pat) Heslop-Harrison
- Department of Genetics and Genome Biology, Institute for Environmental Futures, University of Leicester, Leicester, United Kingdom
- Key Laboratory of Plant Resources Conservation and Sustainable Utilization/Guangdong Provincial Key Laboratory of Applied Botany, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou, China
- South China National Botanical Garden, Chinese Academy of Sciences, Guangzhou, China
| | - Trude Schwarzacher
- Department of Genetics and Genome Biology, Institute for Environmental Futures, University of Leicester, Leicester, United Kingdom
- Key Laboratory of Plant Resources Conservation and Sustainable Utilization/Guangdong Provincial Key Laboratory of Applied Botany, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou, China
- South China National Botanical Garden, Chinese Academy of Sciences, Guangzhou, China
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Lantos E, Krämer R, Richert-Pöggeler KR, Maiss E, König J, Nothnagel T. Host range and molecular and ultrastructural analyses of Asparagus virus 1 pathotypes isolated from garden asparagus Asparagus officinalis L. Front Plant Sci 2023; 14:1187563. [PMID: 37600206 PMCID: PMC10433173 DOI: 10.3389/fpls.2023.1187563] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 03/16/2023] [Accepted: 07/05/2023] [Indexed: 08/22/2023]
Abstract
Asparagus samples were examined from growing areas of Germany and selected European as well as North, Central and South American countries. Overall, 474 samples were analyzed for Asparagus virus 1 (AV1) using DAS-ELISA. In our survey, 19 AV1 isolates were further characterized. Experimental transmission to 11 species belonging to Aizoaceae, Amarantaceae, Asparagaceae, and Solanaceae succeeded. The ultrastructure of AV1 infection in asparagus has been revealed and has been compared with the one in indicator plants. The cylindrical inclusion (CI) protein, a core factor in viral replication, localized within the cytoplasm and in systemic infections adjacent to the plasmodesmata. The majority of isolates referred to pathotype I (PI). These triggered a hypersensitive resistance in inoculated leaves of Chenopodium spp. and were incapable of infecting Nicotiana spp. Only pathotype II (PII) and pathotype III (PIII) infected Nicotiana benthamiana systemically but differed in their virulence when transmitted to Chenopodium spp. The newly identified PIII generated amorphous inclusion bodies and degraded chloroplasts during systemic infection but not in local lesions of infected Chenopodium spp. PIII probably evolved via recombination in asparagus carrying a mixed infection by PI and PII. Phylogeny of the coat protein region recognized two clusters, which did not overlap with the CI-associated grouping of pathotypes. These results provide evidence for ongoing modular evolution of AV1.
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Affiliation(s)
- Edit Lantos
- Julius Kühn-Institut, Federal Research Centre of Cultivated Plants, Institute of Breeding Research on Horticultural Crops, Quedlinburg, Germany
| | - Reiner Krämer
- Julius Kühn-Institut, Federal Research Centre of Cultivated Plants, Institute of Breeding Research on Horticultural Crops, Quedlinburg, Germany
| | - Katja R. Richert-Pöggeler
- Julius Kühn-Institut, Federal Research Centre of Cultivated Plants, Institute for Epidemiology and Pathogen Diagnostics, Braunschweig, Germany
| | - Edgar Maiss
- Leibniz-University Hannover, Institute of Horticultural Production Systems, Hannover, Germany
| | - Janine König
- Julius Kühn-Institut, Federal Research Centre of Cultivated Plants, Institute of Breeding Research on Horticultural Crops, Quedlinburg, Germany
| | - Thomas Nothnagel
- Julius Kühn-Institut, Federal Research Centre of Cultivated Plants, Institute of Breeding Research on Horticultural Crops, Quedlinburg, Germany
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Temple C, Blouin AG, De Jonghe K, Foucart Y, Botermans M, Westenberg M, Schoen R, Gentit P, Visage M, Verdin E, Wipf-Scheibel C, Ziebell H, Gaafar YZA, Zia A, Yan XH, Richert-Pöggeler KR, Ulrich R, Rivarez MPS, Kutnjak D, Vučurović A, Massart S. Biological and Genetic Characterization of Physostegia Chlorotic Mottle Virus in Europe Based on Host Range, Location, and Time. Plant Dis 2022; 106:2797-2807. [PMID: 35394335 DOI: 10.1094/pdis-12-21-2800-re] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/14/2023]
Abstract
Application of high throughput sequencing (HTS) technologies enabled the first identification of Physostegia chlorotic mottle virus (PhCMoV) in 2018 in Austria. Subsequently, PhCMoV was detected in Germany and Serbia on tomatoes showing severe fruit mottling and ripening anomalies. We report here how prepublication data-sharing resulted in an international collaboration across eight laboratories in five countries, enabling an in-depth characterization of PhCMoV. The independent studies converged toward its recent identification in eight additional European countries and confirmed its presence in samples collected 20 years ago (2002). The natural plant host range was expanded from two to nine species across seven families, and we confirmed the association of PhCMoV presence with severe fruit symptoms on economically important crops such as tomato, eggplant, and cucumber. Mechanical inoculations of selected isolates in the greenhouse established the causality of the symptoms on a new indexing host range. In addition, phylogenetic analysis showed a low genomic variation across the 29 near-complete genome sequences available. Furthermore, a strong selection pressure within a specific ecosystem was suggested by nearly identical sequences recovered from different host plants through time. Overall, this study describes the European distribution of PhCMoV on multiple plant hosts, including economically important crops on which the virus can cause severe fruit symptoms. This work demonstrates how to efficiently improve knowledge on an emergent pathogen by sharing HTS data and provides a solid knowledge foundation for further studies on plant rhabdoviruses.[Formula: see text] Copyright © 2022 The Author(s). This is an open access article distributed under the CC BY-NC-ND 4.0 International license.
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Affiliation(s)
- Coline Temple
- Plant Pathology Laboratory, TERRA-Gembloux Agro-Bio Tech, University of Liège (ULIEGE), Gembloux 5030, Belgium
| | - Arnaud G Blouin
- Plant Pathology Laboratory, TERRA-Gembloux Agro-Bio Tech, University of Liège (ULIEGE), Gembloux 5030, Belgium
- Plant Protection Department, Agroscope, 1260 Nyon, Switzerland
| | - Kris De Jonghe
- Plant Sciences Unit, Research Institute for Agriculture, Fisheries and Food (ILVO), Merelbeke 9820, Belgium
| | - Yoika Foucart
- Plant Sciences Unit, Research Institute for Agriculture, Fisheries and Food (ILVO), Merelbeke 9820, Belgium
| | - Marleen Botermans
- National Reference Centre of Plant Health, National Plant Protection Organization of the Netherlands, 6700 HC Wageningen, the Netherlands
| | - Marcel Westenberg
- National Reference Centre of Plant Health, National Plant Protection Organization of the Netherlands, 6700 HC Wageningen, the Netherlands
| | - Ruben Schoen
- National Reference Centre of Plant Health, National Plant Protection Organization of the Netherlands, 6700 HC Wageningen, the Netherlands
| | - Pascal Gentit
- Laboratoire de santé des végétaux, Agence nationale de sécurité sanitaire de l'alimentation, de l'environnement et du travail (ANSES), Angers 49100, France
| | - Michèle Visage
- Laboratoire de santé des végétaux, Agence nationale de sécurité sanitaire de l'alimentation, de l'environnement et du travail (ANSES), Angers 49100, France
| | - Eric Verdin
- Unité de Pathologie Végétale, Institut national de recherche pour l'agriculture, l'alimentation et l'environnement (INRAE), Avignon 84000, France
| | - Catherine Wipf-Scheibel
- Unité de Pathologie Végétale, Institut national de recherche pour l'agriculture, l'alimentation et l'environnement (INRAE), Avignon 84000, France
| | - Heiko Ziebell
- Institute for Epidemiology and Pathogen Diagnostics, Julius Kühn Institute (JKI) - Federal Research Centre for Cultivated Plants, Braunschweig 38104, Germany
| | - Yahya Z A Gaafar
- Institute for Epidemiology and Pathogen Diagnostics, Julius Kühn Institute (JKI) - Federal Research Centre for Cultivated Plants, Braunschweig 38104, Germany
| | - Amjad Zia
- Institute for Epidemiology and Pathogen Diagnostics, Julius Kühn Institute (JKI) - Federal Research Centre for Cultivated Plants, Braunschweig 38104, Germany
| | - Xiao-Hua Yan
- Institute for Epidemiology and Pathogen Diagnostics, Julius Kühn Institute (JKI) - Federal Research Centre for Cultivated Plants, Braunschweig 38104, Germany
| | - Katja R Richert-Pöggeler
- Institute for Epidemiology and Pathogen Diagnostics, Julius Kühn Institute (JKI) - Federal Research Centre for Cultivated Plants, Braunschweig 38104, Germany
| | | | - Mark Paul S Rivarez
- Department of Biotechnology and Systems Biology, National Institute of Biology (NIB), Ljubljana 1000, Slovenia
| | - Denis Kutnjak
- Department of Biotechnology and Systems Biology, National Institute of Biology (NIB), Ljubljana 1000, Slovenia
| | - Ana Vučurović
- Department of Biotechnology and Systems Biology, National Institute of Biology (NIB), Ljubljana 1000, Slovenia
| | - Sébastien Massart
- Plant Pathology Laboratory, TERRA-Gembloux Agro-Bio Tech, University of Liège (ULIEGE), Gembloux 5030, Belgium
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Richert-Pöggeler KR, Iskra-Caruana ML, Kishima Y. Editorial: DNA virus and host plant interactions from antagonism to endogenization. Front Plant Sci 2022; 13:1014516. [PMID: 36161005 PMCID: PMC9493344 DOI: 10.3389/fpls.2022.1014516] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 08/08/2022] [Accepted: 08/24/2022] [Indexed: 06/16/2023]
Affiliation(s)
- Katja R. Richert-Pöggeler
- Julius Kuehn Institute, Federal Research Centre for Cultivated Plants, Institute for Epidemiology and Pathogen Diagnostics, Braunschweig, Germany
| | | | - Yuji Kishima
- Laboratory of Plant Breeding, Research Faculty of Agriculture, Hokkaido University, Sapporo, Japan
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El-Salamouny S, Wennmann JT, Kleespies RG, Richert-Pöggeler KR, Mansour A, Awad M, Agamy E, Salama R, Jehle JA. Identification of a new nucleopolyhedrovirus isolated from the olive leaf moth, Palpita vitrealis, from two locations in Egypt. J Invertebr Pathol 2022; 192:107770. [PMID: 35597278 DOI: 10.1016/j.jip.2022.107770] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2021] [Revised: 05/11/2022] [Accepted: 05/15/2022] [Indexed: 11/25/2022]
Abstract
The olive leaf moth (jasmine moth), Palpita vitrealis (Lepidoptera: Crambidae), is an important insect pest of olives in several Mediterranean countries. A new alphabaculovirus was isolated from diseased larvae of P. vitrealis in Egypt, first in Giza in spring 2005 and again in Marsa Matrouh in 2019.The larvae exhibited typical symptoms of a baculovirus infection. Light and scanning electron microscopy studies revealed polyhedral occlusion bodies. Transmission electron microscopy of ultrathin sections of purified OBs revealed virions with multiple embedded nucleocapsids. The identity of the two virus isolates was confirmed by sequencing the partial polyhedrin and lef-8 genes, and sequence comparison suggested a relationship to group I alphabaculoviruses. Therefore, this virus was termed Palpita vitrealis nucleopolyhedrovirus (PaviNPV). Whole genome sequencing of the PaviNPV isolate from Giza (Gz05) revealed a genome of 117,533 bp, 131 open reading frames (ORFs) and three homologous repeat (hr) regions. Phylogenetic reconstruction and genetic distance analyses using 38 core genes indicated that PaviNPV is most closely related to Thysanoplusia orichalcea nucleopolyhedrovirus (ThorNPV) but should be considered to belong to a novel species within the genus Alphabaculovirus. In bioassays, PaviNPV was highly virulent against second-instar larvae of P. vitrealis. The study reports a novel baculovirus that might have potential as a biological control agent of the olive leaf moth.
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Affiliation(s)
- Said El-Salamouny
- Department of Economic Entomology and Pesticides, Faculty of Agriculture, Cairo University, 12613 Giza, Egypt; Julius Kühn Institute (JKI) - Federal Research Centre for Cultivated Plants, Institute for Biological Control, Heinrichstr. 243, 64287 Darmstadt, Germany
| | - Jörg T Wennmann
- Julius Kühn Institute (JKI) - Federal Research Centre for Cultivated Plants, Institute for Biological Control, Heinrichstr. 243, 64287 Darmstadt, Germany
| | - Regina G Kleespies
- Julius Kühn Institute (JKI) - Federal Research Centre for Cultivated Plants, Institute for Biological Control, Heinrichstr. 243, 64287 Darmstadt, Germany
| | - Katja R Richert-Pöggeler
- Julius Kühn Institute (JKI) - Federal Research Centre for Cultivated Plants, Institute for Epidemiology and Pathogen Diagnostics, Messeweg 11-12, 38104 Braunschweig, Germany
| | - Amany Mansour
- Department of Plant Protection Desert Research Center, Ministry of Agriculture, Matariya, 11753 Cairo, Egypt
| | - Mona Awad
- Department of Economic Entomology and Pesticides, Faculty of Agriculture, Cairo University, 12613 Giza, Egypt
| | - Essam Agamy
- Department of Economic Entomology and Pesticides, Faculty of Agriculture, Cairo University, 12613 Giza, Egypt
| | - Ramadan Salama
- Department of Economic Entomology and Pesticides, Faculty of Agriculture, Cairo University, 12613 Giza, Egypt
| | - Johannes A Jehle
- Julius Kühn Institute (JKI) - Federal Research Centre for Cultivated Plants, Institute for Biological Control, Heinrichstr. 243, 64287 Darmstadt, Germany.
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Richert-Pöggeler KR, Vijverberg K, Alisawi O, Chofong GN, Heslop-Harrison JS(P, Schwarzacher T. Participation of Multifunctional RNA in Replication, Recombination and Regulation of Endogenous Plant Pararetroviruses (EPRVs). Front Plant Sci 2021; 12:689307. [PMID: 34234799 PMCID: PMC8256270 DOI: 10.3389/fpls.2021.689307] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/31/2021] [Accepted: 05/19/2021] [Indexed: 05/11/2023]
Abstract
Pararetroviruses, taxon Caulimoviridae, are typical of retroelements with reverse transcriptase and share a common origin with retroviruses and LTR retrotransposons, presumably dating back 1.6 billion years and illustrating the transition from an RNA to a DNA world. After transcription of the viral genome in the host nucleus, viral DNA synthesis occurs in the cytoplasm on the generated terminally redundant RNA including inter- and intra-molecule recombination steps rather than relying on nuclear DNA replication. RNA recombination events between an ancestral genomic retroelement with exogenous RNA viruses were seminal in pararetrovirus evolution resulting in horizontal transmission and episomal replication. Instead of active integration, pararetroviruses use the host DNA repair machinery to prevail in genomes of angiosperms, gymnosperms and ferns. Pararetrovirus integration - leading to Endogenous ParaRetroViruses, EPRVs - by illegitimate recombination can happen if their sequences instead of homologous host genomic sequences on the sister chromatid (during mitosis) or homologous chromosome (during meiosis) are used as template. Multiple layers of RNA interference exist regulating episomal and chromosomal forms of the pararetrovirus. Pararetroviruses have evolved suppressors against this plant defense in the arms race during co-evolution which can result in deregulation of plant genes. Small RNAs serve as signaling molecules for Transcriptional and Post-Transcriptional Gene Silencing (TGS, PTGS) pathways. Different populations of small RNAs comprising 21-24 nt and 18-30 nt in length have been reported for Citrus, Fritillaria, Musa, Petunia, Solanum and Beta. Recombination and RNA interference are driving forces for evolution and regulation of EPRVs.
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Affiliation(s)
- Katja R. Richert-Pöggeler
- Julius Kühn-Institut, Federal Research Centre for Cultivated Plants, Institute for Epidemiology and Pathogen Diagnostics, Braunschweig, Germany
- *Correspondence: Katja R. Richert-Pöggeler,
| | - Kitty Vijverberg
- Naturalis Biodiversity Center, Evolutionary Ecology Group, Leiden, Netherlands
- Radboud University, Institute for Water and Wetland Research (IWWR), Nijmegen, Netherlands
| | - Osamah Alisawi
- Department of Plant Protection, Faculty of Agriculture, University of Kufa, Najaf, Iraq
| | - Gilbert N. Chofong
- Julius Kühn-Institut, Federal Research Centre for Cultivated Plants, Institute for Epidemiology and Pathogen Diagnostics, Braunschweig, Germany
| | - J. S. (Pat) Heslop-Harrison
- Department of Genetics and Genome Biology, University of Leicester, Leicester, United Kingdom
- Key Laboratory of Plant Resources Conservation and Sustainable Utilization, Guangdong Provincial Key Laboratory of Applied Botany, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou, China
| | - Trude Schwarzacher
- Department of Genetics and Genome Biology, University of Leicester, Leicester, United Kingdom
- Key Laboratory of Plant Resources Conservation and Sustainable Utilization, Guangdong Provincial Key Laboratory of Applied Botany, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou, China
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Teycheney PY, Geering ADW, Dasgupta I, Hull R, Kreuze JF, Lockhart B, Muller E, Olszewski N, Pappu H, Pooggin MM, Richert-Pöggeler KR, Schoelz JE, Seal S, Stavolone L, Umber M, Report Consortium ICTV. ICTV Virus Taxonomy Profile: Caulimoviridae. J Gen Virol 2020; 101:1025-1026. [PMID: 32940596 PMCID: PMC7660458 DOI: 10.1099/jgv.0.001497] [Citation(s) in RCA: 38] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2020] [Accepted: 09/04/2020] [Indexed: 11/29/2022] Open
Abstract
Caulimoviridae is a family of non-enveloped reverse-transcribing plant viruses with non-covalently closed circular dsDNA genomes of 7.1-9.8 kbp in the order Ortervirales. They infect a wide range of monocots and dicots. Some viruses cause economically important diseases of tropical and subtropical crops. Transmission occurs through insect vectors (aphids, mealybugs, leafhoppers, lace bugs) and grafting. Activation of infectious endogenous viral elements occurs in Musa balbisiana, Petunia hybrida and Nicotiana edwardsonii. However, most endogenous caulimovirids are not infectious. This is a summary of the International Committee on Taxonomy of Viruses (ICTV) Report on the family Caulimoviridae, which is available at ictv.global/report/caulimoviridae.
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Affiliation(s)
- Pierre-Yves Teycheney
- CIRAD, UMR AGAP, F-97130 Capesterre-Belle-Eau, Guadeloupe, France
- AGAP, Univ Montpellier, CIRAD, INRAE, Montpellier SupAgro, Montpellier, France
| | - Andrew D. W. Geering
- Queensland Alliance for Agriculture and Food Innovation, The University of Queensland, GPO Box 267, Brisbane, Queensland 4001, Australia
| | - Idranil Dasgupta
- Department of Plant Molecular Biology, University of Delhi South Campus, New Delhi 110021, India
| | - Roger Hull
- Child Okeford, Blandford Forum, Dorset, UK
| | - Jan F. Kreuze
- International Potato Center (CIP), Apartado 1558, Lima 12, Peru
| | - Ben Lockhart
- Department of Plant Pathology, University of Minnesota, St. Paul, Minnesota, USA
| | - Emmanuelle Muller
- CIRAD, UMR BGPI, F-34398 Montpellier, France
- BGPI, Univ Montpellier, CIRAD, INRAE, Montpellier SupAgro, Montpellier, France
| | - Neil Olszewski
- Department of Plant Biology, University of Minnesota, Minneapolis, Minnesota, USA
| | - Hanu Pappu
- Department of Plant Pathology, Washington State University, Pullman, Washington, USA
| | | | | | - James E. Schoelz
- Division of Plant Sciences, University of Missouri, Columbia, Missouri, USA
| | - Susan Seal
- Natural Resources Institute, University of Greenwich, Chatham, Kent ME4 4TB, UK
| | - Livia Stavolone
- Consiglio Nazionale delle Ricerche, Istituto per la Protezione Sostenibile delle Piante, Bari, Italy
- International Institute of Tropical Agriculture, Ibadan, Nigeria
| | - Marie Umber
- INRAE, UR ASTRO, F-97170, Petit-Bourg, Guadeloupe, France
| | - ICTV Report Consortium
- CIRAD, UMR AGAP, F-97130 Capesterre-Belle-Eau, Guadeloupe, France
- AGAP, Univ Montpellier, CIRAD, INRAE, Montpellier SupAgro, Montpellier, France
- Queensland Alliance for Agriculture and Food Innovation, The University of Queensland, GPO Box 267, Brisbane, Queensland 4001, Australia
- Department of Plant Molecular Biology, University of Delhi South Campus, New Delhi 110021, India
- Child Okeford, Blandford Forum, Dorset, UK
- International Potato Center (CIP), Apartado 1558, Lima 12, Peru
- Department of Plant Pathology, University of Minnesota, St. Paul, Minnesota, USA
- CIRAD, UMR BGPI, F-34398 Montpellier, France
- BGPI, Univ Montpellier, CIRAD, INRAE, Montpellier SupAgro, Montpellier, France
- Department of Plant Biology, University of Minnesota, Minneapolis, Minnesota, USA
- Department of Plant Pathology, Washington State University, Pullman, Washington, USA
- INRA, UMR BGPI, F-34398 Montpellier, France
- Julius Kühn-Institut, Institute for Epidemiology and Pathogen Diagnostics, Braunschweig, Germany
- Division of Plant Sciences, University of Missouri, Columbia, Missouri, USA
- Natural Resources Institute, University of Greenwich, Chatham, Kent ME4 4TB, UK
- Consiglio Nazionale delle Ricerche, Istituto per la Protezione Sostenibile delle Piante, Bari, Italy
- International Institute of Tropical Agriculture, Ibadan, Nigeria
- INRAE, UR ASTRO, F-97170, Petit-Bourg, Guadeloupe, France
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Gaafar YZA, Richert-Pöggeler KR, Sieg-Müller A, Lüddecke P, Herz K, Hartrick J, Seide Y, Vetten HJ, Ziebell H. A divergent strain of melon chlorotic spot virus isolated from black medic (Medicago lupulina) in Austria. Virol J 2019; 16:89. [PMID: 31277670 PMCID: PMC6612211 DOI: 10.1186/s12985-019-1195-8] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2019] [Accepted: 06/24/2019] [Indexed: 02/08/2023] Open
Abstract
A tenuivirus, referred to here as JKI 29327, was isolated from a black medic (Medicago lupulina) plant collected in Austria. The virus was mechanically transmitted to Nicotiana benthamiana, M. lupulina, M. sativa, Pisum sativum and Vicia faba. The complete genome was determined by high throughput sequencing. The genome of JKI 29327 consists of eight RNA segments closely related to those of melon chlorotic spot virus (MeCSV) isolate E11-018 from France. Since segments RNA 7 and 8 of JKI 29327 are shorter, its genome is slightly smaller (by 247 nts) than that of E11-018. Pairwise comparisons between the predicted virus proteins of JKI 29327 and their homologues in E11-018 showed aa identities ranging from 80.6 to 97.2%. Plants infected with E11-081 gave intermediate DAS-ELISA reactions with polyclonal antibodies to JKI 29327. Since JKI 29327 and E11-018 appear to be closely related both serologically and genetically, we propose to regard JKI 29327 as the black medic strain of MeCSV. To our knowledge, JKI 29327 represents the second tenuivirus identified from a dicotyledonous plant. Serological and molecular diagnostic methods were developed for future detection.
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Affiliation(s)
- Yahya Z. A. Gaafar
- Julius Kühn Institute, Institute for Epidemiology and Pathogen Diagnostics, Messeweg 11-12, 38104 Braunschweig, Germany
| | - Katja R. Richert-Pöggeler
- Julius Kühn Institute, Institute for Epidemiology and Pathogen Diagnostics, Messeweg 11-12, 38104 Braunschweig, Germany
| | - Angelika Sieg-Müller
- Julius Kühn Institute, Institute for Epidemiology and Pathogen Diagnostics, Messeweg 11-12, 38104 Braunschweig, Germany
| | - Petra Lüddecke
- Julius Kühn Institute, Institute for Epidemiology and Pathogen Diagnostics, Messeweg 11-12, 38104 Braunschweig, Germany
| | - Kerstin Herz
- Julius Kühn Institute, Institute for Epidemiology and Pathogen Diagnostics, Messeweg 11-12, 38104 Braunschweig, Germany
| | - Jonas Hartrick
- Julius Kühn Institute, Institute for Epidemiology and Pathogen Diagnostics, Messeweg 11-12, 38104 Braunschweig, Germany
| | - Yvonne Seide
- Julius Kühn Institute, Institute for Epidemiology and Pathogen Diagnostics, Messeweg 11-12, 38104 Braunschweig, Germany
| | | | - Heiko Ziebell
- Julius Kühn Institute, Institute for Epidemiology and Pathogen Diagnostics, Messeweg 11-12, 38104 Braunschweig, Germany
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Gaafar YZA, Richert-Pöggeler KR, Sieg-Müller A, Lüddecke P, Herz K, Hartrick J, Maaß C, Ulrich R, Ziebell H. Caraway yellows virus, a novel nepovirus from Carum carvi. Virol J 2019; 16:70. [PMID: 31133023 PMCID: PMC6537451 DOI: 10.1186/s12985-019-1181-1] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2019] [Accepted: 05/16/2019] [Indexed: 01/30/2023] Open
Abstract
A novel nepovirus was identified and characterised from caraway, and tentatively named caraway yellows virus (CawYV). Tubular structures with isomeric virus particles typical for nepoviruses were observed in infected tissues by electron microscopy. The whole genome of CawYV was identified by high throughput sequencing (HTS). It consists of two segments with 8026 nt for RNA1 and 6405 nt for RNA2, excluding the poly(A) tails. CawYV-RNA1 shared closest nt identity to peach rosette mosaic virus (PRMV) with 63%, while RNA2 shared 41.5% with blueberry latent spherical virus (BLSV). The amino acid sequences of the CawYV protease-polymerase (Pro-Pol) and capsid protein (CP) regions share the highest identities with those of the subgroup C nepoviruses. The Pro-Pol region shared highest aa identity with PRMV (80.1%), while the CP region shared 39.6% to soybean latent spherical virus. Phylogenetic analysis of the CawYV-Pro-Pol and -CP aa sequences provided additional evidence of their association with nepoviruses subgroup C. Based on particle morphology, genomic organization and phylogenetic analyses, we propose CawYV as a novel species within the genus Nepovirus subgroup C.
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Affiliation(s)
- Yahya Z A Gaafar
- Julius Kühn Institute, Institute for Epidemiology and Pathogen Diagnostics, Messeweg 11-12, 38104, Braunschweig, Germany
| | - Katja R Richert-Pöggeler
- Julius Kühn Institute, Institute for Epidemiology and Pathogen Diagnostics, Messeweg 11-12, 38104, Braunschweig, Germany
| | - Angelika Sieg-Müller
- Julius Kühn Institute, Institute for Epidemiology and Pathogen Diagnostics, Messeweg 11-12, 38104, Braunschweig, Germany
| | - Petra Lüddecke
- Julius Kühn Institute, Institute for Epidemiology and Pathogen Diagnostics, Messeweg 11-12, 38104, Braunschweig, Germany
| | - Kerstin Herz
- Julius Kühn Institute, Institute for Epidemiology and Pathogen Diagnostics, Messeweg 11-12, 38104, Braunschweig, Germany
| | - Jonas Hartrick
- Julius Kühn Institute, Institute for Epidemiology and Pathogen Diagnostics, Messeweg 11-12, 38104, Braunschweig, Germany
| | - Christina Maaß
- Julius Kühn Institute, Institute for Epidemiology and Pathogen Diagnostics, Messeweg 11-12, 38104, Braunschweig, Germany
| | - Roswitha Ulrich
- Regierungspräsidium Gießen, Schanzenfeldstrasse 8, 325578, Wetzlar, Germany
| | - Heiko Ziebell
- Julius Kühn Institute, Institute for Epidemiology and Pathogen Diagnostics, Messeweg 11-12, 38104, Braunschweig, Germany.
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10
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Gaafar YZA, Richert-Pöggeler KR, Maaß C, Vetten HJ, Ziebell H. Characterisation of a novel nucleorhabdovirus infecting alfalfa (Medicago sativa). Virol J 2019; 16:55. [PMID: 31036009 PMCID: PMC6489223 DOI: 10.1186/s12985-019-1147-3] [Citation(s) in RCA: 21] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2018] [Accepted: 03/19/2019] [Indexed: 12/22/2022] Open
Abstract
Background Nucleorhabdoviruses possess bacilliform particles which contain a single-stranded negative-sense RNA genome. They replicate and mature in the nucleus of infected cells. Together with viruses of three other genera of the family Rhabdoviridae, they are known to infect plants and can be transmitted by arthropod vectors, during vegetative propagation, or by mechanical means. In 2010, an alfalfa (Medicago sativa) plant showing virus-like symptoms was collected from Stadl-Paura, Austria and sent to Julius Kühn Institute for analysis. Methods Electron microscopy (EM) of leaf extracts from infected plants revealed the presence of rhabdovirus-like particles and was further used for ultrastructural analyses of infected plant tissue. Partially-purified preparations of rhabdovirus nucleocapsids were used for raising an antiserum. To determine the virus genome sequence, high throughput sequencing (HTS) was performed. RT-PCR primers were designed to confirm virus infection and to be used as a diagnostic tool. Results EM revealed bacilliform virions resembling those of plant-infecting rhabdoviruses. HTS of ribosomal RNA-depleted total RNA extracts revealed a consensus sequence consisting of 13,875 nucleotides (nt) and containing seven open reading frames (ORFs). Homology and phylogenetic analyses suggest that this virus isolate represents a new species of the genus Nucleorhabdovirus (family Rhabdoviridae). Since the virus originated from an alfalfa plant in Austria, the name alfalfa-associated nucleorhabdovirus (AaNV) is proposed. Viroplasms (Vp) and budding virions were observed in the nuclei of infected cells by EM, thus confirming its taxonomic assignment based on sequence data. Conclusions In this study, we identified and characterised a new nucleorhabdovirus from alfalfa. It shared only 39.8% nucleotide sequence identity with its closest known relative, black currant-associated rhabdovirus 1. The virus contains an additional open reading frame (accessory gene) with unknown function, located between the matrix protein and the glycoprotein genes. Serological and molecular diagnostic assays were designed for future screening of field samples. Further studies are needed to identify other natural hosts and potential vectors. Electronic supplementary material The online version of this article (10.1186/s12985-019-1147-3) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Yahya Z A Gaafar
- Julius Kühn Institute, Institute for Epidemiology and Pathogen Diagnostics, Messeweg 11-12, 38104, Braunschweig, Germany
| | - Katja R Richert-Pöggeler
- Julius Kühn Institute, Institute for Epidemiology and Pathogen Diagnostics, Messeweg 11-12, 38104, Braunschweig, Germany
| | - Christina Maaß
- Julius Kühn Institute, Institute for Epidemiology and Pathogen Diagnostics, Messeweg 11-12, 38104, Braunschweig, Germany
| | | | - Heiko Ziebell
- Julius Kühn Institute, Institute for Epidemiology and Pathogen Diagnostics, Messeweg 11-12, 38104, Braunschweig, Germany.
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11
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Patz S, Becker Y, Richert-Pöggeler KR, Berger B, Ruppel S, Huson DH, Becker M. Phage tail-like particles are versatile bacterial nanomachines - A mini-review. J Adv Res 2019; 19:75-84. [PMID: 31341672 PMCID: PMC6629978 DOI: 10.1016/j.jare.2019.04.003] [Citation(s) in RCA: 28] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/03/2019] [Revised: 04/06/2019] [Accepted: 04/14/2019] [Indexed: 11/27/2022] Open
Abstract
Suggestion to simplify and unify the nomenclature of phage tail-like particles. Discovery of kosakonicin, a new bacteriocin and tailocin. Microscopy of kosakonicin from Kosakonia radicincitans DSM 16656. Discovery of multiple tail fiber genes in the kosakonicin gene cluster. Discovery of large genetic diversity in the kosakonicin tail fiber locus among ten Kosakonia strains.
Type VI secretion systems and tailocins, two bacterial phage tail-like particles, have been reported to foster interbacterial competition. Both nanostructures enable their producer to kill other bacteria competing for the same ecological niche. Previously, type VI secretion systems and particularly R-type tailocins were considered highly specific, attacking a rather small range of competitors. Their specificity is conferred by cell surface receptors of the target bacterium and receptor-binding proteins on tailocin tail fibers and tail fiber-like appendages of T6SS. Since many R-type tailocin gene clusters contain only one tail fiber gene it was appropriate to expect small R-type tailocin target ranges. However, recently up to three tail fiber genes and broader target ranges have been reported for one plant-associated Pseudomonas strain. Here, we show that having three tail fiber genes per R-type tailocin gene cluster is a common feature of several strains of Gram-negative (often plant-associated) bacteria of the genus Kosakonia. Knowledge about the specificity of type VI secretion systems binding to target bacteria is even lower than in R-type tailocins. Although the mode of operation implicated specific binding, it was only published recently that type VI secretion systems develop tail fiber-like appendages. Here again Kosakonia, exhibiting up to three different type VI secretion systems, may provide valuable insights into the antagonistic potential of plant-associated bacteria. Current understanding of the diversity and potential of phage tail-like particles is fragmentary due to various synonyms and misleading terminology. Consistency in technical terms is a precondition for concerted and purposeful research, which precedes a comprehensive understanding of the specific interaction between bacteria producing phage tail-like particles and their targets. This knowledge is fundamental for selecting and applying tailored, and possibly engineered, producer bacteria for antagonizing plant pathogenic microorganisms.
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Affiliation(s)
- Sascha Patz
- Algorithms in Bioinformatics, Center for Bioinformatics, University of Tübingen, 72074 Tübingen, Germany
| | - Yvonne Becker
- Institute for Epidemiology and Pathogen Diagnostics, Julius Kühn-Institute - Federal Research Centre for Cultivated Plants, 38104 Braunschweig, Germany
| | - Katja R Richert-Pöggeler
- Institute for Epidemiology and Pathogen Diagnostics, Julius Kühn-Institute - Federal Research Centre for Cultivated Plants, 38104 Braunschweig, Germany
| | - Beatrice Berger
- Institute for National and International Plant Health, Julius Kühn-Institute - Federal Research Centre for Cultivated Plants, 38104 Braunschweig, Germany
| | - Silke Ruppel
- Leibniz Institute of Vegetable and Ornamental Crops, 14979 Grossbeeren, Germany
| | - Daniel H Huson
- Algorithms in Bioinformatics, Center for Bioinformatics, University of Tübingen, 72074 Tübingen, Germany
| | - Matthias Becker
- Institute for National and International Plant Health, Julius Kühn-Institute - Federal Research Centre for Cultivated Plants, 38104 Braunschweig, Germany.,Leibniz Institute of Vegetable and Ornamental Crops, 14979 Grossbeeren, Germany
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12
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Rose H, Döring I, Vetten HJ, Menzel W, Richert-Pöggeler KR, Maiss E. Complete genome sequence and construction of an infectious full-length cDNA clone of celery latent virus - an unusual member of a putative new genus within the Potyviridae. J Gen Virol 2019; 100:308-320. [PMID: 30667354 DOI: 10.1099/jgv.0.001207] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Celery latent virus (CeLV) is an incompletely described plant virus known to be sap and seed transmissible and to possess flexuous filamentous particles measuring about 900 nm in length, suggesting it as a possible member of the family Potyviridae. Here, an Italian isolate of CeLV was transmitted by sap to a number of host plants and shown to have a single-stranded and monopartite RNA genome being 11 519 nucleotides (nts) in size and possessing some unusual features. The RNA contains a large open reading frame (ORF) that is flanked by a short 5' untranslated region (UTR) of 13 nt and a 3' UTR consisting of 586 nt that is not polyadenylated. CeLV RNA shares nt sequence identity of only about 40 % with other members of the Potyviridae (potyvirids). The CeLV polyprotein is notable in that it starts with a signal peptide, has a putative P3N-PIPO ORF and shares low aa sequence identity (about 18 %) with other potyvirids. Although potential cleavage sites were not identified for the N-terminal two-thirds of the polyprotein, the latter possesses a number of sequence motifs, the identity and position of which are characteristic of other potyvirids. Attempts at constructing an infectious full-length cDNA clone of CeLV were successful following Rhizobium radiobacter infiltration of Nicotiana benthamiana and Apium graveolens. CeLV appears to have the largest genome of all known potyvirids and some unique genome features that may warrant the creation of a new genus, for which we propose the name 'celavirus'.
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Affiliation(s)
- Hanna Rose
- 1Department Phytomedicine, Leibniz University Hannover, Institute of Horticultural Production Systems, Herrenhäuser Str. 2, 30419, Hannover, Germany
| | - Ines Döring
- 1Department Phytomedicine, Leibniz University Hannover, Institute of Horticultural Production Systems, Herrenhäuser Str. 2, 30419, Hannover, Germany
| | | | - Wulf Menzel
- 3Leibniz Institute DSMZ, German Collection of Microorganisms and Cell Cultures, Inhoffenstraße 7 B, 38124 Braunschweig, Germany
| | - Katja R Richert-Pöggeler
- 4Julius Kühn Institut JKI, Federal Research Centre for Cultivated Plants, Institute of Epidemiology and Pathogen Diagnostics, Messeweg 11-12, 38104 Braunschweig, Germany
| | - Edgar Maiss
- 1Department Phytomedicine, Leibniz University Hannover, Institute of Horticultural Production Systems, Herrenhäuser Str. 2, 30419, Hannover, Germany
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13
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Richert-Pöggeler KR, Franzke K, Hipp K, Kleespies RG. Electron Microscopy Methods for Virus Diagnosis and High Resolution Analysis of Viruses. Front Microbiol 2019; 9:3255. [PMID: 30666247 PMCID: PMC6330349 DOI: 10.3389/fmicb.2018.03255] [Citation(s) in RCA: 57] [Impact Index Per Article: 11.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2018] [Accepted: 12/14/2018] [Indexed: 01/29/2023] Open
Abstract
The term "virosphere" describes both the space where viruses are found and the space they influence, and can extend to their impact on the environment, highlighting the complexity of the interactions involved. Studying the biology of viruses and the etiology of virus disease is crucial to the prevention of viral disease, efficient and reliable virus diagnosis, and virus control. Electron microscopy (EM) is an essential tool in the detection and analysis of virus replication. New EM methods and ongoing technical improvements offer a broad spectrum of applications, allowing in-depth investigation of viral impact on not only the host but also the environment. Indeed, using the most up-to-date electron cryomicroscopy methods, such investigations are now close to atomic resolution. In combination with bioinformatics, the transition from 2D imaging to 3D remodeling allows structural and functional analyses that extend and augment our knowledge of the astonishing diversity in virus structure and lifestyle. In combination with confocal laser scanning microscopy, EM enables live imaging of cells and tissues with high-resolution analysis. Here, we describe the pivotal role played by EM in the study of viruses, from structural analysis to the biological relevance of the viral metagenome (virome).
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Affiliation(s)
- Katja R. Richert-Pöggeler
- Federal Research Center for Cultivated Plants, Institute for Epidemiology and Pathogen Diagnostics, Julius Kühn Institute, Braunschweig, Germany
| | - Kati Franzke
- Institute of Infectiology, Friedrich-Loeffler-Institut, Federal Research Institute for Animal Health, Greifswald-Insel Riems, Germany
| | - Katharina Hipp
- Electron Microscopy Facility, Max Planck Institute for Developmental Biology, Tübingen, Germany
| | - Regina G. Kleespies
- Federal Research Centre for Cultivated Plants, Institute for Biological Control, Julius Kühn Institute, Darmstadt, Germany
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14
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Abstract
The term "virosphere" describes both the space where viruses are found and the space they influence, and can extend to their impact on the environment, highlighting the complexity of the interactions involved. Studying the biology of viruses and the etiology of virus disease is crucial to the prevention of viral disease, efficient and reliable virus diagnosis, and virus control. Electron microscopy (EM) is an essential tool in the detection and analysis of virus replication. New EM methods and ongoing technical improvements offer a broad spectrum of applications, allowing in-depth investigation of viral impact on not only the host but also the environment. Indeed, using the most up-to-date electron cryomicroscopy methods, such investigations are now close to atomic resolution. In combination with bioinformatics, the transition from 2D imaging to 3D remodeling allows structural and functional analyses that extend and augment our knowledge of the astonishing diversity in virus structure and lifestyle. In combination with confocal laser scanning microscopy, EM enables live imaging of cells and tissues with high-resolution analysis. Here, we describe the pivotal role played by EM in the study of viruses, from structural analysis to the biological relevance of the viral metagenome (virome).
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Affiliation(s)
- Katja R Richert-Pöggeler
- Federal Research Center for Cultivated Plants, Institute for Epidemiology and Pathogen Diagnostics, Julius Kühn Institute, Braunschweig, Germany
| | - Kati Franzke
- Institute of Infectiology, Friedrich-Loeffler-Institut, Federal Research Institute for Animal Health, Greifswald-Insel Riems, Germany
| | - Katharina Hipp
- Electron Microscopy Facility, Max Planck Institute for Developmental Biology, Tübingen, Germany
| | - Regina G Kleespies
- Federal Research Centre for Cultivated Plants, Institute for Biological Control, Julius Kühn Institute, Darmstadt, Germany
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15
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Ashrafi S, Stadler M, Dababat AA, Richert-Pöggeler KR, Finckh MR, Maier W. Monocillium gamsii sp. nov. and Monocillium bulbillosum: two nematode-associated fungi parasitising the eggs of Heterodera filipjevi. MycoKeys 2017. [DOI: 10.3897/mycokeys.27.21254] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
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16
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Erokhina TN, Lazareva EA, Richert-Pöggeler KR, Sheval EV, Solovyev AG, Morozov SY. Subcellular Localization and Detection of Tobacco mosaic virus ORF6 Protein by Immunoelectron Microscopy. Biochemistry (Mosc) 2017; 82:60-66. [PMID: 28320287 DOI: 10.1134/s0006297917010060] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/16/2023]
Abstract
Members of the genus Tobamovirus represent one of the best-characterized groups of plant positive, single stranded RNA viruses. Previous studies have shown that genomes of some tobamoviruses contain not only genes coding for coat protein, movement protein, and the cistron coding for different domains of RNA-polymerase, but also a gene, named ORF6, coding for a poorly conserved small protein. The amino acid sequences of ORF6 proteins encoded by different tobamoviruses are highly divergent. The potential role of ORF6 proteins in replication of tobamoviruses still needs to be elucidated. In this study, using biochemical and immunological methods, we have shown that ORF6 peptide is accumulated after infection in case of two isolates of Tobacco mosaic virus strain U1 (TMV-U1 common and TMV-U1 isolate A15). Unlike virus particles accumulating in the cytoplasm, the product of the ORF6 gene is found mainly in nuclei, which correlates with previously published data about transient expression of ORF6 isolated from TMV-U1. Moreover, we present new data showing the presence of ORF6 genes in genomes of several tobamoviruses. For example, in the genomes of other members of the tobamovirus subgroup 1, including Rehmannia mosaic virus, Paprika mild mottle virus, Tobacco mild green mosaic virus, Tomato mosaic virus, Tomato mottle mosaic virus, and Nigerian tobacco latent virus, sequence comparisons revealed the existence of a similar open reading frame like ORF6 of TMV.
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Affiliation(s)
- T N Erokhina
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, Moscow, 117997, Russia.
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17
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Bombarely A, Moser M, Amrad A, Bao M, Bapaume L, Barry CS, Bliek M, Boersma MR, Borghi L, Bruggmann R, Bucher M, D'Agostino N, Davies K, Druege U, Dudareva N, Egea-Cortines M, Delledonne M, Fernandez-Pozo N, Franken P, Grandont L, Heslop-Harrison JS, Hintzsche J, Johns M, Koes R, Lv X, Lyons E, Malla D, Martinoia E, Mattson NS, Morel P, Mueller LA, Muhlemann J, Nouri E, Passeri V, Pezzotti M, Qi Q, Reinhardt D, Rich M, Richert-Pöggeler KR, Robbins TP, Schatz MC, Schranz ME, Schuurink RC, Schwarzacher T, Spelt K, Tang H, Urbanus SL, Vandenbussche M, Vijverberg K, Villarino GH, Warner RM, Weiss J, Yue Z, Zethof J, Quattrocchio F, Sims TL, Kuhlemeier C. Insight into the evolution of the Solanaceae from the parental genomes of Petunia hybrida. Nat Plants 2016; 2:16074. [PMID: 27255838 DOI: 10.1038/nplants.2016.74] [Citation(s) in RCA: 210] [Impact Index Per Article: 26.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/12/2015] [Accepted: 04/22/2016] [Indexed: 05/21/2023]
Abstract
Petunia hybrida is a popular bedding plant that has a long history as a genetic model system. We report the whole-genome sequencing and assembly of inbred derivatives of its two wild parents, P. axillaris N and P. inflata S6. The assemblies include 91.3% and 90.2% coverage of their diploid genomes (1.4 Gb; 2n = 14) containing 32,928 and 36,697 protein-coding genes, respectively. The genomes reveal that the Petunia lineage has experienced at least two rounds of hexaploidization: the older gamma event, which is shared with most Eudicots, and a more recent Solanaceae event that is shared with tomato and other solanaceous species. Transcription factors involved in the shift from bee to moth pollination reside in particularly dynamic regions of the genome, which may have been key to the remarkable diversity of floral colour patterns and pollination systems. The high-quality genome sequences will enhance the value of Petunia as a model system for research on unique biological phenomena such as small RNAs, symbiosis, self-incompatibility and circadian rhythms.
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Affiliation(s)
- Aureliano Bombarely
- Department of Horticulture, Virginia Polytechnic Institute and State University, 490 West Campus Dr., Blacksburg, Virginia 24061, USA
| | - Michel Moser
- Institute of Plant Sciences, University of Bern, Altenbergrain 21, 3013 Bern, Switzerland
| | - Avichai Amrad
- Institute of Plant Sciences, University of Bern, Altenbergrain 21, 3013 Bern, Switzerland
| | - Manzhu Bao
- Huazhong Agricultural University, Wuhan 430070, P. R. China
| | - Laure Bapaume
- Department of Biology, University of Fribourg, Fribourg, Switzerland, 6 Rte Albert Gockel, CH-1700 Fribourg, Switzerland
| | - Cornelius S Barry
- Department of Horticulture, Michigan State University, East Lansing, Michigan 48824, USA
| | - Mattijs Bliek
- Department of Plant Development and (Epi)Genetics, Swammerdam Institute for Life Sciences, University of Amsterdam, Science Park 904, 1098 XH, Amsterdam, The Netherlands
| | - Maaike R Boersma
- Department of Plant Physiology, University of Amsterdam, Science Park 904, 1098 XH, Amsterdam, The Netherlands
| | - Lorenzo Borghi
- Institute of Plant and Microbiology, University of Zürich, Zollikerstr. 107, CH-8008 Zürich, Switzerland
| | - Rémy Bruggmann
- Interfaculty Bioinformatics Unit, University of Bern, Baltzerstrasse 6, CH-3012 Bern, Switzerland
| | - Marcel Bucher
- Cologne Biocenter, Cluster of Excellence on Plant Sciences (CEPLAS), University of Cologne, Zuelpicher Straße 47b, 50674 Cologne, Germany
| | - Nunzio D'Agostino
- Consiglio per la Ricerca in Agricoltura e l'analisi dell'economia agraria, Centro di Ricerca per l'Orticoltura (CREA-ORT), via Cavalleggeri 25, 84098 Pontecagnano (Sa) Italy
| | - Kevin Davies
- Department of Breeding and Genomics, Plant and Food Research, Auckland, 120 Mt Albert Road, Mount Albert, Sandringham 1142, New Zealand
| | - Uwe Druege
- Department of Plant Propagation, Leibniz Institute of Vegetable and Ornamental Crops (IGZ), Kühnhäuserstr. 101, 99090 Erfurt, Germany
| | - Natalia Dudareva
- Department of Biochemistry, Purdue University, West Lafayette, Indiana 47907-2063, USA
| | - Marcos Egea-Cortines
- Instituto de Biotecnología Vegetal, Universidad Politécnica de Cartagena, 30202, Cartagena, Spain
| | - Massimo Delledonne
- Dipartimento di Biotecnologie, Universita degli Studi di Verona, Strada le Grazie 15, 37134 Verona, Italy
| | - Noe Fernandez-Pozo
- Boyce Thompson Institute for Plant Research, 533 Tower Rd, Ithaca, New York 14853, USA
| | - Philipp Franken
- Department of Plant Propagation, Leibniz Institute of Vegetable and Ornamental Crops (IGZ), Kühnhäuserstr. 101, 99090 Erfurt, Germany
| | - Laurie Grandont
- Biosystematics Group, Wageningen University and Research Center, Droevendaalsesteeg 1, 6708 PB, Wageningen, The Netherlands
| | - J S Heslop-Harrison
- Department of Genetics, University of Leicester, University Road, Leicester LE1 7RH, UK
| | - Jennifer Hintzsche
- Department of Biological Sciences, Northern Illinois University, DeKalb, Illinois 60115, USA
| | - Mitrick Johns
- Department of Biological Sciences, Northern Illinois University, DeKalb, Illinois 60115, USA
| | - Ronald Koes
- Department of Plant Development and (Epi)Genetics, Swammerdam Institute for Life Sciences, University of Amsterdam, Science Park 904, 1098 XH, Amsterdam, The Netherlands
| | - Xiaodan Lv
- Beijing Genomics Institute, Shenzhen 518083, China
| | - Eric Lyons
- School of Plant Sciences, iPlant Collaborative, University of Arizona, Tucson, Arizona 85721, USA
| | - Diwa Malla
- Department of Biological Sciences, Northern Illinois University, DeKalb, Illinois 60115, USA
| | - Enrico Martinoia
- Institute of Plant and Microbiology, University of Zürich, Zollikerstr. 107, CH-8008 Zürich, Switzerland
| | - Neil S Mattson
- School of Integrative Plant Science, Cornell University, Cornell University, Ithaca, New York 14853, USA
| | - Patrice Morel
- Laboratoire Reproduction et Développement des Plantes (RDP), ENS de Lyon/CNRS/INRA/UCBL, 46 Allée d'Italie, 69364 Lyon, France
| | - Lukas A Mueller
- Boyce Thompson Institute for Plant Research, 533 Tower Rd, Ithaca, New York 14853, USA
| | - Joëlle Muhlemann
- Department of Biochemistry, Purdue University, West Lafayette, Indiana 47907-2063, USA
| | - Eva Nouri
- Department of Biology, University of Fribourg, Fribourg, Switzerland, 4 Rte Albert Gockel, CH-1700 Fribourg, Switzerland
| | - Valentina Passeri
- Department of Plant Development and (Epi)Genetics, Swammerdam Institute for Life Sciences, University of Amsterdam, Science Park 904, 1098 XH, Amsterdam, The Netherlands
| | - Mario Pezzotti
- Dipartimento di Biotecnologie, Universita degli Studi di Verona, Strada le Grazie 15, 37134 Verona, Italy
| | - Qinzhou Qi
- Department of Biological Sciences, Northern Illinois University, DeKalb, Illinois 60115, USA
| | - Didier Reinhardt
- Department of Biology, University of Fribourg, Fribourg, Switzerland, 3 Rte Albert Gockel, CH-1700 Fribourg, Switzerland
| | - Melanie Rich
- Department of Biology, University of Fribourg, Fribourg, Switzerland, 5 Rte Albert Gockel, CH-1700 Fribourg, Switzerland
| | - Katja R Richert-Pöggeler
- Institute for Epidemiology and Pathogen Diagnostics, Julius Kühn-Institut (JKI), Federal Research Centre for Cultivated Plants, Messeweg 11-12, 38104 Braunschweig, Germany
| | - Tim P Robbins
- Department of Crop and Plant Sciences, University of Nottingham, Sutton Bonington, Leicestershire, UL LE12 5RD, UK
| | - Michael C Schatz
- Cold Spring Harbor Laboratory, 1 Bungtown Road, Cold Spring Harbor, New York 11724, USA
| | - M Eric Schranz
- Biosystematics Group, Wageningen University and Research Center, Droevendaalsesteeg 1, 6708 PB, Wageningen, The Netherlands
| | - Robert C Schuurink
- Department of Plant Physiology, University of Amsterdam, Science Park 904, 1098 XH, Amsterdam, The Netherlands
| | - Trude Schwarzacher
- Department of Genetics, University of Leicester, University Road, Leicester LE1 7RH, UK
| | - Kees Spelt
- Department of Plant Development and (Epi)Genetics, Swammerdam Institute for Life Sciences, University of Amsterdam, Science Park 904, 1098 XH, Amsterdam, The Netherlands
| | - Haibao Tang
- School of Plant Sciences, iPlant Collaborative, University of Arizona, Tucson, Arizona 85721, USA
| | - Susan L Urbanus
- Department of Plant Development and (Epi)Genetics, Swammerdam Institute for Life Sciences, University of Amsterdam, Science Park 904, 1098 XH, Amsterdam, The Netherlands
| | - Michiel Vandenbussche
- Laboratoire Reproduction et Développement des Plantes (RDP), ENS de Lyon/CNRS/INRA/UCBL, 46 Allée d'Italie, 69364 Lyon, France
| | - Kitty Vijverberg
- Radboud University, FNWI, IWWR, Heyendaalseweg 135, 6525AJ Nijmegen, The Netherlands
| | - Gonzalo H Villarino
- School of Integrative Plant Science, Cornell University, Cornell University, Ithaca, New York 14853, USA
| | - Ryan M Warner
- Department of Horticulture, Michigan State University, East Lansing, Michigan 48824, USA
| | - Julia Weiss
- Instituto de Biotecnología Vegetal, Universidad Politécnica de Cartagena, 30202, Cartagena, Spain
| | - Zhen Yue
- Beijing Genomics Institute, Shenzhen 518083, China
| | - Jan Zethof
- Radboud University, FNWI, IWWR, Heyendaalseweg 135, 6525AJ Nijmegen, The Netherlands
| | - Francesca Quattrocchio
- Department of Plant Development and (Epi)Genetics, Swammerdam Institute for Life Sciences, University of Amsterdam, Science Park 904, 1098 XH, Amsterdam, The Netherlands
| | - Thomas L Sims
- Department of Biological Sciences, Northern Illinois University, DeKalb, Illinois 60115, USA
| | - Cris Kuhlemeier
- Institute of Plant Sciences, University of Bern, Altenbergrain 21, 3013 Bern, Switzerland
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18
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Solovyev AG, Minina EA, Makarova SS, Erokhina TN, Makarov VV, Kaplan IB, Kopertekh L, Schiemann J, Richert-Pöggeler KR, Morozov SY. Subcellular localization and self-interaction of plant-specific Nt-4/1 protein. Biochimie 2013; 95:1360-70. [PMID: 23499290 DOI: 10.1016/j.biochi.2013.02.015] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2013] [Accepted: 02/26/2013] [Indexed: 11/26/2022]
Abstract
The Nicotiana tabacum Nt-4/1 protein is a plant-specific protein of unknown function. Analysis of bacterially expressed Nt-4/1 protein in vitro revealed that the protein secondary structure is mostly alpha-helical and suggested that it could consist of three structural domains. Earlier studies of At-4/1, the Arabidopsis thaliana-encoded ortholog of Nt-4/1, demonstrated that GFP-fused At-4/1 was capable of polar localization in plant cells, association with plasmodesmata, and cell-to-cell transport. Together with the At-4/1 ability to interact with a plant virus movement protein, these data supported the hypothesis of the At-4/1 protein involvement in viral transport through plasmodesmata. Studies of the Nt-4/1-GFP fusion protein reported in this paper revealed that the protein was localized to cytoplasmic bodies, which were co-aligned with actin filaments and capable of actin-dependent intracellular movement. The Nt-4/1-GFP bodies, being non-membrane structures, were found in association with the plasma membrane, the tubular endoplasmic reticulum and endosome-like structures. Bimolecular fluorescence complementation experiments and inhibition of nuclear export showed that the Nt-4/1 protein was capable of nuclear-cytoplasmic transport. The nuclear export signal (NES) was identified in the Nt-4/1 protein by site-directed mutagenesis. The Nt-4/1 NES mutant was localized to the nucleoplasm forming spherical bodies. Immunogold labeling and electron microscopy of cytoplasmic Nt-4/1-containing bodies and nuclear structures containing the Nt-4/1 NES mutant revealed differences in their fine structure. In mammalian cells, Nt-4/1-GFP formed cytoplasmic spherical bodies similar to those found for the Nt-4/1 NES mutant in plant cell nuclei. Using dynamic laser light scattering and electron microscopy, the Nt-4/1 protein was found to form multimeric complexes in vitro.
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Affiliation(s)
- A G Solovyev
- A.N. Belozersky Institute of Physico-Chemical Biology, Moscow State University, Chochlova Str. 1, 119992 Moscow, Russia
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19
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Menzel W, Winter S, Richert-Pöggeler KR. First Report of Malva vein clearing virus Naturally Occurring in Hollyhock in Germany. Plant Dis 2010; 94:276. [PMID: 30754276 DOI: 10.1094/pdis-94-2-0276b] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/09/2023]
Abstract
Hollyhocks are popular garden plants and selected cultivars of Alcea rosea (family Malvaceae) are widespread in Germany. In spring 2009, dozens of A. rosea plants displaying strong vein clearing and veinal yellowing symptoms were found in private gardens in Hannover, Lower Saxony. Electron microscopic examinations of negatively stained adsorption preparations of five randomly selected samples of symptomatic plants or their offshoots revealed flexuous filamentous particles resembling those of potyviruses. Sap extracts also reacted strongly positive in an antigen coated plate (ACP)-ELISA with the broad-spectrum potyvirus antiserum AS-0573/I (DSMZ, Braunschweig, Germany). RNA extracts (RNeasy Kit, Qiagen, Valencia, CA) of the above mentioned leaf samples were used as templates in reverse transcription (RT)-PCR assays with potyvirus specific primers (2) that have been shown to amplify the 3' terminus of the genome of many potyvirus species. For extracts from symptomatic samples, this resulted in a consistent amplification of an ~1.6-kbp fragment, whereas no products were obtained from RNA extracts of asymptomatic plants. From one positive sample, the amplified fragment was cloned and one clone was partially sequenced. The nucleotide (nt) and amino acid sequences showed the highest identities (81 to 83% and 87 to 90%, respectively) to GenBank sequences FJ539084, FM212972, EU884405, and FJ561293 of the potyvirus Malva vein clearing virus (MVCM). On the basis of these identity values and according to the species demarcation criteria in the genus Potyvirus, the virus can be regarded as a German isolate of the recently sequenced MVCV (3,4). Direct sequencing of the 5'-end of the amplified RT-PCR fragment revealed sequences of only one potyvirus species. The virus isolate has been submitted to the DSMZ Plant Virus Collection (Braunschweig, Germany) under accession PV-0963 and the sequence obtained from the cloned cDNA is deposited in GenBank (GQ856544). In addition, sap from affected leaves was mechanically inoculated onto sets of herbaceous indicator plants (Chenopodium quinoa, C. foliosum, C. murale, C. amaranticolor, Datura stramonium, Nicotiana benthamiana, N. hesperis, Petunia hybrida, and Solanum lycopersicum) of which only C. quinoa plants became infected. Symptoms of weak chlorosis along and beside veins of inoculated leaves, but not systemic leaves, became visible 2 weeks postinoculation. Symptomatic leaves contained flexuous filamentous particles and ACP-ELISA and RT-PCR confirmed virus presence. The partially sequenced amplicon showed 99% nt identity to the sequence from the cloned cDNA. To our knowledge, this is the first report of a MVCV isolate naturally occurring in A. rosea and C. quinoa is the first host identified that does not belong to the plant family Malvaceae. In contrast, the MVCV isolate used in the host range study of Lunello et al. (4) did not infect A. rosea and C. quinoa, confirming previous host range descriptions by Brunt et al. (1). Since MVCV infections of hollyhocks seem to cause only leaf symptoms and do not noticeably affect growth or flowering of the plants, this will hopefully not impair the usability of this popular garden plant. References: (1) A. A. Brunt et al. Descriptions and Lists from the VIDE Database. Online publication. Version: 16th January, 1997. (2) J. Chen et al. Arch. Virol. 146:757, 2001. (3) A. Hein Phytopathol. Z. 28:205, 1957. (4) P. Lunello et al. Virus Res. 140:91, 2009.
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Affiliation(s)
- W Menzel
- DSMZ Plant Virus Collection, Inhoffenstrasse 7B, 38124 Braunschweig, Germany
| | - S Winter
- DSMZ Plant Virus Collection, Inhoffenstrasse 7B, 38124 Braunschweig, Germany
| | - K R Richert-Pöggeler
- JKI, Institute for Epidemiology and Pathogen Diagnostics, Messeweg 11-12, 38104 Braunschweig, Germany
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Staginnus C, Iskra-Caruana ML, Lockhart B, Hohn T, Richert-Pöggeler KR. Suggestions for a nomenclature of endogenous pararetroviral sequences in plants. Arch Virol 2009; 154:1189-93. [PMID: 19521659 DOI: 10.1007/s00705-009-0412-y] [Citation(s) in RCA: 28] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2008] [Accepted: 05/25/2009] [Indexed: 10/20/2022]
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21
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Noreen F, Akbergenov R, Hohn T, Richert-Pöggeler KR. Distinct expression of endogenous Petunia vein clearing virus and the DNA transposon dTph1 in two Petunia hybrida lines is correlated with differences in histone modification and siRNA production. Plant J 2007; 50:219-29. [PMID: 17444906 DOI: 10.1111/j.1365-313x.2007.03040.x] [Citation(s) in RCA: 31] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/15/2023]
Abstract
Endogenous viruses exist in all kingdoms. They usually have active mechanisms of integration, as in bacteriophage lambda and animal retroviruses, and sophisticated mechanisms to maintain a proviral state over decades and generations. Plant para retroviruses, however, neither have an integrase, nor genes for maintaining the proviral state. How are those elements controlled, and under what conditions can they be activated? Here we study the proviral state of endogenous petunia vein clearing virus (ePVCV). Our results support the hypothesis that the proviral state is associated with a host silencing mechanism manifested by DNA methylation, chromatin modification and production of small interfering (si) RNAs. PVCV may be induced by applying abiotic stress, leading to the development of viral symptoms and increased transcript and siRNA levels. Similar levels of ePVCV DNA methylation were observed in two different lines of Petunia hybrida, RdC (rose du ciel) and W138, the latter known for its active version of transposon dTph1. In contrast, significant differences in histone modification were detected. The predominant association of ePVCV sequences with histone H3 methylated at lysine 9 (H3mK9) in RdC and with about equal amounts of H3mK9 and H3mK4 in W138 indicates a less repressive proviral state in the latter cultivar.
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Affiliation(s)
- Faiza Noreen
- Friedrich Miescher Institute, Maulbeerstlasse 66, CH-4058 Basel, Switzerland
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22
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Noreen F, Akbergenov R, Hohn T, Richert-Pöggeler KR. Distinct expression of endogenous Petunia vein clearing virus and the DNA transposon dTph1 in two Petunia hybrida lines is correlated with differences in histone modification and siRNA production. Plant J 2007; 50:219-229. [PMID: 17444906 DOI: 10.1071/ap06016] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/22/2023]
Abstract
Endogenous viruses exist in all kingdoms. They usually have active mechanisms of integration, as in bacteriophage lambda and animal retroviruses, and sophisticated mechanisms to maintain a proviral state over decades and generations. Plant para retroviruses, however, neither have an integrase, nor genes for maintaining the proviral state. How are those elements controlled, and under what conditions can they be activated? Here we study the proviral state of endogenous petunia vein clearing virus (ePVCV). Our results support the hypothesis that the proviral state is associated with a host silencing mechanism manifested by DNA methylation, chromatin modification and production of small interfering (si) RNAs. PVCV may be induced by applying abiotic stress, leading to the development of viral symptoms and increased transcript and siRNA levels. Similar levels of ePVCV DNA methylation were observed in two different lines of Petunia hybrida, RdC (rose du ciel) and W138, the latter known for its active version of transposon dTph1. In contrast, significant differences in histone modification were detected. The predominant association of ePVCV sequences with histone H3 methylated at lysine 9 (H3mK9) in RdC and with about equal amounts of H3mK9 and H3mK4 in W138 indicates a less repressive proviral state in the latter cultivar.
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Affiliation(s)
- Faiza Noreen
- Friedrich Miescher Institute, Maulbeerstlasse 66, CH-4058 Basel, Switzerland
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23
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Staginnus C, Richert-Pöggeler KR. Endogenous pararetroviruses: two-faced travelers in the plant genome. Trends Plant Sci 2006; 11:485-91. [PMID: 16949329 DOI: 10.1016/j.tplants.2006.08.008] [Citation(s) in RCA: 80] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/18/2006] [Revised: 06/28/2006] [Accepted: 08/24/2006] [Indexed: 05/07/2023]
Abstract
Endogenous plant pararetroviruses (EPRVs) were identified as integrated counterparts of most members of the plant virus family Caulimoviridae and represent repetitive elements that are ubiquitous in the plant kingdom. They are often located in pericentromeric regions of plant chromosomes in the vicinity of retrotransposon sequences. Depending on their structure and sequence integrity, some EPRVs are able to replicate and to initiate viral infection. However, conservation of integrated sequences in plant genomes might indicate benefits for the host during evolution. Understanding EPRV activation and control by the host could have important implications for plant breeding strategies to prevent viral disease caused by EPRVs in newly generated cultivars.
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Affiliation(s)
- Christina Staginnus
- Gregor Mendel Institute (GMI) for Molecular Plant Biology, Dr.-Bohr-Gasse 3, A-1030 Wien, Austria
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Richert-Pöggeler KR, Noreen F, Schwarzacher T, Harper G, Hohn T. Induction of infectious petunia vein clearing (pararetro) virus from endogenous provirus in petunia. EMBO J 2003; 22:4836-45. [PMID: 12970195 PMCID: PMC212712 DOI: 10.1093/emboj/cdg443] [Citation(s) in RCA: 86] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2003] [Revised: 07/18/2003] [Accepted: 07/21/2003] [Indexed: 11/12/2022] Open
Abstract
Infection by an endogenous pararetrovirus using forms of both episomal and chromosomal origin has been demonstrated and characterized, together with evidence that petunia vein clearing virus (PVCV) is a constituent of the Petunia hybrida genome. Our findings allow comparative and direct analysis of horizontally and vertically transmitted virus forms and demonstrate their infectivity using biolistic transformation of a provirus-free petunia species. Some integrants within the genome of P.hybrida are arranged in tandem, allowing direct release of virus by transcription. In addition to known inducers of endogenous pararetroviruses, such as genome hybridization, tissue culture and abiotic stresses, we observed activation of PVCV after wounding. Our data also support the hypothesis that the host plant uses DNA methylation to control the endogenous pararetrovirus.
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Harper G, Richert-Pöggeler KR, Hohn T, Hull R. Detection of petunia vein-clearing virus: model for the detection of DNA viruses in plants with homologous endogenous pararetrovirus sequences. J Virol Methods 2003; 107:177-84. [PMID: 12505632 DOI: 10.1016/s0166-0934(02)00231-8] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022]
Abstract
A number of cases of plant virus sequence integration into host plant genome have been reported. In at least two cases, endogenous pararetrovirus sequences are correlated strongly with subsequent episomal virus infection and there is circumstantial evidence that this also occurs for Petunia vein-clearing virus (PVCV). The detection of viruses is a critical component of plant health and therefore, it is important to have diagnostic procedures that differentiate between the detection of encapsidated viral DNA and homologous sequences in the host genome. PCR-based detection methods targeted at PVCV DNA have been tested and particular attention was paid to design controls that would indicate the existence of host DNA in the reaction. The use of ion-exchange chromatography for the partial purification of plant viruses from other cellular components, including chromosomal DNA, is described. The methods tested for PVCV detection are used to illustrate general principles for the specific detection of virus infections in host plants that carry homologous virus sequences in their genomes.
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Affiliation(s)
- Glyn Harper
- Department of Disease and Stress Biology, John Innes Centre, Colney Lane, NR47UH, Norwich, UK.
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Abstract
Petunia vein-clearing virus (PVCV) is a plant pararetrovirus that has some features of retrotransposons. It encapsidates dsDNA and has isometric particles and inclusion bodies similar to those of caulimoviruses. The PVCV genome of 7205 bp has two large ORFs in the transcribed strand and a methionine tRNA primer-binding site in its 663-bp intergenic region. The N-terminal position of the large protein (126 kDa) encoded by ORF I has similarity to the movement protein of caulimoviruses. Toward the C-terminus of this same polyprotein are the two distinctive sequence elements [HHCC and DD(35)E] of the integrase function of retroviruses and retrotransposons. ORF II of PVCV encodes a protein of 125 kDa with domains for an RNA-binding element, common to the gag gene of retroelements, followed by consensus sequences for an acid protease, reverse transcriptase, and ribonuclease H. Hence, the gag equivalent (capsid protein) and pol gene of PVCV are part of the same polyprotein. Phylogenetic comparison of the reverse transcriptase of PVCV with that of various other retroelements grouped PVCV between caulimoviruses and the Ty3/gypsy retrotransposons, suggesting that PVCV is a divergent member of the caulimoviruses.
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