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Torralba B, Blanc S, Michalakis Y. Reassortments in single-stranded DNA multipartite viruses: Confronting expectations based on molecular constraints with field observations. Virus Evol 2024; 10:veae010. [PMID: 38384786 PMCID: PMC10880892 DOI: 10.1093/ve/veae010] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2023] [Revised: 11/23/2023] [Accepted: 01/30/2024] [Indexed: 02/23/2024] Open
Abstract
Single-stranded DNA multipartite viruses, which mostly consist of members of the genus Begomovirus, family Geminiviridae, and all members of the family Nanoviridae, partly resolve the cost of genomic integrity maintenance through two remarkable capacities. They are able to systemically infect a host even when their genomic segments are not together in the same host cell, and these segments can be separately transmitted by insect vectors from host to host. These capacities potentially allow such viruses to reassort at a much larger spatial scale, since reassortants could arise from parental genotypes that do not co-infect the same cell or even the same host. To assess the limitations affecting reassortment and their implications in genome integrity maintenance, the objective of this review is to identify putative molecular constraints influencing reassorted segments throughout the infection cycle and to confront expectations based on these constraints with empirical observations. Trans-replication of the reassorted segments emerges as the major constraint, while encapsidation, viral movement, and transmission compatibilities appear more permissive. Confronting the available molecular data and the resulting predictions on reassortments to field population surveys reveals notable discrepancies, particularly a surprising rarity of interspecific natural reassortments within the Nanoviridae family. These apparent discrepancies unveil important knowledge gaps in the biology of ssDNA multipartite viruses and call for further investigation on the role of reassortment in their biology.
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Affiliation(s)
- Babil Torralba
- PHIM, Université Montpellier, IRD, CIRAD, INRAE, Institut Agro, Avenue du Campus d’Agropolis - ZAC de Baillarguet, Montpellier 34980, France
| | - Stéphane Blanc
- PHIM, Université Montpellier, IRD, CIRAD, INRAE, Institut Agro, Avenue du Campus d’Agropolis - ZAC de Baillarguet, Montpellier 34980, France
| | - Yannis Michalakis
- MIVEGEC, Université Montpellier, CNRS, IRD, 911, Avenue Agropolis, Montpellier 34394, France
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2
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Bonnamy M, Brousse A, Pirolles E, Michalakis Y, Blanc S. The genome formula of a multipartite virus is regulated both at the individual segment and the segment group levels. PLoS Pathog 2024; 20:e1011973. [PMID: 38271470 PMCID: PMC10846721 DOI: 10.1371/journal.ppat.1011973] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2023] [Revised: 02/06/2024] [Accepted: 01/14/2024] [Indexed: 01/27/2024] Open
Abstract
Differential accumulation of the distinct genome segments is a common feature of viruses with segmented genomes. The reproducible and specific pattern of genome segment accumulation within the host is referred to as the "genome formula". There is speculation and some experimental support for a functional role of the genome formula by modulating gene expression through copy number variations. However, the mechanisms of genome formula regulation have not yet been identified. In this study, we investigated whether the genome formula of the octopartite nanovirus faba bean necrotic stunt virus (FBNSV) is regulated by processes acting at the individual segment vs. viral population levels. We used a leaf infiltration system to show that the two most accumulated genome segments of the FBNSV possess a greater intrinsic accumulation capacity in Vicia faba tissues than the other segments. Nevertheless, processes acting at the individual segment level are insufficient to generate the genome formula, suggesting the involvement of additional mechanisms acting at the supra-segment level. Indeed, the absence of segments with important functions during systemic infection strongly modifies the relative frequency of the others, indicating that the genome formula is a property of the segment group. Together, these results demonstrate that the FBNSV genome formula is shaped by a complex process acting at both the individual segment and the segment group levels.
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Affiliation(s)
- Mélia Bonnamy
- PHIM, Univ Montpellier, IRD, CIRAD, INRAE, Institut Agro, Montpellier, France
- MIVEGEC, CNRS, IRD, Univ Montpellier, Montpellier, France
| | - Andy Brousse
- PHIM, Univ Montpellier, IRD, CIRAD, INRAE, Institut Agro, Montpellier, France
- MIVEGEC, CNRS, IRD, Univ Montpellier, Montpellier, France
| | - Elodie Pirolles
- PHIM, Univ Montpellier, IRD, CIRAD, INRAE, Institut Agro, Montpellier, France
| | | | - Stéphane Blanc
- PHIM, Univ Montpellier, IRD, CIRAD, INRAE, Institut Agro, Montpellier, France
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3
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Bonnamy M, Blanc S, Michalakis Y. Replication mechanisms of circular ssDNA plant viruses and their potential implication in viral gene expression regulation. mBio 2023; 14:e0169223. [PMID: 37695133 PMCID: PMC10653810 DOI: 10.1128/mbio.01692-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 09/12/2023] Open
Abstract
The replication of members of the two circular single-stranded DNA (ssDNA) virus families Geminiviridae and Nanoviridae, the only ssDNA viruses infecting plants, is believed to be processed by rolling-circle replication (RCR) and recombination-dependent replication (RDR) mechanisms. RCR is a ubiquitous replication mode for circular ssDNA viruses and involves a virus-encoded Replication-associated protein (Rep) which fulfills multiple functions in the replication mechanism. Two key genomic elements have been identified for RCR in Geminiviridae and Nanoviridae: (i) short iterative sequences called iterons which determine the specific recognition of the viral DNA by the Rep and (ii) a sequence enabling the formation of a stem-loop structure which contains a conserved motif and constitutes the origin of replication. In addition, studies in Geminiviridae provided evidence for a second replication mode, RDR, which has also been documented in some double-stranded DNA viruses. Here, we provide a synthesis of the current understanding of the two presumed replication modes of Geminiviridae and Nanoviridae, and we identify knowledge gaps and discuss the possibility that these replication mechanisms could regulate viral gene expression through modulation of gene copy number.
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Affiliation(s)
- Mélia Bonnamy
- PHIM, Univ Montpellier, IRD, CIRAD, INRAE, Institut Agro, Montpellier, France
- MIVEGEC, CNRS, IRD, Univ Montpellier, Montpellier, France
| | - Stéphane Blanc
- PHIM, Univ Montpellier, IRD, CIRAD, INRAE, Institut Agro, Montpellier, France
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Lal A, Shamim A, Kil EJ, Vo TTB, Qureshi MA, Bupi N, Tabassum M, Lee S. Insights into the Differential Composition of Stem-Loop Structures of Nanoviruses and Their Impacts. Microbiol Spectr 2023; 11:e0479822. [PMID: 37367433 PMCID: PMC10434203 DOI: 10.1128/spectrum.04798-22] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2022] [Accepted: 05/03/2023] [Indexed: 06/28/2023] Open
Abstract
Multipartite viruses package their genomic segments independently and mainly infect plants; few of them target animals. Nanoviridae is a family of multipartite single-stranded DNA (ssDNA) plant viruses that individually encapsidate ssDNAs of ~1 kb and transmit them through aphids without replication in aphid vectors, thereby causing important diseases in host plants, mainly leguminous crops. All of these components constitute an open reading frame to perform a specific role in nanovirus infection. All segments contain conserved inverted repeat sequences, potentially forming a stem-loop structure and a conserved nonanucleotide, TAGTATTAC, within a common region. This study investigated the variations in the stem-loop structure of nanovirus segments and their impact using molecular dynamics (MD) simulations and wet lab approaches. Although the accuracy of MD simulations is limited by force field approximations and simulation time scale, explicit solvent MD simulations were successfully used to analyze the important aspects of the stem-loop structure. This study involves the mutants' design, based on the variations in the stem-loop region and construction of infectious clones, followed by their inoculation and expression analysis, based on nanosecond dynamics of the stem-loop structure. The original stem-loop structures showed more conformational stability than mutant stem-loop structures. The mutant structures were expected to alter the neck region of the stem-loop by adding and switching nucleotides. Changes in conformational stability are suggested expression variations of the stem-loop structures found in host plants with nanovirus infection. However, our results can be a starting point for further structural and functional analysis of nanovirus infection. IMPORTANCE Nanoviruses comprise multiple segments, each with a single open reading frame to perform a specific function and an intergenic region with a conserved stem-loop region. The genome expression of a nanovirus has been an intriguing area but is still poorly understood. We attempted to investigate the variations in the stem-loop structure of nanovirus segments and their impact on viral expression. Our results show that the stem-loop composition is essential in controlling the virus segments' expression level.
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Affiliation(s)
- Aamir Lal
- Department of Integrative Biotechnology, Sungkyunkwan University, Suwon, South Korea
- Department of Plant Medicals, College of Life Sciences, Andong National University, Andong, South Korea
- Agricultural Science and Technology Research Institute, Andong National University, Andong, South Korea
| | - Amen Shamim
- Department of Computer Science, University of Agriculture, Faisalabad, Pakistan
| | - Eui-Joon Kil
- Department of Plant Medicals, College of Life Sciences, Andong National University, Andong, South Korea
- Agricultural Science and Technology Research Institute, Andong National University, Andong, South Korea
| | - Thuy T. B. Vo
- Department of Integrative Biotechnology, Sungkyunkwan University, Suwon, South Korea
| | - Muhammad Amir Qureshi
- Department of Integrative Biotechnology, Sungkyunkwan University, Suwon, South Korea
| | - Nattanong Bupi
- Department of Integrative Biotechnology, Sungkyunkwan University, Suwon, South Korea
| | - Marjia Tabassum
- Department of Integrative Biotechnology, Sungkyunkwan University, Suwon, South Korea
| | - Sukchan Lee
- Department of Integrative Biotechnology, Sungkyunkwan University, Suwon, South Korea
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Bashir S, Naqvi SMS, Muhammad A, Hussain I, Ali K, Khan MR, Farrakh S, Yasmin T, Hyder MZ. Banana bunchy top virus genetic diversity in Pakistan and association of diversity with recombination in its genomes. PLoS One 2022; 17:e0263875. [PMID: 35255085 PMCID: PMC8901069 DOI: 10.1371/journal.pone.0263875] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2021] [Accepted: 01/30/2022] [Indexed: 11/30/2022] Open
Abstract
Banana Bunchy top virus (BBTV) is a multipartite circular single strand DNA virus that belongs to genus Babuvirus and family Nanoviridae. It causes significant crop losses worldwide and also in Pakistan. BBTV is present in Pakistan since 1988 however, till now only few (about twenty only) sequence of genomic components have been reported from the country. To have insights into current genetic diversity in Pakistan fifty-seven genomic components including five complete genomes (comprises of DNA-R, -U3, -S, -M, -C and -N components) were sequenced in this study. The genetic diversity analysis of populations from Pakistan showed that DNA-R is highly conserved followed by DNA-N, whereas DNA-U3 is highly diverse with the most diverse Common Region Stem-loop (CR-SL) in BBTV genome, a functional region, which previously been reported to have undergone recombination in Pakistani population. A Maximum Likelihood (ML) phylogenetic analysis of entire genomes of isolates by using sequence of all the components concatenated together with the reported genomes around the world revealed deeper insights about the origin of the disease in Pakistan. A comparison of the genetic diversity of Pakistani and entire BBTV populations around the world indicates that there exists a correlation between genetic diversity and recombination. Population genetics analysis indicated that the degree of selection pressure differs depending on the area and genomic component. A detailed analysis of recombination across various components and functional regions suggested that recombination is closely associated with the functional parts of BBTV genome showing high genetic diversity. Both genetic diversity and recombination analyses suggest that the CR-SL is a recombination hotspot in all BBTV genomes and among the six components DNA-U3 is the only recombined component that has extensively undergone inter and intragenomic recombination. Diversity analysis of recombinant regions results on average one and half fold increase and, in some cases up to four-fold increase due to recombination. These results suggest that recombination is significantly contributing to the genetic diversity of BBTV populations around the world.
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Affiliation(s)
- Sana Bashir
- Department of Biosciences, COMSATS University Islamabad, Islamabad, Pakistan
| | | | - Aish Muhammad
- National Institute for Genomics and Advanced Biotechnology, National Agriculture Research Centre, Islamabad, Pakistan
| | - Iqbal Hussain
- National Institute for Genomics and Advanced Biotechnology, National Agriculture Research Centre, Islamabad, Pakistan
| | - Kazim Ali
- National Institute for Genomics and Advanced Biotechnology, National Agriculture Research Centre, Islamabad, Pakistan
| | - Muhammad Ramzan Khan
- National Institute for Genomics and Advanced Biotechnology, National Agriculture Research Centre, Islamabad, Pakistan
| | - Sumaira Farrakh
- Department of Biosciences, COMSATS University Islamabad, Islamabad, Pakistan
| | - Tayyaba Yasmin
- Department of Biosciences, COMSATS University Islamabad, Islamabad, Pakistan
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6
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Hasanvand V, Heydanejad J, Massumi H, Kleinow T, Jeske H, Fontenele RS, Kraberger S, Varsani A. Genome characterization of parsley severe stunt-associated virus in Iran. Virus Genes 2021; 57:293-301. [PMID: 33881682 DOI: 10.1007/s11262-021-01835-y] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2021] [Accepted: 04/08/2021] [Indexed: 11/28/2022]
Abstract
Parsley severe stunt-associated virus (PSSaV) is a recently identified nanovirus first reported in Germany. During a survey for identification of nanoviruses infecting apiaceous plants in south-eastern Iran, PSSaV was identified and characterized using a combination of rolling circle amplification (RCA) and high-throughput sequencing. Parsley plant samples were collected from vegetable production farms in Kerman province. From two symptomatic samples (39Ba and 40Ba), seven PSSaV components (DNA-C, -S, -M, -R, -N, -U1 and -U2) with two phylogenetically distinct variants of DNA-R (R1 and R2) were identified. In common with the German isolate of PSSaV, no DNA-U4 component was identified. In addition, associated alphasatellite molecules were identified in samples 39Ba [n = 6] and 40Ba [n = 5]. Sequence analyses showed that concatenated component sequences of the two Iranian PSSaVs share 97.2% nucleotide identity with each other and 82% to the German isolate. The coat proteins (CPs) of the PSSaV Iranian sequences share 97.2% amino acid identity and ~ 84% identity with that of the German isolate. Sequence and phylogenetic analyses of a total of 11 recovered alphasatellites from the two samples can be classified into the genera Fabenesatellite [n = 2], Milvetsatellite [n = 1], Mivedwarsatellite [n = 2], Subclovsatellite [n = 2], Sophoyesatellite [n = 4] in the family Alphasatellitidae. Identification of PSSaV and other nanoviruses in wild and cultivated plants in Iran reveals that nanoviruses could be causing yield reduction in crops plants in this country.
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Affiliation(s)
- Vahid Hasanvand
- Department of Plant Protection, College of Agriculture, Shahid Bahonar University of Kerman, 7616914111, Kerman, Iran
| | - Jahangir Heydanejad
- Department of Plant Protection, College of Agriculture, Shahid Bahonar University of Kerman, 7616914111, Kerman, Iran. .,Research and Technology Institute of Plant Production (RTIPP), Shahid Bahonar University of Kerman, 7616914111, Kerman, Iran.
| | - Hossain Massumi
- Department of Plant Protection, College of Agriculture, Shahid Bahonar University of Kerman, 7616914111, Kerman, Iran
| | - Tatjana Kleinow
- Department of Molecular Biology and Plant Virology, Institute of Biomaterials and Biomolecular Systems, University of Stuttgart, Stuttgart, Germany
| | - Holger Jeske
- Department of Molecular Biology and Plant Virology, Institute of Biomaterials and Biomolecular Systems, University of Stuttgart, Stuttgart, Germany
| | - Rafaela S Fontenele
- The Biodesign Center of Fundamental and Applied Microbiomics, School of Life Sciences, Center for Evolution and Medicine, Arizona State University, 1001 S. McAllister Ave, Tempe, AZ, 85287-5001, USA
| | - Simona Kraberger
- The Biodesign Center of Fundamental and Applied Microbiomics, School of Life Sciences, Center for Evolution and Medicine, Arizona State University, 1001 S. McAllister Ave, Tempe, AZ, 85287-5001, USA
| | - Arvind Varsani
- The Biodesign Center of Fundamental and Applied Microbiomics, School of Life Sciences, Center for Evolution and Medicine, Arizona State University, 1001 S. McAllister Ave, Tempe, AZ, 85287-5001, USA.,Structural Biology Research Unit, Department of Clinical Laboratory Sciences, University of Cape Town, Rondebosch, Cape Town, 7701, South Africa
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7
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Lal A, Vo TTB, Sanjaya IGNPW, Ho PT, Kim JK, Kil EJ, Lee S. Nanovirus Disease Complexes: An Emerging Threat in the Modern Era. FRONTIERS IN PLANT SCIENCE 2020; 11:558403. [PMID: 33329624 PMCID: PMC7710663 DOI: 10.3389/fpls.2020.558403] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 05/02/2020] [Accepted: 10/28/2020] [Indexed: 06/12/2023]
Abstract
Multipartite viruses package their genomic segments independently and mainly infect plants; few target animals. Nanoviridae is a family of multipartite single-stranded DNA plant viruses that individually encapsidate single-stranded DNAs of approximately 1 kb and transmit them through aphids without replication in the aphid vectors, thereby causing important diseases of leguminous crops and banana. Significant findings regarding nanoviruses have recently been made on important features, such as their multicellular way of life, the transmission of distinct encapsidated genome segments through the vector body, evolutionary ambiguities, mode of infection, host range and geographical distribution. This review deals with all the above-mentioned features in view of recent advances with special emphasis on the emergence of new species and recognition of new host range of nanoviruses and aims to shed light on the evolutionary linkages, the potentially devastating impact on the world economy, and the future challenges imposed by nanoviruses.
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Affiliation(s)
- Aamir Lal
- Department of Integrative Biotechnology, Sungkyunkwan University, Suwon, South Korea
| | - Thuy Thi Bich Vo
- Department of Integrative Biotechnology, Sungkyunkwan University, Suwon, South Korea
| | | | - Phuong Thi Ho
- Department of Integrative Biotechnology, Sungkyunkwan University, Suwon, South Korea
| | - Ji-Kwang Kim
- Research and Development Bureau, Chungcheongnam-do Agricultural Research and Extension Services, Yesan, South Korea
| | - Eui-Joon Kil
- Department of Integrative Biotechnology, Sungkyunkwan University, Suwon, South Korea
- Department of Plant Medicals, Andong National University, Andong, South Korea
| | - Sukchan Lee
- Department of Integrative Biotechnology, Sungkyunkwan University, Suwon, South Korea
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8
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Hassan-Sheikhi P, Heydarnejad J, Massumi H, Kraberger S, Varsani A. Novel nanovirus and associated alphasatellites identified in milk vetch plants with chlorotic dwarf disease in Iran. Virus Res 2019; 276:197830. [PMID: 31790775 DOI: 10.1016/j.virusres.2019.197830] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2019] [Revised: 11/27/2019] [Accepted: 11/29/2019] [Indexed: 02/03/2023]
Abstract
Members of the family Nanoviridae are multi-component single-stranded DNA viruses that infect a variety of plant species. Using a combination of conventional PCR and high throughput sequencing-based approach, we identified a novel nanovirus infecting two symptomatic milk vetch plants (Astragalus myriacanthus Boiss.; family Fabaceae) showing marginal leaf chlorosis, little leaves and dwarfing in Iran. All eight segments (DNA-C, DNA-M, DNA-N, DNA-R, DNA-S, DNA-U1, DNA-U2 and DNAU4) were recovered and Sanger sequenced. The genome of this new nanovirus, hereby referred to as milk vetch chlorotic dwarf virus (MVCDV), shares 62.2-74.7 % nucleotide pairwise identity with the genomes of other nanoviruses. DNA-C, DNA-M, DNA-N, DNA-S components are most closely related to those of black medic leaf roll virus (BMLRV), sharing between 67.8-81.2 % identity. We also identified three nanoalphasatellites (family Alphasatellitidae) associated with the nanovirus which belong to species Faba bean necrotic yellows alphasatellite 1 (genus Subclovsatellite), Faba bean necrotic yellows alphasatellite 2 (genus Fabenesatellite) and Sophora yellow stunt alphasatellite 5 (genus Clostunsatellite). Given the significant diversity of Astragalus spp. in Iran, it is likely that there could be more nanoviruses circulating in these plants and that these may play a role in the spread of these nanovirus to cultivated fabaceous hosts.
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Affiliation(s)
- Parisa Hassan-Sheikhi
- Department of Plant Protection, College of Agriculture, Shahid Bahonar University of Kerman, Kerman 7616914111, Iran
| | - Jahangir Heydarnejad
- Department of Plant Protection, College of Agriculture, Shahid Bahonar University of Kerman, Kerman 7616914111, Iran; Research and Technology Institute of Plant Production (RTIPP), Shahid Bahonar University of Kerman, 7616914111, Iran.
| | - Hossain Massumi
- Department of Plant Protection, College of Agriculture, Shahid Bahonar University of Kerman, Kerman 7616914111, Iran
| | - Simona Kraberger
- The Biodesign Center of Fundamental and Applied Microbiomics, School of Life Sciences, Center for Evolution and Medicine, Arizona State University, 1001 S. McAllister Ave, Tempe, AZ 85287-5001, USA
| | - Arvind Varsani
- The Biodesign Center of Fundamental and Applied Microbiomics, School of Life Sciences, Center for Evolution and Medicine, Arizona State University, 1001 S. McAllister Ave, Tempe, AZ 85287-5001, USA; Structural Biology Research Unit, Department of Integrative Biomedical Sciences, University of Cape Town, Observatory, Cape Town, South Africa
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9
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Vetten HJ, Knierim D, Rakoski MS, Menzel W, Maiss E, Gronenborn B, Winter S, Krenz B. Identification of a novel nanovirus in parsley. Arch Virol 2019; 164:1883-1887. [PMID: 31079213 DOI: 10.1007/s00705-019-04280-3] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2019] [Accepted: 04/09/2019] [Indexed: 11/30/2022]
Abstract
Using next-generation sequencing to characterize agents associated with a severe stunting disease of parsley from Germany, we identified a hitherto undescribed virus. We sequenced total RNA and rolling-circle-amplified DNA from diseased plants. The genome sequence of the virus shows that it is a member of the genus Nanovirus, but it lacks DNA-U4. In addition to the seven genomic DNAs of the virus, we identified a second DNA-R and seven distinct alphasatellites associated with the disease. We propose the name "parsley severe stunt associated virus" (PSSaV) for this novel nanovirus.
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Affiliation(s)
| | - Dennis Knierim
- Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSMZ), Messeweg 11/12, 38104, Brunswick, Germany
| | - Mirko Sebastian Rakoski
- Department of Phytomedicine, Plant Virology, Institute of Horticultural Production Systems, Leibniz University, 30419, Hannover, Germany
| | - Wulf Menzel
- Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSMZ), Messeweg 11/12, 38104, Brunswick, Germany
| | - Edgar Maiss
- Department of Phytomedicine, Plant Virology, Institute of Horticultural Production Systems, Leibniz University, 30419, Hannover, Germany
| | - Bruno Gronenborn
- Institute for Integrative Biology of the Cell, UMR9198, CNRS, Université Paris-Sud, CEA, Avenue de la Terrasse, 91198, Gif sur Yvette, France
| | - Stephan Winter
- Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSMZ), Messeweg 11/12, 38104, Brunswick, Germany
| | - Björn Krenz
- Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSMZ), Messeweg 11/12, 38104, Brunswick, Germany.
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Kamran A, Hou H, Xie Y, Zhao C, Wei X, Zhang C, Yu X, Wang F, Yang J. Full genome sequence analysis and putative host-shifting of Milk vetch dwarf virus infecting tobacco (Nicotiana tabacum) in China. Virol J 2019; 16:38. [PMID: 30917832 PMCID: PMC6437909 DOI: 10.1186/s12985-019-1129-5] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2018] [Accepted: 02/13/2019] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Tobacco production in China has been affected by plant viruses with Milk vetch dwarf virus (MDV) as a recent invader posing serious concern. According to most of the studies, MDV mainly infects hosts from Fabaceae family but in our previous study we reported its infection in tobacco plant (Nicotiana tabacum L.) in Shandong province. FINDINGS In current study (2016-2017), tobacco plants (Nicotiana tabacum) with severe stunting, yellowing and axillary bunch of new leaves were observed in Zhengning, Gansu province. Isolate GSZN yielded into eight genomic circular single-stranded DNA components while no alphasatellite DNA was obtained. High percent identity of this isolate was recorded in overall nucleotide and amino acid assembly with reported MDV isolates worldwide. Phylogenetic analysis fetched into a separate sub-clade comprising of new isolate along with other tobacco infecting isolates of MDV. While recombination was predicted in DNA-C encoding Clink protein and DNA-U1, which may attribute towards the potential host-shifting phenomenon and ability of this virus to expand its host range. CONCLUSION To our knowledge this is the first full genome annotation of a Nanovirus, infecting tobacco in natural field conditions, also this is the first extended analysis on host-shifting behavior of MDV.
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Affiliation(s)
- Ali Kamran
- Key Laboratory of Tobacco Pest Monitoring Controlling & Integrated Management, Tobacco Research Institute of Chinese Academy of Agricultural Sciences, Qingdao, 266101, China
- Graduate School of Chinese Academy of Agricultural Sciences, Beijing, 100081, China
| | - Han Hou
- Key Laboratory of Tobacco Pest Monitoring Controlling & Integrated Management, Tobacco Research Institute of Chinese Academy of Agricultural Sciences, Qingdao, 266101, China
- Graduate School of Chinese Academy of Agricultural Sciences, Beijing, 100081, China
| | - Yi Xie
- Key Laboratory of Tobacco Pest Monitoring Controlling & Integrated Management, Tobacco Research Institute of Chinese Academy of Agricultural Sciences, Qingdao, 266101, China
| | - Cunxiao Zhao
- Qingyang Tobacco Company, Gansu Tobacco Cooperation, Xifeng, 745000, China
| | - Xiaomin Wei
- Qingyang Tobacco Company, Gansu Tobacco Cooperation, Xifeng, 745000, China
| | - Chaoqun Zhang
- Jiangxi Tobacco Science Institute, Nanchang, 330025, China
| | - Xiangwen Yu
- Sichuan Tobacco Science Institute, Chengdu, 610000, China
| | - Fenglong Wang
- Key Laboratory of Tobacco Pest Monitoring Controlling & Integrated Management, Tobacco Research Institute of Chinese Academy of Agricultural Sciences, Qingdao, 266101, China.
| | - Jinguang Yang
- Key Laboratory of Tobacco Pest Monitoring Controlling & Integrated Management, Tobacco Research Institute of Chinese Academy of Agricultural Sciences, Qingdao, 266101, China.
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11
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Venkataraman S, Selvarajan R. Recent advances in understanding the replication initiator protein of the ssDNA plant viruses of the family Nanoviridae. Virusdisease 2019; 30:22-31. [PMID: 31143829 PMCID: PMC6517469 DOI: 10.1007/s13337-019-00514-9] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2018] [Accepted: 02/13/2019] [Indexed: 12/20/2022] Open
Abstract
The families of viruses possessing single-stranded (ss) circular genome employ a dedicated replication initiator protein (Rep) for making copies of their genome through the process of rolling circle replication. The replication begins at conserved nonanucleotide sequence at the intergenic region. The Rep protein seems to be the most conserved amongst the available proteins of the nanovirids and comprises of the N-terminal endonuclease domain and the C-terminal helicase domain. The structural studies of Faba bean necrotic yellows virus endonuclease domain suggests a α + β fold comprising of central β sheet built from five antiparallel β strands surrounded by outer short α helices. The catalysis is mediated by a conserved Tyr residue and employs divalent metal ions (Mn2+). On one hand, the Reps associate with each other and oligomerize and on the other hand interact with varied host and vector associated proteins for successful infection. The sequence analysis of Reps from previously known nanovirids and the newly found ones from metagenomics data shed light on the evolutionary pattern of nanovirids in comparison to other plant infecting ssDNA viruses.
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Affiliation(s)
- Sangita Venkataraman
- Department of Biotechnology, Acharya Nagarjuna University, Nagarjuna Nagar, Guntur, 522510 India
| | - R. Selvarajan
- ICAR National Research Centre for Banana, Thayanur Post, Tiruchirapalli, 620102 India
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Knierim D, Barrière Q, Grigoras I, Winter S, Vetten HJ, Schwinghamer M, Thomas J, Chu P, Gronenborn B, Timchenko T. Subterranean Clover Stunt Virus Revisited: Detection of Two Missing Genome Components. Viruses 2019; 11:v11020138. [PMID: 30720711 PMCID: PMC6410307 DOI: 10.3390/v11020138] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2019] [Revised: 01/28/2019] [Accepted: 02/01/2019] [Indexed: 01/15/2023] Open
Abstract
Subterranean clover stunt virus (SCSV) is a type species of the genus Nanovirus in the family Nanoviridae. It was the first single-stranded DNA plant virus with a multipartite genome, of which genomic DNA sequences had been determined. All nanoviruses have eight genome components except SCSV, for which homologs of two genome components present in all other nanovirus genomes, DNA-U2 and DNA-U4, were lacking. We analysed archived and more recent samples from SCSV-infected legume plants to verify its genome composition and found the missing genome components. These results indicated that SCSV also has eight genome components and is a typical member of the genus Nanovirus.
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Affiliation(s)
- Dennis Knierim
- Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSMZ), Inhoffenstraße 7B, 38124 Braunschweig, Germany.
| | - Quentin Barrière
- Institute for Integrative Biology of the Cell, UMR9198, CNRS, Université Paris-Sud, CEA, 91198 Gif-sur-Yvette, France.
| | - Ioana Grigoras
- Institute for Integrative Biology of the Cell, UMR9198, CNRS, Université Paris-Sud, CEA, 91198 Gif-sur-Yvette, France.
| | - Stephan Winter
- Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSMZ), Inhoffenstraße 7B, 38124 Braunschweig, Germany.
| | | | - Mark Schwinghamer
- NSW Department of Primary Industries, Tamworth Agricultural Institute, 4 Marsden Park Road, Calala, NSW 2340, Australia
| | - John Thomas
- The University of Queensland, QAAFI, Ecosciences Precinct, GPO Box 267, Brisbane, QLD 4001, Australia.
| | - Paul Chu
- Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, China.
- Megalong Crescent, Harrison, ACT 2914, Australia.
| | - Bruno Gronenborn
- Institute for Integrative Biology of the Cell, UMR9198, CNRS, Université Paris-Sud, CEA, 91198 Gif-sur-Yvette, France.
| | - Tatiana Timchenko
- Institute for Integrative Biology of the Cell, UMR9198, CNRS, Université Paris-Sud, CEA, 91198 Gif-sur-Yvette, France.
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Zhao L, Rosario K, Breitbart M, Duffy S. Eukaryotic Circular Rep-Encoding Single-Stranded DNA (CRESS DNA) Viruses: Ubiquitous Viruses With Small Genomes and a Diverse Host Range. Adv Virus Res 2018; 103:71-133. [PMID: 30635078 DOI: 10.1016/bs.aivir.2018.10.001] [Citation(s) in RCA: 123] [Impact Index Per Article: 20.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Abstract
While single-stranded DNA (ssDNA) was once thought to be a relatively rare genomic architecture for viruses, modern metagenomics sequencing has revealed circular ssDNA viruses in most environments and in association with diverse hosts. In particular, circular ssDNA viruses encoding a homologous replication-associated protein (Rep) have been identified in the majority of eukaryotic supergroups, generating interest in the ecological effects and evolutionary history of circular Rep-encoding ssDNA viruses (CRESS DNA) viruses. This review surveys the explosion of sequence diversity and expansion of eukaryotic CRESS DNA taxonomic groups over the last decade, highlights similarities between the well-studied geminiviruses and circoviruses with newly identified groups known only through their genome sequences, discusses the ecology and evolution of eukaryotic CRESS DNA viruses, and speculates on future research horizons.
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Affiliation(s)
- Lele Zhao
- Department of Ecology, Evolution and Natural Resources, Rutgers, the State University of New Jersey, New Brunswick, NJ, United States
| | - Karyna Rosario
- College of Marine Science, University of South Florida, Saint Petersburg, FL, United States
| | - Mya Breitbart
- College of Marine Science, University of South Florida, Saint Petersburg, FL, United States
| | - Siobain Duffy
- Department of Ecology, Evolution and Natural Resources, Rutgers, the State University of New Jersey, New Brunswick, NJ, United States.
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Alphasatellitidae: a new family with two subfamilies for the classification of geminivirus- and nanovirus-associated alphasatellites. Arch Virol 2018; 163:2587-2600. [PMID: 29740680 DOI: 10.1007/s00705-018-3854-2] [Citation(s) in RCA: 79] [Impact Index Per Article: 13.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2018] [Accepted: 04/25/2018] [Indexed: 10/16/2022]
Abstract
Nanoviruses and geminiviruses are circular, single stranded DNA viruses that infect many plant species around the world. Nanoviruses and certain geminiviruses that belong to the Begomovirus and Mastrevirus genera are associated with additional circular, single stranded DNA molecules (~ 1-1.4 kb) that encode a replication-associated protein (Rep). These Rep-encoding satellite molecules are commonly referred to as alphasatellites and here we communicate the establishment of the family Alphasatellitidae to which these have been assigned. Within the Alphasatellitidae family two subfamilies, Geminialphasatellitinae and Nanoalphasatellitinae, have been established to respectively accommodate the geminivirus- and nanovirus-associated alphasatellites. Whereas the pairwise nucleotide sequence identity distribution of all the known geminialphasatellites (n = 628) displayed a troughs at ~ 70% and 88% pairwise identity, that of the known nanoalphasatellites (n = 54) had a troughs at ~ 67% and ~ 80% pairwise identity. We use these pairwise identity values as thresholds together with phylogenetic analyses to establish four genera and 43 species of geminialphasatellites and seven genera and 19 species of nanoalphasatellites. Furthermore, a divergent alphasatellite associated with coconut foliar decay disease is assigned to a species but not a subfamily as it likely represents a new alphasatellite subfamily that could be established once other closely related molecules are discovered.
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Analysis of DNAs associated with coconut foliar decay disease implicates a unique single-stranded DNA virus representing a new taxon. Sci Rep 2018; 8:5698. [PMID: 29632309 PMCID: PMC5890292 DOI: 10.1038/s41598-018-23739-y] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2018] [Accepted: 03/16/2018] [Indexed: 12/11/2022] Open
Abstract
The unique ecology, pathology and undefined taxonomy of coconut foliar decay virus (CFDV), found associated with coconut foliar decay disease (CFD) in 1986, prompted analyses of old virus samples by modern methods. Rolling circle amplification and deep sequencing applied to nucleic acid extracts from virion preparations and CFD-affected palms identified twelve distinct circular DNAs, eleven of which had a size of about 1.3 kb and one of 641 nt. Mass spectrometry-based protein identification proved that a 24 kDa protein encoded by two 1.3 kb DNAs is the virus capsid protein with highest sequence similarity to that of grabloviruses (family Geminiviridae), even though CFDV particles are not geminate. The nine other 1.3 kb DNAs represent alphasatellites coding for replication initiator proteins that differ clearly from those encoded by nanovirid DNA-R. The 641 nt DNA-gamma is unique and may encode a movement protein. Three DNAs, alphasatellite CFDAR, capsid protein encoding CFDV DNA-S.1 and DNA-gamma share sequence motifs near their replication origins and were consistently present in all samples analysed. These DNAs appear to be integral components of a possibly tripartite CFDV genome, different from those of any Geminiviridae or Nanoviridae family member, implicating CFDV as representative of a new genus and family.
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Molecular characterization of faba bean necrotic yellows viruses in Tunisia. Arch Virol 2017; 163:687-694. [PMID: 29147784 DOI: 10.1007/s00705-017-3651-3] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2017] [Accepted: 11/06/2017] [Indexed: 10/18/2022]
Abstract
Faba bean necrotic yellows virus (FBNYV) (genus Nanovirus; family Nanoviridae) has a genome comprising eight individually encapsidated circular single-stranded DNA components. It has frequently been found infecting faba bean (Vicia faba L.) and chickpea (Cicer arietinum L.) in association with satellite molecules (alphasatellites). Genome sequences of FBNYV from Azerbaijan, Egypt, Iran, Morocco, Spain and Syria have been determined previously and we now report the first five genome sequences of FBNYV and associated alphasatellites from faba bean sampled in Tunisia. In addition, we have determined the genome sequences of two additional FBNYV isolates from chickpea plants sampled in Syria and Iran. All individual FBNYV genome component sequences that were determined here share > 84% nucleotide sequence identity with FBNYV sequences available in public databases, with the DNA-M component displaying the highest degree of diversity. As with other studied nanoviruses, recombination and genome component reassortment occurs frequently both between FBNYV genomes and between genomes of nanoviruses belonging to other species.
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17
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Krenz B, Schießl I, Greiner E, Krapp S. Analyses of pea necrotic yellow dwarf virus-encoded proteins. Virus Genes 2017; 53:454-463. [PMID: 28238159 DOI: 10.1007/s11262-017-1439-x] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2016] [Accepted: 02/17/2017] [Indexed: 10/20/2022]
Abstract
Pea necrotic yellow dwarf virus (PNYDV) is a multipartite, circular, single-stranded DNA plant virus. PNYDV encodes eight proteins and the function of three of which remains unknown-U1, U2, and U4. PNYDV proteins cellular localization was analyzed by GFP tagging and bimolecular fluorescence complementation (BiFC) studies. The interactions of all eight PNYDV proteins were tested pairwise in planta (36 combinations in total). Seven interactions were identified and two (M-Rep with CP and MP with U4) were characterized further. MP and U4 complexes appeared as vesicle-like spots and were localized at the nuclear envelope and cell periphery. These vesicle-like spots were associated with the endoplasmatic reticulum. In addition, a nuclear localization signal (NLS) was mapped for U1, and a mutated U1 with NLS disrupted localized at plasmodesmata and therefore might also have a role in movement. Taken together, this study provides evidence for previously undescribed nanovirus protein-protein interactions and their cellular localization with novel findings not only for those proteins with unknown function, but also for characterized proteins such as the CP.
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Affiliation(s)
- Björn Krenz
- Lehrstuhl für Biochemie, Department Biologie, Universität Erlangen-Nürnberg, Staudtstr. 5, 91058, Erlangen, Germany.
| | - Ingrid Schießl
- Lehrstuhl für Biochemie, Department Biologie, Universität Erlangen-Nürnberg, Staudtstr. 5, 91058, Erlangen, Germany
| | - Eva Greiner
- Lehrstuhl für Biochemie, Department Biologie, Universität Erlangen-Nürnberg, Staudtstr. 5, 91058, Erlangen, Germany
| | - Susanna Krapp
- Lehrstuhl für Biochemie, Department Biologie, Universität Erlangen-Nürnberg, Staudtstr. 5, 91058, Erlangen, Germany
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18
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Heydarnejad J, Kamali M, Massumi H, Kvarnheden A, Male MF, Kraberger S, Stainton D, Martin DP, Varsani A. Identification of a Nanovirus-Alphasatellite Complex in Sophora alopecuroides. Virus Res 2017; 235:24-32. [PMID: 28396284 DOI: 10.1016/j.virusres.2017.03.023] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2017] [Revised: 03/15/2017] [Accepted: 03/18/2017] [Indexed: 10/19/2022]
Abstract
Viruses in the genus Nanovirus of the family Nanoviridae generally have eight individually encapsidated circular genome components and have been predominantly found infecting Fabaceae plants in Europe, Australia, Africa and Asia. For over a decade Sophora alopecuroides L. (Fabaceae) plants have been observed across Iran displaying dwarfing, yellowing, stunted leaves and yellow vein banding. Using a high-throughput sequencing approach, sequences were identified within one such plant that had similarities to nanovirus genome components. From this plant, the nanovirus-like molecules DNA-R (n=4), DNA-C (n=2), DNA-S (n=1), DNA-M (n=1), DNA-N (n=1), DNA-U1 (n=1), DNA-U2 (n=1) and DNA-U4 (n=1) were amplified, cloned and sequenced. Other than for the DNA-R, these components share less than 71% identity with those of other known nanoviruses. The four DNA-R molecules were highly diverse, sharing only 65-71% identity with each other and 64-86% identity with those of other nanoviruses. In the S. alopecuroides plant 14 molecules sharing 57.7-84.6% identity with previously determined sequences of nanovirus-associated alphasatellites were also identified. Given the research activity in the nanovirus field during the last five years coupled with high-throughput sequence technologies, many more diverse nanoviruses and nanovirus-associated satellites are likely to be identified.
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Affiliation(s)
- Jahangir Heydarnejad
- Department of Plant Protection, College of Agriculture, Shahid Bahonar University of Kerman, Kerman, Iran.
| | - Mehdi Kamali
- Department of Plant Protection, College of Agriculture, Shahid Bahonar University of Kerman, Kerman, Iran
| | - Hossain Massumi
- Department of Plant Protection, College of Agriculture, Shahid Bahonar University of Kerman, Kerman, Iran
| | - Anders Kvarnheden
- Department of Plant Biology, Uppsala BioCenter, Linnean Center of Plant Biology in Uppsala, Swedish University of Agricultural Sciences, Box 7080, SE-750 07 Uppsala, Sweden
| | - Maketalena F Male
- School of Biological Sciences, University of Canterbury, Private Bag 4800, Christchurch 8140, New Zealand
| | - Simona Kraberger
- School of Biological Sciences, University of Canterbury, Private Bag 4800, Christchurch 8140, New Zealand; Department of Microbiology, Immunology and Pathology, Colorado State University, Fort Collins, CO 80523, USA
| | - Daisy Stainton
- School of Biological Sciences, University of Canterbury, Private Bag 4800, Christchurch 8140, New Zealand; School of Biological Sciences, The University of Queensland, Brisbane, Queensland 4072, Australia
| | - Darren P Martin
- Computational Biology Group, Institute of Infectious Disease and Molecular Medicine, Faculty of Health Sciences, University of Cape Town, Observatory 7925, Rondebosch, Cape Town, South Africa
| | - Arvind Varsani
- School of Biological Sciences, University of Canterbury, Private Bag 4800, Christchurch 8140, New Zealand; Structural Biology Research Unit, Department of Clinical Laboratory Sciences, University of Cape Town, Rondebosch 7701, Cape Town, South Africa; The Biodesign Center for Fundamental and Applied Microbiomics, Center for Evolution and Medicine, School of Life Sciences, Arizona State University, Tempe, AZ 85287-5001, USA.
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19
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Complete genomic characterization of milk vetch dwarf virus isolates from cowpea and broad bean in Anhui province, China. Arch Virol 2017; 162:2437-2440. [DOI: 10.1007/s00705-017-3348-7] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2016] [Accepted: 03/01/2017] [Indexed: 10/19/2022]
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20
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Stainton D, Martin DP, Collings DA, Varsani A. Comparative analysis of common regions found in babuviruses and alphasatellite molecules. Arch Virol 2016; 162:849-855. [PMID: 27878460 DOI: 10.1007/s00705-016-3168-1] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2016] [Accepted: 10/24/2016] [Indexed: 11/26/2022]
Abstract
Viruses in the genus Babuvirus have multi-component ssDNA genomes and often associate with alphasatellite molecules containing two common motifs, a common-region stem-loop (CR-SL) involved in initiation of rolling-circle replication and a common-region major (CR-M) motif involved in secondary-strand synthesis. We compared known babuvirus genome components and alphasatellite CR-SL and CR-M sequences, defining five divergent CR-SL sequence classes. We identified iterated sequence elements in babuvirus genome components that have particularly conserved sequences and spatial arrangements between known babuviruses.
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Affiliation(s)
- Daisy Stainton
- School of Biological Sciences, University of Canterbury, Christchurch, 8140, New Zealand
| | - Darren P Martin
- Department of Clinical Laboratory Sciences, University of Cape Town, Cape Town, South Africa
| | - David A Collings
- School of Biological Sciences, University of Canterbury, Christchurch, 8140, New Zealand
- School of Environmental and Life Sciences, University of Newcastle, Callaghan, NSW, 2308, Australia
| | - Arvind Varsani
- School of Biological Sciences, University of Canterbury, Christchurch, 8140, New Zealand.
- Department of Clinical Laboratory Sciences, University of Cape Town, Cape Town, South Africa.
- The Biodesign Center for Fundamental and Applied Microbiomics, and School of Life Sciences, Arizona State University, Tempe, AZ, 85287-5001, USA.
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Abstract
Multipartite viruses have one of the most puzzling genetic organizations found in living organisms. These viruses have several genome segments, each containing only a part of the genetic information, and each individually encapsidated into a separate virus particle. While countless studies on molecular and cellular mechanisms of the infection cycle of multipartite viruses are available, just as for other virus types, very seldom is their lifestyle questioned at the viral system level. Moreover, the rare available “system” studies are purely theoretical, and their predictions on the putative benefit/cost balance of this peculiar genetic organization have not received experimental support. In light of ongoing progresses in general virology, we here challenge the current hypotheses explaining the evolutionary success of multipartite viruses and emphasize their shortcomings. We also discuss alternative ideas and research avenues to be explored in the future in order to solve the long-standing mystery of how viral systems composed of interdependent but physically separated information units can actually be functional.
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22
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Asymmetric patterns of reassortment and concerted evolution in Cardamom bushy dwarf virus. INFECTION GENETICS AND EVOLUTION 2014; 24:15-24. [DOI: 10.1016/j.meegid.2014.02.012] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/03/2013] [Revised: 01/10/2014] [Accepted: 02/26/2014] [Indexed: 11/18/2022]
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Grigoras I, Ginzo AIDC, Martin DP, Varsani A, Romero J, Mammadov AC, Huseynova IM, Aliyev JA, Kheyr-Pour A, Huss H, Ziebell H, Timchenko T, Vetten HJ, Gronenborn B. Genome diversity and evidence of recombination and reassortment in nanoviruses from Europe. J Gen Virol 2014; 95:1178-1191. [DOI: 10.1099/vir.0.063115-0] [Citation(s) in RCA: 38] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/26/2023] Open
Abstract
The recent identification of a new nanovirus, pea necrotic yellow dwarf virus, from pea in Germany prompted us to survey wild and cultivated legumes for nanovirus infections in several European countries. This led to the identification of two new nanoviruses: black medic leaf roll virus (BMLRV) and pea yellow stunt virus (PYSV), each considered a putative new species. The complete genomes of a PYSV isolate from Austria and three BMLRV isolates from Austria, Azerbaijan and Sweden were sequenced. In addition, the genomes of five isolates of faba bean necrotic yellows virus (FBNYV) from Azerbaijan and Spain and those of four faba bean necrotic stunt virus (FBNSV) isolates from Azerbaijan were completely sequenced, leading to the first identification of FBNSV occurring in Europe. Sequence analyses uncovered evolutionary relationships, extensive reassortment and potential remnants of mixed nanovirus infections, as well as intra- and intercomponent recombination events within the nanovirus genomes. In some virus isolates, diverse types of the same genome component (paralogues) were observed, a type of genome complexity not described previously for any member of the family Nanoviridae. Moreover, infectious and aphid-transmissible nanoviruses from cloned genomic DNAs of FBNYV and BMLRV were reconstituted that, for the first time, allow experimental reassortments for studying the genome functions and evolution of these nanoviruses.
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Affiliation(s)
- Ioana Grigoras
- Institut des Sciences du Végétal, CNRS, 91198 Gif sur Yvette, France
| | - Ana Isabel del Cueto Ginzo
- Departamento de Protección Vegetal, Instituto Nacional de Investigación y Tecnología Agraria (INIA), Carretera de La Coruna Km. 7.0, Madrid 28040, Spain
| | - Darren P. Martin
- Computational Biology Group, Institute of Infectious Diseases and Molecular Medicine, University of Cape Town, Cape Town, South Africa
| | - Arvind Varsani
- Electron Microscope Unit, University of Cape Town, Rondebosch, 7701, Cape Town, South Africa
- Department of Plant Pathology and Emerging Pathogens Institute, University of Florida, Gainesville, FL, USA
- School of Biological Sciences and Biomolecular Interaction Centre, University of Canterbury, Christchurch, 8140, New Zealand
| | - Javier Romero
- Departamento de Protección Vegetal, Instituto Nacional de Investigación y Tecnología Agraria (INIA), Carretera de La Coruna Km. 7.0, Madrid 28040, Spain
| | - Alamdar Ch. Mammadov
- Department of Fundamental Problems of Biological Productivity, Institute of Botany, Azerbaijan National Academy of Sciences, 40 Badamdar Highway, Baku AZ 1073, Azerbaijan
| | - Irada M. Huseynova
- Department of Fundamental Problems of Biological Productivity, Institute of Botany, Azerbaijan National Academy of Sciences, 40 Badamdar Highway, Baku AZ 1073, Azerbaijan
| | - Jalal A. Aliyev
- Department of Fundamental Problems of Biological Productivity, Institute of Botany, Azerbaijan National Academy of Sciences, 40 Badamdar Highway, Baku AZ 1073, Azerbaijan
| | | | - Herbert Huss
- Lehr- und Forschungszentrum für Landwirtschaft (LFZ) Raumberg-Gumpenstein, Versuchsstation Lambach/Stadl-Paura, 4651 Stadl-Paura, Austria
| | - Heiko Ziebell
- Julius Kühn Institut, Bundesforschungsinstitut für Kulturpflanzen, Institut für Epidemiologie und Pathogendiagnostik, 38104 Braunschweig, Germany
| | - Tatiana Timchenko
- Institut des Sciences du Végétal, CNRS, 91198 Gif sur Yvette, France
| | - Heinrich-Josef Vetten
- Julius Kühn Institut, Bundesforschungsinstitut für Kulturpflanzen, Institut für Epidemiologie und Pathogendiagnostik, 38104 Braunschweig, Germany
| | - Bruno Gronenborn
- Institut des Sciences du Végétal, CNRS, 91198 Gif sur Yvette, France
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Savory FR, Varma V, Ramakrishnan U. Identifying geographic hot spots of reassortment in a multipartite plant virus. Evol Appl 2014; 7:569-79. [PMID: 24944570 PMCID: PMC4055178 DOI: 10.1111/eva.12156] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2013] [Accepted: 03/05/2014] [Indexed: 11/26/2022] Open
Abstract
Reassortment between different species or strains plays a key role in the evolution of multipartite plant viruses and can have important epidemiological implications. Identifying geographic locations where reassortant lineages are most likely to emerge could be a valuable strategy for informing disease management and surveillance efforts. We developed a predictive framework to identify potential geographic hot spots of reassortment based upon spatially explicit analyses of genome constellation diversity. To demonstrate the utility of this approach, we examined spatial variation in the potential for reassortment among Cardamom bushy dwarf virus (CBDV; Nanoviridae, Babuvirus) isolates in Northeast India. Using sequence data corresponding to six discrete genome components for 163 CBDV isolates, a quantitative measure of genome constellation diversity was obtained for locations across the sampling region. Two key areas were identified where viruses with highly distinct genome constellations cocirculate, and these locations were designated as possible geographic hot spots of reassortment, where novel reassortant lineages could emerge. Our study demonstrates that the potential for reassortment can be spatially dependent in multipartite plant viruses and highlights the use of evolutionary analyses to identify locations which could be actively managed to facilitate the prevention of outbreaks involving novel reassortant strains.
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Affiliation(s)
- Fiona R Savory
- National Centre for Biological Sciences, TATA Institute of Fundamental Research Bangalore, India
| | - Varun Varma
- National Centre for Biological Sciences, TATA Institute of Fundamental Research Bangalore, India
| | - Uma Ramakrishnan
- National Centre for Biological Sciences, TATA Institute of Fundamental Research Bangalore, India
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Hull R. Replication of Plant Viruses. PLANT VIROLOGY 2014. [PMCID: PMC7184227 DOI: 10.1016/b978-0-12-384871-0.00007-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 11/05/2022]
Abstract
Viruses replicate using both their own genetic information and host cell components and machinery. The different genome types have different replication pathways which contain controls on linking the process with translation and movement around the cell as well as not compromising the infected cell. This chapter discusses the replication mechanisms, faults in replication and replication of viruses co-infecting cells. Viruses replicate using both their own genetic information and host cell components and machinery. The different genome types have different replication pathways which contain controls on linking the process with translation and movement around the cell as well as not compromising the infected cell. This chapter discusses the replication mechanisms, faults in replication and replication of viruses coinfecting cells.
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26
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New Volvovirus Isolates from Acheta domesticus (Japan) and Gryllus assimilis (United States). GENOME ANNOUNCEMENTS 2013; 1:1/3/e00328-13. [PMID: 23792751 PMCID: PMC3675518 DOI: 10.1128/genomea.00328-13] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Indexed: 12/01/2022]
Abstract
A novel circular single-stranded DNA (ssDNA) virus, volvovirus, from the house cricket has been described recently. Here, we report the isolation of volvoviruses from Acheta domesticus in Japan and Gryllus assimilis in the United States. These Acheta domesticus volvovirus (AdVVV) isolates have genomes of 2,517 and 2,516 nucleotides (nt) and 4 large open reading frames (ORFs).
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Dayaram A, Potter KA, Moline AB, Rosenstein DD, Marinov M, Thomas JE, Breitbart M, Rosario K, Argüello-Astorga GR, Varsani A. High global diversity of cycloviruses amongst dragonflies. J Gen Virol 2013; 94:1827-1840. [PMID: 23596268 DOI: 10.1099/vir.0.052654-0] [Citation(s) in RCA: 53] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022] Open
Abstract
Members of the family Circoviridae, specifically the genus Circovirus, were thought to infect only vertebrates; however, members of a sister group under the same family, the proposed genus Cyclovirus, have been detected recently in insects. In an effort to explore the diversity of cycloviruses and better understand the evolution of these novel ssDNA viruses, here we present five cycloviruses isolated from three dragonfly species (Orthetrum sabina, Xanthocnemis zealandica and Rhionaeschna multicolor) collected in Australia, New Zealand and the USA, respectively. The genomes of these five viruses share similar genome structure to other cycloviruses, with a circular ~1.7 kb genome and two major bidirectionally transcribed ORFs. The genomic sequence data gathered during this study were combined with all cyclovirus genomes available in public databases to identify conserved motifs and regulatory elements in the intergenic regions, as well as determine diversity and recombinant regions within their genomes. The genomes reported here represent four different cyclovirus species, three of which are novel. Our results confirm that cycloviruses circulate widely in winged-insect populations; in eight different cyclovirus species identified in dragonflies to date, some of these exhibit a broad geographical distribution. Recombination analysis revealed both intra- and inter-species recombination events amongst cycloviruses, including genomes recovered from disparate sources (e.g. goat meat and human faeces). Similar to other well-characterized circular ssDNA viruses, recombination may play an important role in cyclovirus evolution.
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Affiliation(s)
- Anisha Dayaram
- School of Biological Sciences, University of Canterbury, Christchurch 8140, New Zealand
| | - Kristen A Potter
- School of Forestry, Northern Arizona University, Flagstaff, AZ 86011, USA
| | - Angela B Moline
- School of Earth Sciences and Environmental Sustainability, Northern Arizona University, Flagstaff, AZ 86011, USA
| | - Dana Drake Rosenstein
- School of Anthropology, University of Arizona, 1009 E South Campus Drive, Tucson, AZ 85721-0030, USA
| | - Milen Marinov
- School of Biological Sciences, University of Canterbury, Christchurch 8140, New Zealand
| | - John E Thomas
- Department of Agriculture, Fisheries and Forestry, Ecosciences Precinct, GPO Box 267, Brisbane, QLD 4001, Australia.,Centre for Plant Science, Queensland Alliance for Agriculture and Food Innovation, The University of Queensland, Ecosciences Precinct, GPO Box 247, Brisbane, QLD 4001, Australia
| | - Mya Breitbart
- College of Marine Science, University of South Florida, St Petersburg, FL 33701, USA
| | - Karyna Rosario
- College of Marine Science, University of South Florida, St Petersburg, FL 33701, USA
| | - Gerardo R Argüello-Astorga
- División de Biología Molecular, Instituto Potosino de Investigación Científica y Tecnológica, Camino a la Presa San José 2055, 78216 San Luis Potosí, S.L.P., Mexico
| | - Arvind Varsani
- Electron Microscope Unit, Division of Medical Biochemistry, Department of Clinical Laboratory Sciences, University of Cape Town, Observatory 7700, South Africa.,Biomolecular Interaction Centre, University of Canterbury, Christchurch 8140, New Zealand.,School of Biological Sciences, University of Canterbury, Christchurch 8140, New Zealand
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28
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Acheta domesticus Volvovirus, a Novel Single-Stranded Circular DNA Virus of the House Cricket. GENOME ANNOUNCEMENTS 2013; 1:e0007913. [PMID: 23516206 PMCID: PMC3623006 DOI: 10.1128/genomea.00079-13] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Indexed: 12/04/2022]
Abstract
The genome of a novel virus of the house cricket consists of a 2,517-nucleotide (nt) circular single-stranded DNA (ssDNA) molecule with 4 open reading frames (ORFs). One ORF had a low identity to circovirus nucleotide sequences (NS). The unique properties of this volvovirus suggested that it belongs to a new virus family or genus.
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29
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Stainton D, Kraberger S, Walters M, Wiltshire EJ, Rosario K, Halafihi M, Lolohea S, Katoa I, Faitua TH, Aholelei W, Taufa L, Thomas JE, Collings DA, Martin DP, Varsani A. Evidence of inter-component recombination, intra-component recombination and reassortment in banana bunchy top virus. J Gen Virol 2012; 93:1103-1119. [PMID: 22278830 DOI: 10.1099/vir.0.040337-0] [Citation(s) in RCA: 35] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Banana bunchy top virus (BBTV; family Nanoviridae, genus Babuvirus) is a multi-component, ssDNA virus, which causes widespread banana crop losses throughout tropical Africa and Australasia. We determined the full genome sequences of 12 BBTV isolates from the Kingdom of Tonga and analysed these together with previously determined BBTV sequences to show that reassortment and both inter- and intra-component recombination have all been relatively frequent occurrences during BBTV evolution. We found that whereas DNA-U3 components display evidence of complex inter- and intra-component recombination, all of the South Pacific DNA-R components have a common intra-component recombinant origin spanning the replication-associated protein gene. Altogether, the DNA-U3 and DNA-M components display a greater degree of inter-component recombination than the DNA-R, -S, -C and -M components. The breakpoint distribution of the inter-component recombination events reveals a primary recombination hotspot around the 5' side of the common region major and, in accordance with recombination hotspots detectable in related ssDNA viruses, a secondary recombination hotspot near the origin of virion-strand replication.
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Affiliation(s)
- Daisy Stainton
- School of Biological Sciences, University of Canterbury, Christchurch 8140, New Zealand
| | - Simona Kraberger
- School of Biological Sciences, University of Canterbury, Christchurch 8140, New Zealand
| | - Matthew Walters
- School of Biological Sciences, University of Canterbury, Christchurch 8140, New Zealand
| | - Elizabeth J Wiltshire
- School of Biological Sciences, University of Canterbury, Christchurch 8140, New Zealand
| | - Karyna Rosario
- College of Marine Science, University of South Florida, St Petersburg, FL 33701, USA
| | - Mana'ia Halafihi
- Ministry of Agriculture and Food, Forests and Fisheries, Nuku'alofa, Tongatapu, Kingdom of Tonga
| | | | - Ika Katoa
- Ministry of Agriculture and Food, Forests and Fisheries, Nuku'alofa, Tongatapu, Kingdom of Tonga
| | | | - Waikato Aholelei
- Ministry of Agriculture and Food, Forests and Fisheries, Nuku'alofa, Tongatapu, Kingdom of Tonga
| | - Luseane Taufa
- Ministry of Agriculture and Food, Forests and Fisheries, Nuku'alofa, Tongatapu, Kingdom of Tonga
| | - John E Thomas
- The University of Queensland, Centre for Plant Science, Queensland Alliance for Agriculture and Food Innovation, Ecosciences Precinct, PO Box 46, Brisbane QLD 4001, Australia
| | - David A Collings
- Biomolecular Interaction Centre, University of Canterbury, Christchurch 8140, New Zealand.,School of Biological Sciences, University of Canterbury, Christchurch 8140, New Zealand
| | - Darren P Martin
- Computational Biology Group, Institute of Infectious Diseases and Molecular Medicine, University of Cape Town, Cape Town, South Africa
| | - Arvind Varsani
- Electron Microscope Unit, University of Cape Town, Rondebosch 7701, Cape Town, South Africa.,Biomolecular Interaction Centre, University of Canterbury, Christchurch 8140, New Zealand.,School of Biological Sciences, University of Canterbury, Christchurch 8140, New Zealand
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30
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Abstract
In the Mediterranean region, pea, bean, and faba bean production is affected by around 17 major viruses. These viruses do not have the same ecology and consequently require a variety of different preventive measures to control them. Some of these viruses have a narrow host range, such as Faba bean necrotic yellows virus (FBNYV), and others, such as Alfalfa mosaic virus (AMV) and Cucumber mosaic virus (CMV), a very wide host range. Such features are important when identifying sources of virus inoculum in a region, and the vectors can transmit viruses from natural reservoirs to the crop plants. Some of these viruses are seed borne and, consequently, can be disseminated long distances through infected seeds. Crop losses caused by these viruses are variable, depending on the sensitivity and susceptibility of the crop to infection. Host resistance genes have been identified for some of these viruses, but in others, such as FBNYV, no resistance genes in faba bean have been identified yet. Significant progress was made in developing precise methods for the identification of these viruses, and new virus problems are being identified every year. This chapter is not intended to be a review for pea, bean, and faba bean viruses, but rather focuses on the major viruses which affect these crops in the Mediterranean basin with focus on the progress made over the past two decades.
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Affiliation(s)
- Khaled Makkouk
- National Council for Scientific Research, Beirut, Lebanon
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31
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Martin DP, Biagini P, Lefeuvre P, Golden M, Roumagnac P, Varsani A. Recombination in eukaryotic single stranded DNA viruses. Viruses 2011; 3:1699-738. [PMID: 21994803 PMCID: PMC3187698 DOI: 10.3390/v3091699] [Citation(s) in RCA: 158] [Impact Index Per Article: 12.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2011] [Revised: 08/18/2011] [Accepted: 09/05/2011] [Indexed: 12/23/2022] Open
Abstract
Although single stranded (ss) DNA viruses that infect humans and their domesticated animals do not generally cause major diseases, the arthropod borne ssDNA viruses of plants do, and as a result seriously constrain food production in most temperate regions of the world. Besides the well known plant and animal-infecting ssDNA viruses, it has recently become apparent through metagenomic surveys of ssDNA molecules that there also exist large numbers of other diverse ssDNA viruses within almost all terrestrial and aquatic environments. The host ranges of these viruses probably span the tree of life and they are likely to be important components of global ecosystems. Various lines of evidence suggest that a pivotal evolutionary process during the generation of this global ssDNA virus diversity has probably been genetic recombination. High rates of homologous recombination, non-homologous recombination and genome component reassortment are known to occur within and between various different ssDNA virus species and we look here at the various roles that these different types of recombination may play, both in the day-to-day biology, and in the longer term evolution, of these viruses. We specifically focus on the ecological, biochemical and selective factors underlying patterns of genetic exchange detectable amongst the ssDNA viruses and discuss how these should all be considered when assessing the adaptive value of recombination during ssDNA virus evolution.
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Affiliation(s)
- Darren P. Martin
- Computational Biology Group, Institute of Infectious Diseases and Molecular Medicine, University of Cape Town, Cape Town 4579, South Africa; E-Mail:
| | - Philippe Biagini
- UMR CNRS 6578 Anthropologie Bioculturelle, Equipe “Emergence et co-évolution virale”, Etablissement Français du Sang Alpes-Méditerranée, Université de la Méditerranée, 27 Bd. Jean Moulin, 13005 Marseille, France; E-Mail:
| | - Pierre Lefeuvre
- CIRAD, UMR 53 PVBMT CIRAD-Université de la Réunion, Pôle de Protection des Plantes, Ligne Paradis, 97410, Saint Pierre, La Réunion, France; E-Mail:
| | - Michael Golden
- Computational Biology Group, Institute of Infectious Diseases and Molecular Medicine, University of Cape Town, Cape Town 4579, South Africa; E-Mail:
| | - Philippe Roumagnac
- CIRAD, UMR BGPI, TA A-54/K, Campus International de Montferrier-Baillarguet, 34398 Montpellier, France; E-Mail:
| | - Arvind Varsani
- Electron Microscope Unit, University of Cape Town, Rondebosch, Cape Town 7701, South Africa; E-Mail:
- Biomolecular Interaction Centre, University of Canterbury, Private Bag 4800, Christchurch 8140, New Zealand
- School of Biological Sciences, University of Canterbury, Private Bag 4800, Christchurch 8140, New Zealand
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32
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Hyder MZ, Shah SH, Hameed S, Naqvi SMS. Evidence of recombination in the Banana bunchy top virus genome. INFECTION GENETICS AND EVOLUTION 2011; 11:1293-300. [PMID: 21539936 DOI: 10.1016/j.meegid.2011.04.015] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/23/2010] [Revised: 04/13/2011] [Accepted: 04/16/2011] [Indexed: 10/18/2022]
Abstract
Viruses serve as good model for evolutionary studies, owing to their short generation times and small genomes. Banana bunchy top virus (BBTV) is a significant subject being multicomponent circular single stranded DNA virus. BBTV belongs to family Nanoviridae and contains DNA-R, -U3, -S, -M, -C, and -N as integral genomic components. Evolutionary studies have shown genetic re-assortment of components among its isolates and revealed a concerted type evolution in non-coding regions of its genome. The DNA U3 having been shown as the most diverse component in our previous studies, was subjected to sequencing from some Pakistani isolates for the first time. Sequence analysis revealed intergenomic recombination in DNA-U3 among the isolates of two sub-groups and a very rare intragenomic recombination in Pakistani BBTV population. This indicates that like other evolutionary processes including intergenomic recombination, intragenomic recombination among the genomic components of the same isolate may also have a significant contribution in the evolution of BBTV genome. Intragenomic recombination therefore appears to be a unique way to generate genetic diversity in the multicomponent ssDNA viruses.
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Affiliation(s)
- Muhammad Zeeshan Hyder
- Department of Biosciences, COMSATS Institute of Information Technology Islamabad, Islamabad 44000, Pakistan
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33
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Amin I, Ilyas M, Qazi J, Bashir R, Yadav JS, Mansoor S, Fauquet CM, Briddon RW. Identification of a major pathogenicity determinant and suppressors of RNA silencing encoded by a South Pacific isolate of Banana bunchy top virus originating from Pakistan. Virus Genes 2011; 42:272-81. [PMID: 21161359 DOI: 10.1007/s11262-010-0559-3] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2010] [Accepted: 11/26/2010] [Indexed: 12/11/2022]
Abstract
Five genes encoded by Banana bunchy top virus (BBTV) originating from Pakistan were expressed in Nicotiana benthamiana using a Potato virus X (PVX) vector. Expression of the master replication-associated protein (mRep) and movement protein (MP) resulted in necrotic cell death of inoculated tissues, as well as leaf curling and necrosis along the veins in newly emerging leaves. The systemic necrosis induced by the expression of MP was discolored (dark) in comparison to that induced by mRep. Expression of the cell-cycle link protein (Clink), the coat protein (CP), and the nuclear shuttle protein from the PVX vector induced somewhat milder symptoms, consisting of mild leaf curling and mosaic, although expression of the CP caused a necrotic response in inoculated leaf. The accumulation of viral RNA was enhanced by MP, Clink, and CP. Of the five BBTV-encoded gene products two, the MP and Clink, stabilized GFP-specific mRNA and reduced GFP-specific small interfering RNA in N. benthamiana line 16c when expressed under the control of the 35S promoter and co-inoculated with a construct for the expression of GFP hairpin RNA construct. These results identified MP and Clink as suppressors of RNA silencing. Taken together the ability of MP to induce severe symptoms in plants and suppress RNA silencing implicates this product as a major pathogenicity determinant of BBTV.
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Affiliation(s)
- Imran Amin
- Agricultural Biotechnology Division, National Institute for Biotechnology and Genetic Engineering, P.O. Box 577, Jhang Road, Faisalabad, Pakistan
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34
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Molecular Characterization of Geographically Different Banana bunchy top virus Isolates in India. INDIAN JOURNAL OF VIROLOGY : AN OFFICIAL ORGAN OF INDIAN VIROLOGICAL SOCIETY 2011; 21:110-6. [PMID: 23637489 DOI: 10.1007/s13337-010-0020-1] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/01/2010] [Accepted: 12/21/2010] [Indexed: 10/18/2022]
Abstract
Banana bunchy top disease (BBTD) caused by Banana bunchy top virus (BBTV) is one of the most devastating diseases of banana and poses a serious threat for cultivars like Hill Banana (Syn: Virupakshi) and Grand Naine in India. In this study, we have cloned and sequenced the complete genome comprised of six DNA components of BBTV infecting Hill Banana grown in lower Pulney hills, Tamil Nadu State, India. The complete genome sequence of this hill banana isolate showed high degree of similarity with the corresponding sequences of BBTV isolates originating from Lucknow, Uttar Pradesh State, India, and from Fiji, Egypt, Pakistan, and Australia. In addition, sixteen coat protein (CP) and thirteen replicase genes (Rep) sequences of BBTV isolates collected from different banana growing states of India were cloned and sequenced. The replicase sequences of 13 isolates showed high degree of similarity with that of South Pacific group of BBTV isolates. However, the CP gene of BBTV isolates from Shervroy and Kodaikanal hills of Tamil Nadu showed higher amino acid sequence variability compared to other isolates. Another hill banana isolate from Meghalaya state had 23 nucleotide substitutions in the CP gene but the amino acid sequence was conserved. This is the first report of the characterization of a complete genome of BBTV occurring in the high altitudes of India. Our study revealed that the Indian BBTV isolates with distinct geographical origins belongs to the South Pacific group, except Shervroy and Kodaikanal hill isolates which neither belong to the South Pacific nor the Asian group.
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35
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Mandal B. Advances in Small Isometric Multicomponent ssDNA Viruses Infecting Plants. INDIAN JOURNAL OF VIROLOGY : AN OFFICIAL ORGAN OF INDIAN VIROLOGICAL SOCIETY 2010; 21:18-30. [PMID: 23637475 PMCID: PMC3550773 DOI: 10.1007/s13337-010-0010-3] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/09/2010] [Accepted: 05/14/2010] [Indexed: 11/26/2022]
Abstract
Multicomponent ssDNA plant viruses were discovered during 1990s. They are associated with bunchy top, yellowing and dwarfing diseases of several economic plants under family Musaceae, Leguminosae and Zingiberaceae. In the current plant virus taxonomy, these viruses are classified under the family Nanoviridae containing two genera, Nanovirus and Babuvirus. The family Nanoviridae was created with five members in 2005 and by 2010, it has expanded with four additional members. The viruses are distributed in the tropical and subtropical regions of Asia, Australia, Europe and Africa. The viruses are not sap or seed transmissible and are naturally transmitted by aphid vector in a persistent manner. The genome is consisted of several circular ssDNAs of about 1 kb each. Up to 12 DNA components have been isolated from the diseased plant. The major viral proteins encoded by these components are replication initiator protein (Rep), coat protein, cell-cycle link protein, movement protein and a nuclear shuttle protein. Each ssDNA contains a single gene and a noncoding region with a stable stem and loop structure. Several Rep encoding components have been reported from each virus, only one of them designated as master Rep has ability to control replication of the other genomic components. Infectivity of the genomic DNAs was demonstrated only for two nanoviruses, Faba bean necrotic yellows virus and Faba bean necrotic stunt virus (FBNSV). A group of eight ssDNA components of FBNSV were necessary for producing disease and biologically active progeny viruses. So far, infectivity of genomic components of Babuvirus has not been demonstrated.
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Affiliation(s)
- Bikash Mandal
- Plant Virology Unit, Division of Plant Pathology, Indian Agricultural Research Institute, New Delhi, 110012 India
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36
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DNA-binding specificity determinants of replication proteins encoded by eukaryotic ssDNA viruses are adjacent to widely separated RCR conserved motifs. Arch Virol 2010; 155:1033-46. [PMID: 20422235 DOI: 10.1007/s00705-010-0674-4] [Citation(s) in RCA: 36] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2009] [Accepted: 03/22/2010] [Indexed: 10/19/2022]
Abstract
Eukaryotic ssDNA viruses encode a rolling-circle replication (RCR) initiation protein, Rep, which binds to iterated DNA elements functioning as essential elements for virus-specific replication. By using the iterons of all known circoviruses, nanoviruses and nanovirus-like satellites as heuristic devices, we have identified certain amino acid residues that presumably determine the DNA-binding specificity of their Rep proteins. These putative "specificity determinants" (SPDs) cluster in two discrete protein regions, which are adjacent to distinct conserved motifs. A comparable distribution of SPDs was uncovered in the Rep protein of geminiviruses. Modeling of the tertiary structure of diverse Rep proteins showed that SPD regions interact to form a small beta-sheet element that has been proposed to be critical for high-affinity DNA-binding of Rep. Our findings indicate that eukaryotic circular ssDNA viruses have a common ancestor and suggest that SPDs present in replication initiators from a huge variety of viral and plasmid RCR systems are associated with the same conserved motifs.
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37
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Abraham AD, Bencharki B, Torok V, Katul L, Varrelmann M, Josef Vetten H. Two distinct nanovirus species infecting faba bean in Morocco. Arch Virol 2009; 155:37-46. [PMID: 20069400 PMCID: PMC3128733 DOI: 10.1007/s00705-009-0548-9] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2009] [Accepted: 10/14/2009] [Indexed: 11/27/2022]
Abstract
Using monoclonal antibodies raised against a Faba bean necrotic yellows virus (FBNYV) isolate from Egypt and a Faba bean necrotic stunt virus (FBNSV) isolate from Ethiopia, a striking serological variability among nanovirus isolates from faba bean in Morocco was revealed. To obtain a better understanding of this nanovirus variability in Morocco, the entire genomes of two serologically contrasting isolates referred to as Mor5 and Mor23 were sequenced. The eight circular ssDNA components, each identified from Mor5- and Mor23-infected tissues and thought to form the complete nanovirus genome, ranged in size from 952 to 1,005 nt for Mor5 and from 980 to 1,004 nt for Mor23 and were structurally similar to previously described nanovirus DNAs. However, Mor5 and Mor23 differed from each other in overall nucleotide and amino acid sequences by 25 and 26%, respectively. Mor23 was most closely related to typical FBNYV isolates described earlier from Egypt and Syria, with which it shared a mean amino acid sequence identity of about 94%. On the other hand, Mor5 most closely resembled a FBNSV isolate from Ethiopia, with which it shared a mean amino acid sequence identity of approximately 89%. The serological and genetic differences observed for Mor5 and Mor23 were comparable to those observed earlier for FBNYV, FBNSV, and Milk vetch dwarf virus. Following the guidelines on nanovirus species demarcation, this suggests that Mor23 and Mor5 represent isolates of FBNYV and FBNSV, respectively. This is the first report not only on the presence of FBNSV in a country other than Ethiopia but also on the occurrence and complete genome sequences of members of two nanovirus species in the same country, thus providing evidence for faba bean crops being infected by members of two distinct nanovirus species in a restricted geographic area.
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Affiliation(s)
- Adane D. Abraham
- Julius Kühn Institute (JKI), Bundesforschungsinstitut für Kulturpflanzen, Institut für Epidemiologie und Pathogendiagnostik, Messeweg 11-12, 38104 Braunschweig, Germany
- Department of Crop Sciences, Section Plant Virology, University of Göttingen, Grisebachstr. 6, 37077 Göttingen, Germany
- Biotechnology Program, Ethiopian Institute of Agricultural Research, P.O. Box 2003, Addis Ababa, Ethiopia
| | - Bouchaib Bencharki
- Faculté des Sciences et Techniques, Université Hassan 1er, P.O. Box 577, Settat, Morocco
| | - Valeria Torok
- Julius Kühn Institute (JKI), Bundesforschungsinstitut für Kulturpflanzen, Institut für Epidemiologie und Pathogendiagnostik, Messeweg 11-12, 38104 Braunschweig, Germany
| | - Lina Katul
- Julius Kühn Institute (JKI), Bundesforschungsinstitut für Kulturpflanzen, Institut für Epidemiologie und Pathogendiagnostik, Messeweg 11-12, 38104 Braunschweig, Germany
| | - Mark Varrelmann
- Department of Crop Sciences, Section Plant Virology, University of Göttingen, Grisebachstr. 6, 37077 Göttingen, Germany
| | - H. Josef Vetten
- Julius Kühn Institute (JKI), Bundesforschungsinstitut für Kulturpflanzen, Institut für Epidemiologie und Pathogendiagnostik, Messeweg 11-12, 38104 Braunschweig, Germany
- Julius Kühn Institute, Federal Research Center for Cultivated Plants (JKI), Messeweg 11/12, 38104 Braunschweig, Germany
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38
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Grigoras I, Timchenko T, Katul L, Grande-Pérez A, Vetten HJ, Gronenborn B. Reconstitution of authentic nanovirus from multiple cloned DNAs. J Virol 2009; 83:10778-87. [PMID: 19656882 PMCID: PMC2753110 DOI: 10.1128/jvi.01212-09] [Citation(s) in RCA: 52] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2009] [Accepted: 07/30/2009] [Indexed: 11/20/2022] Open
Abstract
We describe a new plant single-stranded DNA (ssDNA) virus, a nanovirus isolate originating from the faba bean in Ethiopia. We applied rolling circle amplification (RCA) to extensively copy the individual circular DNAs of the nanovirus genome. By sequence analyses of more than 208 individually cloned genome components, we obtained a representative sample of eight polymorphic swarms of circular DNAs, each about 1 kb in size. From these heterogeneous DNA populations after RCA, we inferred consensus sequences of the eight DNA components of the virus genome. Based on the distinctive molecular and biological properties of the virus, we propose to consider it a new species of the genus Nanovirus and to name it faba bean necrotic stunt virus (FBNSV). Selecting a representative clone of each of the eight DNAs for transfer by T-DNA plasmids of Agrobacterium tumefaciens into Vicia faba plants, we elicited the development of the typical FBNSV disease symptoms. Moreover, we showed that the virus thus produced was readily transmitted by two different aphid vector species, Aphis craccivora and Acyrthosiphon pisum. This represents the first reconstitution of a fully infectious and sustainably insect-transmissible nanovirus from its cloned DNAs and provides compelling evidence that the genome of a legume-infecting nanovirus is typically comprised of eight distinct DNA components.
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Affiliation(s)
- Ioana Grigoras
- Institut des Sciences du Végétal, CNRS, 91198 Gif sur Yvette, France
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39
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Fu HC, Hu JM, Hung TH, Su HJ, Yeh HH. Unusual events involved in Banana bunchy top virus strain evolution. PHYTOPATHOLOGY 2009; 99:812-822. [PMID: 19522579 DOI: 10.1094/phyto-99-7-0812] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/27/2023]
Abstract
Banana bunchy top virus (BBTV) can be transmitted by aphids and consists of at least six integral components (DNA-R, -U3, -S, -M, -C, and -N). Several additional replication-competent components (additional Reps) are associated with some BBTV isolates. A collected BBTV strain (TW3) that causes mild symptoms was selected to study the processes in BBTV evolution. Southern blot hybridization, polymerase chain reaction (PCR), and real-time PCR did not detect DNA-N in TW3. Real-time PCR quantification of BBTV components revealed that, except for the copy number of TW3 DNA-U3, each detected integral component of BBTV TW3 was at least two orders lower than that of the severe strains. No infection was observed in plants inoculated with aphids, which were first given acquisition access to the TW3-infected banana leaves. Recombination analysis revealed recombination between the integral component TW3 DNA-U3 and the additional Rep DNA-Y. All BBTV integral components contain a replication initiation region (stem-loop common region) that share high sequence identity. Sequence alignment revealed that TW3 DNA-R, -S, -M, and -C all have a stem-loop common region containing a characteristic 9-nucleotide deletion found only in all reported DNA-N. Our data suggest that the additional Rep DNAs can serve as sources of additional genetic diversity for integral BBTV components.
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Affiliation(s)
- Hui-Chuan Fu
- Department of Plant Pathology and Microbiology, College of Agriculture, National Taiwan University, 1 Sec. 4 Roosevelt Road, Taipei, Taiwan
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40
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Grigoras I, Timchenko T, Gronenborn B. Transcripts encoding the nanovirus master replication initiator proteins are terminally redundant. J Gen Virol 2008; 89:583-593. [DOI: 10.1099/vir.0.83352-0] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
The multicomponent single-stranded DNA plant nanoviruses encode unique master replication initiator (Rep) proteins. We have mapped the 5′ and 3′ termini of the corresponding polyadenylated mRNAs from faba bean necrotic yellows virus (FBNYV) and subterranean clover stunt virus and found that these are terminally redundant by up to about 160 nt. Moreover, the origin of viral DNA replication is transcribed into RNA that is capable of folding into extended secondary structures. Other nanovirus genome components, such as the FBNYV DNA encoding the protein Clink or an FBNYV DNA encoding a non-essential para-Rep protein, are not transcribed in such a unique fashion. Thus, terminally redundant mRNAs and the resulting transcription of the replication origin appear to be restricted to nanovirus master Rep DNAs. We speculate that this may be a way to regulate the expression of the essential master Rep protein.
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Affiliation(s)
- Ioana Grigoras
- Institut des Sciences du Végétal, CNRS, 91198 Gif sur Yvette, France
| | - Tatiana Timchenko
- Institut des Sciences du Végétal, CNRS, 91198 Gif sur Yvette, France
| | - Bruno Gronenborn
- Institut des Sciences du Végétal, CNRS, 91198 Gif sur Yvette, France
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41
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Amin I, Qazi J, Mansoor S, Ilyas M, Briddon RW. Molecular characterisation of banana bunchy top virus (BBTV) from Pakistan. Virus Genes 2007. [PMID: 17990091 DOI: 10.1007/s11262‐007‐0168‐y] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 09/29/2022]
Abstract
Banana bunchy top disease is caused by a single-stranded circular DNA virus, banana bunchy top virus (BBTV), which is a member of the genus Babuvirus (family Nanoviridae). We have cloned and sequenced five components (DNA-R, DNA-S, DNA-N, DNA-M and DNA-C) of a BBTV isolate originating from Pakistan. In addition, the DNA-R and several other components of five further isolates, originating from geographically distinct sites across the banana-growing area of Sindh province, Pakistan, were cloned and sequenced. Analysis of the sequences indicates that BBTV present in Pakistan belongs to the "South Pacific" group of isolates and that the genetic diversity of the virus in the country is very low. The virus shows the highest levels of sequence identity to BBTV isolates originating from Egypt, India and Australia. The significance of these results with respect to the possible origin of the virus in Pakistan and the prospects for obtaining genetically engineered resistance to the virus are discussed.
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Affiliation(s)
- Imran Amin
- Plant Biotechnology Division, National Institute for Biotechnology and Genetic Engineering, PO Box 577, Faisalabad, Pakistan.
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42
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Amin I, Qazi J, Mansoor S, Ilyas M, Briddon RW. Molecular characterisation of banana bunchy top virus (BBTV) from Pakistan. Virus Genes 2007; 36:191-8. [PMID: 17990091 DOI: 10.1007/s11262-007-0168-y] [Citation(s) in RCA: 29] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2007] [Accepted: 09/28/2007] [Indexed: 11/29/2022]
Abstract
Banana bunchy top disease is caused by a single-stranded circular DNA virus, banana bunchy top virus (BBTV), which is a member of the genus Babuvirus (family Nanoviridae). We have cloned and sequenced five components (DNA-R, DNA-S, DNA-N, DNA-M and DNA-C) of a BBTV isolate originating from Pakistan. In addition, the DNA-R and several other components of five further isolates, originating from geographically distinct sites across the banana-growing area of Sindh province, Pakistan, were cloned and sequenced. Analysis of the sequences indicates that BBTV present in Pakistan belongs to the "South Pacific" group of isolates and that the genetic diversity of the virus in the country is very low. The virus shows the highest levels of sequence identity to BBTV isolates originating from Egypt, India and Australia. The significance of these results with respect to the possible origin of the virus in Pakistan and the prospects for obtaining genetically engineered resistance to the virus are discussed.
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Affiliation(s)
- Imran Amin
- Plant Biotechnology Division, National Institute for Biotechnology and Genetic Engineering, PO Box 577, Faisalabad, Pakistan.
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43
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Leppik L, Gunst K, Lehtinen M, Dillner J, Streker K, de Villiers EM. In vivo and in vitro intragenomic rearrangement of TT viruses. J Virol 2007; 81:9346-56. [PMID: 17596318 PMCID: PMC1951432 DOI: 10.1128/jvi.00781-07] [Citation(s) in RCA: 47] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/05/2023] Open
Abstract
The in vitro replication of the Torque teno virus (TT virus) tth8 full-length genome and particle formation in a Hodgkin's lymphoma-derived cell line after transfection with cloned viral DNA were demonstrated. Analyses of the transcription patterns of tth8 and tth7 TT virus isolates in a number of lymphoma and T-cell leukemia cell lines indicated differential additional splicing events and intragenomic rearrangement generating open reading frames which could not be deducted from the genomic sequence. We also demonstrated the presence of rearranged TT virus genomes in vivo in sera taken from pregnant mothers whose children later developed childhood leukemia, as well as sera from control mothers. Control experiments using religated cloned genomic tth8 DNA mixed with cellular DNA did not result in such subviral molecules. These subviral isolates ranged from 172 bp to full-length TT virus genomes. Possible in vivo selection for specific rearranged molecules was indicated by the presence of one isolate (561 bp) in 11 serum samples. It remains to be clarified whether selected rearranged subviral components resulting from specific TT virus types may contribute to the initiation of disease. These data demonstrate new features of TT viruses suggesting possible similarities to plant viruses of the family Geminiviridae, as well as raise questions about the documented plurality and diversity of anelloviruses.
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MESH Headings
- Cell Line, Tumor
- Child
- DNA Virus Infections/virology
- DNA, Viral/chemistry
- DNA, Viral/genetics
- Female
- Genome, Viral
- Humans
- Infant
- Molecular Sequence Data
- Mothers
- RNA, Messenger/biosynthesis
- RNA, Messenger/genetics
- RNA, Viral/biosynthesis
- RNA, Viral/genetics
- Recombination, Genetic
- Sequence Analysis, DNA
- Serum/virology
- Torque teno virus/genetics
- Torque teno virus/isolation & purification
- Torque teno virus/physiology
- Transcription, Genetic
- Virus Replication
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Affiliation(s)
- Ludmila Leppik
- Division for the Characterization of Tumor Viruses, Deutsches Krebsforschungszentrum, Im Neuenheimer Feld 242, 69120 Heidelberg, Germany
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44
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Vega-Arreguín JC, Gronenborn B, Ramírez BC. Arabidopsis thaliana is a host of the legume nanovirus Faba bean necrotic yellows virus. Virus Res 2007; 128:81-7. [PMID: 17512075 DOI: 10.1016/j.virusres.2007.04.011] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2007] [Revised: 04/09/2007] [Accepted: 04/09/2007] [Indexed: 10/23/2022]
Abstract
We report infection of Arabidopsis thaliana with the legume nanovirus Faba bean necrotic yellows virus (FBNYV) by its insect vector Aphis craccivora. Symptoms of FBNYV infection on A. thaliana include stunting and reduced apical dominance, and are rather mild, compared to the severe necrosis and early plant death induced by the virus in the natural host Vicia faba. An inoculation access period of 6h is sufficient to transmit FBNYV to A. thaliana. FBNYV is readily transmitted back from A. thaliana to V. faba, where it induces the characteristic severe disease symptoms. Hence, passage through A. thaliana does not affect FBNYV pathogenicity. FBNYV accumulates to the highest levels in roots and stems, compared to cauline and rosette leaves. In cauline leaves, the kinetics of virus accumulation correlates with the amount of master Rep protein accumulation.
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Affiliation(s)
- Julio C Vega-Arreguín
- Institut des Sciences du Végétal, CNRS, Avenue de la Terrasse, Bât 23, Gif-sur-Yvette 91198, France.
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45
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Vega-Rocha S, Gronenborn B, Gronenborn AM, Campos-Olivas R. Solution structure of the endonuclease domain from the master replication initiator protein of the nanovirus faba bean necrotic yellows virus and comparison with the corresponding geminivirus and circovirus structures. Biochemistry 2007; 46:6201-12. [PMID: 17472345 PMCID: PMC2577285 DOI: 10.1021/bi700159q] [Citation(s) in RCA: 32] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Nanoviruses are a family of plant viruses that possess a genome of multiple circular single-stranded DNA (ssDNA) components and are strikingly similar in their replication mode to the plant geminiviruses and to the circoviruses that infect birds or mammals. These viruses multiply by rolling circle replication using virus-encoded multifunctional replication initiator proteins (Rep proteins) that catalyze the initiation of replication on a double-stranded DNA (dsDNA) intermediate and the resolution of the ssDNA into circles. Here we report the solution NMR three-dimensional structure of the endonuclease domain from the master Rep (M-Rep) protein of faba bean necrotic yellows virus (FBNYV), a representative of the nanoviruses. The domain comprises amino acids 2-95 (M-Rep2-95), and its global fold is similar to those previously described for the gemini- and circovirus Rep endonuclease domains, consisting of a central 5-stranded antiparallel beta-sheet covered on one side by an alpha-helix and irregular loops and on the other, more open side of the domain, by an alpha-helix containing the catalytic tyrosine residue (the catalytic helix). Longer domain constructs extending to amino acids 117 and 124 were also characterized. They contain an additional alpha-helix, are monomeric, and exhibit catalytic activity indistinguishable from that of M-Rep2-95. The binding site for the catalytic metal was identified by paramagnetic broadening and maps to residues on the exposed face of the central beta-sheet. A comparison with the previously determined Rep endonuclease domain structures of tomato yellow leaf curl Sardinia virus (TYLCSV), a geminivirus, and that of porcine circovirus type 2 (PCV2) Rep allows the identification of a positively charged surface that is most likely involved in dsDNA binding, and reveals common features shared by all endonuclease domains of nanovirus, geminivirus, and circovirus Rep proteins.
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Affiliation(s)
- Susana Vega-Rocha
- Structural and Computational Biology Program. Spanish National Cancer Center (CNIO). Madrid 28029. Spain
| | - Bruno Gronenborn
- Institut des Sciences du Vegetal. Centre National de la Recherche Scientifique. 91198 Gif-sur-Yvette Cedex, France
| | - Angela M. Gronenborn
- Department of Structural Biology. University of Pittsburgh School of Medicine, BST3, 3501 5th Avenue, Pittsburgh, PA 15261. USA
| | - Ramón Campos-Olivas
- Structural and Computational Biology Program. Spanish National Cancer Center (CNIO). Madrid 28029. Spain
- Corresponding author: Ramón Campos-Olivas, Structural and Computational Biology Program., Spanish National Cancer Center (CNIO)., C. Melchor Fernandez Almagro, 3, Madrid 28029. Spain, Tel: +34-912246900, Fax: +34-912246976, E-mail:
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46
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Hu JM, Fu HC, Lin CH, Su HJ, Yeh HH. Reassortment and concerted evolution in banana bunchy top virus genomes. J Virol 2007; 81:1746-61. [PMID: 17135318 PMCID: PMC1797577 DOI: 10.1128/jvi.01390-06] [Citation(s) in RCA: 53] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2006] [Accepted: 11/16/2006] [Indexed: 12/12/2022] Open
Abstract
The nanovirus Banana bunchy top virus (BBTV) has six standard components in its genome and occasionally contains components encoding additional Rep (replication initiation protein) genes. Phylogenetic network analysis of coding sequences of DNA 1 and 3 confirmed the two major groups of BBTV, a Pacific and an Asian group, but show evidence of web-like phylogenies for some genes. Phylogenetic analysis of 102 major common regions (CR-Ms) from all six components showed a possible concerted evolution within the Pacific group, which is likely due to recombination in this region. The CR-M of additional Rep genes is close to that of DNA 1 and 2. Comparison of tree topologies constructed with DNA 1 and DNA 3 coding sequences of 14 BBTV isolates showed distinct phylogenetic histories based on Kishino-Hasegawa and Shimodaira-Hasegawa tests. The results of principal component analysis of amino acid and codon usages indicate that DNA 1 and 3 have a codon bias different from that of all other genes of nanoviruses, including all currently known additional Rep genes of BBTV, which suggests a possible ancient genome reassortment event between distinctive nanoviruses.
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Affiliation(s)
- Jer-Ming Hu
- Institute of Ecology and Evolutionary Biology, National Taiwan University, 1, Sec. 4, Roosevelt Road, Taipei 106, Taiwan.
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47
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Herrera-Valencia VA, Dugdale B, Harding RM, Dale JL. An iterated sequence in the genome of Banana bunchy top virus is essential for efficient replication. J Gen Virol 2006; 87:3409-3412. [PMID: 17030877 DOI: 10.1099/vir.0.82166-0] [Citation(s) in RCA: 26] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Banana bunchy top virus (BBTV) has a multi-component genome of circular, single-stranded DNA. BBTV replicates via a rolling-circle mechanism, probably involving sequence-specific interaction of the replication initiation protein (Rep) with iterated sequences (iterons) within the viral genome. Three putative iterons (designated F1, F2 and R), with the sequence GGGAC, have been identified in the intergenic region of each BBTV component. To investigate their role in replication, each of the iterons was mutated, singularly and in tandem, in a BBTV DNA-N 1.1mer and the ability of these molecules to be replicated by the BBTV 'master' Rep was evaluated in banana cells using transient biolistic assays. All iteron mutants were replicated less efficiently than the native DNA-N. Mutation of the F1 and R iterons caused a 42 and 62 % reduction in DNA-N replication, respectively, whereas mutation of the F2 and combined F1F2 iteron virtually abolished DNA-N replication.
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Affiliation(s)
| | - Benjamin Dugdale
- Science Research Centre, Queensland University of Technology, GPO Box 2434, Brisbane, QLD 4001, Australia
| | - Robert M Harding
- Science Research Centre, Queensland University of Technology, GPO Box 2434, Brisbane, QLD 4001, Australia
| | - James L Dale
- Science Research Centre, Queensland University of Technology, GPO Box 2434, Brisbane, QLD 4001, Australia
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48
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Timchenko T, Katul L, Aronson M, Vega-Arreguín JC, Ramirez BC, Vetten HJ, Gronenborn B. Infectivity of nanovirus DNAs: induction of disease by cloned genome components of Faba bean necrotic yellows virus. J Gen Virol 2006; 87:1735-1743. [PMID: 16690940 DOI: 10.1099/vir.0.81753-0] [Citation(s) in RCA: 37] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Circumstantial evidence suggests that the genome of Faba bean necrotic yellows virus (FBNYV), a nanovirus, consists of eight distinct, circular, single-stranded DNAs, each of about 1 kb and encoding only one protein. Here, the use of cloned full-length FBNYV DNAs for reproducing FBNYV-like symptoms in Vicia faba, the principal natural host of FBNYV, is reported. Characteristic symptoms of FBNYV infection were obtained in faba bean plants following biolistic DNA delivery or agroinoculation with all eight FBNYV DNAs. Although the eight different DNAs have been invariably detected in field samples infected with the various geographical FBNYV isolates, experimental infection with different combinations of fewer than eight DNAs also led to typical FBNYV symptoms. Even only five genome components, DNA-R, DNA-S, DNA-M, DNA-U1 and DNA-U2, were sufficient for inducing disease symptoms in V. faba upon agroinoculation. Symptomatic plants agroinoculated or bombarded with eight DNAs contained typical FBNYV virions; however, the virus was not transmitted by Aphis craccivora or Acyrthosiphon pisum, two efficient aphid vectors of FBNYV.
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Affiliation(s)
- T Timchenko
- Institut des Sciences du Végétal, CNRS, Avenue de la Terrasse, Bât. 23, 91198 Gif sur Yvette, France
| | - L Katul
- Biologische Bundesanstalt für Land und Forstwirtschaft, Institut für Pflanzenvirologie, Mikrobiologie und Biologische Sicherheit, Messeweg 11-12, 38104 Braunschweig, Germany
| | - M Aronson
- Institut des Sciences du Végétal, CNRS, Avenue de la Terrasse, Bât. 23, 91198 Gif sur Yvette, France
| | - J C Vega-Arreguín
- Institut des Sciences du Végétal, CNRS, Avenue de la Terrasse, Bât. 23, 91198 Gif sur Yvette, France
| | - B C Ramirez
- Institut des Sciences du Végétal, CNRS, Avenue de la Terrasse, Bât. 23, 91198 Gif sur Yvette, France
| | - H J Vetten
- Biologische Bundesanstalt für Land und Forstwirtschaft, Institut für Pflanzenvirologie, Mikrobiologie und Biologische Sicherheit, Messeweg 11-12, 38104 Braunschweig, Germany
| | - B Gronenborn
- Institut des Sciences du Végétal, CNRS, Avenue de la Terrasse, Bât. 23, 91198 Gif sur Yvette, France
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49
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Briddon RW, Stanley J. Subviral agents associated with plant single-stranded DNA viruses. Virology 2006; 344:198-210. [PMID: 16364750 DOI: 10.1016/j.virol.2005.09.042] [Citation(s) in RCA: 220] [Impact Index Per Article: 12.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2005] [Accepted: 09/16/2005] [Indexed: 11/18/2022]
Abstract
Begomoviruses (family Geminiviridae) are responsible for many economically important crop diseases worldwide. The majority of these diseases are caused by bipartite begomovirus infections, although a rapidly growing number of diseases of the Old World are associated with monopartite begomoviruses. With the exception of several diseases of tomato, most of these are caused by a monopartite begomovirus in association with a recently discovered essential satellite component (DNA-beta). These begomovirus/satellite disease complexes are widespread and diverse and collectively infect a wide variety of crops, weeds and ornamental plants. Non-essential subviral components (DNA-1) originating from nanoviruses are frequently associated with these disease complexes, and there are tantalizing hints that further novel satellites may also be associated with some begomovirus diseases. DNA-beta components can be maintained in permissive plants by more than one distinct begomovirus, reflecting less stringent requirements for trans-replication that will undoubtedly encourage diversification and adaptation as a consequence of component exchange and recombination. In view of their impact on agriculture, there is a pressing need to develop a more comprehensive picture of the diversity and distribution of the disease complexes. A greater understanding of how they elicit the host response may provide useful information for their control as well as an insight into plant developmental processes.
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Affiliation(s)
- R W Briddon
- Plant Biotechnology Division, National Institute for Biotechnology and Genetic Engineering, Jhang Road, Faisalabad, Pakistan
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50
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Vega-Arreguín JC, Timchenko T, Gronenborn B, Ramírez BC. A functional histidine-tagged replication initiator protein: implications for the study of single-stranded DNA virus replication in planta. J Virol 2005; 79:8422-30. [PMID: 15956586 PMCID: PMC1143747 DOI: 10.1128/jvi.79.13.8422-8430.2005] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/13/2023] Open
Abstract
Replication initiation of nanoviruses, plant viruses with a multipartite circular single-stranded DNA genome, is triggered by the master Rep (M-Rep) protein. To enable the study of interactions between M-Rep and viral or host factors involved in replication, we designed oligohistidine-tagged variants of the nanovirus Faba bean necrotic yellows virus (FBNYV) M-Rep protein that allow affinity purification of enzymatically active M-Rep from plant tissue. The tagged M-Rep protein was able to initiate replication of its cognate and other FBNYV DNAs in Nicotiana benthamiana leaf disks and plants. The replicon encoding the tagged M-Rep protein multiplied and moved systemically in FBNYV-infected Vicia faba plants and was transmitted by the aphid vector of the virus. Using the tagged M-Rep protein, we demonstrated the in planta interaction between wild-type M-Rep and its tagged counterpart. Such a tagged and fully functional replication initiator protein will have bearings on the isolation of protein complexes from plants.
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Affiliation(s)
- Julio C Vega-Arreguín
- Institut des Sciences du Végétal, CNRS, Avenue de la Terrasse, Bât. 23, 91198 Gif sur Yvette Cedex, France
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