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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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2
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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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Dilip D, Louis V, Savithri HS, Namitha PM. Restriction-free cloning for molecular manipulation and augmented expression of banana bunchy top viral coat protein. 3 Biotech 2021; 11:471. [PMID: 34745822 PMCID: PMC8536813 DOI: 10.1007/s13205-021-03017-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2021] [Accepted: 10/05/2021] [Indexed: 10/20/2022] Open
Abstract
Banana bunchy top virus (BBTV) causing bunchy top disease, is one of the most devastating diseases of banana and plantain. All the six genomic components of isolates from different parts of the world have been well characterised, with most of the studies focusing on replicase gene and coat protein gene. Overexpression of coat protein (CP) in Escherichia coli system can contribute significantly in structural as well as immunological studies. In the present investigation, the full length BBTV CP was cloned to pGEX-4T-2 expression vector and overexpressed in various Escherichia coli strains to obtain high quality and quantity of the CP. An augmented overexpression and stability of recombinant coat protein was achieved by molecular manipulation of the clone by restriction-free (RF) cloning platform. The RF cloning was employed to replace the thrombin cleavage site in the vector backbone, which was also present in the protein of interest, and to incorporate TEV protease site to cleave fusion protein at this specific site, and separate the affinity tag. The RF method allows direct transformation of the PCR product to undergo ligation in vivo and obtain the transformants thereby avoiding the restriction digestion and ligation of the product to the linearized plasmid. From a litre culture, 1.084 mg/ml of fusion protein with GST tag was obtained after GSH sepharose affinity column chromatography. The fluorescence spectra indicated partial disordered tertiary structure of the fusion protein. Cleavage of tag was attempted using TEV protease overexpressed and purified in the laboratory. SUPPLEMENTARY INFORMATION The online version contains supplementary material available at 10.1007/s13205-021-03017-x.
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Affiliation(s)
- Darsana Dilip
- Department of Plant Pathology, College of Agriculture, Kerala Agricultural University, Thrissur, Kerala 680656 India
| | - Vimi Louis
- Division of Plant Pathology, Banana Research Station, Kannara, Kerala Agricultural University, Thrissur, Kerala 680652 India
| | - H. S. Savithri
- Department of Biochemistry, Indian Institute of Science, New Biological Sciences Building, Bangalore, 560012 India
| | - P. M. Namitha
- Division of Plant Pathology, Banana Research Station, Kannara, Kerala Agricultural University, Thrissur, Kerala 680652 India
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4
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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: 3] [Impact Index Per Article: 1.0] [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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Tripathi L, Ntui VO, Tripathi JN, Kumar PL. Application of CRISPR/Cas for Diagnosis and Management of Viral Diseases of Banana. Front Microbiol 2021; 11:609784. [PMID: 33584573 PMCID: PMC7873300 DOI: 10.3389/fmicb.2020.609784] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2020] [Accepted: 12/29/2020] [Indexed: 12/26/2022] Open
Abstract
Viral diseases are significant biotic constraints for banana (Musa spp.) production as they affect the yield and limit the international movement of germplasm. Among all the viruses known to infect banana, the banana bunchy top virus and banana streak viruses are widespread and economically damaging. The use of virus-resistant bananas is the most cost-effective option to minimize the negative impacts of viral-diseases on banana production. CRISPR/Cas-based genome editing is emerging as the most powerful tool for developing virus-resistant crop varieties in several crops, including the banana. The availability of a vigorous genetic transformation and regeneration system and a well-annotated whole-genome sequence of banana makes it a compelling candidate for genome editing. A robust CRISPR/Cas9-based genome editing of the banana has recently been established, which can be applied in developing disease-resistant varieties. Recently, the CRISPR system was exploited to detect target gene sequences using Cas9, Cas12, Cas13, and Cas14 enzymes, thereby unveiling the use of this technology for virus diagnosis. This article presents a synopsis of recent advancements and perspectives on the application of CRISPR/Cas-based genome editing for diagnosing and developing resistance against banana viruses and challenges in genome-editing of banana.
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Affiliation(s)
- Leena Tripathi
- International Institute of Tropical Agriculture, Nairobi, Kenya
| | | | | | - P. Lava Kumar
- International Institute of Tropical Agriculture, Ibadan, Nigeria
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6
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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: 11] [Impact Index Per Article: 2.8] [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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7
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Jekayinoluwa T, Tripathi L, Tripathi JN, Ntui VO, Obiero G, Muge E, Dale J. RNAi technology for management of banana bunchy top disease. Food Energy Secur 2020; 9:e247. [PMID: 33381301 PMCID: PMC7757248 DOI: 10.1002/fes3.247] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2020] [Revised: 08/13/2020] [Accepted: 08/16/2020] [Indexed: 12/15/2022] Open
Abstract
Banana bunchy top disease (BBTD) is one of the world's most destructive viral diseases of banana and plantain, causing up to 100% yield loss in severe cases. The disease is vectored by banana aphids (Pentalonia nigronervosa) and carried long distances through the movement of infected plant materials. The banana aphids harboring banana bunchy top virus (BBTV) present in banana producing regions are the sole vector and the most efficient method of transmitting the virus to the healthy plants. Controlling the spread of BBTD has been very challenging since no known banana germplasm is immune to BBTV. The disease can be managed with the use of virus-free planting material and roguing. However, once BBTD is established in the field, it is very difficult to eradicate or manage it. Therefore, a more sustainable way of controlling the disease is developing host plant resistance against the virus and the vector. Biotechnological strategies via RNA interference (RNAi) could be used to target the banana aphid as well as BBTV to reduce virus-associated yield losses of banana and plantain, which feed over 500 million people around the world. This review discusses the status of BBTD and perspectives on effective RNAi technologies for controlling BBTV and the vector, banana aphid, transmitting the virus as sustainable management of the disease.
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Affiliation(s)
- Temitope Jekayinoluwa
- International Institute of Tropical AgricultureNairobiKenya
- Center for Biotechnology and BioinformaticsUniversity of NairobiNairobiKenya
| | - Leena Tripathi
- International Institute of Tropical AgricultureNairobiKenya
| | | | | | - George Obiero
- Center for Biotechnology and BioinformaticsUniversity of NairobiNairobiKenya
| | - Edward Muge
- Department of BiochemistryUniversity of NairobiNairobiKenya
| | - James Dale
- Queensland University of TechnologyBrisbaneQldAustralia
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8
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Morozov SY, Solovyev AG. Small hydrophobic viral proteins involved in intercellular movement of diverse plant virus genomes. AIMS Microbiol 2020; 6:305-329. [PMID: 33134746 PMCID: PMC7595835 DOI: 10.3934/microbiol.2020019] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2020] [Accepted: 09/13/2020] [Indexed: 12/12/2022] Open
Abstract
Most plant viruses code for movement proteins (MPs) targeting plasmodesmata to enable cell-to-cell and systemic spread in infected plants. Small membrane-embedded MPs have been first identified in two viral transport gene modules, triple gene block (TGB) coding for an RNA-binding helicase TGB1 and two small hydrophobic proteins TGB2 and TGB3 and double gene block (DGB) encoding two small polypeptides representing an RNA-binding protein and a membrane protein. These findings indicated that movement gene modules composed of two or more cistrons may encode the nucleic acid-binding protein and at least one membrane-bound movement protein. The same rule was revealed for small DNA-containing plant viruses, namely, viruses belonging to genus Mastrevirus (family Geminiviridae) and the family Nanoviridae. In multi-component transport modules the nucleic acid-binding MP can be viral capsid protein(s), as in RNA-containing viruses of the families Closteroviridae and Potyviridae. However, membrane proteins are always found among MPs of these multicomponent viral transport systems. Moreover, it was found that small membrane MPs encoded by many viruses can be involved in coupling viral replication and cell-to-cell movement. Currently, the studies of evolutionary origin and functioning of small membrane MPs is regarded as an important pre-requisite for understanding of the evolution of the existing plant virus transport systems. This paper represents the first comprehensive review which describes the whole diversity of small membrane MPs and presents the current views on their role in plant virus movement.
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Affiliation(s)
- Sergey Y Morozov
- A. N. Belozersky Institute of Physico-Chemical Biology, Moscow State University, Moscow, Russia.,Department of Virology, Biological Faculty, Moscow State University, Moscow, Russia
| | - Andrey G Solovyev
- A. N. Belozersky Institute of Physico-Chemical Biology, Moscow State University, Moscow, Russia.,Department of Virology, Biological Faculty, Moscow State University, Moscow, Russia.,Institute of Molecular Medicine, Sechenov First Moscow State Medical University, Moscow, Russia
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9
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Gaafar YZA, Ziebell H. Aphid transmission of nanoviruses. ARCHIVES OF INSECT BIOCHEMISTRY AND PHYSIOLOGY 2020; 104:e21668. [PMID: 32212397 DOI: 10.1002/arch.21668] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/13/2019] [Revised: 02/28/2020] [Accepted: 03/03/2020] [Indexed: 06/10/2023]
Abstract
The genus Nanovirus consists of plant viruses that predominantly infect legumes leading to devastating crop losses. Nanoviruses are transmitted by various aphid species. The transmission occurs in a circulative nonpropagative manner. It was long suspected that a virus-encoded helper factor would be needed for successful transmission by aphids. Recently, a helper factor was identified as the nanovirus-encoded nuclear shuttle protein (NSP). The mode of action of NSP is currently unknown in contrast to helper factors from other plant viruses that, for example, facilitate binding of virus particles to receptors within the aphids' stylets. In this review, we are summarizing the current knowledge about nanovirus-aphid vector interactions.
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Affiliation(s)
- Yahya Z A Gaafar
- Institute for Epidemiology and Pathogen Diagnostics, Julius Kuehn Institute, Braunschweig, Lower Saxony, Germany
| | - Heiko Ziebell
- Institute for Epidemiology and Pathogen Diagnostics, Julius Kuehn Institute, Braunschweig, Lower Saxony, Germany
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10
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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: 6] [Impact Index Per Article: 1.2] [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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11
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Yu NT, Xie HM, Zhang YL, Wang JH, Xiong Z, Liu ZX. Independent modulation of individual genomic component transcription and a cis-acting element related to high transcriptional activity in a multipartite DNA virus. BMC Genomics 2019; 20:573. [PMID: 31296162 PMCID: PMC6625112 DOI: 10.1186/s12864-019-5901-0] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2019] [Accepted: 06/12/2019] [Indexed: 02/08/2023] Open
Abstract
Background The genome of Banana bunchy top virus (BBTV) consists of at least six circular, single-stranded DNA components of ~ 1 kb in length. Some BBTV isolates may also carry satellite DNA molecules that are not essential for BBTV infection. The relation between multipartite DNA virus replication and their transcriptional levels and the underlying mechanism remain unclear. Results To understand the coordinated replication and transcription of the multiple genomic components, the absolute amounts of each BBTV DNA component were measured by real-time PCR (qPCR), and their transcriptional levels were determined by RNAseq and reverse transcription-qPCR (qRT-PCR). Significant differences were found in the absolute amounts of individual BBTV genomic components. Transcriptional levels of each BBTV genomic component obtained from the RNAseq data matched closely to those obtained from qRT-PCR, but did not correspond to the absolute amount of each DNA component. The ratio of transcript over DNA copies ranged from 46.21 to 1059.44%, which was possibly regulated by the promoter region in the intergenic region of each component. To further determine this speculation, the promoter region of the DNA-S, −M or -N was constructed to the upstream of green fluorescent protein (GFP) gene for transient expression by agrobacterium-mediated transformation method. The qRT-PCR showed the highest transcriptional activity was promoted by DNA-N promoter, about 386.58% activity comparing with CaMV 35S promoter. Confocal microscopy observation showed that the intensity of green fluorescence was corresponding to that of qRT-PCR. Conclusions Our data clearly showed that BBTV was able to control the transcriptional level of each DNA component independently by through the promoter sequences in the intergenic region. Moreover, a cis-acting element from DNA-N component had a high transcriptional activity. Electronic supplementary material The online version of this article (10.1186/s12864-019-5901-0) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Nai-Tong Yu
- Key Laboratory of Biology and Genetic Resources of Tropical Crops, Ministry of Agriculture and Rural Affairs, Institute of Tropical Bioscience and Biotechnology, Chinese Academy of Tropical Agricultural Sciences, Haikou, 571101, China
| | - Hui-Min Xie
- Key Laboratory of Biology and Genetic Resources of Tropical Crops, Ministry of Agriculture and Rural Affairs, Institute of Tropical Bioscience and Biotechnology, Chinese Academy of Tropical Agricultural Sciences, Haikou, 571101, China
| | - Yu-Liang Zhang
- Key Laboratory of Biology and Genetic Resources of Tropical Crops, Ministry of Agriculture and Rural Affairs, Institute of Tropical Bioscience and Biotechnology, Chinese Academy of Tropical Agricultural Sciences, Haikou, 571101, China
| | - Jian-Hua Wang
- Key Laboratory of Biology and Genetic Resources of Tropical Crops, Ministry of Agriculture and Rural Affairs, Institute of Tropical Bioscience and Biotechnology, Chinese Academy of Tropical Agricultural Sciences, Haikou, 571101, China
| | - Zhongguo Xiong
- School of Plant Sciences and BIO5 Institute, University of Arizona, Tucson, 85721, USA.
| | - Zhi-Xin Liu
- Key Laboratory of Biology and Genetic Resources of Tropical Crops, Ministry of Agriculture and Rural Affairs, Institute of Tropical Bioscience and Biotechnology, Chinese Academy of Tropical Agricultural Sciences, Haikou, 571101, China.
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12
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Zhuang J, Lin W, Coates CJ, Shang P, Wei T, Wu Z, Xie L. Cleavage of the Babuvirus Movement Protein B4 into Functional Peptides Capable of Host Factor Conjugation is Required for Virulence. Virol Sin 2019; 34:295-305. [PMID: 30868360 PMCID: PMC6599508 DOI: 10.1007/s12250-019-00094-4] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2018] [Accepted: 01/18/2019] [Indexed: 11/29/2022] Open
Abstract
Banana bunchy top virus (BBTV) poses a serious danger to banana crops worldwide. BBTV-encoded protein B4 is a determinant of pathogenicity. However, the relevant molecular mechanisms underlying its effects remain unknown. In this study, we found that a functional peptide could be liberated from protein B4, likely via proteolytic processing. Site-directed mutagenesis indicated that the functional processing of protein B4 is required for its pathogenic effects, including dwarfism and sterility, in plants. The released protein fragment targets host proteins, such as the large subunit of RuBisCO (RbcL) and elongation factor 2 (EF2), involved in protein synthesis. Therefore, the peptide released from B4 (also a precursor) may act as a non-canonical modifier to influence host-pathogen interactions involving BBTV and plants.
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Affiliation(s)
- Jun Zhuang
- State Key Laboratory of Ecological Pest Control for Fujian and Taiwan Crops, Fujian Agriculture and Forestry University, Fuzhou, 350002, China.
- Institute of Plant Virology, Fujian Agriculture and Forestry University, Fuzhou, 350002, China.
| | - Wenwu Lin
- State Key Laboratory of Ecological Pest Control for Fujian and Taiwan Crops, Fujian Agriculture and Forestry University, Fuzhou, 350002, China
- Institute of Plant Virology, Fujian Agriculture and Forestry University, Fuzhou, 350002, China
| | - Christopher J Coates
- Department of Biosciences, College of Science, Swansea University, Swansea, SA2 8PP, Wales, UK
| | - Pengxiang Shang
- Institute of Plant Virology, Fujian Agriculture and Forestry University, Fuzhou, 350002, China
| | - Taiyun Wei
- State Key Laboratory of Ecological Pest Control for Fujian and Taiwan Crops, Fujian Agriculture and Forestry University, Fuzhou, 350002, China
- Institute of Plant Virology, Fujian Agriculture and Forestry University, Fuzhou, 350002, China
| | - Zujian Wu
- State Key Laboratory of Ecological Pest Control for Fujian and Taiwan Crops, Fujian Agriculture and Forestry University, Fuzhou, 350002, China
- Institute of Plant Virology, Fujian Agriculture and Forestry University, Fuzhou, 350002, China
| | - Lianhui Xie
- State Key Laboratory of Ecological Pest Control for Fujian and Taiwan Crops, Fujian Agriculture and Forestry University, Fuzhou, 350002, China.
- Institute of Plant Virology, Fujian Agriculture and Forestry University, Fuzhou, 350002, China.
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13
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Ji XL, Yu NT, Qu L, Li BB, Liu ZX. Banana bunchy top virus (BBTV) nuclear shuttle protein interacts and re-distributes BBTV coat protein in Nicotiana benthamiana. 3 Biotech 2019; 9:121. [PMID: 30863700 DOI: 10.1007/s13205-019-1656-1] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2018] [Accepted: 02/26/2019] [Indexed: 01/27/2023] Open
Abstract
Banana bunchy top virus (BBTV) is a circular single-stranded DNA virus with multi-components. The knowledge about interaction between viral proteins and pathogenesis mechanism of BBTV remains unclear. In this study, the coat protein gene (CP, ORF 516 bp) and nuclear shuttle protein gene (NSP, ORF 465 bp) from BBTV B2 isolate of the Southeast-Asia group were cloned. The intracellular localization analysis showed the CP locates in the cell nucleus of tobacco cells, while the NSP distributes in the cell nucleus and cytoplasm. Co-localization analysis indicated the NSP itself does not change distribution, but CP re-distributes to the cell nucleus and cytoplasm, suggesting that NSP interacts with CP and re-locates the CP in the cell. The interaction between CP and NSP was further verified by co-immunoprecipitation (Co-IP) in tobacco protoplasts. The study will help us to understand the interaction between viral proteins and pathogenesis mechanism of BBTV in host plants.
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Affiliation(s)
- Xiao-Long Ji
- Key Laboratory of Biology and Genetic Resources of Tropical Crops, Ministry of Agriculture and Rural Affairs/Hainan Provincial Key Laboratory of Microbiology, Institute of Tropical Bioscience and Biotechnology, Chinese Academy of Tropical Agricultural Sciences, Haikou, 571101 China
| | - Nai-Tong Yu
- Key Laboratory of Biology and Genetic Resources of Tropical Crops, Ministry of Agriculture and Rural Affairs/Hainan Provincial Key Laboratory of Microbiology, Institute of Tropical Bioscience and Biotechnology, Chinese Academy of Tropical Agricultural Sciences, Haikou, 571101 China
| | - Ling Qu
- Key Laboratory of Biology and Genetic Resources of Tropical Crops, Ministry of Agriculture and Rural Affairs/Hainan Provincial Key Laboratory of Microbiology, Institute of Tropical Bioscience and Biotechnology, Chinese Academy of Tropical Agricultural Sciences, Haikou, 571101 China
| | - Bin-Bin Li
- Key Laboratory of Biology and Genetic Resources of Tropical Crops, Ministry of Agriculture and Rural Affairs/Hainan Provincial Key Laboratory of Microbiology, Institute of Tropical Bioscience and Biotechnology, Chinese Academy of Tropical Agricultural Sciences, Haikou, 571101 China
| | - Zhi-Xin Liu
- Key Laboratory of Biology and Genetic Resources of Tropical Crops, Ministry of Agriculture and Rural Affairs/Hainan Provincial Key Laboratory of Microbiology, Institute of Tropical Bioscience and Biotechnology, Chinese Academy of Tropical Agricultural Sciences, Haikou, 571101 China
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14
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Baldodiya GM, Baruah G, Borah BK, Modi MK, Nath PD. Molecular characterization and sequence analyses of Banana bunchy top virus infecting banana cultivar Jahaji (Dwarf Cavendish) in Assam, India. 3 Biotech 2019; 9:110. [PMID: 30863694 DOI: 10.1007/s13205-019-1636-5] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2018] [Accepted: 02/13/2019] [Indexed: 11/25/2022] Open
Abstract
Several isolates of Banana bunchy top virus (BBTV) have been reported worldwide. They are members of either the Pacific Indian Ocean (PIO) or the South East Asian (SEA) group. However, there is only one completely sequenced isolate published from the northeastern part of India till date. Therefore, we obtained the complete sequences of all the six genomic components of a BBTV isolate from the northeastern Indian state of Assam. The isolate was named as BBTV-As-JOR, and its genome showed the presence of the reported conserved motifs. Nevertheless, like other Indian BBTV isolate, the major common regions in DNA-R and DNA-U3 of BBTV-As-JOR had deletions of 26 and 36 nucleotides, respectively. Phylogenetic analysis based on 312 sequences of BBTV DNA-R classified BBTV-As-JOR as a member of the PIO group; similar phylogenetic patterns were also found with the other genomic segments. Analysis with Recombination Detection Program revealed two intra-segment recombination events involving DNA-C of geographically distinct BBTV isolates. On the other hand, DNA-U3 and DNA-N were found to be involved in few inter-segment recombination events in BBTV-As-JOR. This is the first report of a BBTV isolate from Assam and also of another PIO isolate from the region (the other isolate, BBTV-Umiam, was much closer to the SEA group). The detected possible recombinants could emerge as a major future threat for the banana cultivations in the country considering the asexual nature of propagation of banana crop.
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Affiliation(s)
- Gajendra Mohan Baldodiya
- 1Department of Agricultural Biotechnology, Assam Agricultural University, Jorhat, Assam 785013 India
| | - Geetanjali Baruah
- 1Department of Agricultural Biotechnology, Assam Agricultural University, Jorhat, Assam 785013 India
| | - Basanta Kumar Borah
- 1Department of Agricultural Biotechnology, Assam Agricultural University, Jorhat, Assam 785013 India
| | - Mahendra Kumar Modi
- 1Department of Agricultural Biotechnology, Assam Agricultural University, Jorhat, Assam 785013 India
| | - Palash Deb Nath
- 2Department of Plant Pathology, Assam Agricultural University, Jorhat, Assam 785013 India
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15
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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: 2] [Impact Index Per Article: 0.4] [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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16
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Grigoras I, Vetten HJ, Commandeur U, Ziebell H, Gronenborn B, Timchenko T. Nanovirus DNA-N encodes a protein mandatory for aphid transmission. Virology 2018; 522:281-291. [PMID: 30071404 DOI: 10.1016/j.virol.2018.07.001] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2018] [Revised: 07/04/2018] [Accepted: 07/04/2018] [Indexed: 12/15/2022]
Abstract
Nanoviruses possess a multipartite single-stranded DNA genome and are naturally transmitted to plants by various aphid species in a circulative non-propagative manner. Using the cloned genomic DNAs of faba bean necrotic stunt virus (FBNSV) for reconstituting nanovirus infections we analyzed the necessity of different virus components for infection and transmission by aphids. We found that in the absence of DNA-U1 and DNA-U2 symptom severity decreased, and in the absence of DNA-U1 the transmission efficiency decreased. Most significantly, we demonstrated that the protein encoded by DNA-N (NSP) is mandatory for aphid transmission. Moreover, we showed that the NSP of FBNSV could substitute for that of a distantly related nanovirus, pea necrotic yellow dwarf virus. Altering the FBNSV NSP by adding 13 amino acids to its carboxy-terminus resulted in an infectious but non-transmissible virus. We demonstrate that the NSP acts as a nanovirus transmission factor, the existence of which had been hypothesized earlier.
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Affiliation(s)
- Ioana Grigoras
- Institut des Sciences du Végétal, CNRS, 91198 Gif sur Yvette, France
| | | | - Ulrich Commandeur
- Institute for Molecular Biotechnology (Biology VII), RWTH Aachen University, Worringerweg 1, 52074 Aachen, Germany
| | - Heiko Ziebell
- Julius Kühn Institute (JKI), Bundesforschungsinstitut für Kulturpflanzen, Institut für Epidemiologie und Pathogendiagnostik, 38104 Braunschweig, Germany
| | - Bruno Gronenborn
- Institut des Sciences du Végétal, CNRS, 91198 Gif sur Yvette, France; Institute for Integrative Biology of the Cell, UMR 9198, CNRS, Université Paris-Sud, CEA, Avenue de la Terrasse, 91198 Gif sur Yvette, France
| | - Tatiana Timchenko
- Institut des Sciences du Végétal, CNRS, 91198 Gif sur Yvette, France; Institute for Integrative Biology of the Cell, UMR 9198, CNRS, Université Paris-Sud, CEA, Avenue de la Terrasse, 91198 Gif sur Yvette, France.
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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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Zhuang J, Coates CJ, Mao Q, Wu Z, Xie L. The antagonistic effect of Banana bunchy top virus multifunctional protein B4 against Fusarium oxysporum. MOLECULAR PLANT PATHOLOGY 2016; 17:669-679. [PMID: 26369403 PMCID: PMC6638366 DOI: 10.1111/mpp.12319] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/05/2023]
Abstract
The viral-induced banana bunchy top disease and the fungal-induced banana blight are two major causes of concern for industrial scale production of bananas. Banana blight is particularly troublesome, affecting ∼80% of crops worldwide. Strict guidelines and protocols are in place in order to ameliorate the effects of this devastating disease, yet little success has been achieved. From the data presented here, we have found that Banana bunchy top virus (BBTV)-infected bananas are more resistant to Fusarium oxysporum f. sp. cubense (Foc). BBTV appears to be antagonistic towards Foc, thus improving the survivability of plants against blight. The BBTV suppressor of RNA silencing, namely protein B4, displays fungicidal properties in vitro. Furthermore, transgenic tomatoes expressing green fluorescent protein (GFP)-tagged protein B4 demonstrate enhanced resistance to F. oxysporum f. sp. lycopersici (Fol). Differential gene expression analysis indicates that increased numbers of photogenesis-related gene transcripts are present in dark-green leaves of B4-GFP-modified tomato plants relative to those found in WT plants. Conversely, the transcript abundance of immunity-related genes is substantially lower in transgenic tomatoes compared with WT plants, suggesting that plant defences may be influenced by protein B4. This viral-fungal interaction provides new insights into microbial community dynamics within a single host and has potential commercial value for the breeding of transgenic resistance to Fusarium-related blight/wilt.
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Affiliation(s)
- Jun Zhuang
- Fujian Provincial Key Laboratory of Plant Virology, Institute of Plant Virology, Fujian Agriculture and Forestry University, Fuzhou, 350002, China
- Key Laboratory of Biopesticide and Chemical Biology, Fujian Agriculture and Forestry University, Ministry of Education, Fuzhou, 350002, China
| | - Christopher J Coates
- Department of Biosciences, College of Science, Swansea University, Swansea, SA2 8PP, UK
| | - Qianzhuo Mao
- Fujian Provincial Key Laboratory of Plant Virology, Institute of Plant Virology, Fujian Agriculture and Forestry University, Fuzhou, 350002, China
- Key Laboratory of Biopesticide and Chemical Biology, Fujian Agriculture and Forestry University, Ministry of Education, Fuzhou, 350002, China
| | - Zujian Wu
- Fujian Provincial Key Laboratory of Plant Virology, Institute of Plant Virology, Fujian Agriculture and Forestry University, Fuzhou, 350002, China
- Key Laboratory of Biopesticide and Chemical Biology, Fujian Agriculture and Forestry University, Ministry of Education, Fuzhou, 350002, China
| | - Lianhui Xie
- Fujian Provincial Key Laboratory of Plant Virology, Institute of Plant Virology, Fujian Agriculture and Forestry University, Fuzhou, 350002, China
- Key Laboratory of Biopesticide and Chemical Biology, Fujian Agriculture and Forestry University, Ministry of Education, Fuzhou, 350002, China
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20
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Wickramaarachchi WART, Shankarappa KS, Rangaswamy KT, Maruthi MN, Rajapakse RGAS, Ghosh S. Molecular characterization of banana bunchy top virus isolate from Sri Lanka and its genetic relationship with other isolates. Virusdisease 2016; 27:154-60. [PMID: 27366766 DOI: 10.1007/s13337-016-0311-2] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2016] [Accepted: 03/08/2016] [Indexed: 10/22/2022] Open
Abstract
Bunchy top disease of banana caused by Banana bunchy top virus (BBTV, genus Babuvirus family Nanoviridae) is one of the most important constraints in production of banana in the different parts of the world. Six genomic DNA components of BBTV isolate from Kandy, Sri Lanka (BBTV-K) were amplified by polymerase chain reaction (PCR) with specific primers using total DNA extracted from banana tissues showing typical symptoms of bunchy top disease. The amplicons were of expected size of 1.0-1.1 kb, which were cloned and sequenced. Analysis of sequence data revealed the presence of six DNA components; DNA-R, DNA-U3, DNA-S, DNA-N, DNA-M and DNA-C for Sri Lanka isolate. Comparisons of sequence data of DNA components followed by the phylogenetic analysis, grouped Sri Lanka-(Kandy) isolate in the Pacific Indian Oceans (PIO) group. Sri Lanka-(Kandy) isolate of BBTV is classified a new member of PIO group based on analysis of six components of the virus.
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Affiliation(s)
- W A R T Wickramaarachchi
- Division of Plant Pathology, Department of Agriculture, Horticulture Crops Research and Development Institute, Gannoruwa, Peradeniya, 20400 Sri Lanka
| | - K S Shankarappa
- Department of Plant Pathology, K. R. C. College of Horticulture, Arabhavi, University of Horticultural Sciences, Bagalkot, Karnataka India
| | - K T Rangaswamy
- Department of Plant Pathology, University of Agricultural Sciences, GKVK, Bengaluru, 560 065 India
| | - M N Maruthi
- Natural Resources Institute, University of Greenwich, Central Avenue, Chatham Maritime, Kent, ME4 4TB UK
| | - R G A S Rajapakse
- Division of Plant Pathology, Department of Agriculture, Horticulture Crops Research and Development Institute, Gannoruwa, Peradeniya, 20400 Sri Lanka
| | - Saptarshi Ghosh
- Natural Resources Institute, University of Greenwich, Central Avenue, Chatham Maritime, Kent, ME4 4TB UK
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21
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Identification and in silico characterisation of defective molecules associated with isolates of banana bunchy top virus. Arch Virol 2016; 161:1019-26. [DOI: 10.1007/s00705-015-2736-0] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2015] [Accepted: 12/19/2015] [Indexed: 11/28/2022]
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22
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Stainton D, Martin DP, Muhire BM, Lolohea S, Halafihi M, Lepoint P, Blomme G, Crew KS, Sharman M, Kraberger S, Dayaram A, Walters M, Collings DA, Mabvakure B, Lemey P, Harkins GW, Thomas JE, Varsani A. The global distribution of Banana bunchy top virus reveals little evidence for frequent recent, human-mediated long distance dispersal events. Virus Evol 2015; 1:vev009. [PMID: 27774281 PMCID: PMC5014477 DOI: 10.1093/ve/vev009] [Citation(s) in RCA: 40] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/03/2022] Open
Abstract
Banana bunchy top virus (BBTV; family Nanoviridae, genus Babuvirus) is a multi-component single-stranded DNA virus, which infects banana plants in many regions of the world, often resulting in large-scale crop losses. We analyzed 171 banana leaf samples from fourteen countries and recovered, cloned, and sequenced 855 complete BBTV components including ninety-four full genomes. Importantly, full genomes were determined from eight countries, where previously no full genomes were available (Samoa, Burundi, Republic of Congo, Democratic Republic of Congo, Egypt, Indonesia, the Philippines, and the USA [HI]). Accounting for recombination and genome component reassortment, we examined the geographic structuring of global BBTV populations to reveal that BBTV likely originated in Southeast Asia, that the current global hotspots of BBTV diversity are Southeast Asia/Far East and India, and that BBTV populations circulating elsewhere in the world have all potentially originated from infrequent introductions. Most importantly, we find that rather than the current global BBTV distribution being due to increases in human-mediated movements of bananas over the past few decades, it is more consistent with a pattern of infrequent introductions of the virus to different parts of the world over the past 1,000 years.
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Affiliation(s)
- Daisy Stainton
- School of Biological Sciences and Biomolecular Interaction Centre, University of Canterbury, Private Bag 4800, Christchurch, 8140, New Zealand
| | - Darren P Martin
- Department of Clinical Laboratory Sciences, University of Cape Town, Cape Town, South Africa
| | - Brejnev M Muhire
- Department of Clinical Laboratory Sciences, University of Cape Town, Cape Town, South Africa
| | | | - Mana'ia Halafihi
- Ministry of Agriculture and Food, Forests and Fisheries, Kingdom of Tonga
| | | | - Guy Blomme
- Bioversity International Uganda Office, Naguru, Kampala, Uganda
| | - Kathleen S Crew
- Queensland Department of Agriculture, Fisheries and Forestry, Ecosciences Precinct, GPO Box 267, Brisbane, QLD 4001, Australia
| | - Murray Sharman
- Queensland Department of Agriculture, Fisheries and Forestry, Ecosciences Precinct, GPO Box 267, Brisbane, QLD 4001, Australia
| | - Simona Kraberger
- School of Biological Sciences and Biomolecular Interaction Centre, University of Canterbury, Private Bag 4800, Christchurch, 8140, New Zealand
| | - Anisha Dayaram
- School of Biological Sciences and Biomolecular Interaction Centre, University of Canterbury, Private Bag 4800, Christchurch, 8140, New Zealand
| | - Matthew Walters
- School of Biological Sciences and Biomolecular Interaction Centre, University of Canterbury, Private Bag 4800, Christchurch, 8140, New Zealand
| | - David A Collings
- School of Biological Sciences and Biomolecular Interaction Centre, University of Canterbury, Private Bag 4800, Christchurch, 8140, New Zealand
| | - Batsirai Mabvakure
- South African National Bioinformatics Institute, MRC Unit for Bioinformatics Capacity Development, University of the Western Cape, Bellville, 7535, South Africa
| | - Philippe Lemey
- KU Leuven, University of Leuven, Department of Microbiology and Immunology, Rega Institute for Medical Research, Clinical and Epidemiological Virology, Minderbroedersstraat 10, B-3000 Leuven, Belgium
| | - Gordon W Harkins
- South African National Bioinformatics Institute, MRC Unit for Bioinformatics Capacity Development, University of the Western Cape, Bellville, 7535, South Africa
| | - 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
| | - Arvind Varsani
- School of Biological Sciences and Biomolecular Interaction Centre, University of Canterbury, Private Bag 4800, Christchurch, 8140, New Zealand; Department of Clinical Laboratory Sciences, University of Cape Town, Cape Town, South Africa; Department of Plant Pathology and Emerging Pathogens Institute, University of Florida, Gainesville, FL 32611, USA
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Banerjee A, Roy S, Behere GT, Roy SS, Dutta SK, Ngachan SV. Identification and characterization of a distinct banana bunchy top virus isolate of Pacific-Indian Oceans group from North-East India. Virus Res 2014; 183:41-9. [PMID: 24468493 DOI: 10.1016/j.virusres.2014.01.017] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2013] [Revised: 01/15/2014] [Accepted: 01/16/2014] [Indexed: 12/23/2022]
Abstract
Banana bunch top virus (BBTV) is considered to be a serious threat to banana production. A new isolate of the virus (BBTV-Umiam) was identified and characterized from local banana mats growing in mid-hills of Meghalaya in North-East India. The complete nucleotide sequence analysis revealed the presence of six full-length ssDNA components (DNA R, DNA U3, DNA S, DNA M, DNA C and DNA N) sharing major common region (CR-M) and a stem-loop common region (CR-SL). BBTV-Umiam showed a unique deletion of 20 nucleotides in the intergenic region of DNA R, the absence of predicted open reading frame (ORF) in DNA U3 and probability for a small ORF in DNA U3 expecting functional evidence at transcriptional level. Phylogenetic analysis based on 88 complete nucleotide sequence of BBTV DNA R available in GenBank generated two broad clusters of Pacific-Indian Oceans (PIO) and South-East Asian (SEA) groups including BBTV-Umiam within PIO cluster. However, BBTV-Umiam was identified as the most distinct member of the PIO group with 100% bootstrap support. This was further supported by the phylogenetic grouping of each genomic component of BBTV-Umiam at the distant end of PIO group during clustering of 21 complete BBTV sequences. BBTV-Umiam shared relatively less nucleotide identity with PIO group for each genomic component (85.0-95.4%) and corresponding ORF (93.8-97.5%) than that of earlier PIO isolates (91.5-99.6% and 96.0-99.3%, respectively). Recombination analysis revealed two intra-component and five inter-component recombination events in BBTV-Umiam, but none of them was unique. Moreover, the isolate was identified as major parental sequence for intra-component recombination event spanning the replication-associated protein encoding region in Tongan BBTV DNA R. The current study indicated differential evolution of BBTV in North-East India (Meghalaya). The natural occurrence of hybrids of Musa balbisiana and M. acuminata in this geographically isolated region could be the contributing factor in accumulating genetic distinctiveness in BBTV-Umiam which need further characterization.
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Affiliation(s)
- Amrita Banerjee
- Division of Crop Improvement, ICAR Research Complex for NEH Region, Umiam 793 013, Meghalaya, India.
| | - Somnath Roy
- National Bureau of Plant Genetic Resources, Regional Station, Umiam 793 013, Meghalaya, India
| | - Ganesh T Behere
- Division of Crop Improvement, ICAR Research Complex for NEH Region, Umiam 793 013, Meghalaya, India
| | - Subhra Saikat Roy
- ICAR Research Complex for NEH Region, Manipur Centre, Lamphelpat 795 004, Manipur, India
| | - Sudip Kumar Dutta
- ICAR Research Complex for NEH Region, Mizoram Centre, Kolasib 796 081, Mizoram, India
| | - S V Ngachan
- Division of Crop Improvement, ICAR Research Complex for NEH Region, Umiam 793 013, Meghalaya, 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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25
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Watanabe S, Greenwell AM, Bressan A. Localization, concentration, and transmission efficiency of Banana bunchy top virus in four asexual lineages of Pentalonia aphids. Viruses 2013; 5:758-76. [PMID: 23435241 PMCID: PMC3640525 DOI: 10.3390/v5020758] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2013] [Revised: 02/14/2013] [Accepted: 02/14/2013] [Indexed: 02/01/2023] Open
Abstract
Banana bunchy top virus (BBTV) is the most destructive pathogenic virus of banana plants worldwide. The virus is transmitted in a circulative non-propagative manner by the banana aphid, Pentalonia nigronervosa Coquerel. In this work, we examined the localization, accumulation, and transmission efficiency of BBTV in four laboratory-established lineages of Pentalonia aphids derived from four different host plants: taro (Colocasia esculenta), heliconia (Heliconia spp.), red ginger (Alpinia purpurata), and banana (Musa sp.). Mitochondrial sequencing identified three and one lineages as Pentalonia caladii van der Goot, a recently proposed species, and P. nigronervosa, respectively. Microsatellite analysis separated the aphid lineages into four distinct genotypes. The transmission of BBTV was tested using leaf disk and whole-plant assays, both of which showed that all four lineages are competent vectors of BBTV, although the P. caladii from heliconia transmitted BBTV to the leaf disks at a significantly lower rate than did P. nigronervosa. The concentration of BBTV in dissected guts, haemolymph, and salivary glands was quantified by real-time PCR. The BBTV titer reached similar concentrations in the guts, haemolymph, and salivary glands of aphids from all four lineages tested. Furthermore, immunofluorescence assays showed that BBTV antigens localized to the anterior midguts and the principal salivary glands, demonstrating a similar pattern of translocations across the four lineages. The results reported in this study showed for the first time that P. caladii is a competent vector of BBTV.
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Affiliation(s)
- Shizu Watanabe
- Department of Plant and Environmental Protection Sciences, University of Hawaii at Manoa, Honolulu, HI 96822, USA
- Department of Molecular Bioscience and Bioengineering, University of Hawaii, Honolulu, HI 96822; USA; E-Mail: (S.W.)
| | - April M. Greenwell
- Department of Plant and Environmental Protection Sciences, University of Hawaii at Manoa, Honolulu, HI 96822, USA
- NSF-Center for Integrated Pest Management, North Carolina State University, USDA APHIS PPQ office, Honolulu, HI 96850, USA; E-Mail: (A.M.G.)
| | - Alberto Bressan
- Department of Plant and Environmental Protection Sciences, University of Hawaii at Manoa, Honolulu, HI 96822, USA
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26
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Development of Agrobacterium-mediated transformation of highly valued hill banana cultivar Virupakshi (AAB) for resistance to BBTV disease. World J Microbiol Biotechnol 2012. [DOI: 10.1007/s11274-012-1214-z] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/27/2022]
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27
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Yu NT, Zhang YL, Feng TC, Wang JH, Kulye M, Yang WJ, Lin ZS, Xiong Z, Liu ZX. Cloning and sequence analysis of two banana bunchy top virus genomes in Hainan. Virus Genes 2012; 44:488-94. [PMID: 22286609 DOI: 10.1007/s11262-012-0718-9] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2011] [Accepted: 01/12/2012] [Indexed: 11/29/2022]
Abstract
The genome of Banana bunchy top virus (BBTV) consists of six segments of single-stranded DNA of approximately 1 kb in length. We identified and sequenced the complete genomes of two BBTV isolates, one with and one without satellite DNA, from Haikou, Hainan, China. The Haikou-2 isolate contains six genomic segments and an additional satellite DNA while the Haikou-4 isolate contains only six genomic segments. Typical of other babuviruses, each genomic segment encodes a single open reading frame and contains the highly conserved stem-loop and major common regions. Phylogenetic analysis of the two Haikou isolates together with existing sequence records in GenBank confirmed the grouping of BBTV into two large groups and further refined the geographical distribution of each group. To accommodate the changes in the BBTV geographical distribution, the two groups are proposed as the Southeast Asian group and the Pacific-Indian Oceans group. Both the Haikou-2 and Haikou-4 isolates belong to the newly proposed Southeast Asian group.
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Affiliation(s)
- Nai-Tong Yu
- Key Laboratory of Biology and Genetic Resources of Tropical Crops, Ministry of Agriculture, Institute of Tropical Bioscience and Biotechnology, Chinese Academy of Tropical Agricultural Sciences, Haikou 571101, China
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28
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Shekhawat UKS, Ganapathi TR, Hadapad AB. Transgenic banana plants expressing small interfering RNAs targeted against viral replication initiation gene display high-level resistance to banana bunchy top virus infection. J Gen Virol 2012; 93:1804-1813. [DOI: 10.1099/vir.0.041871-0] [Citation(s) in RCA: 75] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023] Open
Abstract
The banana aphid-transmitted Banana bunchy top virus (BBTV) is the most destructive viral pathogen of bananas and plantains worldwide. Lack of natural sources of resistance to BBTV has necessitated the exploitation of proven transgenic technologies for obtaining BBTV-resistant banana cultivars. In this study, we have explored the concept of using intron-hairpin-RNA (ihpRNA) transcripts corresponding to viral master replication initiation protein (Rep) to generate BBTV-resistant transgenic banana plants. Two ihpRNA constructs namely ihpRNA-Rep and ihpRNA-ProRep generated using Rep full coding sequence or Rep partial coding sequence together with its 5′ upstream regulatory region, respectively, and castor bean catalase intron were successfully transformed into banana embryogenic cells. ihpRNA-Rep- and ihpRNA-ProRep-derived transgenic banana plants, selected based on preliminary screening for efficient reporter gene expression, were completely resistant to BBTV infection as indicated by the absence of disease symptoms after 6 months of viruliferous aphid inoculation. The resistance to BBTV infection was also evident by the inability to detect cDNAs coding for viral coat protein, movement protein and Rep protein by RT-PCR from inoculated transgenic leaf extracts. Southern analysis of the two groups of transgenics showed that ihpRNA transgene was stably integrated into the banana genome. The detection of small interfering RNAs (siRNAs) derived from the ihpRNA transgene sequence in transformed BBTV-resistant plants positively established RNA interference as the mechanism underlying the observed resistance to BBTV. Efficient screening of optimal transformants in this vegetatively propagated non-segregating fruit crop ensured that all the transgenic plants assayed were resistant to BBTV infection.
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Affiliation(s)
- Upendra K. S. Shekhawat
- Nuclear Agriculture and Biotechnology Division, Bhabha Atomic Research Centre, Trombay, Mumbai, India
| | - Thumballi R. Ganapathi
- Nuclear Agriculture and Biotechnology Division, Bhabha Atomic Research Centre, Trombay, Mumbai, India
| | - Ashok B. Hadapad
- Nuclear Agriculture and Biotechnology Division, Bhabha Atomic Research Centre, Trombay, Mumbai, India
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29
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Abraham AD, Varrelmann M, Josef Vetten H. Three Distinct Nanoviruses, One of Which Represents a New Species, Infect Faba Bean in Ethiopia. PLANT DISEASE 2012; 96:1045-1053. [PMID: 30727219 DOI: 10.1094/pdis-09-11-0734-re] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/09/2023]
Abstract
In all, 70 of 296 leaf samples (23.6%) collected from faba bean (Vicia faba) plants showing leaf yellowing and stunting in Ethiopia gave nanovirus-positive reactions when studied by triple-antibody sandwich enzyme-linked immunosorbent assay using broad-spectrum monoclonal antibodies (MAbs) specific to nanoviruses. Further analysis of these samples with seven discriminating MAbs revealed contrasting epitope profiles that were categorized into roughly three serogroups, designated A, B, and C. Serogroup A was found in 89% of the nanovirus-positive samples whereas serogroups B and C were infrequently encountered. Sequence analysis of DNA-S and DNA-U1 of serogroup A, B, and C isolates suggested that each represents a distinct nanovirus species. Serogroup A comprised isolates of Faba bean necrotic stunt virus reported earlier only from Ethiopia and Morocco. The DNA-R, -S, -U1, and -U2 sequences of a serogroup B isolate closely resembled those of Faba bean necrotic yellows virus, providing first molecular evidence for its occurrence in Ethiopia. Sequence analysis of the eight genomic DNAs of a representative serogroup C isolate (Eth-231) showed that it shared overall nucleotide and amino acid sequence identities of only ≤70 and ≤74%, respectively, with other nanoviruses. This suggests that Eth-231 represents a new nanovirus species, for which the name faba bean yellow leaf virus is proposed.
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Affiliation(s)
- Adane D Abraham
- Holetta Agricultural Research Center, Ethiopian Institute of Agricultural Research, Addis Ababa, Ethiopia; Julius Kühn Institute, Federal Research Center for Cultivated Plants, 38104, Braunschweig, Germany; and Institute for Plant Pathology and Protection, University of Göttingen, 37077 Göttingen, Germany
| | - Mark Varrelmann
- Institute for Sugar Beet Research, University of Göttingen, 37079 Göttingen, Germany
| | - H Josef Vetten
- Julius Kühn Institute, Federal Research Center for Cultivated Plants, Germany
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30
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Kumar PL, Hanna R, Alabi OJ, Soko MM, Oben TT, Vangu GHP, Naidu RA. Banana bunchy top virus in sub-Saharan Africa: investigations on virus distribution and diversity. Virus Res 2011; 159:171-82. [PMID: 21549775 DOI: 10.1016/j.virusres.2011.04.021] [Citation(s) in RCA: 39] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2011] [Accepted: 04/15/2011] [Indexed: 10/18/2022]
Abstract
Banana bunchy top virus (BBTV) was first reported from sub-Saharan Africa (SSA) from Democratic Republic of Congo (DRC) in the 1950s, has become invasive and spread into 11 countries in the region. To determine the potential threat of BBTV to the production of bananas and plantains (Musa spp.) in the sub-region, field surveys were conducted for the presence of banana bunchy top disease (BBTD) in the DRC, Angola, Cameroon, Gabon and Malawi. Using the DNA-S and DNA-R segments of the virus genome, the genetic diversity of BBTV isolates was also determined from these countries relative to virus isolates across the banana-growing regions around the world. The results established that BBTD is widely prevalent in all parts of DRC, Malawi, Angola and Gabon, in south and western part of Cameroon. Analysis of the nucleotide sequences of DNA-S and DNA-R indicate that BBTV isolates from these countries are genetically identical forming a unique clade within the 'South Pacific' phylogroup that includes isolates from Australia, Egypt, South Asia and South Pacific. These results imply that farmers' traditional practice of transferring vegetative propagules within and between countries, together with virus spread by the widely prevalent banana aphid vector, Pentalonia nigronervosa, could have contributed to the geographic expansion of BBTV in SSA. The results provided a baseline to explore sanitary measures and other 'clean' plant programs for sustainable management of BBTV and its vector in regions where the disease has already been established and prevent the spread of the virus to as yet unaffected regions in SSA.
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Affiliation(s)
- P Lava Kumar
- International Institute of Tropical Agriculture (IITA), PMB 5320, Ibadan, Nigeria.
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31
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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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32
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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: 14] [Impact Index Per Article: 1.1] [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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33
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Rybicki EP, Martin DP. Virus-derived ssDNA vectors for the expression of foreign proteins in plants. Curr Top Microbiol Immunol 2011; 375:19-45. [PMID: 22038412 DOI: 10.1007/82_2011_185] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Plant viruses with ssRNA genomes provide a unique opportunity for generating expression vehicles for biopharming in plants, as constructs containing only the replication origin, with the replication-associated protein (Rep) gene provided in cis or in trans, can be replicationally amplified in vivo by several orders of magnitude, with significant accompanying increases in transcription and expression of gene(s) of interest. Appropriate replicating vectors or replicons may be derived from several different generic geminiviruses (family Geminiviridae) or nanoviruses (family Nanoviridae), for potential expression of a wide range of single or even multiple products in a wide range of plant families. The use of vacuum or other infiltration of whole plants by Agrobacterium tumefaciens suspensions has allowed the development of a set of expression vectors that rival the deconstructed RNA virus vectors in their yield and application, with some potential advantages over the latter that still need to be explored. Several modern applications of ssDNA plant vectors and their future potential will be discussed.
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Affiliation(s)
- Edward P Rybicki
- Institute of Infectious Disease and Molecular Medicine, Cape Town, South Africa,
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34
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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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35
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Niu S, Wang B, Guo X, Yu J, Wang X, Xu K, Zhai Y, Wang J, Liu Z. Identification of two RNA silencing suppressors from banana bunchy top virus. Arch Virol 2009; 154:1775-83. [PMID: 19816653 DOI: 10.1007/s00705-009-0515-5] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2008] [Accepted: 09/02/2009] [Indexed: 01/19/2023]
Abstract
In order to suppress RNA silencing, many plant and some animal viruses encode RNA silencing suppressors to achieve infection. In this study, we report that B3 and B4, encoded by DNA3 and DNA4 of banana bunchy top virus (BBTV), exhibit RNA silencing suppression activity. B3 and B4 were able to increase the transient expression of green fluorescent protein (GFP) and dramatically enhanced the pathogenicity of potato virus X (PVX) in Nicotiana benthamiana. B4 was able to reverse established gene silencing on an inoculated leaf or on an upper leaf. B3, however, was only active during infection of an inoculated leaf. Furthermore, B4, but not B3, was able to enhance GFP expression in the transgenic N. benthamiana line 16c. In conclusion, B3 and B4 are the RNA silencing suppressors of BBTV, and they may act at different steps in the RNA silencing pathways.
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Affiliation(s)
- Shengniao Niu
- Key Laboratory of Tropical Crop Biotechnology of Ministry of Agriculture, Institute of Tropical Bioscience and Biotechnology, Chinese Academy of Tropical Agricultural Science, Haikou, Hainan, China
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36
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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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37
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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: 18] [Impact Index Per Article: 1.2] [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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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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39
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Sharman M, Thomas JE, Skabo S, Holton TA. Abacá bunchy top virus, a new member of the genus Babuvirus (family Nanoviridae). Arch Virol 2007; 153:135-47. [PMID: 17978886 DOI: 10.1007/s00705-007-1077-z] [Citation(s) in RCA: 26] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2007] [Accepted: 09/07/2007] [Indexed: 11/26/2022]
Abstract
Two isolates of a novel babuvirus causing "bunchy top" symptoms were characterised, one from abacá (Musa textilis) from the Philippines and one from banana (Musa sp.) from Sarawak (Malaysia). The name abacá bunchy top virus (ABTV) is proposed. Both isolates have a genome of six circular DNA components, each ca. 1.0-1.1 kb, analogous to those of isolates of Banana bunchy top virus (BBTV). However, unlike BBTV, both ABTV isolates lack an internal ORF in DNA-R, and the ORF in DNA-U3 found in some BBTV isolates is also absent. In all phylogenetic analyses of nanovirid isolates, ABTV and BBTV fall in the same clade, but on separate branches. However, ABTV and BBTV isolates shared only 79-81% amino acid sequence identity for the putative coat protein and 54-76% overall nucleotide sequence identity across all components. Stem-loop and major common regions were present in ABTV, but there was less than 60% identity with the major common region of BBTV. ABTV and BBTV were also shown to be serologically distinct, with only two out of ten BBTV-specific monoclonal antibodies reacting with ABTV. The two ABTV isolates may represent distinct strains of the species as they are less closely related to each other than are isolates of the two geographic subgroups (Asian and South Pacific) of BBTV.
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Affiliation(s)
- M Sharman
- Department of Primary Industries and Fisheries, Horticulture and Forestry Science, Indooroopilly, Queensland, Australia
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40
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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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41
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Herrera-Valencia VA, Dugdale B, Harding RM, Dale JL. Mapping the 5' ends of banana bunchy top virus gene transcripts. Arch Virol 2006; 152:615-20. [PMID: 17187296 DOI: 10.1007/s00705-006-0889-6] [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] [Received: 07/19/2006] [Accepted: 11/06/2006] [Indexed: 10/23/2022]
Abstract
Banana bunchy top virus (BBTV), a multi-component circular ssDNA virus, replicates via a dsDNA intermediate that also serves as a template for virion sense transcription. Seven virus-derived transcripts have been previously identified and analysed in BBTV-infected bananas by northern analysis and 3' rapid amplification of cDNA ends (3' RACE). In this study, we have used RNA ligase-mediated rapid amplification of 5' cDNA ends (RLM-RACE) to complete the mapping of the BBTV gene transcripts and have now fully mapped the transcribed regions of each BBTV component and effectively defined the upstream regulatory region.
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Affiliation(s)
- V A Herrera-Valencia
- Centre for Tropical Crops and Biocommodities, Institute of Health and Biomedical Innovation, Queensland University of Technology, Brisbane, Australia
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42
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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: 31] [Impact Index Per Article: 1.7] [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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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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Abstract
Nanoviruses, single-stranded DNA (ssDNA) plant viruses with a multipartite genome, share similarities with members of the Circoviridae family that infect mammals or birds as well as with the Geminiviridae, the only other plant virus family with circular ssDNA genomes. Although the virions of the latter are unique and different from that of the circoviruses, the mode of replication of viruses with monopartite or multipartite circular ssDNA genomes is strikingly similar. They multiply by rolling circle replication using virus-encoded multifunctional replication initiator proteins (Rep proteins) that catalyse initiation of ssDNA replication and resolution of replicative ssDNA into circular single-stranded virion DNA. All these ssDNA viruses exploit host polymerases for DNA synthesis and code for proteins that modulate the host's cell cycle favourably for virus multiplication. Recent three-dimensional structure analyses of a geminivirus and a parvovirus Rep protein have revealed an intriguing similarity between the catalytic domains of their respective Rep proteins. Furthermore, these structural data revealed that ssDNA virus replication initiator proteins might represent evolutionary intermediates between certain RNA-binding proteins and some multifunctional origin-binding proteins of papovaviruses.
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Affiliation(s)
- Bruno Gronenborn
- Institut des Sciences Végétales, CNRS, 91198, Gif sur Yvette, France.
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Oruetxebarria I, Kvarnheden A, Valkonen JPT. Analysis of putative interactions between potyviral replication proteins and plant retinoblastoma proteins. Virus Genes 2002; 24:65-75. [PMID: 11930964 DOI: 10.1023/a:1014090105049] [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] [Indexed: 11/12/2022]
Abstract
Sequence comparisons suggest that the RNA-dependent RNA polymerase (NIb) of potyviruses and bymoviruses, as well as the viral polymerase of potexviruses may contain a putative retinoblastoma protein (pRb) binding motif. The possibility that the potyviral NIb may function in the nucleus through interactions with plant pRb-related (RBR) proteins, and the modifications of the cell cycle was investigated by a combination of mutagenesis of the NIb and yeast two-hybrid system (YTHS). Mutation of a highly conserved glutamic acid residue in the putative pRb-binding motif of the NIb had no detectable phenotypic effect on replication of Potato virus A (PVA). Furthermore, the NIb proteins from Potato virus V and PVA failed to interact with maize or tobacco RBR proteins in yeast. Although the conservation of the motif for pRb interaction in plant RNA viruses is intriguing, these proteins from plant RNA viruses appear not to interact with plant RBR proteins.
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Solovyev AG, Stroganova TA, Zamyatnin AA, Fedorkin ON, Schiemann J, Morozov SY. Subcellular sorting of small membrane-associated triple gene block proteins: TGBp3-assisted targeting of TGBp2. Virology 2000; 269:113-27. [PMID: 10725204 DOI: 10.1006/viro.2000.0200] [Citation(s) in RCA: 79] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
We studied subcellular distribution of green fluorescent protein (GFP)-tagged movement proteins encoded by the second and the third genes of poa semilatent hordeivirus (PSLV) triple gene block (TGB), 15K TGBp2 and 18K TGBp3. GFP-15K transiently expressed in Nicotiana benthamiana leaf epidermal cells was associated with the endomembrane system elements. GFP-18K appeared in the membrane bodies at cell periphery. Mutation analysis demonstrated that subcellular targeting of GFP-15K depended on the protein transmembrane segment(s), whereas the TGBp3 central hydrophilic region was responsible for targeting of GFP-18K. Coexpression of GFP-15K with the intact 18K protein induced drastic changes in the TGBp2 localization: GFP-15K appeared in the cell peripheral bodies similar to those in the cells expressing GFP-18K alone. Coexpression experiments with mutant forms of both proteins argue against involvement of direct interaction between small TGB proteins in the TGBp3-assisted targeting of TGBp2 to the cell peripheral compartments. This conclusion was further confirmed by similar effects on the PSLV 15K TGBp2 localization induced by TGBp3 proteins of PSLV and potato virus X, which have no detectable sequence similarity to each other.
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Affiliation(s)
- A G Solovyev
- Department of Virology, Moscow State University, Moscow, 119899, Russia.
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