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Iqbal Z, Masood M, Shafiq M, Briddon RW. Temporal changes in the levels of virus and betasatellite DNA in B. tabaci feeding on CLCuD affected cotton during the growing season. Front Microbiol 2024; 15:1410568. [PMID: 38841073 PMCID: PMC11150673 DOI: 10.3389/fmicb.2024.1410568] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2024] [Accepted: 05/06/2024] [Indexed: 06/07/2024] Open
Abstract
Cotton, a key source of income for Pakistan, has suffered significantly by cotton leaf curl disease (CLCuD) since 1990. This disease is caused by a complex of phylogenetically-related begomovirus (genus Begomovirus, family Geminiviridae) species and a specific betasatellite (genus Betasatellite, family Tolecusatellitidae), cotton leaf curl Multan betasatellite. Additionally, another DNA satellite called alphasatellite (family Alphasatellitidae), is also frequently associated. All these virus components are vectored by a single species of whitefly (Bemisia tabaci). While many factors affect cotton productivity, including cotton variety, sowing time, and environmental cues such as temperature, humidity, and rainfall, CLCuD is a major biotic constraint. Although the understanding of begomoviruses transmission by whiteflies has advanced significantly over the past three decades, however, the in-field seasonal dynamics of the viruses in the insect vector remained an enigma. This study aimed to assess the levels of virus and betasatellite in whiteflies collected from cotton plants throughout the cotton growing season from 2014 to 2016. Notably, begomovirus levels showed no consistent pattern, with minimal variations, ranging from 0.0017 to 0.0074 ng.μg-1 of the genomic DNA in 2014, 0.0356 to 0.113 ng.μg-1 of the genomic DNA in 2015, and 0.0517 to 0.0791 ng.μg-1 of the genomic DNA in 2016. However, betasatellite levels exhibited a distinct pattern. During 2014 and 2015, it steadily increased throughout the sampling period (May to September). While 2016 showed a similar trend from the start of sampling (July) to September but a decline in October (end of sampling). Such a study has not been conducted previously, and could potentially provide valuable insights about the epidemiology of the virus complex causing CLCuD and possible means of controlling losses due to it.
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Affiliation(s)
- Zafar Iqbal
- Central Laboratories, King Faisal University, Al-Ahsa, Saudi Arabia
| | - Mariyam Masood
- Department of Zoology, Government College Women University, Faisalabad, Pakistan
| | - Muhammad Shafiq
- Department of Biotechnology, University of Management and Technology, Sialkot Campus, Sialkot, Pakistan
| | - Rob W. Briddon
- Agricultural Biotechnology Division, National Institute for Biotechnology and Genetic Engineering, Faisalabad, Pakistan
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2
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Torralba B, Blanc S, Michalakis Y. Reassortments in single-stranded DNA multipartite viruses: Confronting expectations based on molecular constraints with field observations. Virus Evol 2024; 10:veae010. [PMID: 38384786 PMCID: PMC10880892 DOI: 10.1093/ve/veae010] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2023] [Revised: 11/23/2023] [Accepted: 01/30/2024] [Indexed: 02/23/2024] Open
Abstract
Single-stranded DNA multipartite viruses, which mostly consist of members of the genus Begomovirus, family Geminiviridae, and all members of the family Nanoviridae, partly resolve the cost of genomic integrity maintenance through two remarkable capacities. They are able to systemically infect a host even when their genomic segments are not together in the same host cell, and these segments can be separately transmitted by insect vectors from host to host. These capacities potentially allow such viruses to reassort at a much larger spatial scale, since reassortants could arise from parental genotypes that do not co-infect the same cell or even the same host. To assess the limitations affecting reassortment and their implications in genome integrity maintenance, the objective of this review is to identify putative molecular constraints influencing reassorted segments throughout the infection cycle and to confront expectations based on these constraints with empirical observations. Trans-replication of the reassorted segments emerges as the major constraint, while encapsidation, viral movement, and transmission compatibilities appear more permissive. Confronting the available molecular data and the resulting predictions on reassortments to field population surveys reveals notable discrepancies, particularly a surprising rarity of interspecific natural reassortments within the Nanoviridae family. These apparent discrepancies unveil important knowledge gaps in the biology of ssDNA multipartite viruses and call for further investigation on the role of reassortment in their biology.
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Affiliation(s)
- Babil Torralba
- PHIM, Université Montpellier, IRD, CIRAD, INRAE, Institut Agro, Avenue du Campus d’Agropolis - ZAC de Baillarguet, Montpellier 34980, France
| | - Stéphane Blanc
- PHIM, Université Montpellier, IRD, CIRAD, INRAE, Institut Agro, Avenue du Campus d’Agropolis - ZAC de Baillarguet, Montpellier 34980, France
| | - Yannis Michalakis
- MIVEGEC, Université Montpellier, CNRS, IRD, 911, Avenue Agropolis, Montpellier 34394, France
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3
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Budzyńska D, Zwart MP, Hasiów-Jaroszewska B. Defective RNA Particles of Plant Viruses-Origin, Structure and Role in Pathogenesis. Viruses 2022; 14:2814. [PMID: 36560818 PMCID: PMC9786237 DOI: 10.3390/v14122814] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2022] [Revised: 12/14/2022] [Accepted: 12/15/2022] [Indexed: 12/23/2022] Open
Abstract
The genomes of RNA viruses may be monopartite or multipartite, and sub-genomic particles such as defective RNAs (D RNAs) or satellite RNAs (satRNAs) can be associated with some of them. D RNAs are small, deletion mutants of a virus that have lost essential functions for independent replication, encapsidation and/or movement. D RNAs are common elements associated with human and animal viruses, and they have been described for numerous plant viruses so far. Over 30 years of studies on D RNAs allow for some general conclusions to be drawn. First, the essential condition for D RNA formation is prolonged passaging of the virus at a high cellular multiplicity of infection (MOI) in one host. Second, recombination plays crucial roles in D RNA formation. Moreover, during virus propagation, D RNAs evolve, and the composition of the particle depends on, e.g., host plant, virus isolate or number of passages. Defective RNAs are often engaged in transient interactions with full-length viruses-they can modulate accumulation, infection dynamics and virulence, and are widely used, i.e., as a tool for research on cis-acting elements crucial for viral replication. Nevertheless, many questions regarding the generation and role of D RNAs in pathogenesis remain open. In this review, we summarise the knowledge about D RNAs of plant viruses obtained so far.
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Affiliation(s)
- Daria Budzyńska
- Department of Virology and Bacteriology, Institute of Plant Protection-National Research Institute, Wl Wegorka 20, 60-318 Poznan, Poland
| | - Mark P. Zwart
- Department of Microbial Ecology, Netherlands Institute of Ecology (NIOO-KNAW), Droevendaalsesteeg 10, 6708 PB Wageningen, The Netherlands
| | - Beata Hasiów-Jaroszewska
- Department of Virology and Bacteriology, Institute of Plant Protection-National Research Institute, Wl Wegorka 20, 60-318 Poznan, Poland
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4
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Saunders K, Richardson J, Lawson DM, Lomonossoff GP. Requirements for the Packaging of Geminivirus Circular Single-Stranded DNA: Effect of DNA Length and Coat Protein Sequence. Viruses 2020; 12:E1235. [PMID: 33143128 PMCID: PMC7694086 DOI: 10.3390/v12111235] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2020] [Revised: 10/26/2020] [Accepted: 10/28/2020] [Indexed: 11/16/2022] Open
Abstract
Geminivirus particles, consisting of a pair of twinned isometric structures, have one of the most distinctive capsids in the virological world. Until recently, there was little information as to how these structures are generated. To address this, we developed a system to produce capsid structures following the delivery of geminivirus coat protein and replicating circular single-stranded DNA (cssDNA) by the infiltration of gene constructs into plant leaves. The transencapsidation of cssDNA of the Begomovirus genus by coat protein of different geminivirus genera was shown to occur with full-length but not half-length molecules. Double capsid structures, distinct from geminate capsid structures, were also generated in this expression system. By increasing the length of the encapsidated cssDNA, triple geminate capsid structures, consisting of straight, bent and condensed forms were generated. The straight geminate triple structures generated were similar in morphology to those recorded for a potato-infecting virus from Peru. These finding demonstrate that the length of encapsidated DNA controls both the size and stability of geminivirus particles.
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Affiliation(s)
- Keith Saunders
- Department of Biological Chemistry, John Innes Centre, Norwich Research Park, Norwich NR4 7UH, UK; (D.M.L.); (G.P.L.)
| | - Jake Richardson
- Department of Cell and Developmental Biology, John Innes Centre, Norwich Research Park, Norwich NR4 7UH, UK;
| | - David M. Lawson
- Department of Biological Chemistry, John Innes Centre, Norwich Research Park, Norwich NR4 7UH, UK; (D.M.L.); (G.P.L.)
| | - George P. Lomonossoff
- Department of Biological Chemistry, John Innes Centre, Norwich Research Park, Norwich NR4 7UH, UK; (D.M.L.); (G.P.L.)
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Abstract
Viruses are the most abundant biological entities on Earth. In addition to their impact on animal and plant health, viruses have important roles in ecosystem dynamics as well as in the evolution of the biosphere. Circular Rep-encoding single-stranded (CRESS) DNA viruses are ubiquitous in nature, many are agriculturally important, and they appear to have multiple origins from prokaryotic plasmids. A subset of CRESS-DNA viruses, the cruciviruses, have homologues of capsid proteins encoded by RNA viruses. The genetic structure of cruciviruses attests to the transfer of capsid genes between disparate groups of viruses. However, the evolutionary history of cruciviruses is still unclear. By collecting and analyzing cruciviral sequence data, we provide a deeper insight into the evolutionary intricacies of cruciviruses. Our results reveal an unexpected diversity of this virus group, with frequent recombination as an important determinant of variability. The discovery of cruciviruses revealed the most explicit example of a common protein homologue between DNA and RNA viruses to date. Cruciviruses are a novel group of circular Rep-encoding single-stranded DNA (ssDNA) (CRESS-DNA) viruses that encode capsid proteins that are most closely related to those encoded by RNA viruses in the family Tombusviridae. The apparent chimeric nature of the two core proteins encoded by crucivirus genomes suggests horizontal gene transfer of capsid genes between DNA and RNA viruses. Here, we identified and characterized 451 new crucivirus genomes and 10 capsid-encoding circular genetic elements through de novo assembly and mining of metagenomic data. These genomes are highly diverse, as demonstrated by sequence comparisons and phylogenetic analysis of subsets of the protein sequences they encode. Most of the variation is reflected in the replication-associated protein (Rep) sequences, and much of the sequence diversity appears to be due to recombination. Our results suggest that recombination tends to occur more frequently among groups of cruciviruses with relatively similar capsid proteins and that the exchange of Rep protein domains between cruciviruses is rarer than intergenic recombination. Additionally, we suggest members of the stramenopiles/alveolates/Rhizaria supergroup as possible crucivirus hosts. Altogether, we provide a comprehensive and descriptive characterization of cruciviruses.
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Fontenele RS, Salywon AM, Majure LC, Cobb IN, Bhaskara A, Avalos-Calleros JA, Argüello-Astorga GR, Schmidlin K, Khalifeh A, Smith K, Schreck J, Lund MC, Köhler M, Wojciechowski MF, Hodgson WC, Puente-Martinez R, Van Doorslaer K, Kumari S, Vernière C, Filloux D, Roumagnac P, Lefeuvre P, Ribeiro SG, Kraberger S, Martin DP, Varsani A. A Novel Divergent Geminivirus Identified in Asymptomatic New World Cactaceae Plants. Viruses 2020; 12:E398. [PMID: 32260283 PMCID: PMC7232249 DOI: 10.3390/v12040398] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2020] [Revised: 03/29/2020] [Accepted: 03/31/2020] [Indexed: 12/17/2022] Open
Abstract
Cactaceae comprise a diverse and iconic group of flowering plants which are almost exclusively indigenous to the New World. The wide variety of growth forms found amongst the cacti have led to the trafficking of many species throughout the world as ornamentals. Despite the evolution and physiological properties of these plants having been extensively studied, little research has focused on cactus-associated viral communities. While only single-stranded RNA viruses had ever been reported in cacti, here we report the discovery of cactus-infecting single-stranded DNA viruses. These viruses all apparently belong to a single divergent species of the family Geminiviridae and have been tentatively named Opuntia virus 1 (OpV1). A total of 79 apparently complete OpV1 genomes were recovered from 31 different cactus plants (belonging to 20 different cactus species from both the Cactoideae and Opuntioideae clades) and from nine cactus-feeding cochineal insects (Dactylopius sp.) sampled in the USA and Mexico. These 79 OpV1 genomes all share > 78.4% nucleotide identity with one another and < 64.9% identity with previously characterized geminiviruses. Collectively, the OpV1 genomes display evidence of frequent recombination, with some genomes displaying up to five recombinant regions. In one case, recombinant regions span ~40% of the genome. We demonstrate that an infectious clone of an OpV1 genome can replicate in Nicotiana benthamiana and Opuntia microdasys. In addition to expanding the inventory of viruses that are known to infect cacti, the OpV1 group is so distantly related to other known geminiviruses that it likely represents a new geminivirus genus. It remains to be determined whether, like its cactus hosts, its geographical distribution spans the globe.
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Affiliation(s)
- Rafaela S. Fontenele
- The Biodesign Center for Fundamental and Applied Microbiomics, Arizona State University, Tempe, AZ 85287, USA; (R.S.F.); (I.N.C.); (A.B.); (K.S.); (A.K.); (K.S.); (J.S.); (M.C.L.); (S.K.)
- School of Life Sciences, Arizona State University, Tempe, AZ 85287, USA;
| | - Andrew M. Salywon
- Desert Botanical Garden, Phoenix, AZ 85008, USA; (A.M.S.); (L.C.M.); (W.C.H.); (R.P.-M.)
| | - Lucas C. Majure
- Desert Botanical Garden, Phoenix, AZ 85008, USA; (A.M.S.); (L.C.M.); (W.C.H.); (R.P.-M.)
- Florida Museum of Natural History, University of Florida, Gainesville, FL 32611, USA
| | - Ilaria N. Cobb
- The Biodesign Center for Fundamental and Applied Microbiomics, Arizona State University, Tempe, AZ 85287, USA; (R.S.F.); (I.N.C.); (A.B.); (K.S.); (A.K.); (K.S.); (J.S.); (M.C.L.); (S.K.)
- The University of British Columbia, Vancouver, BC V6T 1Z4, Canada
| | - Amulya Bhaskara
- The Biodesign Center for Fundamental and Applied Microbiomics, Arizona State University, Tempe, AZ 85287, USA; (R.S.F.); (I.N.C.); (A.B.); (K.S.); (A.K.); (K.S.); (J.S.); (M.C.L.); (S.K.)
- Center for Research in Engineering, Science and Technology, Paradise Valley High School, 3950 E Bell Rd, Phoenix, AZ 85032, USA
| | - Jesús A. Avalos-Calleros
- División de Biología Molecular, Instituto Potosino de Investigación Científica y Tecnológica, A.C., Camino a la Presa de San José 2055, Lomas 4ta Secc, San Luis Potosi 78216, S.L.P., Mexico; (J.A.A.-C.); (G.R.A.-A.)
| | - Gerardo R. Argüello-Astorga
- División de Biología Molecular, Instituto Potosino de Investigación Científica y Tecnológica, A.C., Camino a la Presa de San José 2055, Lomas 4ta Secc, San Luis Potosi 78216, S.L.P., Mexico; (J.A.A.-C.); (G.R.A.-A.)
| | - Kara Schmidlin
- The Biodesign Center for Fundamental and Applied Microbiomics, Arizona State University, Tempe, AZ 85287, USA; (R.S.F.); (I.N.C.); (A.B.); (K.S.); (A.K.); (K.S.); (J.S.); (M.C.L.); (S.K.)
- School of Life Sciences, Arizona State University, Tempe, AZ 85287, USA;
| | - Anthony Khalifeh
- The Biodesign Center for Fundamental and Applied Microbiomics, Arizona State University, Tempe, AZ 85287, USA; (R.S.F.); (I.N.C.); (A.B.); (K.S.); (A.K.); (K.S.); (J.S.); (M.C.L.); (S.K.)
- School of Life Sciences, Arizona State University, Tempe, AZ 85287, USA;
| | - Kendal Smith
- The Biodesign Center for Fundamental and Applied Microbiomics, Arizona State University, Tempe, AZ 85287, USA; (R.S.F.); (I.N.C.); (A.B.); (K.S.); (A.K.); (K.S.); (J.S.); (M.C.L.); (S.K.)
- School of Life Sciences, Arizona State University, Tempe, AZ 85287, USA;
| | - Joshua Schreck
- The Biodesign Center for Fundamental and Applied Microbiomics, Arizona State University, Tempe, AZ 85287, USA; (R.S.F.); (I.N.C.); (A.B.); (K.S.); (A.K.); (K.S.); (J.S.); (M.C.L.); (S.K.)
- School of Life Sciences, Arizona State University, Tempe, AZ 85287, USA;
| | - Michael C. Lund
- The Biodesign Center for Fundamental and Applied Microbiomics, Arizona State University, Tempe, AZ 85287, USA; (R.S.F.); (I.N.C.); (A.B.); (K.S.); (A.K.); (K.S.); (J.S.); (M.C.L.); (S.K.)
- School of Life Sciences, Arizona State University, Tempe, AZ 85287, USA;
| | - Matias Köhler
- Departamento de BotânicaPrograma de Pós-Graduação em Botânica, Universidade Federal do Rio Grande do Sul, Porto Alegre, RS 91501970, Brazil;
| | | | - Wendy C. Hodgson
- Desert Botanical Garden, Phoenix, AZ 85008, USA; (A.M.S.); (L.C.M.); (W.C.H.); (R.P.-M.)
| | - Raul Puente-Martinez
- Desert Botanical Garden, Phoenix, AZ 85008, USA; (A.M.S.); (L.C.M.); (W.C.H.); (R.P.-M.)
| | - Koenraad Van Doorslaer
- School of Animal and Comparative Biomedical Sciences, Department of Immunobiology, BIO5 Institute, and UA Cancer Center, University of Arizona, Tucson, AZ 85721, USA;
| | - Safaa Kumari
- International Center for Agricultural Research in the Dry Areas (ICARDA), Terbol Station, Beqa’a, Zahle, Lebanon;
| | - Christian Vernière
- CIRAD, BGPI, 34398 Montpellier, France; (C.V.); (D.F.); (P.R.)
- BGPI, INRAE, CIRAD, SupAgro, Univ Montpellier, 34398 Montpellier, France
| | - Denis Filloux
- CIRAD, BGPI, 34398 Montpellier, France; (C.V.); (D.F.); (P.R.)
- BGPI, INRAE, CIRAD, SupAgro, Univ Montpellier, 34398 Montpellier, France
| | - Philippe Roumagnac
- CIRAD, BGPI, 34398 Montpellier, France; (C.V.); (D.F.); (P.R.)
- BGPI, INRAE, CIRAD, SupAgro, Univ Montpellier, 34398 Montpellier, France
| | | | - Simone G. Ribeiro
- Embrapa Recursos Genéticos e Biotecnologia, Brasília, CEP 70770-917, Brazil;
| | - Simona Kraberger
- The Biodesign Center for Fundamental and Applied Microbiomics, Arizona State University, Tempe, AZ 85287, USA; (R.S.F.); (I.N.C.); (A.B.); (K.S.); (A.K.); (K.S.); (J.S.); (M.C.L.); (S.K.)
| | - Darren P. Martin
- Computational Biology Division, Department of Integrative Biomedical Sciences, Institute of Infectious Diseases and Molecular Medicine, University of Cape Town, Observatory, Cape Town 7925, South Africa;
| | - Arvind Varsani
- The Biodesign Center for Fundamental and Applied Microbiomics, Arizona State University, Tempe, AZ 85287, USA; (R.S.F.); (I.N.C.); (A.B.); (K.S.); (A.K.); (K.S.); (J.S.); (M.C.L.); (S.K.)
- School of Life Sciences, Arizona State University, Tempe, AZ 85287, USA;
- Center for Evolution and Medicine, Arizona State University, Tempe, AZ 85287, USA
- Structural Biology Research Unit, Department of Clinical Laboratory Sciences, University of Cape Town, Cape Town 7925, South Africa
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Abstract
The geminivirus capsid architecture is unique and built from twinned pseudo T=1 icosahedrons with 110 copies of the coat protein (CP). The CP is multifunctional. It performs various functions during the infection of a wide range of agriculturally important plant hosts. The CP multimerizes via pentameric intermediates during assembly and encapsulates the ssDNA genome to generate the unique capsid morphology. The virus capsid protects and transports the genome in the insect vector and plant host enroute to the plant nucleus for replication and the production of progeny. This review further explores CP:CP and CP:DNA interactions, and the environmental conditions that govern the assembly of the geminivirus capsid. This analysis was facilitated by new data available for the family, including three-dimensional structures and molecular biology data for several members. In addition, current and promising new control strategies of plant crop infection, which can lead to starvation for subsistence farmers, are discussed.
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Affiliation(s)
- Antonette Bennett
- Department of Biochemistry and Molecular Biology, College of Medicine, Center for Structural Biology, McKnight Brain Institute, University of Florida, Gainesville, FL, United States
| | - Mavis Agbandje-McKenna
- Department of Biochemistry and Molecular Biology, College of Medicine, Center for Structural Biology, McKnight Brain Institute, University of Florida, Gainesville, FL, United States.
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Bennett A, Rodriguez D, Lister S, Boulton M, McKenna R, Agbandje-McKenna M. Assembly and disassembly intermediates of maize streak geminivirus. Virology 2018; 525:224-236. [PMID: 30300759 DOI: 10.1016/j.virol.2018.09.011] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2018] [Revised: 09/16/2018] [Accepted: 09/16/2018] [Indexed: 11/17/2022]
Abstract
Maize streak virus (MSV) belongs to the Geminiviridae. Four forms of MSV coat protein (CP) assemblages were isolated from infected plants: geminate capsids, T = 1 icosahedral capsids, pentamers and decamers of CPs. Sequential exposure of geminate capsids to increasing pH, from 4.8 to 7.2 was used to monitor capsid disassembly. The capsids remain intact at pH4.8, disassemble to decamers and pentamers by pH6.4 and aggregate by pH7.2. Similarly, high salt and divalent cations cause disassembly. The disassembly process was reversed in low pH and low salt, but resulted in empty (no DNA) single and geminate capsid assemblies. This is likely due to disruption of CP-DNA interactions under acidic conditions and suggests a mechanism of capsid assembly in which the genome is packaged into preformed empty capsids. The pH assay developed in this study provides a method for characterizing the conditions that are the determinants of geminivirus assembly and disassembly.
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Affiliation(s)
- Antonette Bennett
- Department of Biochemistry and Molecular Biology, College of Medicine, Center for Structural Biology, McKnight Brain Institute, University of Florida, Gainesville, FL 32610-0245, United States
| | - David Rodriguez
- Department of Biochemistry and Molecular Biology, College of Medicine, Center for Structural Biology, McKnight Brain Institute, University of Florida, Gainesville, FL 32610-0245, United States
| | - Samantha Lister
- John Innes Center, Norwich Research Park, Colney Lane, Norwich NR4 7UH, UK
| | - Margaret Boulton
- John Innes Center, Norwich Research Park, Colney Lane, Norwich NR4 7UH, UK
| | - Robert McKenna
- Department of Biochemistry and Molecular Biology, College of Medicine, Center for Structural Biology, McKnight Brain Institute, University of Florida, Gainesville, FL 32610-0245, United States
| | - Mavis Agbandje-McKenna
- Department of Biochemistry and Molecular Biology, College of Medicine, Center for Structural Biology, McKnight Brain Institute, University of Florida, Gainesville, FL 32610-0245, United States.
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Alphasatellitidae: a new family with two subfamilies for the classification of geminivirus- and nanovirus-associated alphasatellites. Arch Virol 2018; 163:2587-2600. [PMID: 29740680 DOI: 10.1007/s00705-018-3854-2] [Citation(s) in RCA: 79] [Impact Index Per Article: 13.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2018] [Accepted: 04/25/2018] [Indexed: 10/16/2022]
Abstract
Nanoviruses and geminiviruses are circular, single stranded DNA viruses that infect many plant species around the world. Nanoviruses and certain geminiviruses that belong to the Begomovirus and Mastrevirus genera are associated with additional circular, single stranded DNA molecules (~ 1-1.4 kb) that encode a replication-associated protein (Rep). These Rep-encoding satellite molecules are commonly referred to as alphasatellites and here we communicate the establishment of the family Alphasatellitidae to which these have been assigned. Within the Alphasatellitidae family two subfamilies, Geminialphasatellitinae and Nanoalphasatellitinae, have been established to respectively accommodate the geminivirus- and nanovirus-associated alphasatellites. Whereas the pairwise nucleotide sequence identity distribution of all the known geminialphasatellites (n = 628) displayed a troughs at ~ 70% and 88% pairwise identity, that of the known nanoalphasatellites (n = 54) had a troughs at ~ 67% and ~ 80% pairwise identity. We use these pairwise identity values as thresholds together with phylogenetic analyses to establish four genera and 43 species of geminialphasatellites and seven genera and 19 species of nanoalphasatellites. Furthermore, a divergent alphasatellite associated with coconut foliar decay disease is assigned to a species but not a subfamily as it likely represents a new alphasatellite subfamily that could be established once other closely related molecules are discovered.
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Passion Fruit Chlorotic Mottle Virus: Molecular Characterization of a New Divergent Geminivirus in Brazil. Viruses 2018; 10:v10040169. [PMID: 29614801 PMCID: PMC5923463 DOI: 10.3390/v10040169] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2018] [Revised: 03/27/2018] [Accepted: 03/30/2018] [Indexed: 12/23/2022] Open
Abstract
Brazil is one of the major passion fruit producers worldwide. Viral diseases are among the most important constraints for passion fruit production. Here we identify and characterize a new passion fruit infecting-virus belonging to the family Geminiviridae: passion fruit chlorotic mottle virus (PCMoV). PCMoV is a divergent geminivirus unlike previously characterized passion fruit-infecting geminiviruses that belonged to the genus Begomovirus. Among the presently known geminiviruses, it is most closely related to, and shares ~62% genome-wide identity with citrus chlorotic dwarf associated virus (CCDaV) and camelia chlorotic dwarf associated virus (CaCDaV). The 3743 nt PCMoV genome encodes a capsid protein (CP) and replication-associated protein (Rep) that respectively share 56 and 60% amino acid identity with those encoded by CaCDaV. The CPs of PCMoV, CCDaV, and CaCDaV cluster with those of begomovirus whereas their Reps with those of becurtoviruses. Hence, these viruses likely represent a lineage of recombinant begomo-like and becurto-like ancestral viruses. Furthermore, PCMoV, CCDaV, and CaCDaV genomes are ~12-30% larger than monopartite geminiviruses and this is primarily due to the encoded movement protein (MP; 891-921 nt) and this MP is most closely related to that encoded by the DNA-B component of bipartite begomoviruses. Hence, PCMoV, CCDaV, and CaCDaV lineage of viruses may represent molecules in an intermediary step in the evolution of bipartite begomoviruses (~5.3 kb) from monopartite geminiviruses (~2.7-3 kb). An infectious clone of PCMoV systemically infected Nicotiana benthamina, Arabidopsis thaliana, and Passiflora edulis.
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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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12
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Al Rwahnih M, Alabi OJ, Westrick NM, Golino D, Rowhani A. Description of a Novel Monopartite Geminivirus and Its Defective Subviral Genome in Grapevine. PHYTOPATHOLOGY 2017; 107:240-251. [PMID: 27670772 DOI: 10.1094/phyto-07-16-0282-r] [Citation(s) in RCA: 31] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/06/2023]
Abstract
A novel virus was detected in grapevines by Illumina sequencing during the screening of two table grape (Vitis vinifera) accessions, cultivars Black Beet and Nagano Purple, from South Korea. The monopartite circular ssDNA genome sequence was subsequently confirmed by rolling cycle amplification, cloning and Sanger sequencing. The complete viral genomic sequence from both accessions ranged from 2,903 to 2,907 nucleotides in length and contained the conserved nonanucleotide sequence TAATATT↓AC and other sequence features typical of the family Geminiviridae, including two predicted sense and four complementary-sense open reading frames. Phylogenetic analysis placed the novel virus in a unique taxon within the family Geminiviridae. A naturally occurring defective subviral DNA was also discovered. This defective DNA molecule carried a deletion of approximately 46% of the full-length genome. Both the genomic and defective DNA molecules were graft-transmissible although no disease is yet correlated with their occurrence in Vitis spp. The tentative names Grapevine geminivirus A (GGVA) and GGVA defective DNA (GGVA D-DNA) are proposed. PCR assays developed using primers designed in the coat protein gene led to the detection of GGVA in 1.74% of 1,262 vines derived from 15 grapevine cultivars from six countries across three continents.
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Affiliation(s)
- Maher Al Rwahnih
- First, third, fourth, and fifth authors: Department of Plant Pathology, University of California, Davis, 95616; and second author: Department of Plant Pathology & Microbiology, Texas A&M AgriLife Research and Extension Center, Weslaco 78596
| | - Olufemi J Alabi
- First, third, fourth, and fifth authors: Department of Plant Pathology, University of California, Davis, 95616; and second author: Department of Plant Pathology & Microbiology, Texas A&M AgriLife Research and Extension Center, Weslaco 78596
| | - Nathaniel M Westrick
- First, third, fourth, and fifth authors: Department of Plant Pathology, University of California, Davis, 95616; and second author: Department of Plant Pathology & Microbiology, Texas A&M AgriLife Research and Extension Center, Weslaco 78596
| | - Deborah Golino
- First, third, fourth, and fifth authors: Department of Plant Pathology, University of California, Davis, 95616; and second author: Department of Plant Pathology & Microbiology, Texas A&M AgriLife Research and Extension Center, Weslaco 78596
| | - Adib Rowhani
- First, third, fourth, and fifth authors: Department of Plant Pathology, University of California, Davis, 95616; and second author: Department of Plant Pathology & Microbiology, Texas A&M AgriLife Research and Extension Center, Weslaco 78596
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13
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Hassan I, Orílio AF, Fiallo-Olivé E, Briddon RW, Navas-Castillo J. Infectivity, effects on helper viruses and whitefly transmission of the deltasatellites associated with sweepoviruses (genus Begomovirus, family Geminiviridae). Sci Rep 2016; 6:30204. [PMID: 27453359 PMCID: PMC4958995 DOI: 10.1038/srep30204] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2016] [Accepted: 06/30/2016] [Indexed: 11/08/2022] Open
Abstract
Begomoviruses (family Geminiviridae) are whitefly-transmitted viruses with single-stranded DNA genomes that are frequently associated with DNA satellites. These satellites include non-coding satellites, for which the name deltasatellites has been proposed. Although the first deltasatellite was identified in the late 1990s, little is known about the effects they have on infections of their helper begomoviruses. Recently a group of deltasatellites were identified associated with sweepoviruses, a group of phylogenetically distinct begomoviruses that infect plants of the family Convolvulaceae including sweet potato. In this work, the deltasatellites associated with sweepoviruses are shown to be transreplicated and maintained in plants by the virus with which they were identified, sweet potato leaf curl virus (SPLCV). These deltasatellites were shown generally to reduce symptom severity of the virus infection by reducing virus DNA levels. Additionally they were shown to be maintained in plants, and reduce the symptoms induced by two Old World monopartite begomoviruses, tomato yellow leaf curl virus and tomato yellow leaf curl Sardinia virus. Finally one of the satellites was shown to be transmitted plant-to-plant in the presence of SPLCV by the whitefly vector of the virus, Bemisia tabaci, being the first time a deltasatellite has been shown to be insect transmitted.
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Affiliation(s)
- Ishtiaq Hassan
- Instituto de Hortofruticultura Subtropical y Mediterránea “La Mayora”, Universidad de Málaga - Consejo Superior de Investigaciones Científicas (IHSM-UMA-CSIC), Estación Experimental “La Mayora”, 29750 Algarrobo-Costa, Málaga, Spain
- Agricultural Biotechnology Division, National Institute for Biotechnology and Genetic Engineering, Faisalabad, Pakistan
- Pakistan Institute of Engineering and Applied Sciences, Islamabad, Pakistan
| | - Anelise F. Orílio
- Instituto de Hortofruticultura Subtropical y Mediterránea “La Mayora”, Universidad de Málaga - Consejo Superior de Investigaciones Científicas (IHSM-UMA-CSIC), Estación Experimental “La Mayora”, 29750 Algarrobo-Costa, Málaga, Spain
| | - Elvira Fiallo-Olivé
- Instituto de Hortofruticultura Subtropical y Mediterránea “La Mayora”, Universidad de Málaga - Consejo Superior de Investigaciones Científicas (IHSM-UMA-CSIC), Estación Experimental “La Mayora”, 29750 Algarrobo-Costa, Málaga, Spain
| | - Rob W. Briddon
- Agricultural Biotechnology Division, National Institute for Biotechnology and Genetic Engineering, Faisalabad, Pakistan
| | - Jesús Navas-Castillo
- Instituto de Hortofruticultura Subtropical y Mediterránea “La Mayora”, Universidad de Málaga - Consejo Superior de Investigaciones Científicas (IHSM-UMA-CSIC), Estación Experimental “La Mayora”, 29750 Algarrobo-Costa, Málaga, Spain
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14
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Lozano G, Trenado HP, Fiallo-Olivé E, Chirinos D, Geraud-Pouey F, Briddon RW, Navas-Castillo J. Characterization of Non-coding DNA Satellites Associated with Sweepoviruses (Genus Begomovirus, Geminiviridae) - Definition of a Distinct Class of Begomovirus-Associated Satellites. Front Microbiol 2016; 7:162. [PMID: 26925037 PMCID: PMC4756297 DOI: 10.3389/fmicb.2016.00162] [Citation(s) in RCA: 80] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2015] [Accepted: 02/01/2016] [Indexed: 11/13/2022] Open
Abstract
Begomoviruses (family Geminiviridae) are whitefly-transmitted, plant-infecting single-stranded DNA viruses that cause crop losses throughout the warmer parts of the World. Sweepoviruses are a phylogenetically distinct group of begomoviruses that infect plants of the family Convolvulaceae, including sweet potato (Ipomoea batatas). Two classes of subviral molecules are often associated with begomoviruses, particularly in the Old World; the betasatellites and the alphasatellites. An analysis of sweet potato and Ipomoea indica samples from Spain and Merremia dissecta samples from Venezuela identified small non-coding subviral molecules in association with several distinct sweepoviruses. The sequences of 18 clones were obtained and found to be structurally similar to tomato leaf curl virus-satellite (ToLCV-sat, the first DNA satellite identified in association with a begomovirus), with a region with significant sequence identity to the conserved region of betasatellites, an A-rich sequence, a predicted stem–loop structure containing the nonanucleotide TAATATTAC, and a second predicted stem–loop. These sweepovirus-associated satellites join an increasing number of ToLCV-sat-like non-coding satellites identified recently. Although sharing some features with betasatellites, evidence is provided to suggest that the ToLCV-sat-like satellites are distinct from betasatellites and should be considered a separate class of satellites, for which the collective name deltasatellites is proposed.
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Affiliation(s)
- Gloria Lozano
- Instituto de Hortofruticultura Subtropical y Mediterránea "La Mayora", Universidad de Málaga - Consejo Superior de Investigaciones Científicas Algarrobo-Costa, Spain
| | - Helena P Trenado
- Instituto de Hortofruticultura Subtropical y Mediterránea "La Mayora", Universidad de Málaga - Consejo Superior de Investigaciones Científicas Algarrobo-Costa, Spain
| | - Elvira Fiallo-Olivé
- Instituto de Hortofruticultura Subtropical y Mediterránea "La Mayora", Universidad de Málaga - Consejo Superior de Investigaciones Científicas Algarrobo-Costa, Spain
| | | | | | - Rob W Briddon
- Agricultural Biotechnology Division, National Institute for Biotechnology and Genetic Engineering Faisalabad, Pakistan
| | - Jesús Navas-Castillo
- Instituto de Hortofruticultura Subtropical y Mediterránea "La Mayora", Universidad de Málaga - Consejo Superior de Investigaciones Científicas Algarrobo-Costa, Spain
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15
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Diverse circular replication-associated protein encoding viruses circulating in invertebrates within a lake ecosystem. INFECTION GENETICS AND EVOLUTION 2016; 39:304-316. [PMID: 26873065 DOI: 10.1016/j.meegid.2016.02.011] [Citation(s) in RCA: 56] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/26/2015] [Revised: 01/30/2016] [Accepted: 02/07/2016] [Indexed: 11/24/2022]
Abstract
Over the last five years next-generation sequencing has become a cost effective and efficient method for identifying known and unknown microorganisms. Access to this technique has dramatically changed the field of virology, enabling a wide range of environmental viral metagenome studies to be undertaken of organisms and environmental samples from polar to tropical regions. These studies have led to the discovery of hundreds of highly divergent single stranded DNA (ssDNA) virus-like sequences encoding replication-associated proteins. Yet, few studies have explored how viruses might be shared in an ecosystem through feeding relationships. Here we identify 169 circular molecules (160 CRESS DNA molecules, nine circular molecules) recovered from a New Zealand freshwater lake, that we have tentatively classified into 51 putatively novel species and five previously described species (DflaCV-3, -5, -6, -8, -10). The CRESS DNA viruses identified in this study were recovered from molluscs (Echyridella menzeisii, Musculium novaezelandiae, Potamopyrgus antipodarum and Physella acuta) and insect larvae (Procordulia grayi, Xanthocnemis zealandica, and Chironomus zealandicus) collected from Lake Sarah, as well as from the lake water and benthic sediments. Extensive diversity was observed across most CRESS DNA molecules recovered. The putative capsid protein of one viral species was found to be most similar to those of members of the Tombusviridae family, thus expanding the number of known RNA-DNA hybrid viruses in nature. We noted a strong association between the CRESS DNA viruses and circular molecules identified in the water and browser organisms (C. zealandicus, P. antipodarum and P. acuta), and between water sediments and undefended prey species (C. zealandicus). However, we were unable to find any significant correlation of viral assemblages to the potential feeding relationships of the host aquatic invertebrates.
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16
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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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17
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Analysis of complete genomes of isolates of the Wheat dwarf virus from new geographical locations and descriptions of their defective forms. Virus Genes 2014; 48:133-9. [PMID: 24122067 DOI: 10.1007/s11262-013-0989-9] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2013] [Accepted: 09/25/2013] [Indexed: 10/26/2022]
Abstract
Recently, the importance of the Geminiviruses infecting cereal crops has been appreciated, and they are now being studied in detail. Barley and wheat strains of Wheat dwarf virus are recorded in most European countries. Information on complete sequences of isolates from the United Kingdom, Spain, and Austria are reported here for the first time. Analysis revealed that their sequences are very stable. Recombination between strains was recorded only for the barley strain. We identified several defective forms of the barley strain from barley and wheat, which do not influence symptom expression. Sequences of barley isolates infecting wheat were obtained that did not differ from the isolates from barley. Based on specific features of the SIR of the barley strains, it is suggested that they are assigned to one of the two proposed new clusters, A1 or A2.
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18
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Rosario K, Padilla-Rodriguez M, Kraberger S, Stainton D, Martin DP, Breitbart M, Varsani A. Discovery of a novel mastrevirus and alphasatellite-like circular DNA in dragonflies (Epiprocta) from Puerto Rico. Virus Res 2013; 171:231-7. [DOI: 10.1016/j.virusres.2012.10.017] [Citation(s) in RCA: 43] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2012] [Revised: 10/14/2012] [Accepted: 10/18/2012] [Indexed: 11/28/2022]
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19
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Bi H, Zhang P. Molecular characterization of two sweepoviruses from China and evaluation of the infectivity of cloned SPLCV-JS in Nicotiana benthamiana. Arch Virol 2012; 157:441-54. [PMID: 22179901 DOI: 10.1007/s00705-011-1194-6] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2011] [Accepted: 12/01/2011] [Indexed: 11/25/2022]
Abstract
Sweepoviruses are important begomoviruses that infect Ipomoea plants worldwide and cause sweet potato yield losses and cultivar decline. Two sweepoviruses, sweet potato leaf curl virus-Jiangsu (SPLCV-JS) and sweet potato leaf curl China virus-Zhejiang (SPLCCNV-ZJ), were cloned from diseased sweet potato plants collected in the Jiangsu and Zhejiang provinces of China. Sequence characterization and phylogenetic analysis demonstrated that both are typical monopartite begomoviruses and have close relationships to several reported SPLCV and SPLCCNV isolates, respectively, from Asian countries. Analysis of the protein alignments and subcellular localizations of the six SPLCV-JS proteins was also conducted to verify their putative functions. In Nicotiana benthamiana, an infectivity assay of the infectious SPLCV-JS clone resulted in mild symptoms and weak viral DNA accumulation. Interestingly, SPLCV-JS, together with a heterologous betasatellite DNA (tomato yellow leaf curl China virus isolate Y10 [TYLCCNV-Y10] DNA-β), showed a synergistic effect on enhanced symptom severity and viral DNA accumulation. This is the first reported infectious SPLCV clone.
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Affiliation(s)
- Huiping Bi
- National Key Laboratory of Plant Molecular Genetics, Institute of Plant Physiology and Ecology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, 300 Fenglin Road, Shanghai 200032, China
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20
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Martin DP, Biagini P, Lefeuvre P, Golden M, Roumagnac P, Varsani A. Recombination in eukaryotic single stranded DNA viruses. Viruses 2011; 3:1699-738. [PMID: 21994803 PMCID: PMC3187698 DOI: 10.3390/v3091699] [Citation(s) in RCA: 159] [Impact Index Per Article: 12.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2011] [Revised: 08/18/2011] [Accepted: 09/05/2011] [Indexed: 12/23/2022] Open
Abstract
Although single stranded (ss) DNA viruses that infect humans and their domesticated animals do not generally cause major diseases, the arthropod borne ssDNA viruses of plants do, and as a result seriously constrain food production in most temperate regions of the world. Besides the well known plant and animal-infecting ssDNA viruses, it has recently become apparent through metagenomic surveys of ssDNA molecules that there also exist large numbers of other diverse ssDNA viruses within almost all terrestrial and aquatic environments. The host ranges of these viruses probably span the tree of life and they are likely to be important components of global ecosystems. Various lines of evidence suggest that a pivotal evolutionary process during the generation of this global ssDNA virus diversity has probably been genetic recombination. High rates of homologous recombination, non-homologous recombination and genome component reassortment are known to occur within and between various different ssDNA virus species and we look here at the various roles that these different types of recombination may play, both in the day-to-day biology, and in the longer term evolution, of these viruses. We specifically focus on the ecological, biochemical and selective factors underlying patterns of genetic exchange detectable amongst the ssDNA viruses and discuss how these should all be considered when assessing the adaptive value of recombination during ssDNA virus evolution.
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Affiliation(s)
- Darren P. Martin
- Computational Biology Group, Institute of Infectious Diseases and Molecular Medicine, University of Cape Town, Cape Town 4579, South Africa; E-Mail:
| | - Philippe Biagini
- UMR CNRS 6578 Anthropologie Bioculturelle, Equipe “Emergence et co-évolution virale”, Etablissement Français du Sang Alpes-Méditerranée, Université de la Méditerranée, 27 Bd. Jean Moulin, 13005 Marseille, France; E-Mail:
| | - Pierre Lefeuvre
- CIRAD, UMR 53 PVBMT CIRAD-Université de la Réunion, Pôle de Protection des Plantes, Ligne Paradis, 97410, Saint Pierre, La Réunion, France; E-Mail:
| | - Michael Golden
- Computational Biology Group, Institute of Infectious Diseases and Molecular Medicine, University of Cape Town, Cape Town 4579, South Africa; E-Mail:
| | - Philippe Roumagnac
- CIRAD, UMR BGPI, TA A-54/K, Campus International de Montferrier-Baillarguet, 34398 Montpellier, France; E-Mail:
| | - Arvind Varsani
- Electron Microscope Unit, University of Cape Town, Rondebosch, Cape Town 7701, South Africa; E-Mail:
- Biomolecular Interaction Centre, University of Canterbury, Private Bag 4800, Christchurch 8140, New Zealand
- School of Biological Sciences, University of Canterbury, Private Bag 4800, Christchurch 8140, New Zealand
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21
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Ambivalent effects of defective DNA in beet curly top virus-infected transgenic sugarbeet plants. Virus Res 2011; 158:169-78. [PMID: 21473892 DOI: 10.1016/j.virusres.2011.03.029] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2010] [Revised: 03/29/2011] [Accepted: 03/30/2011] [Indexed: 02/02/2023]
Abstract
Beet curly top virus (BCTV) limits sugarbeet production considerably. Previous studies have shown that infections are associated with the generation of defective DNAs (D-DNA) which may attenuate symptoms. Transgenic sugarbeet lines were established carrying a partial direct repeat construct of D-DNA in order to examine whether they are useful as a means of generating tolerance against BCTV. Thirty four independent transgenic lines were challenged. Viral full-length and D-DNAs were monitored by polymerase chain reaction (PCR) or rolling circle amplification (RCA) and restriction fragment length polymorphism (RFLP). The differential accumulation of both DNA species was compared with symptom severity during the course of infection. RCA/RFLP allowed the discrimination of two D-DNA classes which were either derived from the transgenic construct (D(0)) or had been generated de novo (D(n)). The statistical analysis of the results showed that the presence of D(0)-DNA correlated with increased symptom severity, whereas D(n)-DNAs correlated with attenuated symptoms.
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22
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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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23
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Krupovic M, Ravantti JJ, Bamford DH. Geminiviruses: a tale of a plasmid becoming a virus. BMC Evol Biol 2009; 9:112. [PMID: 19460138 PMCID: PMC2702318 DOI: 10.1186/1471-2148-9-112] [Citation(s) in RCA: 92] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/02/2009] [Accepted: 05/21/2009] [Indexed: 01/21/2023] Open
Abstract
Background Geminiviruses (family Geminiviridae) are small single-stranded (ss) DNA viruses infecting plants. Their virion morphology is unique in the known viral world – two incomplete T = 1 icosahedra are joined together to form twinned particles. Geminiviruses utilize a rolling-circle mode to replicate their genomes. A limited sequence similarity between the three conserved motifs of the rolling-circle replication initiation proteins (RCR Reps) of geminiviruses and plasmids of Gram-positive bacteria allowed Koonin and Ilyina to propose that geminiviruses descend from bacterial replicons. Results Phylogenetic and clustering analyses of various RCR Reps suggest that Rep proteins of geminiviruses share a most recent common ancestor with Reps encoded on plasmids of phytoplasmas, parasitic wall-less bacteria replicating both in plant and insect cells and therefore occupying a common ecological niche with geminiviruses. Capsid protein of Satellite tobacco necrosis virus was found to be the best template for homology-based structural modeling of the geminiviral capsid protein. Good stereochemical quality of the generated models indicates that the geminiviral capsid protein shares the same structural fold, the viral jelly-roll, with the vast majority of icosahedral plant-infecting ssRNA viruses. Conclusion We propose a plasmid-to-virus transition scenario, where a phytoplasmal plasmid acquired a capsid-coding gene from a plant RNA virus to give rise to the ancestor of geminiviruses.
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Affiliation(s)
- Mart Krupovic
- Department of Biological and Environmental Sciences and Institute of Biotechnology, Biocenter 2, PO Box 56 (Viikinkaari 5), FIN-00014 University of Helsinki, Helsinki, Finland.
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24
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van der Walt E, Rybicki EP, Varsani A, Polston JE, Billharz R, Donaldson L, Monjane AL, Martin DP. Rapid host adaptation by extensive recombination. J Gen Virol 2009; 90:734-746. [PMID: 19218220 PMCID: PMC2885065 DOI: 10.1099/vir.0.007724-0] [Citation(s) in RCA: 80] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/02/2008] [Accepted: 11/18/2008] [Indexed: 11/25/2022] Open
Abstract
Experimental investigations into virus recombination can provide valuable insights into the biochemical mechanisms and the evolutionary value of this fundamental biological process. Here, we describe an experimental scheme for studying recombination that should be applicable to any recombinogenic viruses amenable to the production of synthetic infectious genomes. Our approach is based on differences in fitness that generally exist between synthetic chimaeric genomes and the wild-type viruses from which they are constructed. In mixed infections of defective reciprocal chimaeras, selection strongly favours recombinant progeny genomes that recover a portion of wild-type fitness. Characterizing these evolved progeny viruses can highlight both important genetic fitness determinants and the contribution that recombination makes to the evolution of their natural relatives. Moreover, these experiments supply precise information about the frequency and distribution of recombination breakpoints, which can shed light on the mechanistic processes underlying recombination. We demonstrate the value of this approach using the small single-stranded DNA geminivirus, maize streak virus (MSV). Our results show that adaptive recombination in this virus is extremely efficient and can yield complex progeny genomes comprising up to 18 recombination breakpoints. The patterns of recombination that we observe strongly imply that the mechanistic processes underlying rolling circle replication are the prime determinants of recombination breakpoint distributions found in MSV genomes sampled from nature.
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Affiliation(s)
- Eric van der Walt
- Department of Molecular and Cell Biology, University of Cape Town, Cape Town, South Africa
| | - Edward P. Rybicki
- Department of Molecular and Cell Biology, University of Cape Town, Cape Town, South Africa
- Institute of Infectious Disease and Molecular Medicine, University of Cape Town, Cape Town, South Africa
| | - Arvind Varsani
- Department of Molecular and Cell Biology, University of Cape Town, Cape Town, South Africa
- Electron Microscope Unit, University of Cape Town, Cape Town, South Africa
| | - J. E. Polston
- Department of Plant Pathology, University of Florida, Gainesville, FL 32611, USA
| | - Rosalind Billharz
- Department of Microbiology, University of Washington, Seattle, Washington, USA
| | - Lara Donaldson
- Department of Molecular and Cell Biology, University of Cape Town, Cape Town, South Africa
| | - Adérito L. Monjane
- Department of Molecular and Cell Biology, University of Cape Town, Cape Town, South Africa
| | - Darren P. Martin
- Institute of Infectious Disease and Molecular Medicine, University of Cape Town, Cape Town, South Africa
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25
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Qian Y, Tan Z, Liu Y, Briddon RW, Zhou X. Size reversion of a truncated DNAbeta associated with Tobacco curly shoot virus. Virus Res 2008; 131:288-92. [PMID: 17950948 DOI: 10.1016/j.virusres.2007.09.005] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2007] [Revised: 09/05/2007] [Accepted: 09/09/2007] [Indexed: 11/21/2022]
Abstract
Our previous results demonstrated that DNAbeta associated with Tobacco curly shoot virus (TbCSV) is not necessary for infection but intensifies symptoms in some hosts. To better understand the function of DNAbeta in virus infection, a betaC1 deleted infectious clone of the TbCSV DNAbeta was constructed. Agroinoculation showed that the truncated DNAbeta (DNADeltaC1beta) was trans-replicated by TbCSV in tobacco and Petunia hybrida plants. However, PCR and Southern blot analysis demonstrated that the truncated DNAbeta reverted to near wild type component size in some Nicotiana benthamiana, N. glutinosa, N. tabacum Samsun and P. hybrida plants co-inoculated with TbCSV and DNADeltaC1beta. Sequence analysis of four DNADeltaC1beta derivatives revealed that the wild type size DNAbeta molecules were recombinants between TbCSV DNAbeta and the pBinPLUS vector in which dimeric constructs were produced for inoculation. The significance of these findings is discussed with respect to the constraints imposed on begomovirus genome size.
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Affiliation(s)
- Yajuan Qian
- Institute of Biotechnology, Zhejiang University, Hangzhou 310029, PR China
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26
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Jovel J, Preiss W, Jeske H. Characterization of DNA intermediates of an arising geminivirus. Virus Res 2007; 130:63-70. [PMID: 17601624 DOI: 10.1016/j.virusres.2007.05.018] [Citation(s) in RCA: 27] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2007] [Revised: 05/15/2007] [Accepted: 05/18/2007] [Indexed: 11/21/2022]
Abstract
Weeds of the genus Sida collected in Brazil have harbored several geminiviruses persistently over decades of vegetative propagation. They serve as cradles for new geminiviruses originating from pseudorecombination (reassortment) or molecular recombination, as has been exemplified by Sida micrantha mosaic-associated viruses (SimMV). One of such viruses has developed recently and naturally by recombination between a DNA A and a DNA B of different ancestors. We used two-dimensional gel electrophoresis and hybridization to visualize viral DNA intermediates in mixed infections as well as after transfer of single viruses into test plants. DNA intermediates which indicate multitasking in replication (rolling circle and recombination-dependent replication) were readily detected in all cases. A conspicuous increase in multimerization of circular single-stranded (ss) DNA could be attributed to the recently recombined geminivirus, suggesting poor adaptation to the host and/or inefficient gene regulation. Consequences of the accumulation of multimeric ssDNA were analyzed using nucleoprotein particle purification and electron microscopy. SimMV nucleoprotein exhibited pleomorphic structures in addition to the typical twin particles. This report provides the first analysis of DNA intermediates of an arising geminivirus.
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Affiliation(s)
- Juan Jovel
- Department of Molecular Biology and Plant Virology, Institute of Biology, University of Stuttgart, Pfaffenwaldring 57, D-70550 Stuttgart, Germany.
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27
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Behjatnia SAA, Dry IB, Rezaian MA. Characterization and transient replication of tomato leaf curl virus defective DNAs. Arch Virol 2007; 152:1127-38. [PMID: 17347773 DOI: 10.1007/s00705-006-0929-2] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2006] [Accepted: 12/18/2006] [Indexed: 10/23/2022]
Abstract
Distinct subgenomic DNA species known as defective (df) DNA molecules were found in plants infected with tomato leaf curl virus (TLCV). Four df DNAs derived from TLCV Type and Darwin 1 strains were found to contain large deletions that disrupt all of the viral genes required for viral replication, encapsidation and spread. However, the viral origin of replication (ori), including the replication-associated protein (Rep) binding domains, was present in all four df DNAs. Co-agroinfection of leaf strips with tandem repeat constructs of the viral and df DNAs resulted in their replication in the presence of the respective TLCV strain. However, the df DNAs failed to move in whole plants when co-inoculated with TLCV. The df DNAs were shown to be associated with TLCV coat protein, which may indicate encapsidation. Mutational analysis showed the minimum sequence requirements for df DNA replication by TLCV to be the intergenic region containing the Rep-binding domains.
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28
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Patil BL, Dutt N, Briddon RW, Bull SE, Rothenstein D, Borah BK, Dasgupta I, Stanley J, Jeske H. Deletion and recombination events between the DNA-A and DNA-B components of Indian cassava-infecting geminiviruses generate defective molecules in Nicotiana benthamiana. Virus Res 2007; 124:59-67. [PMID: 17109983 DOI: 10.1016/j.virusres.2006.10.003] [Citation(s) in RCA: 29] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2006] [Revised: 10/05/2006] [Accepted: 10/09/2006] [Indexed: 11/17/2022]
Abstract
Cloned DNA-B components, belonging to the bipartite begomoviruses Indian cassava mosaic virus (ICMV) and Sri Lankan cassava mosaic virus (SLCMV), family Geminiviridae, when co-inoculated along with previously cloned DNA-A components of the respective viruses onto the experimental host Nicotiana benthamiana, generated defective DNAs (def-DNA) ranging in size from 549 to 1555 nucleotides. All the cloned def-DNAs contained the common region (CR) as well as portions of either DNA-A or DNA-B and, in a few cases, both DNA-A and DNA-B, representing recombinant products, the junction points of which correspond to repeats of 2-11 bases found in the parental molecules. The DNA-B-derived def-DNAs were, in some cases, associated with a decrease in levels of DNA-B, with a concomitant change in the symptoms from downward leaf curling in the older leaves to upward leaf-rolling in newly emerging leaves, more typical of monopartite begomoviruses.
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Affiliation(s)
- Basavaprabhu L Patil
- University of Delhi South Campus, Department of Plant Molecular Biology, New Delhi 110021, India
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