151
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Leal É, Villanova FE, Lin W, Hu F, Liu Q, Liu Y, Cui S. Interclade recombination in porcine parvovirus strains. J Gen Virol 2012; 93:2692-2704. [DOI: 10.1099/vir.0.045765-0] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 08/30/2023] Open
Abstract
A detailed analysis of the Ns1/Vp1Vp2 genome region of the porcine parvovirus (PPV) strains isolated from vaccinated animals was performed. We found many inconsistencies in the phylogenetic trees of these viral isolates, such as low statistical support and strains with long branches in the phylogenetic trees. Thus, we used distance-based and phylogenetic methods to distinguish de facto recombinants from spurious recombination signals. We found a mosaic virus in which the Ns1 gene was acquired from one PPV clade and the Vp1Vp2 gene was acquired from a distinct phylogenetic clade. We also described the interclade mosaic structure of the Vp1Vp2 gene of a reference strain. If recombination is an adaptive mechanism over the course of PPV evolution, we would likely observe increasing numbers of chimeric strains over time. However, when the PPV sequences isolated from 1964 to 2011 were analysed, only two chimeric strains were detected. Thus, PPV recombination is an independent event, resulting from close contact between animals housed in high-density conditions.
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Affiliation(s)
- Élcio Leal
- Federal University of Pará, Belém, Brazil
| | | | - Wencheng Lin
- Division of Swine Infectious Diseases, State Key Laboratory of Veterinary Biotechnology, Harbin Veterinary Research Institute of CAAS, Heilongjiang, PR China
| | - Feng Hu
- Division of Swine Infectious Diseases, State Key Laboratory of Veterinary Biotechnology, Harbin Veterinary Research Institute of CAAS, Heilongjiang, PR China
| | - Qinfang Liu
- Division of Swine Infectious Diseases, State Key Laboratory of Veterinary Biotechnology, Harbin Veterinary Research Institute of CAAS, Heilongjiang, PR China
| | - Yebing Liu
- China Institute of Veterinary Drug Control, Beijing 100081, PR China
| | - Shangjin Cui
- Division of Swine Infectious Diseases, State Key Laboratory of Veterinary Biotechnology, Harbin Veterinary Research Institute of CAAS, Heilongjiang, PR China
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152
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Davino S, Miozzi L, Panno S, Rubio L, Davino M, Accotto GP. Recombination profiles between Tomato yellow leaf curl virus and Tomato yellow leaf curl Sardinia virus in laboratory and field conditions: evolutionary and taxonomic implications. J Gen Virol 2012; 93:2712-2717. [DOI: 10.1099/vir.0.045773-0] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Tomato yellow leaf curl Sardinia virus and Tomato yellow leaf curl virus have co-existed in Italian tomato crops since 2002 and have reached equilibrium, with plants hosting molecules of both species plus their recombinants being the most frequent case. Recombination events are studied in field samples, as well as in experimental co-infections, when recombinants were detected as early as 45 days following inoculation. In both conditions, recombination breakpoints were essentially absent in regions corresponding to ORFs V2, CP and C4, whereas density was highest in the 3′-terminal portion of ORF C3, next to the region where the two transcription units co-terminate. The vast majority of breakpoints were mapped at antisense ORFs, supporting speculation that the rolling-circle replication mechanism, and the existence of sense and antisense ORFs on the circular genome, may result in clashes between replication and transcription complexes.
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Affiliation(s)
- Salvatore Davino
- DEMETRA Department, University of Palermo, Viale delle Scienze Ed. 5, 90100 Palermo, Italy
| | - Laura Miozzi
- Istituto di Virologia Vegetale, CNR, Strada delle Cacce 73, 10135, Torino, Italy
| | - Stefano Panno
- DEMETRA Department, University of Palermo, Viale delle Scienze Ed. 5, 90100 Palermo, Italy
| | - Luis Rubio
- Instituto Valenciano de Investigaciones Agrarias (IVIA), crt Moncada-Náquera Km 4,5, 46113 Moncada (Valencia), Spain
| | - Mario Davino
- DISPA Department, University of Catania, Via S. Sofia 100, 95100 Catania, Italy
| | - Gian Paolo Accotto
- Istituto di Virologia Vegetale, CNR, Strada delle Cacce 73, 10135, Torino, Italy
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153
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PepGMV rep-protein expression in mammalian cells. Viruses 2012; 4:1792-801. [PMID: 23170183 PMCID: PMC3499830 DOI: 10.3390/v4091792] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2012] [Revised: 09/06/2012] [Accepted: 09/06/2012] [Indexed: 11/17/2022] Open
Abstract
The Geminiviruses genome is a small, single strand DNA that replicates in the plant cell nucleus. Analogous to animal DNA viruses, Geminiviruses depend on the host replication machinery to amplify their genomes and only supply the factors required to initiate their replication. Consequently, Geminiviruses remove the cell-cycle arrest and induce the host replication machinery using an endocycle process. They encode proteins, such as the conserved replication-associated proteins (Rep) that interact with retinoblastoma-like proteins in plants and alter the cell division cycle in yeasts. Therefore, the aim of this work is to analyze the impact of Pepper Golden Mosaic Virus (PepGMV) Rep protein in mammalian cells. Results indicate that the pTracer-SV40:Rep construction obtained in this work can be used to analyze the Rep protein effect in mammalian cells in order to compare the cell cycle regulation mechanisms in plants and animals.
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154
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Rey MEC, Ndunguru J, Berrie LC, Paximadis M, Berry S, Cossa N, Nuaila VN, Mabasa KG, Abraham N, Rybicki EP, Martin D, Pietersen G, Esterhuizen LL. Diversity of dicotyledenous-infecting geminiviruses and their associated DNA molecules in southern Africa, including the South-west Indian ocean islands. Viruses 2012; 4:1753-91. [PMID: 23170182 PMCID: PMC3499829 DOI: 10.3390/v4091753] [Citation(s) in RCA: 43] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2012] [Revised: 09/04/2012] [Accepted: 09/05/2012] [Indexed: 11/16/2022] Open
Abstract
The family Geminiviridae comprises a group of plant-infecting circular ssDNA viruses that severely constrain agricultural production throughout the temperate regions of the world, and are a particularly serious threat to food security in sub-Saharan Africa. While geminiviruses exhibit considerable diversity in terms of their nucleotide sequences, genome structures, host ranges and insect vectors, the best characterised and economically most important of these viruses are those in the genus Begomovirus. Whereas begomoviruses are generally considered to be either monopartite (one ssDNA component) or bipartite (two circular ssDNA components called DNA-A and DNA-B), many apparently monopartite begomoviruses are associated with additional subviral ssDNA satellite components, called alpha- (DNA-αs) or betasatellites (DNA-βs). Additionally, subgenomic molecules, also known as defective interfering (DIs) DNAs that are usually derived from the parent helper virus through deletions of parts of its genome, are also associated with bipartite and monopartite begomoviruses. The past three decades have witnessed the emergence and diversification of various new begomoviral species and associated DI DNAs, in southern Africa, East Africa, and proximal Indian Ocean islands, which today threaten important vegetable and commercial crops such as, tobacco, cassava, tomato, sweet potato, and beans. This review aims to describe what is known about these viruses and their impacts on sustainable production in this sensitive region of the world.
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Affiliation(s)
- Marie E. C. Rey
- Department of Biochemistry, University of Johannesburg, PO Box 524, Auckland Park, 2006, Johannesburg, South Africa;
| | - Joseph Ndunguru
- Mikocheni Agricultural Research Institute, P.O. Box 6226, Dar es Salaam, Tanzania;
| | - Leigh C. Berrie
- National Institute for Communicable Diseases, Private Bag X4, Sandringham, Johannesburg, 2131, South Africa
- Department of Biochemistry, University of Johannesburg, PO Box 524, Auckland Park, 2006, Johannesburg, South Africa;
| | - Maria Paximadis
- National Institute for Communicable Diseases, Private Bag X4, Sandringham, Johannesburg, 2131, South Africa
- Department of Biochemistry, University of Johannesburg, PO Box 524, Auckland Park, 2006, Johannesburg, South Africa;
| | - Shaun Berry
- South African Sugarcane Research Institute, 170 Flanders Drive, Private Bag X02, Mount Edgecombe, 4300, South Africa
- Department of Biochemistry, University of Johannesburg, PO Box 524, Auckland Park, 2006, Johannesburg, South Africa;
| | - Nurbibi Cossa
- The Institute of Agricultural Research of Mozambique, Av. Das FPLM, No. 269 C.P. 3658, Maputo, Mozambique;
| | - Valter N. Nuaila
- Biotechnology Center, Eduardo Mondlane University, Praca 25 de Junho. Caixa, Potal 257, Maputo, Mozambique
- Department of Biochemistry, University of Johannesburg, PO Box 524, Auckland Park, 2006, Johannesburg, South Africa;
| | - Ken G. Mabasa
- Crop Protection and Diagnostic Center, ARC-Roodeplaat-VOPI, Private Bag X134, Pretoria, 0001, South Africa
- Department of Biochemistry, University of Johannesburg, PO Box 524, Auckland Park, 2006, Johannesburg, South Africa;
| | - Natasha Abraham
- Department of Biochemistry, University of Johannesburg, PO Box 524, Auckland Park, 2006, Johannesburg, South Africa;
| | - Edward P. Rybicki
- Institute of Infectious Disease and Molecular Medicine, University of Cape Town, Observatory, Cape Town, 7925, South Africa; (E.P.R.); (D.M.)
| | - Darren Martin
- Institute of Infectious Disease and Molecular Medicine, University of Cape Town, Observatory, Cape Town, 7925, South Africa; (E.P.R.); (D.M.)
| | - Gerhard Pietersen
- ARC-Plant Protection Research Institute and University of Pretoria, Private Bag X134, Pretoria, 0001, South Africa;
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155
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Sim AYL, Lipfert J, Herschlag D, Doniach S. Salt dependence of the radius of gyration and flexibility of single-stranded DNA in solution probed by small-angle x-ray scattering. PHYSICAL REVIEW. E, STATISTICAL, NONLINEAR, AND SOFT MATTER PHYSICS 2012; 86:021901. [PMID: 23005779 DOI: 10.1103/physreve.86.021901] [Citation(s) in RCA: 109] [Impact Index Per Article: 9.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/09/2012] [Indexed: 06/01/2023]
Abstract
Short single-stranded nucleic acids are ubiquitous in biological processes; understanding their physical properties provides insights to nucleic acid folding and dynamics. We used small-angle x-ray scattering to study 8-100 residue homopolymeric single-stranded DNAs in solution, without external forces or labeling probes. Poly-T's structural ensemble changes with increasing ionic strength in a manner consistent with a polyelectrolyte persistence length theory that accounts for molecular flexibility. For any number of residues, poly-A is consistently more elongated than poly-T, likely due to the tendency of A residues to form stronger base-stacking interactions than T residues.
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Affiliation(s)
- Adelene Y L Sim
- Applied Physics Department, Stanford University, Stanford, California 94305, USA
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156
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A field guide to eukaryotic circular single-stranded DNA viruses: insights gained from metagenomics. Arch Virol 2012; 157:1851-71. [DOI: 10.1007/s00705-012-1391-y] [Citation(s) in RCA: 187] [Impact Index Per Article: 15.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2012] [Accepted: 05/16/2012] [Indexed: 10/28/2022]
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157
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Hadfield J, Thomas JE, Schwinghamer MW, Kraberger S, Stainton D, Dayaram A, Parry JN, Pande D, Martin DP, Varsani A. Molecular characterisation of dicot-infecting mastreviruses from Australia. Virus Res 2012; 166:13-22. [PMID: 22406325 DOI: 10.1016/j.virusres.2012.02.024] [Citation(s) in RCA: 37] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2011] [Revised: 02/16/2012] [Accepted: 02/20/2012] [Indexed: 11/24/2022]
Abstract
Monocotyledonous and dicotyledonous plant infecting mastreviruses threaten various agricultural systems throughout Africa, Eurasia and Australasia. In Australia three distinct mastrevirus species are known to infect dicotyledonous hosts such as chickpea, bean and tobacco. Amongst 34 new "dicot-infecting" mastrevirus full genome sequences obtained from these hosts we discovered one new species, four new strains, and various variants of previously described mastrevirus species. Besides providing additional support for the hypothesis that evolutionary processes operating during dicot-infecting mastrevirus evolution (such as patterns of pervasive homologous and non-homologous recombination, and strong purifying selection acting on all genes) have mostly mirrored those found in their monocot-infecting counterparts, we find that the Australian dicot-infecting viruses display patterns of phylogeographic clustering reminiscent of those displayed by monocot infecting mastrevirus species such as Panicum streak virus and Maize streak virus.
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Affiliation(s)
- James Hadfield
- School of Biological Sciences, University of Canterbury, Ilam, Christchurch 8140, New Zealand
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158
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Stainton D, Kraberger S, Walters M, Wiltshire EJ, Rosario K, Halafihi M, Lolohea S, Katoa I, Faitua TH, Aholelei W, Taufa L, Thomas JE, Collings DA, Martin DP, Varsani A. Evidence of inter-component recombination, intra-component recombination and reassortment in banana bunchy top virus. J Gen Virol 2012; 93:1103-1119. [PMID: 22278830 DOI: 10.1099/vir.0.040337-0] [Citation(s) in RCA: 35] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Banana bunchy top virus (BBTV; family Nanoviridae, genus Babuvirus) is a multi-component, ssDNA virus, which causes widespread banana crop losses throughout tropical Africa and Australasia. We determined the full genome sequences of 12 BBTV isolates from the Kingdom of Tonga and analysed these together with previously determined BBTV sequences to show that reassortment and both inter- and intra-component recombination have all been relatively frequent occurrences during BBTV evolution. We found that whereas DNA-U3 components display evidence of complex inter- and intra-component recombination, all of the South Pacific DNA-R components have a common intra-component recombinant origin spanning the replication-associated protein gene. Altogether, the DNA-U3 and DNA-M components display a greater degree of inter-component recombination than the DNA-R, -S, -C and -M components. The breakpoint distribution of the inter-component recombination events reveals a primary recombination hotspot around the 5' side of the common region major and, in accordance with recombination hotspots detectable in related ssDNA viruses, a secondary recombination hotspot near the origin of virion-strand replication.
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Affiliation(s)
- Daisy Stainton
- School of Biological Sciences, University of Canterbury, Christchurch 8140, New Zealand
| | - Simona Kraberger
- School of Biological Sciences, University of Canterbury, Christchurch 8140, New Zealand
| | - Matthew Walters
- School of Biological Sciences, University of Canterbury, Christchurch 8140, New Zealand
| | - Elizabeth J Wiltshire
- School of Biological Sciences, University of Canterbury, Christchurch 8140, New Zealand
| | - Karyna Rosario
- College of Marine Science, University of South Florida, St Petersburg, FL 33701, USA
| | - Mana'ia Halafihi
- Ministry of Agriculture and Food, Forests and Fisheries, Nuku'alofa, Tongatapu, Kingdom of Tonga
| | | | - Ika Katoa
- Ministry of Agriculture and Food, Forests and Fisheries, Nuku'alofa, Tongatapu, Kingdom of Tonga
| | | | - Waikato Aholelei
- Ministry of Agriculture and Food, Forests and Fisheries, Nuku'alofa, Tongatapu, Kingdom of Tonga
| | - Luseane Taufa
- Ministry of Agriculture and Food, Forests and Fisheries, Nuku'alofa, Tongatapu, Kingdom of Tonga
| | - John E Thomas
- The University of Queensland, Centre for Plant Science, Queensland Alliance for Agriculture and Food Innovation, Ecosciences Precinct, PO Box 46, Brisbane QLD 4001, Australia
| | - David A Collings
- Biomolecular Interaction Centre, University of Canterbury, Christchurch 8140, New Zealand.,School of Biological Sciences, University of Canterbury, Christchurch 8140, New Zealand
| | - Darren P Martin
- Computational Biology Group, Institute of Infectious Diseases and Molecular Medicine, University of Cape Town, Cape Town, South Africa
| | - Arvind Varsani
- Electron Microscope Unit, University of Cape Town, Rondebosch 7701, Cape Town, South Africa.,Biomolecular Interaction Centre, University of Canterbury, Christchurch 8140, New Zealand.,School of Biological Sciences, University of Canterbury, Christchurch 8140, New Zealand
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