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Shakir S, Mubin M, Nahid N, Serfraz S, Qureshi MA, Lee TK, Liaqat I, Lee S, Nawaz-ul-Rehman MS. REPercussions: how geminiviruses recruit host factors for replication. Front Microbiol 2023; 14:1224221. [PMID: 37799604 PMCID: PMC10548238 DOI: 10.3389/fmicb.2023.1224221] [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: 05/22/2023] [Accepted: 08/21/2023] [Indexed: 10/07/2023] Open
Abstract
Circular single-stranded DNA viruses of the family Geminiviridae encode replication-associated protein (Rep), which is a multifunctional protein involved in virus DNA replication, transcription of virus genes, and suppression of host defense responses. Geminivirus genomes are replicated through the interaction between virus Rep and several host proteins. The Rep also interacts with itself and the virus replication enhancer protein (REn), which is another essential component of the geminivirus replicase complex that interacts with host DNA polymerases α and δ. Recent studies revealed the structural and functional complexities of geminivirus Rep, which is believed to have evolved from plasmids containing a signature domain (HUH) for single-stranded DNA binding with nuclease activity. The Rep coding sequence encompasses the entire coding sequence for AC4, which is intricately embedded within it, and performs several overlapping functions like Rep, supporting virus infection. This review investigated the structural and functional diversity of the geminivirus Rep.
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Affiliation(s)
- Sara Shakir
- Plant Genetics Lab, Gembloux Agro-Bio Tech, University of Liѐge, Gembloux, Belgium
| | - Muhammad Mubin
- Virology Lab, Center for Agricultural Biochemistry and Biotechnology, University of Agriculture, Faisalabad, Faisalabad, Pakistan
| | - Nazia Nahid
- Department of Bioinformatics and Biotechnology, Government College University, Faisalabad, Pakistan
| | - Saad Serfraz
- Virology Lab, Center for Agricultural Biochemistry and Biotechnology, University of Agriculture, Faisalabad, Faisalabad, Pakistan
| | - Muhammad Amir Qureshi
- Department of Integrative Biotechnology, Sungkyunkwan University, Suwon, Republic of Korea
| | - Taek-Kyun Lee
- Risk Assessment Research Center, Korea Institute of Ocean Science and Technology, Geoje, Republic of Korea
| | - Iram Liaqat
- Microbiology Lab, Department of Zoology, Government College University, Lahore, Pakistan
| | - Sukchan Lee
- Department of Integrative Biotechnology, Sungkyunkwan University, Suwon, Republic of Korea
| | - Muhammad Shah Nawaz-ul-Rehman
- Virology Lab, Center for Agricultural Biochemistry and Biotechnology, University of Agriculture, Faisalabad, Faisalabad, Pakistan
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Qin Y, Zhao J, Wang J, Ye X, Zhou C, Zhou Y. Regulation of Nicotiana benthamiana cell death induced by citrus chlorotic dwarf-associated virus-RepA protein by WRKY 1. FRONTIERS IN PLANT SCIENCE 2023; 14:1164416. [PMID: 37180388 PMCID: PMC10167294 DOI: 10.3389/fpls.2023.1164416] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 02/12/2023] [Accepted: 04/10/2023] [Indexed: 05/16/2023]
Abstract
Citrus chlorotic dwarf-associated virus (CCDaV) is a Citlodavirus species in the Geminiviridae family that causes tremendous economic loss to the citrus industry in China. Some proteins encoded by geminiviruses are crucial for the interaction between the virus and its host plant. However, the exact functions of CCDaV-encoded proteins such as CCDaV-RepA have not been investigated. This study presents evidence that CCDaV-RepA elicits a hypersensitive response (HR)-like cell death in Nicotiana benthamiana that was accompanied by the production of H2O2 and ion leakage, which suggested that CCDaV-RepA is a potential recognition target for inducing host defense responses. Furthermore, the rolling-circle replication motifs of CCDaV-RepA are associated with triggering HR-like cell death in N. benthamiana. Confocal microscopy and deletion mutagenesis assays showed that CCDaV-RepA was located in the nucleus, while the first eight amino acids (aa) at the N terminus and two regions located between aa residues 122-263 and 220-264 of RepA were not associated with nuclear localization. Tobacco rattle virus-induced gene silencing of the key signaling cascade components revealed that HR-like cell death induced by RepA was inhibited in WRKY1-silenced N. benthamiana. Moreover, WRKY1 expression was upregulated in RepA-GFP infiltrated Overall, the results suggest that NbWRKY1 positively regulated CCDaV-RepA -induced cell death in N. benthamiana. These findings provide novel information for further research on the interactions between CCDaV and the host plant.
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Affiliation(s)
| | | | | | | | | | - Yan Zhou
- National Citrus Engineering Research Center, Citrus Research Institute, Southwest University, Chongqing, China
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Mastrevirus Rep and RepA Proteins Suppress de novo Transcriptional Gene Silencing. Int J Mol Sci 2021; 22:ijms222111462. [PMID: 34768892 PMCID: PMC8584122 DOI: 10.3390/ijms222111462] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2021] [Revised: 10/13/2021] [Accepted: 10/19/2021] [Indexed: 01/13/2023] Open
Abstract
Transcriptional gene silencing (TGS) in plants is a defense mechanism against DNA virus infection. The genomes of viruses in the Geminiviridae family encode several TGS suppressors. In this study, we induced de novo TGS against the transgenic GFP gene encoding green fluorescent protein by expressing a hairpin-shaped self-complementary RNA corresponding to the enhancer region of the 35S promoter (hpE35S). In addition, we examined the TGS suppression activity of proteins encoded in the genome of Tobacco yellow dwarf virus (TYDV, genus Mastrevirus). The results show that the replication-associated protein (Rep) and RepA encoded by TYDV have TGS suppressor activity and lead to decreased accumulation of 24-nt siRNAs. These results suggest that Rep and RepA can block the steps before the loading of siRNAs into Argonaute (AGO) proteins. This is the first report of TGS suppressors in the genus Mastrevirus.
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Abstract
Single-stranded (ss)DNA viruses are extremely widespread, infect diverse hosts from all three domains of life and include important pathogens. Most ssDNA viruses possess small genomes that replicate by the rolling-circle-like mechanism initiated by a distinct virus-encoded endonuclease. High throughput genome sequencing and improved bioinformatics tools have yielded vast information on presence of ssDNA viruses in diverse habitats. The simple genome of ssDNA viruses have high propensity to undergo mutation and recombination often emerging as threat to human civilization. Interestingly their genome is found embedded in fossils dating back to million years. The unusual evolutionary history of ssDNA viruses reveal evidences of horizontal gene transfer, sometimes between different species and genera.
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Zhao L, Rosario K, Breitbart M, Duffy S. Eukaryotic Circular Rep-Encoding Single-Stranded DNA (CRESS DNA) Viruses: Ubiquitous Viruses With Small Genomes and a Diverse Host Range. Adv Virus Res 2018; 103:71-133. [PMID: 30635078 DOI: 10.1016/bs.aivir.2018.10.001] [Citation(s) in RCA: 128] [Impact Index Per Article: 21.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Abstract
While single-stranded DNA (ssDNA) was once thought to be a relatively rare genomic architecture for viruses, modern metagenomics sequencing has revealed circular ssDNA viruses in most environments and in association with diverse hosts. In particular, circular ssDNA viruses encoding a homologous replication-associated protein (Rep) have been identified in the majority of eukaryotic supergroups, generating interest in the ecological effects and evolutionary history of circular Rep-encoding ssDNA viruses (CRESS DNA) viruses. This review surveys the explosion of sequence diversity and expansion of eukaryotic CRESS DNA taxonomic groups over the last decade, highlights similarities between the well-studied geminiviruses and circoviruses with newly identified groups known only through their genome sequences, discusses the ecology and evolution of eukaryotic CRESS DNA viruses, and speculates on future research horizons.
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Affiliation(s)
- Lele Zhao
- Department of Ecology, Evolution and Natural Resources, Rutgers, the State University of New Jersey, New Brunswick, NJ, United States
| | - Karyna Rosario
- College of Marine Science, University of South Florida, Saint Petersburg, FL, United States
| | - Mya Breitbart
- College of Marine Science, University of South Florida, Saint Petersburg, FL, United States
| | - Siobain Duffy
- Department of Ecology, Evolution and Natural Resources, Rutgers, the State University of New Jersey, New Brunswick, NJ, United States.
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6
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Borah B, Zarreen F, Baruah G, Dasgupta I. Insights into the control of geminiviral promoters. Virology 2016; 495:101-11. [DOI: 10.1016/j.virol.2016.04.033] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2016] [Revised: 04/26/2016] [Accepted: 04/27/2016] [Indexed: 10/21/2022]
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Fahmy IF, Taha O, El-Ashry AN. First genome analysis and molecular characterization of Chickpea chlorotic dwarf virus Egyptian isolate infecting squash. Virusdisease 2015; 26:33-41. [PMID: 26436119 PMCID: PMC4585055 DOI: 10.1007/s13337-014-0246-4] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2014] [Accepted: 12/29/2014] [Indexed: 10/24/2022] Open
Abstract
This study aims to identifying and characterizing some molecular properties of geminiviruses co-infection in squash field crop cultivated in Egypt. Squash crops observed to be heavily infected with several insect vectors, also severe chlorosis and stunting was observed. Electron microscopic analysis has revealed geminate capsid particles which indicate the infection of Geminiviruses, especially SqLCV which represent an economic problem to squash filed crop in Egypt. We have investigated possible mixed infections with different plant viruses associated with chlorotic stunt diseases and or other genus groups of geminiviruses. The main objective of this study is to investigate the recombination events, possible recombinants and variants among these genera in the same family differing in vector transmission. This is the first report of the molecular characterization, phylogenetic analysis and putative recombination events of the full length genome of the Chickpea Chlorotic Dwarf Mastrevirus in Egypt. And the first report of co-infection with another begomovirus infecting squash plants. A full length clone of both viruses were isolated and characterized at the molecular level. The complete nucleotide sequence of DNA-A was determined (2,572 bp) and submitted to the genbank under accession no. KF692356. The isolate from Egypt has about 97.8 % homology with the Chickpea chlorotic dwarf virus (CpCDV) isolate from Syria DNA-A isolate FR687959, a 83.2 % homology with the Sudan isolate AM933134 and a 82.7 % homology with Pakistan isolate FR687960. To best of our knowledge this is the first report of complete genome of CpCDV that infect squash plants in Egypt and worldwide.
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Affiliation(s)
- Inas Farouk Fahmy
- />Phytopathogen Vector Interaction Lab, Department of Microbiology, Agricultural Research Center (ARC), Agricultural Genetic Engineering Research Institute, Giza, Egypt
| | - Omnia Taha
- />Phytopathogen Vector Interaction Lab, Department of Microbiology, Agricultural Research Center (ARC), Agricultural Genetic Engineering Research Institute, Giza, Egypt
| | - Abdel Nasser El-Ashry
- />Department of Plant Pathology, Faculty of Agriculture, Institute fuer Nutzpflanzenwissenschaften und Ressourcen Schutz, University of Bonn, Bonn, Germany
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8
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Baltes NJ, Gil-Humanes J, Cermak T, Atkins PA, Voytas DF. DNA replicons for plant genome engineering. THE PLANT CELL 2014; 26:151-63. [PMID: 24443519 PMCID: PMC3963565 DOI: 10.1105/tpc.113.119792] [Citation(s) in RCA: 319] [Impact Index Per Article: 31.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/21/2013] [Revised: 12/08/2013] [Accepted: 12/18/2013] [Indexed: 05/17/2023]
Abstract
Sequence-specific nucleases enable facile editing of higher eukaryotic genomic DNA; however, targeted modification of plant genomes remains challenging due to ineffective methods for delivering reagents for genome engineering to plant cells. Here, we use geminivirus-based replicons for transient expression of sequence-specific nucleases (zinc-finger nucleases, transcription activator-like effector nucleases, and the clustered, regularly interspaced, short palindromic repeat/Cas system) and delivery of DNA repair templates. In tobacco (Nicotiana tabacum), replicons based on the bean yellow dwarf virus enhanced gene targeting frequencies one to two orders of magnitude over conventional Agrobacterium tumefaciens T-DNA. In addition to the nuclease-mediated DNA double-strand breaks, gene targeting was promoted by replication of the repair template and pleiotropic activity of the geminivirus replication initiator proteins. We demonstrate the feasibility of using geminivirus replicons to generate plants with a desired DNA sequence modification. By adopting a general plant transformation method, plantlets with a desired DNA change were regenerated in <6 weeks. These results, in addition to the large host range of geminiviruses, advocate the use of replicons for plant genome engineering.
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Affiliation(s)
- Nicholas J. Baltes
- Department of Genetics, Cell Biology, and Development, Center for Genome Engineering, University of Minnesota, Minneapolis, Minnesota 55455
| | - Javier Gil-Humanes
- Department of Genetics, Cell Biology, and Development, Center for Genome Engineering, University of Minnesota, Minneapolis, Minnesota 55455
| | - Tomas Cermak
- Department of Genetics, Cell Biology, and Development, Center for Genome Engineering, University of Minnesota, Minneapolis, Minnesota 55455
| | - Paul A. Atkins
- Department of Genetics, Cell Biology, and Development, Center for Genome Engineering, University of Minnesota, Minneapolis, Minnesota 55455
| | - Daniel F. Voytas
- Department of Genetics, Cell Biology, and Development, Center for Genome Engineering, University of Minnesota, Minneapolis, Minnesota 55455
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Evidence of pervasive biologically functional secondary structures within the genomes of eukaryotic single-stranded DNA viruses. J Virol 2013; 88:1972-89. [PMID: 24284329 DOI: 10.1128/jvi.03031-13] [Citation(s) in RCA: 31] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022] Open
Abstract
Single-stranded DNA (ssDNA) viruses have genomes that are potentially capable of forming complex secondary structures through Watson-Crick base pairing between their constituent nucleotides. A few of the structural elements formed by such base pairings are, in fact, known to have important functions during the replication of many ssDNA viruses. Unknown, however, are (i) whether numerous additional ssDNA virus genomic structural elements predicted to exist by computational DNA folding methods actually exist and (ii) whether those structures that do exist have any biological relevance. We therefore computationally inferred lists of the most evolutionarily conserved structures within a diverse selection of animal- and plant-infecting ssDNA viruses drawn from the families Circoviridae, Anelloviridae, Parvoviridae, Nanoviridae, and Geminiviridae and analyzed these for evidence of natural selection favoring the maintenance of these structures. While we find evidence that is consistent with purifying selection being stronger at nucleotide sites that are predicted to be base paired than at sites predicted to be unpaired, we also find strong associations between sites that are predicted to pair with one another and site pairs that are apparently coevolving in a complementary fashion. Collectively, these results indicate that natural selection actively preserves much of the pervasive secondary structure that is evident within eukaryote-infecting ssDNA virus genomes and, therefore, that much of this structure is biologically functional. Lastly, we provide examples of various highly conserved but completely uncharacterized structural elements that likely have important functions within some of the ssDNA virus genomes analyzed here.
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Abstract
Geminiviruses are a family of plant viruses that cause economically important plant diseases worldwide. These viruses have circular single-stranded DNA genomes and four to eight genes that are expressed from both strands of the double-stranded DNA replicative intermediate. The transcription of these genes occurs under the control of two bidirectional promoters and one monodirectional promoter. The viral proteins function to facilitate virus replication, virus movement, the assembly of virus-specific nucleoprotein particles, vector transmission and to counteract plant host defence responses. Recent research findings have provided new insights into the structure and function of these proteins and have identified numerous host interacting partners. Most of the viral proteins have been shown to be multifunctional, participating in multiple events during the infection cycle and have, indeed, evolved coordinated interactions with host proteins to ensure a successful infection. Here, an up-to-date review of viral protein structure and function is presented, and some areas requiring further research are identified.
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Affiliation(s)
- Vincent N Fondong
- Department of Biological Sciences, Delaware State University, 1200 North DuPont Highway, Dover, DE 19901, USA.
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11
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Ruschhaupt M, Martin DP, Lakay F, Bezuidenhout M, Rybicki EP, Jeske H, Shepherd DN. Replication modes of Maize streak virus mutants lacking RepA or the RepA-pRBR interaction motif. Virology 2013; 442:173-9. [PMID: 23679984 DOI: 10.1016/j.virol.2013.04.012] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2013] [Revised: 04/08/2013] [Accepted: 04/16/2013] [Indexed: 11/16/2022]
Abstract
The plant-infecting mastreviruses (family Geminiviridae) express two distinct replication-initiator proteins, Rep and RepA. Although RepA is essential for systemic infectivity, little is known about its precise function. We therefore investigated its role in replication using 2D-gel electrophoresis to discriminate the replicative forms of Maize streak virus (MSV) mutants that either fail to express RepA (RepA(-)), or express RepA that is unable to bind the plant retinoblastoma related protein, pRBR. Whereas amounts of viral DNA were reduced in two pRBR-binding deficient RepA mutants, their repertoires of replicative forms changed only slightly. While a complete lack of RepA expression was also associated with reduced viral DNA titres, the only traces of replicative intermediates of RepA(-) viruses were those indicative of recombination-dependent replication. We conclude that in MSV, RepA, but not RepA-pRBR binding, is necessary for single-stranded DNA production and efficient rolling circle replication.
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Affiliation(s)
- Moritz Ruschhaupt
- Department of Molecular Biology and Plant Virology, Institute of Biology, University of Stuttgart, Pfaffenwaldring 57, Stuttgart, Germany
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12
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Monjane AL, Pande D, Lakay F, Shepherd DN, van der Walt E, Lefeuvre P, Lett JM, Varsani A, Rybicki EP, Martin DP. Adaptive evolution by recombination is not associated with increased mutation rates in Maize streak virus. BMC Evol Biol 2012; 12:252. [PMID: 23268599 PMCID: PMC3556111 DOI: 10.1186/1471-2148-12-252] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2012] [Accepted: 12/12/2012] [Indexed: 12/29/2022] Open
Abstract
BACKGROUND Single-stranded (ss) DNA viruses in the family Geminiviridae are proving to be very useful in real-time evolution studies. The high mutation rate of geminiviruses and other ssDNA viruses is somewhat mysterious in that their DNA genomes are replicated in host nuclei by high fidelity host polymerases. Although strand specific mutation biases observed in virus species from the geminivirus genus Mastrevirus indicate that the high mutation rates in viruses in this genus may be due to mutational processes that operate specifically on ssDNA, it is currently unknown whether viruses from other genera display similar strand specific mutation biases. Also, geminivirus genomes frequently recombine with one another and an alternative cause of their high mutation rates could be that the recombination process is either directly mutagenic or produces a selective environment in which the survival of mutants is favoured. To investigate whether there is an association between recombination and increased basal mutation rates or increased degrees of selection favoring the survival of mutations, we compared the mutation dynamics of the MSV-MatA and MSV-VW field isolates of Maize streak virus (MSV; Mastrevirus), with both a laboratory constructed MSV recombinant, and MSV recombinants closely resembling MSV-MatA. To determine whether strand specific mutation biases are a general characteristic of geminivirus evolution we compared mutation spectra arising during these MSV experiments with those arising during similar experiments involving the geminivirus Tomato yellow leaf curl virus (Begomovirus genus). RESULTS Although both the genomic distribution of mutations and the occurrence of various convergent mutations at specific genomic sites indicated that either mutation hotspots or selection for adaptive mutations might elevate observed mutation rates in MSV, we found no association between recombination and mutation rates. Importantly, when comparing the mutation spectra of MSV and TYLCV we observed similar strand specific mutation biases arising predominantly from imbalances in the complementary mutations G → T: C → A. CONCLUSIONS While our results suggest that recombination does not strongly influence mutation rates in MSV, they indicate that high geminivirus mutation rates are at least partially attributable to increased susceptibility of all geminivirus genomes to oxidative damage while in a single stranded state.
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Affiliation(s)
- Adérito L Monjane
- Department of Molecular and Cell Biology, University of Cape Town, Rondebosch, Cape Town 7701, South Africa
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13
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Monjane AL, van der Walt E, Varsani A, Rybicki EP, Martin DP. Recombination hotspots and host susceptibility modulate the adaptive value of recombination during maize streak virus evolution. BMC Evol Biol 2011; 11:350. [PMID: 22136133 PMCID: PMC3280948 DOI: 10.1186/1471-2148-11-350] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2011] [Accepted: 12/02/2011] [Indexed: 02/05/2023] Open
Abstract
BACKGROUND Maize streak virus -strain A (MSV-A; Genus Mastrevirus, Family Geminiviridae), the maize-adapted strain of MSV that causes maize streak disease throughout sub-Saharan Africa, probably arose between 100 and 200 years ago via homologous recombination between two MSV strains adapted to wild grasses. MSV recombination experiments and analyses of natural MSV recombination patterns have revealed that this recombination event entailed the exchange of the movement protein - coat protein gene cassette, bounded by the two genomic regions most prone to recombination in mastrevirus genomes; the first surrounding the virion-strand origin of replication, and the second around the interface between the coat protein gene and the short intergenic region. Therefore, aside from the likely adaptive advantages presented by a modular exchange of this cassette, these specific breakpoints may have been largely predetermined by the underlying mechanisms of mastrevirus recombination. To investigate this hypothesis, we constructed artificial, low-fitness, reciprocal chimaeric MSV genomes using alternating genomic segments from two MSV strains; a grass-adapted MSV-B, and a maize-adapted MSV-A. Between them, each pair of reciprocal chimaeric genomes represented all of the genetic material required to reconstruct - via recombination - the highly maize-adapted MSV-A genotype, MSV-MatA. We then co-infected a selection of differentially MSV-resistant maize genotypes with pairs of reciprocal chimaeras to determine the efficiency with which recombination would give rise to high-fitness progeny genomes resembling MSV-MatA. RESULTS Recombinants resembling MSV-MatA invariably arose in all of our experiments. However, the accuracy and efficiency with which the MSV-MatA genotype was recovered across all replicates of each experiment depended on the MSV susceptibility of the maize genotypes used and the precise positions - in relation to known recombination hotspots - of the breakpoints required to re-create MSV-MatA. Although the MSV-sensitive maize genotype gave rise to the greatest variety of recombinants, the measured fitness of each of these recombinants correlated with their similarity to MSV-MatA. CONCLUSIONS The mechanistic predispositions of different MSV genomic regions to recombination can strongly influence the accessibility of high-fitness MSV recombinants. The frequency with which the fittest recombinant MSV genomes arise also correlates directly with the escalating selection pressures imposed by increasingly MSV-resistant maize hosts.
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Affiliation(s)
- Adérito L Monjane
- Department of Molecular and Cell Biology, University of Cape Town, Rondebosch, 7701, Cape Town, South Africa
| | | | - Arvind Varsani
- 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
- Electron Microscope Unit, University of Cape Town, Rondebosch, 7701, Cape Town, South Africa
| | - Edward P Rybicki
- Department of Molecular and Cell Biology, University of Cape Town, Rondebosch, 7701, Cape Town, South Africa
- Computational Biology Group, Institute of Infectious Disease and Molecular Medicine, University of Cape Town, Observatory, 7925, Cape Town, South Africa
| | - Darren P Martin
- Computational Biology Group, Institute of Infectious Disease and Molecular Medicine, University of Cape Town, Observatory, 7925, Cape Town, South Africa
- Centre for High-Performance Computing, Rosebank, Cape Town, South Africa
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14
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Monjane AL, Harkins GW, Martin DP, Lemey P, Lefeuvre P, Shepherd DN, Oluwafemi S, Simuyandi M, Zinga I, Komba EK, Lakoutene DP, Mandakombo N, Mboukoulida J, Semballa S, Tagne A, Tiendrébéogo F, Erdmann JB, van Antwerpen T, Owor BE, Flett B, Ramusi M, Windram OP, Syed R, Lett JM, Briddon RW, Markham PG, Rybicki EP, Varsani A. Reconstructing the history of maize streak virus strain a dispersal to reveal diversification hot spots and its origin in southern Africa. J Virol 2011; 85:9623-36. [PMID: 21715477 PMCID: PMC3165777 DOI: 10.1128/jvi.00640-11] [Citation(s) in RCA: 52] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2011] [Accepted: 06/21/2011] [Indexed: 01/11/2023] Open
Abstract
Maize streak virus strain A (MSV-A), the causal agent of maize streak disease, is today one of the most serious biotic threats to African food security. Determining where MSV-A originated and how it spread transcontinentally could yield valuable insights into its historical emergence as a crop pathogen. Similarly, determining where the major extant MSV-A lineages arose could identify geographical hot spots of MSV evolution. Here, we use model-based phylogeographic analyses of 353 fully sequenced MSV-A isolates to reconstruct a plausible history of MSV-A movements over the past 150 years. We show that since the probable emergence of MSV-A in southern Africa around 1863, the virus spread transcontinentally at an average rate of 32.5 km/year (95% highest probability density interval, 15.6 to 51.6 km/year). Using distinctive patterns of nucleotide variation caused by 20 unique intra-MSV-A recombination events, we tentatively classified the MSV-A isolates into 24 easily discernible lineages. Despite many of these lineages displaying distinct geographical distributions, it is apparent that almost all have emerged within the past 4 decades from either southern or east-central Africa. Collectively, our results suggest that regular analysis of MSV-A genomes within these diversification hot spots could be used to monitor the emergence of future MSV-A lineages that could affect maize cultivation in Africa.
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Affiliation(s)
- Adérito L. Monjane
- Department of Molecular and Cell Biology, University of Cape Town, Rondebosch, 7701, Cape Town, South Africa
| | - Gordon W. Harkins
- South African National Bioinformatics Institute, University of the Western Cape, Cape Town, South Africa
| | - Darren P. Martin
- Institute of Infectious Disease and Molecular Medicine, University of Cape Town, Observatory, 7925, Cape Town, South Africa
- Centre for High-Performance Computing, Rosebank, Cape Town, South Africa
| | - Philippe Lemey
- Department of Microbiology and Immunology, Rega Institute, K.U. Leuven, Leuven, Belgium
| | - Pierre Lefeuvre
- Institute of Infectious Disease and Molecular Medicine, University of Cape Town, Observatory, 7925, Cape Town, South Africa
- CIRAD, UMR 53 PVBMT CIRAD-Université de la Réunion, Pôle de Protection des Plantes, 97410, Saint Pierre, La Réunion, France
| | - Dionne N. Shepherd
- Department of Molecular and Cell Biology, University of Cape Town, Rondebosch, 7701, Cape Town, South Africa
| | - Sunday Oluwafemi
- Department of Crop Production, Soil and Environmental Management, Bowen University, Iwo, Osun State, P.M.B. 284, Nigeria
| | | | - Innocent Zinga
- LASBAD Laboratory, Faculty of Sciences, University of Bangui, BP 908 Bangui, Central African Republic
| | - Ephrem K. Komba
- LASBAD Laboratory, Faculty of Sciences, University of Bangui, BP 908 Bangui, Central African Republic
| | - Didier P. Lakoutene
- LASBAD Laboratory, Faculty of Sciences, University of Bangui, BP 908 Bangui, Central African Republic
| | - Noella Mandakombo
- LASBAD Laboratory, Faculty of Sciences, University of Bangui, BP 908 Bangui, Central African Republic
| | - Joseph Mboukoulida
- LASBAD Laboratory, Faculty of Sciences, University of Bangui, BP 908 Bangui, Central African Republic
| | - Silla Semballa
- LASBAD Laboratory, Faculty of Sciences, University of Bangui, BP 908 Bangui, Central African Republic
| | - Appolinaire Tagne
- Cereals Research Program, Institute of Agricultural Research for Development, Box 2067 Messa, Yaounde, Cameroon
| | - Fidèle Tiendrébéogo
- Centre de Recherche en Sciences Biologiques Alimentaires et Nutritionnelles (CRSBAN), UFR/SVT Université de Ouagadougou, 03 BP 7131 Ouagadougou 03, Burkina Faso
| | - Julia B. Erdmann
- Department of Molecular and Cell Biology, University of Cape Town, Rondebosch, 7701, Cape Town, South Africa
- Institute of Biology, Department of Molecular Biology and Plant Virology, University of Stuttgart, Pfaffenwaldring 57, D-70550 Stuttgart, Germany
| | - Tania van Antwerpen
- South African Sugarcane Research Institute, Mount Edgecombe, KwaZulu Natal, South Africa
| | - Betty E. Owor
- Department of Molecular and Cell Biology, University of Cape Town, Rondebosch, 7701, Cape Town, South Africa
- Department of Plant Sciences, University of Cambridge, Cambridge, United Kingdom, CB2 3EA
| | - Bradley Flett
- Crop Protection, ARC-Grain Crops Institute, Potchefstroom 2520, South Africa
| | - Moses Ramusi
- Crop Protection, ARC-Grain Crops Institute, Potchefstroom 2520, South Africa
| | - Oliver P. Windram
- Warwick HRI Biology Centre, University of Warwick, Wellesbourne, CV35 9EF, England
| | - Rizwan Syed
- Department of Molecular and Cell Biology, University of Cape Town, Rondebosch, 7701, Cape Town, South Africa
| | - Jean-Michel Lett
- CIRAD, UMR 53 PVBMT CIRAD-Université de la Réunion, Pôle de Protection des Plantes, 97410, Saint Pierre, La Réunion, France
| | - Rob W. Briddon
- National Institute for Biotechnology and Genetic Engineering, Jhang Road, P.O. Box 577, Faisalabad, Pakistan
| | - Peter G. Markham
- Department of Disease and Stress Biology, John Innes Centre, Norwich NR4 7UH, United Kingdom
| | - Edward P. Rybicki
- Department of Molecular and Cell Biology, University of Cape Town, Rondebosch, 7701, Cape Town, South Africa
- Institute of Infectious Disease and Molecular Medicine, University of Cape Town, Observatory, 7925, Cape Town, South Africa
| | - Arvind Varsani
- 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
- Electron Microscope Unit, University of Cape Town, Rondebosch, 7701, Cape Town, South Africa
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Collens JI, Mason HS, Curtis WR. Agrobacterium-mediated viral vector-amplified transient gene expression in Nicotiana glutinosa plant tissue culture. Biotechnol Prog 2007; 23:570-6. [PMID: 17425328 DOI: 10.1021/bp060342u] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/25/2023]
Abstract
A viral vector based on the bean yellow dwarf virus was investigated for its potential to increase transient gene expression. An intron-containing GUS reporter gene and the cis-acting viral regulatory elements were incorporated in the viral vector and could be complemented by the viral replication-associated proteins provided on a secondary vector. All vectors were delivered to Nicotiana glutinosa plant cell suspension or hairy root cultures via auxotrophic Agrobacterium tumefaciens. Cell culture generated greater yield of reporter gene expression than did root culture, as a result of the limitation imposed on roots to express the protein only in surface tissue containing actively dividing cells. Reporter gene expression increased for cell culture when the reporter gene construct was co-delivered with the construct supplying both viral replication associated proteins (REP and REPA); gene expression decreased when the construct supplying only the viral REP protein was co-delivered. Reporter protein expression increased from 0.091% for the reporter construct alone to 0.22% total soluble protein (% TSP) when the viral Rep-supplying vector was co-delivered with the reporter gene construct. Reporter protein was generated 3 days after the initiation of bacterial co-culture, providing for rapid generation of heterologous protein in cell culture.
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Affiliation(s)
- Jason I Collens
- Department of Chemical Engineering, The Pennsylvania State University, University Park, Pennsylvania 16802, USA
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