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Ketsela D, Oyeniran KA, Feyissa B, Fontenele RS, Kraberger S, Varsani A. Molecular identification and phylogenetic characterization of A-strain isolates of maize streak virus from western Ethiopia. Arch Virol 2022; 167:2753-2759. [PMID: 36169719 DOI: 10.1007/s00705-022-05614-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2022] [Accepted: 09/22/2022] [Indexed: 12/14/2022]
Abstract
The A-strain of maize streak virus (MSV) causes maize streak disease (MSD), which is a major biotic threat to maize production in sub-Saharan Africa. Previous studies have described different MSV strains of economic importance from southern and eastern African countries and how eastern African regions are hubs for MSV diversification. Despite these efforts, due to a lack of extensive sampling, there is limited knowledge about the MSV-A diversity in Ethiopia. Here, field sampling of maize plants and wild grasses with visible MSD symptoms was carried out in the western Ethiopian regions of Gambela, Oromia, and Benishangul-Gumuz during the maize-growing season of 2019. The complete genomes of MSV isolates (n = 60) were cloned and sequenced by the Sanger method. We used a model-based phylogenetic approach to analyse 725 full MSV genome sequences available in the GenBank database together with newly determined genome sequences from Ethiopia to determine their subtypes and identify recombinant lineages. Of the 127 fields accessed, MSD prevalence was highest, at 96%, in the Gambela region and lowest in Oromia, at 66%. The highest mean symptom severity of 4/5 (where 5 is the highest and 1 the lowest) was observed in Gambela and Benishangul-Gumuz. Our results show that these newly determined MSV isolates belong to recombinant lineage V of the A1 subtype, with the widest dissemination and greatest economic significance in sub-Saharan Africa and the adjacent Indian Ocean islands.
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Affiliation(s)
- Daniel Ketsela
- Virology Research Laboratory, Ambo Agricultural Research Centre, Ethiopian Institute of Agricultural Research, P.O. Box 37, Ambo, Ethiopia
| | - Kehinde A Oyeniran
- 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.
- Department of Biological Sciences, Bamidele Olumilua University of Education, Science and Technology, Ikere-Ekiti, Nigeria.
| | - Berhanu Feyissa
- Virology Research Laboratory, Ambo Agricultural Research Centre, Ethiopian Institute of Agricultural Research, P.O. Box 37, Ambo, Ethiopia
| | - Rafaela S Fontenele
- The Biodesign Center for Fundamental and Applied Microbiomics, Center for Evolution and Medicine, School of Life Sciences, Arizona State University, Tempe, AZ, USA
| | - Simona Kraberger
- The Biodesign Center for Fundamental and Applied Microbiomics, Center for Evolution and Medicine, School of Life Sciences, Arizona State University, Tempe, AZ, USA
| | - Arvind Varsani
- The Biodesign Center for Fundamental and Applied Microbiomics, Center for Evolution and Medicine, School of Life Sciences, Arizona State University, Tempe, AZ, USA
- Structural Biology Research Unit, Department of Integrative Biomedical Sciences, University of Cape Town, Rondebosch, Cape Town, 7700, South Africa
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Tembo M, Adediji AO, Bouvaine S, Chikoti PC, Seal SE, Silva G. A quick and sensitive diagnostic tool for detection of Maize streak virus. Sci Rep 2020; 10:19633. [PMID: 33184360 PMCID: PMC7661706 DOI: 10.1038/s41598-020-76612-2] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2020] [Accepted: 10/29/2020] [Indexed: 11/09/2022] Open
Abstract
Maize streak virus disease (MSVD), caused by Maize streak virus (MSV; genus Mastrevirus), is one of the most severe and widespread viral diseases that adversely reduces maize yield and threatens food security in Africa. An effective control and management of MSVD requires robust and sensitive diagnostic tests capable of rapid detection of MSV. In this study, a loop-mediated isothermal amplification (LAMP) assay was designed for the specific detection of MSV. This test has shown to be highly specific and reproducible and able to detect MSV in as little as 10 fg/µl of purified genomic DNA obtained from a MSV-infected maize plant, a sensitivity 105 times higher to that obtained with polymerase chain reaction (PCR) in current general use. The high degree of sequence identity between Zambian and other African MSV isolates indicate that this LAMP assay can be used for detecting MSV in maize samples from any region in Africa. Furthermore, this assay can be adopted in minimally equipped laboratories and with potential use in plant clinic laboratories across Africa strengthening diagnostic capacity in countries dealing with MSD.
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Affiliation(s)
- Mathias Tembo
- Zambia Agriculture Research Institute, Mount Makulu Research Station, P/Bag 7, Lusaka, Zambia.
| | - Adedapo O Adediji
- Department of Crop Protection and Environmental Biology, Faculty of Agriculture, University of Ibadan, Ibadan, Oyo State, Nigeria
| | - Sophie Bouvaine
- Natural Resources Institute, University of Greenwich, Central Avenue, Chatham Maritime, ME4 4TB, Kent, UK
| | - Patrick C Chikoti
- Zambia Agriculture Research Institute, Mount Makulu Research Station, P/Bag 7, Lusaka, Zambia
| | - Susan E Seal
- Natural Resources Institute, University of Greenwich, Central Avenue, Chatham Maritime, ME4 4TB, Kent, UK
| | - Gonҫalo Silva
- Natural Resources Institute, University of Greenwich, Central Avenue, Chatham Maritime, ME4 4TB, Kent, UK
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3
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Yahaya A, Dangora DB, Alegbejo MD, Kumar PL, Alabi OJ. Identification and molecular characterization of a novel sugarcane streak mastrevirus and an isolate of the A-strain of maize streak virus from sugarcane in Nigeria. Arch Virol 2016; 162:597-602. [PMID: 27815694 DOI: 10.1007/s00705-016-3148-5] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2016] [Accepted: 10/31/2016] [Indexed: 11/27/2022]
Abstract
Sugarcane and maize plants showing symptoms typical of those described for the so-called "African streak viruses" (AfSVs) were encountered during field surveys conducted from February to July 2015 to document viruses infecting both crops across the northern Guinea savannah region of Nigeria. As part of this study, two categories of complete mastrevirus-like genome sequences were obtained from nine samples (maize = 2; sugarcane = 7). In pairwise comparisons, the full-length genomes of the first sequence category (2,687 nt each; maize = 2; sugarcane = 2) shared 96 to 99% identity with global isolates of the A-strain of maize streak virus (MSV-A), indicating that sugarcane may also serve as a reservoir host to MSV-A. Analysis of the complete genomes belonging to the second sequence category (2,757 nt each; sugarcane = 5) showed that they shared 42 to 67% identity with their closest AfSV relatives, thus indicating that they represent sequences of a novel mastrevirus. Both sequence categories shared 61-62% sequence identity with each other. Further analysis revealed that the novel sugarcane-infecting virus, tentatively named as sugarcane chlorotic streak virus (SCSV), arose from a putative interspecific recombination event involving two grass-infecting mastreviruses, eragrostis streak virus and urochloa streak virus, as putative parental sequences. The results of this study add to the repertoire of diverse AfSVs present in cereal and sugarcane mixed cropping landscapes in the northern Guinea savannah region of Nigeria, with implications for disease epidemiology.
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Affiliation(s)
- Adama Yahaya
- Department of Biological Sciences, Ahmadu Bello University, Zaria, Kaduna State, Nigeria
| | - Danladi B Dangora
- Department of Biological Sciences, Ahmadu Bello University, Zaria, Kaduna State, Nigeria
| | - Matthew D Alegbejo
- Department of Crop Protection, Ahmadu Bello University, Zaria, Kaduna State, Nigeria
| | - P Lava Kumar
- International Institute of Tropical Agriculture (IITA), PMB 5320, Ibadan, Nigeria
| | - Olufemi J Alabi
- Department of Plant Pathology & Microbiology, Texas A&M AgriLife Research & Extension Center, Weslaco, TX, 78596, United States of America.
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4
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Shepherd DN, Dugdale B, Martin DP, Varsani A, Lakay FM, Bezuidenhout ME, Monjane AL, Thomson JA, Dale J, Rybicki EP. Inducible resistance to maize streak virus. PLoS One 2014; 9:e105932. [PMID: 25166274 PMCID: PMC4148390 DOI: 10.1371/journal.pone.0105932] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2014] [Accepted: 07/28/2014] [Indexed: 11/18/2022] Open
Abstract
Maize streak virus (MSV), which causes maize streak disease (MSD), is the major viral pathogenic constraint on maize production in Africa. Type member of the Mastrevirus genus in the family Geminiviridae, MSV has a 2.7 kb, single-stranded circular DNA genome encoding a coat protein, movement protein, and the two replication-associated proteins Rep and RepA. While we have previously developed MSV-resistant transgenic maize lines constitutively expressing "dominant negative mutant" versions of the MSV Rep, the only transgenes we could use were those that caused no developmental defects during the regeneration of plants in tissue culture. A better transgene expression system would be an inducible one, where resistance-conferring transgenes are expressed only in MSV-infected cells. However, most known inducible transgene expression systems are hampered by background or "leaky" expression in the absence of the inducer. Here we describe an adaptation of the recently developed INPACT system to express MSV-derived resistance genes in cell culture. Split gene cassette constructs (SGCs) were developed containing three different transgenes in combination with three different promoter sequences. In each SGC, the transgene was split such that it would be translatable only in the presence of an infecting MSV's replication associated protein. We used a quantitative real-time PCR assay to show that one of these SGCs (pSPLITrepIII-Rb-Ubi) inducibly inhibits MSV replication as efficiently as does a constitutively expressed transgene that has previously proven effective in protecting transgenic maize from MSV. In addition, in our cell-culture based assay pSPLITrepIII-Rb-Ubi inhibited replication of diverse MSV strains, and even, albeit to a lesser extent, of a different mastrevirus species. The application of this new technology to MSV resistance in maize could allow a better, more acceptable product.
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Affiliation(s)
- Dionne N. Shepherd
- Department of Molecular and Cell Biology, University of Cape Town, Rondebosch, Cape Town, South Africa
- * E-mail:
| | - Benjamin Dugdale
- Centre for Tropical Crops and Biocommodities, Queensland University of Technology (QUT), Brisbane, Queensland, Australia
| | - Darren P. Martin
- Institute of Infectious Disease and Molecular Medicine, University of Cape Town, Observatory, Cape Town, South Africa
- Centre for High-Performance Computing, Rosebank, Cape Town, South Africa
| | - Arvind Varsani
- School of Biological Sciences and Biomolecular Interaction Centre, University of Canterbury, Christchurch, New Zealand
- Department of Plant Pathology and Emerging Pathogens Institute, University of Florida, Gainesville, Florida, United States of America
- Electron Microscope Unit, Division of Medical Biochemistry, Department of Clinical Laboratory Sciences, University of Cape Town, Observatory, Cape Town, South Africa
| | - Francisco M. Lakay
- Department of Molecular and Cell Biology, University of Cape Town, Rondebosch, Cape Town, South Africa
| | - Marion E. Bezuidenhout
- Department of Molecular and Cell Biology, University of Cape Town, Rondebosch, Cape Town, South Africa
| | - Adérito L. Monjane
- Department of Molecular and Cell Biology, University of Cape Town, Rondebosch, Cape Town, South Africa
- Institute of Infectious Disease and Molecular Medicine, University of Cape Town, Observatory, Cape Town, South Africa
| | - Jennifer A. Thomson
- Department of Molecular and Cell Biology, University of Cape Town, Rondebosch, Cape Town, South Africa
| | - James Dale
- Centre for Tropical Crops and Biocommodities, Queensland University of Technology (QUT), Brisbane, Queensland, Australia
| | - Edward P. Rybicki
- Department of Molecular and Cell Biology, University of Cape Town, Rondebosch, Cape Town, South Africa
- Institute of Infectious Disease and Molecular Medicine, University of Cape Town, Observatory, Cape Town, South Africa
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5
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Monjane AL, Martin DP, Lakay F, Muhire BM, Pande D, Varsani A, Harkins G, Shepherd DN, Rybicki EP. Extensive recombination-induced disruption of genetic interactions is highly deleterious but can be partially reversed by small numbers of secondary recombination events. J Virol 2014; 88:7843-51. [PMID: 24789787 PMCID: PMC4097777 DOI: 10.1128/jvi.00709-14] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2014] [Accepted: 04/22/2014] [Indexed: 01/12/2023] Open
Abstract
Although homologous recombination can potentially provide viruses with vastly more evolutionary options than are available through mutation alone, there are considerable limits on the adaptive potential of this important evolutionary process. Primary among these is the disruption of favorable coevolved genetic interactions that can occur following the transfer of foreign genetic material into a genome. Although the fitness costs of such disruptions can be severe, in some cases they can be rapidly recouped by either compensatory mutations or secondary recombination events. Here, we used a maize streak virus (MSV) experimental model to explore both the extremes of recombination-induced genetic disruption and the capacity of secondary recombination to adaptively reverse almost lethal recombination events. Starting with two naturally occurring parental viruses, we synthesized two of the most extreme conceivable MSV chimeras, each effectively carrying 182 recombination breakpoints and containing thorough reciprocal mixtures of parental polymorphisms. Although both chimeras were severely defective and apparently noninfectious, neither had individual movement-, encapsidation-, or replication-associated genome regions that were on their own "lethally recombinant." Surprisingly, mixed inoculations of the chimeras yielded symptomatic infections with viruses with secondary recombination events. These recombinants had only 2 to 6 breakpoints, had predominantly inherited the least defective of the chimeric parental genome fragments, and were obviously far more fit than their synthetic parents. It is clearly evident, therefore, that even when recombinationally disrupted virus genomes have extremely low fitness and there are no easily accessible routes to full recovery, small numbers of secondary recombination events can still yield tremendous fitness gains. Importance: Recombination between viruses can generate strains with enhanced pathological properties but also runs the risk of producing hybrid genomes with decreased fitness due to the disruption of favorable genetic interactions. Using two synthetic maize streak virus genome chimeras containing alternating genome segments derived from two natural viral strains, we examined both the fitness costs of extreme degrees of recombination (both chimeras had 182 recombination breakpoints) and the capacity of secondary recombination events to recoup these costs. After the severely defective chimeras were introduced together into a suitable host, viruses with between 1 and 3 secondary recombination events arose, which had greatly increased replication and infective capacities. This indicates that even in extreme cases where recombination-induced genetic disruptions are almost lethal, and 91 consecutive secondary recombination events would be required to reconstitute either one of the parental viruses, moderate degrees of fitness recovery can be achieved through relatively small numbers of secondary recombination events.
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Affiliation(s)
- Adérito L Monjane
- Molecular and Cell Biology Department, University of Cape Town, Cape Town, South Africa Institute of Infectious Diseases and Molecular Medicine, University of Cape Town, Cape Town, South Africa
| | - Darren P Martin
- Institute of Infectious Diseases and Molecular Medicine, University of Cape Town, Cape Town, South Africa
| | - Francisco Lakay
- Molecular and Cell Biology Department, University of Cape Town, Cape Town, South Africa
| | - Brejnev M Muhire
- Institute of Infectious Diseases and Molecular Medicine, University of Cape Town, Cape Town, South Africa
| | - Daniel Pande
- Department of Botany and Horticulture, Maseno University, Maseno, Kenya
| | - Arvind Varsani
- School of Biological Sciences and Biomolecular Interaction Centre, University of Canterbury, Christchurch, New Zealand Department of Plant Pathology and Emerging Pathogens Institute, University of Florida, Gainesville, Florida, USA Electron Microscope Unit, Division of Medical Biochemistry, Department of Clinical Laboratory Sciences, University of Cape Town, Cape Town, South Africa
| | - Gordon Harkins
- South African National Bioinformatics Institute, MRC Unit for Bioinformatics Capacity Development, University of the Western Cape, Bellville, South Africa
| | - Dionne N Shepherd
- Molecular and Cell Biology Department, University of Cape Town, Cape Town, South Africa
| | - Edward P Rybicki
- Molecular and Cell Biology Department, University of Cape Town, Cape Town, South Africa Institute of Infectious Diseases and Molecular Medicine, University of Cape Town, Cape Town, South Africa
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6
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Oluwafemi S, Kraberger S, Shepherd DN, Martin DP, Varsani A. A high degree of African streak virus diversity within Nigerian maize fields includes a new mastrevirus from Axonopus compressus. Arch Virol 2014; 159:2765-70. [PMID: 24796552 DOI: 10.1007/s00705-014-2090-7] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2014] [Accepted: 04/10/2014] [Indexed: 11/25/2022]
Abstract
The A-strain of maize streak virus (MSV-A; genus Mastrevirus, family Geminiviridae), the causal agent of maize streak disease, places a major constraint on maize production throughout sub-Saharan Africa. In West-African countries such as Nigeria, where maize is not cultivated year-round, this MSV strain is forced to overwinter in non-maize hosts. In order to both identify uncultivated grasses that might harbour MSV-A during the winter season and further characterise the diversity of related maize-associated streak viruses, we collected maize and grass samples displaying streak symptoms in a number of Nigerian maize fields. From these we isolated and cloned 18 full mastrevirus genomes (seven from maize and 11 from various wild grass species). Although only MSV-A isolates were obtained from maize, both MSV-A and MSV-F isolates were obtained from Digitaria ciliaris. Four non-MSV African streak viruses were also sampled, including sugarcane streak Reunion virus and Urochloa streak virus (USV) from Eleusine coacana, USV from Urochloa sp., maize streak Reunion virus (MSRV) from both Setaria barbata and Rottboellia sp., and a novel highly divergent mastrevirus from Axonopus compressus, which we have tentatively named Axonopus compressus streak virus (ACSV). Besides the discovery of this new mastrevirus species and expanding the known geographical and host ranges of MSRV, we have added D. ciliaris to the list of uncultivated species within which Nigerian MSV-A isolates are possibly able to overwinter.
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Affiliation(s)
- Sunday Oluwafemi
- Department of Crop Production, Soil and Environmental Management, Bowen University, P.M.B. 284, Iwo, Osun State, Nigeria
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7
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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] [What about the content of this article? (0)] [Affiliation(s)] [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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Owor BE, Martin DP, Rybicki EP, Thomson JA, Bezuidenhout ME, Lakay FM, Shepherd DN. A rep-based hairpin inhibits replication of diverse maize streak virus isolates in a transient assay. J Gen Virol 2011; 92:2458-2465. [PMID: 21653753 DOI: 10.1099/vir.0.032862-0] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Maize streak disease, caused by the A strain of the African endemic geminivirus, maize streak mastrevirus (MSV-A), threatens the food security and livelihoods of subsistence farmers throughout sub-Saharan Africa. Using a well-established transient expression assay, this study investigated the potential of a spliceable-intron hairpin RNA (hpRNA) approach to interfere with MSV replication. Two strategies were explored: (i) an inverted repeat of a 662 bp region of the MSV replication-associated protein gene (rep), which is essential for virus replication and is therefore a good target for post-transcriptional gene silencing; and (ii) an inverted repeat of the viral long intergenic region (LIR), considered for its potential to trigger transcriptional silencing of the viral promoter region. After co-bombardment of cultured maize cells with each construct and an infectious partial dimer of the cognate virus genome (MSV-Kom), followed by viral replicative-form-specific PCR, it was clear that, whilst the hairpin rep construct (pHPrepΔI(662)) completely inhibited MSV replication, the LIR hairpin construct was ineffective in this regard. In addition, pHPrepΔI(662) inhibited or reduced replication of six MSV-A genotypes representing the entire breadth of known MSV-A diversity. Further investigation by real-time PCR revealed that the pHPrepΔI(662) inverted repeat was 22-fold more effective at reducing virus replication than a construct containing the sense copy, whilst the antisense copy had no effect on replication when compared with the wild type. This is the first indication that an hpRNA strategy targeting MSV rep has the potential to protect transgenic maize against diverse MSV-A genotypes found throughout sub-Saharan Africa.
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Affiliation(s)
- Betty E Owor
- Department of Molecular and Cell Biology, University of Cape Town, Rondebosch 7701, Cape Town, South Africa
| | - Darren P Martin
- Centre for High-Performance Computing, Rosebank, Cape Town, South Africa
- Institute of Infectious Disease and Molecular Medicine, University of Cape Town, Observatory 7925, Cape Town, South Africa
| | - Edward P Rybicki
- Centre for High-Performance Computing, Rosebank, Cape Town, South Africa
- Department of Molecular and Cell Biology, University of Cape Town, Rondebosch 7701, Cape Town, South Africa
| | - Jennifer A Thomson
- Department of Molecular and Cell Biology, University of Cape Town, Rondebosch 7701, Cape Town, South Africa
| | - Marion E Bezuidenhout
- Department of Molecular and Cell Biology, University of Cape Town, Rondebosch 7701, Cape Town, South Africa
| | - Francisco M Lakay
- Department of Molecular and Cell Biology, University of Cape Town, Rondebosch 7701, Cape Town, South Africa
| | - Dionne N Shepherd
- Department of Molecular and Cell Biology, University of Cape Town, Rondebosch 7701, Cape Town, South Africa
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9
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Escobar C, García A, Aristizábal F, Portillo M, Herreros E, Munoz-Martín MA, Grundler F, Mullineaux PM, Fenoll C. Activation of geminivirus V-sense promoters in roots is restricted to nematode feeding sites. Mol Plant Pathol 2010; 11:409-17. [PMID: 20447288 PMCID: PMC6640434 DOI: 10.1111/j.1364-3703.2010.00611.x] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/08/2023]
Abstract
Obligate sedentary endoparasitic nematodes, such as the root-knot and cyst nematodes, elicit the differentiation of specialized nematode nurse or feeding cells [nematode feeding sites (NFS), giant cells and syncytia, respectively]. During NFS differentiation, marked changes in cell cycle progression occur, partly similar to those induced by some geminiviruses. In this work, we describe the activation of V-sense promoters from the Maize streak virus (MSV) and Wheat dwarf virus (WDV) in NFS formed by root-knot and cyst nematodes. Both promoters were transiently active in microinjection experiments. In tobacco and Arabidopsis transgenic lines carrying promoter-beta-glucuronidase fusions, the MSV V-sense promoter was activated in the vascular tissues of aerial plant parts, primarily leaf and cotyledon phloem tissue and some floral structures. Interestingly, in roots, promoter activation was restricted to syncytia and giant cells tested with four different nematode populations, but undetectable in the rest of the root system. As the activity of the promoter in transgenic rootstocks should be restricted to NFS only, the MSV promoter may have utility in engineering grafted crops for nematode control. Therefore, this study represents a step in the provision of some of the much needed additional data on promoters with restricted activation in NFS useful in biotechnological nematode control strategies.
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Affiliation(s)
- Carolina Escobar
- Facultad de Ciencias del Medio Ambiente, Universidad de Castilla-La Mancha, E-45071 Toledo, Spain.
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Abstract
UNLABELLED Maize streak virus (MSV; Genus Mastrevirus, Family Geminiviridae) occurs throughout Africa, where it causes what is probably the most serious viral crop disease on the continent. It is obligately transmitted by as many as six leafhopper species in the Genus Cicadulina, but mainly by C. mbila Naudé and C. storeyi. In addition to maize, it can infect over 80 other species in the Family Poaceae. Whereas 11 strains of MSV are currently known, only the MSV-A strain is known to cause economically significant streak disease in maize. Severe maize streak disease (MSD) manifests as pronounced, continuous parallel chlorotic streaks on leaves, with severe stunting of the affected plant and, usuallly, a failure to produce complete cobs or seed. Natural resistance to MSV in maize, and/or maize infections caused by non-maize-adapted MSV strains, can result in narrow, interrupted streaks and no obvious yield losses. MSV epidemiology is primarily governed by environmental influences on its vector species, resulting in erratic epidemics every 3-10 years. Even in epidemic years, disease incidences can vary from a few infected plants per field, with little associated yield loss, to 100% infection rates and complete yield loss. TAXONOMY The only virus species known to cause MSD is MSV, the type member of the Genus Mastrevirus in the Family Geminiviridae. In addition to the MSV-A strain, which causes the most severe form of streak disease in maize, 10 other MSV strains (MSV-B to MSV-K) are known to infect barley, wheat, oats, rye, sugarcane, millet and many wild, mostly annual, grass species. Seven other mastrevirus species, many with host and geographical ranges partially overlapping those of MSV, appear to infect primarily perennial grasses. PHYSICAL PROPERTIES MSV and all related grass mastreviruses have single-component, circular, single-stranded DNA genomes of approximately 2700 bases, encapsidated in 22 x 38-nm geminate particles comprising two incomplete T = 1 icosahedra, with 22 pentameric capsomers composed of a single 32-kDa capsid protein. Particles are generally stable in buffers of pH 4-8. DISEASE SYMPTOMS In infected maize plants, streak disease initially manifests as minute, pale, circular spots on the lowest exposed portion of the youngest leaves. The only leaves that develop symptoms are those formed after infection, with older leaves remaining healthy. As the disease progresses, newer leaves emerge containing streaks up to several millimetres in length along the leaf veins, with primary veins being less affected than secondary or tertiary veins. The streaks are often fused laterally, appearing as narrow, broken, chlorotic stripes, which may extend over the entire length of severely affected leaves. Lesion colour generally varies from white to yellow, with some virus strains causing red pigmentation on maize leaves and abnormal shoot and flower bunching in grasses. Reduced photosynthesis and increased respiration usually lead to a reduction in leaf length and plant height; thus, maize plants infected at an early stage become severely stunted, producing undersized, misshapen cobs or giving no yield at all. Yield loss in susceptible maize is directly related to the time of infection: infected seedlings produce no yield or are killed, whereas plants infected at later times are proportionately less affected. DISEASE CONTROL Disease avoidance can be practised by only planting maize during the early season when viral inoculum loads are lowest. Leafhopper vectors can also be controlled with insecticides such as carbofuran. However, the development and use of streak-resistant cultivars is probably the most effective and economically viable means of preventing streak epidemics. Naturally occurring tolerance to MSV (meaning that, although plants become systemically infected, they do not suffer serious yield losses) has been found, which has primarily been attributed to a single gene, msv-1. However, other MSV resistance genes also exist and improved resistance has been achieved by concentrating these within individual maize genotypes. Whereas true MSV immunity (meaning that plants cannot be symptomatically infected by the virus) has been achieved in lines that include multiple small-effect resistance genes together with msv-1, it has proven difficult to transfer this immunity into commercial maize genotypes. An alternative resistance strategy using genetic engineering is currently being investigated in South Africa. USEFUL WEBSITES http://www.mcb.uct.ac.za/MSV/mastrevirus.htm; http://www.danforthcenter.org/iltab/geminiviridae/geminiaccess/mastrevirus/Mastrevirus.htm.
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Affiliation(s)
- Dionne N Shepherd
- Department of Molecular and Cell Biology, University of Cape Town, PB Rondebosch, 7701, South Africa.
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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] [What about the content of this article? (0)] [Affiliation(s)] [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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Varsani A, Shepherd DN, Monjane AL, Owor BE, Erdmann JB, Rybicki EP, Peterschmitt M, Briddon RW, Markham PG, Oluwafemi S, Windram OP, Lefeuvre P, Lett JM, Martin DP. Recombination, decreased host specificity and increased mobility may have driven the emergence of maize streak virus as an agricultural pathogen. J Gen Virol 2008; 89:2063-2074. [PMID: 18753214 PMCID: PMC2886952 DOI: 10.1099/vir.0.2008/003590-0] [Citation(s) in RCA: 90] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2008] [Accepted: 06/17/2008] [Indexed: 01/20/2023] Open
Abstract
Maize streak virus (MSV; family Geminiviridae, genus Mastrevirus), the causal agent of maize streak disease, ranks amongst the most serious biological threats to food security in subSaharan Africa. Although five distinct MSV strains have been currently described, only one of these - MSV-A - causes severe disease in maize. Due primarily to their not being an obvious threat to agriculture, very little is known about the 'grass-adapted' MSV strains, MSV-B, -C, -D and -E. Since comparing the genetic diversities, geographical distributions and natural host ranges of MSV-A with the other MSV strains could provide valuable information on the epidemiology, evolution and emergence of MSV-A, we carried out a phylogeographical analysis of MSVs found in uncultivated indigenous African grasses. Amongst the 83 new MSV genomes presented here, we report the discovery of six new MSV strains (MSV-F to -K). The non-random recombination breakpoint distributions detectable with these and other available mastrevirus sequences partially mirror those seen in begomoviruses, implying that the forces shaping these breakpoint patterns have been largely conserved since the earliest geminivirus ancestors. We present evidence that the ancestor of all MSV-A variants was the recombinant progeny of ancestral MSV-B and MSV-G/-F variants. While it remains unknown whether recombination influenced the emergence of MSV-A in maize, our discovery that MSV-A variants may both move between and become established in different regions of Africa with greater ease, and infect more grass species than other MSV strains, goes some way towards explaining why MSV-A is such a successful maize pathogen.
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Affiliation(s)
- Arvind Varsani
- Electron Microscope Unit, University of Cape Town, Rondebosch, Cape Town 7701, South Africa
- Department of Molecular and Cell Biology, University of Cape Town, Rondebosch, Cape Town 7701, South Africa
| | - Dionne N. Shepherd
- Department of Molecular and Cell Biology, University of Cape Town, Rondebosch, Cape Town 7701, South Africa
| | - Adérito L. Monjane
- Department of Molecular and Cell Biology, University of Cape Town, Rondebosch, Cape Town 7701, South Africa
| | - Betty E. Owor
- Department of Molecular and Cell Biology, University of Cape Town, Rondebosch, Cape Town 7701, South Africa
| | - Julia B. Erdmann
- Department of Molecular and Cell Biology, University of Cape Town, Rondebosch, Cape Town 7701, South Africa
- Institute of Biology, Department of Molecular Biology and Plant Virology, University of Stuttgart, Pfaffenwaldring 57, D-70550 Stuttgart, Germany
| | - Edward P. Rybicki
- Department of Molecular and Cell Biology, University of Cape Town, Rondebosch, Cape Town 7701, South Africa
- Institute of Infectious Disease and Molecular Medicine, University of Cape Town, Anzio Road, Observatory, Cape Town 7925, South Africa
| | - Michel Peterschmitt
- CIRAD, UMR BGPI, TA A54/K, Campus International de Baillarguet, 34398 Montpellier Cedex 5, France
| | - Rob W. Briddon
- National Institute for Biotechnology and Genetic Engineering, Jhang Road, PO Box 577, Faisalabad, Pakistan
| | - Peter G. Markham
- Department of Disease and Stress Biology, John Innes Centre, Norwich NR4 7UH, UK
| | - Sunday Oluwafemi
- Department of Crop, Soil and Environmental Management, Bowen University, PMB 284, Iwo, Osun State, Nigeria
| | - Oliver P. Windram
- Warwick HRI Biology Centre, University of Warwick, Wellesbourne CV35 9EF, UK
| | - Pierre Lefeuvre
- CIRAD, UMR 53 PVBMT CIRAD-Université de la Réunion, Pôle de Protection des Plantes, Ligne Paradis, 97410 Saint Pierre, La Réunion, France
| | - Jean-Michel Lett
- CIRAD, UMR 53 PVBMT CIRAD-Université de la Réunion, Pôle de Protection des Plantes, Ligne Paradis, 97410 Saint Pierre, La Réunion, France
| | - Darren P. Martin
- Institute of Infectious Disease and Molecular Medicine, University of Cape Town, Anzio Road, Observatory, Cape Town 7925, South Africa
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Willment JA, Martin DP, Palmer KE, Schnippenkoetter WH, Shepherd DN, Rybicki EP. Identification of long intergenic region sequences involved in maize streak virus replication. J Gen Virol 2007; 88:1831-1841. [PMID: 17485545 DOI: 10.1099/vir.0.82513-0] [Citation(s) in RCA: 15] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
The main cis-acting control regions for replication of the single-stranded DNA genome of maize streak virus (MSV) are believed to reside within an approximately 310 nt long intergenic region (LIR). However, neither the minimum LIR sequence required nor the sequence determinants of replication specificity have been determined experimentally. There are iterated sequences, or iterons, both within the conserved inverted-repeat sequences with the potential to form a stem-loop structure at the origin of virion-strand replication, and upstream of the rep gene TATA box (the rep-proximal iteron or RPI). Based on experimental analyses of similar iterons in viruses from other geminivirus genera and their proximity to known Rep-binding sites in the distantly related mastrevirus wheat dwarf virus, it has been hypothesized that the iterons may be Rep-binding and/or -recognition sequences. Here, a series of LIR deletion mutants was used to define the upper bounds of the LIR sequence required for replication. After identifying MSV strains and distinct mastreviruses with incompatible replication-specificity determinants (RSDs), LIR chimaeras were used to map the primary MSV RSD to a 67 nt sequence containing the RPI. Although the results generally support the prevailing hypothesis that MSV iterons are functional analogues of those found in other geminivirus genera, it is demonstrated that neither the inverted-repeat nor RPI sequences are absolute determinants of replication specificity. Moreover, widely divergent mastreviruses can trans-replicate one another. These results also suggest that sequences in the 67 nt region surrounding the RPI interact in a sequence-specific manner with those of the inverted repeat.
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Affiliation(s)
- Janet A Willment
- Institute of Infectious Diseases and Molecular Medicine, Faculty of Health Sciences, University of Cape Town, Observatory 7925, South Africa
| | - Darrin P Martin
- Institute of Infectious Diseases and Molecular Medicine, Faculty of Health Sciences, University of Cape Town, Observatory 7925, South Africa
| | - Kenneth E Palmer
- Department of Pharmacology and Toxicology, University of Louisville, 570 South Preston Street, Louisville, KY 40202, USA
- James Graham Brown Cancer Center, University of Louisville, 529 South Jackson Street, Louisville, KY 40202, USA
| | | | - Dionne N Shepherd
- Department of Molecular and Cell Biology, University of Cape Town, Private Bag, Rondebosch, Cape Town 7701, South Africa
| | - Edward P Rybicki
- Department of Molecular and Cell Biology, University of Cape Town, Private Bag, Rondebosch, Cape Town 7701, South Africa
- Institute of Infectious Diseases and Molecular Medicine, Faculty of Health Sciences, University of Cape Town, Observatory 7925, South Africa
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Owor BE, Shepherd DN, Taylor NJ, Edema R, Monjane AL, Thomson JA, Martin DP, Varsani A. Successful application of FTA® Classic Card technology and use of bacteriophage ϕ29 DNA polymerase for large-scale field sampling and cloning of complete maize streak virus genomes. J Virol Methods 2007; 140:100-5. [PMID: 17174409 DOI: 10.1016/j.jviromet.2006.11.004] [Citation(s) in RCA: 57] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2006] [Revised: 11/01/2006] [Accepted: 11/08/2006] [Indexed: 10/23/2022]
Abstract
Leaf samples from 155 maize streak virus (MSV)-infected maize plants were collected from 155 farmers' fields in 23 districts in Uganda in May/June 2005 by leaf-pressing infected samples onto FTA Classic Cards. Viral DNA was successfully extracted from cards stored at room temperature for 9 months. The diversity of 127 MSV isolates was analysed by PCR-generated RFLPs. Six representative isolates having different RFLP patterns and causing either severe, moderate or mild disease symptoms, were chosen for amplification from FTA cards by bacteriophage phi29 DNA polymerase using the TempliPhi system. Full-length genomes were inserted into a cloning vector using a unique restriction enzyme site, and sequenced. The 1.3-kb PCR product amplified directly from FTA-eluted DNA and used for RFLP analysis was also cloned and sequenced. Comparison of cloned whole genome sequences with those of the original PCR products indicated that the correct virus genome had been cloned and that no errors were introduced by the phi29 polymerase. This is the first successful large-scale application of FTA card technology to the field, and illustrates the ease with which large numbers of infected samples can be collected and stored for downstream molecular applications such as diversity analysis and cloning of potentially new virus genomes.
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Affiliation(s)
- Betty E Owor
- Department of Molecular and Cell Biology, University of Cape Town, Private Bag, Rondebosch 7701, South Africa
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15
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Shepherd DN, Mangwende T, Martin DP, Bezuidenhout M, Thomson JA, Rybicki EP. Inhibition of maize streak virus (MSV) replication by transient and transgenic expression of MSV replication-associated protein mutants. J Gen Virol 2007; 88:325-336. [PMID: 17170465 DOI: 10.1099/vir.0.82338-0] [Citation(s) in RCA: 29] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Maize streak disease is a severe agricultural problem in Africa and the development of maize genotypes resistant to the causal agent, Maize streak virus (MSV), is a priority. A transgenic approach to engineering MSV-resistant maize was developed and tested in this study. A pathogen-derived resistance strategy was adopted by using targeted deletions and nucleotide-substitution mutants of the multifunctional MSV replication-associated protein gene (rep). Various rep gene constructs were tested for their efficacy in limiting replication of wild-type MSV by co-bombardment of maize suspension cells together with an infectious genomic clone of MSV and assaying replicative forms of DNA by quantitative PCR. Digitaria sanguinalis, an MSV-sensitive grass species used as a model monocot, was then transformed with constructs that had inhibited virus replication in the transient-expression system. Challenge experiments using leafhopper-transmitted MSV indicated significant MSV resistance--from highly resistant to immune--in regenerated transgenic D. sanguinalis lines. Whereas regenerated lines containing a mutated full-length rep gene displayed developmental and growth defects, those containing a truncated rep gene both were fertile and displayed no growth defects, making the truncated gene a suitable candidate for the development of transgenic MSV-resistant maize.
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Affiliation(s)
- Dionne N Shepherd
- Department of Molecular and Cell Biology, University of Cape Town, Private Bag, Rondebosch, Cape Town 7701, South Africa
| | - Tichaona Mangwende
- Division of Pharmacology, University of Cape Town, Cape Town, South Africa
- Department of Molecular and Cell Biology, University of Cape Town, Private Bag, Rondebosch, Cape Town 7701, South Africa
| | - Darren P Martin
- Institute of Infectious Disease and Molecular Medicine, University of Cape Town, Observatory, Anzio Road, Cape Town 7925, South Africa
| | - Marion Bezuidenhout
- Department of Molecular and Cell Biology, University of Cape Town, Private Bag, Rondebosch, Cape Town 7701, South Africa
| | - Jennifer A Thomson
- Department of Molecular and Cell Biology, University of Cape Town, Private Bag, Rondebosch, Cape Town 7701, South Africa
| | - Edward P Rybicki
- Institute of Infectious Disease and Molecular Medicine, University of Cape Town, Observatory, Anzio Road, Cape Town 7925, South Africa
- Department of Molecular and Cell Biology, University of Cape Town, Private Bag, Rondebosch, Cape Town 7701, South Africa
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Martin DP, van der Walt E, Posada D, Rybicki EP. The evolutionary value of recombination is constrained by genome modularity. PLoS Genet 2006; 1:e51. [PMID: 16244707 PMCID: PMC1262190 DOI: 10.1371/journal.pgen.0010051] [Citation(s) in RCA: 93] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2005] [Accepted: 09/22/2005] [Indexed: 11/19/2022] Open
Abstract
Genetic recombination is a fundamental evolutionary mechanism promoting biological adaptation. Using engineered recombinants of the small single-stranded DNA plant virus, Maize streak virus (MSV), we experimentally demonstrate that fragments of genetic material only function optimally if they reside within genomes similar to those in which they evolved. The degree of similarity necessary for optimal functionality is correlated with the complexity of intragenomic interaction networks within which genome fragments must function. There is a striking correlation between our experimental results and the types of MSV recombinants that are detectable in nature, indicating that obligatory maintenance of intragenome interaction networks strongly constrains the evolutionary value of recombination for this virus and probably for genomes in general. Genetic exchange between organisms, called recombination, occurs in all biological kingdoms and is also common in viruses in which it may threaten the long-term control of important human pathogens such as HIV and influenza. Although recombination can produce advantageous gene combinations, bioinformatic analyses of bacterial genomes have suggested that recombination is not well tolerated when it involves exchanges of genes that interact with a lot of other genes. Using laboratory-constructed recombinants of a small plant virus called MSV, Martin and co-workers provide the first direct experimental evidence that the evolutionary value of exchanging a genome fragment is constrained by the number of ways in which the fragment interacts with the rest of the genome. They note that fitness losses suffered by artificial MSV recombinants increase with decreasing parental relatedness. Furthermore, these losses accurately anticipate the patterns of genetic exchange detectable in natural MSV recombinants, suggesting that they accurately reflect the impact of deleterious selection on natural isolates of the virus.
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Affiliation(s)
- Darren P Martin
- Institute of Infectious Diseases and Molecular Medicine, University of Cape Town, Cape Town, South Africa.
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Tsai CW, Redinbaugh MG, Willie KJ, Reed S, Goodin M, Hogenhout SA. Complete genome sequence and in planta subcellular localization of maize fine streak virus proteins. J Virol 2005; 79:5304-14. [PMID: 15827145 PMCID: PMC1082748 DOI: 10.1128/jvi.79.9.5304-5314.2005] [Citation(s) in RCA: 65] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/03/2004] [Accepted: 12/09/2004] [Indexed: 11/20/2022] Open
Abstract
The genome of the nucleorhabdovirus maize fine streak virus (MFSV) consists of 13,782 nucleotides of nonsegmented, negative-sense, single-stranded RNA. The antigenomic strand consisted of seven open reading frames (ORFs), and transcripts of all ORFs were detected in infected plants. ORF1, ORF6, and ORF7 had significant similarities to the nucleocapsid protein (N), glycoprotein (G), and polymerase (L) genes of other rhabdoviruses, respectively, whereas the ORF2, ORF3, ORF4, and ORF5 proteins had no significant similarities. The N (ORF1), ORF4, and ORF5 proteins localized to nuclei, consistent with the presence of nuclear localization signals (NLSs) in these proteins. ORF5 likely encodes the matrix protein (M), based on its size, the position of its NLS, and the localization of fluorescent protein fusions to the nucleus. ORF2 probably encodes the phosphoprotein (P) because, like the P protein of Sonchus yellow net virus (SYNV), it was spread throughout the cell when expressed alone but was relocalized to a subnuclear locus when coexpressed with the MFSV N protein. Unexpectedly, coexpression of the MFSV N and P proteins, but not the orthologous proteins of SYNV, resulted in accumulations of both proteins in the nucleolus. The N and P protein relocalization was specific to cognate proteins of each virus. The subcellular localizations of the MFSV ORF3 and ORF4 proteins were distinct from that of the SYNV sc4 protein, suggesting different functions. To our knowledge, this is the first comparative study of the cellular localizations of plant rhabdoviral proteins. This study indicated that plant rhabdoviruses are diverse in genome sequence and viral protein interactions.
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Affiliation(s)
- Chi-Wei Tsai
- Department of Entomology, The Ohio State University-Ohio Agricultural Research and Development Center (OARDC), 1680 Madison Ave., Wooster, OH 44691, USA
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Shepherd DN, Martin DP, McGivern DR, Boulton MI, Thomson JA, Rybicki EP. A three-nucleotide mutation altering the Maize streak virus Rep pRBR-interaction motif reduces symptom severity in maize and partially reverts at high frequency without restoring pRBR–Rep binding. J Gen Virol 2005; 86:803-813. [PMID: 15722543 DOI: 10.1099/vir.0.80694-0] [Citation(s) in RCA: 47] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022] Open
Abstract
Geminivirus infectivity is thought to depend on interactions between the virus replication-associated proteins Rep or RepA and host retinoblastoma-related proteins (pRBR), which control cell-cycle progression. It was determined that the substitution of two amino acids in the Maize streak virus (MSV) RepA pRBR-interaction motif (LLCNE to LLCLK) abolished detectable RepA–pRBR interaction in yeast without abolishing infectivity in maize. Although the mutant virus was infectious in maize, it induced less severe symptoms than the wild-type virus. Sequence analysis of progeny viral DNA isolated from infected maize enabled detection of a high-frequency single-nucleotide reversion of C(601)A in the 3 nt mutated sequence of the Rep gene. Although it did not restore RepA–pRBR interaction in yeast, sequence-specific PCR showed that, in five out of eight plants, the C(601)A reversion appeared by day 10 post-inoculation. In all plants, the C(601)A revertant eventually completely replaced the original mutant population, indicating a high selection pressure for the single-nucleotide reversion. Apart from potentially revealing an alternative or possibly additional function for the stretch of DNA that encodes the apparently non-essential pRBR-interaction motif of MSV Rep, the consistent emergence and eventual dominance of the C(601)A revertant population might provide a useful tool for investigating aspects of MSV biology, such as replication, mutation and evolution rates, and complex population phenomena, such as competition between quasispecies and population turnover.
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Affiliation(s)
- Dionne N Shepherd
- Department of Molecular and Cell Biology, University of Cape Town, Rondebosch 7701, South Africa
| | - Darren P Martin
- Department of Molecular and Cell Biology, University of Cape Town, Rondebosch 7701, South Africa
| | - David R McGivern
- John Innes Centre, Norwich Research Park, Colney, Norwich NR4 7UH, UK
| | | | - Jennifer A Thomson
- Department of Molecular and Cell Biology, University of Cape Town, Rondebosch 7701, South Africa
| | - Edward P Rybicki
- Department of Molecular and Cell Biology, University of Cape Town, Rondebosch 7701, South Africa
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Casado CG, Javier Ortiz G, Padron E, Bean SJ, McKenna R, Agbandje-McKenna M, Boulton MI. Isolation and characterization of subgenomic DNAs encapsidated in “single” T = 1 isometric particles of Maize streak virus. Virology 2004; 323:164-71. [PMID: 15165828 DOI: 10.1016/j.virol.2004.02.014] [Citation(s) in RCA: 29] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2003] [Revised: 01/29/2004] [Accepted: 02/19/2004] [Indexed: 11/25/2022]
Abstract
"Single" T = 1 isometric particles of Maize streak virus (MSV) have been isolated from infected maize leaves. Biochemical and genetic characterizations show that these particles contain subgenomic (sg) MSV DNA encapsidated by the MSV coat protein. The largest sg DNA is 1.56 kb, slightly larger than half genome size, although sg DNAs as small as 0.2 kb were also cloned. The sg DNAs are not infectious, and they do not appear to play a role in the pathogenicity of MSV. This is the first report of sg DNAs for MSV and, to our knowledge, the first time that encapsidated sg DNAs have been characterized at the sequence level for any geminivirus. These data will assist in our investigations into the role of genomic DNA in the formation of the unique geminate capsid architecture of the Geminiviridae.
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Affiliation(s)
- Carolina G Casado
- Department of Biochemistry and Molecular Biology, College of Medicine, McKnight Brain Institute, University of Florida, Gainesville, FL 32610-0245, USA
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Abstract
The infectivity of cloned unit-length genomes of Maize streak virus (MSV) was tested using vascular puncture inoculation (VPI). VPI of kernels with plasmid DNA (pUC19) carrying a tandem repeat of the MSV genome produced 33+/-8% infection. Similar plasmids carrying the unit-length MSV genome were not infectious. If the MSV genome was released from the plasmid prior to VPI, 16+/-4% of plants became infected. Ligation of the free linear MSV genome did not increase infectivity. The three infective inocula produced symptoms of similar severity in maize. Bioassay of systemically infected leaves indicated the virus was equally infectious regardless of inoculum. In Southern blots of bioassay plants, no differences in MSV genome restriction endonuclease sites were observed. Thus, inoculation with the free linear or circularized MSV unit-length genome produced infections similar to those with plasmids carrying tandemly repeated genomes. The infectivity of free linear MSV unit-length genomes will facilitate molecular analysis of MSV, because cloning steps are minimized.
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Affiliation(s)
- M G Redinbaugh
- Department of Plant Pathology, Ohio Agriculture Research and Development Center, The Ohio State University, 1680 Madison Avenue, Wooster, OH 44691, USA.
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Muñoz-Martín A, Collin S, Herreros E, Mullineaux PM, Fernández-Lobato M, Fenoll C. Regulation of MSV and WDV virion-sense promoters by WDV nonstructural proteins: a role for their retinoblastoma protein-binding motifs. Virology 2003; 306:313-23. [PMID: 12642104 DOI: 10.1016/s0042-6822(02)00072-7] [Citation(s) in RCA: 18] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/27/2022]
Abstract
In this work we demonstrate that wheat dwarf virus (WDV) RepA can activate WDV and maize streak virus (MSV) virion (V)-sense expression in plant tissues. Rep alone does not have any effect on the silent WDV promoter and it represses the basal MSV promoter activity. MSV promoter activation by RepA depends on an intact RepA retinoblastoma protein (RB)-binding domain. Promoter repression by Rep also depends on this domain to some extent. Mutation of the RepA RB-binding domain has no effect on WDV promoter activation. The WDV promoter contains two sites that fit the consensus E2F-binding site. One, WDV1, binds human E2F-1 in one-hybrid assays in yeast. It also binds specifically to maize and wheat proteins in vitro and, when fused to a minimal 35S promoter, it confers responsiveness to RepA only when the RepA RB-binding domain and the WDV1 site are intact. In the whole WDV V-sense promoter context, mutations of this sequence have no effect, suggesting that additional sequences are important for RepA-mediated promoter activation.
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Affiliation(s)
- Angeles Muñoz-Martín
- Facultad de Ciencias del Medio Ambiente, Universidad de Castilla-La Mancha, E-45071, Toledo, Spain
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23
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Abstract
Genes and intergenic regions were reciprocally exchanged between a highly pathogenic Maize streak virus (MSV) isolate (MSV-MatA) and three less pathogenic isolates (MSV-Kom, MSV-R2, and MSV-VW) to determine the contribution of individual genome constituents to MSV pathogenicity in maize. Comparison of disease symptoms produced by the 54 resulting chimaeras and parental viruses enabled identification of genome constituents that are primarily responsible for the heightened pathogenicity of MSV-MatA in maize. Whereas pathogenicity determinants were detected in all of the MSV genomic regions examined, generally only chimaeras containing the MSV-MatA long intergenic region, coat protein gene, and/or movement protein gene were more pathogenic than the milder MSV isolates from which most of their genomes were derived. The pathogenicity of chimeras was strongly influenced by the relatedness of their parental viruses and evidence was found of nucleotide sequence-dependent interactions between both coding and intergenic regions.
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Affiliation(s)
- D P Martin
- Department of Molecular and Cell Biology, University of Cape Town, Private Bag, Rondebosch, 7701, Western Cape, South Africa
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24
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Abstract
Recombination between divergent virus genomes is believed to be a major mechanism for generation of novel virus genotypes. We have examined the recombination process in geminiviruses by forcing recombination between two distinct isolates of Maize streak virus (MSV), MSV-Kom and MSV-Set. Heterodimeric agroinfectious constructs containing tandemly cloned mixtures of complete or partial MSV-Set and MSV-Kom genomes were used to simulate a circular dimeric form similar to that which would be expected to occur following a single intermolecular crossing-over event between MSV-Set and MSV-Kom replicative form DNAs at the long intergenic region (LIR)-movement protein gene (MP) interface. We isolated, analysed and biologically characterized many of the recombinant MSV genomes that were generated from the constructs in planta. Apart from having the same simulated breakpoint at the LIR-MP interface, all the genomes examined had a second breakpoint that had been generated through either intramolecular homologous recombination or a replicational release mechanism. The pathogenicities of six predominantly MSV-Kom-like recombinants were tested in maize. While all were capable of producing a symptomatic infection in this host, none was more virulent than MSV-Kom and only two were more virulent than MSV-Set. The two most virulent recombinants were leafhopper transmitted to a range of differentially MSV-resistant maize, wheat and barley genotypes and both were found to have unique biological properties.
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Affiliation(s)
- W H Schnippenkoetter
- Department of Molecular and Cell Biology, University of Cape Town, Private Bag, Cape Town 7000, South Africa1
| | - D P Martin
- Department of Molecular and Cell Biology, University of Cape Town, Private Bag, Cape Town 7000, South Africa1
| | - J A Willment
- Department of Molecular and Cell Biology, University of Cape Town, Private Bag, Cape Town 7000, South Africa1
| | - E P Rybicki
- Department of Molecular and Cell Biology, University of Cape Town, Private Bag, Cape Town 7000, South Africa1
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25
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Abstract
Restriction analysis and cloning of virus-specific double-stranded DNA isolated from plants infected with wheat dwarf virus (WDV) indicated that the virus genome, like that of maize streak virus (MSV), consists of a single DNA circle. The complete nucleotide sequence of cloned WDV DNA (2749 nucleotides) has been determined. Comparison of the potential coding regions in WDV DNA with those in the DNA of two strains of MSV suggests that these viruses encode at least two functional proteins, the coat protein read in the virion (+) DNA sense and a composite protein, formed from two open reading regions, in the complementary (-) DNA sense. Although WDV and MSV are serologically unrelated their coat proteins showed 35% direct amino acid sequence and their DNAs showed 46% nucleotide sequence homology. There was too little homology between the DNAs of WDV and those of two geminiviruses with bipartite genomes, cassava latent virus (CLV) and tomato golden mosaic virus (TGMV), to align the sequences. However comparison of the amino acid sequences of predicted proteins of WDV, MSV, TGMV and CLV revealed clear relationships between these viruses and suggested that the monopartite and the bipartite geminiviruses have a common ancestral origin. Four inverted repeat sequences which have the potential to form hairpin structures of deltaG >/= -14 kcal/mol were detected in WDV DNA. The sequence TAATATTAC present in the loop of one of these hairpins is conserved in similar putative structures in MSV DNA and in both DNA components of CLV and TGMV and may function as a recognition sequence for a protein involved in virus DNA replication.
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Affiliation(s)
- S W MacDowell
- Department of Pure and Applied Biology, Imperial College of Science and Technology, London SW7 2BB, UK
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