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Zhong X, Wang ZQ, Xiao R, Cao L, Wang Y, Xie Y, Zhou X. Mimic Phosphorylation of a βC1 Protein Encoded by TYLCCNB Impairs Its Functions as a Viral Suppressor of RNA Silencing and a Symptom Determinant. J Virol 2017; 91:e00300-17. [PMID: 28539450 PMCID: PMC5533934 DOI: 10.1128/jvi.00300-17] [Citation(s) in RCA: 37] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2017] [Accepted: 05/17/2017] [Indexed: 01/03/2023] Open
Abstract
Phosphorylation of the βC1 protein encoded by the betasatellite of tomato yellow leaf curl China virus (TYLCCNB-βC1) by SNF1-related protein kinase 1 (SnRK1) plays a critical role in defense of host plants against geminivirus infection in Nicotiana benthamiana However, how phosphorylation of TYLCCNB-βC1 impacts its pathogenic functions during viral infection remains elusive. In this study, we identified two additional tyrosine residues in TYLCCNB-βC1 that are phosphorylated by SnRK1. The effects of TYLCCNB-βC1 phosphorylation on its functions as a viral suppressor of RNA silencing (VSR) and a symptom determinant were investigated via phosphorylation mimic mutants in N. benthamiana plants. Mutations that mimic phosphorylation of TYLCCNB-βC1 at tyrosine 5 and tyrosine 110 attenuated disease symptoms during viral infection. The phosphorylation mimics weakened the ability of TYLCCNB-βC1 to reverse transcriptional gene silencing and to suppress posttranscriptional gene silencing and abolished its interaction with N. benthamiana ASYMMETRIC LEAVES 1 in N. benthamiana leaves. The mimic phosphorylation of TYLCCNB-βC1 had no impact on its protein stability, subcellular localization, or self-association. Our data establish an inhibitory effect of phosphorylation of TYLCCNB-βC1 on its pathogenic functions as a VSR and a symptom determinant and provide a mechanistic explanation of how SnRK1 functions as a host defense factor.IMPORTANCE Tomato yellow leaf curl China virus (TYLCCNV), which causes a severe yellow leaf curl disease in China, is a monopartite geminivirus associated with the betasatellite (TYLCCNB). TYLCCNB encodes a single pathogenicity protein, βC1 (TYLCCNB-βC1), which functions as both a viral suppressor of RNA silencing (VSR) and a symptom determinant. Here, we show that mimicking phosphorylation of TYLCCNB-βC1 weakens its ability to reverse transcriptional gene silencing, to suppress posttranscriptional gene silencing, and to interact with N. benthamiana ASYMMETRIC LEAVES 1. To our knowledge, this is the first report establishing an inhibitory effect of phosphorylation of TYLCCNB-βC1 on its pathogenic functions as both a VSR and a symptom determinant and to provide a mechanistic explanation of how SNF1-related protein kinase 1 acts as a host defense factor. These findings expand the scope of phosphorylation-mediated defense mechanisms and contribute to further understanding of plant defense mechanisms against geminiviruses.
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Affiliation(s)
- Xueting Zhong
- State Key Laboratory of Rice Biology, Institute of Biotechnology, Zhejiang University, Hangzhou, China
| | - Zhan Qi Wang
- State Key Laboratory of Rice Biology, Institute of Biotechnology, Zhejiang University, Hangzhou, China
| | - Ruyuan Xiao
- State Key Laboratory of Rice Biology, Institute of Biotechnology, Zhejiang University, Hangzhou, China
| | - Linge Cao
- State Key Laboratory of Rice Biology, Institute of Biotechnology, Zhejiang University, Hangzhou, China
| | - Yaqin Wang
- State Key Laboratory of Rice Biology, Institute of Biotechnology, Zhejiang University, Hangzhou, China
| | - Yan Xie
- State Key Laboratory of Rice Biology, Institute of Biotechnology, Zhejiang University, Hangzhou, China
| | - Xueping Zhou
- State Key Laboratory of Rice Biology, Institute of Biotechnology, Zhejiang University, Hangzhou, China
- State Key Laboratory for Biology of Plant Diseases and Insect Pests, Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing, China
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152
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Wang ZZ, Bing XL, Liu SS, Chen XX. RNA interference of an antimicrobial peptide, Btdef, reduces Tomato yellow leaf curl China virus accumulation in the whitefly Bemisia tabaci. PEST MANAGEMENT SCIENCE 2017; 73:1421-1427. [PMID: 27804213 DOI: 10.1002/ps.4472] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/28/2016] [Revised: 10/03/2016] [Accepted: 11/02/2016] [Indexed: 06/06/2023]
Abstract
BACKGROUND The whitefly Bemisia tabaci (Gennadius) is considered one of the main pests for agriculture. One important problem with the whitefly is its notorious status as a vector for plant viruses, primarily begomoviruses. We have previously identified a defensin-like antimicrobial peptide, Btdef, from the whitefly B. tabaci MEAM1. However, the function of Btdef in the immune system of the insect vector and begomovirus transmission has yet to be explored. RESULTS To explore the role of Btdef during begomovirus transmission, we firstly investigated the transcriptional response of Btdef following acquisition of Tomato yellow leaf curl China virus (TYLCCNV). The expression of Btdef was up-regulated in the viruliferous whiteflies. After RNA silencing of the Btdef gene in adult whiteflies fed with dsRNA, they were allowed to feed on TYLCCNV-infected plants and then quantified for TYLCCNV DNA titre. Unexpectedly, silencing the Btdef gene reduced both the abundance and expressions of TYLCCNV genes in the whiteflies. In the meantime, the density of the endosymbiont Rickettsia was significantly reduced in dsBtdef-fed whiteflies. CONCLUSION Our data provide evidence that Btdef is involved in begomovirus infection, possibly through symbiont-mediated alteration of begomovirus-whitefly interactions. These findings indicate that Btdef may be targeted for the development of new technology for the control of whitefly-transmitted begomoviruses. © 2016 Society of Chemical Industry.
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Affiliation(s)
- Zhi-Zhi Wang
- Ministry of Agriculture Key Lab of Agricultural Entomology, Institute of Insect Sciences, Zhejiang University, Hangzhou, China
| | - Xiao-Li Bing
- Ministry of Agriculture Key Lab of Agricultural Entomology, Institute of Insect Sciences, Zhejiang University, Hangzhou, China
| | - Shu-Sheng Liu
- Ministry of Agriculture Key Lab of Agricultural Entomology, Institute of Insect Sciences, Zhejiang University, Hangzhou, China
| | - Xue-Xin Chen
- Ministry of Agriculture Key Lab of Agricultural Entomology, Institute of Insect Sciences, Zhejiang University, Hangzhou, China
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153
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Mar TB, Mendes IR, Lau D, Fiallo-Olivé E, Navas-Castillo J, Alves MS, Murilo Zerbini F. Interaction between the New World begomovirus Euphorbia yellow mosaic virus and its associated alphasatellite: effects on infection and transmission by the whitefly Bemisia tabaci. J Gen Virol 2017; 98:1552-1562. [PMID: 28590236 DOI: 10.1099/jgv.0.000814] [Citation(s) in RCA: 34] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022] Open
Abstract
The majority of Old World monopartite begomoviruses (family Geminiviridae) are associated with satellite DNAs. Alphasatellites are capable of autonomous replication, but depend on the helper virus for movement, encapsidation and transmission by the insect vector. Recently, Euphorbia yellow mosaic alphasatellite (EuYMA) was found in association with Euphorbia yellow mosaic virus (EuYMV) infecting Euphorbia heterophylla plants in Brazil. The geographical range of EuYMA was assessed in a representative sampling of E. heterophylla plants collected in several states of Brazil from 2009 to 2014. Infectious clones were generated and used to assess the phenotype of viral infection in the presence or absence of the alphasatellite in tomato, E. heterophylla, Nicotiana benthamiana, Arabidopsis thaliana and Crotalaria juncea. Phenotypic differences of EuYMV infection in the presence or absence of EuYMA were observed in A. thaliana, N. benthamiana and E. heterophylla. Symptoms were more severe when EuYMV was inoculated in combination with EuYMA in N. benthamiana and E. heterophylla, and the presence of the alphasatellite was determinant for symptom development in A. thaliana. Quantification of EuYMV and EuYMA indicated that EuYMA affects the accumulation of EuYMV during infection on a host-dependent basis. Transmission assays indicated that EuYMA negatively affects the transmission of EuYMV by Bemisia tabaci MEAM1. Together, these results indicate that EuYMA is capable of modulating symptoms, viral accumulation and whitefly transmission of EuYMV, potentially interfering with virus dissemination in the field.
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Affiliation(s)
- Talita Bernardon Mar
- Dep de Fitopatologia/BIOAGRO, Universidade Federal de Viçosa, Viçosa, MG 36570-900, Brazil.,National Research Institute for Plant-Pest Interactions, Universidade Federal de Viçosa, Viçosa, MG 36570-900, Brazil
| | - Igor Rodrigues Mendes
- Dep de Fitopatologia/BIOAGRO, Universidade Federal de Viçosa, Viçosa, MG 36570-900, Brazil.,National Research Institute for Plant-Pest Interactions, Universidade Federal de Viçosa, Viçosa, MG 36570-900, Brazil
| | - Douglas Lau
- Embrapa Trigo, Rodovia BR-285, CP 3081, Passo Fundo, RS, 99001-970, Brazil
| | - Elvira Fiallo-Olivé
- National Research Institute for Plant-Pest Interactions, Universidade Federal de Viçosa, Viçosa, MG 36570-900, Brazil.,Instituto de Hortofruticultura Subtropical y Mediterránea ''La Mayora'', Universidad de Málaga - Consejo Superior de Investigaciones Científicas (IHSM-UMA-CSIC), Estación Experimental ''La Mayora'', 29750 Algarrobo-Costa, Málaga, Spain
| | - Jesús Navas-Castillo
- National Research Institute for Plant-Pest Interactions, Universidade Federal de Viçosa, Viçosa, MG 36570-900, Brazil.,Instituto de Hortofruticultura Subtropical y Mediterránea ''La Mayora'', Universidad de Málaga - Consejo Superior de Investigaciones Científicas (IHSM-UMA-CSIC), Estación Experimental ''La Mayora'', 29750 Algarrobo-Costa, Málaga, Spain
| | - Murilo Siqueira Alves
- Dep de Fitopatologia/BIOAGRO, Universidade Federal de Viçosa, Viçosa, MG 36570-900, Brazil.,National Research Institute for Plant-Pest Interactions, Universidade Federal de Viçosa, Viçosa, MG 36570-900, Brazil
| | - F Murilo Zerbini
- Dep de Fitopatologia/BIOAGRO, Universidade Federal de Viçosa, Viçosa, MG 36570-900, Brazil.,National Research Institute for Plant-Pest Interactions, Universidade Federal de Viçosa, Viçosa, MG 36570-900, Brazil
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154
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Sattar MN, Iqbal Z, Tahir MN, Ullah S. The Prediction of a New CLCuD Epidemic in the Old World. Front Microbiol 2017; 8:631. [PMID: 28469604 PMCID: PMC5395620 DOI: 10.3389/fmicb.2017.00631] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2016] [Accepted: 03/28/2017] [Indexed: 12/05/2022] Open
Abstract
Cotton leaf curl disease (CLCuD), the most complex disease of cotton, is a major limiting biotic factor to worldwide cotton productivity. Several whitefly-transmitted monopartite begomoviruses causing CLCuD have been characterized and designated as CLCuD-associated begomoviruses. Despite of being reported over 100 years ago in Africa, CLCuD became economically pandemic causing massive losses to cotton production in Pakistan and India during past couple of decades. In Asia, cotton has faced two major epidemics during this period viz. "Multan epidemic" and "Burewala epidemic." The "Multan epidemic" era was 1988-1999 after which the virus remained calm until 2002 when "Burewala epidemic" broke into the cotton fields in Indo-Pak subcontinent, till 2013-2014. However, both the epidemics were caused by monopartite begomovirus complex. Similarly in Africa, Cotton leaf curl Gezira virus with associated DNA-satellites causes CLCuD. Quite recently, in the Old World (both Asia and Africa), bipartite begomoviruses have started appearing in the areas under cotton cultivation. Under such aggravated circumstances, it seems we are heading toward another epidemic of CLCuD in the Old World. Here we articulate the causes and potential emergence of the third epidemic of CLCuD in Asia. The current situation of CLCuD in Asia and Africa is also discussed.
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Affiliation(s)
- Muhammad N. Sattar
- Department of Environment and Natural Resources, Faculty of Agriculture and Food Science, King Faisal UniversityAl-Hasa, Saudi Arabia
| | - Zafar Iqbal
- Akhuwat-Faisalabad Institute of Research, Science and TechnologyFaisalabad, Pakistan
| | | | - Sami Ullah
- University College of Agriculture, University of SargodhaSargodha, Pakistan
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155
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Zaidi SSEA, Mansoor S. Viral Vectors for Plant Genome Engineering. FRONTIERS IN PLANT SCIENCE 2017; 8:539. [PMID: 28443125 PMCID: PMC5386974 DOI: 10.3389/fpls.2017.00539] [Citation(s) in RCA: 60] [Impact Index Per Article: 8.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/14/2017] [Accepted: 03/27/2017] [Indexed: 05/19/2023]
Abstract
Recent advances in genome engineering (GE) has made it possible to precisely alter DNA sequences in plant cells, providing specifically engineered plants with traits of interest. Gene targeting efficiency depends on the delivery-method of both sequence-specific nucleases and repair templates, to plant cells. Typically, this is achieved using Agrobacterium mediated transformation or particle bombardment, both of which transform only a subset of cells in treated tissues. The alternate in planta approaches, stably integrating nuclease-encoding cassettes and repair templates into the plant genome, are time consuming, expensive and require extra regulations. More efficient GE reagents delivery methods are clearly needed if GE is to become routine, especially in economically important crops that are difficult to transform. Recently, autonomously replicating virus-based vectors have been demonstrated as efficient means of delivering GE reagents in plants. Both DNA viruses (Bean yellow dwarf virus, Wheat dwarf virus and Cabbage leaf curl virus) and RNA virus (Tobacco rattle virus) have demonstrated efficient gene targeting frequencies in model plants (Nicotiana benthamiana) and crops (potato, tomato, rice, and wheat). Here we discuss the recent advances using viral vectors for plant genome engineering, the current limitations and future directions.
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Affiliation(s)
- Syed Shan-e-Ali Zaidi
- Molecular Virology and Gene Silencing Laboratory, Agricultural Biotechnology Division, National Institute for Biotechnology and Genetic EngineeringFaisalabad, Pakistan
| | - Shahid Mansoor
- Molecular Virology and Gene Silencing Laboratory, Agricultural Biotechnology Division, National Institute for Biotechnology and Genetic EngineeringFaisalabad, Pakistan
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156
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Heydarnejad J, Kamali M, Massumi H, Kvarnheden A, Male MF, Kraberger S, Stainton D, Martin DP, Varsani A. Identification of a Nanovirus-Alphasatellite Complex in Sophora alopecuroides. Virus Res 2017; 235:24-32. [PMID: 28396284 DOI: 10.1016/j.virusres.2017.03.023] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2017] [Revised: 03/15/2017] [Accepted: 03/18/2017] [Indexed: 10/19/2022]
Abstract
Viruses in the genus Nanovirus of the family Nanoviridae generally have eight individually encapsidated circular genome components and have been predominantly found infecting Fabaceae plants in Europe, Australia, Africa and Asia. For over a decade Sophora alopecuroides L. (Fabaceae) plants have been observed across Iran displaying dwarfing, yellowing, stunted leaves and yellow vein banding. Using a high-throughput sequencing approach, sequences were identified within one such plant that had similarities to nanovirus genome components. From this plant, the nanovirus-like molecules DNA-R (n=4), DNA-C (n=2), DNA-S (n=1), DNA-M (n=1), DNA-N (n=1), DNA-U1 (n=1), DNA-U2 (n=1) and DNA-U4 (n=1) were amplified, cloned and sequenced. Other than for the DNA-R, these components share less than 71% identity with those of other known nanoviruses. The four DNA-R molecules were highly diverse, sharing only 65-71% identity with each other and 64-86% identity with those of other nanoviruses. In the S. alopecuroides plant 14 molecules sharing 57.7-84.6% identity with previously determined sequences of nanovirus-associated alphasatellites were also identified. Given the research activity in the nanovirus field during the last five years coupled with high-throughput sequence technologies, many more diverse nanoviruses and nanovirus-associated satellites are likely to be identified.
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Affiliation(s)
- Jahangir Heydarnejad
- Department of Plant Protection, College of Agriculture, Shahid Bahonar University of Kerman, Kerman, Iran.
| | - Mehdi Kamali
- Department of Plant Protection, College of Agriculture, Shahid Bahonar University of Kerman, Kerman, Iran
| | - Hossain Massumi
- Department of Plant Protection, College of Agriculture, Shahid Bahonar University of Kerman, Kerman, Iran
| | - Anders Kvarnheden
- Department of Plant Biology, Uppsala BioCenter, Linnean Center of Plant Biology in Uppsala, Swedish University of Agricultural Sciences, Box 7080, SE-750 07 Uppsala, Sweden
| | - Maketalena F Male
- School of Biological Sciences, University of Canterbury, Private Bag 4800, Christchurch 8140, New Zealand
| | - Simona Kraberger
- School of Biological Sciences, University of Canterbury, Private Bag 4800, Christchurch 8140, New Zealand; Department of Microbiology, Immunology and Pathology, Colorado State University, Fort Collins, CO 80523, USA
| | - Daisy Stainton
- School of Biological Sciences, University of Canterbury, Private Bag 4800, Christchurch 8140, New Zealand; School of Biological Sciences, The University of Queensland, Brisbane, Queensland 4072, Australia
| | - Darren P Martin
- Computational Biology Group, Institute of Infectious Disease and Molecular Medicine, Faculty of Health Sciences, University of Cape Town, Observatory 7925, Rondebosch, Cape Town, South Africa
| | - Arvind Varsani
- School of Biological Sciences, University of Canterbury, Private Bag 4800, Christchurch 8140, New Zealand; Structural Biology Research Unit, Department of Clinical Laboratory Sciences, University of Cape Town, Rondebosch 7701, Cape Town, South Africa; The Biodesign Center for Fundamental and Applied Microbiomics, Center for Evolution and Medicine, School of Life Sciences, Arizona State University, Tempe, AZ 85287-5001, USA.
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157
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Zubair M, Zaidi SSEA, Shakir S, Farooq M, Amin I, Scheffler JA, Scheffler BE, Mansoor S. Multiple begomoviruses found associated with cotton leaf curl disease in Pakistan in early 1990 are back in cultivated cotton. Sci Rep 2017; 7:680. [PMID: 28386113 PMCID: PMC5429635 DOI: 10.1038/s41598-017-00727-2] [Citation(s) in RCA: 30] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2016] [Accepted: 03/10/2017] [Indexed: 11/09/2022] Open
Abstract
The first epidemic of cotton leaf curl disease (CLCuD) in early 1990's in the Indian subcontinent was associated with several distinct begomoviruses along with a disease-specific betasatellite. Resistant cotton varieties were introduced in late 1990's but soon resistance was broken and was associated with a single recombinant begomovirus named Burewala strain of Cotton leaf curl Kokhran virus that lacks a full complement of a gene encoding a transcription activator protein (TrAP). In order to understand the ongoing changes in CLCuD complex in Pakistan, CLCuD affected plants from cotton fields at Vehari were collected. Illumina sequencing was used to assess the diversity of CLCuD complex. At least three distinct begomoviruses characterized from the first epidemic; Cotton leaf curl Multan virus, Cotton leaf curl Kokhran virus and Cotton leaf curl Alabad virus, several distinct species of alphasatellites and cotton leaf curl Multan betasatellite were found associated with CLCuD. These viruses were also cloned and sequenced through Sanger sequencing to confirm the identity of the begomoviruses and that all clones possessed a full complement of the TrAP gene. A new strain of betasatellite was identified here and named CLCuMuBVeh. The implications of these findings in efforts to control CLCuD are discussed.
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Affiliation(s)
- Muhammad Zubair
- National Institute for Biotechnology and Genetic Engineering, Faisalabad, Pakistan.,Pakistan Institute of Engineering and Applied Sciences, Nilore, Islamabad, Pakistan
| | - Syed Shan-E-Ali Zaidi
- National Institute for Biotechnology and Genetic Engineering, Faisalabad, Pakistan.,Pakistan Institute of Engineering and Applied Sciences, Nilore, Islamabad, Pakistan
| | - Sara Shakir
- Centre for Agricultural Biochemistry and Biotechnology, University of Agriculture, Faisalabad, Pakistan
| | - Muhammad Farooq
- National Institute for Biotechnology and Genetic Engineering, Faisalabad, Pakistan
| | - Imran Amin
- National Institute for Biotechnology and Genetic Engineering, Faisalabad, Pakistan
| | - Jodi A Scheffler
- USDA-ARS, Crop Genetics Research Unit, 141 Experiment Station Rd, Stoneville, MS, 38776, USA
| | - Brian E Scheffler
- USDA-ARS, Genomics and Bioinformatics Research Unit, 141 Experiment Station Rd, Stoneville, MS, 38776, USA
| | - Shahid Mansoor
- National Institute for Biotechnology and Genetic Engineering, Faisalabad, Pakistan.
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158
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Vinoth Kumar R, Singh D, Singh AK, Chakraborty S. Molecular diversity, recombination and population structure of alphasatellites associated with begomovirus disease complexes. INFECTION, GENETICS AND EVOLUTION : JOURNAL OF MOLECULAR EPIDEMIOLOGY AND EVOLUTIONARY GENETICS IN INFECTIOUS DISEASES 2017; 49:39-47. [PMID: 28062387 DOI: 10.1016/j.meegid.2017.01.001] [Citation(s) in RCA: 43] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/28/2016] [Revised: 12/21/2016] [Accepted: 01/02/2017] [Indexed: 11/21/2022]
Abstract
The genus, begomovirus (family Geminiviridae) includes a large number of viruses infecting a wide range of plant species worldwide. The majority of monopartite begomoviruses are associated with satellites (betasatellites) and/or satellite-like molecules (alphasatellites). In spite of the Indo-China region being regarded as the centre of origin of begomoviruses and satellites, a detailed study on the emergence and evolution of alphasatellites in India has not yet conducted. Our present analysis indicated the association of 22 alphasatellites with monopartite and bipartite begomovirus-betasatellite complexes in India. Based on sequence pairwise identity, these alphasatellites were categorized into five distinct groups: Cotton leaf curl alphasatellite, Gossypium darwinii symptomless alphasatellite, Gossypium mustelinum symptomless alphasatellite, Okra leaf curl alphasatellite and an unreported Chilli leaf curl alphasatellite (ChiLCA). Furthermore, infectivity analysis of the cloned ChiLCA along with the viral components of either cognate or non-cognate chilli-infecting begomoviruses on Nicotiana benthamiana suggested that ChiLCA is dispensable for leaf curl disease development. It is noteworthy that in the presence of ChiLCA, a marginal decrease in betasatellite DNA level was noticed. Additionally, high genetic variability and diverse recombination patterns were detected among these alphasatellites, and the nucleotide substitution rate for the Rep gene of ChiLCA was determined to be 2.25×10-3nucleotides/site/year. This study highlights the genetic distribution, and likely contribution of recombination and nucleotide diversity in facilitating the emergence of alphasatellites.
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Affiliation(s)
- R Vinoth Kumar
- Molecular Virology Laboratory, School of Life Sciences, Jawaharlal Nehru University, New Delhi -110 067, India
| | - Divya Singh
- Molecular Virology Laboratory, School of Life Sciences, Jawaharlal Nehru University, New Delhi -110 067, India
| | - Achuit K Singh
- Molecular Virology Laboratory, School of Life Sciences, Jawaharlal Nehru University, New Delhi -110 067, India
| | - S Chakraborty
- Molecular Virology Laboratory, School of Life Sciences, Jawaharlal Nehru University, New Delhi -110 067, India.
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159
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Kulshreshtha A, Roshan P, Sharma D, Hallan V. Molecular characterization of a new begomovirus infecting Mirabilis jalapa in northern India. Arch Virol 2017; 162:2163-2167. [PMID: 28342034 DOI: 10.1007/s00705-017-3330-4] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2016] [Accepted: 03/09/2017] [Indexed: 11/30/2022]
Abstract
Begomoviruses are whitefly-transmitted single-stranded DNA viruses that are responsible for considerable economic losses. A begomovirus, alphasatellite and betasatellite were characterized in a Mirabilis jalapa plant exhibiting severe leaf curling and mottling symptoms. The complete viral genome shared highest sequence identity of 87% with pedilanthus leaf curl virus (AM712436), reported from Pakistan. Additionally, the viral genome was 84% identical to that of chilli leaf curl India virus (KX951415) and 83% identical to that of tobacco curly shoot virus (GU1999584), which were previously reported to infect M. jalapa in India and China, respectively. Based on the ICTV criterion for begomovirus species demarcation (≥91% sequence identity for the complete genome), the virus represents a new species, for which we propose the name Mirabilis leaf curl virus. The alphasatellite and betasatellite sequences were similar to the corresponding sequences of ageratum yellow vein India alphasatellite (KU852743; 99% identity) and tomato leaf curl Patna betasatellite (HQ180394; 86% identity) sequences, respectively. This report describes a new begomovirus-satellite disease complex in M. jalapa.
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Affiliation(s)
- Aditya Kulshreshtha
- Academy of Scientific and Innovative Research (AcSIR), CSIR-Institute of Himalayan Bioresource Technology, Palampur, Himachal Pradesh, 176061, India.,CSIR-IHBT, Palampur, Himachal Pradesh, 176061, India
| | - Poonam Roshan
- Academy of Scientific and Innovative Research (AcSIR), CSIR-Institute of Himalayan Bioresource Technology, Palampur, Himachal Pradesh, 176061, India.,CSIR-IHBT, Palampur, Himachal Pradesh, 176061, India
| | - Dolly Sharma
- CSIR-IHBT, Palampur, Himachal Pradesh, 176061, India
| | - Vipin Hallan
- Academy of Scientific and Innovative Research (AcSIR), CSIR-Institute of Himalayan Bioresource Technology, Palampur, Himachal Pradesh, 176061, India. .,CSIR-IHBT, Palampur, Himachal Pradesh, 176061, India.
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160
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Al Rwahnih M, Alabi OJ, Westrick NM, Golino D, Rowhani A. Description of a Novel Monopartite Geminivirus and Its Defective Subviral Genome in Grapevine. PHYTOPATHOLOGY 2017; 107:240-251. [PMID: 27670772 DOI: 10.1094/phyto-07-16-0282-r] [Citation(s) in RCA: 31] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/06/2023]
Abstract
A novel virus was detected in grapevines by Illumina sequencing during the screening of two table grape (Vitis vinifera) accessions, cultivars Black Beet and Nagano Purple, from South Korea. The monopartite circular ssDNA genome sequence was subsequently confirmed by rolling cycle amplification, cloning and Sanger sequencing. The complete viral genomic sequence from both accessions ranged from 2,903 to 2,907 nucleotides in length and contained the conserved nonanucleotide sequence TAATATT↓AC and other sequence features typical of the family Geminiviridae, including two predicted sense and four complementary-sense open reading frames. Phylogenetic analysis placed the novel virus in a unique taxon within the family Geminiviridae. A naturally occurring defective subviral DNA was also discovered. This defective DNA molecule carried a deletion of approximately 46% of the full-length genome. Both the genomic and defective DNA molecules were graft-transmissible although no disease is yet correlated with their occurrence in Vitis spp. The tentative names Grapevine geminivirus A (GGVA) and GGVA defective DNA (GGVA D-DNA) are proposed. PCR assays developed using primers designed in the coat protein gene led to the detection of GGVA in 1.74% of 1,262 vines derived from 15 grapevine cultivars from six countries across three continents.
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Affiliation(s)
- Maher Al Rwahnih
- First, third, fourth, and fifth authors: Department of Plant Pathology, University of California, Davis, 95616; and second author: Department of Plant Pathology & Microbiology, Texas A&M AgriLife Research and Extension Center, Weslaco 78596
| | - Olufemi J Alabi
- First, third, fourth, and fifth authors: Department of Plant Pathology, University of California, Davis, 95616; and second author: Department of Plant Pathology & Microbiology, Texas A&M AgriLife Research and Extension Center, Weslaco 78596
| | - Nathaniel M Westrick
- First, third, fourth, and fifth authors: Department of Plant Pathology, University of California, Davis, 95616; and second author: Department of Plant Pathology & Microbiology, Texas A&M AgriLife Research and Extension Center, Weslaco 78596
| | - Deborah Golino
- First, third, fourth, and fifth authors: Department of Plant Pathology, University of California, Davis, 95616; and second author: Department of Plant Pathology & Microbiology, Texas A&M AgriLife Research and Extension Center, Weslaco 78596
| | - Adib Rowhani
- First, third, fourth, and fifth authors: Department of Plant Pathology, University of California, Davis, 95616; and second author: Department of Plant Pathology & Microbiology, Texas A&M AgriLife Research and Extension Center, Weslaco 78596
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161
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Khan ZA, Khan JA. Characterization of a new begomovirus and betasatellite associated with chilli leaf curl disease in India. Arch Virol 2017; 162:561-565. [PMID: 27738844 DOI: 10.1007/s00705-016-3096-0] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2016] [Accepted: 09/29/2016] [Indexed: 11/27/2022]
Abstract
Chilli leaf curl disease (ChiLCD) is a serious problem and a major limitation to chilli (Capsicum spp.) cultivation in India. Leaves of a chilli plant showing leaf curl symptoms were collected from the Gonda district in Uttar Pradesh, India, in April, 2013. Full-length genomes of a begomovirus and an associated betasatellite were amplified, cloned and sequenced. The size of the begomovirus genome and the betasatellite were 2760 bp and 1374 bp, respectively. The nucleotide sequence of the begomovirus genome shared maximum identity (89 %) with pepper leaf curl Bangladesh virus-India isolate Chhapra (PepLCBV, JN663853), below the threshold for species demarcation. Sequence analysis showed that the begomovirus is a potential recombinant between viruses related to PepLCBV and chilli leaf curl virus (ChiLCV). The name chilli leaf curl Gonda virus (ChiLCGV) is being proposed. The betasatellite associated with ChiLCGV was identified as tomato leaf curl Bangladesh betasatellite (ToLCBDB). Agroinoculation of the viral genome along with betasatellite induced severe leaf curl symptoms in Nicotiana benthamiana. ChiLCGV and ToLCBDB characterized in this study represent a new begomovirus-betasatellite complex infecting Capsicum.
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Affiliation(s)
- Zainul A Khan
- Plant Virus Laboratory, Department of Biosciences, Jamia Millia Islamia (Central University), New Delhi, 110025, India.
| | - Jawaid A Khan
- Plant Virus Laboratory, Department of Biosciences, Jamia Millia Islamia (Central University), New Delhi, 110025, India
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162
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Zhong X, Wang ZQ, Xiao R, Wang Y, Xie Y, Zhou X. iTRAQ analysis of the tobacco leaf proteome reveals that RNA-directed DNA methylation (RdDM) has important roles in defense against geminivirus-betasatellite infection. J Proteomics 2017; 152:88-101. [PMID: 27989946 DOI: 10.1016/j.jprot.2016.10.015] [Citation(s) in RCA: 31] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2016] [Revised: 10/10/2016] [Accepted: 10/27/2016] [Indexed: 11/22/2022]
Abstract
Geminiviruses have caused serious losses in crop production. To investigate the mechanisms underlying host defenses against geminiviruses, an isobaric tags for relative and absolute quantification (iTRAQ)-based quantitative proteomic approach was used to explore the expression profiles of proteins in Nicotiana benthamiana (N. benthamiana) leaves in response to tomato yellow leaf curl China virus (TYLCCNV) with its betasatellite (TYLCCNB) at an early phase. In total, 4155 proteins were identified and 272 proteins were changed differentially in response to TYLCCNV/TYLCCNB infection. Bioinformatics analysis indicated that S-adenosyl-l-methionine cycle II was the most significantly up-regulated biochemical process during TYLCCNV/TYLCCNB infection. The mRNA levels of three proteins in S-adenosyl-l-methionine cycle II were further analyzed by qPCR, each was found significantly up-regulated in TYLCCNV/TYLCCNB-infected N. benthamiana. This result suggested a strong promotion of the biosynthesis of available methyl groups during geminivirus infections. We further tested the potential role of RdDM in N. benthamiana by virus-induced gene silencing (VIGS) and found that a disruption in RdDM resulted in more severe infectious symptoms and higher accumulation of viral DNA after TYLCCNV/TYLCCNB infection. Although the precise functions of these proteins still need to be determined, our proteomic results enhance the understanding of plant antiviral mechanisms. BIOLOGICAL SIGNIFICANCE One of the major limitations to crop growth in the worldwide is the prevalence of geminiviruses. They are able to infect food and cash crops and cause serious crop failures and economic losses worldwide, especially in Africa and Asia. Tomato yellow leaf curl China virus (TYLCCNV), which causes severe viral diseases in China, is a monopartite geminivirus associated with the betasatellite (TYLCCNB). However, the mechanisms underlying the TYLCCNV/TYLCCNB defense in plants are still not fully understood at the molecular level. In this study, the combined proteomic, bioinformatic and VIGS analyses revealed that TYLCCNV/TYLCCNB invasion caused complex proteomic alterations in the leaves of N. benthamiana involving the processes of stress and defense, energy production, photosynthesis, protein homeostasis, metabolism, cell structure, signal transduction, transcription, transportation, and cell growth/division. Promotion of available methyl groups via the S-adenosyl-l-methionine cycle II pathway in N. benthamiana appeared crucial for antiviral responses. These findings enhance our understanding in the proteomic aspects of host antiviral defenses against geminiviruses, and also demonstrate that the combination of proteomics with bioinformatics and VIGS analysis is an effective approach to investigate systemic plant responses to geminiviruses and to shed light on plant-virus interactions.
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Affiliation(s)
- Xueting Zhong
- State Key Laboratory of Rice Biology, Institute of Biotechnology, Zhejiang University, Hangzhou 310058, China.
| | - Zhan Qi Wang
- State Key Laboratory of Rice Biology, Institute of Biotechnology, Zhejiang University, Hangzhou 310058, China.
| | - Ruyuan Xiao
- State Key Laboratory of Rice Biology, Institute of Biotechnology, Zhejiang University, Hangzhou 310058, China.
| | - Yaqin Wang
- State Key Laboratory of Rice Biology, Institute of Biotechnology, Zhejiang University, Hangzhou 310058, China.
| | - Yan Xie
- State Key Laboratory of Rice Biology, Institute of Biotechnology, Zhejiang University, Hangzhou 310058, China.
| | - Xueping Zhou
- State Key Laboratory of Rice Biology, Institute of Biotechnology, Zhejiang University, Hangzhou 310058, China; State Key Laboratory for Biology of Plant Diseases and Insect Pests, Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing 100193, China.
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163
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Srivastava A, Agrawal L, Raj R, Jaidi M, Raj SK, Gupta S, Dixit R, Singh PC, Tripathi T, Sidhu OP, Singh BN, Shukla S, Chauhan PS, Kumar S. Ageratum enation virus Infection Induces Programmed Cell Death and Alters Metabolite Biosynthesis in Papaver somniferum. FRONTIERS IN PLANT SCIENCE 2017; 8:1172. [PMID: 28729873 PMCID: PMC5498505 DOI: 10.3389/fpls.2017.01172] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/08/2017] [Accepted: 06/19/2017] [Indexed: 05/06/2023]
Abstract
A previously unknown disease which causes severe vein thickening and inward leaf curl was observed in a number of opium poppy (Papaver somniferum L.) plants. The sequence analysis of full-length viral genome and associated betasatellite reveals the occurrence of Ageratum enation virus (AEV) and Ageratum leaf curl betasatellite (ALCB), respectively. Co-infiltration of cloned agroinfectious DNAs of AEV and ALCB induces the leaf curl and vein thickening symptoms as were observed naturally. Infectivity assay confirmed this complex as the cause of disease and also satisfied the Koch's postulates. Comprehensive microscopic analysis of infiltrated plants reveals severe structural anomalies in leaf and stem tissues represented by unorganized cell architecture and vascular bundles. Moreover, the characteristic blebs and membranous vesicles formed due to the virus-induced disintegration of the plasma membrane and intracellular organelles were also present. An accelerated nuclear DNA fragmentation was observed by Comet assay and confirmed by TUNEL and Hoechst dye staining assays suggesting virus-induced programmed cell death. Virus-infection altered the biosynthesis of several important metabolites. The biosynthesis potential of morphine, thebaine, codeine, and papaverine alkaloids reduced significantly in infected plants except for noscapine whose biosynthesis was comparatively enhanced. The expression analysis of corresponding alkaloid pathway genes by real time-PCR corroborated well with the results of HPLC analysis for alkaloid perturbations. The changes in the metabolite and alkaloid contents affect the commercial value of the poppy plants.
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Affiliation(s)
- Ashish Srivastava
- Plant Molecular Virology Laboratory, Council of Scientific and Industrial Research – National Botanical Research InstituteLucknow, India
- Amity Institute of Virology and Immunology, Amity UniversityNoida, India
| | - Lalit Agrawal
- Division of Plant Microbe Interaction, Council of Scientific and Industrial Research – National Botanical Research InstituteLucknow, India
| | - Rashmi Raj
- Plant Molecular Virology Laboratory, Council of Scientific and Industrial Research – National Botanical Research InstituteLucknow, India
| | - Meraj Jaidi
- Plant Molecular Virology Laboratory, Council of Scientific and Industrial Research – National Botanical Research InstituteLucknow, India
| | - Shri K. Raj
- Plant Molecular Virology Laboratory, Council of Scientific and Industrial Research – National Botanical Research InstituteLucknow, India
| | - Swati Gupta
- Division of Plant Microbe Interaction, Council of Scientific and Industrial Research – National Botanical Research InstituteLucknow, India
| | - Ritu Dixit
- Division of Plant Microbe Interaction, Council of Scientific and Industrial Research – National Botanical Research InstituteLucknow, India
| | - Poonam C. Singh
- Division of Plant Microbe Interaction, Council of Scientific and Industrial Research – National Botanical Research InstituteLucknow, India
| | - Tusha Tripathi
- Division of Phytochemistry, Council of Scientific and Industrial Research – National Botanical Research InstituteLucknow, India
| | - Om P. Sidhu
- Division of Phytochemistry, Council of Scientific and Industrial Research – National Botanical Research InstituteLucknow, India
| | - Brahma N. Singh
- Division of Pharmacognosy and Ethnopharmacology, Council of Scientific and Industrial Research – National Botanical Research InstituteLucknow, India
| | - Sudhir Shukla
- Plant Breeding Laboratory, Council of Scientific and Industrial Research – National Botanical Research InstituteLucknow, India
| | - Puneet S. Chauhan
- Division of Plant Microbe Interaction, Council of Scientific and Industrial Research – National Botanical Research InstituteLucknow, India
| | - Susheel Kumar
- Plant Molecular Virology Laboratory, Council of Scientific and Industrial Research – National Botanical Research InstituteLucknow, India
- *Correspondence: Susheel Kumar,
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164
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Stainton D, Martin DP, Collings DA, Varsani A. Comparative analysis of common regions found in babuviruses and alphasatellite molecules. Arch Virol 2016; 162:849-855. [PMID: 27878460 DOI: 10.1007/s00705-016-3168-1] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2016] [Accepted: 10/24/2016] [Indexed: 11/26/2022]
Abstract
Viruses in the genus Babuvirus have multi-component ssDNA genomes and often associate with alphasatellite molecules containing two common motifs, a common-region stem-loop (CR-SL) involved in initiation of rolling-circle replication and a common-region major (CR-M) motif involved in secondary-strand synthesis. We compared known babuvirus genome components and alphasatellite CR-SL and CR-M sequences, defining five divergent CR-SL sequence classes. We identified iterated sequence elements in babuvirus genome components that have particularly conserved sequences and spatial arrangements between known babuviruses.
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Affiliation(s)
- Daisy Stainton
- School of Biological Sciences, University of Canterbury, Christchurch, 8140, New Zealand
| | - Darren P Martin
- Department of Clinical Laboratory Sciences, University of Cape Town, Cape Town, South Africa
| | - David A Collings
- School of Biological Sciences, University of Canterbury, Christchurch, 8140, New Zealand
- School of Environmental and Life Sciences, University of Newcastle, Callaghan, NSW, 2308, Australia
| | - Arvind Varsani
- School of Biological Sciences, University of Canterbury, Christchurch, 8140, New Zealand.
- Department of Clinical Laboratory Sciences, University of Cape Town, Cape Town, South Africa.
- The Biodesign Center for Fundamental and Applied Microbiomics, and School of Life Sciences, Arizona State University, Tempe, AZ, 85287-5001, USA.
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165
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Zaidi SSEA, Tashkandi M, Mansoor S, Mahfouz MM. Engineering Plant Immunity: Using CRISPR/Cas9 to Generate Virus Resistance. FRONTIERS IN PLANT SCIENCE 2016; 7:1673. [PMID: 27877187 PMCID: PMC5099147 DOI: 10.3389/fpls.2016.01673] [Citation(s) in RCA: 88] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/31/2016] [Accepted: 10/24/2016] [Indexed: 05/19/2023]
Abstract
Plant viruses infect many economically important crops, including wheat, cotton, maize, cassava, and other vegetables. These viruses pose a serious threat to agriculture worldwide, as decreases in cropland area per capita may cause production to fall short of that required to feed the increasing world population. Under these circumstances, conventional strategies can fail to control rapidly evolving and emerging plant viruses. Genome-engineering strategies have recently emerged as promising tools to introduce desirable traits in many eukaryotic species, including plants. Among these genome engineering technologies, the CRISPR (clustered regularly interspaced palindromic repeats)/CRISPR-associated 9 (CRISPR/Cas9) system has received special interest because of its simplicity, efficiency, and reproducibility. Recent studies have used CRISPR/Cas9 to engineer virus resistance in plants, either by directly targeting and cleaving the viral genome, or by modifying the host plant genome to introduce viral immunity. Here, we briefly describe the biology of the CRISPR/Cas9 system and plant viruses, and how different genome engineering technologies have been used to target these viruses. We further describe the main findings from recent studies of CRISPR/Cas9-mediated viral interference and discuss how these findings can be applied to improve global agriculture. We conclude by pinpointing the gaps in our knowledge and the outstanding questions regarding CRISPR/Cas9-mediated viral immunity.
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Affiliation(s)
- Syed Shan-e-Ali Zaidi
- Laboratory for Genome Engineering, Division of Biological Sciences, King Abdullah University of Science and TechnologyThuwal, Saudi Arabia
- National Institute for Biotechnology and Genetic EngineeringFaisalabad, Pakistan
| | - Manal Tashkandi
- Laboratory for Genome Engineering, Division of Biological Sciences, King Abdullah University of Science and TechnologyThuwal, Saudi Arabia
| | - Shahid Mansoor
- National Institute for Biotechnology and Genetic EngineeringFaisalabad, Pakistan
| | - Magdy M. Mahfouz
- Laboratory for Genome Engineering, Division of Biological Sciences, King Abdullah University of Science and TechnologyThuwal, Saudi Arabia
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166
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Kumar S, Srivastava A, Jaidi M, Chauhan PS, Raj SK. Molecular Characterization of a Begomovirus, α-Satellite, and β-Satellite Associated with Leaf Curl Disease of Parthenium hysterophorus in India. PLANT DISEASE 2016; 100:2299-2305. [PMID: 30682918 DOI: 10.1094/pdis-09-15-0982-re] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/09/2023]
Abstract
Parthenium hysterophorus plants exhibiting severe leaf curl and stunting symptoms were observed near agriculture fields in Lucknow, India. The association of a begomovirus, β-satellite, and α-satellite with these symptoms of a Parthenium disease was investigated by sequence analyses of virus and satellite DNA amplified by rolling circle amplification and polymerase chain reaction. The highest sequence identities and closest phylogenetic relationships for the begomovirus, β-satellite, and α-satellite detected in P. hysterophorus plants were to Tomato leaf curl virus (ToLCV), papaya leaf curl β-satellite (PaLCuB), and Ageratum yellow vein India α-satellite (AYVIA), respectively. These findings identified the virus and satellites infecting the Parthenium sp. as ToLCV, PaLCuB, and AYVIA, respectively. P. hysterophorus and tomato seedlings infected with cloned ToLCV, PaLCuB, and AYVIA by agroinoculation developed leaf curl symptoms, whereas plants infected with ToLCV alone or with ToLCV and AYVIA developed mild yellowing. The results show that this complex infects and causes disease in P. hysterophorus and tomato. P. hysterophorus is an invasive weed commonly found around agricultural fields and along roadsides in India. These results indicate that P. hysterophorus plants infected with ToLCV and associated satellite DNA act as an alternate host (reservoir), and that could lead to increased incidence of tomato leaf curl disease.
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Affiliation(s)
- Susheel Kumar
- Plant Molecular Virology Laboratory, Centre for Plant Molecular Biology Division, Council of Scientific and Industrial Research-National Botanical Research Institute (CSIR-NBRI), Lucknow-226001, U.P., India
| | - Ashish Srivastava
- Department of Plant Molecular Biology, University of Delhi South Campus; and Plant Molecular Virology Laboratory, CSIR-NBRI, Lucknow-226001, U.P., India
| | - Meraj Jaidi
- Division of Plant-Microbe Interactions, CSIR-NBRI, Lucknow-226001, U.P., India
| | | | - S K Raj
- Plant Molecular Virology Laboratory, CSIR-NBRI, Lucknow-226001, U.P., India
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167
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Fiallo-Olivé E, Tovar R, Navas-Castillo J. Deciphering the biology of deltasatellites from the New World: maintenance by New World begomoviruses and whitefly transmission. THE NEW PHYTOLOGIST 2016; 212:680-692. [PMID: 27400152 DOI: 10.1111/nph.14071] [Citation(s) in RCA: 42] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/27/2016] [Accepted: 05/23/2016] [Indexed: 06/06/2023]
Abstract
Deltasatellites are small noncoding DNA satellites associated with begomoviruses. The study presented here has investigated the biology of two deltasatellites found in wild malvaceous plants in the New World (NW). Infectious clones of two NW deltasatellites (from Malvastrum coromandelianum and Sidastrum micranthum) and associated begomoviruses were constructed. Infectivity in Nicotiana benthamiana and their natural malvaceous hosts was assessed. The NW deltasatellites were not able to spread autonomously in planta, whereas they were maintained by the associated bipartite begomovirus. Furthermore, NW deltasatellites were transreplicated by a monopartite NW begomovirus, tomato leaf deformation virus. However, they were not maintained by begomoviruses from the Old World (tomato yellow leaf curl virus, tomato yellow leaf curl Sardinia virus and African cassava mosaic virus) or a curtovirus (beet curly top virus). NW deltasatellites did not affect the symptoms induced by the helper viruses but in some cases reduced their accumulation. Moreover, one NW deltasatellite was shown to be transmitted by the whitefly Bemisia tabaci, the vector of its helper begomoviruses. These results confirm that these molecules are true satellites. The availability of infectious clones and the observation that NW deltasatellites reduced virus accumulation paves the way for further studies of the effect on their helper begomoviruses.
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Affiliation(s)
- Elvira Fiallo-Olivé
- Instituto de Hortofruticultura Subtropical y Mediterránea 'La Mayora', Universidad de Málaga - Consejo Superior de Investigaciones Científicas (IHSM-UMA-CSIC), Estación Experimental 'La Mayora', 29750, Algarrobo-Costa, Málaga, Spain
| | - Remedios Tovar
- Instituto de Hortofruticultura Subtropical y Mediterránea 'La Mayora', Universidad de Málaga - Consejo Superior de Investigaciones Científicas (IHSM-UMA-CSIC), Estación Experimental 'La Mayora', 29750, Algarrobo-Costa, Málaga, Spain
| | - Jesús Navas-Castillo
- Instituto de Hortofruticultura Subtropical y Mediterránea 'La Mayora', Universidad de Málaga - Consejo Superior de Investigaciones Científicas (IHSM-UMA-CSIC), Estación Experimental 'La Mayora', 29750, Algarrobo-Costa, Málaga, Spain.
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168
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Ju Z, Wang L, Cao D, Zuo J, Zhu H, Fu D, Luo Y, Zhu B. A viral satellite DNA vector-induced transcriptional gene silencing via DNA methylation of gene promoter in Nicotiana benthamiana. Virus Res 2016; 223:99-107. [PMID: 27422476 DOI: 10.1016/j.virusres.2016.07.005] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2016] [Revised: 07/05/2016] [Accepted: 07/08/2016] [Indexed: 11/19/2022]
Abstract
Virus-induced gene silencing (VIGS) has been widely used for plant functional genomics study at the post-transcriptional level using various DNA or RNA viral vectors. However, while virus-induced transcriptional gene silencing (VITGS) via DNA methylation of gene promoter was achieved using several plant RNA viral vectors, it has not yet been done using a satellite DNA viral vector. In this study, a viral satellite DNA associated with tomato yellow leaf curl China virus (TYLCCNV), which has been modified as a VIGS vector in previous research, was developed as a VITGS vector. Firstly, the viral satellite DNA VIGS vector was further optimized to a more convenient p1.7A+2mβ vector with high silencing efficiency of the phytoene desaturase (PDS) gene in Nicotiana benthamiana plants. Secondly, the constructed VITGS vector (TYLCCNV:35S), which carried a portion of the cauliflower mosaic virus 35S promoter, could successfully induce heritable transcriptional gene silencing (TGS) of the green fluorescent protein (GFP) gene in the 35S-GFP transgenic N. benthamiana line 16c plants. Moreover, bisulfite sequencing results revealed higher methylated cytosine residues at CG, CHG and CHH sites of the 35S promoter sequence in TYLCCNV:35S-inoculated plants than in TYLCCNV-inoculated line 16c plants (control). Overall, these results demonstrated that the viral satellite DNA vector could be used as an effective VITGS vector to study DNA methylation in plant genomes.
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Affiliation(s)
- Zheng Ju
- College of Food Science and Nutritional Engineering, China Agricultural University, Beijing 100083, China.
| | - Lei Wang
- College of Food Science and Nutritional Engineering, China Agricultural University, Beijing 100083, China.
| | - Dongyan Cao
- College of Food Science and Nutritional Engineering, China Agricultural University, Beijing 100083, China.
| | - Jinhua Zuo
- National Engineering Research Center for Vegetables, Beijing Academy of Agriculture and Forestry Sciences, Beijing 100097, China.
| | - Hongliang Zhu
- College of Food Science and Nutritional Engineering, China Agricultural University, Beijing 100083, China.
| | - Daqi Fu
- College of Food Science and Nutritional Engineering, China Agricultural University, Beijing 100083, China.
| | - Yunbo Luo
- College of Food Science and Nutritional Engineering, China Agricultural University, Beijing 100083, China.
| | - Benzhong Zhu
- College of Food Science and Nutritional Engineering, China Agricultural University, Beijing 100083, China.
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169
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Rasool G, Yousaf S, Akram A, Mansoor S, Briddon RW, Saeed M. G5, a Phage Single-Stranded DNA-Binding Protein, Fused with a Nuclear Localization Signal, Attenuates Symptoms and Reduces Begomovirus-Betasatellite Accumulation in Transgenic Plants. Mol Biotechnol 2016; 58:595-602. [PMID: 27364491 DOI: 10.1007/s12033-016-9959-5] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Cotton leaf curl disease is caused by several monopartite begomoviruses and is the major threat to cotton production in the Indian subcontinent. The disease has been shown to be associated with four distinct species, including Cotton leaf curl Kokhran virus (CLCuKoV), and a specific betasatellite-Cotton leaf curl Multan betasatellite (CLCuMuB). Transgenic Nicotiana benthamiana plants were produced which constitutively express the Escherichia coli phage M13 encoded, sequence nonspecific single-stranded (ss) DNA-binding protein, G5 alone and fused with the maize opaque-2 nuclear localization signal (NLS), to evaluate resistance against CLCuKoV-CLCuMuB. Transgenic plants expressing only G5 performed poorly exhibiting symptoms of infection and high virus DNA levels upon inoculation with CLCuKoV and CLCuKoV with CLCuMuB. In contrast, plants transformed with G5 fused to the NLS developed mild symptoms and showed a reduction in virus and betasatellite DNA levels in comparison to nontransformed plants. The results show that G5 may be useful in developing broad-spectrum resistance against ssDNA viruses.
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Affiliation(s)
- Ghulam Rasool
- Agricultural Biotechnology Division, National Institute for Biotechnology and Genetic Engineering, Nuclear Institute for Agriculture and Biology, Jhang Road, Faisalabad, 38000, P O Box # 128, Pakistan
- Pakistan Institute of Engineering & Applied Sciences (PIEAS), Nilore, Islamabad, Pakistan
| | - Sumaira Yousaf
- Agricultural Biotechnology Division, National Institute for Biotechnology and Genetic Engineering, Nuclear Institute for Agriculture and Biology, Jhang Road, Faisalabad, 38000, P O Box # 128, Pakistan
- Pakistan Institute of Engineering & Applied Sciences (PIEAS), Nilore, Islamabad, Pakistan
| | - Afzal Akram
- Agricultural Biotechnology Division, National Institute for Biotechnology and Genetic Engineering, Nuclear Institute for Agriculture and Biology, Jhang Road, Faisalabad, 38000, P O Box # 128, Pakistan
- Pakistan Institute of Engineering & Applied Sciences (PIEAS), Nilore, Islamabad, Pakistan
| | - Shahid Mansoor
- Agricultural Biotechnology Division, National Institute for Biotechnology and Genetic Engineering, Nuclear Institute for Agriculture and Biology, Jhang Road, Faisalabad, 38000, P O Box # 128, Pakistan
- Pakistan Institute of Engineering & Applied Sciences (PIEAS), Nilore, Islamabad, Pakistan
| | - Rob W Briddon
- Agricultural Biotechnology Division, National Institute for Biotechnology and Genetic Engineering, Nuclear Institute for Agriculture and Biology, Jhang Road, Faisalabad, 38000, P O Box # 128, Pakistan
- Pakistan Institute of Engineering & Applied Sciences (PIEAS), Nilore, Islamabad, Pakistan
| | - Muhammad Saeed
- Agricultural Biotechnology Division, National Institute for Biotechnology and Genetic Engineering, Nuclear Institute for Agriculture and Biology, Jhang Road, Faisalabad, 38000, P O Box # 128, Pakistan.
- Pakistan Institute of Engineering & Applied Sciences (PIEAS), Nilore, Islamabad, Pakistan.
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170
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Hassan I, Orílio AF, Fiallo-Olivé E, Briddon RW, Navas-Castillo J. Infectivity, effects on helper viruses and whitefly transmission of the deltasatellites associated with sweepoviruses (genus Begomovirus, family Geminiviridae). Sci Rep 2016; 6:30204. [PMID: 27453359 PMCID: PMC4958995 DOI: 10.1038/srep30204] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2016] [Accepted: 06/30/2016] [Indexed: 11/08/2022] Open
Abstract
Begomoviruses (family Geminiviridae) are whitefly-transmitted viruses with single-stranded DNA genomes that are frequently associated with DNA satellites. These satellites include non-coding satellites, for which the name deltasatellites has been proposed. Although the first deltasatellite was identified in the late 1990s, little is known about the effects they have on infections of their helper begomoviruses. Recently a group of deltasatellites were identified associated with sweepoviruses, a group of phylogenetically distinct begomoviruses that infect plants of the family Convolvulaceae including sweet potato. In this work, the deltasatellites associated with sweepoviruses are shown to be transreplicated and maintained in plants by the virus with which they were identified, sweet potato leaf curl virus (SPLCV). These deltasatellites were shown generally to reduce symptom severity of the virus infection by reducing virus DNA levels. Additionally they were shown to be maintained in plants, and reduce the symptoms induced by two Old World monopartite begomoviruses, tomato yellow leaf curl virus and tomato yellow leaf curl Sardinia virus. Finally one of the satellites was shown to be transmitted plant-to-plant in the presence of SPLCV by the whitefly vector of the virus, Bemisia tabaci, being the first time a deltasatellite has been shown to be insect transmitted.
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Affiliation(s)
- Ishtiaq Hassan
- Instituto de Hortofruticultura Subtropical y Mediterránea “La Mayora”, Universidad de Málaga - Consejo Superior de Investigaciones Científicas (IHSM-UMA-CSIC), Estación Experimental “La Mayora”, 29750 Algarrobo-Costa, Málaga, Spain
- Agricultural Biotechnology Division, National Institute for Biotechnology and Genetic Engineering, Faisalabad, Pakistan
- Pakistan Institute of Engineering and Applied Sciences, Islamabad, Pakistan
| | - Anelise F. Orílio
- Instituto de Hortofruticultura Subtropical y Mediterránea “La Mayora”, Universidad de Málaga - Consejo Superior de Investigaciones Científicas (IHSM-UMA-CSIC), Estación Experimental “La Mayora”, 29750 Algarrobo-Costa, Málaga, Spain
| | - Elvira Fiallo-Olivé
- Instituto de Hortofruticultura Subtropical y Mediterránea “La Mayora”, Universidad de Málaga - Consejo Superior de Investigaciones Científicas (IHSM-UMA-CSIC), Estación Experimental “La Mayora”, 29750 Algarrobo-Costa, Málaga, Spain
| | - Rob W. Briddon
- Agricultural Biotechnology Division, National Institute for Biotechnology and Genetic Engineering, Faisalabad, Pakistan
| | - Jesús Navas-Castillo
- Instituto de Hortofruticultura Subtropical y Mediterránea “La Mayora”, Universidad de Málaga - Consejo Superior de Investigaciones Científicas (IHSM-UMA-CSIC), Estación Experimental “La Mayora”, 29750 Algarrobo-Costa, Málaga, Spain
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Jia Q, Liu N, Xie K, Dai Y, Han S, Zhao X, Qian L, Wang Y, Zhao J, Gorovits R, Xie D, Hong Y, Liu Y. CLCuMuB βC1 Subverts Ubiquitination by Interacting with NbSKP1s to Enhance Geminivirus Infection in Nicotiana benthamiana. PLoS Pathog 2016; 12:e1005668. [PMID: 27315204 PMCID: PMC4912122 DOI: 10.1371/journal.ppat.1005668] [Citation(s) in RCA: 71] [Impact Index Per Article: 8.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2016] [Accepted: 05/10/2016] [Indexed: 11/21/2022] Open
Abstract
Viruses interfere with and usurp host machinery and circumvent defense responses to create a suitable cellular environment for successful infection. This is usually achieved through interactions between viral proteins and host factors. Geminiviruses are a group of plant-infecting DNA viruses, of which some contain a betasatellite, known as DNAβ. Here, we report that Cotton leaf curl Multan virus (CLCuMuV) uses its sole satellite-encoded protein βC1 to regulate the plant ubiquitination pathway for effective infection. We found that CLCuMu betasatellite (CLCuMuB) βC1 interacts with NbSKP1, and interrupts the interaction of NbSKP1s with NbCUL1. Silencing of either NbSKP1s or NbCUL1 enhances the accumulation of CLCuMuV genomic DNA and results in severe disease symptoms in plants. βC1 impairs the integrity of SCFCOI1 and the stabilization of GAI, a substrate of the SCFSYL1 to hinder responses to jasmonates (JA) and gibberellins (GA). Moreover, JA treatment reduces viral accumulation and symptoms. These results suggest that CLCuMuB βC1 inhibits the ubiquitination function of SCF E3 ligases through interacting with NbSKP1s to enhance CLCuMuV infection and symptom induction in plants.
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Affiliation(s)
- Qi Jia
- MOE Key Laboratory of Bioinformatics, Center for Plant Biology, School of Life Sciences, Tsinghua University, Beijing, China
| | - Na Liu
- MOE Key Laboratory of Bioinformatics, Center for Plant Biology, School of Life Sciences, Tsinghua University, Beijing, China
| | - Ke Xie
- MOE Key Laboratory of Bioinformatics, Center for Plant Biology, School of Life Sciences, Tsinghua University, Beijing, China
| | - Yanwan Dai
- MOE Key Laboratory of Bioinformatics, Center for Plant Biology, School of Life Sciences, Tsinghua University, Beijing, China
- College of Biological Sciences, China Agricultural University, Beijing, China
| | - Shaojie Han
- MOE Key Laboratory of Bioinformatics, Center for Plant Biology, School of Life Sciences, Tsinghua University, Beijing, China
| | - Xijuan Zhao
- MOE Key Laboratory of Bioinformatics, Center for Plant Biology, School of Life Sciences, Tsinghua University, Beijing, China
| | - Lichao Qian
- MOE Key Laboratory of Bioinformatics, Center for Plant Biology, School of Life Sciences, Tsinghua University, Beijing, China
| | - Yunjing Wang
- MOE Key Laboratory of Bioinformatics, Center for Plant Biology, School of Life Sciences, Tsinghua University, Beijing, China
| | - Jinping Zhao
- MOE Key Laboratory of Bioinformatics, Center for Plant Biology, School of Life Sciences, Tsinghua University, Beijing, China
- Institute of Virology and Biotechnology, Zhejiang Academy of Agricultural Sciences, Hangzhou, China
| | - Rena Gorovits
- Institute of Plant Sciences and Genetics in Agriculture, Robert H. Smith Faculty of Agriculture, Food and Environment, Hebrew University of Jerusalem, Rehovot, Israel
| | - Daoxin Xie
- MOE Key Laboratory of Bioinformatics, Center for Plant Biology, School of Life Sciences, Tsinghua University, Beijing, China
| | - Yiguo Hong
- Research Centre for Plant RNA Signaling, College of Life and Environmental Sciences, Hangzhou Normal University, Hangzhou, China
| | - Yule Liu
- MOE Key Laboratory of Bioinformatics, Center for Plant Biology, School of Life Sciences, Tsinghua University, Beijing, China
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172
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Zaidi SSEA, Shafiq M, Amin I, Scheffler BE, Scheffler JA, Briddon RW, Mansoor S. Frequent Occurrence of Tomato Leaf Curl New Delhi Virus in Cotton Leaf Curl Disease Affected Cotton in Pakistan. PLoS One 2016; 11:e0155520. [PMID: 27213535 PMCID: PMC4877078 DOI: 10.1371/journal.pone.0155520] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2016] [Accepted: 04/29/2016] [Indexed: 11/18/2022] Open
Abstract
Cotton leaf curl disease (CLCuD) is the major biotic constraint to cotton production on the Indian subcontinent, and is caused by monopartite begomoviruses accompanied by a specific DNA satellite, Cotton leaf curl Multan betasatellite (CLCuMB). Since the breakdown of resistance against CLCuD in 2001/2002, only one virus, the "Burewala" strain of Cotton leaf curl Kokhran virus (CLCuKoV-Bur), and a recombinant form of CLCuMB have consistently been identified in cotton across the major cotton growing areas of Pakistan. Unusually a bipartite isolate of the begomovirus Tomato leaf curl virus was identified in CLCuD-affected cotton recently. In the study described here we isolated the bipartite begomovirus Tomato leaf curl New Delhi virus (ToLCNDV) from CLCuD-affected cotton. To assess the frequency and geographic occurrence of ToLCNDV in cotton, CLCuD-symptomatic cotton plants were collected from across the Punjab and Sindh provinces between 2013 and 2015. Analysis of the plants by diagnostic PCR showed the presence of CLCuKoV-Bur in all 31 plants examined and ToLCNDV in 20 of the samples. Additionally, a quantitative real-time PCR analysis of the levels of the two viruses in co-infected plants suggests that coinfection of ToLCNDV with the CLCuKoV-Bur/CLCuMB complex leads to an increase in the levels of CLCuMB, which encodes the major pathogenicity (symptom) determinant of the complex. The significance of these results are discussed.
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Affiliation(s)
- Syed Shan-e-Ali Zaidi
- Agricultural Biotechnology Division, National Institute for Biotechnology and Genetic Engineering, P O Box 577, Jhang Road, Faisalabad, Pakistan
- Pakistan Institute of Engineering and Applied Sciences (PIEAS), Islamabad, Pakistan
| | - Muhammad Shafiq
- Agricultural Biotechnology Division, National Institute for Biotechnology and Genetic Engineering, P O Box 577, Jhang Road, Faisalabad, Pakistan
- Pakistan Institute of Engineering and Applied Sciences (PIEAS), Islamabad, Pakistan
| | - Imran Amin
- Agricultural Biotechnology Division, National Institute for Biotechnology and Genetic Engineering, P O Box 577, Jhang Road, Faisalabad, Pakistan
| | - Brian E. Scheffler
- Genomics and Bioinformatics Research Unit, 141 Experiment Station Rd., Stoneville, Mississippi, 38776, United States of America
| | - Jodi A. Scheffler
- Crop Genetics Research Unit, United States Department of Agriculture-Agricultural Research Service (USDA-ARS), Stoneville, Mississippi, United States of America
| | - Rob W. Briddon
- Agricultural Biotechnology Division, National Institute for Biotechnology and Genetic Engineering, P O Box 577, Jhang Road, Faisalabad, Pakistan
| | - Shahid Mansoor
- Agricultural Biotechnology Division, National Institute for Biotechnology and Genetic Engineering, P O Box 577, Jhang Road, Faisalabad, Pakistan
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173
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Akbar F, Iqbal Z, Briddon RW, Vazquez F, Saeed M. The 35-amino acid C2 protein of Cotton leaf curl Kokhran virus, Burewala, implicated in resistance breaking in cotton, retains some activities of the full-length protein. Virus Genes 2016; 52:688-97. [PMID: 27209537 DOI: 10.1007/s11262-016-1357-3] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2015] [Accepted: 05/12/2016] [Indexed: 11/26/2022]
Abstract
With one exception, all the begomoviruses characterized so far encode an ~134-amino acid (aa) (A)C2 protein. The exception is the "Burewala" strain of Cotton leaf curl Kokhran virus (CLCuKoV-Bu), associated with resistance breaking in cotton across Pakistan and northwestern India, that encodes a truncated 35-aa C2. The C2 protein encoded by begomoviruses performs multiple functions including suppression of post-transcriptional gene silencing (PTGS), modulating microRNA (miRNA) expression and may be a pathogenicity determinant. The study described here was designed to investigate whether the CLCuKoV-Bu 35-aa C2 retains the activities of the full-length C2 protein. The results showed the 35-aa C2 of CLCuKoV-Bu acts as a pathogenicity determinant, suppresses PTGS and upregulates miRNA expression when expressed from a Potato virus X vector in Nicotiana benthamiana. The symptoms induced by expression of full-length C2 were more severe than those induced by the 35-aa C2. The accumulation of most developmental miRNAs decreases with the full-length C2 protein and increases with the 35-aa peptide of CLCuKoV-Bu. The study also revealed that 35-aa peptide of CLCuKoV-Bu maintains suppressor of silencing activity at a level equal to that of full-length C2. The significance of the results with respect to virus fitness and resistance breaking is discussed.
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Affiliation(s)
- Fazal Akbar
- Agricultural Biotechnology Division, National Institute for Biotechnology and Genetic Engineering, Jhang Road, Faisalabad, Pakistan
- Botanical Institute of the University of Basel, Zürich-Basel Plant Science Center, Part of the Swiss Plant Science Web, Schnbeinstrasse 6, 4056, Basel, Switzerland
- Centre for Biotechnology and Microbiology, University of Swat, Swat, Pakistan
| | - Zafar Iqbal
- Agricultural Biotechnology Division, National Institute for Biotechnology and Genetic Engineering, Jhang Road, Faisalabad, Pakistan
- Institute of Biochemistry and Biotechnology, University of the Punjab, Lahore, Pakistan
| | - Rob W Briddon
- Agricultural Biotechnology Division, National Institute for Biotechnology and Genetic Engineering, Jhang Road, Faisalabad, Pakistan
| | - Franck Vazquez
- Botanical Institute of the University of Basel, Zürich-Basel Plant Science Center, Part of the Swiss Plant Science Web, Schnbeinstrasse 6, 4056, Basel, Switzerland
- MDPI AG, Klybeckstrasse 64, 4057, Basel, Switzerland
| | - Muhammad Saeed
- Agricultural Biotechnology Division, National Institute for Biotechnology and Genetic Engineering, Jhang Road, Faisalabad, Pakistan.
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174
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The minimal sequence essential for replication and movement of Cotton leaf curl Multan betasatellite DNA by a helper virus in plant cells. Virus Genes 2016; 52:679-87. [PMID: 27193570 DOI: 10.1007/s11262-016-1354-6] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2016] [Accepted: 05/09/2016] [Indexed: 10/21/2022]
Abstract
Betasatellites are single-stranded circular DNAs associated with a number of monopartite begomoviruses. Betasatellites rely on the helper begomoviruses for replication and movement in plant tissues and plant-to-plant transmission by vectors. Their genomes are approximately half the size of the helper viruses and consist of three main regions including the βC1 gene, an adenine-rich (A-rich) region, and the satellite conserved region (SCR). In this study, we investigated the minimal sequences required for Cotton leaf curl Multan betasatellite (CLCuMB) replication and movement. Mutational analysis of CLCuMB DNA genome indicated that βC1 gene and A-rich region were not required for trans-replication and movement of CLCuMB in host plants by a helper virus. Deletion of βC1 gene and a fragment (135 nt in length) upstream of this gene impaired CLCuMB replication. However, CLCuMB mutant with deletion of βC1 gene and a further 163 nucleotides replicated at a lower level as compared to the wild-type betasatellite. This suggests that there are essential elements in the fragment upstream of βC1 gene, which are required for the replication of CLCuMB rather than the size limitation of CLCuMB DNA.
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175
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Ndunguru J, De León L, Doyle CD, Sseruwagi P, Plata G, Legg JP, Thompson G, Tohme J, Aveling T, Ascencio-Ibáñez JT, Hanley-Bowdoin L. Two Novel DNAs That Enhance Symptoms and Overcome CMD2 Resistance to Cassava Mosaic Disease. J Virol 2016; 90:4160-4173. [PMID: 26865712 PMCID: PMC4810563 DOI: 10.1128/jvi.02834-15] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2015] [Accepted: 02/03/2016] [Indexed: 11/20/2022] Open
Abstract
UNLABELLED Cassava mosaic begomoviruses (CMBs) cause cassava mosaic disease (CMD) across Africa and the Indian subcontinent. Like all members of the geminivirus family, CMBs have small, circular single-stranded DNA genomes. We report here the discovery of two novel DNA sequences, designated SEGS-1 and SEGS-2 (forsequencesenhancinggeminivirussymptoms), that enhance symptoms and break resistance to CMD. The SEGS are characterized by GC-rich regions and the absence of long open reading frames. Both SEGS enhanced CMD symptoms in cassava (Manihot esculentaCrantz) when coinoculated withAfrican cassava mosaic virus(ACMV),East African cassava mosaic Cameroon virus(EACMCV), orEast African cassava mosaic virus-Uganda(EACMV-UG). SEGS-1 also overcame resistance of a cassava landrace carrying the CMD2 resistance locus when coinoculated with EACMV-UG. Episomal forms of both SEGS were detected in CMB-infected cassava but not in healthy cassava. SEGS-2 episomes were also found in virions and whiteflies. SEGS-1 has no homology to geminiviruses or their associated satellites, but the cassava genome contains a sequence that is 99% identical to full-length SEGS-1. The cassava genome also includes three sequences with 84 to 89% identity to SEGS-2 that together encompass all of SEGS-2 except for a 52-bp region, which includes the episomal junction and a 26-bp sequence related to alphasatellite replication origins. These results suggest that SEGS-1 is derived from the cassava genome and facilitates CMB infection as an integrated copy and/or an episome, while SEGS-2 was originally from the cassava genome but now is encapsidated into virions and transmitted as an episome by whiteflies. IMPORTANCE Cassava is a major crop in the developing world, with its production in Africa being second only to maize. CMD is one of the most important diseases of cassava and a serious constraint to production across Africa. CMD2 is a major CMD resistance locus that has been deployed in many cassava cultivars through large-scale breeding programs. In recent years, severe, atypical CMD symptoms have been observed occasionally on resistant cultivars, some of which carry the CMD2 locus, in African fields. In this report, we identified and characterized two DNA sequences, SEGS-1 and SEGS-2, which produce similar symptoms when coinoculated with cassava mosaic begomoviruses onto a susceptible cultivar or a CMD2-resistant landrace. The ability of SEGS-1 to overcome CMD2 resistance and the transmission of SEGS-2 by whiteflies has major implications for the long-term durability of CMD2 resistance and underscore the need for alternative sources of resistance in cassava.
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Affiliation(s)
- Joseph Ndunguru
- Mikocheni Agricultural Research Institute, Dar es Salaam, Tanzania
| | - Leandro De León
- Department of Molecular and Structural Biochemistry, North Carolina State University, Raleigh, North Carolina, USA
| | - Catherine D Doyle
- Department of Plant and Microbial Biology, North Carolina State University, Raleigh, North Carolina, USA
| | - Peter Sseruwagi
- Mikocheni Agricultural Research Institute, Dar es Salaam, Tanzania
| | - German Plata
- Center for Computational Biology and Bioinformatics, Columbia University, New York, New York, USA
| | - James P Legg
- International Institute of Tropical Agriculture-Tanzania, Dar es Salaam, Tanzania
| | - Graham Thompson
- ARC-Institute for Industrial Crops, Rusternburg, South Africa
| | - Joe Tohme
- International Center for Tropical Agriculture, Cali, Colombia
| | - Theresa Aveling
- University of Pretoria, Department of Microbiology and Plant Pathology, Pretoria, South Africa
| | - Jose T Ascencio-Ibáñez
- Department of Molecular and Structural Biochemistry, North Carolina State University, Raleigh, North Carolina, USA
| | - Linda Hanley-Bowdoin
- Department of Plant and Microbial Biology, North Carolina State University, Raleigh, North Carolina, USA
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176
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Nascimento LD, Silva SJC, Sobrinho RR, Ferro MMM, Oliveira MHC, Zerbini FM, Assunção IP, Lima GSA. Complete nucleotide sequence of a new begomovirus infecting a malvaceous weed in Brazil. Arch Virol 2016; 161:1735-8. [PMID: 27020569 DOI: 10.1007/s00705-016-2822-y] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2015] [Accepted: 03/07/2016] [Indexed: 11/25/2022]
Abstract
Begomoviruses are single-strand DNA plant viruses that infect economically important crops worldwide, exhibiting high genetic variability and species diversity. Based on the current taxonomic criteria established for the genus Begomovirus, a new member of this genus infecting a malvaceous weed is reported here. The name triumfetta yellow mosaic virus is proposed. At least one recombination event was detected in this new begomovirus, with putative parents being begomoviruses from tomato and Centrosema.
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Affiliation(s)
- Liliane D Nascimento
- Departamento de Fitossanidade, Universidade Federal Rural de Pernambuco, Recife, PE, 52171-900, Brazil.,Setor de Fitossanidade/CECA, Universidade Federal de Alagoas, Rio Largo, AL, 57100-000, Brazil
| | - Sarah J C Silva
- Setor de Fitossanidade/CECA, Universidade Federal de Alagoas, Rio Largo, AL, 57100-000, Brazil
| | - Roberto Ramos Sobrinho
- Setor de Fitossanidade/CECA, Universidade Federal de Alagoas, Rio Largo, AL, 57100-000, Brazil
| | - Mayra M M Ferro
- Setor de Fitossanidade/CECA, Universidade Federal de Alagoas, Rio Largo, AL, 57100-000, Brazil
| | - Maria H C Oliveira
- Setor de Fitossanidade/CECA, Universidade Federal de Alagoas, Rio Largo, AL, 57100-000, Brazil
| | - Francisco M Zerbini
- Departamento de Fitopatologia/BIOAGRO, Universidade Federal de Viçosa, Viçosa, MG, 36570-900, Brazil
| | - Iraildes P Assunção
- Setor de Fitossanidade/CECA, Universidade Federal de Alagoas, Rio Largo, AL, 57100-000, Brazil
| | - Gaus S A Lima
- Setor de Fitossanidade/CECA, Universidade Federal de Alagoas, Rio Largo, AL, 57100-000, Brazil.
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177
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Betancourt M, Fraile A, Milgroom MG, García-Arenal F. Aphid vector population density determines the emergence of necrogenic satellite RNAs in populations of cucumber mosaic virus. J Gen Virol 2016; 97:1453-1457. [PMID: 26916424 DOI: 10.1099/jgv.0.000435] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
The satellite RNAs of cucumber mosaic virus (CMV) that induce systemic necrosis in tomato plants (N-satRNA) multiply to high levels in the infected host while severely depressing CMV accumulation and, hence, its aphid transmission efficiency. As N-satRNAs are transmitted into CMV particles, the conditions for N-satRNA emergence are not obvious. Model analyses with realistic parameter values have predicted that N-satRNAs would invade CMV populations only when transmission rates are high. Here, we tested this hypothesis experimentally by passaging CMV or CMV+N-satRNAs at low or high aphid densities (2 or 8 aphids/plant). As predicted, high aphid densities were required for N-satRNA emergence. The results showed that at low aphid densities, random effects due to population bottlenecks during transmission dominate the epidemiological dynamics of CMV/CMV+N-satRNA. The results suggest that maintaining aphid populations at low density will prevent the emergence of highly virulent CMV+N-satRNA isolates.
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Affiliation(s)
- Mónica Betancourt
- Centro de Biotecnología y Genómica de Plantas UPM-INIA and ETSI Agrónomos, Universidad Politécnica de Madrid, Campus de Montegancedo. 28223 Pozuelo de Alarcón, Madrid, Spain
| | - Aurora Fraile
- Centro de Biotecnología y Genómica de Plantas UPM-INIA and ETSI Agrónomos, Universidad Politécnica de Madrid, Campus de Montegancedo. 28223 Pozuelo de Alarcón, Madrid, Spain
| | - Michael G Milgroom
- Plant Pathology and Plant-Microbe Biology Section, School of Integrative Plant, Science, Cornell University, Ithaca, NY 14853, USA
| | - Fernando García-Arenal
- Centro de Biotecnología y Genómica de Plantas UPM-INIA and ETSI Agrónomos, Universidad Politécnica de Madrid, Campus de Montegancedo. 28223 Pozuelo de Alarcón, Madrid, Spain
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178
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Lozano G, Trenado HP, Fiallo-Olivé E, Chirinos D, Geraud-Pouey F, Briddon RW, Navas-Castillo J. Characterization of Non-coding DNA Satellites Associated with Sweepoviruses (Genus Begomovirus, Geminiviridae) - Definition of a Distinct Class of Begomovirus-Associated Satellites. Front Microbiol 2016; 7:162. [PMID: 26925037 PMCID: PMC4756297 DOI: 10.3389/fmicb.2016.00162] [Citation(s) in RCA: 80] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2015] [Accepted: 02/01/2016] [Indexed: 11/13/2022] Open
Abstract
Begomoviruses (family Geminiviridae) are whitefly-transmitted, plant-infecting single-stranded DNA viruses that cause crop losses throughout the warmer parts of the World. Sweepoviruses are a phylogenetically distinct group of begomoviruses that infect plants of the family Convolvulaceae, including sweet potato (Ipomoea batatas). Two classes of subviral molecules are often associated with begomoviruses, particularly in the Old World; the betasatellites and the alphasatellites. An analysis of sweet potato and Ipomoea indica samples from Spain and Merremia dissecta samples from Venezuela identified small non-coding subviral molecules in association with several distinct sweepoviruses. The sequences of 18 clones were obtained and found to be structurally similar to tomato leaf curl virus-satellite (ToLCV-sat, the first DNA satellite identified in association with a begomovirus), with a region with significant sequence identity to the conserved region of betasatellites, an A-rich sequence, a predicted stem–loop structure containing the nonanucleotide TAATATTAC, and a second predicted stem–loop. These sweepovirus-associated satellites join an increasing number of ToLCV-sat-like non-coding satellites identified recently. Although sharing some features with betasatellites, evidence is provided to suggest that the ToLCV-sat-like satellites are distinct from betasatellites and should be considered a separate class of satellites, for which the collective name deltasatellites is proposed.
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Affiliation(s)
- Gloria Lozano
- Instituto de Hortofruticultura Subtropical y Mediterránea "La Mayora", Universidad de Málaga - Consejo Superior de Investigaciones Científicas Algarrobo-Costa, Spain
| | - Helena P Trenado
- Instituto de Hortofruticultura Subtropical y Mediterránea "La Mayora", Universidad de Málaga - Consejo Superior de Investigaciones Científicas Algarrobo-Costa, Spain
| | - Elvira Fiallo-Olivé
- Instituto de Hortofruticultura Subtropical y Mediterránea "La Mayora", Universidad de Málaga - Consejo Superior de Investigaciones Científicas Algarrobo-Costa, Spain
| | | | | | - Rob W Briddon
- Agricultural Biotechnology Division, National Institute for Biotechnology and Genetic Engineering Faisalabad, Pakistan
| | - Jesús Navas-Castillo
- Instituto de Hortofruticultura Subtropical y Mediterránea "La Mayora", Universidad de Málaga - Consejo Superior de Investigaciones Científicas Algarrobo-Costa, Spain
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179
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Zhang T, Xu X, Huang C, Qian Y, Li Z, Zhou X. A Novel DNA Motif Contributes to Selective Replication of a Geminivirus-Associated Betasatellite by a Helper Virus-Encoded Replication-Related Protein. J Virol 2016; 90:2077-89. [PMID: 26656709 PMCID: PMC4734014 DOI: 10.1128/jvi.02290-15] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2015] [Accepted: 12/02/2015] [Indexed: 11/20/2022] Open
Abstract
UNLABELLED Rolling-circle replication of single-stranded genomes of plant geminiviruses is initiated by sequence-specific DNA binding of the viral replication-related protein (Rep) to its cognate genome at the replication origin. Monopartite begomovirus-associated betasatellites can be trans replicated by both cognate and some noncognate helper viruses, but the molecular basis of replication promiscuity of betasatellites remains uncharacterized. Earlier studies showed that when tomato yellow leaf curl China virus (TYLCCNV) or tobacco curly shoot virus (TbCSV) is coinoculated with both cognate and noncognate betasatellites, the cognate betasatellite dominates over the noncognate one at the late stages of infection. In this study, we constructed reciprocal chimeric betasatellites between tomato yellow leaf curl China betasatellite and tobacco curly shoot betasatellite and assayed their competitiveness against wild-type betasatellite when coinoculated with TYLCCNV or TbCSV onto plants. We mapped a region immediately upstream of the conserved rolling-circle cruciform structure of betasatellite origin that confers the cognate Rep-mediated replication advantage over the noncognate satellite. DNase I protection and in vitro binding assays further identified a novel sequence element termed Rep-binding motif (RBM), which specifically binds to the cognate Rep protein and to the noncognate Rep, albeit at lower affinity. Furthermore, we showed that RBM-Rep binding affinity is correlated with betasatellite replication efficiency in protoplasts. Our data suggest that although strict specificity of Rep-mediated replication does not exist, betasatellites have adapted to their cognate Reps for efficient replication during coevolution. IMPORTANCE Begomoviruses are numerous circular DNA viruses that cause devastating diseases of crops worldwide. Monopartite begomoviruses are frequently associated with betasatellites which are essential for induction of typical disease symptoms. Coexistence of two distinct betasatellites with one helper virus is rare in nature. Our previous research showed that begomoviruses can trans replicate cognate betasatellites to higher levels than noncognate ones. However, the molecular mechanisms of betasatellites selective replication remain largely unknown. We investigated the interaction between the begomovirus replication-associated protein and betasatellite DNA. We found that the replication-associated protein specifically binds to a motif in betasatellites, with higher affinity for the cognate motif than the noncognate motif. This preference for cognate motif binding determines the selective replication of betasatellites. We also demonstrated that this motif is essential for betasatellite replication. These findings shed new light on the promiscuous yet selective replication of betasatellites by helper geminiviruses.
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Affiliation(s)
- Tong Zhang
- State Key Laboratory of Rice Biology, Institute of Biotechnology, Zhejiang University, Hangzhou, People's Republic of China
| | - Xiongbiao Xu
- State Key Laboratory of Rice Biology, Institute of Biotechnology, Zhejiang University, Hangzhou, People's Republic of China
| | - Changjun Huang
- State Key Laboratory of Rice Biology, Institute of Biotechnology, Zhejiang University, Hangzhou, People's Republic of China
| | - Yajuan Qian
- State Key Laboratory of Rice Biology, Institute of Biotechnology, Zhejiang University, Hangzhou, People's Republic of China
| | - Zhenghe Li
- State Key Laboratory of Rice Biology, Institute of Biotechnology, Zhejiang University, Hangzhou, People's Republic of China
| | - Xueping Zhou
- State Key Laboratory of Rice Biology, Institute of Biotechnology, Zhejiang University, Hangzhou, People's Republic of China State Key Laboratory for Biology of Plant Diseases and Insect Pests, Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing, People's Republic of China
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180
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Male MF, Kraberger S, Stainton D, Kami V, Varsani A. Cycloviruses, gemycircularviruses and other novel replication-associated protein encoding circular viruses in Pacific flying fox (Pteropus tonganus) faeces. INFECTION GENETICS AND EVOLUTION 2016; 39:279-292. [PMID: 26873064 DOI: 10.1016/j.meegid.2016.02.009] [Citation(s) in RCA: 52] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/26/2015] [Revised: 01/27/2016] [Accepted: 02/06/2016] [Indexed: 12/13/2022]
Abstract
Viral metagenomic studies have demonstrated that animal faeces can be a good sampling source for exploring viral diversity associated with the host and its environment. As part of an continuing effort to identify novel circular replication-associated protein encoding single-stranded (CRESS) DNA viruses circulating in the Tongan archipelago, coupled with the fact that bats are a reservoir species of a large number of viruses, we used a metagenomic approach to investigate the CRESS DNA virus diversity in Pacific flying fox (Pteropus tonganus) faeces. Faecal matter from four roosting sites located in Ha'avakatolo, Kolovai, Ha'ateiho and Lapaha on Tongatapu Island was collected in April 2014 and January 2015. From these samples we identified five novel cycloviruses representing three putative species, 25 gemycircularviruses representing at least 14 putative species, 17 other CRESS DNA viruses (15 putative species), two circular DNA molecules and a putative novel multi-component virus for which we have identified three cognate molecules. This study demonstrates that there exists a large diversity of CRESS DNA viruses in Pacific flying fox faeces.
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Affiliation(s)
- Maketalena F Male
- School of Biological Sciences and Biomolecular Interaction Centre, University of Canterbury, Private Bag 4800, Christchurch 8140, New Zealand
| | - Simona Kraberger
- School of Biological Sciences and Biomolecular Interaction Centre, University of Canterbury, Private Bag 4800, Christchurch 8140, New Zealand
| | - Daisy Stainton
- School of Biological Sciences and Biomolecular Interaction Centre, University of Canterbury, Private Bag 4800, Christchurch 8140, New Zealand
| | | | - Arvind Varsani
- School of Biological Sciences and Biomolecular Interaction Centre, University of Canterbury, Private Bag 4800, Christchurch 8140, New Zealand; Structural Biology Research Unit, Division of Medical Biochemistry, Department of Clinical Laboratory Sciences, University of Cape Town, Observatory 7700, South Africa; Department of Plant Pathology and Emerging Pathogens Institute, University of Florida, Gainesville, USA.
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181
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Rosario K, Marr C, Varsani A, Kraberger S, Stainton D, Moriones E, Polston JE, Breitbart M. Begomovirus-Associated Satellite DNA Diversity Captured Through Vector-Enabled Metagenomic (VEM) Surveys Using Whiteflies (Aleyrodidae). Viruses 2016; 8:v8020036. [PMID: 26848679 PMCID: PMC4776191 DOI: 10.3390/v8020036] [Citation(s) in RCA: 28] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2015] [Revised: 01/15/2016] [Accepted: 01/22/2016] [Indexed: 01/23/2023] Open
Abstract
Monopartite begomoviruses (Geminiviridae), which are whitefly-transmitted single-stranded DNA viruses known for causing devastating crop diseases, are often associated with satellite DNAs. Since begomovirus acquisition or exchange of satellite DNAs may lead to adaptation to new plant hosts and emergence of new disease complexes, it is important to investigate the diversity and distribution of these molecules. This study reports begomovirus-associated satellite DNAs identified during a vector-enabled metagenomic (VEM) survey of begomoviruses using whiteflies collected in various locations (California (USA), Guatemala, Israel, Puerto Rico, and Spain). Protein-encoding satellite DNAs, including alphasatellites and betasatellites, were identified in Israel, Puerto Rico, and Guatemala. Novel alphasatellites were detected in samples from Guatemala and Puerto Rico, resulting in the description of a phylogenetic clade (DNA-3-type alphasatellites) dominated by New World sequences. In addition, a diversity of small (~640-750 nucleotides) satellite DNAs similar to satellites associated with begomoviruses infecting Ipomoea spp. were detected in Puerto Rico and Spain. A third class of satellite molecules, named gammasatellites, is proposed to encompass the increasing number of reported small (<1 kilobase), non-coding begomovirus-associated satellite DNAs. This VEM-based survey indicates that, although recently recovered begomovirus genomes are variations of known genetic themes, satellite DNAs hold unexplored genetic diversity.
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Affiliation(s)
- Karyna Rosario
- College of Marine Science, University of South Florida, Saint Petersburg, FL 33701, USA.
| | - Christian Marr
- College of Marine Science, University of South Florida, Saint Petersburg, FL 33701, USA.
| | - Arvind Varsani
- School of Biological Sciences and Biomolecular Interaction Centre, University of Canterbury, Ilam, Christchurch 8041, New Zealand.
- Department of Plant Pathology, University of Florida, Gainesville, FL 32611, USA.
- Structural Biology Research Unit, Department of Clinical Laboratory Sciences, University of Cape Town, Rondebosch, Cape Town 7701, South Africa.
| | - Simona Kraberger
- School of Biological Sciences and Biomolecular Interaction Centre, University of Canterbury, Ilam, Christchurch 8041, New Zealand.
| | - Daisy Stainton
- School of Biological Sciences and Biomolecular Interaction Centre, University of Canterbury, Ilam, Christchurch 8041, New Zealand.
| | - Enrique Moriones
- Instituto de Hortofruticultura Subtropical y Mediterránea ''La Mayora'' (IHSM-UMA-CSIC), Consejo Superior de Investigaciones Científicas, Estación Experimental ''La Mayora'', Algarrobo-Costa, Málaga 29750, Spain.
| | - Jane E Polston
- Department of Plant Pathology, University of Florida, Gainesville, FL 32611, USA.
| | - Mya Breitbart
- College of Marine Science, University of South Florida, Saint Petersburg, FL 33701, USA.
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182
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Wang B, Wang L, Chen F, Yang X, Ding M, Zhang Z, Liu SS, Wang XW, Zhou X. MicroRNA profiling of the whitefly Bemisia tabaci Middle East-Aisa Minor I following the acquisition of Tomato yellow leaf curl China virus. Virol J 2016; 13:20. [PMID: 26837429 PMCID: PMC4736103 DOI: 10.1186/s12985-016-0469-7] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2015] [Accepted: 01/17/2016] [Indexed: 12/19/2022] Open
Abstract
Background The begomoviruses are the largest and most economically important group of plant viruses exclusively vectored by whitefly (Bemisia tabaci) in a circulative, persistent manner. During this process, begomoviruses and whitefly vectors have developed close relationships and complex interactions. However, the molecular mechanisms underlying these interactions remain largely unknown, and the microRNA profiles for viruliferous and nonviruliferous whiteflies have not been studied. Methods Sequences of Argonaute 1(Ago1) and Dicer 1 (Dcr1) genes were cloned from B. tabaci MEAM1 cDNAs. Subsequently, deep sequencing of small RNA libraries from uninfected and Tomato yellow leaf curl China virus (TYLCCNV)-infected whiteflies was performed. The conserved and novel miRNAs were identified using the release of miRBase Version 19.0 and the prediction software miRDeep2, respectively. The sequencing results of selected deregulated and novel miRNAs were further confirmed using quantitative reverse transcription-PCR. Moreover, the previously published B. tabaci MEAM1 transcriptome database and the miRNA target prediction algorithm miRanda 3.1 were utilized to predict potential targets for miRNAs. Gene Ontology (GO) analysis was also used to classify the potential enriched functional groups of their putative targets. Results Ago1 and Dcr1orthologs with conserved domains were identified from B. tabaci MEAM1. BLASTn searches and sequence analysis identified 112 and 136 conserved miRNAs from nonviruliferous and viruliferous whitefly libraries respectively, and a comparison of the conserved miRNAs of viruliferous and nonviruliferous whiteflies revealed 15 up- and 9 down-regulated conserved miRNAs. 7 novel miRNA candidates with secondary pre-miRNA hairpin structures were also identified. Potential targets of conserved and novel miRNAs were predicted using GO analysis, for the targets of up- and down-regulated miRNAs, eight and nine GO terms were significantly enriched. Conclusions We identified Ago1 and Dcr1 orthologs from whiteflies, which indicated that miRNA-mediated silencing is present in whiteflies. Our comparative analysis of miRNAs from TYLCCNV viruliferous and nonviruliferous whiteflies revealed the relevance of deregulated miRNAs for the post-transcriptional gene regulation in these whiteflies. The potential targets of all expressed miRNAs were also predicted. These results will help to acquire a better understanding of the molecular mechanism underlying the complex interactions between begomoviruses and whiteflies. Electronic supplementary material The online version of this article (doi:10.1186/s12985-016-0469-7) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Bi Wang
- State Key Laboratory of Rice Biology, Institute of Biotechnology, Zhejiang University, Hangzhou, 310058, People's Republic of China. .,State Key Laboratory for Biology of Plant Diseases and Insect Pests, Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing, 100193, People's Republic of China.
| | - Lanlan Wang
- Ministry of Agriculture Key Laboratory of Agricultural Entomology, Institute of Insect Sciences, Zhejiang University, Hangzhou, 310058, People's Republic of China.
| | - Fangyuan Chen
- State Key Laboratory of Rice Biology, Institute of Biotechnology, Zhejiang University, Hangzhou, 310058, People's Republic of China.
| | - Xiuling Yang
- State Key Laboratory of Rice Biology, Institute of Biotechnology, Zhejiang University, Hangzhou, 310058, People's Republic of China. .,State Key Laboratory for Biology of Plant Diseases and Insect Pests, Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing, 100193, People's Republic of China.
| | - Ming Ding
- Institute of Biotechnology and Genetic Resources, Yunnan Academy of Agricultural Sciences, Kunming, Yunnan, 650223, People's Republic of China.
| | - Zhongkai Zhang
- Institute of Biotechnology and Genetic Resources, Yunnan Academy of Agricultural Sciences, Kunming, Yunnan, 650223, People's Republic of China.
| | - Shu-Sheng Liu
- Ministry of Agriculture Key Laboratory of Agricultural Entomology, Institute of Insect Sciences, Zhejiang University, Hangzhou, 310058, People's Republic of China.
| | - Xiao-Wei Wang
- Ministry of Agriculture Key Laboratory of Agricultural Entomology, Institute of Insect Sciences, Zhejiang University, Hangzhou, 310058, People's Republic of China.
| | - Xueping Zhou
- State Key Laboratory of Rice Biology, Institute of Biotechnology, Zhejiang University, Hangzhou, 310058, People's Republic of China. .,State Key Laboratory for Biology of Plant Diseases and Insect Pests, Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing, 100193, People's Republic of China.
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183
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Sun YW, Tee CS, Ma YH, Wang G, Yao XM, Ye J. Attenuation of Histone Methyltransferase KRYPTONITE-mediated transcriptional gene silencing by Geminivirus. Sci Rep 2015; 5:16476. [PMID: 26602265 PMCID: PMC4658475 DOI: 10.1038/srep16476] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2015] [Accepted: 10/06/2015] [Indexed: 01/07/2023] Open
Abstract
Although histone H3K9 methylation has been intensively studied in animals and a model plant Arabidopsis thaliana, little is known about the evolution of the histone methyltransferase and its roles in plant biotic stress response. Here we identified a Nicotiana benthamiana homolog of H3K9 histone methyltransferase KRYPTONITE (NbKYP) and demonstrated its fundamental roles on methylation of plant and virus, beside of leading to the suppression of endogenous gene expression and virus replication. NbKYP and another gene encoding DNA methyltransferase CHROMOMETHYLTRANSFERASE 3 (NbCMT3-1) were further identified as the key components of maintenance of transcriptional gene silencing, a DNA methylation involved anti-virus machinery. All three types of DNA methylations (asymmetric CHH and symmetric CHG/CG) were severely affected in NbKYP-silenced plants, but only severe reduction of CHG methylation found in NbCMT3-1-silenced plants. Attesting to the importance of plant histone H3K9 methylation immunity to virus, the virulence of geminiviruses requires virus-encoded trans-activator AC2 which inhibits the expression of KYP via activation of an EAR-motif-containing transcription repressor RAV2 (RELATED TO ABI3 and VP1). The reduction of KYP was correlated with virulence of various similar geminiviruses. These findings provide a novel mechanism of how virus trans-activates a plant endogenous anti-silencing machinery to gain high virulence.
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Affiliation(s)
- Yan-Wei Sun
- State Key Laboratory of Plant Genomics, Institute of
Microbiology, Chinese Academy of Sciences, Beijing
100101, China
| | - Chuan-Sia Tee
- Temasek Life Sciences Laboratory, National University of
Singapore, Singapore
117604, Singapore
| | - Yong-Huan Ma
- State Key Laboratory of Plant Genomics, Institute of
Microbiology, Chinese Academy of Sciences, Beijing
100101, China
| | - Gang Wang
- Temasek Life Sciences Laboratory, National University of
Singapore, Singapore
117604, Singapore
| | - Xiang-Mei Yao
- State Key Laboratory of Plant Genomics, Institute of
Microbiology, Chinese Academy of Sciences, Beijing
100101, China
| | - Jian Ye
- State Key Laboratory of Plant Genomics, Institute of
Microbiology, Chinese Academy of Sciences, Beijing
100101, China
- Temasek Life Sciences Laboratory, National University of
Singapore, Singapore
117604, Singapore
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184
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Gilbertson RL, Batuman O, Webster CG, Adkins S. Role of the Insect SupervectorsBemisia tabaciandFrankliniella occidentalisin the Emergence and Global Spread of Plant Viruses. Annu Rev Virol 2015; 2:67-93. [DOI: 10.1146/annurev-virology-031413-085410] [Citation(s) in RCA: 247] [Impact Index Per Article: 27.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Affiliation(s)
- Robert L. Gilbertson
- Department of Plant Pathology, University of California, Davis, California 95616; ,
| | - Ozgur Batuman
- Department of Plant Pathology, University of California, Davis, California 95616; ,
| | - Craig G. Webster
- US Horticultural Research Laboratory, Agricultural Research Service, US Department of Agriculture, Fort Pierce, Florida 34945; ,
| | - Scott Adkins
- US Horticultural Research Laboratory, Agricultural Research Service, US Department of Agriculture, Fort Pierce, Florida 34945; ,
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185
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Rosario K, Seah YM, Marr C, Varsani A, Kraberger S, Stainton D, Moriones E, Polston JE, Duffy S, Breitbart M. Vector-Enabled Metagenomic (VEM) Surveys Using Whiteflies (Aleyrodidae) Reveal Novel Begomovirus Species in the New and Old Worlds. Viruses 2015; 7:5553-70. [PMID: 26516898 PMCID: PMC4632403 DOI: 10.3390/v7102895] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2015] [Revised: 10/16/2015] [Accepted: 10/19/2015] [Indexed: 01/16/2023] Open
Abstract
Whitefly-transmitted viruses belonging to the genus Begomovirus (family Geminiviridae) represent a substantial threat to agricultural food production. The rapid evolutionary potential of these single-stranded DNA viruses combined with the polyphagous feeding behavior of their whitefly vector (Bemisia tabaci) can lead to the emergence of damaging viral strains. Therefore, it is crucial to characterize begomoviruses circulating in different regions and crops globally. This study utilized vector-enabled metagenomics (VEM) coupled with high-throughput sequencing to survey begomoviruses directly from whiteflies collected in various locations (California (USA), Guatemala, Israel, Puerto Rico, and Spain). Begomoviruses were detected in all locations, with the highest diversity identified in Guatemala where up to seven different species were identified in a single field. Both bipartite and monopartite viruses were detected, including seven new begomovirus species from Guatemala, Puerto Rico, and Spain. This begomovirus survey extends the known diversity of these highly damaging plant viruses. However, the new genomes described here and in the recent literature appear to reflect the outcome of interactions between closely-related species, often resulting from recombination, instead of unique, highly divergent species.
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Affiliation(s)
- Karyna Rosario
- College of Marine Science, University of South Florida, Saint Petersburg, FL 33701, USA.
| | - Yee Mey Seah
- Microbiology and Molecular Genetics, Rutgers, The State University of New Jersey, New Brunswick, NJ 08901, USA.
| | - Christian Marr
- College of Marine Science, University of South Florida, Saint Petersburg, FL 33701, USA.
| | - Arvind Varsani
- School of Biological Sciences and Biomolecular Interaction Centre, University of Canterbury, Ilam, Christchurch 8041, New Zealand.
- Department of Plant Pathology, University of Florida, Gainesville, FL 32611, USA.
- Structural Biology Research Unit, Department of Clinical Laboratory Sciences, University of Cape Town, Rondebosch, Cape Town 7701, South Africa.
| | - Simona Kraberger
- School of Biological Sciences and Biomolecular Interaction Centre, University of Canterbury, Ilam, Christchurch 8041, New Zealand.
| | - Daisy Stainton
- School of Biological Sciences and Biomolecular Interaction Centre, University of Canterbury, Ilam, Christchurch 8041, New Zealand.
| | - Enrique Moriones
- Instituto de Hortofruticultura Subtropical y Mediterránea "La Mayora" (IHSM-UMA-CSIC), Consejo Superior de Investigaciones Científicas, Estación Experimental "La Mayora", Algarrobo-Costa, Málaga 29750, Spain.
| | - Jane E Polston
- Department of Plant Pathology, University of Florida, Gainesville, FL 32611, USA.
| | - Siobain Duffy
- Department of Ecology, Evolution and Natural Resources, Rutgers, The State University of New Jersey, New Brunswick, NJ 08901, USA.
| | - Mya Breitbart
- College of Marine Science, University of South Florida, Saint Petersburg, FL 33701, USA.
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186
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Saeed M, Briddon RW, Dalakouras A, Krczal G, Wassenegger M. Functional Analysis of Cotton Leaf Curl Kokhran Virus/Cotton Leaf Curl Multan Betasatellite RNA Silencing Suppressors. BIOLOGY 2015; 4:697-714. [PMID: 26512705 PMCID: PMC4690014 DOI: 10.3390/biology4040697] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/29/2015] [Revised: 10/15/2015] [Accepted: 10/16/2015] [Indexed: 12/13/2022]
Abstract
In South Asia, Cotton leaf curl disease (CLCuD) is caused by a complex of phylogenetically-related begomovirus species and a specific betasatellite, Cotton leaf curl Multan betasatellite (CLCuMuB). The post-transcriptional gene silencing (PTGS) suppression activities of the transcriptional activator protein (TrAP), C4, V2 and βC1 proteins encoded by Cotton leaf curl Kokhran virus (CLCuKoV)/CLCuMuB were assessed in Nicotiana benthamiana. A variable degree of local silencing suppression was observed for each viral protein tested, with V2 protein exhibiting the strongest suppression activity and only the C4 protein preventing the spread of systemic silencing. The CLCuKoV-encoded TrAP, C4, V2 and CLCuMuB-encoded βC1 proteins were expressed in Escherichia coli and purified. TrAP was shown to bind various small and long nucleic acids including single-stranded (ss) and double-stranded (ds) RNA and DNA molecules. C4, V2, and βC1 bound ssDNA and dsDNA with varying affinities. Transgenic expression of C4 under the constitutive 35S Cauliflower mosaic virus promoter and βC1 under a dexamethasone inducible promoter induced severe developmental abnormalities in N. benthamiana. The results indicate that homologous proteins from even quite closely related begomoviruses may differ in their suppressor activity and mechanism of action. The significance of these findings is discussed.
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Affiliation(s)
- Muhammad Saeed
- RLP AgroScience GmbH, AlPlanta-Institute for Plant Research, Breitenweg 71, Neustadt D-67435, Germany.
- National Institute for Biotechnology and Genetic Engineering, Jhang Road, PO Box 577, Faisalabad 38000, Pakistan.
| | - Rob W Briddon
- National Institute for Biotechnology and Genetic Engineering, Jhang Road, PO Box 577, Faisalabad 38000, Pakistan.
| | - Athanasios Dalakouras
- RLP AgroScience GmbH, AlPlanta-Institute for Plant Research, Breitenweg 71, Neustadt D-67435, Germany.
| | - Gabi Krczal
- RLP AgroScience GmbH, AlPlanta-Institute for Plant Research, Breitenweg 71, Neustadt D-67435, Germany.
| | - Michael Wassenegger
- RLP AgroScience GmbH, AlPlanta-Institute for Plant Research, Breitenweg 71, Neustadt D-67435, Germany.
- Centre for Organismal Studies (COS) Heidelberg, University of Heidelberg, Im Neuenheimer Feld 360, Heidelberg D-69120, Germany.
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187
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Du Z, Tang Y, He Z, She X. High genetic homogeneity points to a single introduction event responsible for invasion of Cotton leaf curl Multan virus and its associated betasatellite into China. Virol J 2015; 12:163. [PMID: 26445958 PMCID: PMC4596356 DOI: 10.1186/s12985-015-0397-y] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2015] [Accepted: 10/01/2015] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Cotton leaf curl Multan virus (CLCuMuV) is a Whitefly Transmitted Geminivirus (WTG) endemic to the India subcontinent and is notorious as a causal agent of cotton leaf curl disease (CLCuD), a major constraint to cotton production in south Asia. We found CLCuMuV infecting Hibiscus rosa-sinensis in Guangzhou, China in 2006. The spread and evolution of the invading CLCuMuV were monitored in the following nine years. FINDINGS CLCuMuV spread rapidly in the last nine years and became established in Southern China. It infects at least five malvaceous plant species, H. rosa-sinensis, H. esculentus, Malvaiscus arboreus, Gossypium hirsutum and H. cannabinus. Complete nucleotide sequences of 34 geographically and/or temporally distinct CLCuMuV isolates were determined and analyzed together with six other publicly available genomes of CLCuMuV occurring in China. The 40 CLCuMuV isolates were found to share > 99 % nucleotide sequence identity with each other. In all cases tested, the CLCuMuVs were associated with a CLCuMuB. The 36 CLCuMuBs (30 sequenced by us) shared > 98 % nucleotide sequence identity. CONCLUSION The high genetic homogeneity of CLCuMuV and CLCuMuB in China suggests the establishment of them from a single founder event.
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Affiliation(s)
- Zhenguo Du
- Plant Protection Research Institute, Guangdong Academy of Agricultural Sciences, Guangzhou, 510640, China.,Guangdong Provincial Key Laboratory of High Technology for Plant Protection, Guangzhou, 510640, China
| | - Yafei Tang
- Plant Protection Research Institute, Guangdong Academy of Agricultural Sciences, Guangzhou, 510640, China.,Guangdong Provincial Key Laboratory of High Technology for Plant Protection, Guangzhou, 510640, China
| | - Zifu He
- Plant Protection Research Institute, Guangdong Academy of Agricultural Sciences, Guangzhou, 510640, China. .,Guangdong Provincial Key Laboratory of High Technology for Plant Protection, Guangzhou, 510640, China.
| | - Xiaoman She
- Plant Protection Research Institute, Guangdong Academy of Agricultural Sciences, Guangzhou, 510640, China.,Guangdong Provincial Key Laboratory of High Technology for Plant Protection, Guangzhou, 510640, China
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188
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Geminivirus Activates ASYMMETRIC LEAVES 2 to Accelerate Cytoplasmic DCP2-Mediated mRNA Turnover and Weakens RNA Silencing in Arabidopsis. PLoS Pathog 2015; 11:e1005196. [PMID: 26431425 PMCID: PMC4592220 DOI: 10.1371/journal.ppat.1005196] [Citation(s) in RCA: 38] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2014] [Accepted: 09/08/2015] [Indexed: 11/25/2022] Open
Abstract
Aberrant viral RNAs produced in infected plant cells serve as templates for the synthesis of dsRNAs. The derived virus-related small interfering RNAs (siRNA) mediate cleavage of viral RNAs by post-transcriptional gene silencing (PTGS), thus blocking virus multiplication. Here, we identified ASYMMETRIC LEAVES2 (AS2) as a new component of plant P body complex which mediates mRNA decapping and degradation. We found that AS2 promotes DCP2 decapping activity, accelerates mRNA turnover rate, inhibits siRNA accumulation and functions as an endogenous suppressor of PTGS. Consistent with these findings, as2 mutant plants are resistant to virus infection whereas AS2 over-expression plants are hypersensitive. The geminivirus nuclear shuttle protein BV1 protein, which shuttles between nuclei and cytoplasm, induces AS2 expression, causes nuclear exit of AS2 to activate DCP2 decapping activity and renders infected plants more sensitive to viruses. These principles of gene induction and shuttling of induced proteins to promote mRNA decapping in the cytosol may be used by viral pathogens to weaken antiviral defenses in host plants. In higher plants, aberrant RNAs generated during virus replication serve as templates to make small interfering RNAs. These small RNAs are used by host as a defense mechanism to cleave viral RNAs thereby blocking virus replication. The anti-virus defense is attenuated by the host cellular mRNA turnover machinery which clears aberrant RNAs. Viruses may use encoded component(s) to activate host cellular mRNA turnover for their own benefits. In this study, we identified ASYMMETRIC LEAVES2 (AS2) as an activator of mRNA decapping and degradation and an endogenous suppressor of virus silencing. We showed that the geminivirus BV1 protein induces AS2 expression, causes nuclear exit of AS2 to activate mRNA decapping activity and renders infected plants more sensitive to viruses. Similar mechanisms may be used by other viral pathogens to weaken antiviral defenses in host plants and also mammals.
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189
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Li F, Xu X, Huang C, Gu Z, Cao L, Hu T, Ding M, Li Z, Zhou X. The AC5 protein encoded by Mungbean yellow mosaic India virus is a pathogenicity determinant that suppresses RNA silencing-based antiviral defenses. THE NEW PHYTOLOGIST 2015; 208:555-69. [PMID: 26010321 DOI: 10.1111/nph.13473] [Citation(s) in RCA: 60] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/07/2014] [Accepted: 04/16/2015] [Indexed: 06/04/2023]
Abstract
It is generally accepted that begomoviruses in the family Geminiviridae encode four proteins (from AC1/C1 to AC4/C4) using the complementary-sense DNA as template. Although AC5/C5 coding sequences are increasingly annotated in databases for many begomoviruses, the evolutionary relationships and functions of this putative protein in viral infection are obscure. Here, we demonstrate several important functions of the AC5 protein of a bipartite begomovirus, Mungbean yellow mosaic India virus (MYMIV). Mutational analyses and transgenic expression showed that AC5 plays a critical role in MYMIV infection. Ectopic expression of AC5 from a Potato virus X (PVX) vector resulted in severe mosaic symptoms followed by a hypersensitive-like response in Nicotiana benthamiana. Furthermore, MYMIV AC5 effectively suppressed post-transcriptional gene silencing induced by single-stranded but not double-stranded RNA. AC5 was also able to reverse transcriptional gene silencing of a green fluorescent protein transgene by reducing methylation of promoter sequences, probably through repressing expression of a CHH cytosine methyltransferase (DOMAINS REARRANGED METHYLTRANSFERASE2) in N. benthamiana. Our results demonstrate that MYMIV AC5 is a pathogenicity determinant and a potent RNA silencing suppressor that employs novel mechanisms to suppress antiviral defenses, and suggest that the AC5 function may be conserved among many begomoviruses.
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Affiliation(s)
- Fangfang Li
- State Key Laboratory of Rice Biology, Zhejiang University, Hangzhou, Zhejiang, 310058, China
- State Key Laboratory for Biology of Plant Diseases and Insect Pests, Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing, 100193, China
| | - Xiongbiao Xu
- State Key Laboratory of Rice Biology, Zhejiang University, Hangzhou, Zhejiang, 310058, China
| | - Changjun Huang
- State Key Laboratory of Rice Biology, Zhejiang University, Hangzhou, Zhejiang, 310058, China
| | - Zhouhang Gu
- State Key Laboratory of Rice Biology, Zhejiang University, Hangzhou, Zhejiang, 310058, China
| | - Linge Cao
- State Key Laboratory of Rice Biology, Zhejiang University, Hangzhou, Zhejiang, 310058, China
| | - Tao Hu
- State Key Laboratory of Rice Biology, Zhejiang University, Hangzhou, Zhejiang, 310058, China
| | - Ming Ding
- Institute of Plant Protection, Yunnan Provincial Academy of Agricultural Sciences, Kunming, Yunnan, 650205, China
| | - Zhenghe Li
- State Key Laboratory of Rice Biology, Zhejiang University, Hangzhou, Zhejiang, 310058, China
| | - Xueping Zhou
- State Key Laboratory of Rice Biology, Zhejiang University, Hangzhou, Zhejiang, 310058, China
- State Key Laboratory for Biology of Plant Diseases and Insect Pests, Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing, 100193, China
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190
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Acyl-CoA N-acyltransferase influences fertility by regulating lipid metabolism and jasmonic acid biogenesis in cotton. Sci Rep 2015; 5:11790. [PMID: 26134787 PMCID: PMC4488762 DOI: 10.1038/srep11790] [Citation(s) in RCA: 33] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2015] [Accepted: 06/04/2015] [Indexed: 11/08/2022] Open
Abstract
Cotton (Gossypium spp.) is an important economic crop and there is obvious heterosis in cotton, fertility has played an important role in this heterosis. However, the genes that exhibit critical roles in anther development and fertility are not well understood. Here, we report an acyl-CoA N-acyltransferase (EC2.3; GhACNAT) that plays a key role in anther development and fertility. Suppression of GhACNAT by virus-induced gene silencing in transgenic cotton (G. hirsutum L. cv. C312) resulted in indehiscent anthers that were full of pollen, diminished filaments and stamens, and plant sterility. We found GhACNAT was involved in lipid metabolism and jasmonic acid (JA) biosynthesis. The genes differentially expressed in GhACNAT-silenced plants and C312 were mainly involved in catalytic activity and transcription regulator activity in lipid metabolism. In GhACNAT-silenced plants, the expression levels of genes involved in lipid metabolism and jasmonic acid biosynthesis were significantly changed, the amount of JA in leaves and reproductive organs was significantly decreased compared with the amounts in C312. Treatments with exogenous methyl jasmonate rescued anther dehiscence and pollen release in GhACNAT-silenced plants and caused self-fertility. The GhACNAT gene may play an important role in controlling cotton fertility by regulating the pathways of lipid synthesis and JA biogenesis.
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191
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Sudarshana MR, Perry KL, Fuchs MF. Grapevine Red Blotch-Associated Virus, an Emerging Threat to the Grapevine Industry. PHYTOPATHOLOGY 2015; 105:1026-1032. [PMID: 25738551 DOI: 10.1094/phyto-12-14-0369-fi] [Citation(s) in RCA: 66] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/28/2023]
Abstract
Grapevine red blotch-associated virus (GRBaV) is a newly identified virus of grapevines and a putative member of a new genus within the family Geminiviridae. This virus is associated with red blotch disease that was first reported in California in 2008. It affects the profitability of vineyards by substantially reducing fruit quality and ripening. In red-berried grapevine cultivars, foliar disease symptoms consist of red blotches early in the season that can expand and coalesce across most of the leaf blade later in the season. In white-berried grapevine cultivars, foliar disease symptoms are less conspicuous and generally involve irregular chlorotic areas that may become necrotic late in the season. Determining the GRBaV genome sequence yielded critical information for the design of primers for polymerase chain reaction-based diagnostics. To date, GRBaV has been reported in the major grape-growing areas in North America and two distinct phylogenetic clades have been described. Spread of GRBaV is suspected in certain vineyards but a vector of epidemiological significance has yet to be identified. Future research will need to focus on virus spread, the production of clean planting stocks, and the development of management options that are effective, economical, and environmentally friendly.
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Affiliation(s)
- Mysore R Sudarshana
- First author: United States Department of Agriculture-Agricultural Research Service, Department of Plant Pathology, University of California, Davis 95616; second author: Section of Plant Pathology and Plant-Microbe Biology, School of Integrative Plant Science, 334 Plant Science, Cornell University, Ithaca, NY 14853; and third author: Section of Plant Pathology and Plant-Microbe Biology, School of Integrative Plant Science, Cornell University, New York State Agricultural Experiment Station, Geneva, NY 14456
| | - Keith L Perry
- First author: United States Department of Agriculture-Agricultural Research Service, Department of Plant Pathology, University of California, Davis 95616; second author: Section of Plant Pathology and Plant-Microbe Biology, School of Integrative Plant Science, 334 Plant Science, Cornell University, Ithaca, NY 14853; and third author: Section of Plant Pathology and Plant-Microbe Biology, School of Integrative Plant Science, Cornell University, New York State Agricultural Experiment Station, Geneva, NY 14456
| | - Marc F Fuchs
- First author: United States Department of Agriculture-Agricultural Research Service, Department of Plant Pathology, University of California, Davis 95616; second author: Section of Plant Pathology and Plant-Microbe Biology, School of Integrative Plant Science, 334 Plant Science, Cornell University, Ithaca, NY 14853; and third author: Section of Plant Pathology and Plant-Microbe Biology, School of Integrative Plant Science, Cornell University, New York State Agricultural Experiment Station, Geneva, NY 14456
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192
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Ma Y, Navarro B, Zhang Z, Lu M, Zhou X, Chi S, Di Serio F, Li S. Identification and molecular characterization of a novel monopartite geminivirus associated with mulberry mosaic dwarf disease. J Gen Virol 2015; 96:2421-2434. [PMID: 25953916 DOI: 10.1099/vir.0.000175] [Citation(s) in RCA: 49] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/13/2023] Open
Abstract
High-throughput sequencing of small RNAs allowed the identification of a novel DNA virus in a Chinese mulberry tree affected by a disease showing mosaic and dwarfing symptoms. Rolling-circle amplification and PCR with specific primers, followed by sequencing of eleven independent full-length clones, showed that this virus has a monopartite circular DNA genome (∼ 2.95 kb) containing ORFs in both polarity strands, as reported previously for geminiviruses. A field survey showed the close association of the virus with diseased mulberries, so we tentatively named the virus mulberry mosaic dwarf-associated virus (MMDaV). The MMDaV genome codes for five and two putative proteins in the virion-sense and in the complementary-sense strands, respectively. Although three MMDaV virion-sense putative proteins did not share sequence homology with any protein in the databases, functional domains [coiled-coil and transmembrane (TM) domains] were identified in two of them. In addition, the protein containing a TM domain was encoded by an ORF located in a similar genomic position in MMDaV and in several other geminiviruses. As reported for members of the genera Mastrevirus and Becurtovirus, MMDaV replication-associated proteins are expressed through the alternative splicing of an intron, which was shown to be functional in vivo. A similar intron was found in the genome of citrus chlorotic dwarf-associated virus (CCDaV), a divergent geminivirus found recently in citrus. On the basis of pairwise comparisons and phylogenetic analyses, CCDaV and MMDaV appear to be closely related to each other, thus supporting their inclusion in a putative novel genus in the family Geminiviridae.
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Affiliation(s)
- Yuxin Ma
- State Key Laboratory for Biology of Plant Diseases and Insect Pests, Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Yuanmingyuan West Road No. 2, Haidian District, Beijing 100193, PR China
| | - Beatriz Navarro
- Istituto per la Protezione Sostenibile delle Piante CNR, UO Bari, Via Amendola, 70126 Bari, Italy
| | - Zhixiang Zhang
- State Key Laboratory for Biology of Plant Diseases and Insect Pests, Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Yuanmingyuan West Road No. 2, Haidian District, Beijing 100193, PR China
| | - Meiguang Lu
- State Key Laboratory for Biology of Plant Diseases and Insect Pests, Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Yuanmingyuan West Road No. 2, Haidian District, Beijing 100193, PR China
| | - Xueping Zhou
- State Key Laboratory for Biology of Plant Diseases and Insect Pests, Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Yuanmingyuan West Road No. 2, Haidian District, Beijing 100193, PR China
| | - Shengqi Chi
- College of Agronomy and Plant Protection, Qingdao Agricultural University, Changcheng Road No. 700, Chengyang District, Qingdao 266000, PR China
| | - Francesco Di Serio
- Istituto per la Protezione Sostenibile delle Piante CNR, UO Bari, Via Amendola, 70126 Bari, Italy
| | - Shifang Li
- State Key Laboratory for Biology of Plant Diseases and Insect Pests, Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Yuanmingyuan West Road No. 2, Haidian District, Beijing 100193, PR China
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193
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Maredza AT, Allie F, Plata G, Rey MEC. Sequences enhancing cassava mosaic disease symptoms occur in the cassava genome and are associated with South African cassava mosaic virus infection. Mol Genet Genomics 2015; 291:1467-85. [PMID: 25920485 DOI: 10.1007/s00438-015-1049-z] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/06/2015] [Accepted: 04/10/2015] [Indexed: 10/23/2022]
Abstract
Cassava is an important food security crop in Sub-Saharan Africa. Two episomal begomovirus-associated sequences, named Sequences Enhancing Geminivirus Symptoms (SEGS1 and SEGS2), were identified in field cassava affected by the devastating cassava mosaic disease (CMD). The sequences reportedly exacerbated CMD symptoms in the tolerant cassava landrace TME3, and the model plants Arabidopsis thaliana and Nicotiana benthamiana, when biolistically co-inoculated with African cassava mosaic virus-Cameroon (ACMV-CM) or East African cassava mosaic virus-UG2 (EACMV-UG2). Following the identification of small SEGS fragments in the cassava EST database, the intention of this study was to confirm their presence in the genome, and investigate a possible role for these sequences in CMD. We report that multiple copies of varying lengths of both SEGS1 and SEGS2 are widely distributed in the sequenced cassava genome and are present in several other cassava accessions screened by PCR. The endogenous SEGS1 and SEGS2 are in close proximity or overlapping with cassava genes, suggesting a possible role in regulation of specific biological processes. We confirm the expression of SEGS in planta using EST data and RT-PCR. The sequence features of endogenous SEGS (iSEGS) are unique but resemble non-autonomous transposable elements (TEs) such as MITEs and helitrons. Furthermore, many SEGS-associated genes, some involved in virus-host interactions, are differentially expressed in susceptible (T200) and tolerant TME3) cassava landraces infected by South African cassava mosaic virus (SACMV) of susceptible (T200) and tolerant (TME3) cassava landraces. Abundant SEGS-derived small RNAs were also present in mock-inoculated and SACMV-infected T200 and TME3 leaves. Given the known role of TEs and associated genes in gene regulation and plant immune responses, our observations are consistent with a role of these DNA elements in the host's regulatory response to geminiviruses.
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Affiliation(s)
- A T Maredza
- School of Molecular and Cell Biology, University of the Witwatersrand, Johannesburg, Wits, 2050, South Africa
| | - F Allie
- School of Molecular and Cell Biology, University of the Witwatersrand, Johannesburg, Wits, 2050, South Africa
| | - G Plata
- Department of Systems Biology, Columbia University in the City of New York, 1130 St Nicholas Avenue, New York, NY, USA
| | - M E C Rey
- School of Molecular and Cell Biology, University of the Witwatersrand, Johannesburg, Wits, 2050, South Africa.
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194
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Saeed M, Krczal G, Wassenegger M. Three gene products of a begomovirus-betasatellite complex restore expression of a transcriptionally silenced green fluorescent protein transgene in Nicotiana benthamiana. Virus Genes 2015; 50:340-4. [PMID: 25537949 DOI: 10.1007/s11262-014-1155-8] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2014] [Accepted: 12/04/2014] [Indexed: 11/30/2022]
Abstract
Single-stranded DNA geminiviruses replicate via double-stranded DNA intermediates forming mini-chromosomes that are targets for transcriptional gene silencing (TGS) in plants. The ability of the cotton leaf curl Kokhran virus (CLCuKoV)-cotton leaf curl Multan betasatellite (CLCuMuB) proteins, replication-associated protein (Rep), transcriptional activator protein (TrAP), C4, V2 and βC1, to suppress TGS was investigated by using the Nicotiana benthamiana line 16-TGS (16-TGS) harbouring a transcriptionally silenced green fluorescent protein (GFP) transgene. Inoculation of 16-TGS plants with a recombinant potato virus X vector carrying Rep, TrAP or βC1 resulted in re-expression of GFP. Northern blot analysis confirmed that the observed GFP fluorescence was associated with GFP mRNA accumulation. These results indicated that Rep, TrAP and βC1 proteins of CLCuKoV-CLCuMuB can re-activate the expression of a transcriptionally silenced GFP transgene in N. benthamiana. Although Rep, TrAP, or βC1 proteins have, for other begomoviruses or begomoviruses-betasatellites, been previously shown to have TGS suppressor activity, this is the first report demonstrating that a single begomovirus-betasatellite complex encodes three suppressors of TGS.
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Affiliation(s)
- Muhammad Saeed
- RLP AgroScience GmbH, AlPlanta-Institute for Plant Research, Breitenweg 71, 67435, Neustadt, Germany,
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195
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Lefeuvre P, Moriones E. Recombination as a motor of host switches and virus emergence: geminiviruses as case studies. Curr Opin Virol 2015; 10:14-9. [DOI: 10.1016/j.coviro.2014.12.005] [Citation(s) in RCA: 75] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2014] [Revised: 11/26/2014] [Accepted: 12/03/2014] [Indexed: 10/24/2022]
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196
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Jeyabharathy C, Shakila H, Usha R. Development of a VIGS vector based on the β-satellite DNA associated with bhendi yellow vein mosaic virus. Virus Res 2015; 195:73-8. [PMID: 25169741 DOI: 10.1016/j.virusres.2014.08.009] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2014] [Revised: 08/17/2014] [Accepted: 08/18/2014] [Indexed: 10/24/2022]
Abstract
Bhendi yellow vein mosaic virus (BYMV) is a monopartite begomovirus with an associated β-satellite. βC1 ORF encoded by the β-satellite is the symptom determinant and a strong suppressor of post transcriptional gene silencing. To create a virus induced gene silencing vector based upon the β-satellite associated with BYVMV the βC1 ORF was replaced with multiple cloning sites. GFP transgene and plant endogenous genes Su, PDS, PCNA and AGO1 were cloned into β-satellite based VIGS vector. GFP expression was silenced in the GFP expressing transgenic 16c Nicotiana benthamiana plants infiltrated with VIGS vector carrying GFP gene inside. N. benthamiana plants infiltrated with the VIGS vector harboring the endogenous genes Su, PDS, PCNA and AGO1 produced the phenotypic symptoms yellowing of the veins, photobleaching of the veins, stunting of the plant and upward leaf curling, respectively. Real time PCR analyses revealed a reduction in the levels of the corresponding transgene or endogenous target mRNA. The β-satellite based VIGS vector was able to silence the target genes effectively. Hence, BYVMV β-satellite based VIGS vector can be used in functional genomics studies.
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Affiliation(s)
- C Jeyabharathy
- School of Biotechnology, Madurai Kamaraj University, Department of Plant Biotechnology, Madurai 625021, Tamil Nadu, India
| | - H Shakila
- School of Biotechnology, Madurai Kamaraj University, Department of Plant Biotechnology, Madurai 625021, Tamil Nadu, India
| | - R Usha
- School of Biotechnology, Madurai Kamaraj University, Department of Plant Biotechnology, Madurai 625021, Tamil Nadu, India.
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197
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Kumar J, Gunapati S, Kumar J, Kumari A, Kumar A, Tuli R, Singh SP. Virus-induced gene silencing using a modified betasatellite: a potential candidate for functional genomics of crops. Arch Virol 2014; 159:2109-13. [PMID: 24610555 DOI: 10.1007/s00705-014-2039-x] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2013] [Accepted: 02/27/2014] [Indexed: 10/25/2022]
Abstract
Betasatellites are geminivirus-associated single-stranded DNA molecules that play an important role in symptom modulation. A VIGS vector was developed by modifying cotton leaf curl Multan betasatellite (CLCuMB). CLCuMB DNA was modified by replacing the βC1 gene with a multiple cloning site. The silencing ability of the modified CLCuMB was investigated by cloning a fragment of a host gene (Su) or a reporter transgene (uidA) into the modified CLCuMB and co-agroinoculation with cotton leaf curl Multan virus, cotton leaf curl Kokhran virus, and ageratum enation virus, separately. The inoculated Nicotiana tabacum, N. benthamiana, Solanum lycopersicum, Arabidopsis thaliana and Gossypium hirsutum plants showed efficient silencing of the cognate genes.
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Affiliation(s)
- Jitendra Kumar
- National Agri-Food Biotechnology Institute, Mohali, 160071, Punjab, India,
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198
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Gu Z, Huang C, Li F, Zhou X. A versatile system for functional analysis of genes and microRNAs in cotton. PLANT BIOTECHNOLOGY JOURNAL 2014; 12:638-49. [PMID: 24521483 DOI: 10.1111/pbi.12169] [Citation(s) in RCA: 97] [Impact Index Per Article: 9.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/05/2013] [Revised: 11/26/2013] [Accepted: 01/02/2014] [Indexed: 05/20/2023]
Abstract
Cotton is an important economic crop worldwide. Due to its long growth cycle, large genome size and recalcitrance to stable transformation, traditional methods for the analysis of gene function in this crop are difficult and labour intensive. Here, we report a cotton leaf crumple virus (CLCrV)-based vector and its application in gene function analysis through virus-induced gene silencing (VIGS) and overexpression of microRNAs (miRNAs), small tandem target mimic (STTM) and artificial miRNA (amiRNA) in cotton via an Agrobacterium-mediated infiltration approach. Using this system, we were able to efficiently silence two endogenous genes, magnesium chelatase subunit I (CHLI) and elongation factor-1α (EF-1α), in Gossypium species and the Bacillus thuringiensis cry1A gene in transgenic cotton. Furthermore, our results show that this vector can be used to ectopically express endogenous miR156 in G. hirsutum, causing a reduction in miR156-targeted RNA transcripts resulting in the development of abnormal leaf phenotypes. Ectopic expression of miR165/166 STTM with this vector led to downward curling and crumpled leaves, and a significant increase in the miR165/166 target mRNAs. This versatile system is easy to use and can provide more uniform and persistent gene silencing in cotton, thereby providing a powerful approach for gene discovery in cotton.
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Affiliation(s)
- Zhouhang Gu
- State Key Laboratory of Rice Biology, Institute of Biotechnology, Zhejiang University, Hangzhou, China
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199
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Jones R. Trends in plant virus epidemiology: Opportunities from new or improved technologies. Virus Res 2014; 186:3-19. [DOI: 10.1016/j.virusres.2013.11.003] [Citation(s) in RCA: 37] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2013] [Revised: 10/30/2013] [Accepted: 11/01/2013] [Indexed: 12/16/2022]
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200
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Association of satellites with a mastrevirus in natural infection: complexity of Wheat dwarf India virus disease. J Virol 2014; 88:7093-104. [PMID: 24719407 DOI: 10.1128/jvi.02911-13] [Citation(s) in RCA: 60] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
UNLABELLED In contrast to begomoviruses, mastreviruses have not previously been shown to interact with satellites. This study reports the first identification of the association of satellites with a mastrevirus in field-grown plants. Two alphasatellite species were detected in different field samples of wheat infected with Wheat Dwarf India Virus (WDIV), a Cotton leaf curl Multan alphasatellite (CLCuMA) and a Guar leaf curl alphasatellite (GLCuA). In addition to the alphasatellites, a betasatellite, Ageratum yellow leaf curl betasatellite (AYLCB), was also identified in the wheat samples. No begomovirus was detected in the wheat samples, thus establishing association of the above-named satellites with WDIV. Agrobacterium-mediated inoculation of WDIV in wheat, in the presence of either of the alphasatellites or the betasatellite, resulted in infections inducing more severe symptoms. WDIV efficiently maintained each of the alphasatellites and the betasatellite in wheat. The satellites enhanced the level of WDIV DNA in wheat. Inoculation of the satellites isolated from wheat with various begomoviruses into Nicotiana tabacum demonstrated that these remain capable of interacting with the viruses with which they were first identified. Virus-specific small RNAs accumulated in wheat upon infection with WDIV but were lower in abundance in plants coinfected with the satellites, suggesting that both the alphasatellites and the betasatellite suppress RNA silencing. These results suggest that the selective advantage for the maintenance of the alphasatellites and the betasatellite by WDIV in the field is in overcoming RNA silencing-mediated host defense. IMPORTANCE Wheat is the most widely cultivated cereal crop in the world. A number of viruses are important pathogens of wheat, including the viruses of the genus Mastrevirus, family Geminiviridae. This study reports the association of subgenomic components, called satellites (alpha- and betasatellites), with a mastrevirus, Wheat Dwarf India Virus (WDIV), isolated from two distant locations in India. This study reports the first identification of the satellites in a monocot plant. The satellites enhanced accumulation of WDIV and severity of disease symptoms. The satellites lowered the concentration of virus-specific small RNAs in wheat plants, indicating their silencing suppressor activity. The involvement of the satellites in symptom severity of the mastrevirus can have implications in the form of economic impact of the virus on crop yield. Understanding the role of the satellites in disease severity is important for developing disease management strategies.
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