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Naresh M, Purkayastha A, Dasgupta I. P4 protein of an Indian isolate of rice tungro bacilliform virus modulates gene silencing. Virus Genes 2024; 60:55-64. [PMID: 38055154 DOI: 10.1007/s11262-023-02039-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2023] [Accepted: 11/09/2023] [Indexed: 12/07/2023]
Abstract
Plant hosts and their viral pathogens are engaged in a constant cycle of defense and counter-defense as part of a molecular arms race, principal among them being the plant RNAi defense and the viral RNAi suppressor counter-defense. Rice tungro bacilliform virus (RTBV), member of the family Caulimoviridae, genus Tungrovirus, species Tungrovirus oryzae, infects rice in South- and Southeast Asia and causes severe symptoms of stunting, yellow-orange discoloration and twisting of leaf tips. To better understand the possible counter-defensive roles of RTBV against the host RNAi defense system, we explored the ability of the P4 protein of an Indian isolate of RTBV to act as a possible modulator of RNAi. Using a transient silencing and silencing suppression assay in Nicotiana benthamiana, we show that P4 not only displays an RNAi suppressor function, but also potentially enhances RNAi. The results also suggests that the N-terminal 168 amino acid residues of P4 are sufficient to maintain RNAi suppressor activity. Taken together with the earlier reports this work strengthens the view that the P4 protein carries out RNAi suppressor and a potential RNAi enhancer function.
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Affiliation(s)
- Madhvi Naresh
- Department of Plant Molecular Biology, University of Delhi South Campus, New Delhi, 110021, India
| | - Arunima Purkayastha
- Department of Plant Molecular Biology, University of Delhi South Campus, New Delhi, 110021, India
| | - Indranil Dasgupta
- Department of Plant Molecular Biology, University of Delhi South Campus, New Delhi, 110021, India.
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2
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Silencing suppressor protein PRT of rice tungro bacilliform virus interacts with the plant RNA silencing-related protein SGS3. Virology 2023; 581:71-80. [PMID: 36921478 DOI: 10.1016/j.virol.2023.02.013] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2022] [Revised: 02/16/2023] [Accepted: 02/22/2023] [Indexed: 03/08/2023]
Abstract
BACKGROUND Rice tungro bacilliform virus (RTBV) is a double stranded DNA containing virus which causes the devastating tungro disease of rice in association with an RNA virus, rice tungro spherical virus. RNA silencing is an evolutionarily conserved antiviral defence pathway in plants as well as in several classes of higher organisms. Many viruses, in turn, encode proteins which are termed Viral Suppressor of RNA Silencing (VSR) because they downregulate or suppress RNA silencing. RESULTS Using an RNA silencing suppressor assay we show that RTBV protease (PRT) acts as a mild VSR. A truncated version of PRT gene abolished the silencing suppression activity. We also show in planta interaction of PRT with the SGS3 protein of Solanum tuberosum and Arabidopsis thaliana using bimolecular fluorescence complementation assay (BIFC). Transient expression of PRT in Nicotiana benthamiana caused an increased accumulation of the begomovirus Sri Lankan cassava mosaic virus (SLCMV) DNA-A, which indicated a virulence function imparted on an unrelated virus. CONCLUSION The finding supports the idea that PRT acts as suppressor of RNA silencing and this action may be mediated by its interaction with SGS3.
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3
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A consolidative synopsis of the MALDI-TOF MS accomplishments for the rapid diagnosis of microbial plant disease pathogens. Trends Analyt Chem 2022. [DOI: 10.1016/j.trac.2022.116713] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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4
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Read DA, Roberts R, Swanevelder D, Pietersen G, Thompson GD. Novel viruses associated with plants of the family Amaryllidaceae in South Africa. Arch Virol 2021; 166:2817-2823. [PMID: 34279720 DOI: 10.1007/s00705-021-05170-3] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2021] [Accepted: 05/23/2021] [Indexed: 11/28/2022]
Abstract
Nineteen samples from members of the plant genera Agapanthus, Clivia, Hippeastrum, and Scadoxus were collected from gardens in the Gauteng and Western Cape provinces of South Africa. The plants displayed highly variable symptoms of viral disease, including chlorosis, necrosis, streaking, and ringspot. RNAtag-seq was used to characterize the associated viral populations. Plants of the genus Agapanthus were found to be associated with three novel viruses from the families Caulimoviridae, Closteroviridae, and Betaflexiviridae; plants of the genus Clivia were associated with novel members of the families Potyviridae and Betaflexiviridae; and plants of the genus Scadoxus were associated with a novel member of the family Tospoviridae. Nerine latent virus was associated with plants of the genera Agapanthus, Clivia, and Hippeastrum, while hippeastrum mosaic virus was associated exclusively with a Hippeastrum cultivar.
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Affiliation(s)
- David A Read
- Agricultural Research Council (ARC) - Biotechnology Platform, 100 Old Soutpan Road, Onderstepoort, Pretoria, 0110, South Africa. .,Forestry and Agricultural Biotechnology Institute (FABI), University of Pretoria, Private Bag X20, Hatfield, 0028, South Africa.
| | - Ronel Roberts
- ARC - Plant Health and Protection, Private Bag X134, Queenswood, Pretoria, 0121, South Africa
| | - Dirk Swanevelder
- Agricultural Research Council (ARC) - Biotechnology Platform, 100 Old Soutpan Road, Onderstepoort, Pretoria, 0110, South Africa
| | - Gerhard Pietersen
- Department of Genetics, Stellenbosch University, Stellenbosch, 7600, South Africa
| | - Genevieve D Thompson
- Agricultural Research Council (ARC) - Biotechnology Platform, 100 Old Soutpan Road, Onderstepoort, Pretoria, 0110, South Africa.,Gene Vantage, 34 Monte Carlo Crescent, Kyalami Business Park, Johannesburg, 1684, South Africa
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5
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The titers of rice tungro bacilliform virus dictate the expression levels of genes related to cell wall dynamics in rice plants affected by tungro disease. Arch Virol 2021; 166:1325-1336. [PMID: 33660107 DOI: 10.1007/s00705-021-05006-0] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2020] [Accepted: 01/04/2021] [Indexed: 10/22/2022]
Abstract
Rice tungro disease (RTD) is a devastating disease of rice caused by combined infection with rice tungro bacilliform virus (RTBV) and rice tungro spherical virus (RTSV), with one of the main symptoms being stunting. To dissect the molecular events responsible for RTD-induced stunting, the expression patterns of 23 cell-wall-related genes were examined in different rice lines with the same titers of RTSV but different titers of RTBV and in lines where only RTBV was present. Genes encoding cellulose synthases, expansins, glycosyl hydrolases, exostosins, and xyloglucan galactosyl transferase showed downregulation, whereas those encoding defensin or defensin-like proteins showed upregulation with increasing titers of RTBV. RTSV titers did not affect the expression levels of these genes. A similar relationship was seen for the reduction in the cellulose and pectin content and the accumulation of lignin. In silico analysis of promoters of the genes indicated a possible link to transcription factors reported earlier to respond to viral titers in rice. These results suggest a common network in which the genes related to the cell wall components are affected during infection with diverse viruses in rice.
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6
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Nguyen TH, Wang D, Rahman SU, Bai H, Yao X, Chen D, Tao S. Analysis of codon usage patterns and influencing factors in rice tungro bacilliform virus. INFECTION GENETICS AND EVOLUTION 2021; 90:104750. [PMID: 33548490 DOI: 10.1016/j.meegid.2021.104750] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/11/2020] [Revised: 01/08/2021] [Accepted: 01/29/2021] [Indexed: 12/17/2022]
Abstract
Rice tungro bacilliform virus (RTBV) belongs to genus Tungrovirus within the family Caulimoviridae harbors circular double-stranded DNA (dsDNA). Rice tungro disease (RTD) caused by RTBV, responsible for severe rice yield losses in South and Southeast Asia. Here, we performed a systematic evolutionary and codon usage bias (CUB) analysis of RTBV genome sequences. We analysed different bioinformatics techniques to calculate the nucleotide compositions, the relative synonymous codon usage (RSCU), and other indices. The results indicated slightly or low codon usage bias in RTBV isolates. Mutation and natural selection pressures have equally contributed to this low codon usage bias. Additionally, multiple factors such as host, geographical distribution also affect codon usage patterns in RTBV genomes. RSCU analysis revealed that RTBV shows mutation bias and prefers A and U ended codons to code amino acids. Codon usage patterns of RTBV were also found to be influenced by its host. This indicates that RTBV have evolved codon usage patterns that are specific to its host. The findings from this study are expected to increase our understanding of factors leading to viral evolution and fitness with respect to hosts and the environment.
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Affiliation(s)
- Thi Hung Nguyen
- College of Life Sciences and State Key Laboratory of Crop Stress Biology in Arid Areas, Northwest A&F University, Yangling, Shaanxi 712100, China; Department of Genetic Engineering, Agricultural Genetics Institute, Tuliem, Hanoi 100000, Viet Nam
| | - Dong Wang
- China animal health and epidemiology center, Qingdao, Shandong, China
| | - Siddiq Ur Rahman
- College of Life Sciences and State Key Laboratory of Crop Stress Biology in Arid Areas, Northwest A&F University, Yangling, Shaanxi 712100, China; Department of Computer Science and Bioinformatics, Khushal Khan Khattak university, Karak, Khyber Pakhtunkhwa 27200, Pakistan
| | - Haoxiang Bai
- College of Life Sciences and State Key Laboratory of Crop Stress Biology in Arid Areas, Northwest A&F University, Yangling, Shaanxi 712100, China
| | - Xiaoting Yao
- College of Veterinary Medicine, Northwest A&F University, Yangling, Shaanxi 712100, China
| | - Dekun Chen
- College of Veterinary Medicine, Northwest A&F University, Yangling, Shaanxi 712100, China.
| | - Shiheng Tao
- College of Life Sciences and State Key Laboratory of Crop Stress Biology in Arid Areas, Northwest A&F University, Yangling, Shaanxi 712100, China.
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7
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Kannan M, Mohamad Saad M, Zainal Z, Kassim H, Ismail I, Talip N, Baharum SN, Bunawan H. Sequence and Phylogenetic Analysis of the First Complete Genome of Ricetungro spherical virus in Malaysia. IRANIAN JOURNAL OF BIOTECHNOLOGY 2020; 18:e2566. [PMID: 34056024 PMCID: PMC8148635 DOI: 10.30498/ijb.2020.2566] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Background: Rice tungro disease (RTD) is a viral disease mainly affecting rice in Asia. RTD caused by Rice tungro bacilliform virus and Rice tungro spherical virus. To date, there are only 5 RTSV isolates have been reported. Objectives: In this study, we aimed to report the complete nucleotide sequence of Malaysian isolate of Rice tungro spherical virus Seberang Perai (RTSV-SP) for the first time. RTSV-SP was characterized and its evolutionary relationship with previously reported Indian and Philippines isolates were elucidated. Materials and Methods: RTSV-SP isolate was isolated from a recent outbreak in a paddy field in Seberang Perai zone of Malaysia. Its complete genome was amplified by RT-PCR, cloned and sequenced. Results: Sequence analysis indicated that the genome of RTSV-SP consisted of 12,173 nucleotides (nt). Comparative analysis of 6 complete genome sequences using Clustal Omega showed that Seberang Perai isolate shared the highest nucleotide identity (96.04%) with Philippine-A isolate, except that the sORF-2 of RTSV-SP is shorter than RTSV Philippine-A by 27 amino acid residues. RTSV-SP found to cluster in Southeast Asia (SEA) group based on the whole genome sequence phylogenetic analysis using MEGA X software. Conclusions: Phylogenetic classification of RTSV isolates based on the complete nucleotide sequences showed more distinctive clustering pattern with the addition of RTSV-SP whole genome to the available isolates. Present study described the isolation and molecular characterization of RTSV-SP.
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Affiliation(s)
- Maathavi Kannan
- Institute of Systems Biology, Universiti Kebangsaan Malaysia, 43600 Bangi, Malaysia
| | - Maisarah Mohamad Saad
- Institute of Rice Research Centre, MARDI Seberang Perai, Jalan Paya Keladi/ Pinang Tunggal, 13200 Kepala Batas, Penang, Malaysia
| | - Zamri Zainal
- Institute of Systems Biology, Universiti Kebangsaan Malaysia, 43600 Bangi, Malaysia.,School of Biosciences and Biotechnology, Universiti Kebangsaan Malaysia, 43600 Bangi Selangor, Malaysia
| | - Hakimi Kassim
- Institute of Systems Biology, Universiti Kebangsaan Malaysia, 43600 Bangi, Malaysia
| | - Ismanizan Ismail
- Institute of Systems Biology, Universiti Kebangsaan Malaysia, 43600 Bangi, Malaysia.,School of Biosciences and Biotechnology, Universiti Kebangsaan Malaysia, 43600 Bangi Selangor, Malaysia
| | - Noraini Talip
- School of Environmental and Natural Resource Sciences, Universiti Kebangsaan Malaysia, 43600 Bangi Selangor, Malaysia
| | | | - Hamidun Bunawan
- Institute of Systems Biology, Universiti Kebangsaan Malaysia, 43600 Bangi, Malaysia
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8
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Kumar G, Dasgupta I. Comprehensive molecular insights into the stress response dynamics of rice (Oryza sativa L.) during rice tungro disease by RNA-seq-based comparative whole transcriptome analysis. J Biosci 2020. [DOI: 10.1007/s12038-020-9996-x] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
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9
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Bernardes WS, Menossi M. Plant 3' Regulatory Regions From mRNA-Encoding Genes and Their Uses to Modulate Expression. FRONTIERS IN PLANT SCIENCE 2020; 11:1252. [PMID: 32922424 PMCID: PMC7457121 DOI: 10.3389/fpls.2020.01252] [Citation(s) in RCA: 30] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/25/2020] [Accepted: 07/29/2020] [Indexed: 05/08/2023]
Abstract
Molecular biotechnology has made it possible to explore the potential of plants for different purposes. The 3' regulatory regions have a great diversity of cis-regulatory elements directly involved in polyadenylation, stability, transport and mRNA translation, essential to achieve the desired levels of gene expression. A complex interaction between the cleavage and polyadenylation molecular complex and cis-elements determine the polyadenylation site, which may result in the choice of non-canonical sites, resulting in alternative polyadenylation events, involved in the regulation of more than 80% of the genes expressed in plants. In addition, after transcription, a wide array of RNA-binding proteins interacts with cis-acting elements located mainly in the 3' untranslated region, determining the fate of mRNAs in eukaryotic cells. Although a small number of 3' regulatory regions have been identified and validated so far, many studies have shown that plant 3' regulatory regions have a higher potential to regulate gene expression in plants compared to widely used 3' regulatory regions, such as NOS and OCS from Agrobacterium tumefaciens and 35S from cauliflower mosaic virus. In this review, we discuss the role of 3' regulatory regions in gene expression, and the superior potential that plant 3' regulatory regions have compared to NOS, OCS and 35S 3' regulatory regions.
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10
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Kumar G, Dasgupta I. Comprehensive molecular insights into the stress response dynamics of rice ( Oryza sativa L.) during rice tungro disease by RNA-seq-based comparative whole transcriptome analysis. J Biosci 2020; 45:27. [PMID: 32020909] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/10/2023]
Abstract
Rice tungro is a serious viral disease of rice resulting from infection by two viruses, Rice tungro bacilliform virus and Rice tungro spherical virus. To gain molecular insights into the global gene expression changes in rice during tungro, a comparative whole genome transcriptome study was performed on healthy and tungroaffected rice plants using Illumina Hiseq 2500. About 10 GB of sequenced data comprising about 50 million paired end reads per sample were then aligned on to the rice genome. Gene expression analysis revealed around 959 transcripts, related to various cellular pathways concerning stress response and hormonal homeostasis to be differentially expressed. The data was validated through qRT-PCR. Gene ontology and pathway analyses revealed enrichment of transcripts and processes similar to the differentially expressed genes categories. In short, the present study is a comprehensive coverage of the differential gene expression landscape and provides molecular insights into the infection dynamics of the rice-tungro virus system.
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Affiliation(s)
- Gaurav Kumar
- Department of Plant Molecular Biology, University of Delhi South Campus, New Delhi 110 021, India
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11
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Complete Genome Sequence of Rice Tungro Bacilliform Virus Infecting Asian Rice (Oryza sativa) in Malaysia. Microbiol Resour Announc 2019; 8:8/20/e00262-19. [PMID: 31097500 PMCID: PMC6522785 DOI: 10.1128/mra.00262-19] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022] Open
Abstract
Rice tungro disease was discovered in Malaysia in the 1930s. The first and only genome of Rice tungro bacilliform virus (RTBV) isolated from rice in Malaysia was sequenced in 1999. Rice tungro disease was discovered in Malaysia in the 1930s. The first and only genome of Rice tungro bacilliform virus (RTBV) isolated from rice in Malaysia was sequenced in 1999. After nearly two decades, here, we present the complete genome sequence of an RTBV isolate in rice from Seberang Perai, Malaysia.
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12
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Assessment of resistance to rice tungro disease in popular rice varieties in India by introgression of a transgene against Rice tungro bacilliform virus. Arch Virol 2019; 164:1005-1013. [PMID: 30734111 DOI: 10.1007/s00705-019-04159-3] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2018] [Accepted: 01/03/2019] [Indexed: 10/27/2022]
Abstract
Rice crops in South and Southeast Asian countries suffer critical yield losses due to rice tungro disease caused by joint infection with rice tungro bacilliform virus (RTBV) and rice tungro spherical virus (RTSV). Previously, for generating RNA interference-based transgenic resistance against tungro viruses, RTBV ORF IV was used as a transgene to develop RTBV resistance in a popular high-yielding scented rice variety. The transgene from this line was then introgressed into five popular high-yielding but tungro-susceptible rice varieties by marker-assisted backcross breeding with a view to combine the resistant trait with the agronomic traits. The present work includes a resistance assay of the BC3F5 lines of these varieties under glasshouse conditions. Out of a total of 28 lines tested, each consisting of 12 individual plants, eight lines showed significant amelioration in height reduction and 100- to 1000-fold reduction in RTBV titers. The RNAi-mediated resistance was clearly manifested by the presence of virus-derived small RNA (vsRNA) specific for RTBV ORF IV in the transgenic backcrossed lines.
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13
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Zarreen F, Kumar G, Johnson AMA, Dasgupta I. Small RNA-based interactions between rice and the viruses which cause the tungro disease. Virology 2018; 523:64-73. [PMID: 30081310 DOI: 10.1016/j.virol.2018.07.022] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2018] [Revised: 07/20/2018] [Accepted: 07/20/2018] [Indexed: 10/28/2022]
Abstract
Rice tungro disease is caused by a complex of two viruses, Rice tungro bacilliform virus (RTBV) and Rice tungro spherical virus (RTSV). To examine the RNAi-based defence response in rice during tungro disease, we characterized the virus-derived small RNAs and miRNAs by Deep Sequencing. We found that, while 21 nt/22 nt (nucleotide) siRNAs are predominantly produced in a continuous, overlapping and asymmetrical manner from RTBV, siRNA accumulation from RTSV were negligible. Additionally, 54 previously known miRNAs from rice, predicted to be regulating genes involved in plant defence, hormone signaling and developmental pathways were differentially expressed in the infected samples, compared to the healthy ones. This is the first study of sRNA profile of tungro virus complex from infected rice plants. The biased response of the host antiviral machinery against the two viruses and the differentially-expressed miRNAs are novel observations, which entail further studies.
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Affiliation(s)
- Fauzia Zarreen
- Department of Plant Molecular Biology, University of Delhi South Campus, New Delhi 110021, India
| | - Gaurav Kumar
- Department of Plant Molecular Biology, University of Delhi South Campus, New Delhi 110021, India
| | - A M Anthony Johnson
- Department of Botany, Sri Krishnadevaraya University, Anantapur 515003, Andhra Pradesh, India
| | - Indranil Dasgupta
- Department of Plant Molecular Biology, University of Delhi South Campus, New Delhi 110021, India.
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14
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Sharma S, Kumar G, Dasgupta I. Simultaneous resistance against the two viruses causing rice tungro disease using RNA interference. Virus Res 2018; 255:157-164. [PMID: 30031045 DOI: 10.1016/j.virusres.2018.07.011] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2018] [Revised: 07/14/2018] [Accepted: 07/17/2018] [Indexed: 02/09/2023]
Abstract
Rice tungro is the most important viral disease affecting rice in South and Southeast Asia, caused by two viruses rice tungro bacilliform virus (RTBV) and rice tungro spherical virus (RTSV). Transgenic resistance using RNA-interference (RNAi) has been reported individually against RTBV and RTSV earlier. Here we report the development of transgenic rice plants expressing RNAi against both RTBV and RTSV simultaneously. A DNA construct carrying 300 bp of RTBV DNA and 300 bp of RTSV cDNA were cloned as the two arms in hairpin orientation in a binary plasmid background to generate RNAi against both viruses simultaneously. Transgenic rice plants were raised using the above construct and their resistance against RTBV and RTSV was quantified at the T1 plants. Levels of both the viral nucleic acids showed a fall of 100- to 500-fold in the above plants, compared with the non-transgenic controls, coupled with the amelioration of stunting. The transgenic plants also retained higher chlorophyll levels than the control non-transgenic plants after infection with RTBV and RTSV. Small RNA analysis of virus inoculated transgenic plants indicated the presence of 21 nt and 22 nt siRNAs specific to RTBV and RTSV. The evidence points towards an active RNAi mechanism leading to resistance against the tungro viruses in the plants analysed.
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Affiliation(s)
- Shweta Sharma
- Department of Plant Molecular Biology, University of Delhi South Campus, Benito Juarez Road, New Delhi, 110021, India
| | - Gaurav Kumar
- Department of Plant Molecular Biology, University of Delhi South Campus, Benito Juarez Road, New Delhi, 110021, India
| | - Indranil Dasgupta
- Department of Plant Molecular Biology, University of Delhi South Campus, Benito Juarez Road, New Delhi, 110021, India.
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15
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Noncoding RNAs in Retrovirus Replication. RETROVIRUS-CELL INTERACTIONS 2018. [PMCID: PMC7173536 DOI: 10.1016/b978-0-12-811185-7.00012-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
Abstract
Although a limited percentage of the genome produces proteins, approximately 90% is transcribed, indicating important roles for noncoding RNA (ncRNA). It is now known that these ncRNAs have a multitude of cellular functions ranging from the regulation of gene expression to roles as structural elements in ribonucleoprotein complexes. ncRNA is also represented at nearly every step of viral life cycles. This chapter will focus on ncRNAs of both host and viral origin and their roles in retroviral life cycles. Cellular ncRNA represents a significant portion of material packaged into retroviral virions and includes transfer RNAs, 7SL RNA, U RNA, and vault RNA. Initially thought to be random packaging events, these host RNAs are now proposed to contribute to viral assembly and infectivity. Within the cell, long ncRNA and endogenous retroviruses have been found to regulate aspects of the retroviral life cycle in diverse ways. Additionally, the HIV-1 transactivating response element RNA is thought to impact viral infection beyond the well-characterized role as a transcription activator. RNA interference, thought to be an early version of the innate immune response to viral infection, can still be observed in plants and invertebrates today. The ability of retroviral infection to manipulate the host RNAi pathway is described here. Finally, RNA-based therapies, including gene editing approaches, are being explored as antiretroviral treatments and are discussed.
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16
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Kant R, Dasgupta I. Phenotyping of VIGS-mediated gene silencing in rice using a vector derived from a DNA virus. PLANT CELL REPORTS 2017; 36:1159-1170. [PMID: 28540496 DOI: 10.1007/s00299-017-2156-6] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/17/2016] [Accepted: 05/15/2017] [Indexed: 05/09/2023]
Abstract
Target genes in rice can be optimally silenced if inserted in antisense or hairpin orientation in the RTBV-derived VIGS vector and plants grown at 28 °C and 80% humidity after inoculation. Virus induced gene silencing (VIGS) is a method used to transiently silence genes in dicot as well as monocot plants. For the important monocot species rice, the Rice tungro bacilliform virus (RTBV)-derived VIGS system (RTBV-VIGS), which uses agroinoculation to initiate silencing, has not been standardized for optimal use. Here, using RTBV-VIGS, three sets of conditions were tested to achieve optimal silencing of the rice marker gene phytoene desaturase (pds). The effect of orientation of the insert in the RTBV-VIGS plasmid (sense, antisense and hairpin) on the silencing of the target gene was then evaluated using rice magnesium chelatase subunit H (chlH). Finally, the rice Xa21 gene, conferring resistance against bacterial leaf blight disease (BLB) was silenced using RTBV-VIGS system. In each case, real-time PCR-based assessment indicated approximately 40-80% fall in the accumulation levels of the transcripts of pds, chlH and Xa21. In the case of pds, the appearance of white streaks in the emerging leaves, and for chlH, chlorophyll levels and F v/F m ratio were assessed as phenotypes for silencing. For Xa21, the resistance levels to BLB were assessed by measuring the lesion length and the percent diseased areas of leaves, following challenge inoculation with Xanthomonas oryzae. In each case, the RTBV-MVIGS system gave rise to a discernible phenotype indicating the silencing of the respective target gene using condition III (temperature 28 °C, humidity 80% and 1 mM MES and 20 µM acetosyringone in secondary agrobacterium culture), which revealed the robustness of this gene silencing system for rice.
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Affiliation(s)
- Ravi Kant
- Department of Plant Molecular Biology, University of Delhi South Campus, Benito Juarez Road, New Delhi, 110021, India
| | - Indranil Dasgupta
- Department of Plant Molecular Biology, University of Delhi South Campus, Benito Juarez Road, New Delhi, 110021, India.
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17
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Valarmathi P, Kumar G, Robin S, Manonmani S, Dasgupta I, Rabindran R. Evaluation of virus resistance and agronomic performance of rice cultivar ASD 16 after transfer of transgene against Rice tungro bacilliform virus by backcross breeding. Virus Genes 2016; 52:521-9. [PMID: 26983604 DOI: 10.1007/s11262-016-1318-x] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2015] [Accepted: 03/07/2016] [Indexed: 11/28/2022]
Abstract
Severe losses of rice yield in south and southeast Asia are caused by Rice tungro disease (RTD) induced by mixed infection of Rice tungro bacilliform virus (RTBV) and Rice tungro spherical virus (RTSV). In order to develop transgene-based resistance against RTBV, one of its genes, ORF IV, was used to generate transgenic resistance based on RNA-interference in the easily transformed rice variety Pusa Basmati-1, and the transgene was subsequently introgressed to rice variety ASD 16, a variety popular in southern India, using transgene marker-assisted selection. Here, we report the evaluation of BC3F4 and BC3F5 generation rice plants for resistance to RTBV as well as for agronomic traits under glasshouse conditions. The BC3F4 and BC3F5 generation rice plants tested showed variable levels of resistance, which was manifested by an average of twofold amelioration in height reduction, 1.5-fold decrease in the reduction in chlorophyll content, and 100- to 10,000-fold reduction in the titers of RTBV, but no reduction of RTSV titers, in three backcrossed lines when compared with the ASD 16 parent. Agronomic traits of some of the backcrossed lines recorded substantial improvements when compared with the ASD 16 parental line after inoculation by RTBV and RTSV. This work represents an important step in transferring RTD resistance to a susceptible popular rice variety, hence enhancing its yield in areas threatened by the disease.
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Affiliation(s)
- P Valarmathi
- Department of Plant Pathology, ICAR-Indian Institute of Rice Research (IIRR), Hyderabad, 500030, India
| | - G Kumar
- Department of Plant Molecular Biology, University of Delhi South Campus, New Delhi, 110021, India
| | - S Robin
- Department of Rice, Tamil Nadu Agricultural University, Coimbatore, Tamil Nadu, 641003, India
| | - S Manonmani
- Department of Rice, Tamil Nadu Agricultural University, Coimbatore, Tamil Nadu, 641003, India
| | - I Dasgupta
- Department of Plant Molecular Biology, University of Delhi South Campus, New Delhi, 110021, India.
| | - R Rabindran
- Department of Plant Pathology, Tamil Nadu Agricultural University, Coimbatore, Tamil Nadu, 641003, India
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Villacreses J, Rojas-Herrera M, Sánchez C, Hewstone N, Undurraga SF, Alzate JF, Manque P, Maracaja-Coutinho V, Polanco V. Deep sequencing reveals the complete genome and evidence for transcriptional activity of the first virus-like sequences identified in Aristotelia chilensis (Maqui Berry). Viruses 2015; 7:1685-99. [PMID: 25855242 PMCID: PMC4411674 DOI: 10.3390/v7041685] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2014] [Revised: 03/12/2015] [Accepted: 03/25/2015] [Indexed: 01/01/2023] Open
Abstract
Here, we report the genome sequence and evidence for transcriptional activity of a virus-like element in the native Chilean berry tree Aristotelia chilensis. We propose to name the endogenous sequence as Aristotelia chilensis Virus 1 (AcV1). High-throughput sequencing of the genome of this tree uncovered an endogenous viral element, with a size of 7122 bp, corresponding to the complete genome of AcV1. Its sequence contains three open reading frames (ORFs): ORFs 1 and 2 shares 66%–73% amino acid similarity with members of the Caulimoviridae virus family, especially the Petunia vein clearing virus (PVCV), Petuvirus genus. ORF1 encodes a movement protein (MP); ORF2 a Reverse Transcriptase (RT) and a Ribonuclease H (RNase H) domain; and ORF3 showed no amino acid sequence similarity with any other known virus proteins. Analogous to other known endogenous pararetrovirus sequences (EPRVs), AcV1 is integrated in the genome of Maqui Berry and showed low viral transcriptional activity, which was detected by deep sequencing technology (DNA and RNA-seq). Phylogenetic analysis of AcV1 and other pararetroviruses revealed a closer resemblance with Petuvirus. Overall, our data suggests that AcV1 could be a new member of Caulimoviridae family, genus Petuvirus, and the first evidence of this kind of virus in a fruit plant.
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Affiliation(s)
- Javier Villacreses
- Centro de Genómica y Bioinformática, Facultad de Ciencias, Universidad Mayor, Santiago 8580000, Chile.
| | - Marcelo Rojas-Herrera
- Centro de Genómica y Bioinformática, Facultad de Ciencias, Universidad Mayor, Santiago 8580000, Chile.
| | - Carolina Sánchez
- Centro de Genómica y Bioinformática, Facultad de Ciencias, Universidad Mayor, Santiago 8580000, Chile.
| | | | - Soledad F Undurraga
- Centro de Genómica y Bioinformática, Facultad de Ciencias, Universidad Mayor, Santiago 8580000, Chile.
| | - Juan F Alzate
- Centro Nacional de Secuenciación Genómica, Universidad de Antioquia, Medellín, Colombia.
| | - Patricio Manque
- Centro de Genómica y Bioinformática, Facultad de Ciencias, Universidad Mayor, Santiago 8580000, Chile.
| | | | - Victor Polanco
- Centro de Genómica y Bioinformática, Facultad de Ciencias, Universidad Mayor, Santiago 8580000, Chile.
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Kant R, Sharma S, Dasgupta I. Virus-induced gene silencing (VIGS) for functional genomics in rice using Rice tungro bacilliform virus (RTBV) as a vector. Methods Mol Biol 2015; 1287:201-17. [PMID: 25740367 DOI: 10.1007/978-1-4939-2453-0_15] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
The large-scale functional analysis of genes in plants depends heavily on robust techniques for gene silencing. Virus-induced gene silencing (VIGS) is a transient gene silencing method for plants, triggered by the inoculation of a modified viral vector carrying a fragment of the gene targeted for silencing. Here we describe a VIGS protocol for rice, based on the Rice tungro bacilliform virus (RTBV, a DNA virus). We present an updated and detailed protocol for silencing of the gene encoding Phytoene desaturase in rice, using the RTBV-VIGS system.
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Affiliation(s)
- Ravi Kant
- Department of Plant Molecular Biology, University of Delhi South Campus, Benito Juarez Road, New Delhi, 110021, India
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20
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Rajeswaran R, Golyaev V, Seguin J, Zvereva AS, Farinelli L, Pooggin MM. Interactions of Rice tungro bacilliform pararetrovirus and its protein P4 with plant RNA-silencing machinery. MOLECULAR PLANT-MICROBE INTERACTIONS : MPMI 2014; 27:1370-8. [PMID: 25122481 DOI: 10.1094/mpmi-07-14-0201-r] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/10/2023]
Abstract
Small interfering RNA (siRNA)-directed gene silencing plays a major role in antiviral defense. Virus-derived siRNAs inhibit viral replication in infected cells and potentially move to neighboring cells, immunizing them from incoming virus. Viruses have evolved various ways to evade and suppress siRNA production or action. Here, we show that 21-, 22-, and 24-nucleotide (nt) viral siRNAs together constitute up to 19% of total small RNA population of Oryza sativa plants infected with Rice tungro bacilliform virus (RTBV) and cover both strands of the RTBV DNA genome. However, viral siRNA hotspots are restricted to a short noncoding region between transcription and reverse-transcription start sites. This region generates double-stranded RNA (dsRNA) precursors of siRNAs and, in pregenomic RNA, forms a stable secondary structure likely inaccessible to siRNA-directed cleavage. In transient assays, RTBV protein P4 suppressed cell-to-cell spread of silencing but enhanced cell-autonomous silencing, which correlated with reduced 21-nt siRNA levels and increased 22-nt siRNA levels. Our findings imply that RTBV generates decoy dsRNA that restricts siRNA production to the structured noncoding region and thereby protects other regions of the viral genome from repressive action of siRNAs, while the viral protein P4 interferes with cell-to-cell spread of antiviral silencing.
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Rice genomes recorded ancient pararetrovirus activities: Virus genealogy and multiple origins of endogenization during rice speciation. Virology 2014; 471-473:141-52. [PMID: 25461539 DOI: 10.1016/j.virol.2014.09.014] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2014] [Accepted: 09/11/2014] [Indexed: 11/21/2022]
Abstract
Viral fossils in rice genomes are a best entity to understand ancient pararetrovirus activities through host plant history because of our advanced knowledge of the genomes and evolutionary history with rice and its related species. Here, we explored organization, geographic origins and genealogy of rice pararetroviruses, which were turned into endogenous rice tungro bacilliform virus-like (eRTBVL) sequences. About 300 eRTBVL sequences from three representative rice genomes were clearly classified into six families. Most of the endogenization events of the eRTBVLs were initiated before differentiation of the rice progenitor (> 160,000 years ago). We successfully followed the genealogy of old relic viruses during rice speciation, and inferred the geographical origins for these viruses. Possible virus genomic sequences were explained mostly by recombinations between different virus families. Interestingly, we discovered that only a few recombination events among the numerous occasions had determined the virus genealogy.
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Wang Y, Wang H, Xu K, Ni P, Zhang H, Ma J, Yang H, Xu F. A survey of overlooked viral infections in biological experiment systems. PLoS One 2014; 9:e105348. [PMID: 25144530 PMCID: PMC4140767 DOI: 10.1371/journal.pone.0105348] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2014] [Accepted: 07/23/2014] [Indexed: 12/04/2022] Open
Abstract
It is commonly accepted that there are many unknown viruses on the planet. For the known viruses, do we know their prevalence, even in our experimental systems? Here we report a virus survey using recently published small (s)RNA sequencing datasets. The sRNA reads were assembled and contigs were screened for virus homologues against the NCBI nucleotide (nt) database using the BLASTn program. To our surprise, approximately 30% (28 out of 94) of publications had highly scored viral sequences in their datasets. Among them, only two publications reported virus infections. Though viral vectors were used in some of the publications, virus sequences without any identifiable source appeared in more than 20 publications. By determining the distributions of viral reads and the antiviral RNA interference (RNAi) pathways using the sRNA profiles, we showed evidence that many of the viruses identified were indeed infecting and generated host RNAi responses. As virus infections affect many aspects of host molecular biology and metabolism, the presence and impact of viruses needs to be actively investigated in experimental systems.
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Affiliation(s)
- Yajing Wang
- College of Biotechnology, Tianjin University of Science and Technology, Tianjin, China
- College of Pharmacy, State Key Laboratory of Medicinal Chemical Biology and Tianjin Key Laboratory of Molecular Drug Research, Nankai University, Tianjin, China
| | - Hui Wang
- NERC/Centre for Ecology and Hydrology, Wallingford, Oxfordshire, United Kingdom
- Beijing Genome Institute (BGI), Yantian District, Shenzhen, China
- Department of Zoology, University of Oxford, Oxford, United Kingdom
| | - Kunhan Xu
- Tianjin International Joint Academy of Biotechnology and Medicine, Tianjin, China
| | - Peixiang Ni
- BGI-Tianjin, Airport Economic Area, Tianjin, China
| | - Huan Zhang
- College of Pharmacy, State Key Laboratory of Medicinal Chemical Biology and Tianjin Key Laboratory of Molecular Drug Research, Nankai University, Tianjin, China
- Tianjin International Joint Academy of Biotechnology and Medicine, Tianjin, China
| | - Jinmin Ma
- Beijing Genome Institute (BGI), Yantian District, Shenzhen, China
| | - Huanming Yang
- Beijing Genome Institute (BGI), Yantian District, Shenzhen, China
- Department of Zoology, University of Oxford, Oxford, United Kingdom
- Prince Aljawhra Center of Excellence in Research of Hereditary Disorders, King Abdulaziz University, Jeddah, Saudi Arabia
- James D. Watson Institute of Genome Science, Hangzhou, China
| | - Feng Xu
- College of Pharmacy, State Key Laboratory of Medicinal Chemical Biology and Tianjin Key Laboratory of Molecular Drug Research, Nankai University, Tianjin, China
- Tianjin International Joint Academy of Biotechnology and Medicine, Tianjin, China
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23
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Borah BK, Sharma S, Kant R, Johnson AMA, Saigopal DVR, Dasgupta I. Bacilliform DNA-containing plant viruses in the tropics: commonalities within a genetically diverse group. MOLECULAR PLANT PATHOLOGY 2013; 14:759-71. [PMID: 23763585 PMCID: PMC6638767 DOI: 10.1111/mpp.12046] [Citation(s) in RCA: 36] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/25/2023]
Abstract
UNLABELLED Plant viruses, possessing a bacilliform shape and containing double-stranded DNA, are emerging as important pathogens in a number of agricultural and horticultural crops in the tropics. They have been reported from a large number of countries in African and Asian continents, as well as from islands from the Pacific region. The viruses, belonging to two genera, Badnavirus and Tungrovirus, within the family Caulimoviridae, have genomes displaying a common plan, yet are highly variable, sometimes even between isolates of the same virus. In this article, we summarize the current knowledge with a view to revealing the common features embedded within the genetic diversity of this group of viruses. TAXONOMY Virus; order Unassigned; family Caulimoviridae; genera Badnavirus and Tungrovirus; species Banana streak viruses, Bougainvillea spectabilis chlorotic vein banding virus, Cacao swollen shoot virus, Citrus yellow mosaic badnavirus, Dioscorea bacilliform viruses, Rice tungro bacilliform virus, Sugarcane bacilliform viruses and Taro bacilliform virus. MICROBIOLOGICAL PROPERTIES Bacilliform in shape; length, 60-900 nm; width, 35-50 nm; circular double-stranded DNA of approximately 7.5 kbp with one or more single-stranded discontinuities. HOST RANGE Each virus generally limited to its own host, including banana, bougainvillea, black pepper, cacao, citrus species, Dioscorea alata, rice, sugarcane and taro. DISEASE SYMPTOMS Foliar streaking in banana and sugarcane, swelling of shoots in cacao, yellow mosaic in leaves and stems in citrus, brown spot in the tubers in yam and yellow-orange discoloration and stunting in rice. USEFUL WEBSITES http://www.dpvweb.net.
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Affiliation(s)
- Basanta K Borah
- Department of Plant Molecular Biology, Delhi University South Campus, New Delhi 110021, India
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24
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Mathur S, Dasgupta I. Further support of genetic conservation in Indian isolates of Rice tungro bacilliform virus by sequence analysis of an isolate from North-Western India. Virus Genes 2012. [PMID: 23197138 DOI: 10.1007/s11262-012-0857-z] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
The genomic sequence of an isolate of Rice tungro bacilliform virus (RTBV), collected from the state of Punjab (Pb), a non-endemic tungro region from North-Western India was determined. In silico comparison of the 7931-bp sequence with isolates from Southeast Asia and the three previously characterized Indian isolates, revealed not only similar genome size to other Indian isolates but also high degree of homology both at nucleotide (>93 %) and amino acid (>96 %) levels among them. On the other hand, like the other Indian isolates, RTBV-Pb showed much lower nucleotide (<87 %) and amino acid (<90 % in most of the open reading frames) identities with the Southeast Asian isolates owing to several nucleotide substitutions and indels. In-depth annotation comparisons reinforce the hypothesis that Indian isolates of RTBV have diverged sufficiently from the Southeast Asian ones to form a separate group.
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Affiliation(s)
- Saloni Mathur
- Department of Plant Molecular Biology, University of Delhi South Campus, New Delhi 110021, India
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25
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Development of SYBR Green I based real-time PCR assays for quantitative detection of Rice tungro bacilliform virus and Rice tungro spherical virus. J Virol Methods 2012; 181:86-92. [DOI: 10.1016/j.jviromet.2012.01.018] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2011] [Revised: 01/16/2012] [Accepted: 01/24/2012] [Indexed: 11/24/2022]
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26
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The large intergenic region of Rice tungro bacilliform virus evolved differentially among geographically distinguished isolates. Virus Genes 2011; 44:312-8. [PMID: 21989904 DOI: 10.1007/s11262-011-0680-y] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2011] [Accepted: 09/29/2011] [Indexed: 10/17/2022]
Abstract
Rice tungro bacilliform virus (RTBV) is a plant pararetrovirus. The large intergenic region (LIGR) of RTBV having a single transcriptional promoter produces more than genome length pregenomic RNA (pgRNA) which directs synthesis of circular double-stranded viral DNA and serves as a polycistronic mRNA. By computer-aided analysis of LIGR, the 11 RTBV isolates sequenced so far were compared with respect to structural organization of promoter and pgRNA 5'-leader. The results revealed only 74.90% identity at LIGR between 'Southeast Asian' (SEA) and 'South Asian' (SA) isolates of RTBV indicating considerable variation between two groups which was also reflected during analysis of promoter and leader sequence. The predicted promoter region of SA isolates exhibited major variations in terms of transcription start site and consensus sequences of cis motifs expecting further exploitation of promoter region of SA isolates. The reduced length of leader sequence along with less numbers and different arrangements of small open reading frames (sORFs) in case of SA isolates might have some alterations in the control of expression of ORF II and III between the two groups. In spite of these variations, the leader sequence of both SEA and SA type isolates showed formation of stable secondary or stem-loop structure having identical features for efficient translation. The conservation of sORF1 at seven nucleotides upstream of stable stem-loop, CU-rich sequence following the sORF1 stop codon and AU-rich shunt landing sequence immediately downstream of the secondary structure suggested conservation of ribosomal shunt mechanism in all RTBV isolates irrespective of their geographical distribution.
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Phylogenetic analysis of Rice tungro bacilliform virus ORFs revealed strong correlation between evolution and geographical distribution. Virus Genes 2011; 43:398-408. [PMID: 21796436 DOI: 10.1007/s11262-011-0647-z] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2011] [Accepted: 07/15/2011] [Indexed: 10/17/2022]
Abstract
A new isolate of Rice tungro bacilliform virus (RTBV) was collected from Chinsura, West Bengal, India. The full genome was sequenced and deposited to GenBank designating the new one as Chinsura isolate. The four open reading frames (ORFs) of the new isolate were compared with those of previously reported 'South-east Asian' (SEA) and 'South Asian' (SA) isolates emphasizing the ORF3, which is the largest and functionally most important gene of RTBV. In the ORFs, Chinsura isolate shared 90.0-100.0% identity at amino acid level with SA isolates, but only 58.76-88.63% identity with SEA isolates for the same. Similarly, the amino acid identity of ORFs between SEA and SA isolates ranged from 58.77 to 88.64, whereas within each group the corresponding value was >96.0%. The phylogenetic analysis based on nucleotide and amino acid sequences of each ORF made two broad clusters of SEA- and SA-types including Chinsura isolate within SA cluster. Moreover, the relative positions and length of functional domains corresponding to movement protein (MP), coat protein (CP), aspartate protease (PR) and reverse transcriptase/ribonuclease H (RT/RNase H) of ORF3 of Chinsura isolate were completely identical with SA isolates. The clustering pattern indicated strong influence of geographical habitat on genomic evolution. Comparison of ORF3 among all the isolates revealed major variations at non-functional regions in between the functional domains and at the hypervariable 3'-terminal end of ORF3, while PR appeared to have evolved differentially in SA isolates expecting further characterization.
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28
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Cuellar WJ, De Souza J, Barrantes I, Fuentes S, Kreuze JF. Distinct cavemoviruses interact synergistically with sweet potato chlorotic stunt virus (genus Crinivirus) in cultivated sweet potato. J Gen Virol 2011; 92:1233-1243. [PMID: 21307225 DOI: 10.1099/vir.0.029975-0] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Two serologically unrelated sweet potato viruses causing symptoms of vein clearing in the indicator plant Ipomoea setosa were isolated and their genomes have been sequenced. They are associated with symptomless infections in sweet potato but distinct vein-clearing symptoms and higher virus titres were observed when these viruses co-infected with sweet potato chlorotic stunt virus (SPCSV), a virus that is distributed worldwide and is a mediator of severe virus diseases in this crop. Molecular characterization and phylogenetic analysis revealed an overall nucleotide identity of 47.6 % and an arrangement of the movement protein and coat protein domains characteristic of members of the genus Cavemovirus, in the family Caulimoviridae. We detected both cavemoviruses in cultivated sweet potato from East Africa, Central America and the Caribbean islands, but not in samples from South America. One of the viruses characterized showed a similar genome organization as, and formed a phylogenetic sublineage with, tobacco vein clearing virus (TVCV), giving further support to the previously suggested separation of TVCV, and related viral sequences, into a new caulimovirid genus. Given their geographical distribution and previous reports of similar but yet unidentified viruses, sweet potato cavemoviruses may co-occur with SPCSV more often than previously thought and they could therefore contribute to the extensive yield losses and cultivar decline caused by mixed viral infections in sweet potato.
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Affiliation(s)
- Wilmer J Cuellar
- Virology Laboratory, Crop Management & Production Systems Division, International Potato Center (CIP), Av. La Molina 1895, Lima 12, Peru
| | - Joao De Souza
- Virology Laboratory, Crop Management & Production Systems Division, International Potato Center (CIP), Av. La Molina 1895, Lima 12, Peru
| | - Israel Barrantes
- Magdeburg Centre for Systems Biology (MaCS), Otto von Guericke University, Sandtorstr. 1, D-39106 Magdeburg, Germany
| | - Segundo Fuentes
- Virology Laboratory, Crop Management & Production Systems Division, International Potato Center (CIP), Av. La Molina 1895, Lima 12, Peru
| | - Jan F Kreuze
- Applied Biotechnology Laboratory, Germplasm Enhancement & Crop Improvement Division, International Potato Center (CIP), Av. La Molina 1895, Lima 12, Peru
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Purkayastha A, Mathur S, Verma V, Sharma S, Dasgupta I. Virus-induced gene silencing in rice using a vector derived from a DNA virus. PLANTA 2010; 232:1531-40. [PMID: 20872012 DOI: 10.1007/s00425-010-1273-z] [Citation(s) in RCA: 45] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/03/2010] [Accepted: 09/02/2010] [Indexed: 05/08/2023]
Abstract
Virus-induced gene silencing (VIGS) is a method of rapid and transient gene silencing in plants using viral vectors. A VIGS vector for gene silencing in rice has been developed from Rice tungro bacilliform virus (RTBV), a rice-infecting virus containing DNA as the genetic material. A full-length RTBV DNA cloned as a partial dimer in a binary plasmid accumulated in rice plants when inoculated through Agrobacterium (agroinoculation) within 2 weeks and produced detectable levels of RTBV coat protein. Deletion of two of the four viral ORFs did not compromise the ability of the cloned RTBV DNA to accumulate in rice plants. To modify the cloned RTBV DNA as a VIGS vector (pRTBV-MVIGS), the tissue-specific RTBV promoter was replaced by the constitutively expressed maize ubiquitin promoter, sequences comprising the tRNA-binding site were incorporated to ensure reverse transcription-mediated replication, sequences to ensure optimal context for translation initiation of the viral genes were added and a multi-cloning site for the ease of cloning DNA fragments was included. The silencing ability of pRTBV-MVIGS was tested using the rice phytoene desaturase (pds) gene on rice. More than half of the agroinoculated rice plants showed white streaks in leaves within 21 days post-inoculation (dpi), which continued to appear in all emerging leaves till approximately 60-70 dpi. Compared to control samples, real-time PCR showed only 10-40% accumulation of pds transcripts in the leaves showing the streaks. This is the first report of the construction of a VIGS vector for rice which can be introduced by agroinoculation.
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Affiliation(s)
- Arunima Purkayastha
- Department of Plant Molecular Biology, University of Delhi South Campus, Benito Juarez Road, New Delhi, 110021, India
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30
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Ordiz MI, Magnenat L, Barbas CF, Beachy RN. Negative regulation of the RTBV promoter by designed zinc finger proteins. PLANT MOLECULAR BIOLOGY 2010; 72:621-630. [PMID: 20169401 DOI: 10.1007/s11103-010-9600-0] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/02/2009] [Accepted: 01/08/2010] [Indexed: 05/28/2023]
Abstract
The symptoms of rice tungro disease are caused by infection by a DNA-containing virus, rice tungro bacilliform virus (RTBV). To reduce expression of the RTBV promoter, and to ultimately reduce virus replication, we tested three synthetic zinc finger protein transcription factors (ZF-TFs), each comprised of six finger domains, designed to bind to sequences between -58 and +50 of the promoter. Two of these ZF-TFs reduced expression from the promoter in transient assays and in transgenic Arabidopsis thaliana plants. One of the ZF-TFs had significant effects on plant regeneration, apparently as a consequence of binding to multiple sites in the A. thaliana genome. Expression from the RTBV promoter was reduced by approximately 45% in transient assays and was reduced by up to 80% in transgenic plants. Co-expression of two different ZF-TFs did not further reduce expression of the promoter. These experiments suggest that ZF-TFs may be used to reduce replication of RTBV and thereby offer a potential method for control of an important crop disease.
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Affiliation(s)
- M Isabel Ordiz
- Donald Danforth Plant Science Center, 975 N. Warson Road, St. Louis, MO 63132, USA
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31
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Balconi C, Lanzanova C, Motto M. Ribosome-Inactivating Proteins in Cereals. TOXIC PLANT PROTEINS 2010. [DOI: 10.1007/978-3-642-12176-0_8] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/14/2023]
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32
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Encabo JR, Cabauatan PQ, Cabunagan RC, Satoh K, Lee JH, Kwak DY, De Leon TB, Macalalad RJA, Kondoh H, Kikuchi S, Choi IR. Suppression of two tungro viruses in rice by separable traits originating from cultivar Utri Merah. MOLECULAR PLANT-MICROBE INTERACTIONS : MPMI 2009; 22:1268-1281. [PMID: 19737100 DOI: 10.1094/mpmi-22-10-1268] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/28/2023]
Abstract
Rice tungro disease (RTD) is caused by Rice tungro spherical virus (RTSV) and Rice tungro bacilliform virus (RTBV) transmitted by green leafhoppers. Rice cv. Utri Merah is highly resistant to RTD. To define the RTD resistance of Utri Merah, near-isogenic lines (NIL, BC(5) or BC(6)) developed from Utri Merah and susceptible cv. Taichung Native 1 (TN1) were evaluated for reactions to RTSV and RTBV. TW16 is an NIL (BC(5)) resistant to RTD. RTBV was able to infect both TN1 and TW16 but the levels of RTBV were usually significantly lower in TW16 than in TN1. Infection of RTSV was confirmed in TN1 by a serological test but not in TW16. However, the global gene-expression pattern in an RTSV-resistant NIL (BC(6)), TW16-69, inoculated with RTSV indicated that RTSV can also infect the resistant NIL. Infection of RTSV in TW16 was later confirmed by reverse-transcription polymerase chain reaction but the level of RTSV was considerably lower in TW16 than in TN1. Examination for virus accumulation in another NIL (BC(6)), TW16-1029, indicated that all plants of TW16-1029 were resistant to RTSV, whereas the resistance to RTBV and symptom severity were segregating among the individual plants of TW16-1029. Collectively, these results suggest that RTD resistance of Utri Merah involves suppression of interacting RTSV and RTBV but the suppression trait for RTSV and for RTBV is inherited separately.
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Affiliation(s)
- Jaymee R Encabo
- Plant Breeding, Genetics, and Biotechnology Division, International Rice Research Institute, DAPO Box 7777, Metro Manila, Philippines
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33
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Ganesan U, Suri SS, Rajasubramaniam S, Rajam MV, Dasgupta I. Transgenic expression of coat protein gene of Rice tungro bacilliform virus in rice reduces the accumulation of viral DNA in inoculated plants. Virus Genes 2009; 39:113-9. [PMID: 19387813 DOI: 10.1007/s11262-009-0359-9] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2009] [Accepted: 04/07/2009] [Indexed: 10/20/2022]
Abstract
Rice tungro, a devastating disease of rice in south and southeast Asia, is caused by the joint infection of Rice tungro bacilliform virus (RTBV) and Rice tungro spherical virus (RTSV). In order to obtain transgenic resistance against RTBV, indica rice cultivar Pusa Basmati-1 was transformed to express the coat protein (CP) gene of an Indian isolate of RTBV. Rice plants containing the transgene integrated in low copy numbers were obtained, in which the CP was shown to accumulate in the leaf tissue. The progenies representing three independent transformation events were challenged with Indian isolates of RTBV using viruliferous Green leafhoppers, and the viral titers in the inoculated plants were monitored using DNA dot-blot hybridization. As compared to non-transgenic controls, two independent transgenic lines showed significantly low levels of RTBV DNA, especially towards later stages of infection and a concomitant reduction of tungro symptoms.
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Affiliation(s)
- Uma Ganesan
- Plant Polyamine and Transgenic Research Laboratory, Department of Genetics, University of Delhi, South Campus, New Delhi 110021, India
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Harper G, Hart D, Moult S, Hull R, Geering A, Thomas J. The diversity of Banana streak virus isolates in Uganda. Arch Virol 2005; 150:2407-20. [PMID: 16096705 DOI: 10.1007/s00705-005-0610-1] [Citation(s) in RCA: 41] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/01/2005] [Accepted: 06/24/2005] [Indexed: 11/29/2022]
Abstract
In a study of the variation among isolates of Banana streak virus (BSV) in Uganda, 140 sequences were obtained from 49 samples by PCR across the conserved reverse transcriptase/RNaseH region of the genome. Pairwise comparison of these sequences suggested that they represented 15 different species and phylogenetic analyses showed that all species fell into three major clades based on 28% sequence difference. In addition to the Ugandan sequences, clade I also contained BSV species that are known as both integrated sequences and episomal viruses; clade II also contained integrated BSV sequences but which have not previously been identified as episomal viruses. Clade III comprised of Sugarcane bacilliform virus isolates and Ugandan BSV sequences and for which there is no evidence of integration. The possible reasons for the extraordinary levels of virus sequence variation and the potential origins and epidemiology of these viruses causing banana streak disease are discussed.
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Affiliation(s)
- G Harper
- Department of Disease and Stress Biology, John Innes Centre, Colney Lane, Norwich, UK.
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Guerra-Peraza O, Kirk D, Seltzer V, Veluthambi K, Schmit AC, Hohn T, Herzog E. Coat proteins of Rice tungro bacilliform virus and Mungbean yellow mosaic virus contain multiple nuclear-localization signals and interact with importin alpha. J Gen Virol 2005; 86:1815-1826. [PMID: 15914861 DOI: 10.1099/vir.0.80920-0] [Citation(s) in RCA: 43] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Transport of the viral genome into the nucleus is an obligatory step in the replication cycle of plant pararetro- and geminiviruses. In both these virus types, the multifunctional coat protein (CP) is thought to be involved in this process. Here, a green fluorescent protein tagging approach was used to demonstrate nuclear import of the CPs of Rice tungro bacilliform virus (RTBV) and Mungbean yellow mosaic virus--Vigna (MYMV) in Nicotiana plumbaginifolia protoplasts. In both cases, at least two nuclear localization signals (NLSs) were identified and characterized. The NLSs of RTBV CP are located within both N- and C-terminal regions (residues 479KRPK/497KRK and 744KRK/758RRK), and those of MYMV CP within the N-terminal part (residues 3KR and 41KRRR). The MYMV and RTBV CP NLSs resemble classic mono- and bipartite NLSs, respectively. However, the N-terminal MYMV CP NLS and both RTBV CP NLSs show peculiarities in the number and position of basic residues. In vitro pull-down assays revealed interaction of RTBV and MYMV CPs with the nuclear import factor importin alpha, suggesting that both CPs are imported into the nucleus via an importin alpha-dependent pathway. The possibility that this pathway could serve for docking of virions to the nucleus is discussed.
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Affiliation(s)
- O Guerra-Peraza
- Friedrich Miescher Institute, Maulbeerstrasse 66, 4058 Basel, Switzerland
| | - D Kirk
- Friedrich Miescher Institute, Maulbeerstrasse 66, 4058 Basel, Switzerland
| | - V Seltzer
- Institut de Biologie Moléculaire des Plantes, UPR-CNRS 2357, Université Louis Pasteur, 12 rue du Général Zimmer, 67084 Strasbourg Cedex, France
| | - K Veluthambi
- Department of Plant Biotechnology, School of Biotechnology, Madurai Kamaraj University, Madurai 625021, India
| | - A C Schmit
- Department of Plant Biotechnology, School of Biotechnology, Madurai Kamaraj University, Madurai 625021, India
| | - T Hohn
- University of Basel, Botanical Institute, Plant Health Unit, Schoenbeinstrasse 6, 4056 Basel, Switzerland
- Friedrich Miescher Institute, Maulbeerstrasse 66, 4058 Basel, Switzerland
| | - E Herzog
- Department of Plant Biotechnology, School of Biotechnology, Madurai Kamaraj University, Madurai 625021, India
- Friedrich Miescher Institute, Maulbeerstrasse 66, 4058 Basel, Switzerland
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36
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Marmey P, Rojas-Mendoza A, de Kochko A, Beachy RN, Fauquet CM. Characterization of the protease domain of Rice tungro bacilliform virus responsible for the processing of the capsid protein from the polyprotein. Virol J 2005; 2:33. [PMID: 15831103 PMCID: PMC1087892 DOI: 10.1186/1743-422x-2-33] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2005] [Accepted: 04/14/2005] [Indexed: 11/21/2022] Open
Abstract
Background Rice tungro bacilliform virus (RTBV) is a pararetrovirus, and a member of the family Caulimoviridae in the genus Badnavirus. RTBV has a long open reading frame that encodes a large polyprotein (P3). Pararetroviruses show similarities with retroviruses in molecular organization and replication. P3 contains a putative movement protein (MP), the capsid protein (CP), the aspartate protease (PR) and the reverse transcriptase (RT) with a ribonuclease H activity. PR is a member of the cluster of retroviral proteases and serves to proteolytically process P3. Previous work established the N- and C-terminal amino acid sequences of CP and RT, processing of RT by PR, and estimated the molecular mass of PR by western blot assays. Results A molecular mass of a protein that was associated with virions was determined by in-line HPLC electrospray ionization mass spectral analysis. Comparison with retroviral proteases amino acid sequences allowed the characterization of a putative protease domain in this protein. Structural modelling revealed strong resemblance with retroviral proteases, with overall folds surrounding the active site being well conserved. Expression in E. coli of putative domain was affected by the presence or absence of the active site in the construct. Analysis of processing of CP by PR, using pulse chase labelling experiments, demonstrated that the 37 kDa capsid protein was dependent on the presence of the protease in the constructs. Conclusion The findings suggest the characterization of the RTBV protease domain. Sequence analysis, structural modelling, in vitro expression studies are evidence to consider the putative domain as being the protease domain. Analysis of expression of different peptides corresponding to various domains of P3 suggests a processing of CP by PR. This work clarifies the organization of the RTBV polyprotein, and its processing by the RTBV protease.
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Affiliation(s)
- Philippe Marmey
- IRD, UMR «DGPC», B.P. 64501, 34394 Montpellier cedex 5, France
| | - Ana Rojas-Mendoza
- Protein Design Group, Centro Nacional de Biotecnologia, Campus Universidad Autonoma Cantoblanco, 28049 Madrid, Spain
| | | | - Roger N Beachy
- Donald Danforth Plant Science Center, 975 North Warson Road, St. Louis, MO 63132, USA
| | - Claude M Fauquet
- Donald Danforth Plant Science Center, 975 North Warson Road, St. Louis, MO 63132, USA
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Abstract
Banana streak virus (BSV) is a badnavirus that causes a viral leaf streak disease of banana and plantain (Musa spp.). Identified in essentially all Musa growing areas of the world, it has a deleterious effect on the productivity of infected plants as well as being a major constraint to Musa breeding programmes and germplasm dissemination. Banana is a staple food in Uganda which is, per capita, one of the worlds largest banana producers and consumers. BSV was isolated from infected plants sampled across the Ugandan Musa growing area and the isolates were analysed using molecular and serological techniques. These analyses showed that BSV is very highly variable in Uganda. They suggest that the variability is, in part, due to a series of introductions of banana into Uganda, each with a different complement of infecting viruses.
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Affiliation(s)
- Glyn Harper
- Department of Disease and Stress Biology, John lnnes Centre, Colney Lane, Norwich NR4 7UH, UK.
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38
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Abstract
Mobile genetic elements, by virtue of their ability to move to new chromosomal locations, are considered important in shaping the evolutionary course of the genome. They are widespread in the biological kingdom. Among the protozoan parasites several types of transposable elements are encountered. The largest variety is seen in the trypanosomatids-Trypanosoma brucei, Trypanosoma cruzi and Crithidia fasciculata. They contain elements that insert site-specifically in the spliced-leader RNA genes, and others that are dispersed in a variety of genomic locations. Giardia lamblia contains three families of transposable elements. Two of these are subtleomeric in location while one is chromosome-internal. Entamoeba histolytica has an abundant retrotransposon dispersed in the genome. Nucleotide sequence analysis of all the elements shows that they are all retrotransposons, and, with the exception of one class of elements in T. cruzi, all of them are non-long-terminal-repeat retrotransposons. Although most copies have accumulated mutations, they can potentially encode reverse transcriptase, endonuclease and nucleic-acid-binding activities. Functionally and phylogenetically they do not belong to a single lineage, showing that retrotransposons were acquired early in the evolution of protozoan parasites. Many of the potentially autonomous elements that encode their own transposition functions have nonautonomous counterparts that probably utilize the functions in trans. In this respect these elements are similar to the mammalian LINEs and SINEs (long and short interspersed DNA elements), showing a common theme in the evolution of retrotransposons. So far there is no report of a DNA transposon in any protozoan parasite. The genome projects that are under way for most of these organisms will help understand the evolution and possible function of these genetic elements.
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Affiliation(s)
- Sudha Bhattacharya
- School of Environmental Sciences, Jawaharlal Nehru University, New Delhi 110 067, India.
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Huang Q, Hartung JS. Cloning and sequence analysis of an infectious clone of Citrus yellow mosaic virus that can infect sweet orange via Agrobacterium-mediated inoculation. J Gen Virol 2001; 82:2549-2558. [PMID: 11562547 DOI: 10.1099/0022-1317-82-10-2549] [Citation(s) in RCA: 48] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Citrus yellow mosaic virus (CYMV), a member of the family Caulimoviridae, genus Badnavirus, causes citrus mosaic disease, a disease that occurs commonly in India. The CYMV genome has been cloned and its complete nucleotide sequence determined. Its DNA genome is 7559 bp in length and contains six putative open reading frames (ORFs), all on the plus-strand of the genome and each capable of encoding proteins with a molecular mass of greater than 10 kDa. ORF 3, the largest ORF, encodes a putative polyprotein for functions involved in virus movement, assembly and replication. The other ORFs encode proteins whose exact functions are not completely understood. The genome also contains a plant tRNA(met)-binding site, which may serve as a primer for minus-strand DNA synthesis, in its intergenic region. Phylogenetic analysis of the badnaviruses revealed that CYMV is most closely related to Cacao swollen shoot virus. It was demonstrated that a construct containing 1.4 copies of the cloned CYMV genome could infect sweet orange via Agrobacterium-mediated inoculation.
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Affiliation(s)
- Qi Huang
- USDA, Agriculture Research Service, Fruit Laboratory, Bldg 010A, BARC-West, 10300 Baltimore Avenue, Beltsville, MD 20705, USA1
| | - John S Hartung
- USDA, Agriculture Research Service, Fruit Laboratory, Bldg 010A, BARC-West, 10300 Baltimore Avenue, Beltsville, MD 20705, USA1
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40
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Petruccelli S, Dai S, Carcamo R, Yin Y, Chen S, Beachy RN. Transcription factor RF2a alters expression of the rice tungro bacilliform virus promoter in transgenic tobacco plants. Proc Natl Acad Sci U S A 2001; 98:7635-40. [PMID: 11390974 PMCID: PMC34720 DOI: 10.1073/pnas.121186398] [Citation(s) in RCA: 29] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 04/16/2001] [Indexed: 11/18/2022] Open
Abstract
The promoter from rice tungro bacilliform badnavirus (RTBV) is expressed only in phloem tissues in transgenic rice plants. RF2a, a b-Zip protein from rice, is known to bind to the Box II cis element near the TATA box of the promoter. Here, we report that the full-length RTBV promoter and a truncated fragment E of the promoter, comprising nucleotides -164 to +45, result in phloem-specific expression of beta-glucuronidase (GUS) reporter genes in transgenic tobacco plants. When a fusion gene comprising the cauliflower mosaic virus 35S promoter and RF2a cDNA was coexpressed with the GUS reporter genes, GUS activity was increased by 2-20-fold. The increase in GUS activity was positively correlated with the amount of RF2a, and the expression pattern of the RTBV promoter was altered from phloem-specific to constitutive. Constitutive expression of RF2a did not induce morphological changes in the transgenic plants. In contrast, constitutive overexpression of the b-ZIP domain of RF2a had a strong effect on the development of transgenic plants. These studies suggest that expression of the b-Zip domain can interfere with the function of homologues of RF2a that regulate development of tobacco plants.
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Affiliation(s)
- S Petruccelli
- The Scripps Research Institute, La Jolla, CA 92037, USA
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41
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Rothnie HM, Chen G, Fütterer J, Hohn T. Polyadenylation in rice tungro bacilliform virus: cis-acting signals and regulation. J Virol 2001; 75:4184-94. [PMID: 11287568 PMCID: PMC114164 DOI: 10.1128/jvi.75.9.4184-4194.2001] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
The polyadenylation signal of rice tungro bacilliform virus (RTBV) was characterized by mutational and deletion analysis. The cis-acting signals required to direct polyadenylation conformed to what is known for plant poly(A) signals in general and were very similar to those of the related cauliflower mosaic virus. Processing was directed by a canonical AAUAAA poly(A) signal, an upstream UG-rich region considerably enhanced processing efficiency, and sequences downstream of the cleavage site were not required. When present at the end of a transcription unit, the cis-acting signals for 3'-end processing were highly efficient in both monocot (rice) and dicot (Nicotiana plumbaginifolia) protoplasts. In a promoter-proximal position, as in the viral genome, the signal was also efficiently processed in rice protoplasts, giving rise to an abundant "short-stop" (SS-) RNA. The proportion of SS-RNA was considerably lower in N. plumbaginifolia protoplasts. In infected plants, SS-RNA was hardly detectable, suggesting either that SS-RNA is unstable in infected plants or that read-through of the promoter-proximal poly(A) site is very efficient. SS-RNA is readily detectable in transgenic rice plants (A. Klöti, C. Henrich, S. Bieri, X. He, G. Chen, P. K. Burkhardt, J. Wünn, P. Lucca, T. Hohn, I. Potrylus, and J. Fütterer, 1999. Plant Mol. Biol. 40:249-266), thus the absence of SS-RNA in infected plants can be attributed to poly(A) site bypass in the viral context to ensure production of the full-length pregenomic viral RNA. RTBV poly(A) site suppression thus depends both on context and the expression system; our results suggest that the circular viral minichromosome directs assembly of a transcription-processing complex with specific properties to effect read-through of the promoter-proximal poly(A) signal.
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Affiliation(s)
- H M Rothnie
- Friedrich Miescher Institute, CH-4002 Basel, Switzerland.
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42
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He X, Hohn T, Fütterer J. Transcriptional activation of the rice tungro bacilliform virus gene is critically dependent on an activator element located immediately upstream of the TATA box. J Biol Chem 2000; 275:11799-808. [PMID: 10766804 DOI: 10.1074/jbc.275.16.11799] [Citation(s) in RCA: 21] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
To investigate the transcriptional mechanisms of rice tungro bacilliform virus, we have systematically analyzed an activator element located immediately upstream of the TATA box in the rice tungro bacilliform virus promoter and its cognate trans-acting factors. Using electrophoretic mobility shift assays, we showed that rice nuclear proteins bind to the activator element, forming multiple specific DNA-protein complexes via protein-protein interactions. Copper-phenanthroline footprinting and DNA methylation interference analysis indicated that multiple DNA-protein complexes share a common binding site located between positions -60 to -39, and the proteins contact the activator element in the major groove. DNA UV cross-linking assays further showed that two nuclear proteins (36 and 33 kDa), found in rice cell suspension and shoot nuclear extracts, and one (27 kDa), present in root nuclear extracts, bind to this activator element. In protoplasts derived from a rice (Oryza sativa) suspension culture, the activator element is a prerequisite for promoter activity and its function is critically dependent on its position relative to the TATA box. Thus, transcriptional activation may function via interactions with the basal transcriptional machinery, and we propose that this activation is mediated by protein-protein interactions in a position-dependent mechanism.
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Affiliation(s)
- X He
- Friedrich Miescher Institute, P. O. Box 2543, CH-4002 Basel, Switzerland
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43
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Guerra-Peraza O, de Tapia M, Hohn T, Hemmings-Mieszczak M. Interaction of the cauliflower mosaic virus coat protein with the pregenomic RNA leader. J Virol 2000; 74:2067-72. [PMID: 10666236 PMCID: PMC111687 DOI: 10.1128/jvi.74.5.2067-2072.2000] [Citation(s) in RCA: 38] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/02/2023] Open
Abstract
Using the yeast three-hybrid system, the interaction of the Cauliflower mosaic virus (CaMV) pregenomic 35S RNA (pgRNA) leader with the viral coat protein, its precursor, and a series of derivatives was studied. The purine-rich domain in the center of the pgRNA leader was found to specifically interact with the coat protein. The zinc finger motif of the coat protein and the preceding basic domain were essential for this interaction. Removal of the N-terminal portion of the basic domain led to loss of specificity but did not affect the strength of the interaction. Mutations of the zinc finger motif abolished not only the interaction with the RNA but also viral infectivity. In the presence of the very acidic C-terminal domain, which is part of the preprotein but is not present in the mature CP, the interaction with the RNA was undetectable.
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44
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Herzog E, Guerra-Peraza O, Hohn T. The rice tungro bacilliform virus gene II product interacts with the coat protein domain of the viral gene III polyprotein. J Virol 2000; 74:2073-83. [PMID: 10666237 PMCID: PMC111688 DOI: 10.1128/jvi.74.5.2073-2083.2000] [Citation(s) in RCA: 22] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Rice tungro bacilliform virus (RTBV) is a plant pararetrovirus whose DNA genome contains four genes encoding three proteins and a large polyprotein. The function of most of the viral proteins is still unknown. To investigate the role of the gene II product (P2), we searched for interactions between this protein and other RTBV proteins. P2 was shown to interact with the coat protein (CP) domain of the viral gene III polyprotein (P3) both in the yeast two-hybrid system and in vitro. Domains involved in the P2-CP association have been identified and mapped on both proteins. To determine the importance of this interaction for viral multiplication, the infectivity of RTBV gene II mutants was investigated by agroinoculation of rice plants. The results showed that virus viability correlates with the ability of P2 to interact with the CP domain of P3. This study suggests that P2 could participate in RTBV capsid assembly.
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Affiliation(s)
- E Herzog
- Friedrich Miescher Institute, CH-4002 Basel, Switzerland
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45
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Vazquez M, Ben-Dov C, Lorenzi H, Moore T, Schijman A, Levin MJ. The short interspersed repetitive element of Trypanosoma cruzi, SIRE, is part of VIPER, an unusual retroelement related to long terminal repeat retrotransposons. Proc Natl Acad Sci U S A 2000; 97:2128-33. [PMID: 10688909 PMCID: PMC15765 DOI: 10.1073/pnas.050578397] [Citation(s) in RCA: 29] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
The short interspersed repetitive element (SIRE) of Trypanosoma cruzi was first detected when comparing the sequences of loci that encode the TcP2beta genes. It is present in about 1,500-3,000 copies per genome, depending on the strain, and it is distributed in all chromosomes. An initial analysis of SIRE sequences from 21 genomic fragments allowed us to derive a consensus nucleotide sequence and structure for the element, consisting of three regions (I, II, and III) each harboring distinctive features. Analysis of 158 transcribed SIREs demonstrates that the consensus is highly conserved. The sequences of 51 cDNAs show that SIRE is included in the 3' end of several mRNAs, always transcribed from the sense strand, contributing the polyadenylation site in 63% of the cases. This study led to the characterization of VIPER (vestigial interposed retroelement), a 2,326-bp-long unusual retroelement. VIPER's 5' end is formed by the first 182 bp of SIRE, whereas its 3' end is formed by the last 220 bp of the element. Both SIRE moieties are connected by a 1,924-bp-long fragment that carries a unique ORF encoding a complete reverse transcriptase-RNase H gene whose 15 C-terminal amino acids derive from codons specified by SIRE's region II. The amino acid sequence of VIPER's reverse transcriptase-RNase H shares significant homology to that of long terminal repeat retrotransposons. The fact that SIRE and VIPER sequences are found only in the T. cruzi genome may be of relevance for studies concerning the evolution and the genome flexibility of this protozoan parasite.
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Affiliation(s)
- M Vazquez
- Laboratorio de Biología Molecular de la Enfermedad de Chagas, Instituto de Investigaciones en Ingenieria Genética y Biologia Molecular, Vuelta de Obligado 2490, 1428 Buenos Aires, Argentina
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46
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Affiliation(s)
- E P Rybicki
- Department of Microbiology, University of Cape Town, South Africa
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47
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Briddon RW, Phillips S, Brunt A, Hull R. Analysis of the sequence of dioscorea Alata bacilliform virus: comparison to others members of the badnavirus group. Virus Genes 1999; 18:277-83. [PMID: 10456795 DOI: 10.1023/a:1008076420783] [Citation(s) in RCA: 32] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
Abstract
The complete nucleotide sequence of the genome of Dioscorea alata bacilliform virus (DaBV) has been determined from cloned fragments. Features of the genome confirm DaBV to be a pararetrovirus of the genus Badnavirus which is more similar to other mealy-bug transmitted badnaviruses, in particular to cacao swollen shoot virus, than to rice tungro bacilliform virus. Sequence variability between cloned fragments suggests that the genetic variability of the virus may be quite high (up to 11% nucleotide sequence variation for some small regions of the genome) although the overall variability detected was 4.2% at the nucleotide level.
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Affiliation(s)
- R W Briddon
- Department of Virus Research, John Innes Centre, Norwich, UK.
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48
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Cabauatan PQ, Melcher U, Ishikawa K, Omura T, Hibino H, Koganezawa H, Azzam O. Sequence changes in six variants of rice tungro bacilliform virus and their phylogenetic relationships. J Gen Virol 1999; 80 ( Pt 8):2229-2237. [PMID: 10466823 DOI: 10.1099/0022-1317-80-8-2229] [Citation(s) in RCA: 15] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
The DNA of three biological variants, G1, Ic and G2, which originated from the same greenhouse isolate of rice tungro bacilliform virus (RTBV) at the International Rice Research Institute (IRRI), was cloned and sequenced. Comparison of the sequences revealed small differences in genome sizes. The variants were between 95 and 99% identical at the nucleotide and amino acid levels. Alignment of the three genome sequences with those of three published RTBV sequences (Phi-1, Phi-2 and Phi-3) revealed numerous nucleotide substitutions and some insertions and deletions. The published RTBV sequences originated from the same greenhouse isolate at IRRI 20, 11 and 9 years ago. All open reading frames (ORFs) and known functional domains were conserved across the six variants. The cysteine-rich region of ORF3 showed the greatest variation. When the six DNA sequences from IRRI were compared with that of an isolate from Malaysia (Serdang), similar changes were observed in the cysteine-rich region in addition to other nucleotide substitutions and deletions across the genome. The aligned nucleotide sequences of the IRRI variants and Serdang were used to analyse phylogenetic relationships by the bootstrapped parsimony, distance and maximum-likelihood methods. The isolates clustered in three groups: Serdang alone; Ic and G1; and Phi-1, Phi-2, Phi-3 and G2. The distribution of phylogenetically informative residues in the IRRI sequences shared with the Serdang sequence and the differing tree topologies for segments of the genome suggested that recombination, as well as substitutions and insertions or deletions, has played a role in the evolution of RTBV variants. The significance and implications of these evolutionary forces are discussed in comparison with badnaviruses and caulimoviruses.
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Affiliation(s)
- Pepito Q Cabauatan
- Entomology and Plant Pathology Division, International Rice Research Institute, PO Box 933, 1099 Manila, Philippines1
| | | | - Koichi Ishikawa
- National Agriculture Research Center, Tsukuba 305-0856, Japan3
| | - Toshihiro Omura
- National Agriculture Research Center, Tsukuba 305-0856, Japan3
| | - Hiroyuki Hibino
- National Institute for Agroenvironmental Science, Tsukuba 305-8604, Japan4
| | - Hiroki Koganezawa
- Shikoku National Agricultural Experiment Station, Zentsuji, Kagawa 765-0001, Japan5
| | - Ossmat Azzam
- Entomology and Plant Pathology Division, International Rice Research Institute, PO Box 933, 1099 Manila, Philippines1
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49
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Pooggin MM, Fütterer J, Skryabin KG, Hohn T. A short open reading frame terminating in front of a stable hairpin is the conserved feature in pregenomic RNA leaders of plant pararetroviruses. J Gen Virol 1999; 80 ( Pt 8):2217-2228. [PMID: 10466822 DOI: 10.1099/0022-1317-80-8-2217] [Citation(s) in RCA: 59] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
In plant pararetroviruses, pregenomic RNA (pgRNA) directs synthesis of circular double-stranded viral DNA and serves as a polycistronic mRNA. By computer-aided analysis, the 14 plant pararetroviruses sequenced so far were compared with respect to structural organization of their pgRNA 5'-leader. The results revealed that the pgRNA of all these viruses carries a long leader sequence containing several short ORFs and having the potential to form a large stem-loop structure; both features are known to be inhibitory for downstream translation. Formation of the structure brings the first long ORF into the close spatial vicinity of a 5'-proximal short ORF that terminates 5 to 10 nt upstream of the stable structural element. The first long ORF on the pgRNA is translated by a ribosome shunt mechanism discovered in cauliflower mosaic (CaMV) and rice tungro bacilliform viruses, representing the two major groups of plant pararetroviruses. Both the short ORF and the structure have been implicated in the shunt process for CaMV pgRNA translation. The conservation of these elements among all plant pararetroviruses suggests conservation of the ribosome shunt mechanism. For some of the less well-studied viruses, the localization of the conserved elements also allowed predictions of the pgRNA promoter region and the translation start site of the first long ORF.
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Affiliation(s)
- Mikhail M Pooggin
- Centre 'Bioengineering', Russian Academy of Sciences, 117312 Moscow, Russia2
- Friedrich Miescher Institute, PO Box 2543, CH-4002 Basel, Switzerland1
| | - Johannes Fütterer
- Institute for Plant Sciences, ETH Zentrum, CH-8092 Zürich, Switzerland3
| | | | - Thomas Hohn
- Friedrich Miescher Institute, PO Box 2543, CH-4002 Basel, Switzerland1
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50
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Klöti A, Henrich C, Bieri S, He X, Chen G, Burkhardt PK, Wünn J, Lucca P, Hohn T, Potrykus I, Fütterer J. Upstream and downstream sequence elements determine the specificity of the rice tungro bacilliform virus promoter and influence RNA production after transcription initiation. PLANT MOLECULAR BIOLOGY 1999; 40:249-266. [PMID: 10412904 DOI: 10.1023/a:1006119517262] [Citation(s) in RCA: 17] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/23/2023]
Abstract
The contribution of sequences upstream and downstream of the transcription start site to the strength and specificity of the promoter of rice tungro bacilliform virus was analysed in transgenic rice plants. The promoter is strongly stimulated by downstream sequences which include an intron and is active in all vascular and epidermal cells. Expression in the vascular tissue requires a promoter element located between -100 and -164 to which protein(s) from rice nuclear extracts bind. Elimination of this region leads to specificity for the epidermis. Due to the presence of a polyadenylation signal in the intron, short-stop RNA is produced from the promoter in addition to full-length primary transcript and its spliced derivatives. The ratio between short-stop RNA and full-length or spliced RNA is determined by upstream promoter sequences, suggesting the assembly of RNA polymerase complexes with different processivity on this promoter.
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Affiliation(s)
- A Klöti
- Institute of Plant Sciences, ETH Zürich, Switzerland
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