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Ranasinghe P, Addison ML, Dear JW, Webb DJ. Small interfering RNA: Discovery, pharmacology and clinical development-An introductory review. Br J Pharmacol 2023; 180:2697-2720. [PMID: 36250252 DOI: 10.1111/bph.15972] [Citation(s) in RCA: 28] [Impact Index Per Article: 28.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2022] [Revised: 08/23/2022] [Accepted: 09/29/2022] [Indexed: 11/28/2022] Open
Abstract
Post-transcriptional gene silencing targets and degrades mRNA transcripts, silencing the expression of specific genes. RNA interference technology, using synthetic structurally well-defined short double-stranded RNA (small interfering RNA [siRNA]), has advanced rapidly in recent years. This introductory review describes the utility of siRNA, by exploring the underpinning biology, pharmacology, recent advances and clinical developments, alongside potential limitations and ongoing challenges. Mediated by the RNA-induced silencing complex, siRNAs bind to specific complementary mRNAs, which are subsequently degraded. siRNA therapy offers advantages over other therapeutic approaches, including ability of specifically designed siRNAs to potentially target any mRNA and improved patient adherence through infrequent administration associated with a very long duration of action. Key pharmacokinetic and pharmacodynamic challenges include targeted administration, poor tissue penetration, nuclease inactivation, rapid renal elimination, immune activation and off-target effects. These have been overcome by chemical modification of siRNA and/or by utilising a range of delivery systems, increasing bioavailability and stability to allow successful clinical translation. Patisiran (hereditary transthyretin-mediated amyloidosis) was the first licensed siRNA, followed by givosiran (acute hepatic porphyria), lumasiran (primary hyperoxaluria type 1) and inclisiran (familial hypercholesterolaemia), which all use N-acetylgalactosamine (GalNAc) linkage for effective liver-directed delivery. Others are currently under development for indications varying from rare genetic diseases to common chronic non-communicable diseases (hypertension, cancer). Technological advances are paving the way for broader clinical use. Ongoing challenges remain in targeting organs beyond the liver and reaching special sites (e.g., brain). By overcoming these barriers, siRNA therapy has the potential to substantially widen its therapeutic impact.
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Affiliation(s)
- Priyanga Ranasinghe
- Department of Pharmacology, Faculty of Medicine, University of Colombo, Colombo, Sri Lanka
- University/British Heart Foundation Centre for Cardiovascular Science, The University of Edinburgh, Edinburgh, UK
| | - Melisande L Addison
- University/British Heart Foundation Centre for Cardiovascular Science, The University of Edinburgh, Edinburgh, UK
| | - James W Dear
- University/British Heart Foundation Centre for Cardiovascular Science, The University of Edinburgh, Edinburgh, UK
| | - David J Webb
- University/British Heart Foundation Centre for Cardiovascular Science, The University of Edinburgh, Edinburgh, UK
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2
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López-Márquez D, Del-Espino Á, Ruiz-Albert J, Bejarano ER, Brodersen P, Beuzón CR. Regulation of plant immunity via small RNA-mediated control of NLR expression. J Exp Bot 2023; 74:6052-6068. [PMID: 37449766 PMCID: PMC10575705 DOI: 10.1093/jxb/erad268] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/17/2023] [Accepted: 07/13/2023] [Indexed: 07/18/2023]
Abstract
Plants use different receptors to detect potential pathogens: membrane-anchored pattern recognition receptors (PRRs) activated upon perception of pathogen-associated molecular patterns (PAMPs) that elicit pattern-triggered immunity (PTI); and intracellular nucleotide-binding leucine-rich repeat proteins (NLRs) activated by detection of pathogen-derived effectors, activating effector-triggered immunity (ETI). The interconnections between PTI and ETI responses have been increasingly reported. Elevated NLR levels may cause autoimmunity, with symptoms ranging from fitness cost to developmental arrest, sometimes combined with run-away cell death, making accurate control of NLR dosage key for plant survival. Small RNA-mediated gene regulation has emerged as a major mechanism of control of NLR dosage. Twenty-two nucleotide miRNAs with the unique ability to trigger secondary siRNA production from target transcripts are particularly prevalent in NLR regulation. They enhance repression of the primary NLR target, but also bring about repression of NLRs only complementary to secondary siRNAs. We summarize current knowledge on miRNAs and siRNAs in the regulation of NLR expression with an emphasis on 22 nt miRNAs and propose that miRNA and siRNA regulation of NLR levels provides additional links between PTI and NLR defense pathways to increase plant responsiveness against a broad spectrum of pathogens and control an efficient deployment of defenses.
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Affiliation(s)
- Diego López-Márquez
- Department of Biology, University of Copenhagen, Copenhagen N, DK-2200, Denmark
| | - Ángel Del-Espino
- Instituto de Hortofruticultura Subtropical y Mediterránea ‘La Mayora’, Universidad de Málaga-Consejo Superior de Investigaciones Científicas (IHSM-UMA-CSIC), Depto. Biología Celular, Genética y Fisiología, Málaga, Spain
| | - Javier Ruiz-Albert
- Instituto de Hortofruticultura Subtropical y Mediterránea ‘La Mayora’, Universidad de Málaga-Consejo Superior de Investigaciones Científicas (IHSM-UMA-CSIC), Depto. Biología Celular, Genética y Fisiología, Málaga, Spain
| | - Eduardo R Bejarano
- Instituto de Hortofruticultura Subtropical y Mediterránea ‘La Mayora’, Universidad de Málaga-Consejo Superior de Investigaciones Científicas (IHSM-UMA-CSIC), Depto. Biología Celular, Genética y Fisiología, Málaga, Spain
| | - Peter Brodersen
- Department of Biology, University of Copenhagen, Copenhagen N, DK-2200, Denmark
| | - Carmen R Beuzón
- Instituto de Hortofruticultura Subtropical y Mediterránea ‘La Mayora’, Universidad de Málaga-Consejo Superior de Investigaciones Científicas (IHSM-UMA-CSIC), Depto. Biología Celular, Genética y Fisiología, Málaga, Spain
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3
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Alam MS, Islam MN, Das M, Islam SF, Rabbane MG, Karim E, Roy A, Alam MS, Ahmed R, Kibria ASM. RNAi-Based Therapy: Combating Shrimp Viral Diseases. Viruses 2023; 15:2050. [PMID: 37896827 PMCID: PMC10612085 DOI: 10.3390/v15102050] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2023] [Revised: 09/18/2023] [Accepted: 09/23/2023] [Indexed: 10/29/2023] Open
Abstract
Shrimp aquaculture has become a vital industry, meeting the growing global demand for seafood. Shrimp viral diseases have posed significant challenges to the aquaculture industry, causing major economic losses worldwide. Conventional treatment methods have proven to be ineffective in controlling these diseases. However, recent advances in RNA interference (RNAi) technology have opened new possibilities for combating shrimp viral diseases. This cutting-edge technology uses cellular machinery to silence specific viral genes, preventing viral replication and spread. Numerous studies have shown the effectiveness of RNAi-based therapies in various model organisms, paving the way for their use in shrimp health. By precisely targeting viral pathogens, RNAi has the potential to provide a sustainable and environmentally friendly solution to combat viral diseases in shrimp aquaculture. This review paper provides an overview of RNAi-based therapy and its potential as a game-changer for shrimp viral diseases. We discuss the principles of RNAi, its application in combating viral infections, and the current progress made in RNAi-based therapy for shrimp viral diseases. We also address the challenges and prospects of this innovative approach.
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Affiliation(s)
- Md. Shahanoor Alam
- Department of Genetics and Fish Breeding, Bangabandhu Sheikh Mujibur Rahman Agricultural University, Gazipur 1706, Bangladesh;
| | - Mohammad Nazrul Islam
- Department of Biotechnology, Sher-e-Bangla Agricultural University, Dhaka 1207, Bangladesh;
| | - Mousumi Das
- Department of Aquaculture, Bangabandhu Sheikh Mujibur Rahman Agricultural University, Gazipur 1706, Bangladesh;
| | - Sk. Farzana Islam
- Department of Fisheries (DoF), Government of the People’s Republic of Bangladesh, Matshya Bhaban, Ramna, Dhaka 1000, Bangladesh; (S.F.I.); (R.A.)
| | - Md. Golam Rabbane
- Department of Fisheries, Faculty of Biological Sciences, University of Dhaka, Dhaka 1000, Bangladesh;
| | - Ehsanul Karim
- Bangladesh Fisheries Research Institute, Mymensingh 2201, Bangladesh;
| | - Animesh Roy
- Department of Fisheries Biology and Aquatic Environment, Bangabandhu Sheikh Mujibur Rahman Agricultural University, Gazipur 1706, Bangladesh;
| | - Mohammad Shafiqul Alam
- Department of Genetics and Fish Breeding, Bangabandhu Sheikh Mujibur Rahman Agricultural University, Gazipur 1706, Bangladesh;
| | - Raju Ahmed
- Department of Fisheries (DoF), Government of the People’s Republic of Bangladesh, Matshya Bhaban, Ramna, Dhaka 1000, Bangladesh; (S.F.I.); (R.A.)
| | - Abu Syed Md. Kibria
- Department of Aquaculture, Hajee Mohammad Danesh Science and Technology University, Dinajpur 5200, Bangladesh;
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Kyndt T. Loss of susceptibility, an underexplored approach for durable resistance to plant-parasitic nematodes. J Exp Bot 2023; 74:5422-5425. [PMID: 37773262 DOI: 10.1093/jxb/erad287] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/01/2023]
Abstract
This article comments on:
Noureddine Y, da Rocha M, An J, Médina C, Mejias J, Mulet K, Quentin M, Abad P, Zouine M, Favery B, Jaubert-Possamai S. 2023. AUXIN RESPONSIVE FACTOR8 regulates development of the feeding site induced by root-knot nematodes in tomato. Journal of Experimental Botany 74, 5752–5766.
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Affiliation(s)
- Tina Kyndt
- Department Biotechnology, Faculty of Bioscience Engineering, Ghent University, 9000 Gent, Belgium
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de Felippes FF, Waterhouse PM. Plant terminators: the unsung heroes of gene expression. J Exp Bot 2023; 74:2239-2250. [PMID: 36477559 PMCID: PMC10082929 DOI: 10.1093/jxb/erac467] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 09/21/2022] [Accepted: 11/25/2022] [Indexed: 06/06/2023]
Abstract
To be properly expressed, genes need to be accompanied by a terminator, a region downstream of the coding sequence that contains the information necessary for the maturation of the mRNA 3' end. The main event in this process is the addition of a poly(A) tail at the 3' end of the new transcript, a critical step in mRNA biology that has important consequences for the expression of genes. Here, we review the mechanism leading to cleavage and polyadenylation of newly transcribed mRNAs and how this process can affect the final levels of gene expression. We give special attention to an aspect often overlooked, the effect that different terminators can have on the expression of genes. We also discuss some exciting findings connecting the choice of terminator to the biogenesis of small RNAs, which are a central part of one of the most important mechanisms of regulation of gene expression in plants.
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Affiliation(s)
| | - Peter M Waterhouse
- Centre for Agriculture and the Bioeconomy, Institute for Future Environments, Queensland University of Technology (QUT), Brisbane, QLD, Australia
- ARC Centre of Excellence for Plant Success in Nature & Agriculture, QUT, Brisbane, QLD, Australia
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Spada M, Pugliesi C, Fambrini M, Palpacelli D, Pecchia S. Knockdown of Bmp1 and Pls1 Virulence Genes by Exogenous Application of RNAi-Inducing dsRNA in Botrytis cinerea. Int J Mol Sci 2023; 24. [PMID: 36902297 DOI: 10.3390/ijms24054869] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2022] [Revised: 02/09/2023] [Accepted: 02/24/2023] [Indexed: 03/06/2023] Open
Abstract
Botrytis cinerea is a pathogen of wide agronomic and scientific importance partly due to its tendency to develop fungicide resistance. Recently, there has been great interest in the use of RNA interference as a control strategy against B. cinerea. In order to reduce the possible effects on non-target species, the sequence-dependent nature of RNAi can be used as an advantage to customize the design of dsRNA molecules. We selected two genes related to virulence: BcBmp1 (a MAP kinase essential for fungal pathogenesis) and BcPls1 (a tetraspanin related to appressorium penetration). After performing a prediction analysis of small interfering RNAs, dsRNAs of 344 (BcBmp1) and 413 (BcPls1) nucleotides were synthesized in vitro. We tested the effect of topical applications of dsRNAs, both in vitro by a fungal growth assay in microtiter plates and in vivo on artificially inoculated detached lettuce leaves. In both cases, topical applications of dsRNA led to gene knockdown with a delay in conidial germination for BcBmp1, an evident growth retardation for BcPls1, and a strong reduction in necrotic lesions on lettuce leaves for both genes. Furthermore, a strongly reduced expression of the BcBmp1 and BcPls1 genes was observed in both in vitro and in vivo experiments, suggesting that these genes could be promising targets for the development of RNAi-based fungicides against B. cinerea.
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Valli AA, Gonzalo-Magro I, Sanchez DH. Rearranged Endogenized Plant Pararetroviruses as Evidence of Heritable RNA-based Immunity. Mol Biol Evol 2022; 40:6794085. [PMID: 36322467 PMCID: PMC9868043 DOI: 10.1093/molbev/msac240] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2022] [Revised: 09/05/2022] [Accepted: 10/25/2022] [Indexed: 01/24/2023] Open
Abstract
Eukaryotic genomics frequently revealed historical spontaneous endogenization events of external invading nucleic acids, such as viral elements. In plants, an extensive occurrence of endogenous plant pararetroviruses (EPRVs) is usually believed to endow hosts with an additional layer of internal suppressive weaponry. However, an actual demonstration of this activity remains speculative. We analyzed the EPRV component and accompanying silencing effectors of Solanum lycopersicum, documenting that intronic/intergenic pararetroviral integrations bearing inverted-repeats fuel the plant's RNA-based immune system with suitable transcripts capable of evoking a silencing response. A surprisingly small set of rearrangements explained a substantial fraction of pararetroviral-derived endogenous small-interfering (si)RNAs, enriched in 22-nt forms typically associated with anti-viral post-transcriptional gene silencing. We provide preliminary evidence that such genetic and immunological signals may be found in other species outside the genus Solanum. Based on molecular dating, bioinformatics, and empirical explorations, we propose that homology-dependent silencing emerging from particular immuno-competent rearranged chromosomal areas that constitute an adaptive heritable trans-acting record of past infections, with potential impact against the unlocking of plant latent EPRVs and cognate-free pararetroviruses.
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Affiliation(s)
| | - Irene Gonzalo-Magro
- Centro Nacional de Biotecnología (CNB-CSIC), Calle Darwin 3, 28049 Madrid, Spain
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8
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Matchett-Oates L, Spangenberg GC, Cogan NOI. Manipulation of Cannabinoid Biosynthesis via Transient RNAi Expression. Front Plant Sci 2021; 12:773474. [PMID: 35035388 PMCID: PMC8757041 DOI: 10.3389/fpls.2021.773474] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/10/2021] [Accepted: 11/08/2021] [Indexed: 05/04/2023]
Abstract
Cannabis sativa L. produces unique phytocannabinoids, which are used for their pharmaceutical benefits. To date, there are no reports of in vivo engineering targeting the cannabinoid biosynthesis genes to greater elucidate the role each of these genes play in synthesis of these medically important compounds. Reported here is the first modulation of cannabinoid biosynthesis genes using RNAi via agroinfiltration. Vacuum infiltrated leaf segments of the Cannbio-2 C. sativa strain, transfected with different RNAi constructs corresponding to THCAS, CBDAS, and CBCAS gene sequences, showed significant downregulation of all cannabinoid biosynthesis genes using real-time quantitative PCR. Using RNAi, significant off-targeting occurs resulting in the downregulation of highly homologous transcripts. Significant (p < 0.05) downregulation was observed for THCAS (92%), CBDAS (97%), and CBCAS (70%) using pRNAi-GG-CBDAS-UNIVERSAL. Significant (p < 0.05) upregulation of CBCAS (76%) and non-significant upregulation of THCAS (13%) were observed when transfected with pRNAi-GG-CBCAS, suggesting the related gene's ability to synthesize multiple cannabinoids. Using this approach, increased understanding of the relationship between cannabinoid biosynthesis genes can be further elucidated. This RNAi approach enables functional genomics screens for further reverse genetic studies as well as the development of designer cannabis strains with over-expression and/or downregulation of targeted cannabinoid biosynthesis genes. Functional genomics screens, such as these, will further provide insights into gene regulation of cannabinoid biosynthesis in Cannabis.
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Affiliation(s)
- Lennon Matchett-Oates
- Agriculture Victoria, AgriBio, The Centre for AgriBioscience, Bundoora, VIC, Australia
- School of Applied Systems Biology, La Trobe University, Bundoora, VIC, Australia
| | - German C. Spangenberg
- Agriculture Victoria, AgriBio, The Centre for AgriBioscience, Bundoora, VIC, Australia
- School of Applied Systems Biology, La Trobe University, Bundoora, VIC, Australia
| | - Noel O. I. Cogan
- Agriculture Victoria, AgriBio, The Centre for AgriBioscience, Bundoora, VIC, Australia
- School of Applied Systems Biology, La Trobe University, Bundoora, VIC, Australia
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9
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Fei Y, Pyott DE, Molnar A. Temperature modulates virus-induced transcriptional gene silencing via secondary small RNAs. New Phytol 2021; 232:356-371. [PMID: 34185326 DOI: 10.1111/nph.17586] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/25/2021] [Accepted: 06/17/2021] [Indexed: 05/08/2023]
Abstract
Virus-induced gene silencing (VIGS) can be harnessed to sequence-specifically degrade host transcripts and induce heritable epigenetic modifications referred to as virus-induced post-transcriptional gene silencing (ViPTGS) and virus-induced transcriptional gene silencing (ViTGS), respectively. Both ViPTGS and ViTGS enable manipulation of endogenous gene expression without the need for transgenesis. Although VIGS has been widely used in many plant species, it is not always uniform or highly efficient. The efficiency of VIGS is affected by developmental, physiological and environmental factors. Here, we use recombinant Tobacco rattle viruses (TRV) to study the effect of temperature on ViPTGS and ViTGS using GFP as a reporter gene of silencing in N. benthamiana 16c plants. We found that unlike ViPTGS, ViTGS was impaired at high temperature. Using a novel mismatch-small interfering RNA (siRNA) tool, which precisely distinguishes virus-derived (primary) from target-generated (secondary) siRNAs, we demonstrated that the lack of secondary siRNA production/amplification was responsible for inefficient ViTGS at 29°C. Moreover, inefficient ViTGS at 29°C inhibited the transmission of epigenetic gene silencing to the subsequent generations. Our finding contributes to understanding the impact of environmental conditions on primary and secondary siRNA production and may pave the way to design/optimize ViTGS for transgene-free crop improvement.
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Affiliation(s)
- Yue Fei
- Institute of Molecular Plant Sciences, University of Edinburgh, Max Born Crescent, Edinburgh, EH9 3BF, UK
| | - Douglas E Pyott
- Institute of Molecular Plant Sciences, University of Edinburgh, Max Born Crescent, Edinburgh, EH9 3BF, UK
| | - Attila Molnar
- Institute of Molecular Plant Sciences, University of Edinburgh, Max Born Crescent, Edinburgh, EH9 3BF, UK
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El-Sappah AH, Yan K, Huang Q, Islam MM, Li Q, Wang Y, Khan MS, Zhao X, Mir RR, Li J, El-Tarabily KA, Abbas M. Comprehensive Mechanism of Gene Silencing and Its Role in Plant Growth and Development. Front Plant Sci 2021; 12:705249. [PMID: 34589097 PMCID: PMC8475493 DOI: 10.3389/fpls.2021.705249] [Citation(s) in RCA: 29] [Impact Index Per Article: 9.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/04/2021] [Accepted: 08/10/2021] [Indexed: 05/19/2023]
Abstract
Gene silencing is a negative feedback mechanism that regulates gene expression to define cell fate and also regulates metabolism and gene expression throughout the life of an organism. In plants, gene silencing occurs via transcriptional gene silencing (TGS) and post-transcriptional gene silencing (PTGS). TGS obscures transcription via the methylation of 5' untranslated region (5'UTR), whereas PTGS causes the methylation of a coding region to result in transcript degradation. In this review, we summarized the history and molecular mechanisms of gene silencing and underlined its specific role in plant growth and crop production.
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Affiliation(s)
- Ahmed H. El-Sappah
- School of Agriculture, Forestry and Food Engineering, Yibin University, Yibin, China
- Genetics Department, Faculty of Agriculture, Zagazig University, Zagazig, Egypt
- Key Laboratory of Sichuan Province for Refining Sichuan Tea, Yibin, China
| | - Kuan Yan
- School of Agriculture, Forestry and Food Engineering, Yibin University, Yibin, China
- Key Laboratory of Sichuan Province for Refining Sichuan Tea, Yibin, China
| | - Qiulan Huang
- School of Agriculture, Forestry and Food Engineering, Yibin University, Yibin, China
- Key Laboratory of Sichuan Province for Refining Sichuan Tea, Yibin, China
- College of Tea Science, Yibin University, Yibin, China
| | | | - Quanzi Li
- State Key Laboratory of Tree Genetics and Breeding, Chinese Academy of Forestry, Beijing, China
- Research Institute of Forestry, Chinese Academy of Forestry, Beijing, China
| | - Yu Wang
- School of Agriculture, Forestry and Food Engineering, Yibin University, Yibin, China
- Key Laboratory of Sichuan Province for Refining Sichuan Tea, Yibin, China
| | - Muhammad Sarwar Khan
- Center of Agriculture Biochemistry and Biotechnology, University of Agriculture, Faisalabad, Pakistan
| | - Xianming Zhao
- School of Agriculture, Forestry and Food Engineering, Yibin University, Yibin, China
- Key Laboratory of Sichuan Province for Refining Sichuan Tea, Yibin, China
| | - Reyazul Rouf Mir
- Division of Genetics and Plant Breeding, Faculty of Agriculture (FoA), Sher-e-Kashmir University of Agricultural Sciences and Technology (SKUAST–K), Sopore, India
| | - Jia Li
- School of Agriculture, Forestry and Food Engineering, Yibin University, Yibin, China
- Key Laboratory of Sichuan Province for Refining Sichuan Tea, Yibin, China
| | - Khaled A. El-Tarabily
- Department of Biology, College of Science, United Arab Emirates University, Al-Ain, United Arab Emirates
- Harry Butler Institute, Murdoch University, Murdoch, WA, Australia
| | - Manzar Abbas
- School of Agriculture, Forestry and Food Engineering, Yibin University, Yibin, China
- Key Laboratory of Sichuan Province for Refining Sichuan Tea, Yibin, China
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Kuriyama K, Tabara M, Moriyama H, Kanazawa A, Koiwa H, Takahashi H, Fukuhara T. Disturbance of floral colour pattern by activation of an endogenous pararetrovirus, petunia vein clearing virus, in aged petunia plants. Plant J 2020; 103:497-511. [PMID: 32100385 PMCID: PMC7496347 DOI: 10.1111/tpj.14728] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/09/2020] [Accepted: 02/04/2020] [Indexed: 05/22/2023]
Abstract
White areas of star-type bicolour petals of petunia (Petunia hybrida) are caused by post-transcriptional gene silencing (PTGS) of the key enzyme of anthocyanin biosynthesis. We observed blotched flowers and a vein-clearing symptom in aged petunia plants. To determine the cause of blotched flowers, we focused on an endogenous pararetrovirus, petunia vein clearing virus (PVCV), because this virus may have a suppressor of PTGS (VSR). Transcripts and episomal DNAs derived from proviral PVCVs accumulated in aged plants, indicating that PVCV was activated as the host plant aged. Furthermore, DNA methylation of CG and CHG sites in the promoter region of proviral PVCV decreased in aged plants, suggesting that poor maintenance of DNA methylation activates PVCV. In parallel, de novo DNA methylation of CHH sites in its promoter region was also detected. Therefore, both activation and inactivation of PVCV occurred in aged plants. The accumulation of PVCV transcripts and episomal DNAs in blotched regions and the detection of VSR activity support a mechanism in which suppression of PTGS by PVCV causes blotched flowers.
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Affiliation(s)
- Kazunori Kuriyama
- Department of Applied Biological SciencesTokyo University of Agriculture and Technology3‐5‐8 SaiwaichoFuchuTokyo183‐8509Japan
| | - Midori Tabara
- Department of Applied Biological SciencesTokyo University of Agriculture and Technology3‐5‐8 SaiwaichoFuchuTokyo183‐8509Japan
- Institute of Global Innovation ResearchTokyo University of Agriculture and Technology3‐5‐8 SaiwaichoFuchuTokyo183‐8509Japan
| | - Hiromitsu Moriyama
- Department of Applied Biological SciencesTokyo University of Agriculture and Technology3‐5‐8 SaiwaichoFuchuTokyo183‐8509Japan
| | - Akira Kanazawa
- Research Faculty of AgricultureHokkaido UniversityKita 9, Nishi 9, Kita‐kuSapporo060‐8589Japan
| | - Hisashi Koiwa
- Institute of Global Innovation ResearchTokyo University of Agriculture and Technology3‐5‐8 SaiwaichoFuchuTokyo183‐8509Japan
- Department of Horticultural SciencesTexas A&M UniversityCollege StationTX77843USA
| | - Hideki Takahashi
- Graduate School of Agricultural ScienceTohoku University468‐1, Aramaki‐Aza‐AobaSendai980‐0845Japan
| | - Toshiyuki Fukuhara
- Department of Applied Biological SciencesTokyo University of Agriculture and Technology3‐5‐8 SaiwaichoFuchuTokyo183‐8509Japan
- Institute of Global Innovation ResearchTokyo University of Agriculture and Technology3‐5‐8 SaiwaichoFuchuTokyo183‐8509Japan
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Zhang Y, Wu X, Yuan L. Distinct non-coding RNAs confer root-dependent sense transgene-induced post-transcriptional gene silencing and nitrogen-dependent post-transcriptional regulation to AtAMT1;1 transcripts in Arabidopsis roots. Plant J 2020; 102:823-837. [PMID: 31901180 DOI: 10.1111/tpj.14667] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/22/2019] [Revised: 12/19/2019] [Accepted: 12/23/2019] [Indexed: 06/10/2023]
Abstract
High-affinity ammonium uptake in roots mediate by AMT1-type ammonium transporters, which are tightly controlled at multiple regulatory levels for adapting various nitrogen availability. For Arabidopsis AtAMT1;1 gene, in addition to the transcriptional and post-translational controls, an organ-dependent and N-dependent post-transcriptional regulation was suggested as an additional regulatory step for fine tuning ammonium uptake, but the underlying mechanisms remain to be elucidated. Here, we showed that degradation of AtAMT1;1 transcript in roots of Pro35s:AtAMT1;1-transformed atamt1;1-1 Arabidopsis plants resulted from RDR6-dependent sense transgene-induced post-transcriptional gene silencing (S-PTGS). The siRNAs for S-PTGS may derive from the aberrant RNA, of which the production was co-determined by sequence feature and excessive expression of AtAMT1;1. Switching to the expression of AtAMT1;1 driven by ProAtUBQ10 or of AtAMT1;1 mutated at two siRNA-targeted hotspots reduced AtAMT1;1-specific siRNAs and overcame S-PTGS in roots. In roots of these lines, however, the steady-state transcript levels of AtAMT1;1 still significantly decreased under conditions of N-sufficiency compared with N-deficiency, confirming a N-dependent post-transcriptional regulatory manner. A crucial role of the 207-bp 3'-end sequence of AtAMT1;1 was further demonstrated by N-dependent accumulation of chimeric-AtAMT1;1 transcript in T-DNA insertion lines and of GFP-tagged chimeric-AtAMT1;1 transcript in transgenic lines. A novel non-coding RNA (ncRNA), which was highly abundant in N-sufficient roots, may target the above-identified 3'-end region for the degrading AtAMT1;1 transcript. This degradation could be prevented by a mutation on the AtAMT1;1 transcript at a potential cleavage site (+1458). These results suggested two distinct mechanisms of regulating AtAMT1;1 mRNA turnover by ncRNA for strictly control of ammonium uptake in roots.
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Affiliation(s)
- Yongjian Zhang
- Key Laboratory of Plant-Soil Interaction, MOE, College of Resources and Environmental Sciences, China Agricultural University, 100193, Beijing, China
| | - Xiangyu Wu
- Key Laboratory of Plant-Soil Interaction, MOE, College of Resources and Environmental Sciences, China Agricultural University, 100193, Beijing, China
| | - Lixing Yuan
- Key Laboratory of Plant-Soil Interaction, MOE, College of Resources and Environmental Sciences, China Agricultural University, 100193, Beijing, China
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13
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de Felippes FF, Waterhouse PM. The Whys and Wherefores of Transitivity in Plants. Front Plant Sci 2020; 11:579376. [PMID: 32983223 PMCID: PMC7488869 DOI: 10.3389/fpls.2020.579376] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/02/2020] [Accepted: 08/14/2020] [Indexed: 05/05/2023]
Abstract
Transitivity in plants is a mechanism that produces secondary small interfering RNAs (siRNAs) from a transcript targeted by primary small RNAs (sRNAs). It expands the silencing signal to additional sequences of the transcript. The process requires RNA-dependent RNA polymerases (RDRs), which convert single-stranded RNA targets into a double-stranded (ds) RNA, the precursor of siRNAs and is critical for effective and amplified responses to virus infection. It is also important for the production of endogenous secondary siRNAs, such as phased siRNAs (phasiRNAs), which regulate several genes involved in development and adaptation. Transitivity on endogenous transcripts is very specific, utilizing special primary sRNAs, such as miRNAs with unique features, and particular ARGONAUTEs. In contrast, transitivity on transgene and virus (exogenous) transcripts is more generic. This dichotomy of responses implies the existence of a mechanism that differentiates self from non-self targets. In this work, we examine the possible mechanistic process behind the dichotomy and the intriguing counter-intuitive directionality of transitive sequence-spread in plants.
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14
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Ban Y, Morita Y, Ogawa M, Higashi K, Nakatsuka T, Nishihara M, Nakayama M. Inhibition of post-transcriptional gene silencing of chalcone synthase genes in petunia picotee petals by fluacrypyrim. J Exp Bot 2019; 70:1513-1523. [PMID: 30690559 DOI: 10.1093/jxb/erz009] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/05/2018] [Accepted: 01/29/2019] [Indexed: 06/09/2023]
Abstract
In petals of picotee petunia (Petunia hybrida) cultivars, margin-specific post-transcriptional gene silencing (PTGS) of chalcone synthase A (CHSA) inhibits anthocyanin biosynthesis, resulting in marginal white tissue formation. In this study, we found that a low molecular mass compound, fluacrypyrim, inhibits PTGS of CHSA, and we explored the site-specific PTGS mechanism of operation. Fluacrypyrim treatment abolished the picotee pattern and eliminated site-specific differences in the levels of anthocyanin-related compounds, CHSA expression, and CHSA small interfering RNA (siRNA). In addition, fluacrypyrim abolished the petunia star-type pattern, which is also caused by PTGS of CHSA. Fluacrypyrim treatment was effective only at the early floral developmental stage and predominantly eliminated siRNA derived from CHS genes; i.e. siRNA derived from other genes remained at a comparable level. Fluacrypyrim probably targets the induction of PTGS that specifically operates for CHS genes in petunia picotee flowers, rather than common PTGS maintenance mechanisms that degrade mRNAs and generate siRNA. Upon treatment, the proportion of colored tissue increased due to a shift of the border between white and colored sites toward the margin in a time- and dose-dependent manner. These findings imply that the fluacrypyrim-targeted PTGS induction is completed gradually and its strength is attenuated from the margins to the center of petunia picotee petals.
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Affiliation(s)
- Yusuke Ban
- Institute of Vegetable and Floriculture Science, National Agriculture and Food Research Organization (NARO), Tsukuba, Ibaraki, Japan
- Western Region Agricultural Research Center, NARO, Fukuyama, Hiroshima, Japan
| | - Yasumasa Morita
- Institute of Vegetable and Floriculture Science, National Agriculture and Food Research Organization (NARO), Tsukuba, Ibaraki, Japan
- Experimental Farm, Faculty of Agriculture, Meijo University, Kasugai, Aichi, Japan
| | - Mika Ogawa
- Teikyo University of Science, Adachi, Tokyo, Japan
| | | | - Takashi Nakatsuka
- Iwate Biotechnology Research Center, Kitakami, Iwate, Japan
- Graduate School of Agriculture, Shizuoka University, Shizuoka, Shizuoka, Japan
| | | | - Masayoshi Nakayama
- Institute of Vegetable and Floriculture Science, National Agriculture and Food Research Organization (NARO), Tsukuba, Ibaraki, Japan
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15
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Njaci I, Williams B, Castillo-González C, Dickman MB, Zhang X, Mundree S. Genome-Wide Investigation of the Role of MicroRNAs in Desiccation Tolerance in the Resurrection Grass Tripogon loliiformis. Plants (Basel) 2018; 7:E68. [PMID: 30200279 PMCID: PMC6161015 DOI: 10.3390/plants7030068] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/31/2018] [Revised: 08/24/2018] [Accepted: 08/29/2018] [Indexed: 12/15/2022]
Abstract
Drought causes approximately two-thirds of crop and yield loss worldwide. To sustain future generations, there is a need to develop robust crops with enhanced water use efficiency. Resurrection plants are naturally resilient and tolerate up to 95% water loss with the ability to revive upon watering. Stress is genetically encoded and resilient species may garner tolerance by tightly regulating the expression of stress-related genes. MicroRNAs (miRNAs) post-transcriptionally regulate development and other stress response processes in eukaryotes. However, their role in resurrection plant desiccation tolerance is poorly understood. In this study, small RNA sequencing and miRNA expression profiling was conducted using Tripogon loliiformis plants subjected to extreme water deficit conditions. Differentially expressed miRNA profiles, target mRNAs, and their regulatory processes were elucidated. Gene ontology enrichment analysis revealed that development, stress response, and regulation of programmed cell death biological processes; Oxidoreductase and hydrolyase molecular activities; and SPL, MYB, and WRKY transcription factors were targeted by miRNAs during dehydration stress, indicating the indispensable regulatory role of miRNAs in desiccation tolerance. This study provides insights into the molecular mechanisms of desiccation tolerance in the resurrection plant T. loliiformis. This information will be useful in devising strategies for crop improvement on enhanced drought tolerance and water use efficiency.
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Affiliation(s)
- Isaac Njaci
- Centre for Tropical Crops and Biocommodities, Queensland University of Technology, Brisbane, QLD 4000, Australia.
| | - Brett Williams
- Centre for Tropical Crops and Biocommodities, Queensland University of Technology, Brisbane, QLD 4000, Australia.
| | - Claudia Castillo-González
- Department of Biochemistry and Biophysics, Institute for Plant Genomics and Biotechnology, Texas A&M University, College Station, TX 77843, USA.
| | - Martin B Dickman
- Department of Plant Pathology and Microbiology, Institute for Plant Genomics and Biotechnology, Texas A&M University, College Station, TX 77843, USA.
| | - Xiuren Zhang
- Department of Biochemistry and Biophysics, Institute for Plant Genomics and Biotechnology, Texas A&M University, College Station, TX 77843, USA.
| | - Sagadevan Mundree
- Centre for Tropical Crops and Biocommodities, Queensland University of Technology, Brisbane, QLD 4000, Australia.
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16
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Huang TK, Falk BW, Dandekar AM, McDonald KA. Enhancement of Recombinant Protein Production in Transgenic Nicotiana benthamiana Plant Cell Suspension Cultures with Co-Cultivation of Agrobacterium Containing Silencing Suppressors. Int J Mol Sci 2018; 19:E1561. [PMID: 29882931 PMCID: PMC6032394 DOI: 10.3390/ijms19061561] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2018] [Revised: 05/06/2018] [Accepted: 05/18/2018] [Indexed: 11/16/2022] Open
Abstract
We have previously demonstrated that the inducible plant viral vector (CMViva) in transgenic plant cell cultures can significantly improve the productivity of extracellular functional recombinant human alpha-1-antiryspin (rAAT) compared with either a common plant constitutive promoter (Cauliflower mosaic virus (CaMV) 35S) or a chemically inducible promoter (estrogen receptor-based XVE) system. For a transgenic plant host system, however, viral or transgene-induced post-transcriptional gene silencing (PTGS) has been identified as a host response mechanism that may dramatically reduce the expression of a foreign gene. Previous studies have suggested that viral gene silencing suppressors encoded by a virus can block or interfere with the pathways of transgene-induced PTGS in plant cells. In this study, the capability of nine different viral gene silencing suppressors were evaluated for improving the production of rAAT protein in transgenic plant cell cultures (CMViva, XVE or 35S system) using an Agrobacterium-mediated transient expression co-cultivation process in which transgenic plant cells and recombinant Agrobacterium carrying the viral gene silencing suppressor were grown together in suspension cultures. Through the co-cultivation process, the impacts of gene silencing suppressors on the rAAT production were elucidated, and promising gene silencing suppressors were identified. Furthermore, the combinations of gene silencing suppressors were optimized using design of experiments methodology. The results have shown that in transgenic CMViva cell cultures, the functional rAAT as a percentage of total soluble protein is increased 5.7 fold with the expression of P19, and 17.2 fold with the co-expression of CP, P19 and P24.
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Affiliation(s)
- Ting-Kuo Huang
- Department of Chemical Engineering and Materials Science, University of California, 1 Shields Avenue, Davis, CA 95616, USA.
| | - Bryce W Falk
- Department of Plant Pathology, University of California, 1 Shields Avenue, Davis, CA 95616, USA.
| | - Abhaya M Dandekar
- Department of Plant Sciences, University of California, 1 Shields Avenue, Davis, CA 95616, USA.
| | - Karen A McDonald
- Department of Chemical Engineering and Materials Science, University of California, 1 Shields Avenue, Davis, CA 95616, USA.
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17
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Park EJ, Kim TH. Fine-Tuning of Gene Expression by tRNA-Derived Fragments during Abiotic Stress Signal Transduction. Int J Mol Sci 2018; 19:E518. [PMID: 29419808 DOI: 10.3390/ijms19020518] [Citation(s) in RCA: 33] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2018] [Revised: 01/30/2018] [Accepted: 02/06/2018] [Indexed: 11/17/2022] Open
Abstract
When plants are subjected to unfavorable environmental conditions, overall gene expression in stressed cells is altered from a programmed pattern for normal development to an adaptive pattern for survival. Rapid changes in plant gene expression include production of stress responsive proteins for protection as well as reduction of irrelevant proteins to minimize energy consumption during growth. In addition to the many established mechanisms known to modulate gene expression in eukaryotes, a novel strategy involving tRNA-derived fragments (tRFs) was recently reported to control gene expression. In animals, tRFs are shown to play a certain role in infected or cancer cells. However, tRFs are expected to function in the regulation of gene expression against abiotic stress conditions in plants. Moreover, the underlying mechanism linking up-regulation of tRFs under stress conditions with the stress tolerant response remains unknown. In this review, the biogenesis and putative function of diverse tRFs in abiotic stress signaling are discussed with a focus on tRFs as a transcriptional/post-transcriptional/translational regulator.
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18
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Wu YY, Hou BH, Lee WC, Lu SH, Yang CJ, Vaucheret H, Chen HM. DCL2- and RDR6-dependent transitive silencing of SMXL4 and SMXL5 in Arabidopsis dcl4 mutants causes defective phloem transport and carbohydrate over-accumulation. Plant J 2017; 90:1064-1078. [PMID: 28267232 DOI: 10.1111/tpj.13528] [Citation(s) in RCA: 31] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/10/2016] [Revised: 02/02/2017] [Accepted: 02/28/2017] [Indexed: 05/25/2023]
Abstract
DICER-LIKE (DCL) enzymes process double-stranded RNA into small RNAs that act as regulators of gene expression. Arabidopsis DCL4 and DCL2 each allow the post-transcriptional gene silencing (PTGS) of viruses and transgenes, but primary PTGS-prone DCL4 outcompetes transitive PTGS-prone DCL2 in wild-type plants. This hierarchy likely prevents DCL2 having any detrimental effects on endogenous genes. Indeed, dcl4 mutants exhibit developmental defects and increased sensitivity to genotoxic stress. In this study, the mechanism underlying dcl4 defects was investigated using genetic, biochemical and high-throughput sequencing approaches. We show that the purple phenotype of dcl4 leaves correlates with carbohydrate over-accumulation and defective phloem transport, and depends on the activity of SUPPRESSOR OF GENE SILENCING 3, RNA-DEPENDENT RNA POLYMERASE 6 (RDR6) and DCL2. This phenotype correlates with the downregulation of two genes expressed in the apex and the vasculature, SMAX1-LIKE 4 (SMXL4) and SMXL5, and the accumulation of DCL2- and RDR6-dependent small interfering RNAs derived from these two genes. Supporting a causal effect, smxl4 smxl5 double mutants exhibit leaf pigmentation, enhanced starch accumulation and defective phloem transport, similar to dcl4 plants. Overall, this study elucidates the detrimental action of DCL2 when DCL4 is absent, and indicates that DCL4 outcompeting DCL2 in wild-type plants is crucial to prevent the degradation of endogenous transcripts by DCL2- and RDR6-dependent transitive PTGS.
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Affiliation(s)
- Yu-Yi Wu
- Agricultural Biotechnology Research Center, Academia Sinica, Taipei, 11529, Taiwan
| | - Bo-Han Hou
- Agricultural Biotechnology Research Center, Academia Sinica, Taipei, 11529, Taiwan
| | - Wen-Chi Lee
- Agricultural Biotechnology Research Center, Academia Sinica, Taipei, 11529, Taiwan
| | - Shin-Hua Lu
- Agricultural Biotechnology Research Center, Academia Sinica, Taipei, 11529, Taiwan
| | - Chen-Jui Yang
- Agricultural Biotechnology Research Center, Academia Sinica, Taipei, 11529, Taiwan
| | - Hervé Vaucheret
- Institut Jean-Pierre Bourgin, UMR 1318, INRA, SPS Saclay Plant Sciences, Versailles, France
| | - Ho-Ming Chen
- Agricultural Biotechnology Research Center, Academia Sinica, Taipei, 11529, Taiwan
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19
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Jaime-Pérez N, Pineda B, García-Sogo B, Atares A, Athman A, Byrt CS, Olías R, Asins MJ, Gilliham M, Moreno V, Belver A. The sodium transporter encoded by the HKT1;2 gene modulates sodium/potassium homeostasis in tomato shoots under salinity. Plant Cell Environ 2017; 40:658-671. [PMID: 27987209 DOI: 10.1111/pce.12883] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/14/2016] [Accepted: 12/05/2016] [Indexed: 05/20/2023]
Abstract
Excessive soil salinity diminishes crop yield and quality. In a previous study in tomato, we identified two closely linked genes encoding HKT1-like transporters, HKT1;1 and HKT1;2, as candidate genes for a major quantitative trait locus (kc7.1) related to shoot Na+ /K+ homeostasis - a major salt tolerance trait - using two populations of recombinant inbred lines (RILs). Here, we determine the effectiveness of these genes in conferring improved salt tolerance by using two near-isogenic lines (NILs) that were homozygous for either the Solanum lycopersicum allele (NIL17) or for the Solanum cheesmaniae allele (NIL14) at both HKT1 loci; transgenic lines derived from these NILs in which each HKT1;1 and HKT1;2 had been silenced by stable transformation were also used. Silencing of ScHKT1;2 and SlHKT1;2 altered the leaf Na+ /K+ ratio and caused hypersensitivity to salinity in plants cultivated under transpiring conditions, whereas silencing SlHKT1;1/ScHKT1;1 had a lesser effect. These results indicate that HKT1;2 has the more significant role in Na+ homeostasis and salinity tolerance in tomato.
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Affiliation(s)
- Noelia Jaime-Pérez
- Department of Biochemistry, Molecular and Cellular Biology of Plants, Estación Experimental del Zaidín, Consejo Superior de Investigaciones Científicas (CSIC), C/Prof. Albareda 1, E-18008, Granada, Spain
| | - Benito Pineda
- Laboratory of Tissue Culture and Plant Breeding, Institute of Plant Molecular and Cellular Biology, CSIC, Polytechnic University of Valencia, Valencia, 46022, Spain
| | - Begoña García-Sogo
- Laboratory of Tissue Culture and Plant Breeding, Institute of Plant Molecular and Cellular Biology, CSIC, Polytechnic University of Valencia, Valencia, 46022, Spain
| | - Alejandro Atares
- Laboratory of Tissue Culture and Plant Breeding, Institute of Plant Molecular and Cellular Biology, CSIC, Polytechnic University of Valencia, Valencia, 46022, Spain
| | - Asmini Athman
- ARC Centre of Excellence in Plant Energy Biology, School of Agriculture, Food and Wine and Waite Research Institute, Waite Research Precinct, University of Adelaide, Glen Osmond, SA 5064, Australia
| | - Caitlin S Byrt
- ARC Centre of Excellence in Plant Energy Biology, School of Agriculture, Food and Wine and Waite Research Institute, Waite Research Precinct, University of Adelaide, Glen Osmond, SA 5064, Australia
| | - Raquel Olías
- Department of Biochemistry, Molecular and Cellular Biology of Plants, Estación Experimental del Zaidín, Consejo Superior de Investigaciones Científicas (CSIC), C/Prof. Albareda 1, E-18008, Granada, Spain
| | - Maria José Asins
- Plant Protection and Biotechnology Center, Instituto Valenciano de Investigaciones Agrarias (IVIA), E46113 Moncada, Valencia, Spain
| | - Matthew Gilliham
- ARC Centre of Excellence in Plant Energy Biology, School of Agriculture, Food and Wine and Waite Research Institute, Waite Research Precinct, University of Adelaide, Glen Osmond, SA 5064, Australia
| | - Vicente Moreno
- Laboratory of Tissue Culture and Plant Breeding, Institute of Plant Molecular and Cellular Biology, CSIC, Polytechnic University of Valencia, Valencia, 46022, Spain
| | - Andrés Belver
- Department of Biochemistry, Molecular and Cellular Biology of Plants, Estación Experimental del Zaidín, Consejo Superior de Investigaciones Científicas (CSIC), C/Prof. Albareda 1, E-18008, Granada, Spain
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20
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Hewezi T, Piya S, Qi M, Balasubramaniam M, Rice JH, Baum TJ. Arabidopsis miR827 mediates post-transcriptional gene silencing of its ubiquitin E3 ligase target gene in the syncytium of the cyst nematode Heterodera schachtii to enhance susceptibility. Plant J 2016; 88:179-192. [PMID: 27304416 DOI: 10.1111/tpj.13238] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/04/2016] [Accepted: 06/08/2016] [Indexed: 05/02/2023]
Abstract
MicroRNAs (miRNAs) are a major class of small non-coding RNAs with emerging functions in biotic and abiotic interactions. Here, we report on a new functional role of Arabidopsis miR827 and its NITROGEN LIMITATION ADAPTATION (NLA) target gene in mediating plant susceptibility to the beet cyst nematode Heterodera schachtii. Cyst nematodes are sedentary endoparasites that induce the formation of multinucleated feeding structures termed syncytia in the roots of host plants. Using promoter:GUS fusion assays we established that miR827 was activated in the initial feeding cells and this activation was maintained in the syncytium during all sedentary stages of nematode development. Meanwhile, the NLA target gene, which encodes an ubiquitin E3 ligase enzyme, was post-transcriptionally silenced in the syncytium to permanently suppress its activity during all nematode parasitic stages. Overexpression of miR827 in Arabidopsis resulted in hyper-susceptibility to H. schachtii. In contrast, inactivation of miR827 activity through target mimicry or by overexpression a miR827-resistant cDNA of NLA produced the opposite phenotype of reduced plant susceptibility to H. schachtii. Gene expression analysis of several pathogenesis-related genes together with Agrobacterium-mediated transient expression in Nicotiana benthamiana provided strong evidence that miR827-mediated downregulation of NLA to suppress basal defense pathways. In addition, using yeast two-hybrid screens we identified several candidates of NLA-interacting proteins that are involved in a wide range of biological processes and molecular functions, including three pathogenesis-related proteins. Taken together, we conclude that nematode-activated miR827 in the syncytium is necessary to suppress immune responses in order to establish infection and cause disease.
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Affiliation(s)
- Tarek Hewezi
- Department of Plant Sciences, University of Tennessee, Knoxville, TN, 37996, USA
| | - Sarbottam Piya
- Department of Plant Sciences, University of Tennessee, Knoxville, TN, 37996, USA
| | - Mingsheng Qi
- Department of Plant Pathology and Microbiology, Iowa State University, Ames, IA, 50011, USA
| | | | - J Hollis Rice
- Department of Plant Sciences, University of Tennessee, Knoxville, TN, 37996, USA
| | - Thomas J Baum
- Department of Plant Pathology and Microbiology, Iowa State University, Ames, IA, 50011, USA
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21
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Meziadi C, Blanchet S, Richard MMS, Pilet-Nayel ML, Geffroy V, Pflieger S. Bean pod mottle virus: a new powerful tool for functional genomics studies in Pisum sativum. Plant Biotechnol J 2016; 14:1777-87. [PMID: 26896301 PMCID: PMC5067550 DOI: 10.1111/pbi.12537] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/26/2015] [Revised: 11/13/2015] [Accepted: 01/06/2016] [Indexed: 05/08/2023]
Abstract
Pea (Pisum sativum L.) is an important legume worldwide. The importance of pea in arable rotations and nutritional value for both human and animal consumption have fostered sustained production and different studies to improve agronomic traits of interest. Moreover, complete sequencing of the pea genome is currently underway and will lead to the identification of a large number of genes potentially associated with important agronomic traits. Because stable genetic transformation is laborious for pea, virus-induced gene silencing (VIGS) appears as a powerful alternative technology for determining the function of unknown genes. In this work, we present a rapid and efficient viral inoculation method using DNA infectious plasmids of Bean pod mottle virus (BPMV)-derived VIGS vector. Six pea genotypes with important genes controlling biotic and/or abiotic stresses were found susceptible to BPMV carrying a GFP reporter gene and showed fluorescence in both shoots and roots. In a second step, we investigated 37 additional pea genotypes and found that 30 were susceptible to BPMV and only 7 were resistant. The capacity of BPMV to induce silencing of endogenes was investigated in the most susceptible genotype using two visual reporter genes: PsPDS and PsKORRIGAN1 (PsKOR1) encoding PHYTOENE DESATURASE and a 1,4-β-D-glucanase, respectively. The features of the 'one-step' BPMV-derived VIGS vector include (i) the ease of rub-inoculation, without any need for biolistic or agro-inoculation procedures, (ii) simple cost-effective procedure and (iii) noninterference of viral symptoms with silencing. These features make BPMV the most adapted VIGS vector in pea to make low- to high-throughput VIGS studies.
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Affiliation(s)
- Chouaib Meziadi
- Institute of Plant Sciences Paris-Saclay (IPS2), CNRS, INRA, Université Paris-Sud, Université d'Evry, Université Paris-Diderot Sorbonne Paris-Cité, Université Paris-Saclay, Orsay, France
| | - Sophie Blanchet
- Institute of Plant Sciences Paris-Saclay (IPS2), CNRS, INRA, Université Paris-Sud, Université d'Evry, Université Paris-Diderot Sorbonne Paris-Cité, Université Paris-Saclay, Orsay, France
| | - Manon M S Richard
- Institute of Plant Sciences Paris-Saclay (IPS2), CNRS, INRA, Université Paris-Sud, Université d'Evry, Université Paris-Diderot Sorbonne Paris-Cité, Université Paris-Saclay, Orsay, France
| | | | - Valérie Geffroy
- Institute of Plant Sciences Paris-Saclay (IPS2), CNRS, INRA, Université Paris-Sud, Université d'Evry, Université Paris-Diderot Sorbonne Paris-Cité, Université Paris-Saclay, Orsay, France
| | - Stéphanie Pflieger
- Institute of Plant Sciences Paris-Saclay (IPS2), CNRS, INRA, Université Paris-Sud, Université d'Evry, Université Paris-Diderot Sorbonne Paris-Cité, Université Paris-Saclay, Orsay, France
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22
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Abstract
Multicellular organisms, like higher plants, need to coordinate their growth and development and to cope with environmental cues. To achieve this, various signal molecules are transported between neighboring cells and distant organs to control the fate of the recipient cells and organs. RNA silencing produces cell non-autonomous signal molecules that can move over short or long distances leading to the sequence specific silencing of a target gene in a well defined area of cells or throughout the entire plant, respectively. The nature of these signal molecules, the route of silencing spread, and the genes involved in their production, movement and reception are discussed in this review. Additionally, a short section on features of silencing spread in animal models is presented at the end of this review.
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Affiliation(s)
- Glykeria Mermigka
- Department of Biology, University of Crete, Heraklion, Crete, Greece
| | - Frédéric Verret
- Institute of Molecular Biology and Biotechnology, Foundation for Research and Technology, Heraklion, Crete, Greece
| | - Kriton Kalantidis
- Department of Biology, University of Crete, Heraklion, Crete, Greece
- Institute of Molecular Biology and Biotechnology, Foundation for Research and Technology, Heraklion, Crete, Greece
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23
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Abstract
RNA interference is widely employed as a gene-silencing system in eukaryotes for host defence against invading nucleic acids. In response to invading double-stranded RNA (dsRNA), mRNA is degraded in sequence-specific manner. So far, however, DNA interference (DNAi) has been reported only in plants, ciliates and archaea, and has not been explored in Metazoa. Here, we demonstrate that linear double-stranded DNA promotes both sequence-specific transcription blocking and mRNA degradation in developing embryos of the appendicularian Oikopleura dioica. Introduced polymerase chain reaction (PCR) products or linearized plasmids encoding Brachyury induced tail malformation and mRNA degradation. This malformation was also promoted by DNA fragments of the putative 5'-flanking region and intron without the coding region. PCR products encoding Zic-like1 and acetylcholine esterase also induced loss of sensory organ and muscle acetylcholinesterase activity, respectively. Co-injection of mRNA encoding EGFP and mCherry, and PCR products encoding these fluorescent proteins, induced sequence-specific decrease in the green or red fluorescence, respectively. These results suggest that O. dioica possesses a defence system against exogenous DNA and RNA, and that DNA fragment-induced gene silencing would be mediated through transcription blocking as well as mRNA degradation. This is the first report of DNAi in Metazoa.
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Affiliation(s)
- Tatsuya Omotezako
- Department of Biological Sciences, Graduate School of Science, Osaka University, 1-1 Machikaneyama-cho, Toyonaka, Osaka 560-0043, Japan
| | - Takeshi A Onuma
- Department of Biological Sciences, Graduate School of Science, Osaka University, 1-1 Machikaneyama-cho, Toyonaka, Osaka 560-0043, Japan
| | - Hiroki Nishida
- Department of Biological Sciences, Graduate School of Science, Osaka University, 1-1 Machikaneyama-cho, Toyonaka, Osaka 560-0043, Japan
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Lee WS, Fu SF, Li Z, Murphy AM, Dobson EA, Garland L, Chaluvadi SR, Lewsey MG, Nelson RS, Carr JP. Salicylic acid treatment and expression of an RNA-dependent RNA polymerase 1 transgene inhibit lethal symptoms and meristem invasion during tobacco mosaic virus infection in Nicotiana benthamiana. BMC Plant Biol 2016; 16:15. [PMID: 26757721 PMCID: PMC4710973 DOI: 10.1186/s12870-016-0705-8] [Citation(s) in RCA: 46] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/16/2015] [Accepted: 01/06/2016] [Indexed: 05/23/2023]
Abstract
BACKGROUND Host RNA-dependent RNA polymerases (RDRs) 1 and 6 contribute to antiviral RNA silencing in plants. RDR6 is constitutively expressed and was previously shown to limit invasion of Nicotiana benthamiana meristem tissue by potato virus X and thereby inhibit disease development. RDR1 is inducible by salicylic acid (SA) and several other phytohormones. But although it contributes to basal resistance to tobacco mosaic virus (TMV) it is dispensable for SA-induced resistance in inoculated leaves. The laboratory accession of N. benthamiana is a natural rdr1 mutant and highly susceptible to TMV. However, TMV-induced symptoms are ameliorated in transgenic plants expressing Medicago truncatula RDR1. RESULTS In MtRDR1-transgenic N. benthamiana plants the spread of TMV expressing the green fluorescent protein (TMV.GFP) into upper, non-inoculated, leaves was not inhibited. However, in these plants exclusion of TMV.GFP from the apical meristem and adjacent stem tissue was greater than in control plants and this exclusion effect was enhanced by SA. TMV normally kills N. benthamiana plants but although MtRDR1-transgenic plants initially displayed virus-induced necrosis they subsequently recovered. Recovery from disease was markedly enhanced by SA treatment in MtRDR1-transgenic plants whereas in control plants SA delayed but did not prevent systemic necrosis and death. Following SA treatment of MtRDR1-transgenic plants, extractable RDR enzyme activity was increased and Western blot analysis of RDR extracts revealed a band cross-reacting with an antibody raised against MtRDR1. Expression of MtRDR1 in the transgenic N. benthamiana plants was driven by a constitutive 35S promoter derived from cauliflower mosaic virus, confirmed to be non-responsive to SA. This suggests that the effects of SA on MtRDR1 are exerted at a post-transcriptional level. CONCLUSIONS MtRDR1 inhibits severe symptom development by limiting spread of virus into the growing tips of infected plants. Thus, RDR1 may act in a similar fashion to RDR6. MtRDR1 and SA acted additively to further promote recovery from disease symptoms in MtRDR1-transgenic plants. Thus it is possible that SA promotes MtRDR1 activity and/or stability through post-transcriptional effects.
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Affiliation(s)
- Wing-Sham Lee
- Department of Plant Sciences, University of Cambridge, Downing Street, Cambridge, CB2 3EA, UK.
- Rothamsted Research, Harpenden, Hertfordshire, AL5 2JQ, UK.
| | - Shih-Feng Fu
- Department of Plant Sciences, University of Cambridge, Downing Street, Cambridge, CB2 3EA, UK.
- Department of Biology, National Changhua University of Education, 1 Jin-De Road, Changhua City, 500, Taiwan.
| | - Zheng Li
- Department of Plant Sciences, University of Cambridge, Downing Street, Cambridge, CB2 3EA, UK.
| | - Alex M Murphy
- Department of Plant Sciences, University of Cambridge, Downing Street, Cambridge, CB2 3EA, UK.
| | - Elizabeth A Dobson
- Department of Plant Sciences, University of Cambridge, Downing Street, Cambridge, CB2 3EA, UK.
| | - Laura Garland
- Department of Plant Sciences, University of Cambridge, Downing Street, Cambridge, CB2 3EA, UK.
| | - Srinivasa Rao Chaluvadi
- Plant Biology Division, Samuel Roberts Noble Foundation, Inc, 2510 Sam Noble Parkway, Ardmore, OK, 73401, USA.
| | - Mathew G Lewsey
- Department of Plant Sciences, University of Cambridge, Downing Street, Cambridge, CB2 3EA, UK.
- Centre for AgriBioscience, Department of Animal, Plant and Soil Science, School of Life Science, La Trobe University, Bundoora, Australia.
| | - Richard S Nelson
- Plant Biology Division, Samuel Roberts Noble Foundation, Inc, 2510 Sam Noble Parkway, Ardmore, OK, 73401, USA.
| | - John P Carr
- Department of Plant Sciences, University of Cambridge, Downing Street, Cambridge, CB2 3EA, UK.
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Muthamilselvan T, Lee CW, Cho YH, Wu FC, Hu CC, Liang YC, Lin NS, Hsu YH. A transgenic plant cell-suspension system for expression of epitopes on chimeric Bamboo mosaic virus particles. Plant Biotechnol J 2016; 14:231-9. [PMID: 25879277 DOI: 10.1111/pbi.12377] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/25/2014] [Revised: 03/05/2015] [Accepted: 03/12/2015] [Indexed: 06/04/2023]
Abstract
We describe a novel strategy to produce vaccine antigens using a plant cell-suspension culture system in lieu of the conventional bacterial or animal cell-culture systems. We generated transgenic cell-suspension cultures from Nicotiana benthamiana leaves carrying wild-type or chimeric Bamboo mosaic virus (BaMV) expression constructs encoding the viral protein 1 (VP1) epitope of foot-and-mouth disease virus (FMDV). Antigens accumulated to high levels in BdT38 and BdT19 transgenic cell lines co-expressing silencing suppressor protein P38 or P19. BaMV chimeric virus particles (CVPs) were subsequently purified from the respective cell lines (1.5 and 2.1 mg CVPs/20 g fresh weight of suspended biomass, respectively), and the resulting CVPs displayed VP1 epitope on the surfaces. Guinea pigs vaccinated with purified CVPs produced humoral antibodies. This study represents an important advance in the large-scale production of immunopeptide vaccines in a cost-effective manner using a plant cell-suspension culture system.
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Affiliation(s)
| | - Chin-Wei Lee
- Graduate Institute of Biotechnology, National Chung Hsing University, Taichung, Taiwan
| | - Yu-Hsin Cho
- Graduate Institute of Biotechnology, National Chung Hsing University, Taichung, Taiwan
| | - Feng-Chao Wu
- Graduate Institute of Biotechnology, National Chung Hsing University, Taichung, Taiwan
| | - Chung-Chi Hu
- Graduate Institute of Biotechnology, National Chung Hsing University, Taichung, Taiwan
| | - Yu-Chuan Liang
- Agricultural Biotechnology Research Center, Academia Sinica, Nankang, Taipei, Taiwan
| | - Na-Sheng Lin
- Graduate Institute of Biotechnology, National Chung Hsing University, Taichung, Taiwan
- Institute of Plant and Microbial Biology, Academia Sinica, Nankang, Taipei, Taiwan
| | - Yau-Heiu Hsu
- Graduate Institute of Biotechnology, National Chung Hsing University, Taichung, Taiwan
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26
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Ivanov KI, Eskelin K, Bašić M, De S, Lõhmus A, Varjosalo M, Mäkinen K. Molecular insights into the function of the viral RNA silencing suppressor HCPro. Plant J 2016; 85:30-45. [PMID: 26611351 DOI: 10.1111/tpj.13088] [Citation(s) in RCA: 69] [Impact Index Per Article: 8.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/21/2015] [Revised: 11/13/2015] [Accepted: 11/16/2015] [Indexed: 05/23/2023]
Abstract
Potyviral helper component proteinase (HCPro) is a well-characterized suppressor of antiviral RNA silencing, but its mechanism of action is not yet fully understood. In this study, we used affinity purification coupled with mass spectrometry to identify binding partners of HCPro in potyvirus-infected plant cells. This approach led to identification of various HCPro interactors, including two key enzymes of the methionine cycle, S-adenosyl-L-methionine synthase and S-adenosyl-L-homocysteine hydrolase. This finding, together with the results of enzymatic activity and gene knockdown experiments, suggests a mechanism in which HCPro complexes containing viral and host proteins act to suppress antiviral RNA silencing through local disruption of the methionine cycle. Another group of HCPro interactors identified in this study comprised ribosomal proteins. Immunoaffinity purification of ribosomes demonstrated that HCPro is associated with ribosomes in virus-infected cells. Furthermore, we show that HCPro and ARGONAUTE1 (AGO1), the core component of the RNA-induced silencing complex (RISC), interact with each other and are both associated with ribosomes in planta. These results, together with the fact that AGO1 association with ribosomes is a hallmark of RISC-mediated translational repression, suggest a second mechanism of HCPro action, whereby ribosome-associated multiprotein complexes containing HCPro relieve viral RNA translational repression through interaction with AGO1.
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Affiliation(s)
- Konstantin I Ivanov
- Department of Food and Environmental Sciences, Viikki Plant Science Centre, University of Helsinki, Helsinki, 00014, Finland
| | - Katri Eskelin
- Department of Food and Environmental Sciences, Viikki Plant Science Centre, University of Helsinki, Helsinki, 00014, Finland
| | - Marta Bašić
- Department of Food and Environmental Sciences, Viikki Plant Science Centre, University of Helsinki, Helsinki, 00014, Finland
| | - Swarnalok De
- Department of Food and Environmental Sciences, Viikki Plant Science Centre, University of Helsinki, Helsinki, 00014, Finland
| | - Andres Lõhmus
- Department of Food and Environmental Sciences, Viikki Plant Science Centre, University of Helsinki, Helsinki, 00014, Finland
| | - Markku Varjosalo
- Institute of Biotechnology, University of Helsinki, Helsinki, 00014, Finland
| | - Kristiina Mäkinen
- Department of Food and Environmental Sciences, Viikki Plant Science Centre, University of Helsinki, Helsinki, 00014, Finland
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Zhang X, Zhu Y, Wu H, Guo H. Post-transcriptional gene silencing in plants: a double-edged sword. Sci China Life Sci 2016; 59:271-6. [PMID: 26718356 DOI: 10.1007/s11427-015-4972-7] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/18/2015] [Accepted: 09/08/2015] [Indexed: 01/08/2023]
Abstract
In plants, post-transcriptional gene silencing (PTGS) protects the genome from foreign genes and restricts the expression of certain endogenous genes for proper development. Here, we review the recent progress about how the unwanted PTGS is avoided in plants. As a decision-making step of PTGS, aberrant transcripts from most endogenous coding genes are strictly sorted to the bidirectional RNA decay pathways in cytoplasm but not to the short interference RNA (siRNA)-mediated PTGS, with the exception of a few development-relevant endogenous siRNA-producing genes. We also discuss a finely balanced PTGS threshold model that plants fully take advantage of the power of PTGS without self-harm.
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Saeed M, Briddon RW, Dalakouras A, Krczal G, Wassenegger M. Functional Analysis of Cotton Leaf Curl Kokhran Virus/Cotton Leaf Curl Multan Betasatellite RNA Silencing Suppressors. Biology (Basel) 2015; 4:697-714. [PMID: 26512705 PMCID: PMC4690014 DOI: 10.3390/biology4040697] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/29/2015] [Revised: 10/15/2015] [Accepted: 10/16/2015] [Indexed: 12/13/2022]
Abstract
In South Asia, Cotton leaf curl disease (CLCuD) is caused by a complex of phylogenetically-related begomovirus species and a specific betasatellite, Cotton leaf curl Multan betasatellite (CLCuMuB). The post-transcriptional gene silencing (PTGS) suppression activities of the transcriptional activator protein (TrAP), C4, V2 and βC1 proteins encoded by Cotton leaf curl Kokhran virus (CLCuKoV)/CLCuMuB were assessed in Nicotiana benthamiana. A variable degree of local silencing suppression was observed for each viral protein tested, with V2 protein exhibiting the strongest suppression activity and only the C4 protein preventing the spread of systemic silencing. The CLCuKoV-encoded TrAP, C4, V2 and CLCuMuB-encoded βC1 proteins were expressed in Escherichia coli and purified. TrAP was shown to bind various small and long nucleic acids including single-stranded (ss) and double-stranded (ds) RNA and DNA molecules. C4, V2, and βC1 bound ssDNA and dsDNA with varying affinities. Transgenic expression of C4 under the constitutive 35S Cauliflower mosaic virus promoter and βC1 under a dexamethasone inducible promoter induced severe developmental abnormalities in N. benthamiana. The results indicate that homologous proteins from even quite closely related begomoviruses may differ in their suppressor activity and mechanism of action. The significance of these findings is discussed.
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Affiliation(s)
- Muhammad Saeed
- RLP AgroScience GmbH, AlPlanta-Institute for Plant Research, Breitenweg 71, Neustadt D-67435, Germany.
- National Institute for Biotechnology and Genetic Engineering, Jhang Road, PO Box 577, Faisalabad 38000, Pakistan.
| | - Rob W Briddon
- National Institute for Biotechnology and Genetic Engineering, Jhang Road, PO Box 577, Faisalabad 38000, Pakistan.
| | - Athanasios Dalakouras
- RLP AgroScience GmbH, AlPlanta-Institute for Plant Research, Breitenweg 71, Neustadt D-67435, Germany.
| | - Gabi Krczal
- RLP AgroScience GmbH, AlPlanta-Institute for Plant Research, Breitenweg 71, Neustadt D-67435, Germany.
| | - Michael Wassenegger
- RLP AgroScience GmbH, AlPlanta-Institute for Plant Research, Breitenweg 71, Neustadt D-67435, Germany.
- Centre for Organismal Studies (COS) Heidelberg, University of Heidelberg, Im Neuenheimer Feld 360, Heidelberg D-69120, Germany.
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29
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Wagner A, Bock CT, Fechner H, Kurreck J. Application of modified antisense oligonucleotides and siRNAs as antiviral drugs. Future Med Chem 2015; 7:1637-42. [PMID: 26381598 DOI: 10.4155/fmc.15.114] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/21/2023] Open
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30
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Rajeevkumar S, Anunanthini P, Sathishkumar R. Epigenetic silencing in transgenic plants. Front Plant Sci 2015; 6:693. [PMID: 26442010 PMCID: PMC4564723 DOI: 10.3389/fpls.2015.00693] [Citation(s) in RCA: 80] [Impact Index Per Article: 8.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/14/2015] [Accepted: 08/21/2015] [Indexed: 05/18/2023]
Abstract
Epigenetic silencing is a natural phenomenon in which the expression of genes is regulated through modifications of DNA, RNA, or histone proteins. It is a mechanism for defending host genomes against the effects of transposable elements and viral infection, and acts as a modulator of expression of duplicated gene family members and as a silencer of transgenes. A major breakthrough in understanding the mechanism of epigenetic silencing was the discovery of silencing in transgenic tobacco plants due to the interaction between two homologous promoters. The molecular mechanism of epigenetic mechanism is highly complicated and it is not completely understood yet. Two different molecular routes have been proposed for this, that is, transcriptional gene silencing, which is associated with heavy methylation of promoter regions and blocks the transcription of transgenes, and post-transcriptional gene silencing (PTGS), the basic mechanism is degradation of the cytosolic mRNA of transgenes or endogenous genes. Undesired transgene silencing is of major concern in the transgenic technologies used in crop improvement. A complete understanding of this phenomenon will be very useful for transgenic applications, where silencing of specific genes is required. The current status of epigenetic silencing in transgenic technology is discussed and summarized in this mini-review.
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Affiliation(s)
- Sarma Rajeevkumar
- Molecular Plant Biology and Biotechnology Division, Central Institute of Medicinal and Aromatic Plants Research Centre, BangaloreIndia
| | - Pushpanathan Anunanthini
- Plant Genetic Engineering Laboratory, Department of Biotechnology, Bharathiar University, CoimbatoreIndia
| | - Ramalingam Sathishkumar
- Plant Genetic Engineering Laboratory, Department of Biotechnology, Bharathiar University, CoimbatoreIndia
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Pflieger S, Blanchet S, Meziadi C, Richard MMS, Thareau V, Mary F, Mazoyer C, Geffroy V. The "one-step" Bean pod mottle virus (BPMV)-derived vector is a functional genomics tool for efficient overexpression of heterologous protein, virus-induced gene silencing and genetic mapping of BPMV R-gene in common bean (Phaseolus vulgaris L.). BMC Plant Biol 2014; 14:232. [PMID: 25168520 PMCID: PMC4163167 DOI: 10.1186/s12870-014-0232-4] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/11/2014] [Accepted: 08/20/2014] [Indexed: 05/11/2023]
Abstract
BACKGROUND Over the last two years, considerable advances have been made in common bean (Phaseolus vulgaris L.) genomics, especially with the completion of the genome sequence and the availability of RNAseq data. However, as common bean is recalcitrant to stable genetic transformation, much work remains to be done for the development of functional genomics tools adapted to large-scale studies. RESULTS Here we report the successful implementation of an efficient viral vector system for foreign gene expression, virus-induced gene silencing (VIGS) and genetic mapping of a BPMV resistance gene in common bean, using a "one-step" BPMV vector originally developed in soybean. With the goal of developing this vector for high-throughput VIGS studies in common bean, we optimized the conditions for rub-inoculation of infectious BPMV-derived plasmids in common bean cv. Black Valentine. We then tested the susceptibility to BPMV of six cultivars, and found that only Black Valentine and JaloEEP558 were susceptible to BPMV. We used a BPMV-GFP construct to detect the spatial and temporal infection patterns of BPMV in vegetative and reproductive tissues. VIGS of the PHYTOENE DESATURASE (PvPDS) marker gene was successfully achieved with recombinant BPMV vectors carrying fragments ranging from 132 to 391 bp. Finally, we mapped a gene for resistance to BPMV (R-BPMV) at one end of linkage group 2, in the vicinity of a locus (I locus) previously shown to be involved in virus resistance. CONCLUSIONS The "one-step" BPMV vector system therefore enables rapid and simple functional studies in common bean, and could be suitable for large-scale analyses. In the post-genomic era, these advances are timely for the common bean research community.
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Affiliation(s)
- Stéphanie Pflieger
- />CNRS, Institut de Biologie des Plantes, UMR 8618, Université Paris Sud, Saclay Plant Sciences (SPS), 91405 Orsay, France
- />Univ Paris Diderot, Sorbonne Paris Cité, 75205 Paris, France
| | - Sophie Blanchet
- />CNRS, Institut de Biologie des Plantes, UMR 8618, Université Paris Sud, Saclay Plant Sciences (SPS), 91405 Orsay, France
| | - Chouaib Meziadi
- />CNRS, Institut de Biologie des Plantes, UMR 8618, Université Paris Sud, Saclay Plant Sciences (SPS), 91405 Orsay, France
| | - Manon MS Richard
- />CNRS, Institut de Biologie des Plantes, UMR 8618, Université Paris Sud, Saclay Plant Sciences (SPS), 91405 Orsay, France
| | - Vincent Thareau
- />CNRS, Institut de Biologie des Plantes, UMR 8618, Université Paris Sud, Saclay Plant Sciences (SPS), 91405 Orsay, France
| | - Fanny Mary
- />CNRS, Institut de Biologie des Plantes, UMR 8618, Université Paris Sud, Saclay Plant Sciences (SPS), 91405 Orsay, France
| | - Céline Mazoyer
- />CNRS, Institut de Biologie des Plantes, UMR 8618, Université Paris Sud, Saclay Plant Sciences (SPS), 91405 Orsay, France
| | - Valérie Geffroy
- />CNRS, Institut de Biologie des Plantes, UMR 8618, Université Paris Sud, Saclay Plant Sciences (SPS), 91405 Orsay, France
- />INRA, Unité Mixte de Recherche de Génétique Végétale, Université Paris Sud, IDEEV FR3284, Ferme du Moulon, 91190 Gif-sur-Yvette, France
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Zhao M, San León D, Delgadillo MO, García JA, Simón-Mateo C. Virus-induced gene silencing in transgenic plants: transgene silencing and reactivation associate with two patterns of transgene body methylation. Plant J 2014; 79:440-452. [PMID: 24916614 DOI: 10.1111/tpj.12579] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/25/2014] [Revised: 05/09/2014] [Accepted: 05/21/2014] [Indexed: 06/03/2023]
Abstract
We used bisulfite sequencing to study the methylation of a viral transgene whose expression was silenced upon plum pox virus infection of the transgenic plant and its subsequent recovery as a consequence of so-called virus-induced gene silencing (VIGS). VIGS was associated with a general increase in the accumulation of small RNAs corresponding to the coding region of the viral transgene. After VIGS, the transgene promoter was not methylated and the coding region showed uneven methylation, with the 5' end being mostly unmethylated in the recovered tissue or mainly methylated at CG sites in regenerated silenced plants. The methylation increased towards the 3' end, which showed dense methylation in all three contexts (CG, CHG and CHH). This methylation pattern and the corresponding silenced status were maintained after plant regeneration from recovered silenced tissue and did not spread into the promoter region, but were not inherited in the sexual offspring. Instead, a new pattern of methylation was observed in the progeny plants consisting of disappearance of the CHH methylation, similar CHG methylation at the 3' end, and an overall increase in CG methylation in the 5' end. The latter epigenetic state was inherited over several generations and did not correlate with transgene silencing and hence virus resistance. These results suggest that the widespread CG methylation pattern found in body gene bodies located in euchromatic regions of plant genomes may reflect an older silencing event, and most likely these genes are no longer silenced.
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Affiliation(s)
- Mingmin Zhao
- Centro Nacional de Biotecnología, Consejo Superior de Investigaciones Científicas or (CNB-CSIC), Campus Universidad Autónoma de Madrid, 28049, Madrid, Spain
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Sohn SH, Frost J, Kim YH, Choi SK, Lee Y, Seo MS, Lim SH, Choi Y, Kim KH, Lomonossoff G. Cell-autonomous-like silencing of GFP-partitioned transgenic Nicotiana benthamiana. J Exp Bot 2014; 65:4271-83. [PMID: 24868037 DOI: 10.1093/jxb/eru200] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/03/2023]
Abstract
We previously reported the novel partitioning of regional GFP-silencing on leaves of 35S-GFP transgenic plants, coining the term "partitioned silencing". We set out to delineate the mechanism of partitioned silencing. Here, we report that the partitioned plants were hemizygous for the transgene, possessing two direct-repeat copies of 35S-GFP. The detection of both siRNA expression (21 and 24 nt) and DNA methylation enrichment specifically at silenced regions indicated that both post-transcriptional gene silencing (PTGS) and transcriptional gene silencing (TGS) were involved in the silencing mechanism. Using in vivo agroinfiltration of 35S-GFP/GUS and inoculation of TMV-GFP RNA, we demonstrate that PTGS, not TGS, plays a dominant role in the partitioned silencing, concluding that the underlying mechanism of partitioned silencing is analogous to RNA-directed DNA methylation (RdDM). The initial pattern of partitioned silencing was tightly maintained in a cell-autonomous manner, although partitioned-silenced regions possess a potential for systemic spread. Surprisingly, transcriptome profiling through next-generation sequencing demonstrated that expression levels of most genes involved in the silencing pathway were similar in both GFP-expressing and silenced regions although a diverse set of region-specific transcripts were detected.This suggests that partitioned silencing can be triggered and regulated by genes other than the genes involved in the silencing pathway.
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Affiliation(s)
- Seong-Han Sohn
- National Academy of Agricultural Science (NAAS), Rural Development Administration (RDA), Suwon 441-707, Korea
| | - Jennifer Frost
- College of Natural Resources, University of California, Berkeley CA94720, USA
| | - Yoon-Hee Kim
- National Academy of Agricultural Science (NAAS), Rural Development Administration (RDA), Suwon 441-707, Korea
| | - Seung-Kook Choi
- National Academy of Agricultural Science (NAAS), Rural Development Administration (RDA), Suwon 441-707, Korea
| | - Yi Lee
- College of Agricultural, Life and Environmental Sciences, Chungbuk National University, Cheongju 361-763, Korea
| | - Mi-Suk Seo
- National Academy of Agricultural Science (NAAS), Rural Development Administration (RDA), Suwon 441-707, Korea
| | - Sun-Hyung Lim
- National Academy of Agricultural Science (NAAS), Rural Development Administration (RDA), Suwon 441-707, Korea
| | - Yeonhee Choi
- Department of Biological Sciences, Seoul National University, Seoul 151-747, Korea
| | - Kook-Hyung Kim
- College of Agriculture and Life Sciences (CALS), Seoul National University, Seoul 151-747, Korea
| | - George Lomonossoff
- Department of Biological Chemistry, John Innes Centre (JIC), Colney Lane, Norwich NR4 7UH, UK
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Ramegowda V, Mysore KS, Senthil-Kumar M. Virus-induced gene silencing is a versatile tool for unraveling the functional relevance of multiple abiotic-stress-responsive genes in crop plants. Front Plant Sci 2014; 5:323. [PMID: 25071806 PMCID: PMC4085877 DOI: 10.3389/fpls.2014.00323] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/12/2014] [Accepted: 06/19/2014] [Indexed: 05/03/2023]
Abstract
Virus-induced gene silencing (VIGS) is an effective tool for gene function analysis in plants. Over the last decade, VIGS has been successfully used as both a forward and reverse genetics technique for gene function analysis in various model plants, as well as crop plants. With the increased identification of differentially expressed genes under various abiotic stresses through high-throughput transcript profiling, the application of VIGS is expected to be important in the future for functional characterization of a large number of genes. In the recent past, VIGS was proven to be an elegant tool for functional characterization of genes associated with abiotic stress responses. In this review, we provide an overview of how VIGS is used in different crop species to characterize genes associated with drought-, salt-, oxidative- and nutrient-deficiency-stresses. We describe the examples from studies where abiotic stress related genes are characterized using VIGS. In addition, we describe the major advantages of VIGS over other currently available functional genomics tools. We also summarize the recent improvements, limitations and future prospects of using VIGS as a tool for studying plant responses to abiotic stresses.
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Affiliation(s)
- Venkategowda Ramegowda
- Department of Crop Physiology, University of Agricultural Sciences, GKVKBangalore, India
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35
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Affiliation(s)
- Carlos Fernández-Hernando
- From the Vascular Biology and Therapeutics Program, and Integrative Cell Signalling and Neurobiology of Metabolism Program, Section of Comparative Medicine, Yale University School of Medicine, New Haven, CT.
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Chen ZH, Jia FF, Hu JQ, Pang JL, Xu L, Wang LL. Virus-induced gene silencing of PEAM4 affects floral morphology by altering the expression pattern of PsSOC1a and PsPVP in pea. J Plant Physiol 2014; 171:148-53. [PMID: 24331430 DOI: 10.1016/j.jplph.2013.08.010] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/21/2013] [Revised: 06/29/2013] [Accepted: 08/15/2013] [Indexed: 06/03/2023]
Abstract
pea-MADS4 (PEAM4) regulates floral morphology in Pisum sativum L., however, its molecular mechanisms still remain unclear. Virus-induced gene silencing (VIGS) is a recently developed reverse genetic approach that facilities an easier and more rapid study of gene functions. In this study, the PEAM4 gene was effectively silenced by VIGS using a pea early browning virus (PEBV) in wild type pea JI992. The infected plants showed abnormal phenotypes, as the floral organs, especially the sepals and petals changed in both size and shape, which made the corolla less closed. The petals changed in morphology and internal symmetry with, the stamens reduced and carpel dehisced. Larger sepals and longer tendrils with small cauline leaves appeared, with some sepals turning into bracts, and secondary inflorescences with fused floral organs were formed, indicating a flower-to-inflorescence change. The infected plants also displayed a delayed and prolonged flowering time. The PEAM4-VIGS plants with altered floral morphology were similar to the pim (proliferating inflorescence meristem) mutant and also mimicked the phenotypes of ap1 mutants in Arabidopsis. The expression pattern of the homologous genes PsSOC1a and PsSVP, which were involved in flowering time and florescence morphological control downstream of PEAM4, were analyzed by real-time RT-PCR and mRNA in situ hybridization. PsSOC1a and PsSVP were ectopically expressed and enhanced in the floral meristems from PEAM4-silenced plants. Our data suggests that PEAM4 may have a similar molecular mechanism as AtAP1, which inhibits the expression of PsSOC1a and PsSVP in the floral meristem from the early stages of flower development. As such, in this way PEAM4 plays a crucial role in maintaining floral organ identity and flower development in pea.
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Affiliation(s)
- Zhe-Hao Chen
- College of Life and Environmental Sciences, Hangzhou Normal University, Hangzhou 310036, Zhejiang, China
| | - Fei-Fei Jia
- College of Life and Environmental Sciences, Hangzhou Normal University, Hangzhou 310036, Zhejiang, China
| | - Jiang-Qin Hu
- College of Life and Environmental Sciences, Hangzhou Normal University, Hangzhou 310036, Zhejiang, China
| | - Ji-Liang Pang
- College of Life and Environmental Sciences, Hangzhou Normal University, Hangzhou 310036, Zhejiang, China
| | - Lei Xu
- College of Life and Environmental Sciences, Hangzhou Normal University, Hangzhou 310036, Zhejiang, China
| | - Li-Lin Wang
- College of Life and Environmental Sciences, Hangzhou Normal University, Hangzhou 310036, Zhejiang, China.
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Abstract
With the discovery of post-transcriptional silencing, the idea of targeted therapies became an approachable goal. The widespread involvement of microRNAs (miRNAs) was thought to be the magic bullet against multiple diseases. However, several hurdles, ranging from targeted delivery to side effects still have to be resolved. In this review, we discuss recent progress on delivery as well as current applications for miRNAs as therapeutic agents.
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Dehury B, Panda D, Sahu J, Sahu M, Sarma K, Barooah M, Sen P, Modi MK. In silico identification and characterization of conserved miRNAs and their target genes in sweet potato (Ipomoea batatas L.) expressed sequence tags (ESTs). Plant Signal Behav 2013; 8:e26543. [PMID: 24067297 PMCID: PMC4091516 DOI: 10.4161/psb.26543] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/03/2023]
Abstract
The endogenous small non-coding micro RNAs (miRNAs), which are typically ~21-24 nt nucleotides, play a crucial role in regulating the intrinsic normal growth of cells and development of the plants as well as in maintaining the integrity of genomes. These small non-coding RNAs function as the universal specificity factors in post-transcriptional gene silencing. Discovering miRNAs, identifying their targets, and further inferring miRNA functions is a routine process to understand normal biological processes of miRNAs and their roles in the development of plants. Comparative genomics based approach using expressed sequence tags (EST) and genome survey sequences (GSS) offer a cost-effective platform for identification and characterization of miRNAs and their target genes in plants. Despite the fact that sweet potato (Ipomoea batatas L.) is an important staple food source for poor small farmers throughout the world, the role of miRNA in various developmental processes remains largely unknown. In this paper, we report the computational identification of miRNAs and their target genes in sweet potato from their ESTs. Using comparative genomics-based approach, 8 potential miRNA candidates belonging to miR168, miR2911, and miR156 families were identified from 23 406 ESTs in sweet potato. A total of 42 target genes were predicted and their probable functions were illustrated. Most of the newly identified miRNAs target transcription factors as well as genes involved in plant growth and development, signal transduction, metabolism, defense, and stress response. The identification of miRNAs and their targets is expected to accelerate the pace of miRNA discovery, leading to an improved understanding of the role of miRNA in development and physiology of sweet potato, as well as stress response.
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Abstract
MicroRNAs play central roles in controlling gene expression in human cells. Sequencing data show that many miRNAs are produced at different levels and as multiple isoforms that can vary in length at their 5' or 3' ends, but the biogenesis and functional significance of these RNAs are largely unknown. We show here that the human trans-activation response (TAR) RNA binding protein (TRBP), a known molecular partner of the miRNA processing enzyme Dicer, changes the rates of pre-miRNA cleavage in an RNA-structure-specific manner. Furthermore, TRBP can trigger the generation of iso-miRNAs (isomiRs) that are longer than the canonical sequence by one nucleotide. We show that this change in miRNA processing site can alter guide strand selection, resulting in preferential silencing of a different mRNA target. These results implicate TRBP as a key regulator of miRNA processing and targeting in humans.
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Affiliation(s)
| | - Jennifer A. Doudna
- Department of Molecular and Cell Biology
- Howard Hughes Medical Institute and
- Department of Chemistry, University of California, Berkeley, Berkeley, California 94720, USA
- Physical Biosciences Division, Lawrence Berkeley National Laboratory, Berkeley, California 94720, USA
- Corresponding authorE-mail
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Kasai M, Kanazawa A. RNA silencing as a tool to uncover gene function and engineer novel traits in soybean. Breed Sci 2012; 61:468-79. [PMID: 23136487 PMCID: PMC3406797 DOI: 10.1270/jsbbs.61.468] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/04/2011] [Accepted: 09/14/2011] [Indexed: 05/10/2023]
Abstract
RNA silencing refers collectively to diverse RNA-mediated pathways of nucleotide-sequence-specific inhibition of gene expression. It has been used to analyze gene function and engineer novel traits in various organisms. Here, we review the application of RNA silencing in soybean. To produce soybean lines, in which a particular gene is stably silenced, researchers have frequently used a transgene that transcribes inverted repeats of a target gene segment. Suppression of gene expression in developing soybean embryos has been one of the main focuses of metabolic engineering using transgene-induced silencing. Plants that have enhanced resistance against diseases caused by viruses or cyst nematode have also been produced. Meanwhile, Agrobacterium rhizogenes-mediated transformation has been used to induce RNA silencing in roots, which enabled analysis of the roles of gene products in nodulation or disease resistance. RNA silencing has also been induced using viral vectors, which is particularly useful for gene function analysis. So far, three viral vectors for virus-induced gene silencing have been developed for soybean. One of the features of the soybean genome is the presence of a large number of duplicated genes. Potential use of RNA silencing technology in combination with forward genetic approaches for analyzing duplicated genes is discussed.
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Affiliation(s)
- Megumi Kasai
- Research Faculty of Agriculture, Hokkaido University, Sapporo, Hokkaido 060-8589, Japan
| | - Akira Kanazawa
- Research Faculty of Agriculture, Hokkaido University, Sapporo, Hokkaido 060-8589, Japan
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Wang H, Zhang X, Liu J, Kiba T, Woo J, Ojo T, Hafner M, Tuschl T, Chua NH, Wang XJ. Deep sequencing of small RNAs specifically associated with Arabidopsis AGO1 and AGO4 uncovers new AGO functions. Plant J 2011; 67:292-304. [PMID: 21457371 PMCID: PMC3135789 DOI: 10.1111/j.1365-313x.2011.04594.x] [Citation(s) in RCA: 101] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/28/2011] [Revised: 03/21/2011] [Accepted: 03/28/2011] [Indexed: 05/18/2023]
Abstract
As important components of small RNA (smRNA) pathways, Argonaute (AGO) proteins mediate the interaction of incorporated smRNAs with their targets. Arabidopsis contains 10 AGO proteins with specialized or redundant functions. Among them, AGO1 mainly acts in microRNA (miRNA) and small-interfering RNA (siRNA) pathways for post-transcriptional gene silencing (PTGS), whereas AGO4 regulates transcriptional gene silencing (TGS) via endogenous 24-nucleotide (nt) smRNAs. To fully characterize smRNAs associated with AGO1 and AGO4, we developed a two-step protocol to purify AGO/smRNA complexes from flowers, leaves, roots and seedlings with enhanced purity, and sequenced the smRNAs by Illumina technology. Besides recovering most previously annotated smRNAs, we also identified some additional miRNAs, phased smRNA clusters and small-interfering RNAs derived from the overlapping region of natural antisense transcript pairs (NAT) (nat-siRNAs). We also identified a smRNA distribution feature on miRNA precursors which may help to identify authentic miRNAs. Organ-specific sequencing provided digital expression profiles of all obtained smRNAs, especially miRNAs. The presence and conservation of collateral miRNAs on known miRNA precursors were also investigated. Intriguingly, about 30% of AGO1-associated smRNAs were 24-nt long and unrelated to the 21-nt species. Further analysis showed that DNA-dependent RNA polymerase IV (Pol IV)-dependent smRNAs were mainly 24 nt and associated with AGO4, whereas the majority of the potential Pol V-dependent ones were 21-nt smRNAs and bound to AGO1, suggesting the potential involvement of AGO1 in Pol V-related pathways.
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Affiliation(s)
- Huan Wang
- Laboratory of Plant Molecular Biology, The Rockefeller UniversityNew York, NY 10065, USA
- Graduate University of the Chinese Academy of SciencesBeijing, 100101, China
| | - Xiuren Zhang
- Laboratory of Plant Molecular Biology, The Rockefeller UniversityNew York, NY 10065, USA
- Department of Biochemistry and Biophysics, Institute for Plant Genomics and Biotechnology, Norman Borlaug Center 112A, 2123 TAMU, Texas A&M UniversityCollege Station, TX 77843, USA
| | - Jun Liu
- Laboratory of Plant Molecular Biology, The Rockefeller UniversityNew York, NY 10065, USA
| | - Takatoshi Kiba
- Laboratory of Plant Molecular Biology, The Rockefeller UniversityNew York, NY 10065, USA
- RIKEN Plant Science CenterSuehiro 1-7-22, Tsurumi, Yokohama 230-0045, Japan
| | - Jongchan Woo
- Laboratory of Plant Molecular Biology, The Rockefeller UniversityNew York, NY 10065, USA
| | - Tolulope Ojo
- Howard Hughes Medical Institute, Laboratory of RNA Molecular Biology, The Rockefeller University1230 York Avenue, New York, NY 10065, USA
| | - Markus Hafner
- Howard Hughes Medical Institute, Laboratory of RNA Molecular Biology, The Rockefeller University1230 York Avenue, New York, NY 10065, USA
| | - Thomas Tuschl
- Howard Hughes Medical Institute, Laboratory of RNA Molecular Biology, The Rockefeller University1230 York Avenue, New York, NY 10065, USA
| | - Nam-Hai Chua
- Laboratory of Plant Molecular Biology, The Rockefeller UniversityNew York, NY 10065, USA
- *For correspondence (fax +212 327 8327; e-mail or fax +86 10 64873428; e-mail )
| | - Xiu-Jie Wang
- State Key Laboratory of Plant Genomics, Institute of Genetics and Developmental Biology, Chinese Academy of SciencesBeijing, 100101, China
- *For correspondence (fax +212 327 8327; e-mail or fax +86 10 64873428; e-mail )
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Borges F, Pereira PA, Slotkin RK, Martienssen RA, Becker JD. MicroRNA activity in the Arabidopsis male germline. J Exp Bot 2011; 62:1611-20. [PMID: 21357774 PMCID: PMC5536363 DOI: 10.1093/jxb/erq452] [Citation(s) in RCA: 102] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/15/2010] [Revised: 12/13/2010] [Accepted: 12/15/2010] [Indexed: 05/19/2023]
Abstract
Most of the core proteins involved in the microRNA (miRNA) pathway in plants have been identified, and almost simultaneously hundreds of miRNA sequences processed in the Arabidopsis sporophyte have been discovered by exploiting next-generation sequencing technologies. However, there is very limited understanding about potentially distinct mechanisms of post-transcriptional regulation between different cell lineages. In this review the focus is on the Arabidopsis male gametophyte (pollen), where the germline differentiates after meiosis giving rise to the male gametes. Based on comparative analysis of miRNAs identified in sperm cells by in-depth sequencing, their possible functions during germ cell specification and beyond fertilization are discussed. In addition, 25 potentially novel miRNAs processed in sperm cells and pollen were identified, as well as enriched variations in the sequence length of known miRNAs, which might indicate subfunctionalization by association with a putative germline-specific Argonaute complex. ARGONAUTE 5 (AGO5), by close homology to AGO1 and localizing preferentially to the sperm cell cytoplasm in mature pollen, may be part of such a complex.
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Wege S, Scholz A, Gleissberg S, Becker A. Highly efficient virus-induced gene silencing (VIGS) in California poppy (Eschscholzia californica): an evaluation of VIGS as a strategy to obtain functional data from non-model plants. Ann Bot 2007; 100:641-9. [PMID: 17616562 PMCID: PMC2533598 DOI: 10.1093/aob/mcm118] [Citation(s) in RCA: 78] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/08/2007] [Accepted: 05/10/2007] [Indexed: 05/16/2023]
Abstract
BACKGROUND AND AIMS Eschscholzia californica (California poppy) is an emerging model plant for 'evo-devo' studies from the basal eudicot clade of Papaveraceae. California poppy has a relatively small genome, a short life cycle and, most importantly, it is amenable for transformation. However, since this transformation protocol is time consuming, virus-induced gene silencing (VIGS) was evaluated as a fast method to obtain functional data for California poppy genes. METHODS Commercially available California poppy plants were infiltrated with Agrobacterium tumefaciens carrying the tobacco rattle virus plasmids pTRV1 and pTRV2. pTRV2 contained part of the eschscholzia Phytoene Desaturase (EcPDS) gene whose loss of function results in photobleaching of the green parts of the plant and in a lack of floral coloration. The degree and duration of these symptoms was evaluated for vegetative rosettes and plants in flower. KEY RESULTS It is shown that VIGS is able to effectively down-regulate the EcPDS gene in eschscholzia. Various degrees of silencing were observed starting <2 weeks after infiltration with Agrobacterium tumefaciens in 92 % of the plants. Tissue with silencing symptoms also showed complete or strong reduction of EcPDS transcripts. Strong silencing resulted in almost completely white petals, fruits, shoots and leaves. Plants with a strong degree of silencing will eventually die off; however, others are able to produce EcPDS gene product even after a strong initial silencing and will recover. Silencing was found to be not always systemic, but was often restricted to certain organs or parts of organs. CONCLUSIONS VIGS is an effective, fast and transient method to down-regulate gene expression in eschscholzia. It serves well to detect prominent phenotypes which may become obvious even if some target gene transcript remains in the plant tissue. However, subtle phenotypes will be more difficult to detect, as extremely strong silencing effects occur in <10 % of all flowers from infected plants.
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Affiliation(s)
- Stefanie Wege
- Evolutionary Developmental Genetics Group, University of Bremen, Leobener Str., UFT, D-28139 Bremen, Germany
| | - Andrea Scholz
- Institut für Spezielle Botanik, Johannes-Gutenberg-Universität Mainz, Bentzelweg 9a, D-55099 Mainz, Germany
| | - Stefan Gleissberg
- Institut für Spezielle Botanik, Johannes-Gutenberg-Universität Mainz, Bentzelweg 9a, D-55099 Mainz, Germany
| | - Annette Becker
- Evolutionary Developmental Genetics Group, University of Bremen, Leobener Str., UFT, D-28139 Bremen, Germany
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Davuluri GR, van Tuinen A, Mustilli AC, Manfredonia A, Newman R, Burgess D, Brummell DA, King SR, Palys J, Uhlig J, Pennings HMJ, Bowler C. Manipulation of DET1 expression in tomato results in photomorphogenic phenotypes caused by post-transcriptional gene silencing. Plant J 2004; 40:344-54. [PMID: 15469492 PMCID: PMC3855349 DOI: 10.1111/j.1365-313x.2004.02218.x] [Citation(s) in RCA: 31] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/22/2023]
Abstract
The tomato HIGH PIGMENT-2 gene encodes an orthologue of the Arabidopsis nuclear protein DE-ETIOLATED 1 (DET1). From genetic analyses it has been proposed that DET1 is a negative regulator of light signal transduction, and recent results indicate that it may control light-regulated gene expression at the level of chromatin remodelling. To gain further understanding about the function of DET1 during plant development, we generated a range of overexpression constructs and introduced them into tomato. Unexpectedly, we only observed phenotypes characteristic of DET1 inactivation, i.e. hyper-responsiveness to light. Molecular analysis indicated in all cases that these phenotypes were a result of suppression of endogenous DET1 expression, due to post-transcriptional gene silencing. DET1 silencing was often lethal when it occurred at relatively early stages of plant development, whereas light hyper-responsive phenotypes were obtained when silencing occurred later on. The appearance of phenotypes correlated with the generation of siRNAs but not DNA hypermethylation, and was most efficient when using constructs with mutations in the DET1 coding sequence or with constructs containing only the 3'-terminal portion of the gene. These results indicate an important function for DET1 throughout plant development and demonstrate that silencing of DET1 in fruits results in increased carotenoids, which may have biotechnological potential.
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Affiliation(s)
- Ganga Rao Davuluri
- Laboratory of Molecular Plant Biology, Stazione Zoologica, Villa Comunale, I-80121 Naples, Italy
| | - Ageeth van Tuinen
- Laboratory of Molecular Plant Biology, Stazione Zoologica, Villa Comunale, I-80121 Naples, Italy
| | - Anna Chiara Mustilli
- Laboratory of Molecular Plant Biology, Stazione Zoologica, Villa Comunale, I-80121 Naples, Italy
| | - Alessandro Manfredonia
- Laboratory of Molecular Plant Biology, Stazione Zoologica, Villa Comunale, I-80121 Naples, Italy
| | - Robert Newman
- DNA Plant Technology, 6701 San Pablo Avenue, Oakland, CA 94608, USA
| | - Diane Burgess
- DNA Plant Technology, 6701 San Pablo Avenue, Oakland, CA 94608, USA
| | | | - Stephen R. King
- Seminis Vegetable Seeds, Inc., 37437 State Highway 16, Woodland, CA 95695, USA
| | - Joe Palys
- Seminis Vegetable Seeds, Inc., 37437 State Highway 16, Woodland, CA 95695, USA
| | - John Uhlig
- Seminis Vegetable Seeds, Inc., 37437 State Highway 16, Woodland, CA 95695, USA
| | - Henk M. J. Pennings
- Seminis Vegetable Seeds, Inc., 37437 State Highway 16, Woodland, CA 95695, USA
| | - Chris Bowler
- Laboratory of Molecular Plant Biology, Stazione Zoologica, Villa Comunale, I-80121 Naples, Italy
- CNRS/ENS FRE2433, Organismes Photosynthétiques et Environnement, Département de Biologie, Ecole Normale Supérieure, 46 Rue d'Ulm, 75230 Paris Cedex 05, France
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45
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Fermin G, Inglessis V, Garboza C, Rangel S, Dagert M, Gonsalves D. Engineered Resistance Against Papaya ringspot virus in Venezuelan Transgenic Papayas. Plant Dis 2004; 88:516-522. [PMID: 30812656 DOI: 10.1094/pdis.2004.88.5.516] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/09/2023]
Abstract
Local varieties of papaya grown in the Andean foothills of Mérida, Venezuela, were transformed independently with the coat protein (CP) gene from two different geographical Papaya ringspot virus (PRSV) isolates, designated VE and LA, via Agrobacterium tumefaciens. The CP genes of both PRSV isolates show 92 and 96% nucleotide and amino acid sequence similarity, respectively. Four PRSV-resistant R0 plants were intercrossed or selfed, and the progenies were tested for resistance against the homologous isolates VE and LA, and the heterologous isolates HA (Hawaii) and TH (Thailand) in greenhouse conditions. Resistance was affected by sequence similarity between the transgenes and the challenge viruses: resistance values were higher for plants challenged with the homologous isolates (92 to 100% similarity) than with the Hawaiian (94% similarity) and, lastly, Thailand isolates (88 to 89% similarity). Our results show that PRSV CP gene effectively protects local varieties of papaya against homologous and heterologous isolates of PRSV.
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Affiliation(s)
- Gustavo Fermin
- Department of Biology, Universidad de Los Andes, Mérida, Venezuela
| | | | - Cesar Garboza
- Department of Biology, Universidad de Los Andes, Mérida, Venezuela
| | - Sairo Rangel
- Department of Biology, Universidad de Los Andes, Mérida, Venezuela
| | - Manuel Dagert
- Department of Biology, Universidad de Los Andes, Mérida, Venezuela
| | - Dennis Gonsalves
- USDA - Pacific West Area, Pacific Basin Agricultural Research Center, Hilo, HI 96720
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46
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Abstract
• The association of viral-induced gene silencing (VIGS) elicited by a DNA virus with DNA methylation of the silenced transgene was studied. • 35S-Green fluorescent protein (GFP) transgenic Nicotiana benthamiana were treated with an inhibitor of DNA methylation, 5-azacytidine (5-Aza-C), and VIGS of the transgene was observed upon inoculation with tomato golden mosaic virus carrying the GFP coding sequence. • The onset of VIGS of the 35S-GFP transgene occurred 14-16 d after inoculation in both control and 5-Aza-C-treated plants. At this stage, the silencing was observed in localized regions. Silencing was uniform by 30 d after inoculation in plants that had methylated GFP-DNA, whereas plants that continued to display the same phenotype as seen at 14-15 d after inoculation had hypomethylated GFP-DNA. Viral expression of GFP persisted in pockets throughout the life of infected plants. • This is the first demonstration of a correlation between post transcriptional gene silencing induced by a DNA virus, and transgene methylation. The results suggest that, while DNA methylation is not necessary for the initiation of silencing, the progression of silencing is affected by inhibition of DNA methylation.
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Affiliation(s)
- Michele K Rodman
- BCS & E, Central R & D, DuPont Experimental Station, Wilmington, DE 19880, USA
| | - Narendra S Yadav
- BCS & E, Central R & D, DuPont Experimental Station, Wilmington, DE 19880, USA
| | - Nancy N Artus
- Biology Department, West Chester University, West Chester, PA 19383, USA
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47
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Abstract
Double-stranded RNA (dsRNA) directs gene-specific, post-transcriptional silencing in many organisms, including vertebrates, and has provided a new tool for studying gene function. The biochemical mechanisms underlying this dsRNA interference (RNAi) are unknown. Here we report the development of a cell-free system from syncytial blastoderm Drosophila embryos that recapitulates many of the features of RNAi. The interference observed in this reaction is sequence specific, is promoted by dsRNA but not single-stranded RNA, functions by specific mRNA degradation, and requires a minimum length of dsRNA. Furthermore, preincubation of dsRNA potentiates its activity. These results demonstrate that RNAi can be mediated by sequence-specific processes in soluble reactions.
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Affiliation(s)
- T Tuschl
- The Whitehead Institute for Biomedical Research, Cambridge, Massachusetts 02142, USA.
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