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Zhao X, Gao Q, Wang H, Yue J, An D, Li B, Yan F, Carmen SM, Zhao Y, Zhou H, Zhao M. syn-tasiRnas targeting the coat protein of potato virus Y confer antiviral resistance in Nicotiana benthamiana. PLANT SIGNALING & BEHAVIOR 2024; 19:2358270. [PMID: 38796845 PMCID: PMC11135832 DOI: 10.1080/15592324.2024.2358270] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/31/2024] [Accepted: 05/10/2024] [Indexed: 05/29/2024]
Abstract
Trans-acting small interfering RNAs (tasiRNAs) are 21-nt phased (phased siRNAs) resulting from successive DCL-catalyzed processing from the end of a double-stranded RNA substrate originating from the RDR of an AGO-catalyzed cleaved RNA at a micro RNA target site. Plant tasiRNAs have been synthesized to produce synthetic tasiRNAs (syn-tasiRNAs) targeting viral RNAs that confer viral resistance. In this study, we engineered syn-tasiRNAs to target potato virus Y (PVY) infection by replacing five native siRNAs of TAS1c with 210-bp fragments from the coat protein (CP) region of the PVY genome. The results showed that the transient expression of syn-tasiR-CPpvy2 in Nicotiana benthamiana (N. benthamiana) plants conferred antiviral resistance, supported by the absence of PVY infection symptoms and viral accumulation. This indicated that syn-tasiR-CPpvy2 successfully targeted and silenced the PVY CP gene, effectively inhibiting viral infection. syn-tasiR-CPpvy1 displayed attenuated symptoms and decreased viral accumulation in these plants However, severe symptoms of PVY infection and a similar amount of viral accumulation as the control were observed in plants expressing syn-tasiR-CPpvy3. syn-tasiR-CPpvy/pvx, which targets both PVY and potato virus X (PVX), was engineered using a single precursor. After the transient expression of syn-tasiR-CPpvy/pvx3 and syn-tasiR-CPpvy/pvx5 in N. benthamiana, the plants were resistant to both PVY and PVX. These results suggested that engineered syn-tasiRNAs could not only specifically induce antiviral resistance against one target virus but could also be designed for multi-targeted silencing of different viruses, thereby preventing complex virus infection in plants.
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Affiliation(s)
- Xingyue Zhao
- College of Horticulture and Plant Protection, Inner Mongolia Agricultural University, Hohhot, China
| | - Qian Gao
- College of Horticulture and Plant Protection, Inner Mongolia Agricultural University, Hohhot, China
| | - Haijuan Wang
- College of Horticulture and Plant Protection, Inner Mongolia Agricultural University, Hohhot, China
| | - Jianying Yue
- College of Horticulture and Plant Protection, Inner Mongolia Agricultural University, Hohhot, China
| | - Derong An
- College of Plant Protection, Northwest A&F University, Yangling, China
| | - Bin Li
- Department of Tabacco Production, Sichuan Province Company of Tobacco Corporation in China, Chengdu, China
| | - Fangfang Yan
- Panzhihua City company of Sichuan province company of Tobacco Corporation in China, Panzhihua city, Sichuan provience, China
| | | | - Yuanzheng Zhao
- Department of Plant Protection, Inner Mongolia Academy of Agricultural and Animal Husbandry Sciences, Hohhot, China
| | - Hongyou Zhou
- College of Horticulture and Plant Protection, Inner Mongolia Agricultural University, Hohhot, China
| | - Mingmin Zhao
- College of Horticulture and Plant Protection, Inner Mongolia Agricultural University, Hohhot, China
- Department of Plant protection, Key Laboratory of the Development and Resource Utilization of Biological Pesticide in Inner Mongolia, Hohhot, China
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Cisneros AE, Martín-García T, Primc A, Kuziuta W, Sánchez-Vicente J, Aragonés V, Daròs JA, Carbonell A. Transgene-free, virus-based gene silencing in plants by artificial microRNAs derived from minimal precursors. Nucleic Acids Res 2023; 51:10719-10736. [PMID: 37713607 PMCID: PMC10602918 DOI: 10.1093/nar/gkad747] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2023] [Revised: 08/24/2023] [Accepted: 09/01/2023] [Indexed: 09/17/2023] Open
Abstract
Artificial microRNAs (amiRNAs) are highly specific, 21-nucleotide (nt) small RNAs designed to silence target transcripts. In plants, their application as biotechnological tools for functional genomics or crop improvement is limited by the need of transgenically expressing long primary miRNA (pri-miRNA) precursors to produce the amiRNAs in vivo. Here, we analyzed the minimal structural and sequence requirements for producing effective amiRNAs from the widely used, 521-nt long AtMIR390a pri-miRNA from Arabidopsis thaliana. We functionally screened in Nicotiana benthamiana a large collection of constructs transiently expressing amiRNAs against endogenous genes and from artificially shortened MIR390-based precursors and concluded that highly effective and accurately processed amiRNAs can be produced from a chimeric precursor of only 89 nt. This minimal precursor was further validated in A. thaliana transgenic plants expressing amiRNAs against endogenous genes. Remarkably, minimal but not full-length precursors produce authentic amiRNAs and induce widespread gene silencing in N. benthamiana when expressed from an RNA virus, which can be applied into leaves by spraying infectious crude extracts. Our results reveal that the length of amiRNA precursors can be shortened without affecting silencing efficacy, and that viral vectors including minimal amiRNA precursors can be applied in a transgene-free manner to induce whole-plant gene silencing.
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Affiliation(s)
- Adriana E Cisneros
- Instituto de Biología Molecular y Celular de Plantas (IBMCP), CSIC-Universitat Politècnica de València, Av. de los Naranjos s/n, 46022 Valencia, Spain
| | - Tamara Martín-García
- Instituto de Biología Molecular y Celular de Plantas (IBMCP), CSIC-Universitat Politècnica de València, Av. de los Naranjos s/n, 46022 Valencia, Spain
| | - Anamarija Primc
- Instituto de Biología Molecular y Celular de Plantas (IBMCP), CSIC-Universitat Politècnica de València, Av. de los Naranjos s/n, 46022 Valencia, Spain
| | - Wojtek Kuziuta
- Instituto de Biología Molecular y Celular de Plantas (IBMCP), CSIC-Universitat Politècnica de València, Av. de los Naranjos s/n, 46022 Valencia, Spain
| | - Javier Sánchez-Vicente
- Instituto de Biología Molecular y Celular de Plantas (IBMCP), CSIC-Universitat Politècnica de València, Av. de los Naranjos s/n, 46022 Valencia, Spain
| | - Verónica Aragonés
- Instituto de Biología Molecular y Celular de Plantas (IBMCP), CSIC-Universitat Politècnica de València, Av. de los Naranjos s/n, 46022 Valencia, Spain
| | - José-Antonio Daròs
- Instituto de Biología Molecular y Celular de Plantas (IBMCP), CSIC-Universitat Politècnica de València, Av. de los Naranjos s/n, 46022 Valencia, Spain
| | - Alberto Carbonell
- Instituto de Biología Molecular y Celular de Plantas (IBMCP), CSIC-Universitat Politècnica de València, Av. de los Naranjos s/n, 46022 Valencia, Spain
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Cisneros AE, de la Torre‐Montaña A, Carbonell A. Systemic silencing of an endogenous plant gene by two classes of mobile 21-nucleotide artificial small RNAs. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2022; 110:1166-1181. [PMID: 35277899 PMCID: PMC9310713 DOI: 10.1111/tpj.15730] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 12/07/2021] [Revised: 03/02/2022] [Accepted: 03/03/2022] [Indexed: 06/14/2023]
Abstract
Artificial small RNAs (art-sRNAs) are 21-nucleotide small RNAs (sRNAs) computationally designed to silence plant genes or pathogenic RNAs with high efficacy and specificity. They are typically produced in transgenic plants to induce silencing at the whole-organism level, although their expression in selected tissues for inactivating genes in distal tissues has not been reported. Here, art-sRNAs designed against the magnesium chelatase subunit CHLI-encoding SULFUR gene (NbSu) were agroinfiltrated in Nicotiana benthamiana leaves, and the induction of local and systemic silencing was analyzed phenotypically by monitoring the appearance of the characteristic bleached phenotype, as well as molecularly by analyzing art-sRNA processing, accumulation and targeting activity and efficacy. We found that the two classes of art-sRNAs, artificial microRNAs (amiRNAs) and synthetic trans-acting small interfering RNAs (syn-tasiRNAs), are able to induce systemic silencing of NbSu, which requires high art-sRNA expression in the vicinity of the leaf petiole but is independent on the production of secondary sRNAs from NbSu mRNAs. Moreover, we revealed that 21-nucleotide amiRNA and syn-tasiRNA duplexes, and not their precursors, are the molecules moving between cells and through the phloem to systemically silence NbSu in upper leaves. In sum, our results indicate that 21-nucleotide art-sRNAs can move throughout the plant to silence plant genes in tissues different from where they are produced. This highlights the biotechnological potential of art-sRNAs, which might be applied locally for triggering whole-plant and highly specific silencing to regulate gene expression or induce resistance against pathogenic RNAs in next-generation crops. The present study demonstrates that artificial small RNAs, such as artificial microRNAs and synthetic trans-acting small interfering RNAs, can move long distances in plants as 21-nucleotide duplexes, specifically silencing endogenous genes in tissues different from where they are applied. This highlights the biotechnological potential of artificial small RNAs, which might be applied locally for triggering whole-plant, highly specific silencing to regulate gene expression or induce resistance against pathogenic RNAs in next-generation crops.
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Affiliation(s)
- Adriana E. Cisneros
- Instituto de Biología Molecular y Celular de Plantas (Consejo Superior de Investigaciones Científicas – Universitat Politècnica de València)46022ValenciaSpain
| | - Ainhoa de la Torre‐Montaña
- Instituto de Biología Molecular y Celular de Plantas (Consejo Superior de Investigaciones Científicas – Universitat Politècnica de València)46022ValenciaSpain
| | - Alberto Carbonell
- Instituto de Biología Molecular y Celular de Plantas (Consejo Superior de Investigaciones Científicas – Universitat Politècnica de València)46022ValenciaSpain
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Singh RK, Prasad A, Maurya J, Prasad M. Regulation of small RNA-mediated high temperature stress responses in crop plants. PLANT CELL REPORTS 2022; 41:765-773. [PMID: 34228188 DOI: 10.1007/s00299-021-02745-x] [Citation(s) in RCA: 15] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/14/2021] [Accepted: 06/24/2021] [Indexed: 05/20/2023]
Abstract
Small RNAs have emerged as key players of gene expression regulation. Several lines of evidences highlight their role in modulating high temperature stress responsiveness in plants. Throughout their life cycle, plants have to regulate their gene expression at various developmental phases, physiological changes, and in response to biotic or environmental stress. High temperature is one the most common abiotic stress for crop plants, that results in impaired morphology, physiology, and yield. However, plants have certain mechanisms that enable them to withstand such conditions by modulating the expression of stress-related genes. Small RNA (sRNA)-regulated gene expression is one such mechanism which is ubiquitous in all eukaryotes. The sRNAs mainly include micro RNAs (miRNAs) and small interfering RNAs (siRNAs). They are primarily associated with the gene silencing either through translation inhibition, mRNA degradation, or DNA methylation. During high temperature stress the increased or decreased level of miRNAs altered the protein accumulation of target transcripts and, therefore, regulate stress responses. Several reports are available in plants which are genetically engineered through expressing artificial miRNAs resulted in thermotolerance. sRNAs have also been reported to bring the epigenetic changes on chromatin region through RNA-dependent DNA methylation (RdDM). The present article draws a brief illustration of sRNA origin, their functional mechanisms, role in high temperature stress, and possible application for developing stress tolerant crop plants.
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Affiliation(s)
- Roshan Kumar Singh
- National Institute of Plant Genome Research, Aruna Asaf Ali Marg, New Delhi, 110067, India
| | - Ashish Prasad
- National Institute of Plant Genome Research, Aruna Asaf Ali Marg, New Delhi, 110067, India
| | - Jyoti Maurya
- National Institute of Plant Genome Research, Aruna Asaf Ali Marg, New Delhi, 110067, India
| | - Manoj Prasad
- National Institute of Plant Genome Research, Aruna Asaf Ali Marg, New Delhi, 110067, India.
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Cao X, Zhao R, Wang H, Zhang H, Zhao X, Khan LU, Huang X. Genomic diversity of Areca Palm Velarivirus 1 (APV1) in Areca palm (Areca catechu) plantations in Hainan, China. BMC Genomics 2021; 22:725. [PMID: 34620080 PMCID: PMC8499421 DOI: 10.1186/s12864-021-07976-6] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2021] [Accepted: 08/30/2021] [Indexed: 11/16/2022] Open
Abstract
Background Areca palm (Areca catechu L.) is an important commercial crop in southeast Asia, but its cultivation is threatened by yellowing leaf disease (YLD). Areca palm velarivirus 1 (APV1) was recently associated with YLD, but little is known regarding its population and genetic diversity. To assess the diversity of YLD, the APV1 genome was sequenced in YLD samples collected from different sites in Hainan. Results Twenty new and complete APV1 genomes were identified. The APV1 isolates had highly conserved sequences in seven open reading frames (ORFs; > 95% nucleotide [nt] identity) at the 3′ terminal, but there was diversity (81–87% nt identity) in three ORFs at the 5′ terminal. Phylogenetic analysis divided the APV1 isolates into three phylogroups, with 16 isolates (> 70%) in phylogroup A. Mixed infections with different genotypes in the same tree were identified; this was closely correlated with higher levels of genetic recombination. Conclusions Phylogroup A is the most prevalent APV1 genotype in areca palm plantations in Hainan, China. Mixed infection with different genotypes can lead to genomic recombination of APV1. Our data provide a foundation for accurate diagnostics, characterization of etiology, and elucidation of the evolutionary relationships of APV1 populations. Supplementary Information The online version contains supplementary material available at 10.1186/s12864-021-07976-6.
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Affiliation(s)
- Xianmei Cao
- Hainan Key Laboratory for Sustainable Utilization of Tropical Bioresources, College of Tropical Crops, Hainan University, Haikou, 570228, Hainan, People's Republic of China
| | - Ruibai Zhao
- Hainan Key Laboratory for Sustainable Utilization of Tropical Bioresources, College of Tropical Crops, Hainan University, Haikou, 570228, Hainan, People's Republic of China
| | - Hongxing Wang
- Hainan Key Laboratory for Sustainable Utilization of Tropical Bioresources, College of Tropical Crops, Hainan University, Haikou, 570228, Hainan, People's Republic of China
| | - Huaiwen Zhang
- Hainan Key Laboratory for Sustainable Utilization of Tropical Bioresources, College of Tropical Crops, Hainan University, Haikou, 570228, Hainan, People's Republic of China
| | - Xue Zhao
- Hainan Key Laboratory for Sustainable Utilization of Tropical Bioresources, College of Tropical Crops, Hainan University, Haikou, 570228, Hainan, People's Republic of China
| | - Latif Ullah Khan
- Hainan Key Laboratory for Sustainable Utilization of Tropical Bioresources, College of Tropical Crops, Hainan University, Haikou, 570228, Hainan, People's Republic of China
| | - Xi Huang
- Hainan Key Laboratory for Sustainable Utilization of Tropical Bioresources, College of Tropical Crops, Hainan University, Haikou, 570228, Hainan, People's Republic of China.
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Ashraf MA, Ashraf F, Feng X, Hu X, Shen L, Khan J, Zhang S. Potential targets for evaluation of sugarcane yellow leaf virus resistance in sugarcane cultivars: in silico sugarcane miRNA and target network prediction. BIOTECHNOL BIOTEC EQ 2021. [DOI: 10.1080/13102818.2022.2041483] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022] Open
Affiliation(s)
- Muhammad Aleem Ashraf
- Institute of Tropical Bioscience and Biotechnology, Sugarcane Research Centre of Chinese Academy of Tropical Agricultural Sciences, Key Laboratory of Biology and Genetic Resources of Tropical Crops, Ministry of Agriculture, Haikou, PR China
- Department of Bioscience and Technology, Khwaja Fareed University of Engineering and Information Technology, Rahim Yar Khan, Pakistan
| | - Fakiha Ashraf
- Institute of Tropical Bioscience and Biotechnology, Sugarcane Research Centre of Chinese Academy of Tropical Agricultural Sciences, Key Laboratory of Biology and Genetic Resources of Tropical Crops, Ministry of Agriculture, Haikou, PR China
| | - Xiaoyan Feng
- Institute of Tropical Bioscience and Biotechnology, Sugarcane Research Centre of Chinese Academy of Tropical Agricultural Sciences, Key Laboratory of Biology and Genetic Resources of Tropical Crops, Ministry of Agriculture, Haikou, PR China
- Hainan Academy of Tropical Agricultural Resources, Chinese Academy of Tropical Agricultural Sciences, Haikou, PR China
| | - Xiaowen Hu
- Zhanjiang Experimental Station, Chinese Academy of Tropical Agricultural Sciences, Zhanjiang, PR China
| | - Linbo Shen
- Institute of Tropical Bioscience and Biotechnology, Sugarcane Research Centre of Chinese Academy of Tropical Agricultural Sciences, Key Laboratory of Biology and Genetic Resources of Tropical Crops, Ministry of Agriculture, Haikou, PR China
| | - Jallat Khan
- Department of Chemistry, Khwaja Fareed University of Engineering and Information Technology, Rahim Yar Khan, Pakistan
| | - Shuzhen Zhang
- Institute of Tropical Bioscience and Biotechnology, Sugarcane Research Centre of Chinese Academy of Tropical Agricultural Sciences, Key Laboratory of Biology and Genetic Resources of Tropical Crops, Ministry of Agriculture, Haikou, PR China
- Hainan Academy of Tropical Agricultural Resources, Chinese Academy of Tropical Agricultural Sciences, Haikou, PR China
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Kotowska-Zimmer A, Pewinska M, Olejniczak M. Artificial miRNAs as therapeutic tools: Challenges and opportunities. WILEY INTERDISCIPLINARY REVIEWS-RNA 2021; 12:e1640. [PMID: 33386705 DOI: 10.1002/wrna.1640] [Citation(s) in RCA: 29] [Impact Index Per Article: 9.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/01/2020] [Revised: 12/02/2020] [Accepted: 12/07/2020] [Indexed: 12/21/2022]
Abstract
RNA interference (RNAi) technology has been used for almost two decades to study gene functions and in therapeutic approaches. It uses cellular machinery and small, designed RNAs in the form of synthetic small interfering RNAs (siRNAs) or vector-based short hairpin RNAs (shRNAs), and artificial miRNAs (amiRNAs) to inhibit a gene of interest. Artificial miRNAs, known also as miRNA mimics, shRNA-miRs, or pri-miRNA-like shRNAs have the most complex structures and undergo two-step processing in cells to form mature siRNAs, which are RNAi effectors. AmiRNAs are composed of a target-specific siRNA insert and scaffold based on a natural primary miRNA (pri-miRNA). siRNAs serve as a guide to search for complementary sequences in transcripts, whereas pri-miRNA scaffolds ensure proper processing and transport. The dynamics of siRNA maturation and siRNA levels in the cell resemble those of endogenous miRNAs; therefore amiRNAs are safer than other RNAi triggers. Delivered as viral vectors and expressed under tissue-specific polymerase II (Pol II) promoters, amiRNAs provide long-lasting silencing and expression in selected tissues. Therefore, amiRNAs are useful therapeutic tools for a broad spectrum of human diseases, including neurodegenerative diseases, cancers and viral infections. Recent reports on the role of sequence and structure in pri-miRNA processing may contribute to the improvement of the amiRNA tools. In addition, the success of a recently initiated clinical trial for Huntington's disease could pave the way for other amiRNA-based therapies, if proven effective and safe. This article is categorized under: RNA Processing > Processing of Small RNAs Regulatory RNAs/RNAi/Riboswitches > RNAi: Mechanisms of Action RNA in Disease and Development > RNA in Disease.
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Affiliation(s)
- Anna Kotowska-Zimmer
- Department of Genome Engineering, Institute of Bioorganic Chemistry PAS, Poznan, Poland
| | - Marianna Pewinska
- Department of Genome Engineering, Institute of Bioorganic Chemistry PAS, Poznan, Poland
| | - Marta Olejniczak
- Department of Genome Engineering, Institute of Bioorganic Chemistry PAS, Poznan, Poland
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López-Dolz L, Spada M, Daròs JA, Carbonell A. Fine-tune control of targeted RNAi efficacy by plant artificial small RNAs. Nucleic Acids Res 2020; 48:6234-6250. [PMID: 32396204 PMCID: PMC7293048 DOI: 10.1093/nar/gkaa343] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2020] [Revised: 04/08/2020] [Accepted: 04/23/2020] [Indexed: 12/04/2022] Open
Abstract
Eukaryotic RNA interference (RNAi) results in gene silencing upon the sequence-specific degradation of target transcripts by complementary small RNAs (sRNAs). In plants, RNAi-based tools have been optimized for high efficacy and high specificity, and are extensively used in gene function studies and for crop improvement. However, efficient methods for finely adjusting the degree of induced silencing are missing. Here, we present two different strategies based on artificial sRNAs for fine-tuning targeted RNAi efficacy in plants. First, the degree of silencing induced by synthetic-trans-acting small interfering RNAs (syn-tasiRNAs) can be adjusted by modifying the precursor position from which the syn-tasiRNA is expressed. The accumulation and efficacy of Arabidopsis TAS1c-based syn-tasiRNAs progressively decrease as the syn-tasiRNA is expressed from positions more distal to the trigger miR173 target site. And second, syn-tasiRNA activity can also be tweaked by modifying the degree of base-pairing between the 3' end of the syn-tasiRNA and the 5' end of the target RNA. Both strategies were used to finely modulate the degree of silencing of endogenous and exogenous target genes in Arabidopsis thaliana and Nicotiana benthamiana. New high-throughput syn-tasiRNA vectors were developed and functionally analyzed, and should facilitate the precise control of gene expression in multiple plant species.
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Affiliation(s)
- Lucio López-Dolz
- Instituto de Biología Molecular y Celular de Plantas, Consejo Superior de Investigaciones Científicas-Universitat Politècnica de València, 46022 Valencia, Spain
| | - Maria Spada
- Instituto de Biología Molecular y Celular de Plantas, Consejo Superior de Investigaciones Científicas-Universitat Politècnica de València, 46022 Valencia, Spain
| | - José-Antonio Daròs
- Instituto de Biología Molecular y Celular de Plantas, Consejo Superior de Investigaciones Científicas-Universitat Politècnica de València, 46022 Valencia, Spain
| | - Alberto Carbonell
- Instituto de Biología Molecular y Celular de Plantas, Consejo Superior de Investigaciones Científicas-Universitat Politècnica de València, 46022 Valencia, Spain
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Cisneros AE, Carbonell A. Artificial Small RNA-Based Silencing Tools for Antiviral Resistance in Plants. PLANTS 2020; 9:plants9060669. [PMID: 32466363 PMCID: PMC7356032 DOI: 10.3390/plants9060669] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/04/2020] [Revised: 05/20/2020] [Accepted: 05/21/2020] [Indexed: 01/05/2023]
Abstract
Artificial small RNAs (art-sRNAs), such as artificial microRNAs (amiRNAs) and synthetic trans-acting small interfering RNAs (syn-tasiRNAs), are highly specific 21-nucleotide small RNAs designed to recognize and silence complementary target RNAs. Art-sRNAs are extensively used in gene function studies or for improving crops, particularly to protect plants against viruses. Typically, antiviral art-sRNAs are computationally designed to target one or multiple sites in viral RNAs with high specificity, and art-sRNA constructs are generated and introduced into plants that are subsequently challenged with the target virus(es). Numerous studies have reported the successful application of art-sRNAs to induce resistance against a large number of RNA and DNA viruses in model and crop species. However, the application of art-sRNAs as an antiviral tool has limitations, such as the difficulty to predict the efficacy of a particular art-sRNA or the emergence of virus variants with mutated target sites escaping to art-sRNA-mediated degradation. Here, we review the different classes, features, and uses of art-sRNA-based tools to induce antiviral resistance in plants. We also provide strategies for the rational design of antiviral art-sRNAs and discuss the latest advances in developing art-sRNA-based methodologies for enhanced resistance to plant viruses.
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Ashraf F, Ashraf MA, Hu X, Zhang S. A novel computational approach to the silencing of Sugarcane Bacilliform Guadeloupe A Virus determines potential host-derived MicroRNAs in sugarcane ( Saccharum officinarum L.). PeerJ 2020; 8:e8359. [PMID: 31976180 PMCID: PMC6964690 DOI: 10.7717/peerj.8359] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/04/2019] [Accepted: 12/05/2019] [Indexed: 01/24/2023] Open
Abstract
Sugarcane Bacilliform Guadeloupe A Virus (SCBGAV, genus Badnavirus, family Caulimoviridae) is an emerging, deleterious pathogen of sugarcane which presents a substantial barrier to producing high sugarcane earnings. Sugarcane bacilliform viruses (SCBVs) are one of the main species that infect sugarcane. During the last 30 years, significant genetic changes in SCBV strains have been observed with a high risk of disease incidence associated with crop damage. SCBV infection may lead to significant losses in biomass production in susceptible sugarcane cultivars. The circular, double-stranded (ds) DNA genome of SCBGAV (7.4 Kb) is composed of three open reading frames (ORFs) on the positive strand that replicate by a reverse transcriptase. SCBGAV can infect sugarcane in a semipersistent manner via the insect vectors sugarcane mealybug species. In the current study, we used miRNA target prediction algorithms to identify and comprehensively analyze the genome-wide sugarcane (Saccharum officinarum L.)-encoded microRNA (miRNA) targets against the SCBGAV. Mature miRNA target sequences were retrieved from the miRBase (miRNA database) and were further analyzed for hybridization to the SCBGAV genome. Multiple computational approaches—including miRNA-target seed pairing, multiple target positions, minimum free energy, target site accessibility, maximum complementarity, pattern recognition and minimum folding energy for attachments—were considered by all algorithms. Among them, sof-miR396 was identified as the top effective candidate, capable of targeting the vital ORF3 of the SCBGAV genome. miRanda, RNA22 and RNAhybrid algorithms predicted hybridization of sof-miR396 at common locus position 3394. The predicted sugarcane miRNAs against viral mRNA targets possess antiviral activities, leading to translational inhibition by mRNA cleavage. Interaction network of sugarcane-encoded miRNAs with SCBGAV genes, created using Circos, allow analyze new targets. The finding of the present study acts as a first step towards the creation of SCBGAV-resistant sugarcane through the expression of the identified miRNAs.
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Affiliation(s)
- Fakiha Ashraf
- Institute of Tropical Bioscience and Biotechnology, Chinese Academy of Tropical Agricultural Sciences, Haikou, Hainan, China
| | - Muhammad Aleem Ashraf
- Haikou Experimental Station, Chinese Academy of Tropical Agricultural Sciences, Haikou, Hainan, China.,Department of Plant Breeding and Genetics, University College of Agriculture and Environmental Sciences, Islamia University of Bahawalpur, Baghdad-Ul-Jadeed Campus, Bahwalpur, Pakistan
| | - Xiaowen Hu
- Zhanjiang Experimental Station, Chinese Academy of Tropical Agricultural Sciences, Zhanjiang, Guandong, China
| | - Shuzhen Zhang
- Institute of Tropical Bioscience and Biotechnology, Chinese Academy of Tropical Agricultural Sciences, Haikou, Hainan, China
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Rubio L, Galipienso L, Ferriol I. Detection of Plant Viruses and Disease Management: Relevance of Genetic Diversity and Evolution. FRONTIERS IN PLANT SCIENCE 2020; 11:1092. [PMID: 32765569 PMCID: PMC7380168 DOI: 10.3389/fpls.2020.01092] [Citation(s) in RCA: 110] [Impact Index Per Article: 27.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/02/2020] [Accepted: 07/02/2020] [Indexed: 05/04/2023]
Abstract
Plant viruses cause considerable economic losses and are a threat for sustainable agriculture. The frequent emergence of new viral diseases is mainly due to international trade, climate change, and the ability of viruses for rapid evolution. Disease control is based on two strategies: i) immunization (genetic resistance obtained by plant breeding, plant transformation, cross-protection, or others), and ii) prophylaxis to restrain virus dispersion (using quarantine, certification, removal of infected plants, control of natural vectors, or other procedures). Disease management relies strongly on a fast and accurate identification of the causal agent. For known viruses, diagnosis consists in assigning a virus infecting a plant sample to a group of viruses sharing common characteristics, which is usually referred to as species. However, the specificity of diagnosis can also reach higher taxonomic levels, as genus or family, or lower levels, as strain or variant. Diagnostic procedures must be optimized for accuracy by detecting the maximum number of members within the group (sensitivity as the true positive rate) and distinguishing them from outgroup viruses (specificity as the true negative rate). This requires information on the genetic relationships within-group and with members of other groups. The influence of the genetic diversity of virus populations in diagnosis and disease management is well documented, but information on how to integrate the genetic diversity in the detection methods is still scarce. Here we review the techniques used for plant virus diagnosis and disease control, including characteristics such as accuracy, detection level, multiplexing, quantification, portability, and designability. The effect of genetic diversity and evolution of plant viruses in the design and performance of some detection and disease control techniques are also discussed. High-throughput or next-generation sequencing provides broad-spectrum and accurate identification of viruses enabling multiplex detection, quantification, and the discovery of new viruses. Likely, this technique will be the future standard in diagnostics as its cost will be dropping and becoming more affordable.
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Affiliation(s)
- Luis Rubio
- Centro de Protección Vegetal y Biotecnology, Instituto Valenciano de Investigaciones Agrarias, Moncada, Spain
- *Correspondence: Luis Rubio,
| | - Luis Galipienso
- Centro de Protección Vegetal y Biotecnology, Instituto Valenciano de Investigaciones Agrarias, Moncada, Spain
| | - Inmaculada Ferriol
- Plant Responses to Stress Programme, Centre for Research in Agricultural Genomics (CRAG-CSIC_UAB-UB) Cerdanyola del Vallès, Barcelona, Spain
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Carbonell A, Lisón P, Daròs J. Multi-targeting of viral RNAs with synthetic trans-acting small interfering RNAs enhances plant antiviral resistance. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2019; 100:720-737. [PMID: 31350772 PMCID: PMC6899541 DOI: 10.1111/tpj.14466] [Citation(s) in RCA: 23] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/30/2019] [Revised: 07/10/2019] [Accepted: 07/12/2019] [Indexed: 05/15/2023]
Abstract
RNA interference (RNAi)-based tools are used in multiple organisms to induce antiviral resistance through the sequence-specific degradation of target RNAs by complementary small RNAs. In plants, highly specific antiviral RNAi-based tools include artificial microRNAs (amiRNAs) and synthetic trans-acting small interfering RNAs (syn-tasiRNAs). syn-tasiRNAs have emerged as a promising antiviral tool allowing for the multi-targeting of viral RNAs through the simultaneous expression of several syn-tasiRNAs from a single precursor. Here, we compared in tomato plants the effects of an amiRNA construct expressing a single amiRNA and a syn-tasiRNA construct expressing four different syn-tasiRNAs against Tomato spotted wilt virus (TSWV), an economically important pathogen affecting tomato crops worldwide. Most of the syn-tasiRNA lines were resistant to TSWV, whereas the majority of the amiRNA lines were susceptible and accumulated viral progenies with mutations in the amiRNA target site. Only the two amiRNA lines with higher amiRNA accumulation were resistant, whereas resistance in syn-tasiRNA lines was not exclusive of lines with high syn-tasiRNA accumulation. Collectively, these results suggest that syn-tasiRNAs induce enhanced antiviral resistance because of the combined silencing effect of each individual syn-tasiRNA, which minimizes the possibility that the virus simultaneously mutates all different target sites to fully escape each syn-tasiRNA.
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Affiliation(s)
- Alberto Carbonell
- Instituto de Biología Molecular y Celular de PlantasConsejo Superior de Investigaciones Científicas‐Universitat Politècnica de València46022ValenciaSpain
| | - Purificación Lisón
- Instituto de Biología Molecular y Celular de PlantasConsejo Superior de Investigaciones Científicas‐Universitat Politècnica de València46022ValenciaSpain
| | - José‐Antonio Daròs
- Instituto de Biología Molecular y Celular de PlantasConsejo Superior de Investigaciones Científicas‐Universitat Politècnica de València46022ValenciaSpain
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Abstract
Artificial microRNAs (amiRNAs) and synthetic trans-acting small interfering RNAs (syn-tasiRNAs) are two classes of 21-nucleotide artificial small RNAs (sRNAs) designed to selectively silence transcripts in plants with high efficacy and specificity. Despite their extensive use during the last decade, methods for designing and generating artificial sRNA constructs have not been optimized for time- and cost-effectiveness and high-throughput applicability since recently. In this chapter, I detail the protocols for both the rationale design and high-throughput generation of plant artificial sRNA constructs using the P-SAMS ("Plant Small RNA Maker Suite") web tool and a new generation of BsaI/ccdB (B/c) vectors optimized for one-step cloning of artificial sRNA inserts. These protocols allow for the efficient generation of large number of amiRNA and syn-tasiRNA constructs for potent, selective, and specific gene silencing in plants.
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