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Hu W, Dai Z, Liu P, Deng C, Shen W, Li Z, Cui H. The Single Distinct Leader Protease Encoded by Alpinia oxyphylla Mosaic Virus (Genus Macluravirus) Suppresses RNA Silencing Through Interfering with Double-Stranded RNA Synthesis. PHYTOPATHOLOGY 2023; 113:1103-1114. [PMID: 36576401 DOI: 10.1094/phyto-10-22-0371-r] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/17/2023]
Abstract
The genomic 5'-terminal regions of viruses in the family Potyviridae (potyvirids) encode two types of leader proteases: serine-protease (P1) and cysteine-protease (HCPro), which differ greatly in the arrangement and sequence composition among inter-genus viruses. Most potyvirids have the same tandemly arranged P1 and HCPro, whereas viruses in the genus Macluravirus encode a single distinct leader protease, a truncated version of HCPro with yet-unknown functions. We investigated the RNA silencing suppression (RSS) activity and its underpinning mechanism of the distinct HCPro from alpinia oxyphylla mosaic macluravirus (aHCPro). Sequence analysis revealed that macluraviral HCPros have obvious truncations in the N-terminal and middle regions when aligned to their counterparts in potyviruses (well-characterized viral suppressors of RNA silencing). Nearly all defined elements essential for the RSS activity of potyviral counterparts are not distinguished in macluraviral HCPros. Here, we demonstrated that aHCPro exhibits a similar anti-silencing activity with the potyviral counterpart. However, aHCPro fails to block both the local and systemic spreading of RNA silencing. In line, aHCPro interferes with the dsRNA synthesis, an upstream step in the RNA silencing pathway. Affinity-purification and NanoLC-MS/MS analysis revealed that aHCPro has no association with core components or their potential interactors involving in dsRNA synthesis from the protein layer. Instead, the ectopic expression of aHCPro significantly reduces the transcript abundance of RDR2, RDR6, SGS3, and SDE5. This study represents the first report on the anti-silencing function of Macluravirus-encoded HCPro and the underlying molecular mechanism.
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Affiliation(s)
- Weiyao Hu
- Sanya Nanfan Research Institute, Key Laboratory of Green Prevention and Control of Tropical Plant Diseases and Pests (Ministry of Education) and College of Plant Protection, Hainan University, Haikou, Hainan, 570228, China
| | - Zhaoji Dai
- Sanya Nanfan Research Institute, Key Laboratory of Green Prevention and Control of Tropical Plant Diseases and Pests (Ministry of Education) and College of Plant Protection, Hainan University, Haikou, Hainan, 570228, China
| | - Peilan Liu
- Sanya Nanfan Research Institute, Key Laboratory of Green Prevention and Control of Tropical Plant Diseases and Pests (Ministry of Education) and College of Plant Protection, Hainan University, Haikou, Hainan, 570228, China
| | - Changhui Deng
- Sanya Nanfan Research Institute, Key Laboratory of Green Prevention and Control of Tropical Plant Diseases and Pests (Ministry of Education) and College of Plant Protection, Hainan University, Haikou, Hainan, 570228, China
| | - Wentao Shen
- Institute of Tropical Bioscience and Biotechnology, Chinese Academy of Tropical Agricultural Sciences, Haikou, Hainan, 571101, China
| | - Zengping Li
- Sanya Nanfan Research Institute, Key Laboratory of Green Prevention and Control of Tropical Plant Diseases and Pests (Ministry of Education) and College of Plant Protection, Hainan University, Haikou, Hainan, 570228, China
| | - Hongguang Cui
- Sanya Nanfan Research Institute, Key Laboratory of Green Prevention and Control of Tropical Plant Diseases and Pests (Ministry of Education) and College of Plant Protection, Hainan University, Haikou, Hainan, 570228, China
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Kumar M, Tripathi PK, Ayzenshtat D, Marko A, Forotan Z, Bocobza SE. Increased rates of gene-editing events using a simplified RNAi configuration designed to reduce gene silencing. PLANT CELL REPORTS 2022; 41:1987-2003. [PMID: 35849200 DOI: 10.1007/s00299-022-02903-9] [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: 05/25/2022] [Accepted: 06/30/2022] [Indexed: 06/15/2023]
Abstract
An optimal RNAi configuration that could restrict gene expression most efficiently was determined. This approach was also used to target PTGS and yielded higher rates of gene-editing events. Although it was characterized long ago, transgene silencing still strongly impairs transgene overexpression, and thus is a major barrier to plant crop gene-editing. The development of strategies that could prevent transgene silencing is therefore essential to the success of gene editing assays. Transgene silencing occurs via the RNA silencing process, which regulates the expression of essential genes and protects the plant from viral infections. The RNA silencing machinery thereby controls central biological processes such as growth, development, genome integrity, and stress resistance. RNA silencing is typically induced by aberrant RNA, that may lack 5' or 3' processing, or may consist in double-stranded or hairpin RNA, and involves DICER and ARGONAUTE family proteins. In this study, RNAi inducing constructs were designed in eleven different configurations and were evaluated for their capacity to induce silencing in Nicotiana spp. using transient and stable transformation assays. Using reporter genes, it was found that the overexpression of a hairpin consisting of a forward tandem inverted repeat that started with an ATG and that was not followed downstream by a transcription terminator, could downregulate gene expression most potently. Furthermore, using this method, the downregulation of the NtSGS3 gene caused a significant increase in transgene expression both in transient and stable transformation assays. This SGS3 silencing approach was also employed in gene-editing assays and caused higher rates of gene-editing events. Taken together, these findings suggested the optimal genetic configuration to cause RNA silencing and showed that this strategy may be used to restrict PTGS during gene-editing experiments.
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Affiliation(s)
- Manoj Kumar
- Department of Ornamental Plants and Agricultural Biotechnology, The Institute of Plant Sciences, The Volcani Center, ARO, Beit Dagan, Israel
| | - Pankaj Kumar Tripathi
- Department of Ornamental Plants and Agricultural Biotechnology, The Institute of Plant Sciences, The Volcani Center, ARO, Beit Dagan, Israel
| | - Dana Ayzenshtat
- Department of Ornamental Plants and Agricultural Biotechnology, The Institute of Plant Sciences, The Volcani Center, ARO, Beit Dagan, Israel
| | - Adar Marko
- Department of Ornamental Plants and Agricultural Biotechnology, The Institute of Plant Sciences, The Volcani Center, ARO, Beit Dagan, Israel
| | - Zohar Forotan
- Department of Ornamental Plants and Agricultural Biotechnology, The Institute of Plant Sciences, The Volcani Center, ARO, Beit Dagan, Israel
| | - Samuel E Bocobza
- Department of Ornamental Plants and Agricultural Biotechnology, The Institute of Plant Sciences, The Volcani Center, ARO, Beit Dagan, Israel.
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Cooperative recruitment of RDR6 by SGS3 and SDE5 during small interfering RNA amplification in Arabidopsis. Proc Natl Acad Sci U S A 2021; 118:2102885118. [PMID: 34408020 DOI: 10.1073/pnas.2102885118] [Citation(s) in RCA: 23] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Small interfering RNAs (siRNAs) are often amplified from transcripts cleaved by RNA-induced silencing complexes (RISCs) containing a small RNA (sRNA) and an Argonaute protein. Amplified siRNAs, termed secondary siRNAs, are important for reinforcement of target repression. In plants, target cleavage by RISCs containing 22-nucleotide (nt) sRNA and Argonaute 1 (AGO1) triggers siRNA amplification. In this pathway, the cleavage fragment is converted into double-stranded RNA (dsRNA) by RNA-dependent RNA polymerase 6 (RDR6), and the dsRNA is processed into siRNAs by Dicer-like proteins. Because nonspecific RDR6 recruitment causes nontarget siRNA production, it is critical that RDR6 is specifically recruited to the target RNA that serves as a template for dsRNA formation. Previous studies showed that Suppressor of Gene Silencing 3 (SGS3) binds and stabilizes 22-nt sRNA-containing AGO1 RISCs associated with cleaved target, but how RDR6 is recruited to targets cleaved by 22-nt sRNA-containing AGO1 RISCs remains unknown. Here, using cell-free extracts prepared from suspension-cultured Arabidopsis thaliana cells, we established an in vitro system for secondary siRNA production in which 22-nt siRNA-containing AGO1-RISCs but not 21-nt siRNA-containing AGO1-RISCs induce secondary siRNA production. In this system, addition of recombinant Silencing Defective 5 (SDE5) protein remarkably enhances secondary siRNA production. We show that RDR6 is recruited to a cleavage fragment by 22-nt siRNA-containing AGO1-RISCs in coordination with SGS3 and SDE5. The SGS3-SDE5-RDR6 multicomponent recognition system and the poly(A) tail inhibition may contribute to securing specificity of siRNA amplification.
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Sakurai Y, Baeg K, Lam AYW, Shoji K, Tomari Y, Iwakawa HO. Cell-free reconstitution reveals the molecular mechanisms for the initiation of secondary siRNA biogenesis in plants. Proc Natl Acad Sci U S A 2021; 118:e2102889118. [PMID: 34330830 PMCID: PMC8346886 DOI: 10.1073/pnas.2102889118] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022] Open
Abstract
Secondary small interfering RNA (siRNA) production, triggered by primary small RNA targeting, is critical for proper development and antiviral defense in many organisms. RNA-dependent RNA polymerase (RDR) is a key factor in this pathway. However, how RDR specifically converts the targets of primary small RNAs into double-stranded RNA (dsRNA) intermediates remains unclear. Here, we develop an in vitro system that allows for dissection of the molecular mechanisms underlying the production of trans-acting siRNAs, a class of plant secondary siRNAs that play roles in organ development and stress responses. We find that a combination of the dsRNA-binding protein, SUPPRESSOR OF GENE SILENCING3; the putative nuclear RNA export factor, SILENCING DEFECTIVE5, primary small RNA, and Argonaute is required for physical recruitment of RDR6 to target RNAs. dsRNA synthesis by RDR6 is greatly enhanced by the removal of the poly(A) tail, which can be achieved by the cleavage at a second small RNA-binding site bearing appropriate mismatches. Importantly, when the complementarity of the base pairing at the second target site is too strong, the small RNA-Argonaute complex remains at the cleavage site, thereby blocking the initiation of dsRNA synthesis by RDR6. Our data highlight the light and dark sides of double small RNA targeting in the secondary siRNA biogenesis.
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Affiliation(s)
- Yuriki Sakurai
- Institute for Quantitative Biosciences, The University of Tokyo, Bunkyo-ku, Tokyo 113-0032, Japan
- Department of Computational Biology and Medical Sciences, Graduate School of Frontier Sciences, The University of Tokyo, Bunkyo-ku, Tokyo 113-0032, Japan
| | - Kyungmin Baeg
- Institute for Quantitative Biosciences, The University of Tokyo, Bunkyo-ku, Tokyo 113-0032, Japan
| | - Andy Y W Lam
- Institute for Quantitative Biosciences, The University of Tokyo, Bunkyo-ku, Tokyo 113-0032, Japan
- Department of Computational Biology and Medical Sciences, Graduate School of Frontier Sciences, The University of Tokyo, Bunkyo-ku, Tokyo 113-0032, Japan
| | - Keisuke Shoji
- Institute for Quantitative Biosciences, The University of Tokyo, Bunkyo-ku, Tokyo 113-0032, Japan
| | - Yukihide Tomari
- Institute for Quantitative Biosciences, The University of Tokyo, Bunkyo-ku, Tokyo 113-0032, Japan;
- Department of Computational Biology and Medical Sciences, Graduate School of Frontier Sciences, The University of Tokyo, Bunkyo-ku, Tokyo 113-0032, Japan
| | - Hiro-Oki Iwakawa
- Institute for Quantitative Biosciences, The University of Tokyo, Bunkyo-ku, Tokyo 113-0032, Japan;
- Precursory Research for Embryonic Science and Technology (PRESTO), Japan Science and Technology Agency (JST), Saitama 332-0012, Japan
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Kang DR, Zhu Y, Li SL, Ai PH, Khan MA, Ding HX, Wang Y, Wang ZC. Transcriptome analysis of differentially expressed genes in chrysanthemum MET1 RNA interference lines. PHYSIOLOGY AND MOLECULAR BIOLOGY OF PLANTS : AN INTERNATIONAL JOURNAL OF FUNCTIONAL PLANT BIOLOGY 2021; 27:1455-1468. [PMID: 34366589 PMCID: PMC8295425 DOI: 10.1007/s12298-021-01022-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/08/2020] [Revised: 06/02/2021] [Accepted: 06/07/2021] [Indexed: 05/14/2023]
Abstract
UNLABELLED DNA methylation is the most important epigenetic modification involved in many essential biological processes. MET1 is one of DNA methyltransferases that affect the level of methylation in the entire genome. To explore the effect of MET1 gene silencing on gene expression profile of Chrysanthemum × morifolium 'Zijingling'. The stem section and leaves at the young stage were taken for transcriptome sequencing. MET1-RNAi leaves had 8 differentially expressed genes while 156 differentially expressed genes were observed in MET1-RNAi stem compared with control leaves and stem. These genes encode many key proteins in plant biological processes, such as transcription factors, signal transduction mechanisms, secondary metabolite synthesis, transport and catabolism and interaction. In general, 34.58% of the differentially expressed genes in leaves and stems were affected by the reduction of the MET1 gene. The differentially expressed genes in stem and leaves of transgenic plants went through significant changes. We found adequate amount of candidate genes associated with flowering, however, the number of genes with significant differences between transgenic and control lines was not too high. Several flowering related genes were screened out for gene expression verification and all of them were obseved as consistent with transcriptome data. These candidate genes may play important role in flowering variation of chrysanthemum. This study reveals the mechanism of CmMET1 interference on the growth and development of chrysanthemum at the transcriptional level, which provides the basis for further research on the epigenetic regulation mechanism in flower induction and development. SUPPLEMENTARY INFORMATION The online version contains supplementary material available at 10.1007/s12298-021-01022-1.
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Affiliation(s)
- Dong-ru Kang
- State Key Laboratory of Crop Stress Adaptation and Improvement, Plant Germplasm Resources and Genetic Laboratory, Kaifeng Key Laboratory of Chrysanthemum Biology, School of Life Sciences, Henan University. Jinming Road, Kaifeng, 475004 Henan China
| | - Yi Zhu
- State Key Laboratory of Crop Stress Adaptation and Improvement, Plant Germplasm Resources and Genetic Laboratory, Kaifeng Key Laboratory of Chrysanthemum Biology, School of Life Sciences, Henan University. Jinming Road, Kaifeng, 475004 Henan China
| | - Shuai-lei Li
- State Key Laboratory of Crop Stress Adaptation and Improvement, Plant Germplasm Resources and Genetic Laboratory, Kaifeng Key Laboratory of Chrysanthemum Biology, School of Life Sciences, Henan University. Jinming Road, Kaifeng, 475004 Henan China
| | - Peng-hui Ai
- State Key Laboratory of Crop Stress Adaptation and Improvement, Plant Germplasm Resources and Genetic Laboratory, Kaifeng Key Laboratory of Chrysanthemum Biology, School of Life Sciences, Henan University. Jinming Road, Kaifeng, 475004 Henan China
| | - Muhammad Ayoub Khan
- State Key Laboratory of Crop Stress Adaptation and Improvement, Plant Germplasm Resources and Genetic Laboratory, Kaifeng Key Laboratory of Chrysanthemum Biology, School of Life Sciences, Henan University. Jinming Road, Kaifeng, 475004 Henan China
| | - Hong-xu Ding
- State Key Laboratory of Crop Stress Adaptation and Improvement, Plant Germplasm Resources and Genetic Laboratory, Kaifeng Key Laboratory of Chrysanthemum Biology, School of Life Sciences, Henan University. Jinming Road, Kaifeng, 475004 Henan China
| | - Ying Wang
- State Key Laboratory of Crop Stress Adaptation and Improvement, Plant Germplasm Resources and Genetic Laboratory, Kaifeng Key Laboratory of Chrysanthemum Biology, School of Life Sciences, Henan University. Jinming Road, Kaifeng, 475004 Henan China
| | - Zi-cheng Wang
- State Key Laboratory of Crop Stress Adaptation and Improvement, Plant Germplasm Resources and Genetic Laboratory, Kaifeng Key Laboratory of Chrysanthemum Biology, School of Life Sciences, Henan University. Jinming Road, Kaifeng, 475004 Henan China
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Liu S, Jaouannet M, Dempsey DA, Imani J, Coustau C, Kogel KH. RNA-based technologies for insect control in plant production. Biotechnol Adv 2020; 39:107463. [DOI: 10.1016/j.biotechadv.2019.107463] [Citation(s) in RCA: 60] [Impact Index Per Article: 15.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2019] [Revised: 10/24/2019] [Accepted: 10/26/2019] [Indexed: 12/23/2022]
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7
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Heinemann JA. Should dsRNA treatments applied in outdoor environments be regulated? ENVIRONMENT INTERNATIONAL 2019; 132:104856. [PMID: 31174887 DOI: 10.1016/j.envint.2019.05.050] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/22/2019] [Revised: 05/15/2019] [Accepted: 05/17/2019] [Indexed: 06/09/2023]
Abstract
The New Zealand Environmental Protection Authority (EPA) issued a Decision that makes the use of externally applied double-stranded (ds)RNA molecules on eukaryotic cells or organisms technically out of scope of legislation on new organisms, making risk assessments of such treatments in the open environment unnecessary. The Decision was based on its view that the treatment does not create new or genetically modified organisms and rests on the EPA's conclusions that dsRNA is not heritable and is not a mutagen. For these reasons EPA decided that treatments using dsRNA do not modify genes or other genetic material. I found from an independent review of the literature on the topic indicated, however, that each of the major scientific justifications relied upon by the EPA was based on either an inaccurate interpretation of evidence or failure to consult the research literature pertaining to additional types of eukaryotes. The Decision also did not take into account the unknown and unique eukaryotic biodiversity of New Zealand. The safe use of RNA-based technology holds promise for addressing complex and persistent challenges in public health, agriculture and conservation. However, by failing to restrict the source or means of modifying the dsRNA, the EPA removed regulatory oversight that could prevent unintended consequences of this new technology such as suppression of genes other than those selected for suppression or the release of viral genes or genomes by failing to restrict the source or means of modifying the dsRNA.
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Affiliation(s)
- Jack A Heinemann
- School of Biological Sciences, Centre for Integrative Research in Biosafety, Centre for Integrative Ecology, University of Canterbury, Christchurch, New Zealand.
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Rajamäki ML, Lemmetty A, Laamanen J, Roininen E, Vishwakarma A, Streng J, Latvala S, Valkonen JPT. Small-RNA analysis of pre-basic mother plants and conserved accessions of plant genetic resources for the presence of viruses. PLoS One 2019; 14:e0220621. [PMID: 31390343 PMCID: PMC6685626 DOI: 10.1371/journal.pone.0220621] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2019] [Accepted: 06/12/2019] [Indexed: 11/17/2022] Open
Abstract
Pathogen-free stocks of vegetatively propagated plants are crucial in certified plant production. They require regular monitoring of the plant germplasm for pathogens, especially of the stocks maintained in the field. Here we tested pre-basic mother plants of Fragaria, Rubus and Ribes spp., and conserved accessions of the plant genetic resources of Rubus spp. maintained at research stations in Finland, for the presence of viruses using small interfering RNA (siRNA) -based diagnostics (VirusDetect). The advance of the method is that unrelated viruses can be detected simultaneously without resumptions of the viruses present. While no virus was detected in pre-basic mother plants of Fragaria and Ribes species, rubus yellow net virus (RYNV) was detected in pre-basic mother plants of Rubus. Raspberry bushy dwarf virus (RBDV), black raspberry necrosis virus (BRNV), raspberry vein chlorosis virus (RVCV) and RYNV were detected in the Rubus genetic resource collection. The L polymerase encoding sequence characterized from seven RVCV isolates showed considerable genetic variation. The data provide the first molecular biological evidence for the presence of RYNV in Finland. RYNV was not revealed in virus indexing by indicator plants, which suggests that it may be endogenously present in some raspberry cultivars. In addition, a putative new RYNV-like badnavirus was detected in Rubus spp. Blackcurrant reversion virus (BRV) and gooseberry vein banding associated virus (GVBaV) were detected in symptomatic Ribes plants grown in the field. Results were consistent with those obtained using PCR or reverse transcription PCR and suggest that the current virus indexing methods of pre-basic mother plants work as expected. Furthermore, many new viruses were identified in the collections of plant genetic resources not previously tested for viruses. In the future, siRNA-based diagnostics could be a useful supplement for the currently used virus detection methods in certified plant production and thus rationalize and simplify the current testing system.
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Affiliation(s)
| | - Anne Lemmetty
- Natural Resources Institute Finland (Luke), Jokioinen, Finland
| | - Jaana Laamanen
- Natural Resources Institute Finland (Luke), Jyväskylä, Finland
| | - Elina Roininen
- University of Helsinki, Department of Agricultural Sciences, Helsinki, Finland
| | - Archana Vishwakarma
- University of Helsinki, Department of Agricultural Sciences, Helsinki, Finland
| | - Janne Streng
- University of Helsinki, Department of Agricultural Sciences, Helsinki, Finland
| | - Satu Latvala
- Natural Resources Institute Finland (Luke), Jokioinen, Finland
| | - Jari P T Valkonen
- University of Helsinki, Department of Agricultural Sciences, Helsinki, Finland
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Abstract
RNA interference (RNAi) is the biological process of mRNA degradation induced by complementary sequences double-stranded (ds) small interfering RNAs (siRNA) and suppression of target gene expression. Exogenous siRNAs (perfectly paired dsRNAs of ∼21–25 nt in length) play an important role in host defense against RNA viruses and in transcriptional and post-transcriptional gene regulation in plants and other eukaryotes. Using RNAi technology by transfecting synthetic siRNAs into eukaryotic cells to silence genes has become an indispensable tool to investigate gene functions, and siRNA-based therapy is being developed to knockdown genes implicated in diseases. Other examples of RNAi technology include method of producing highly potent and purified siRNAs directly from Escherichiacoli cells, based on an unexpected discovery that ectopic expression of p19, a plant viral siRNA-binding protein, stabilizes a cryptic siRNA-like RNA species in bacteria. Those siRNAs, named as pro-siRNA for “prokaryotic siRNA”, are bacterial RNase III products that have chemical and functional properties that like eukaryotic siRNAs.
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10
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CMV2b-Dependent Regulation of Host Defense Pathways in the Context of Viral Infection. Viruses 2018; 10:v10110618. [PMID: 30423959 PMCID: PMC6265714 DOI: 10.3390/v10110618] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2018] [Revised: 11/06/2018] [Accepted: 11/08/2018] [Indexed: 01/26/2023] Open
Abstract
RNA silencing (or RNA interference, RNAi) plays direct roles in plant host defenses against viruses. Viruses encode suppressors of RNAi (VSRs) to counteract host antiviral defenses. The generation of transgenic plants expressing VSRs facilitates the understanding of the mechanisms of VSR-mediated interference with the endogenous silencing pathway. However, studying VSRs independent of other viral components simplifies the complex roles of VSRs during natural viral infection. While suppression of transgene silencing by the VSR 2b protein encoded by cucumber mosaic virus (CMV) requires 2b-small RNA (sRNA) binding activity, suppression of host antiviral defenses requires the binding activity of both sRNAs and AGOs proteins. This study, aimed to understand the functions of 2b in the context of CMV infection; thus, we performed genome-wide analyses of differential DNA methylation regions among wild-type CMV-infected, CMVΔ2b-infected, and 2b-transgenic Arabidopsis plants. These analyses, together with transcriptome sequencing and RT-qPCR analyses, show that while the majority of induced genes in 2b-transgenic plants were involved in extensive metabolic pathways, CMV-infection 2b-dependent induced genes were enriched in plant immunity pathways, including salicylic acid (SA) signaling. Together with infection with CMV mutants that expressed the 2b functional domains of sRNA or AGO binding, our data demonstrate that CMV-accelerated SA signaling depends on 2b-sRNA binding activity which is also responsible for virulence.
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Kukushkin NV. Taking memory beyond the brain: Does tobacco dream of the mosaic virus? Neurobiol Learn Mem 2018; 153:111-116. [PMID: 29396326 DOI: 10.1016/j.nlm.2018.01.003] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2017] [Revised: 01/05/2018] [Accepted: 01/21/2018] [Indexed: 10/18/2022]
Abstract
Memory is typically defined through animal behavior, but this point of view may limit our understanding of many related processes in diverse biological systems. The concept of memory can be broadened meaningfully by considering it from the perspective of time and homeostasis. On the one hand, this theoretical angle can help explain and predict the behavior of various non-neural systems such as insulin-secreting cells, plants, or signaling cascades. On the other hand, it emphasizes biological continuity between neural phenomena, such as synaptic plasticity, and their evolutionary precursors in cellular signaling.
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Affiliation(s)
- Nikolay V Kukushkin
- Center for Neural Science, New York University, 4 Washington Pl, New York, NY 10003, USA.
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12
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Donaire L, Ayllón MA. Deep sequencing of mycovirus-derived small RNAs from Botrytis species. MOLECULAR PLANT PATHOLOGY 2017; 18:1127-1137. [PMID: 27578449 PMCID: PMC6638239 DOI: 10.1111/mpp.12466] [Citation(s) in RCA: 41] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/23/2016] [Revised: 08/05/2016] [Accepted: 08/09/2016] [Indexed: 05/25/2023]
Abstract
RNA silencing is an ancient regulatory mechanism operating in all eukaryotic cells. In fungi, it was first discovered in Neurospora crassa, although its potential as a defence mechanism against mycoviruses was first reported in Cryphonectria parasitica and, later, in several fungal species. There is little evidence of the antiviral potential of RNA silencing in the phytopathogenic species of the fungal genus Botrytis. Moreover, little is known about the RNA silencing components in these fungi, although the analysis of public genome databases identified two Dicer-like genes in B. cinerea, as in most of the ascomycetes sequenced to date. In this work, we used deep sequencing to study the virus-derived small RNA (vsiRNA) populations from different mycoviruses infecting field isolates of Botrytis spp. The mycoviruses under study belong to different genera and species, and have different types of genome [double-stranded RNA (dsRNA), (+)single-stranded RNA (ssRNA) and (-)ssRNA]. In general, vsiRNAs derived from mycoviruses are mostly of 21, 20 and 22 nucleotides in length, possess sense or antisense orientation, either in a similar ratio or with a predominance of sense polarity depending on the virus species, have predominantly U at their 5' end, and are unevenly distributed along the viral genome, showing conspicuous hotspots of vsiRNA accumulation. These characteristics reveal striking similarities with vsiRNAs produced by plant viruses, suggesting similar pathways of viral targeting in plants and fungi. We have shown that the fungal RNA silencing machinery acts against the mycoviruses used in this work in a similar manner independent of their viral or fungal origin.
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Affiliation(s)
- Livia Donaire
- Centro de Investigaciones BiológicasConsejo Superior de Investigaciones Científicas (CIB‐CSIC)Madrid28040Spain
| | - María A. Ayllón
- Centro de Biotecnología y Genómica de PlantasUniversidad Politécnica de Madrid (UPM)‐Instituto Nacional de Investigación Agraria y Alimentaria (INIA), Campus de Montegancedo, Pozuelo de AlarcónMadrid28223Spain
- Departamento Biotecnología‐Biología VegetalE.T.S.I. Agronómica, Alimentaria y de Biosistemas, UPMMadrid28040Spain
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Efficient Generation of diRNAs Requires Components in the Posttranscriptional Gene Silencing Pathway. Sci Rep 2017; 7:301. [PMID: 28331197 PMCID: PMC5428250 DOI: 10.1038/s41598-017-00374-7] [Citation(s) in RCA: 30] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2016] [Accepted: 02/21/2017] [Indexed: 11/17/2022] Open
Abstract
It has been reported that double-stranded break (DSB)-induced small RNAs (diRNAs) are generated via the RNA-directed DNA methylation pathway and function in DSB repair in Arabidposis. However, important questions remain regarding the biogenesis and function of diRNAs. Here, we used CRISPR/Cas9- or TALEN-triggered DSBs to characterize diRNAs in Arabidopsis and rice. We found that 21-nt diRNAs were generated from a 35S promoter::GU-US reporter transgene targeted by CRISPR/Cas9. Unexpectedly, Pol II transcription of the transgene was required for efficient diRNA production and the level of diRNA accumulation correlated with the expression level of the transgene. diRNAs were not detected from CRISPR/Cas9- or TALEN-induced DSBs within the examined endogenous genes in Arabidopsis or rice. We also found that DCL4 and RDR6 that are known to be involved in posttranscriptional gene silencing were required to generate diRNAs. Our results suggest that DSBs are necessary but not sufficient for efficient diRNA generation and a high level of diRNAs is not necessary for DSB repair.
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14
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Baykal U, Liu H, Chen X, Nguyen HT, Zhang ZJ. Novel constructs for efficient cloning of sRNA-encoding DNA and uniform silencing of plant genes employing artificial trans-acting small interfering RNA. PLANT CELL REPORTS 2016; 35:2137-50. [PMID: 27417696 DOI: 10.1007/s00299-016-2024-9] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/11/2016] [Accepted: 07/03/2016] [Indexed: 05/28/2023]
Abstract
KEY MESSAGE TAS atasiRNA-producing region swapping used one-step, high efficiency, and high fidelity directional TC-cloning. Uniform silencing was achieved without lethality using miRNA trigger- TAS overexpression fusion cassettes to generate 21-nt atasiRNA. Plant transgenic technologies are very important for basic plant research and biotechnology. Artificial trans-acting small interfering RNA (atasiRNA) represents an attractive platform with certain advantages over other silencing approaches, such as hairpin RNA, artificial microRNA (amiRNA), and virus-induced gene silencing (VIGS). In this study, we developed two types of constructs for atasiRNA-mediated gene silencing in plants. To functionally validate our constructs, we chose TAS1a as a test model. Type 1 constructs had miR173-precursor sequence fused with TAS1a locus driven by single promoter-terminator cassette, which simplified the expression cassette and resulted in uniform gene silencing. Type 2 constructs contained two separate cassettes for miR173 and TAS1a co-expression. The constructs in each type were further improved by deploying the XcmI-based TC-cloning system for highly efficient directional cloning of short DNA fragments encoding atasiRNAs into TAS1a locus. The effectiveness of the constructs was demonstrated by cloning an atasiRNA DNA into the TC site of engineered TAS1a and silencing of CHLORINA 42 (CH42) gene in Arabidopsis. Our results show that the directional TC-cloning of the atasiRNA DNA into the engineered TAS1a is highly efficient and the miR173-TAS1a fusion system provides an attractive alternative to achieve moderate but more uniform gene silencing without lethality, as compared to conventional two separate cassettes for miR173 and TAS locus co-expression system. The design principles described here should be applicable to other TAS loci such as TAS1b, TAS1c, TAS2, or TAS3, and cloning of amiRNA into amiRNA stem-loop.
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Affiliation(s)
- Ulku Baykal
- Plant Transformation Core Facility, Division of Plant Sciences, University of Missouri, 1-33 Agriculture Building, Columbia, MO, 65211, USA
| | - Hua Liu
- Plant Transformation Core Facility, Division of Plant Sciences, University of Missouri, 1-33 Agriculture Building, Columbia, MO, 65211, USA
| | - Xinlu Chen
- Plant Transformation Core Facility, Division of Plant Sciences, University of Missouri, 1-33 Agriculture Building, Columbia, MO, 65211, USA
- Department of Plant Sciences, University of Tennessee, 347/359 Plant Biotech, Knoxville, TX, 37996, USA
| | - Henry T Nguyen
- Plant Transformation Core Facility, Division of Plant Sciences, University of Missouri, 1-33 Agriculture Building, Columbia, MO, 65211, USA
| | - Zhanyuan J Zhang
- Plant Transformation Core Facility, Division of Plant Sciences, University of Missouri, 1-33 Agriculture Building, Columbia, MO, 65211, USA.
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Fang YY, Zhao JH, Liu SW, Wang S, Duan CG, Guo HS. CMV2b-AGO Interaction Is Required for the Suppression of RDR-Dependent Antiviral Silencing in Arabidopsis. Front Microbiol 2016; 7:1329. [PMID: 27605926 PMCID: PMC4995204 DOI: 10.3389/fmicb.2016.01329] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2016] [Accepted: 08/11/2016] [Indexed: 12/02/2022] Open
Abstract
Using a transient plant system, it was previously found that the suppression of Cucumber mosaic virus (CMV) 2b protein relies on its double-strand (ds) RNA binding capacity, but it is independent of its interaction with ARGONAUTE (AGO) proteins. Thus, the biological meaning of the 2b-AGO interaction in the context of virus infection remains elusive. In this study, we created infectious clones of CMV mutants that expressed the 2b functional domains of dsRNA or AGO binding and tested the effect of these CMV mutants on viral pathogenicity. We found that the mutant CMV2b(1–76) expressing the 2b dsRNA-binding domain exhibited the same virulence as wild-type CMV in infection with either wild-type Arabidopsis or rdr1/6 plants with RDR1- and RDR6-deficient mutations. However, remarkably reduced viral RNA levels and increased virus (v)siRNAs were detected in CMV2b(1–76)-infected Arabidopsis in comparison to CMV infection, which demonstrated that the 2b(1–76) deleted AGO-binding domain failed to suppress the RDR1/RDR6-dependent degradation of viral RNAs. The mutant CMV2b(8–111) expressing mutant 2b, in which the N-terminal 7 amino acid (aa) was deleted, exhibited slightly reduced virulence, but not viral RNA levels, in both wild-type and rdr1/6 plants, which indicated that 2b retained the AGO-binding activity acquired the counter-RDRs degradation of viral RNAs. The deletion of the N-terminal 7 aa of 2b affected virulence due to the reduced affinity for long dsRNA. The mutant CMV2b(18–111) expressing mutant 2b lacked the N-terminal 17 aa but retained its AGO-binding activity greatly reduced virulence and viral RNA level. Together with the instability of both 2b(18–111)-EGFP and RFP-AGO4 proteins when co-expressed in Nicotiana benthamiana leaves, our data demonstrates that the effect of 2b-AGO interaction on counter-RDRs antiviral defense required the presence of 2b dsRNA-binding activity. Taken together, our findings demonstrate that the dsRNA-binding activity of the 2b was essential for virulence, whereas the 2b-AGO interaction was necessary for interference with RDR1/6-dependent antiviral silencing in Arabidopsis.
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Affiliation(s)
- Yuan-Yuan Fang
- State Key Laboratory of Plant Genomics, Institute of Microbiology, Chinese Academy of Sciences Beijing, China
| | - Jian-Hua Zhao
- State Key Laboratory of Plant Genomics, Institute of Microbiology, Chinese Academy of Sciences Beijing, China
| | - Shang-Wu Liu
- State Key Laboratory of Plant Genomics, Institute of Microbiology, Chinese Academy of SciencesBeijing, China; Virus-free Seedling Research Institute, Heilongjiang Academy of Agricultural SciencesHarbin, China
| | - Sheng Wang
- State Key Laboratory of Plant Genomics, Institute of Microbiology, Chinese Academy of Sciences Beijing, China
| | - Cheng-Guo Duan
- State Key Laboratory of Plant Genomics, Institute of Microbiology, Chinese Academy of Sciences Beijing, China
| | - Hui-Shan Guo
- State Key Laboratory of Plant Genomics, Institute of Microbiology, Chinese Academy of SciencesBeijing, China; College of Life Sciences, University of Chinese Academy of SciencesBeijing, China
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16
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Götz U, Marker S, Cheaib M, Andresen K, Shrestha S, Durai DA, Nordström KJ, Schulz MH, Simon M. Two sets of RNAi components are required for heterochromatin formation in trans triggered by truncated transgenes. Nucleic Acids Res 2016; 44:5908-23. [PMID: 27085807 PMCID: PMC4937312 DOI: 10.1093/nar/gkw267] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2015] [Accepted: 04/04/2016] [Indexed: 12/13/2022] Open
Abstract
Across kingdoms, RNA interference (RNAi) has been shown to control gene expression at the transcriptional- or the post-transcriptional level. Here, we describe a mechanism which involves both aspects: truncated transgenes, which fail to produce intact mRNA, induce siRNA accumulation and silencing of homologous loci in trans in the ciliate Paramecium. We show that silencing is achieved by co-transcriptional silencing, associated with repressive histone marks at the endogenous gene. This is accompanied by secondary siRNA accumulation, strictly limited to the open reading frame of the remote locus. Our data shows that in this mechanism, heterochromatic marks depend on a variety of RNAi components. These include RDR3 and PTIWI14 as well as a second set of components, which are also involved in post-transcriptional silencing: RDR2, PTIWI13, DCR1 and CID2. Our data indicates differential processing of nascent un-spliced and long, spliced transcripts thus suggesting a hitherto-unrecognized functional interaction between post-transcriptional and co-transcriptional RNAi. Both sets of RNAi components are required for efficient trans-acting RNAi at the chromatin level and our data indicates similar mechanisms contributing to genome wide regulation of gene expression by epigenetic mechanisms.
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Affiliation(s)
- Ulrike Götz
- Molecular Cell Dynamics Saarland University, Centre for Human and Molecular Biology, Campus A2 4, 66123 Saarbrücken, Germany Department of Biology, University of Kaiserslautern, Erwin-Schrödinger Straße, Building Nr. 14, 67663 Kaiserslautern, Germany
| | - Simone Marker
- Molecular Cell Dynamics Saarland University, Centre for Human and Molecular Biology, Campus A2 4, 66123 Saarbrücken, Germany
| | - Miriam Cheaib
- Molecular Cell Dynamics Saarland University, Centre for Human and Molecular Biology, Campus A2 4, 66123 Saarbrücken, Germany Department of Biology, University of Kaiserslautern, Erwin-Schrödinger Straße, Building Nr. 14, 67663 Kaiserslautern, Germany
| | - Karsten Andresen
- Institute of Biotechnology and Drug Research, Erwin-Schrödinger-Str. 56, 67663 Kaiserslautern, Germany
| | - Simon Shrestha
- Molecular Cell Dynamics Saarland University, Centre for Human and Molecular Biology, Campus A2 4, 66123 Saarbrücken, Germany Department of Biology, University of Kaiserslautern, Erwin-Schrödinger Straße, Building Nr. 14, 67663 Kaiserslautern, Germany
| | - Dilip A Durai
- Cluster of Excellence, Multimodal Computing and Interaction and Max Planck Institute for Informatics Saarland University, Department for Computational Biology and Applied Algorithmics, Campus E1 4, 66123 Saarbrücken, Germany
| | - Karl J Nordström
- Department for Genetics, Saarland University, Centre for Human and Molecular Biology, Campus A2 4, 66123 Saarbrücken, Germany
| | - Marcel H Schulz
- Cluster of Excellence, Multimodal Computing and Interaction and Max Planck Institute for Informatics Saarland University, Department for Computational Biology and Applied Algorithmics, Campus E1 4, 66123 Saarbrücken, Germany
| | - Martin Simon
- Molecular Cell Dynamics Saarland University, Centre for Human and Molecular Biology, Campus A2 4, 66123 Saarbrücken, Germany
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17
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Qian X, Hamid FM, El Sahili A, Darwis DA, Wong YH, Bhushan S, Makeyev EV, Lescar J. Functional Evolution in Orthologous Cell-encoded RNA-dependent RNA Polymerases. J Biol Chem 2016; 291:9295-309. [PMID: 26907693 PMCID: PMC4861493 DOI: 10.1074/jbc.m115.685933] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2015] [Indexed: 12/15/2022] Open
Abstract
Many eukaryotic organisms encode more than one RNA-dependent RNA polymerase (RdRP) that probably emerged as a result of gene duplication. Such RdRP paralogs often participate in distinct RNA silencing pathways and show characteristic repertoires of enzymatic activities in vitro However, to what extent members of individual paralogous groups can undergo functional changes during speciation remains an open question. We show that orthologs of QDE-1, an RdRP component of the quelling pathway in Neurospora crassa, have rapidly diverged in evolution at the amino acid sequence level. Analyses of purified QDE-1 polymerases from N. crassa (QDE-1(Ncr)) and related fungi, Thielavia terrestris (QDE-1(Tte)) and Myceliophthora thermophila (QDE-1(Mth)), show that all three enzymes can synthesize RNA, but the precise modes of their action differ considerably. Unlike their QDE-1(Ncr) counterpart favoring processive RNA synthesis, QDE-1(Tte) and QDE-1(Mth) produce predominantly short RNA copies via primer-independent initiation. Surprisingly, a 3.19 Å resolution crystal structure of QDE-1(Tte) reveals a quasisymmetric dimer similar to QDE-1(Ncr) Further electron microscopy analyses confirm that QDE-1(Tte) occurs as a dimer in solution and retains this status upon interaction with a template. We conclude that divergence of orthologous RdRPs can result in functional innovation while retaining overall protein fold and quaternary structure.
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Affiliation(s)
- Xinlei Qian
- From the Division of Structural Biology and Biochemistry, School of Biological Sciences, Nanyang Technological University, 138673 Singapore, Singapore
| | - Fursham M Hamid
- From the Division of Structural Biology and Biochemistry, School of Biological Sciences, Nanyang Technological University, 138673 Singapore, Singapore
| | - Abbas El Sahili
- From the Division of Structural Biology and Biochemistry, School of Biological Sciences, Nanyang Technological University, 138673 Singapore, Singapore
| | - Dina Amallia Darwis
- From the Division of Structural Biology and Biochemistry, School of Biological Sciences, Nanyang Technological University, 138673 Singapore, Singapore
| | - Yee Hwa Wong
- From the Division of Structural Biology and Biochemistry, School of Biological Sciences, Nanyang Technological University, 138673 Singapore, Singapore
| | - Shashi Bhushan
- From the Division of Structural Biology and Biochemistry, School of Biological Sciences, Nanyang Technological University, 138673 Singapore, Singapore
| | - Eugene V Makeyev
- From the Division of Structural Biology and Biochemistry, School of Biological Sciences, Nanyang Technological University, 138673 Singapore, Singapore, the Medical Research Council Centre for Developmental Neurobiology, King's College, London SE1 1UL, United Kingdom, and
| | - Julien Lescar
- From the Division of Structural Biology and Biochemistry, School of Biological Sciences, Nanyang Technological University, 138673 Singapore, Singapore, UPMC UMRS CR7-CNRS ERL 8255-INSERM U1135 Centre d' Immunologie et des Maladies Infectieuses, Faculté de Médecine Pierre et Marie Curie, Centre Hospitalier Universitaire Pitié-Salpêtrière, 75031 Paris, France
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18
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PRIMEGENSw3: a web-based tool for high-throughput primer and probe design. Methods Mol Biol 2015; 1275:181-99. [PMID: 25697661 DOI: 10.1007/978-1-4939-2365-6_14] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/24/2022]
Abstract
Highly specific and efficient primer and probe design has been a major hurdle in many high-throughput techniques. Successful implementation of any PCR or probe hybridization technique depends on the quality of primers and probes used in terms of their specificity and cross-hybridization. Here we describe PRIMEGENSw3, a set of web-based utilities for high-throughput primer and probe design. These utilities allow users to select genomic regions and to design primer/probe for selected regions in an interactive, user-friendly, and automatic fashion. The system runs the PRIMEGENS algorithm in the back-end on the high-performance server with the stored genomic database or user-provided custom database for cross-hybridization check. Cross-hybridization is checked not only using BLAST but also by checking mismatch positions and energy calculation of potential hybridization hits. The results can be visualized online and also can be downloaded. The average success rate of primer design using PRIMEGENSw3 is ~90 %. The web server also supports primer design for methylated sequences, which is used in epigenetic studies. Stand-alone version of the software is also available for download at the website.
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O’Neill EC, Trick M, Henrissat B, Field RA. Euglena in time: Evolution, control of central metabolic processes and multi-domain proteins in carbohydrate and natural product biochemistry. ACTA ACUST UNITED AC 2015. [DOI: 10.1016/j.pisc.2015.07.002] [Citation(s) in RCA: 34] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023]
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20
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Saeed M, Briddon RW, Dalakouras A, Krczal G, Wassenegger M. Functional Analysis of Cotton Leaf Curl Kokhran Virus/Cotton Leaf Curl Multan Betasatellite RNA Silencing Suppressors. BIOLOGY 2015; 4:697-714. [PMID: 26512705 PMCID: PMC4690014 DOI: 10.3390/biology4040697] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/29/2015] [Revised: 10/15/2015] [Accepted: 10/16/2015] [Indexed: 12/13/2022]
Abstract
In South Asia, Cotton leaf curl disease (CLCuD) is caused by a complex of phylogenetically-related begomovirus species and a specific betasatellite, Cotton leaf curl Multan betasatellite (CLCuMuB). The post-transcriptional gene silencing (PTGS) suppression activities of the transcriptional activator protein (TrAP), C4, V2 and βC1 proteins encoded by Cotton leaf curl Kokhran virus (CLCuKoV)/CLCuMuB were assessed in Nicotiana benthamiana. A variable degree of local silencing suppression was observed for each viral protein tested, with V2 protein exhibiting the strongest suppression activity and only the C4 protein preventing the spread of systemic silencing. The CLCuKoV-encoded TrAP, C4, V2 and CLCuMuB-encoded βC1 proteins were expressed in Escherichia coli and purified. TrAP was shown to bind various small and long nucleic acids including single-stranded (ss) and double-stranded (ds) RNA and DNA molecules. C4, V2, and βC1 bound ssDNA and dsDNA with varying affinities. Transgenic expression of C4 under the constitutive 35S Cauliflower mosaic virus promoter and βC1 under a dexamethasone inducible promoter induced severe developmental abnormalities in N. benthamiana. The results indicate that homologous proteins from even quite closely related begomoviruses may differ in their suppressor activity and mechanism of action. The significance of these findings is discussed.
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Affiliation(s)
- Muhammad Saeed
- RLP AgroScience GmbH, AlPlanta-Institute for Plant Research, Breitenweg 71, Neustadt D-67435, Germany.
- National Institute for Biotechnology and Genetic Engineering, Jhang Road, PO Box 577, Faisalabad 38000, Pakistan.
| | - Rob W Briddon
- National Institute for Biotechnology and Genetic Engineering, Jhang Road, PO Box 577, Faisalabad 38000, Pakistan.
| | - Athanasios Dalakouras
- RLP AgroScience GmbH, AlPlanta-Institute for Plant Research, Breitenweg 71, Neustadt D-67435, Germany.
| | - Gabi Krczal
- RLP AgroScience GmbH, AlPlanta-Institute for Plant Research, Breitenweg 71, Neustadt D-67435, Germany.
| | - Michael Wassenegger
- RLP AgroScience GmbH, AlPlanta-Institute for Plant Research, Breitenweg 71, Neustadt D-67435, Germany.
- Centre for Organismal Studies (COS) Heidelberg, University of Heidelberg, Im Neuenheimer Feld 360, Heidelberg D-69120, Germany.
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Zhao M, San León D, Mesel F, García JA, Simón-Mateo C. Assorted Processing of Synthetic Trans-Acting siRNAs and Its Activity in Antiviral Resistance. PLoS One 2015; 10:e0132281. [PMID: 26147769 PMCID: PMC4492489 DOI: 10.1371/journal.pone.0132281] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2015] [Accepted: 06/11/2015] [Indexed: 11/18/2022] Open
Abstract
The use of syn-tasiRNAs has been proposed as an RNA interference technique alternative to those previously described: hairpin based, virus induced gene silencing or artificial miRNAs. In this study we engineered the TAS1c locus to impair Plum pox virus (PPV) infection by replacing the five native siRNAs with two 210-bp fragments from the CP and the 3´NCR regions of the PPV genome. Deep sequencing analysis of the small RNA species produced by both constructs in planta has shown that phased processing of the syn-tasiRNAs is construct-specific. While in syn-tasiR-CP construct the processing was as predicted 21-nt phased in register with miR173-guided cleavage, the processing of syn-tasiR-3NCR is far from what was expected. A 22-nt species from the miR173-guided cleavage was a guide of two series of phased small RNAs, one of them in an exact 21-nt register, and the other one in a mixed of 21-/22-nt frame. In addition, both constructs produced abundant PPV-derived small RNAs in the absence of miR173 as a consequence of a strong sense post-transcriptional gene silencing induction. The antiviral effect of both constructs was also evaluated in the presence or absence of miR173 and showed that the impairment of PPV infection was not significantly higher when miR173 was present. The results show that syn-tasiRNAs processing depends on construct-specific factors that should be further studied before the so-called MIGS (miRNA-induced gene silencing) technology can be used reliably.
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Affiliation(s)
- Mingmin Zhao
- Departamento de Genética Molecular de Plantas, Centro Nacional de Biotecnología (CNB-CSIC), Campus Universidad Autónoma de Madrid, 28049, Madrid, Spain
| | - David San León
- Departamento de Genética Molecular de Plantas, Centro Nacional de Biotecnología (CNB-CSIC), Campus Universidad Autónoma de Madrid, 28049, Madrid, Spain
| | - Frida Mesel
- Departamento de Genética Molecular de Plantas, Centro Nacional de Biotecnología (CNB-CSIC), Campus Universidad Autónoma de Madrid, 28049, Madrid, Spain
| | - Juan Antonio García
- Departamento de Genética Molecular de Plantas, Centro Nacional de Biotecnología (CNB-CSIC), Campus Universidad Autónoma de Madrid, 28049, Madrid, Spain
| | - Carmen Simón-Mateo
- Departamento de Genética Molecular de Plantas, Centro Nacional de Biotecnología (CNB-CSIC), Campus Universidad Autónoma de Madrid, 28049, Madrid, Spain
- College of Agriculture, Yangtze University, Jingzhou, Hubei, 434025, P.R. China
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Weinheimer I, Jiu Y, Rajamäki ML, Matilainen O, Kallijärvi J, Cuellar WJ, Lu R, Saarma M, Holmberg CI, Jäntti J, Valkonen JPT. Suppression of RNAi by dsRNA-degrading RNaseIII enzymes of viruses in animals and plants. PLoS Pathog 2015; 11:e1004711. [PMID: 25747942 PMCID: PMC4352025 DOI: 10.1371/journal.ppat.1004711] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2014] [Accepted: 01/28/2015] [Indexed: 01/08/2023] Open
Abstract
Certain RNA and DNA viruses that infect plants, insects, fish or poikilothermic animals encode Class 1 RNaseIII endoribonuclease-like proteins. dsRNA-specific endoribonuclease activity of the RNaseIII of rock bream iridovirus infecting fish and Sweet potato chlorotic stunt crinivirus (SPCSV) infecting plants has been shown. Suppression of the host antiviral RNA interference (RNAi) pathway has been documented with the RNaseIII of SPCSV and Heliothis virescens ascovirus infecting insects. Suppression of RNAi by the viral RNaseIIIs in non-host organisms of different kingdoms is not known. Here we expressed PPR3, the RNaseIII of Pike-perch iridovirus, in the non-hosts Nicotiana benthamiana (plant) and Caenorhabditis elegans (nematode) and found that it cleaves double-stranded small interfering RNA (ds-siRNA) molecules that are pivotal in the host RNA interference (RNAi) pathway and thereby suppresses RNAi in non-host tissues. In N. benthamiana, PPR3 enhanced accumulation of Tobacco rattle tobravirus RNA1 replicon lacking the 16K RNAi suppressor. Furthermore, PPR3 suppressed single-stranded RNA (ssRNA)--mediated RNAi and rescued replication of Flock House virus RNA1 replicon lacking the B2 RNAi suppressor in C. elegans. Suppression of RNAi was debilitated with the catalytically compromised mutant PPR3-Ala. However, the RNaseIII (CSR3) produced by SPCSV, which cleaves ds-siRNA and counteracts antiviral RNAi in plants, failed to suppress ssRNA-mediated RNAi in C. elegans. In leaves of N. benthamiana, PPR3 suppressed RNAi induced by ssRNA and dsRNA and reversed silencing; CSR3, however, suppressed only RNAi induced by ssRNA and was unable to reverse silencing. Neither PPR3 nor CSR3 suppressed antisense-mediated RNAi in Drosophila melanogaster. These results show that the RNaseIII enzymes of RNA and DNA viruses suppress RNAi, which requires catalytic activities of RNaseIII. In contrast to other viral silencing suppression proteins, the RNaseIII enzymes are homologous in unrelated RNA and DNA viruses and can be detected in viral genomes using gene modeling and protein structure prediction programs.
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Affiliation(s)
- Isabel Weinheimer
- Department of Agricultural Sciences, University of Helsinki, Helsinki, Finland
| | - Yaming Jiu
- Institute of Biotechnology, University of Helsinki, Helsinki, Finland
| | | | - Olli Matilainen
- Research Programs Unit, Translational Cancer Biology, and Institute of Biomedicine, Biomedicum Helsinki, University of Helsinki, Helsinki, Finland
| | - Jukka Kallijärvi
- Institute of Biotechnology, University of Helsinki, Helsinki, Finland
| | - Wilmer J. Cuellar
- Department of Agricultural Sciences, University of Helsinki, Helsinki, Finland
| | - Rui Lu
- Department of Biological Sciences, Louisiana State University, Baton Rouge, Louisiana, United States of America
| | - Mart Saarma
- Institute of Biotechnology, University of Helsinki, Helsinki, Finland
| | - Carina I. Holmberg
- Research Programs Unit, Translational Cancer Biology, and Institute of Biomedicine, Biomedicum Helsinki, University of Helsinki, Helsinki, Finland
| | - Jussi Jäntti
- Institute of Biotechnology, University of Helsinki, Helsinki, Finland
- VTT Technical Research Centre of Finland, Espoo, Finland
| | - Jari P. T. Valkonen
- Department of Agricultural Sciences, University of Helsinki, Helsinki, Finland
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Carradec Q, Götz U, Arnaiz O, Pouch J, Simon M, Meyer E, Marker S. Primary and secondary siRNA synthesis triggered by RNAs from food bacteria in the ciliate Paramecium tetraurelia. Nucleic Acids Res 2015; 43:1818-33. [PMID: 25593325 PMCID: PMC4330347 DOI: 10.1093/nar/gku1331] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
Abstract
In various organisms, an efficient RNAi response can be triggered by feeding cells with bacteria producing double-stranded RNA (dsRNA) against an endogenous gene. However, the detailed mechanisms and natural functions of this pathway are not well understood in most cases. Here, we studied siRNA biogenesis from exogenous RNA and its genetic overlap with endogenous RNAi in the ciliate Paramecium tetraurelia by high-throughput sequencing. Using wild-type and mutant strains deficient for dsRNA feeding we found that high levels of primary siRNAs of both strands are processed from the ingested dsRNA trigger by the Dicer Dcr1, the RNA-dependent RNA polymerases Rdr1 and Rdr2 and other factors. We further show that this induces the synthesis of secondary siRNAs spreading along the entire endogenous mRNA, demonstrating the occurrence of both 3′-to-5′ and 5′-to-3′ transitivity for the first time in the SAR clade of eukaryotes (Stramenopiles, Alveolates, Rhizaria). Secondary siRNAs depend on Rdr2 and show a strong antisense bias; they are produced at much lower levels than primary siRNAs and hardly contribute to RNAi efficiency. We further provide evidence that the Paramecium RNAi machinery also processes single-stranded RNAs from its bacterial food, broadening the possible natural functions of exogenously induced RNAi in this organism.
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Affiliation(s)
- Quentin Carradec
- Institut de Biologie de l'ENS, IBENS, Ecole Normale Supérieure, Inserm, U1024, CNRS, UMR 8197, 75005 Paris, France UPMC, IFD, Sorbonne Universités, 4 place Jussieu, 75252 Paris cedex 05, France
| | - Ulrike Götz
- Zentrum für Human- und Molekularbiologie, Molekulare Zelldynamik, Universität des Saarlandes, Campus A2 4, 66123 Saarbrücken, Germany
| | - Olivier Arnaiz
- Centre de Génétique Moléculaire, CNRS UPR3404, 91198 Gif-sur-Yvette cedex, France
| | - Juliette Pouch
- Institut de Biologie de l'ENS, IBENS, Ecole Normale Supérieure, Inserm, U1024, CNRS, UMR 8197, 75005 Paris, France
| | - Martin Simon
- Zentrum für Human- und Molekularbiologie, Molekulare Zelldynamik, Universität des Saarlandes, Campus A2 4, 66123 Saarbrücken, Germany
| | - Eric Meyer
- Institut de Biologie de l'ENS, IBENS, Ecole Normale Supérieure, Inserm, U1024, CNRS, UMR 8197, 75005 Paris, France
| | - Simone Marker
- Institut de Biologie de l'ENS, IBENS, Ecole Normale Supérieure, Inserm, U1024, CNRS, UMR 8197, 75005 Paris, France Zentrum für Human- und Molekularbiologie, Molekulare Zelldynamik, Universität des Saarlandes, Campus A2 4, 66123 Saarbrücken, Germany
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Ruiz-Vázquez RM, Nicolás FE, Torres-Martínez S, Garre V. Distinct RNAi Pathways in the Regulation of Physiology and Development in the Fungus Mucor circinelloides. ADVANCES IN GENETICS 2015; 91:55-102. [DOI: 10.1016/bs.adgen.2015.07.002] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
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Galvez LC, Banerjee J, Pinar H, Mitra A. Engineered plant virus resistance. PLANT SCIENCE : AN INTERNATIONAL JOURNAL OF EXPERIMENTAL PLANT BIOLOGY 2014; 228:11-25. [PMID: 25438782 DOI: 10.1016/j.plantsci.2014.07.006] [Citation(s) in RCA: 32] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/04/2014] [Revised: 07/16/2014] [Accepted: 07/18/2014] [Indexed: 06/04/2023]
Abstract
Virus diseases are among the key limiting factors that cause significant yield loss and continuously threaten crop production. Resistant cultivars coupled with pesticide application are commonly used to circumvent these threats. One of the limitations of the reliance on resistant cultivars is the inevitable breakdown of resistance due to the multitude of variable virus populations. Similarly, chemical applications to control virus transmitting insect vectors are costly to the farmers, cause adverse health and environmental consequences, and often result in the emergence of resistant vector strains. Thus, exploiting strategies that provide durable and broad-spectrum resistance over diverse environments are of paramount importance. The development of plant gene transfer systems has allowed for the introgression of alien genes into plant genomes for novel disease control strategies, thus providing a mechanism for broadening the genetic resources available to plant breeders. Genetic engineering offers various options for introducing transgenic virus resistance into crop plants to provide a wide range of resistance to viral pathogens. This review examines the current strategies of developing virus resistant transgenic plants.
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Affiliation(s)
- Leny C Galvez
- Department of Plant Pathology, University of Nebarska, Lincoln, NE 68583-0722, USA
| | - Joydeep Banerjee
- Department of Plant Pathology, University of Nebarska, Lincoln, NE 68583-0722, USA
| | - Hasan Pinar
- Department of Plant Pathology, University of Nebarska, Lincoln, NE 68583-0722, USA
| | - Amitava Mitra
- Department of Plant Pathology, University of Nebarska, Lincoln, NE 68583-0722, USA.
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26
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Zhang ZJ. Artificial trans-acting small interfering RNA: a tool for plant biology study and crop improvements. PLANTA 2014; 239:1139-46. [PMID: 24643516 DOI: 10.1007/s00425-014-2054-x] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/24/2013] [Accepted: 03/05/2014] [Indexed: 05/25/2023]
Abstract
Completion of whole genome sequencing in many plant species including economically important crop species not only opens up new opportunities but also imposes challenges for plant science research community. Functional validation and utilization of these enormous DNA sequences necessitate new or improved tools with high accuracy and efficiency. Of various tools, small RNA-mediated gene silencing platform plays an important and unique role in functional verification of plant genes and trait improvements. Artificial trans-acting small interfering RNA (atasiRNA) has emerged as a potent and specific gene silencing platform which overcomes major limitations of other small RNA silencing approaches including double-stranded RNA, artificial microRNA (amiRNA), and microRNA-induced gene silencing. To best utilize atasiRNA platform, it is essential to be able to test candidate atasiRNAs efficiently through either in vivo or in vitro validation approach. Very recently, a breakthrough has been made in developing a new method for in vitro screen of amiRNA candidates, named "epitope-tagged protein-based amiRNA screens". Such a screen can be readily employed to validate atasiRNA candidates and thus accelerate the deployment of atasiRNA technology. Therefore, atasiRNA as an emerging tool shall accelerate both plant biology study and crop genetic improvements including trait stacking.
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Affiliation(s)
- Zhanyuan J Zhang
- Plant Transformation Core Facility, Division of Plant Sciences, University of Missouri, 1-33 Agriculture Building, Columbia, MO, 65211, USA,
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Marker S, Carradec Q, Tanty V, Arnaiz O, Meyer E. A forward genetic screen reveals essential and non-essential RNAi factors in Paramecium tetraurelia. Nucleic Acids Res 2014; 42:7268-80. [PMID: 24860163 PMCID: PMC4066745 DOI: 10.1093/nar/gku223] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022] Open
Abstract
In most eukaryotes, small RNA-mediated gene silencing pathways form complex interacting networks. In the ciliate Paramecium tetraurelia, at least two RNA interference (RNAi) mechanisms coexist, involving distinct but overlapping sets of protein factors and producing different types of short interfering RNAs (siRNAs). One is specifically triggered by high-copy transgenes, and the other by feeding cells with double-stranded RNA (dsRNA)-producing bacteria. In this study, we designed a forward genetic screen for mutants deficient in dsRNA-induced silencing, and a powerful method to identify the relevant mutations by whole-genome sequencing. We present a set of 47 mutant alleles for five genes, revealing two previously unknown RNAi factors: a novel Paramecium-specific protein (Pds1) and a Cid1-like nucleotidyl transferase. Analyses of allelic diversity distinguish non-essential and essential genes and suggest that the screen is saturated for non-essential, single-copy genes. We show that non-essential genes are specifically involved in dsRNA-induced RNAi while essential ones are also involved in transgene-induced RNAi. One of the latter, the RNA-dependent RNA polymerase RDR2, is further shown to be required for all known types of siRNAs, as well as for sexual reproduction. These results open the way for the dissection of the genetic complexity, interconnection, mechanisms and natural functions of RNAi pathways in P. tetraurelia.
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Affiliation(s)
- Simone Marker
- Ecole Normale Supérieure, Institut de Biologie de l'ENS, IBENS, Inserm, U1024, CNRS, UMR 8197, Paris F-75005, France
| | - Quentin Carradec
- Ecole Normale Supérieure, Institut de Biologie de l'ENS, IBENS, Inserm, U1024, CNRS, UMR 8197, Paris F-75005, France Sorbonne Universités, UPMC Univ., IFD, 4 place Jussieu, F-75252 Paris cedex 05, France
| | - Véronique Tanty
- Ecole Normale Supérieure, Institut de Biologie de l'ENS, IBENS, Inserm, U1024, CNRS, UMR 8197, Paris F-75005, France
| | - Olivier Arnaiz
- CNRS UPR3404 Centre de Génétique Moléculaire, Gif-sur-Yvette F-91198 cedex, France; Université Paris-Sud, Département de Biologie, Orsay, F-91405, France
| | - Eric Meyer
- Ecole Normale Supérieure, Institut de Biologie de l'ENS, IBENS, Inserm, U1024, CNRS, UMR 8197, Paris F-75005, France
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Yoshikawa M. Biogenesis of trans-acting siRNAs, endogenous secondary siRNAs in plants. Genes Genet Syst 2014; 88:77-84. [PMID: 23832299 DOI: 10.1266/ggs.88.77] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022] Open
Abstract
Trans-acting small interfering RNAs (tasiRNAs) are plant-specific endogenous siRNAs that control non-identical mRNAs via cleavage. The production of tasiRNAs is triggered by cleavage of capped and polyadenylated primary TAS transcripts (pri-TASs) by specific miRNAs. Following miRNA-directed cleavage, either 5' or 3' cleavage fragments are converted into double-stranded RNAs (dsRNAs) by RNA-DEPENDENT RNA POLYMERASE 6. The dsRNAs are processed to tasiRNAs by DICER-LIKE 4 in a phasing manner. There are two forms of pri-TASs; One has a single miRNA target site that is targeted by 22-nucleotide microRNAs, and the other has two miR390 target sites. Secondary siRNAs that are important for the amplification of RNA silencing are defined as siRNAs whose production is initiated by the cleavage of primary small RNA-containing RNA-induced silencing complexes. Thus, tasiRNA production is a model system of secondary siRNA production in plants. This review focuses on the production of tasiRNAs that are endogenous secondary siRNAs.
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Affiliation(s)
- Manabu Yoshikawa
- Division of Plant Sciences, National Institute of Agrobiological Sciences, Kannondai 2-1-2, Tsukuba, Ibaraki 305-8602, Japan.
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29
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Weinheimer I, Boonrod K, Moser M, Wassenegger M, Krczal G, Butcher SJ, Valkonen JPT. Binding and processing of small dsRNA molecules by the class 1 RNase III protein encoded by sweet potato chlorotic stunt virus. J Gen Virol 2013; 95:486-495. [PMID: 24187016 DOI: 10.1099/vir.0.058693-0] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023] Open
Abstract
Sweet potato chlorotic stunt virus (SPCSV; genus Crinivirus, family Closteroviridae) causes heavy yield losses in sweet potato plants co-infected with other viruses. The dsRNA-specific class 1 RNase III-like endoribonuclease (RNase3) encoded by SPCSV suppresses post-transcriptional gene silencing and eliminates antiviral defence in sweet potato plants in an endoribonuclease activity-dependent manner. RNase3 can cleave long dsRNA molecules, synthetic small interfering RNAs (siRNAs), and plant- and virus-derived siRNAs extracted from sweet potato plants. In this study, conditions for efficient expression and purification of enzymically active recombinant RNase3 were established. Similar to bacterial class 1 RNase III enzymes, RNase3-Ala (a dsRNA cleavage-deficient mutant) bound to and processed double-stranded siRNA (ds-siRNA) as a dimer. The results support the classification of SPCSV RNase3 as a class 1 RNase III enzyme. There is little information about the specificity of RNase III enzymes on small dsRNAs. In vitro assays indicated that ds-siRNAs and microRNAs (miRNAs) with a regular A-form conformation were cleaved by RNase3, but asymmetrical bulges, extensive mismatches and 2'-O-methylation of ds-siRNA and miRNA interfered with processing. Whereas Mg(2+) was the cation that best supported the catalytic activity of RNase3, binding of 21 nt small dsRNA molecules was most efficient in the presence of Mn(2+). Processing of long dsRNA by RNase3 was efficient at pH 7.5 and 8.5, whereas ds-siRNA was processed more efficiently at pH 8.5. The results revealed factors that influence binding and processing of small dsRNA substrates by class 1 RNase III in vitro or make them unsuitable for processing by the enzyme.
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Affiliation(s)
- Isabel Weinheimer
- AgroScience GmbH, AlPlanta-Institute for Plant Research, Breitenweg 71, Neustadt a.d.W., Germany.,Department of Agricultural Sciences, PO Box 27, 00014 University of Helsinki, Helsinki, Finland
| | - Kajohn Boonrod
- AgroScience GmbH, AlPlanta-Institute for Plant Research, Breitenweg 71, Neustadt a.d.W., Germany
| | - Mirko Moser
- AgroScience GmbH, AlPlanta-Institute for Plant Research, Breitenweg 71, Neustadt a.d.W., Germany
| | - Michael Wassenegger
- Centre for Organismal Studies (COS) Heidelberg, Im Neuenheimer Feld 230, Heidelberg, Germany.,AgroScience GmbH, AlPlanta-Institute for Plant Research, Breitenweg 71, Neustadt a.d.W., Germany
| | - Gabi Krczal
- AgroScience GmbH, AlPlanta-Institute for Plant Research, Breitenweg 71, Neustadt a.d.W., Germany
| | - Sarah J Butcher
- Institute of Biotechnology, PO Box 65, 00014 University of Helsinki, Helsinki, Finland
| | - Jari P T Valkonen
- Department of Agricultural Sciences, PO Box 27, 00014 University of Helsinki, Helsinki, Finland
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Haikonen T, Rajamäki ML, Valkonen JPT. Improved silencing suppression and enhanced heterologous protein expression are achieved using an engineered viral helper component proteinase. J Virol Methods 2013; 193:687-92. [PMID: 23933077 DOI: 10.1016/j.jviromet.2013.07.054] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2013] [Revised: 07/20/2013] [Accepted: 07/22/2013] [Indexed: 12/14/2022]
Abstract
RNA silencing limits transient expression of heterologous proteins in plants. Co-expression of viral silencing suppressor proteins can increase and prolong protein expression, but highly efficient silencing suppressors may stress plant tissue and be detrimental to protein yields. Little is known whether silencing suppression could be improved without harm to plant tissues. This study reports development of enhanced silencing suppressors by engineering the helper component proteinase (HCpro) of Potato virus A (PVA). Mutations were introduced to a short region of HCpro (positions 330-335 in PVA HCpro), which is hypervariable among potyviruses. Three out of the four HCpro mutants suppressed RNA silencing more efficiently and sustained expression of co-expressed jellyfish green fluorescent protein for a longer time than wild-type HCpro in agroinfiltrated leaves of Nicotiana benthamiana. Leaf tissues remained healthy-looking without any visible signs of stress.
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Affiliation(s)
- T Haikonen
- Department of Agricultural Sciences, P.O. Box 27, University of Helsinki, FIN-00014 Helsinki, Finland
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Feng L, Duan CG, Guo HS. Inhibition of in vivo Slicer activity of Argonaute protein 1 by the viral 2b protein independent of its dsRNA-binding function. MOLECULAR PLANT PATHOLOGY 2013; 14:617-22. [PMID: 23621279 PMCID: PMC6638910 DOI: 10.1111/mpp.12033] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/21/2023]
Abstract
The 2b protein of Cucumber mosaic virus (CMV) has several unique properties, such as targeting to the nucleolus and interaction with both Argonautes (AGOs) and short and long double-stranded RNA (dsRNA). We have recently uncoupled the domain requirements for dsRNA binding and nucleolar targeting from the physical interactions with AGO proteins, and have found that the direct 2b-AGO interaction is sufficient to inhibit the in vitro AGO1 Slicer function independent of the other biochemical properties of 2b. Because the AGO binding activity of 2b is not required for its suppressor function in vivo, this raises the question of whether in vivo 2b-AGO interaction is possible to inhibit the in vivo AGO Slicer function. In this study, by taking advantage of a technology for the production of artificial trans-acting small interfering RNA (tasiRNA), a process uniquely associated with AGO1-mediated in vivo Slicer activity, we demonstrated that the expression of the 2b protein in planta interfered with the production of tasiRNA. Through further detailed analysis with deletion mutants of 2b proteins, we found that the inhibition of in vivo AGO1 Slicer function required the nucleolar localization signal (NoLS), in addition to the AGO-binding domain, of the 2b protein. Our finding demonstrates that in vivo 2b-AGO1 interaction is sufficient to inhibit AGO1 Slicer function independent of the dsRNA-binding activity of the 2b protein.
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Affiliation(s)
- Lei Feng
- State Key Laboratory of Plant Genomics and National Center for Plant Gene Research, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, China
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Yaegashi H, Yoshikawa N, Ito T, Kanematsu S. A mycoreovirus suppresses RNA silencing in the white root rot fungus, Rosellinia necatrix. Virology 2013; 444:409-16. [PMID: 23896640 DOI: 10.1016/j.virol.2013.07.010] [Citation(s) in RCA: 46] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2013] [Revised: 07/10/2013] [Accepted: 07/10/2013] [Indexed: 12/23/2022]
Abstract
RNA silencing is a fundamental antiviral response in eukaryotic organisms. We investigated the counterdefense strategy of a fungal virus (mycovirus) against RNA silencing in the white root rot fungus, Rosellinia necatrix. We generated an R. necatrix strain that constitutively induced RNA silencing of the exogenous green fluorescent protein (GFP) gene, and infected it with each of four unrelated mycoviruses, including a partitivirus, a mycoreovirus, a megabirnavirus, and a quadrivirus. Infection with a mycoreovirus (R. necatrix mycoreovirus 3; RnMyRV3) suppressed RNA silencing of GFP, while the other mycoviruses did not. RnMyRV3 reduced accumulation of GFP-small interfering (si) RNAs and increased accumulation of GFP-double-stranded (ds) RNA; suggesting that the virus interferes with the dicing of dsRNA. Moreover, an agroinfiltration assay in planta revealed that the S10 gene of RnMyRV3 has RNA silencing suppressor activity. These data corroborate the counterdefense strategy of RnMyRV3 against host RNA silencing.
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Affiliation(s)
- Hajime Yaegashi
- Apple Research Station, National Institute of Fruit Tree Science, National Agriculture and Food Research Organization (NARO), 92 Shimokuriyagawa, Morioka, Iwate 020-0123, Japan.
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Harmoko R, Fanata WID, Yoo JY, Ko KS, Rim YG, Uddin MN, Siswoyo TA, Lee SS, Kim DY, Lee SY, Lee KO. RNA-dependent RNA polymerase 6 is required for efficient hpRNA-induced gene silencing in plants. Mol Cells 2013; 35:202-9. [PMID: 23456296 PMCID: PMC3887914 DOI: 10.1007/s10059-013-2203-2] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2012] [Revised: 01/08/2013] [Accepted: 01/09/2013] [Indexed: 01/03/2023] Open
Abstract
In plants, transgenes with inverted repeats are used to induce efficient RNA silencing, which is also frequently induced by highly transcribed sense transgenes. RNA silencing induced by sense transgenes is dependent on RNA-dependent RNA polymerase 6 (RDR6), which converts single-stranded (ss) RNA into double-stranded (ds) RNA. By contrast, it has been proposed that RNA silencing induced by self-complementary hairpin RNA (hpRNA) does not require RDR6, because the hpRNA can directly fold back on itself to form dsRNA. However, it is unclear whether RDR6 plays a role in hpRNA-induced RNA silencing by amplifying dsRNA to spread RNA silencing within the plant. To address the efficiency of hpRNA-induced RNA silencing in the presence or absence of RDR6, Wild type (WT, Col-0) and rdr6-11 Arabidopsis thaliana lines expressing green fluorescent protein (GFP) were generated and transformed with a GFP-RNA interference (RNAi) construct. Whereas most GFP-RNAi-transformed WT lines exhibited almost complete silencing of GFP expression in the T1 generation, various levels of GFP expression remained among the GFP-RNAi-transformed rdr6-11 lines. Homozygous expression of GFP-RNAi in the T3 generation was not sufficient to induce complete GFP silencing in several rdr6-11 lines. Our results indicate that RDR6 is required for efficient hpRNA-induced RNA silencing in plants.
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Affiliation(s)
- Rikno Harmoko
- Division of Applied Life Science (Brain Korea 21 Program) and Plant Molecular Biology Biotechnology Research Center (PMBBRC), Gyeongsang National University, Jinju 660–701,
Korea
| | - Wahyu Indra Duwi Fanata
- Division of Applied Life Science (Brain Korea 21 Program) and Plant Molecular Biology Biotechnology Research Center (PMBBRC), Gyeongsang National University, Jinju 660–701,
Korea
| | - Jae Yong Yoo
- Division of Applied Life Science (Brain Korea 21 Program) and Plant Molecular Biology Biotechnology Research Center (PMBBRC), Gyeongsang National University, Jinju 660–701,
Korea
| | - Ki Seong Ko
- Division of Applied Life Science (Brain Korea 21 Program) and Plant Molecular Biology Biotechnology Research Center (PMBBRC), Gyeongsang National University, Jinju 660–701,
Korea
| | - Yeong Gil Rim
- Division of Applied Life Science (Brain Korea 21 Program) and Plant Molecular Biology Biotechnology Research Center (PMBBRC), Gyeongsang National University, Jinju 660–701,
Korea
| | - Mohammad Nazim Uddin
- Division of Applied Life Science (Brain Korea 21 Program) and Plant Molecular Biology Biotechnology Research Center (PMBBRC), Gyeongsang National University, Jinju 660–701,
Korea
| | | | | | | | - Sang Yeol Lee
- Division of Applied Life Science (Brain Korea 21 Program) and Plant Molecular Biology Biotechnology Research Center (PMBBRC), Gyeongsang National University, Jinju 660–701,
Korea
| | - Kyun Oh Lee
- Division of Applied Life Science (Brain Korea 21 Program) and Plant Molecular Biology Biotechnology Research Center (PMBBRC), Gyeongsang National University, Jinju 660–701,
Korea
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Role of RNA interference (RNAi) in the Moss Physcomitrella patens. Int J Mol Sci 2013; 14:1516-40. [PMID: 23344055 PMCID: PMC3565333 DOI: 10.3390/ijms14011516] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2012] [Revised: 12/09/2012] [Accepted: 12/10/2012] [Indexed: 01/21/2023] Open
Abstract
RNA interference (RNAi) is a mechanism that regulates genes by either transcriptional (TGS) or posttranscriptional gene silencing (PTGS), required for genome maintenance and proper development of an organism. Small non-coding RNAs are the key players in RNAi and have been intensively studied in eukaryotes. In plants, several classes of small RNAs with specific sizes and dedicated functions have evolved. The major classes of small RNAs include microRNAs (miRNAs) and small interfering RNAs (siRNAs), which differ in their biogenesis. miRNAs are synthesized from a short hairpin structure while siRNAs are derived from long double-stranded RNAs (dsRNA). Both miRNA and siRNAs control the expression of cognate target RNAs by binding to reverse complementary sequences mediating cleavage or translational inhibition of the target RNA. They also act on the DNA and cause epigenetic changes such as DNA methylation and histone modifications. In the last years, the analysis of plant RNAi pathways was extended to the bryophyte Physcomitrella patens, a non-flowering, non-vascular ancient land plant that diverged from the lineage of seed plants approximately 450 million years ago. Based on a number of characteristic features and its phylogenetic key position in land plant evolution P. patens emerged as a plant model species to address basic as well as applied topics in plant biology. Here we summarize the current knowledge on the role of RNAi in P. patens that shows functional overlap with RNAi pathways from seed plants, and also unique features specific to this species.
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Vetukuri RR, Åsman AKM, Tellgren-Roth C, Jahan SN, Reimegård J, Fogelqvist J, Savenkov E, Söderbom F, Avrova AO, Whisson SC, Dixelius C. Evidence for small RNAs homologous to effector-encoding genes and transposable elements in the oomycete Phytophthora infestans. PLoS One 2012; 7:e51399. [PMID: 23272103 PMCID: PMC3522703 DOI: 10.1371/journal.pone.0051399] [Citation(s) in RCA: 65] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2012] [Accepted: 10/31/2012] [Indexed: 12/03/2022] Open
Abstract
Phytophthora infestans is the oomycete pathogen responsible for the devastating late blight disease on potato and tomato. There is presently an intense research focus on the role(s) of effectors in promoting late blight disease development. However, little is known about how they are regulated, or how diversity in their expression may be generated among different isolates. Here we present data from investigation of RNA silencing processes, characterized by non-coding small RNA molecules (sRNA) of 19-40 nt. From deep sequencing of sRNAs we have identified sRNAs matching numerous RxLR and Crinkler (CRN) effector protein genes in two isolates differing in pathogenicity. Effector gene-derived sRNAs were present in both isolates, but exhibited marked differences in abundance, especially for CRN effectors. Small RNAs in P. infestans grouped into three clear size classes of 21, 25/26 and 32 nt. Small RNAs from all size classes mapped to RxLR effector genes, but notably 21 nt sRNAs were the predominant size class mapping to CRN effector genes. Some effector genes, such as PiAvr3a, to which sRNAs were found, also exhibited differences in transcript accumulation between the two isolates. The P. infestans genome is rich in transposable elements, and the majority of sRNAs of all size classes mapped to these sequences, predominantly to long terminal repeat (LTR) retrotransposons. RNA silencing of Dicer and Argonaute genes provided evidence that generation of 21 nt sRNAs is Dicer-dependent, while accumulation of longer sRNAs was impacted by silencing of Argonaute genes. Additionally, we identified six microRNA (miRNA) candidates from our sequencing data, their precursor sequences from the genome sequence, and target mRNAs. These miRNA candidates have features characteristic of both plant and metazoan miRNAs.
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Affiliation(s)
- Ramesh R Vetukuri
- Department of Plant Biology and Forest Genetics, Uppsala BioCenter, Swedish University of Agricultural Sciences and Linnean Center for Plant Biology, Uppsala, Sweden.
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Russell SD, Gou X, Wong CE, Wang X, Yuan T, Wei X, Bhalla PL, Singh MB. Genomic profiling of rice sperm cell transcripts reveals conserved and distinct elements in the flowering plant male germ lineage. THE NEW PHYTOLOGIST 2012; 195:560-573. [PMID: 22716952 DOI: 10.1111/j.1469-8137.2012.04199.x] [Citation(s) in RCA: 48] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/06/2023]
Abstract
Genomic assay of sperm cell RNA provides insight into functional control, modes of regulation, and contributions of male gametes to double fertilization. Sperm cells of rice (Oryza sativa) were isolated from field-grown, disease-free plants and RNA was processed for use with the full-genome Affymetrix microarray. Comparison with Gene Expression Omnibus (GEO) reference arrays confirmed expressionally distinct gene profiles. A total of 10,732 distinct gene sequences were detected in sperm cells, of which 1668 were not expressed in pollen or seedlings. Pathways enriched in male germ cells included ubiquitin-mediated pathways, pathways involved in chromatin modeling including histones, histone modification and nonhistone epigenetic modification, and pathways related to RNAi and gene silencing. Genome-wide expression patterns in angiosperm sperm cells indicate common and divergent themes in the male germline that appear to be largely self-regulating through highly up-regulated chromatin modification pathways. A core of highly conserved genes appear common to all sperm cells, but evidence is still emerging that another class of genes have diverged in expression between monocots and dicots since their divergence. Sperm cell transcripts present at fusion may be transmitted through plasmogamy during double fertilization to effect immediate post-fertilization expression of early embryo and (or) endosperm development.
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Affiliation(s)
- Scott D Russell
- Department of Microbiology and Plant Biology, University of Oklahoma, Norman, OK 73019, USA
| | - Xiaoping Gou
- Department of Microbiology and Plant Biology, University of Oklahoma, Norman, OK 73019, USA
| | - Chui E Wong
- Plant Molecular Biology and Biotechnology Laboratory, Australian Research Council Centre of Excellence for Integrative Legume Research, Melbourne School of Land and Environment, University of Melbourne, Parkville, Victoria 3010, Australia
| | - Xinkun Wang
- Higuchi Biosciences Center, University of Kansas, Lawrence, KS 66047, USA
| | - Tong Yuan
- Department of Microbiology and Plant Biology, University of Oklahoma, Norman, OK 73019, USA
| | - Xiaoping Wei
- Department of Microbiology and Plant Biology, University of Oklahoma, Norman, OK 73019, USA
| | - Prem L Bhalla
- Plant Molecular Biology and Biotechnology Laboratory, Australian Research Council Centre of Excellence for Integrative Legume Research, Melbourne School of Land and Environment, University of Melbourne, Parkville, Victoria 3010, Australia
| | - Mohan B Singh
- Plant Molecular Biology and Biotechnology Laboratory, Australian Research Council Centre of Excellence for Integrative Legume Research, Melbourne School of Land and Environment, University of Melbourne, Parkville, Victoria 3010, Australia
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Cotranscriptional Chromatin Remodeling by Small RNA Species: An HTLV-1 Perspective. LEUKEMIA RESEARCH AND TREATMENT 2012; 2012:984754. [PMID: 23213554 PMCID: PMC3504244 DOI: 10.1155/2012/984754] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/23/2011] [Revised: 10/28/2011] [Accepted: 11/03/2011] [Indexed: 12/22/2022]
Abstract
Cell type specificity of human T cell leukemia virus 1 has been proposed as a possible reason for differential viral outcome in primary target cells versus secondary. Through chromatin remodeling, the HTLV-1 transactivator protein Tax interacts with cellular factors at the chromosomally integrated viral promoter to activate downstream genes and control viral transcription. RNA interference is the host innate defense mechanism mediated by short RNA species (siRNA or miRNA) that regulate gene expression. There exists a close collaborative functioning of cellular transcription factors with miRNA in order to regulate the expression of a number of eukaryotic genes including those involved in suppression of cell growth, induction of apoptosis, as well as repressing viral replication and propagation. In addition, it has been suggested that retroviral latency is influenced by chromatin alterations brought about by miRNA. Since Tax requires the assembly of transcriptional cofactors to carry out viral gene expression, there might be a close association between miRNA influencing chromatin alterations and Tax-mediated LTR activation. Herein we explore the possible interplay between HTLV-1 infection and miRNA pathways resulting in chromatin reorganization as one of the mechanisms determining HTLV-1 cell specificity and viral fate in different cell types.
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38
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Calo S, Nicolás FE, Vila A, Torres-Martínez S, Ruiz-Vázquez RM. Two distinct RNA-dependent RNA polymerases are required for initiation and amplification of RNA silencing in the basal fungus Mucor circinelloides. Mol Microbiol 2011; 83:379-94. [DOI: 10.1111/j.1365-2958.2011.07939.x] [Citation(s) in RCA: 49] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
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Seifi A. Write 'systemic small RNAs': read 'systemic immunity'. FUNCTIONAL PLANT BIOLOGY : FPB 2011; 38:747-752. [PMID: 32480931 DOI: 10.1071/fp11100] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/24/2011] [Accepted: 06/28/2011] [Indexed: 06/11/2023]
Abstract
About 50 years ago, it was reported that pathogen-infected plants are less susceptible to a broad spectrum of the subsequent pathogen attacks. This form of induced resistance, which resembles the immunisation in mammalian cells, is called systemic acquired resistance (SAR). In the last 10 years, plant molecular biology has been revolutionised by the discovery of RNA silencing, which is also a systemic phenomenon and also contributes to plant immunity. Here, I review these two systemic phenomena in a comparative way to highlight the possibility that systemic silencing contributes to systemic immunity. This potential contribution could be in the process of gene expression reprogramming, which is needed for SAR induction, and/or in SAR signal complex, and/or in establishing SAR in remote tissues and forming priming status.
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Hou WN, Duan CG, Fang RX, Zhou XY, Guo HS. Satellite RNA reduces expression of the 2b suppressor protein resulting in the attenuation of symptoms caused by Cucumber mosaic virus infection. MOLECULAR PLANT PATHOLOGY 2011; 12:595-605. [PMID: 21722297 PMCID: PMC6640352 DOI: 10.1111/j.1364-3703.2010.00696.x] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/05/2023]
Abstract
Satellite RNAs (satRNAs) depend on cognate helper viruses for replication, encapsidation, movement and transmission. Many satRNAs with different symptom modulation effects have been reported. The pathogenicity of satRNAs is thought to be the result of a direct interaction among the satRNA, helper viruses and host factors by unknown mechanisms. To understand the effect of satRNA of Cucumber mosaic virus (a severe field ShanDong strain, SD-CMV) on pathogenicity, and the possible involvement of host RNA silencing pathways in pathogenicity, we constructed biologically active CMV cDNA clones and a CMV-Δ2b mutant lacking the open reading frame of 2b, a silencing suppressor protein, in order to infect Nicotiana benthamiana and Arabidopsis with or without SD-satRNA. We found that SD-satRNA reduced the accumulation of the 2b protein and its coding RNA4A and attenuated the yellowing caused by SD-CMV infection. Small RNA analysis indicated that the 2b protein interfered with RNA silencing, specifically in the synthesis of CMV RNA3-derived small interfering RNAs (R3-siRNAs). The accumulation of R3-siRNAs in CMV-Δ2b infection was reduced in the presence of satRNA, for which greater accumulation of satRNA-derived siRNAs (satsiRNAs) was detected. Our results suggest that abundant SD-satRNA serving as target for RNA silencing may play a role in protecting helper CMV RNA, especially, subgenomic RNA4, from being targeted by RNA silencing. This compensates for the increase in RNA silencing resulting from the reduction in expression of the 2b suppressor in the presence of satRNA. Our data provide evidence that a plant silencing mechanism is involved in the pathogenicity of satRNA.
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Affiliation(s)
- Wei-Na Hou
- State Key Laboratory of Plant Genomics and National Center for Plant Gene Research (Beijing), Institute of Microbiology, Chinese Academy of Sciences, China
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41
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RNA interference in protozoan parasites: achievements and challenges. EUKARYOTIC CELL 2011; 10:1156-63. [PMID: 21764910 DOI: 10.1128/ec.05114-11] [Citation(s) in RCA: 102] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/24/2023]
Abstract
Protozoan parasites that profoundly affect mankind represent an exceptionally diverse group of organisms, including Plasmodium, Toxoplasma, Entamoeba, Giardia, trypanosomes, and Leishmania. Despite the overwhelming impact of these parasites, there remain many aspects to be discovered about mechanisms of pathogenesis and how these organisms survive in the host. Combined with the ever-increasing availability of sequenced genomes, RNA interference (RNAi), discovered a mere 13 years ago, has enormously facilitated the analysis of gene function, especially in organisms that are not amenable to classical genetic approaches. Here we review the current status of RNAi in studies of parasitic protozoa, with special emphasis on its use as a postgenomic tool.
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Crombach A, Hogeweg P. Is RNA-dependent RNA polymerase essential for transposon control? BMC SYSTEMS BIOLOGY 2011; 5:104. [PMID: 21714914 PMCID: PMC3155503 DOI: 10.1186/1752-0509-5-104] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/07/2011] [Accepted: 06/29/2011] [Indexed: 11/29/2022]
Abstract
Background Eukaryotes use RNA interference and RNA-based epigenetic regulation to control transposon activity. In the standard pathways of RNA-based transcriptional and post-transcriptional silencing the protein complex RNA-dependent RNA polymerase (RdRP) plays a crucial role. However, alternative pathways that bypass RdRP have recently been described. Hence two important questions are: is RdRP truly a necessary component for transposon control, and are the alternative RNA-based strategies also capable of controlling transposable elements? Results We have studied the interplay between host RNAi pathways and transposons using mathematical models. We show that the canonical RdRP-based model controls transposons tightly, mainly via the feedback of cytoplasmic small RNA amplification. Next, we consider two variants lacking RdRP and instead employing antisense transcription of transposons. We show that transposon activity is also controlled by the alternative pathways, although cytoplasmic small RNA amplification is absent. Instead, control occurs in the nucleus, through a feedback in the epigenetic regulation. Conclusions Concluding, our models show that the control of transposon activity can be achieved by alternative pathways that lack RdRP and act through different feedback mechanisms. Thus, although RdRP activity is ubiquitous in eukaryotes, it need not be a general requirement for transposon control.
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Affiliation(s)
- Anton Crombach
- Theoretical Biology and Bioinformatics Group, Utrecht University, Padualaan 8, 3584 CH Utrecht, The Netherlands.
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43
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Abstract
Small RNAs (sRNAs) have made a large impact on many recent scientific discoveries. MicroRNAs (miRNAs) are a type of sRNA molecule and, although usually just 20-22 nucleotides in length, they are potent regulators of gene expression. Therefore, identification of miRNAs and profiling their abundance are fundamental to understanding an organism's or tissue's gene regulatory network. Next-generation sequencing methods have allowed researchers to quickly sequence and profile sRNA populations. This chapter describes a cloning procedure to identify the sRNAs or miRNAs present in an RNA sample.
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Affiliation(s)
- Ericka R Havecker
- Department of Plant Sciences, University of Cambridge, Cambridge, UK.
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Hohn T, Vazquez F. RNA silencing pathways of plants: silencing and its suppression by plant DNA viruses. BIOCHIMICA ET BIOPHYSICA ACTA-GENE REGULATORY MECHANISMS 2011; 1809:588-600. [PMID: 21683815 DOI: 10.1016/j.bbagrm.2011.06.002] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/02/2011] [Revised: 06/01/2011] [Accepted: 06/02/2011] [Indexed: 02/02/2023]
Abstract
RNA silencing refers to processes that depend on small (s)RNAs to regulate the expression of eukaryotic genomes. In plants, these processes play critical roles in development, in responses to a wide array of stresses, in maintaining genome integrity and in defense against viral and bacterial pathogens. We provide here an updated view on the array of endogenous sRNA pathways, including microRNAs (miRNAs), discovered in the model plant Arabidopsis, which are also the basis for antiviral silencing. We emphasize the current knowledge as well as the recent advances made on understanding the defense and counter-defense strategies evolved in the arms race between plants and DNA viruses on both the nuclear and the cytoplasmic front. This article is part of a Special Issue entitled: MicroRNA's in viral gene regulation.
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Affiliation(s)
- Thomas Hohn
- Institute of Botany, University of Basel, Basel, Switzerland.
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45
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The emerging world of small silencing RNAs in protozoan parasites. Trends Parasitol 2011; 27:321-7. [PMID: 21497553 DOI: 10.1016/j.pt.2011.03.002] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2011] [Revised: 03/15/2011] [Accepted: 03/16/2011] [Indexed: 12/14/2022]
Abstract
A new RNA world has emerged in the past 10 years with the discovery of a plethora of 20- to 30-nucleotide long small RNAs that are involved in various gene silencing mechanisms. These small RNAs have considerably changed our view of the regulation of gene expression in eukaryotic organisms, with a major shift towards epigenetic and post-transcriptional mechanisms. In this article, we focus on the striking diversity of small silencing RNAs that have been identified in several protozoan parasites and their potential biological role.
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46
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van Wolfswinkel JC, Ketting RF. The role of small non-coding RNAs in genome stability and chromatin organization. J Cell Sci 2010; 123:1825-39. [PMID: 20484663 DOI: 10.1242/jcs.061713] [Citation(s) in RCA: 81] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Small non-coding RNAs make up much of the RNA content of a cell and have the potential to regulate gene expression on many different levels. Initial discoveries in the 1990s and early 21st century focused on determining mechanisms of post-transcriptional regulation mediated by small-interfering RNAs (siRNAs) and microRNAs (miRNAs). More recent research, however, has identified new classes of RNAs and new regulatory mechanisms, expanding the known regulatory potential of small non-coding RNAs to encompass chromatin regulation. In this Commentary, we provide an overview of these chromatin-related mechanisms and speculate on the extent to which they are conserved among eukaryotes.
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Affiliation(s)
- Josien C van Wolfswinkel
- Hubrecht Institute-KNAW and University Medical Centre Utrecht, Uppsalalaan 8, 3584 CT Utrecht, The Netherlands
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Marker S, Le Mouël A, Meyer E, Simon M. Distinct RNA-dependent RNA polymerases are required for RNAi triggered by double-stranded RNA versus truncated transgenes in Paramecium tetraurelia. Nucleic Acids Res 2010; 38:4092-107. [PMID: 20200046 PMCID: PMC2896523 DOI: 10.1093/nar/gkq131] [Citation(s) in RCA: 38] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2010] [Revised: 02/13/2010] [Accepted: 02/15/2010] [Indexed: 12/12/2022] Open
Abstract
In many eukaryotes, RNA-dependent RNA polymerases (RdRPs) play key roles in the RNAi pathway. They have been implicated in the recognition and processing of aberrant transcripts triggering the process, and in amplification of the silencing response. We have tested the functions of RdRP genes from the ciliate Paramecium tetraurelia in experimentally induced and endogenous mechanisms of gene silencing. In this organism, RNAi can be triggered either by high-copy, truncated transgenes or by directly feeding cells with double-stranded RNA (dsRNA). Surprisingly, dsRNA-induced silencing depends on the putatively functional RDR1 and RDR2 genes, which are required for the accumulation of both primary siRNAs and a distinct class of small RNAs suggestive of secondary siRNAs. In contrast, a third gene with a highly divergent catalytic domain, RDR3, is required for siRNA accumulation when RNAi is triggered by truncated transgenes. Our data further implicate RDR3 in the accumulation of previously described endogenous siRNAs and in the regulation of the surface antigen gene family. While only one of these genes is normally expressed in any clonal cell line, the knockdown of RDR3 leads to co-expression of multiple antigens. These results provide evidence for a functional specialization of Paramecium RdRP genes in distinct RNAi pathways operating during vegetative growth.
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Affiliation(s)
- Simone Marker
- Department of Biology, University of Kaiserslautern, Gottlieb-Daimler Street, 67663 Kaiserslautern, Germany, Institut de Biologie de l’Ecole Normale Supérieure, CNRS UMR8197, INSERM U1024, 46 rue d'Ulm, 75005 Paris and UMR7216 Epigénétique et Destin Cellulaire, CNRS, Université Paris-Diderot/Paris 7, 35 rue Hélène Brion, 75013, Paris, France
| | - Anne Le Mouël
- Department of Biology, University of Kaiserslautern, Gottlieb-Daimler Street, 67663 Kaiserslautern, Germany, Institut de Biologie de l’Ecole Normale Supérieure, CNRS UMR8197, INSERM U1024, 46 rue d'Ulm, 75005 Paris and UMR7216 Epigénétique et Destin Cellulaire, CNRS, Université Paris-Diderot/Paris 7, 35 rue Hélène Brion, 75013, Paris, France
| | - Eric Meyer
- Department of Biology, University of Kaiserslautern, Gottlieb-Daimler Street, 67663 Kaiserslautern, Germany, Institut de Biologie de l’Ecole Normale Supérieure, CNRS UMR8197, INSERM U1024, 46 rue d'Ulm, 75005 Paris and UMR7216 Epigénétique et Destin Cellulaire, CNRS, Université Paris-Diderot/Paris 7, 35 rue Hélène Brion, 75013, Paris, France
| | - Martin Simon
- Department of Biology, University of Kaiserslautern, Gottlieb-Daimler Street, 67663 Kaiserslautern, Germany, Institut de Biologie de l’Ecole Normale Supérieure, CNRS UMR8197, INSERM U1024, 46 rue d'Ulm, 75005 Paris and UMR7216 Epigénétique et Destin Cellulaire, CNRS, Université Paris-Diderot/Paris 7, 35 rue Hélène Brion, 75013, Paris, France
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Ying XB, Dong L, Zhu H, Duan CG, Du QS, Lv DQ, Fang YY, Garcia JA, Fang RX, Guo HS. RNA-dependent RNA polymerase 1 from Nicotiana tabacum suppresses RNA silencing and enhances viral infection in Nicotiana benthamiana. THE PLANT CELL 2010; 22:1358-72. [PMID: 20400679 PMCID: PMC2879737 DOI: 10.1105/tpc.109.072058] [Citation(s) in RCA: 85] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/09/2009] [Revised: 03/24/2010] [Accepted: 04/02/2010] [Indexed: 05/18/2023]
Abstract
Endogenous eukaryotic RNA-dependent RNA polymerases (RDRs) produce double-stranded RNA intermediates in diverse processes of small RNA synthesis in RNA silencing pathways. RDR6 is required in plants for posttranscriptional gene silencing induced by sense transgenes (S-PTGS) and has an important role in amplification of antiviral silencing. Whereas RDR1 is also involved in antiviral defense in plants, this does not necessarily proceed through triggering silencing. In this study, we show that Nicotiana benthamiana transformed with RDR1 from Nicotiana tabacum (Nt-RDR1 plants) exhibits hypersusceptibility to Plum pox potyvirus and other viruses, resembling RDR6-silenced (RDR6i) N. benthamiana. Analysis of transient induction of RNA silencing in N. benthamiana Nt-RDR1 and RDR6i plants revealed that Nt-RDR1 possesses silencing suppression activity. We found that Nt-RDR1 does not interfere with RDR6-dependent siRNA accumulation but turns out to suppress RDR6-dependent S-PTGS. Our results, together with previously published data, suggest that RDR1 might have a dual role, contributing, on one hand, to salicylic acid-mediated antiviral defense, and suppressing, on the other hand, the RDR6-mediated antiviral RNA silencing. We propose a scenario in which the natural loss-of-function variant of RDR1 in N. benthamiana may be the outcome of selective pressure to maintain a high RDR6-dependent antiviral defense, which would be required to face the hypersensitivity of this plant to a large number of viruses.
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Affiliation(s)
- Xiao-Bao Ying
- State Key Laboratory of Plant Genomics and National Center for Plant Gene Research (Beijing), Institute of Microbiology, Chinese Academy of Sciences, Beijing, 100101, China
- Graduate University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Li Dong
- State Key Laboratory of Plant Genomics and National Center for Plant Gene Research (Beijing), Institute of Microbiology, Chinese Academy of Sciences, Beijing, 100101, China
| | - Hui Zhu
- State Key Laboratory of Plant Genomics and National Center for Plant Gene Research (Beijing), Institute of Microbiology, Chinese Academy of Sciences, Beijing, 100101, China
- Graduate University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Cheng-Guo Duan
- State Key Laboratory of Plant Genomics and National Center for Plant Gene Research (Beijing), Institute of Microbiology, Chinese Academy of Sciences, Beijing, 100101, China
| | - Quan-Sheng Du
- State Key Laboratory of Plant Genomics and National Center for Plant Gene Research (Beijing), Institute of Microbiology, Chinese Academy of Sciences, Beijing, 100101, China
| | - Dian-Qiu Lv
- State Key Laboratory of Plant Genomics and National Center for Plant Gene Research (Beijing), Institute of Microbiology, Chinese Academy of Sciences, Beijing, 100101, China
- Virus-Free Seedling Institute of Heilongjiang Academy of Agricultural Sciences, Heilongjiang, 150086, Haerbin
| | - Yuan-Yuan Fang
- State Key Laboratory of Plant Genomics and National Center for Plant Gene Research (Beijing), Institute of Microbiology, Chinese Academy of Sciences, Beijing, 100101, China
| | - Juan Antonio Garcia
- Department of Plant Molecular Genetics, Centro National de Biotecnologia (Consejo Superior de Investigaciones Científicas), Campus Universidad Autonoma de Madrid, 28049 Madrid, Spain
| | - Rong-Xiang Fang
- State Key Laboratory of Plant Genomics and National Center for Plant Gene Research (Beijing), Institute of Microbiology, Chinese Academy of Sciences, Beijing, 100101, China
| | - Hui-Shan Guo
- State Key Laboratory of Plant Genomics and National Center for Plant Gene Research (Beijing), Institute of Microbiology, Chinese Academy of Sciences, Beijing, 100101, China
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49
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Hairpin RNA induces secondary small interfering RNA synthesis and silencing in trans in fission yeast. EMBO Rep 2010; 11:112-8. [PMID: 20062003 DOI: 10.1038/embor.2009.273] [Citation(s) in RCA: 53] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2009] [Revised: 12/01/2009] [Accepted: 12/01/2009] [Indexed: 12/28/2022] Open
Abstract
RNA interference (RNAi) is widespread in eukaryotes and regulates gene expression transcriptionally or post-transcriptionally. In fission yeast, RNAi is tightly coupled to template transcription and chromatin modifications that establish heterochromatin in cis. Exogenous double-stranded RNA (dsRNA) triggers seem to induce heterochromatin formation in trans only when certain silencing proteins are overexpressed. Here, we show that green fluorescent protein (GFP) hairpin dsRNA allows production of high levels of Argonaute-associated small interfering RNAs (siRNAs), which can induce heterochromatin formation at a remote locus. This silencing does not require any manipulation apart from hairpin expression. In cells expressing a ura4(+)-GFP fusion gene, production of GFP siRNAs causes the appearance of ura4 siRNAs from the target gene. Production of these secondary siRNAs depends on RNA-dependent RNA polymerase Rdp1 (RDRP(Rdp1)) function and other RNAi pathway components. This demonstrates that transitivity occurs in fission yeast and implies that RDRP(Rdp1) can synthesize RNA from targeted RNA templates in vivo, generating siRNAs not homologous to the hairpin.
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50
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Kung YJ, Bau HJ, Wu YL, Huang CH, Chen TM, Yeh SD. Generation of transgenic papaya with double resistance to Papaya ringspot virus and Papaya leaf-distortion mosaic virus. PHYTOPATHOLOGY 2009; 99:1312-1320. [PMID: 19821736 DOI: 10.1094/phyto-99-11-1312] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/28/2023]
Abstract
During the field tests of coat protein (CP)-transgenic papaya lines resistant to Papaya ringspot virus (PRSV), another Potyvirus sp., Papaya leaf-distortion mosaic virus (PLDMV), appeared as an emerging threat to the transgenic papaya. In this investigation, an untranslatable chimeric construct containing the truncated CP coding region of the PLDMV P-TW-WF isolate and the truncated CP coding region with the complete 3' untranslated region of PRSV YK isolate was transferred into papaya (Carica papaya cv. Thailand) via Agrobacterium-mediated transformation to generate transgenic plants with resistance to PLDMV and PRSV. Seventy-five transgenic lines were obtained and challenged with PRSV YK or PLDMV P-TW-WF by mechanical inoculation under greenhouse conditions. Thirty-eight transgenic lines showing no symptoms 1 month after inoculation were regarded as highly resistant lines. Southern and Northern analyses revealed that four weakly resistant lines have one or two inserts of the construct and accumulate detectable amounts of transgene transcript, whereas nine resistant lines contain two or three inserts without significant accumulation of transgene transcript. The results indicated that double virus resistance in transgenic lines resulted from double or more copies of the insert through the mechanism of RNA-mediated posttranscriptional gene silencing. Furthermore, three of nine resistant lines showed high levels of resistance to heterologous PRSV strains originating from Hawaii, Thailand, and Mexico. Our transgenic lines have great potential for controlling a number of PRSV strains and PLDMV in Taiwan and elsewhere.
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Affiliation(s)
- Yi-Jung Kung
- Department of Plant Pathology, National Chung Hsing University, Taichung, Taiwan, R.O.C
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