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Wang Y, Shi Y, Li H, Chang J. Understanding Citrus Viroid Interactions: Experience and Prospects. Viruses 2024; 16:577. [PMID: 38675919 PMCID: PMC11053686 DOI: 10.3390/v16040577] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2024] [Revised: 03/28/2024] [Accepted: 04/05/2024] [Indexed: 04/28/2024] Open
Abstract
Citrus is the natural host of at least eight viroid species, providing a natural platform for studying interactions among viroids. The latter manifests as antagonistic or synergistic phenomena. The antagonistic effect among citrus viroids intuitively leads to reduced symptoms caused by citrus viroids, while the synergistic effect leads to an increase in symptom severity. The interaction phenomenon is complex and interesting, and a deep understanding of the underlying mechanisms induced during this viroid interaction is of great significance for the prevention and control of viroid diseases. This paper summarizes the research progress of citrus viroids in recent years, focusing on the interaction phenomenon and analyzing their interaction mechanisms. It points out the core role of the host RNA silencing mechanism and viroid-derived siRNA (vd-siRNA), and provides suggestions for future research directions.
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Affiliation(s)
- Yafei Wang
- College of Plant Protection, Henan Agricultural University, Zhengzhou 450002, China; (Y.S.); (H.L.); (J.C.)
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2
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Zaheer U, Munir F, Salum YM, He W. Function and regulation of plant ARGONAUTE proteins in response to environmental challenges: a review. PeerJ 2024; 12:e17115. [PMID: 38560454 PMCID: PMC10979746 DOI: 10.7717/peerj.17115] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2023] [Accepted: 02/26/2024] [Indexed: 04/04/2024] Open
Abstract
Environmental stresses diversely affect multiple processes related to the growth, development, and yield of many crops worldwide. In response, plants have developed numerous sophisticated defense mechanisms at the cellular and subcellular levels to react and adapt to biotic and abiotic stressors. RNA silencing, which is an innate immune mechanism, mediates sequence-specific gene expression regulation in higher eukaryotes. ARGONAUTE (AGO) proteins are essential components of the RNA-induced silencing complex (RISC). They bind to small noncoding RNAs (sRNAs) and target complementary RNAs, causing translational repression or triggering endonucleolytic cleavage pathways. In this review, we aim to illustrate the recently published molecular functions, regulatory mechanisms, and biological roles of AGO family proteins in model plants and cash crops, especially in the defense against diverse biotic and abiotic stresses, which could be helpful in crop improvement and stress tolerance in various plants.
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Affiliation(s)
- Uroosa Zaheer
- Plant Protection, State Key Laboratory for Ecological Pest Control of Fujian and Taiwan Crops, Institute of Applied Ecology, Fujian Agriculture and Forestry University, Fuzhou, Fujian, China
- Plant Protection, International Joint Research Laboratory of Ecological Pest Control, Ministry of Education, Fujian Agriculture and Forestry University, Fuzhou, Fujian, China
- Plant Protection, Ministerial and Provincial Joint Innovation Centre for Safety Production of Cross-Strait Crops, Fujian Agriculture and Forestry University, Fuzhou, Fujian, China
| | - Faisal Munir
- Plant Protection, State Key Laboratory for Ecological Pest Control of Fujian and Taiwan Crops, Institute of Applied Ecology, Fujian Agriculture and Forestry University, Fuzhou, Fujian, China
- Plant Protection, International Joint Research Laboratory of Ecological Pest Control, Ministry of Education, Fujian Agriculture and Forestry University, Fuzhou, Fujian, China
- Plant Protection, Ministerial and Provincial Joint Innovation Centre for Safety Production of Cross-Strait Crops, Fujian Agriculture and Forestry University, Fuzhou, Fujian, China
| | - Yussuf Mohamed Salum
- Plant Protection, State Key Laboratory for Ecological Pest Control of Fujian and Taiwan Crops, Institute of Applied Ecology, Fujian Agriculture and Forestry University, Fuzhou, Fujian, China
- Plant Protection, International Joint Research Laboratory of Ecological Pest Control, Ministry of Education, Fujian Agriculture and Forestry University, Fuzhou, Fujian, China
- Plant Protection, Ministerial and Provincial Joint Innovation Centre for Safety Production of Cross-Strait Crops, Fujian Agriculture and Forestry University, Fuzhou, Fujian, China
| | - Weiyi He
- Plant Protection, State Key Laboratory for Ecological Pest Control of Fujian and Taiwan Crops, Institute of Applied Ecology, Fujian Agriculture and Forestry University, Fuzhou, Fujian, China
- Plant Protection, International Joint Research Laboratory of Ecological Pest Control, Ministry of Education, Fujian Agriculture and Forestry University, Fuzhou, Fujian, China
- Plant Protection, Ministerial and Provincial Joint Innovation Centre for Safety Production of Cross-Strait Crops, Fujian Agriculture and Forestry University, Fuzhou, Fujian, China
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3
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Barre-Villeneuve C, Laudié M, Carpentier MC, Kuhn L, Lagrange T, Azevedo-Favory J. The unique dual targeting of AGO1 by two types of PRMT enzymes promotes phasiRNA loading in Arabidopsis thaliana. Nucleic Acids Res 2024; 52:2480-2497. [PMID: 38321923 PMCID: PMC10954461 DOI: 10.1093/nar/gkae045] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2023] [Revised: 12/18/2023] [Accepted: 01/12/2024] [Indexed: 02/08/2024] Open
Abstract
Arginine/R methylation (R-met) of proteins is a widespread post-translational modification (PTM), deposited by a family of protein arginine/R methyl transferase enzymes (PRMT). Regulations by R-met are involved in key biological processes deeply studied in metazoan. Among those, post-transcriptional gene silencing (PTGS) can be regulated by R-met in animals and in plants. It mainly contributes to safeguard processes as protection of genome integrity in germlines through the regulation of piRNA pathway in metazoan, or response to bacterial infection through the control of AGO2 in plants. So far, only PRMT5 has been identified as the AGO/PIWI R-met writer in higher eukaryotes. We uncovered that AGO1, the main PTGS effector regulating plant development, contains unique R-met features among the AGO/PIWI superfamily, and outstanding in eukaryotes. Indeed, AGO1 contains both symmetric (sDMA) and asymmetric (aDMA) R-dimethylations and is dually targeted by PRMT5 and by another type I PRMT in Arabidopsis thaliana. We showed also that loss of sDMA didn't compromise AtAGO1 subcellular trafficking in planta. Interestingly, we underscored that AtPRMT5 specifically promotes the loading of phasiRNA in AtAGO1. All our observations bring to consider this dual regulation of AtAGO1 in plant development and response to environment, and pinpoint the complexity of AGO1 post-translational regulation.
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Affiliation(s)
- Clément Barre-Villeneuve
- CNRS, Laboratoire Génome et Développement des Plantes, UMR 5096, 66860 Perpignan, France
- Université Perpignan Via Domitia, Laboratoire Génome et Développement des Plantes, UMR 5096, F-66860 Perpignan, France
| | - Michèle Laudié
- CNRS, Laboratoire Génome et Développement des Plantes, UMR 5096, 66860 Perpignan, France
- Université Perpignan Via Domitia, Laboratoire Génome et Développement des Plantes, UMR 5096, F-66860 Perpignan, France
| | - Marie-Christine Carpentier
- CNRS, Laboratoire Génome et Développement des Plantes, UMR 5096, 66860 Perpignan, France
- Université Perpignan Via Domitia, Laboratoire Génome et Développement des Plantes, UMR 5096, F-66860 Perpignan, France
| | - Lauriane Kuhn
- Plateforme protéomique Strasbourg – Esplanade, CNRS FR1589, Université de Strasbourg, IBMC, 2 allée Konrad Roentgen, F-67084 Strasbourg, France
- Fédération de Recherche CNRS FR1589, France
| | - Thierry Lagrange
- CNRS, Laboratoire Génome et Développement des Plantes, UMR 5096, 66860 Perpignan, France
- Université Perpignan Via Domitia, Laboratoire Génome et Développement des Plantes, UMR 5096, F-66860 Perpignan, France
| | - Jacinthe Azevedo-Favory
- CNRS, Laboratoire Génome et Développement des Plantes, UMR 5096, 66860 Perpignan, France
- Université Perpignan Via Domitia, Laboratoire Génome et Développement des Plantes, UMR 5096, F-66860 Perpignan, France
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Čermák V, Kašpar T, Fischer L. SPT6L, a newly discovered ancestral component of the plant RNA-directed DNA methylation pathway. Front Plant Sci 2024; 15:1372880. [PMID: 38576781 PMCID: PMC10991848 DOI: 10.3389/fpls.2024.1372880] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 01/18/2024] [Accepted: 02/20/2024] [Indexed: 04/06/2024]
Abstract
RNA-directed DNA methylation (RdDM) is driven by small RNAs (sRNAs) complementary to the nascent transcript of RNA polymerase V (Pol V). sRNAs associated with ARGONAUTE (AGO) proteins are tethered to Pol V mainly by the AGO-hook domain of its subunit NRPE1. We found, by in silico analyses, that Pol V strongly colocalizes on chromatin with another AGO-hook protein, SPT6-like (SPT6L), which is a known essential transcription elongation factor of Pol II. Our phylogenetic analysis revealed that SPT6L acquired its AGO-binding capacity already in the most basal streptophyte algae, even before the emergence of Pol V, suggesting that SPT6L might be a driving force behind the RdDM evolution. Since its emergence, SPT6L with the AGO-hook represents the only conserved SPT6 homolog in Viridiplantae, implying that the same protein is involved in both Pol II and Pol V complexes. To better understand the role of SPT6L in the Pol V complex, we characterized genomic loci where these two colocalize and uncovered that DNA methylation there is more dynamic, driven by higher levels of sRNAs often from non-canonical RdDM pathways and more dependent on chromatin modifying and remodeling proteins like MORC. Pol V loci with SPT6L are highly depleted in helitrons but enriched in gene promoters for which locally and temporally precise methylation is necessary. In view of these results, we discuss potential roles of multiple AGO-hook domains present in the Pol V complex and speculate that SPT6L mediates de novo methylation of naïve loci by interconnecting Pol II and Pol V activities.
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Affiliation(s)
- Vojtěch Čermák
- Laboratory of Plant Cell Biology and Biotechnology, Faculty of Science, Department of Experimental Plant Biology, Charles University, Prague, Czechia
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Qiu Y, Wang Y, Wu Y, Yang H, Yang M, Zhou C, Cao M. Effects of RNA silencing during antagonism between citrus exocortis viroid and citrus bark cracking viroid in Etrog citron (Citrus medica). Mol Plant Pathol 2024; 25:e13408. [PMID: 38041680 PMCID: PMC10788473 DOI: 10.1111/mpp.13408] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/28/2023] [Revised: 11/06/2023] [Accepted: 11/07/2023] [Indexed: 12/03/2023]
Abstract
Citrus exocortis viroid (CEVd) and citrus bark cracking viroid (CBCVd) are two important viroids that infect citrus plants and frequently occur as mixed infections in orchards. However, the mechanism of antagonism between the two viroids in mixed infections remains unclear. The CEVd/CBCVd-citron system and small RNA sequencing (sRNA-seq) were used to study the antagonism. When CBCVd was inoculated before CEVd, the CEVd titre was significantly reduced and the symptoms were attenuated. Viroid-derived sRNAs (vd-sRNAs) from CEVd and CBCVd were predominantly 21-nucleotide (nt) and 22-nt in length and had similar 5' base biases. Homologous sequences of the two viroids in the terminal right (TR) region are rich in vd-sRNAs, and the high frequency vd-sRNAs selected from the CBCVd TR region can be used to degrade the transcripts of CEVd in vivo directly. These results suggest that RNA silencing may play an important role in the antagonism of the two viroids, thus deepening our understanding of the molecular interaction of long noncoding RNAs in woody plants.
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Affiliation(s)
- Yuanjian Qiu
- National Citrus Engineering Research Center, Integrative Science Center of Germplasm Creation in Western China (Chongqing) Science CityCitrus Research Institute, Southwest UniversityChongqingChina
- Academy of Agricultural SciencesSouthwest UniversityChongqingChina
| | - Yafei Wang
- National Citrus Engineering Research Center, Integrative Science Center of Germplasm Creation in Western China (Chongqing) Science CityCitrus Research Institute, Southwest UniversityChongqingChina
- College of Plant ProtectionHenan Agricultural UniversityZhengzhouChina
| | - Yujiao Wu
- National Citrus Engineering Research Center, Integrative Science Center of Germplasm Creation in Western China (Chongqing) Science CityCitrus Research Institute, Southwest UniversityChongqingChina
- Academy of Agricultural SciencesSouthwest UniversityChongqingChina
| | - Han Yang
- National Citrus Engineering Research Center, Integrative Science Center of Germplasm Creation in Western China (Chongqing) Science CityCitrus Research Institute, Southwest UniversityChongqingChina
- Academy of Agricultural SciencesSouthwest UniversityChongqingChina
| | - Mengxue Yang
- National Citrus Engineering Research Center, Integrative Science Center of Germplasm Creation in Western China (Chongqing) Science CityCitrus Research Institute, Southwest UniversityChongqingChina
- Academy of Agricultural SciencesSouthwest UniversityChongqingChina
| | - Changyong Zhou
- National Citrus Engineering Research Center, Integrative Science Center of Germplasm Creation in Western China (Chongqing) Science CityCitrus Research Institute, Southwest UniversityChongqingChina
- Academy of Agricultural SciencesSouthwest UniversityChongqingChina
| | - Mengji Cao
- National Citrus Engineering Research Center, Integrative Science Center of Germplasm Creation in Western China (Chongqing) Science CityCitrus Research Institute, Southwest UniversityChongqingChina
- Academy of Agricultural SciencesSouthwest UniversityChongqingChina
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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] [What about the content of this article? (0)] [Affiliation(s)] [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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Sheng C, Li X, Xia S, Zhang Y, Yu Z, Tang C, Xu L, Wang Z, Zhang X, Zhou T, Nie P, Baig A, Niu D, Zhao H. An OsPRMT5-OsAGO2/miR1875-OsHXK1 module regulates rice immunity to blast disease. J Integr Plant Biol 2023; 65:1077-1095. [PMID: 36511124 DOI: 10.1111/jipb.13430] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/20/2022] [Accepted: 12/11/2022] [Indexed: 06/17/2023]
Abstract
Rice ARGONAUTE2 (OsAGO2) is a core component of the rice RNA-induced silencing complex (RISC), which is repressed by Magnaporthe oryzae (M. oryzae) infection. Whether and how OsAGO2-mediated gene silencing plays a role in rice blast resistance and which sRNAs participate in this process are unknown. Our results indicate that OsAGO2 is a key immune player that manipulates rice defense responses against blast disease. OsAGO2 associates with the 24-nt miR1875 and binds to the promoter region of HEXOKINASE1 (OsHXK1), which causes DNA methylation and leads to gene silencing. Our multiple genetic evidence showed that, without M. oryzae infection, OsAGO2/miR1875 RISC promoted OsHXK1 promoter DNA methylation and OsHXK1 silencing; after M. oryzae infection, the reduced OsAGO2/miR1875 led to a relatively activated OsHXK1 expression. OsHXK1 acts as a positive regulator of blast disease resistance that OsHXK1-OE rice exhibited enhanced resistance, whereas Cas9-Oshxk1 rice showed reduced resistance against M. oryzae infection. OsHXK1 may function through its sugar sensor activity as glucose induced defense-related gene expression and reactive oxygen species (ROS) accumulation in Nipponbare and OsHXK1-OE but not in Cas9-Oshxk1 rice. OsAGO2 itself is delicately regulated by OsPRMT5, which senses M. oryzae infection and attenuates OsAGO2-mediated gene silencing through OsAGO2 arginine methylation. Our study reveals an OsPRMT5-OsAGO2/miR1875-OsHXK1 regulatory module that fine tunes the rice defense response to blast disease.
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Affiliation(s)
- Cong Sheng
- Department of Plant Pathology, College of Plant Protection, Nanjing Agricultural University, Nanjing, 210095, China
- Laboratory of Bio-interactions and Crop Health, Nanjing Agricultural University, Nanjing, 210095, China
| | - Xuan Li
- Department of Plant Pathology, College of Plant Protection, Nanjing Agricultural University, Nanjing, 210095, China
- Laboratory of Bio-interactions and Crop Health, Nanjing Agricultural University, Nanjing, 210095, China
| | - Shengge Xia
- Department of Plant Pathology, College of Plant Protection, Nanjing Agricultural University, Nanjing, 210095, China
- Laboratory of Bio-interactions and Crop Health, Nanjing Agricultural University, Nanjing, 210095, China
| | - Yimai Zhang
- Department of Plant Pathology, College of Plant Protection, Nanjing Agricultural University, Nanjing, 210095, China
- Laboratory of Bio-interactions and Crop Health, Nanjing Agricultural University, Nanjing, 210095, China
| | - Ze Yu
- Department of Plant Pathology, College of Plant Protection, Nanjing Agricultural University, Nanjing, 210095, China
- Laboratory of Bio-interactions and Crop Health, Nanjing Agricultural University, Nanjing, 210095, China
| | - Cheng Tang
- Department of Plant Pathology, College of Plant Protection, Nanjing Agricultural University, Nanjing, 210095, China
- Laboratory of Bio-interactions and Crop Health, Nanjing Agricultural University, Nanjing, 210095, China
| | - Le Xu
- Department of Plant Pathology, College of Plant Protection, Nanjing Agricultural University, Nanjing, 210095, China
- Laboratory of Bio-interactions and Crop Health, Nanjing Agricultural University, Nanjing, 210095, China
| | - Zhaoyun Wang
- Key Laboratory of Food Quality and Safety, Institute of Plant Protection, Jiangsu Academy of Agricultural Sciences, Nanjing, 210095, China
| | - Xin Zhang
- Institute of Industrial Crops, Shanxi Agricultural University, Taiyuan, 030000, China
| | - Tong Zhou
- Key Laboratory of Food Quality and Safety, Institute of Plant Protection, Jiangsu Academy of Agricultural Sciences, Nanjing, 210095, China
| | - Pingping Nie
- College of Life Sciences, Zaozhuang University, Zaozhuang, 277000, China
| | - Ayesha Baig
- Department of Biotechnology, COMSATS University Islamabad Abbottabad Campus, Abbottabad, Pakistan
| | - Dongdong Niu
- Department of Plant Pathology, College of Plant Protection, Nanjing Agricultural University, Nanjing, 210095, China
- Laboratory of Bio-interactions and Crop Health, Nanjing Agricultural University, Nanjing, 210095, China
| | - Hongwei Zhao
- Department of Plant Pathology, College of Plant Protection, Nanjing Agricultural University, Nanjing, 210095, China
- Laboratory of Bio-interactions and Crop Health, Nanjing Agricultural University, Nanjing, 210095, China
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Gui X, Zhang P, Wang D, Ding Z, Wu X, Shi J, Shen QH, Xu YZ, Ma W, Qiao Y. Phytophthora effector PSR1 hijacks the host pre-mRNA splicing machinery to modulate small RNA biogenesis and plant immunity. Plant Cell 2022; 34:3443-3459. [PMID: 35699507 PMCID: PMC9421478 DOI: 10.1093/plcell/koac176] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/09/2021] [Accepted: 06/06/2022] [Indexed: 05/29/2023]
Abstract
Phytophthora effector PSR1 suppresses small RNA (sRNA)-mediated immunity in plants, but the underlying mechanism remains unknown. Here, we show that Phytophthora suppressor of RNA silencing 1 (PSR1) contributes to the pathogenicity of Phytophthora sojae and specifically binds to three conserved C-terminal domains of the eukaryotic PSR1-Interacting Protein 1 (PINP1). PINP1 encodes PRP16, a core pre-mRNA splicing factor that unwinds RNA duplexes and binds to primary microRNA transcripts and general RNAs. Intriguingly, PSR1 decreased both RNA helicase and RNA-binding activity of PINP1, thereby dampening sRNA biogenesis and RNA metabolism. The PSR1-PINP1 interaction caused global changes in alternative splicing (AS). A total of 5,135 genes simultaneously exhibited mis-splicing in both PSR1-overexpressing and PINP1-silenced plants. AS upregulated many mRNA transcripts that had their introns retained. The high occurrence of intron retention in AS-induced transcripts significantly promoted Phytophthora pathogen infection in Nicotiana benthamiana, and this might be caused by the production of truncated proteins. Taken together, our findings reveal a key role for PINP1 in regulating sRNA biogenesis and plant immunity.
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Affiliation(s)
- Xinmeng Gui
- Shanghai Key Laboratory of Plant Molecular Sciences, College of Life Sciences, Shanghai Normal University, Shanghai 200234, China
| | - Peng Zhang
- Shanghai Key Laboratory of Plant Molecular Sciences, College of Life Sciences, Shanghai Normal University, Shanghai 200234, China
- College of Agriculture, Yangtze University, Jingzhou 434025, China
| | - Dan Wang
- Shanghai Key Laboratory of Plant Molecular Sciences, College of Life Sciences, Shanghai Normal University, Shanghai 200234, China
| | - Zhan Ding
- Key Laboratory of Insect Developmental and Evolutionary Biology, CAS Center for Excellence in Molecular Plant Sciences, Shanghai Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, Shanghai 200032, China
- State Key Laboratory of Virology, Hubei Key Laboratory of Cell Homeostasis, College of Life Science, Wuhan University, Hubei 430072, China
| | - Xian Wu
- Shanghai Key Laboratory of Plant Molecular Sciences, College of Life Sciences, Shanghai Normal University, Shanghai 200234, China
| | - Jinxia Shi
- Shanghai Key Laboratory of Plant Molecular Sciences, College of Life Sciences, Shanghai Normal University, Shanghai 200234, China
| | - Qian-Hua Shen
- State Key Laboratory of Plant Cell and Chromosome Engineering, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Innovation Academy for Seed Design, Beijing 100101, China
| | - Yong-Zhen Xu
- Key Laboratory of Insect Developmental and Evolutionary Biology, CAS Center for Excellence in Molecular Plant Sciences, Shanghai Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, Shanghai 200032, China
- State Key Laboratory of Virology, Hubei Key Laboratory of Cell Homeostasis, College of Life Science, Wuhan University, Hubei 430072, China
| | - Wenbo Ma
- The Sainsbury Laboratory, Norwich Research Park, Norwich NR4 7UH, UK
| | - Yongli Qiao
- Shanghai Key Laboratory of Plant Molecular Sciences, College of Life Sciences, Shanghai Normal University, Shanghai 200234, China
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9
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Gardiner J, Ghoshal B, Wang M, Jacobsen SE. CRISPR-Cas-mediated transcriptional control and epi-mutagenesis. Plant Physiol 2022; 188:1811-1824. [PMID: 35134247 PMCID: PMC8968285 DOI: 10.1093/plphys/kiac033] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/01/2021] [Accepted: 01/13/2022] [Indexed: 05/24/2023]
Abstract
Tools for sequence-specific DNA binding have opened the door to new approaches in investigating fundamental questions in biology and crop development. While there are several platforms to choose from, many of the recent advances in sequence-specific targeting tools are focused on developing Clustered Regularly Interspaced Short Palindromic Repeats- CRISPR Associated (CRISPR-Cas)-based systems. Using a catalytically inactive Cas protein (dCas), this system can act as a vector for different modular catalytic domains (effector domains) to control a gene's expression or alter epigenetic marks such as DNA methylation. Recent trends in developing CRISPR-dCas systems include creating versions that can target multiple copies of effector domains to a single site, targeting epigenetic changes that, in some cases, can be inherited to the next generation in the absence of the targeting construct, and combining effector domains and targeting strategies to create synergies that increase the functionality or efficiency of the system. This review summarizes and compares DNA targeting technologies, the effector domains used to target transcriptional control and epi-mutagenesis, and the different CRISPR-dCas systems used in plants.
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Affiliation(s)
| | | | - Ming Wang
- Department of Molecular, Cell and Developmental Biology, University of California at Los Angeles, Los Angeles, California, USA
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10
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Uslu VV, Dalakouras A, Steffens VA, Krczal G, Wassenegger M. High-pressure sprayed siRNAs influence the efficiency but not the profile of transitive silencing. Plant J 2022; 109:1199-1212. [PMID: 34882879 DOI: 10.1111/tpj.15625] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/30/2021] [Revised: 11/18/2021] [Accepted: 11/26/2021] [Indexed: 06/13/2023]
Abstract
In plants, small interfering RNAs (siRNAs) are a quintessential class of RNA interference (RNAi)-inducing molecules produced by the endonucleolytic cleavage of double-stranded RNAs (dsRNAs). In order to ensure robust RNAi, siRNAs are amplified through a positive feedback mechanism called transitivity. Transitivity relies on RNA-DIRECTED RNA POLYMERASE 6 (RDR6)-mediated dsRNA synthesis using siRNA-targeted RNA. The newly synthesized dsRNA is subsequently cleaved into secondary siRNAs by DICER-LIKE (DCL) endonucleases. Just like primary siRNAs, secondary siRNAs are also loaded into ARGONAUTE proteins (AGOs) to form an RNA-induced silencing complex reinforcing the cleavage of the target RNA. Although the molecular players underlying transitivity are well established, the mode of action of transitivity remains elusive. In this study, we investigated the influence of primary target sites on transgene silencing and transitivity using the green fluorescent protein (GFP)-expressing Nicotiana benthamiana 16C line, high-pressure spraying protocol, and synthetic 22-nucleotide (nt) long siRNAs. We found that the 22-nt siRNA targeting the 3' of the GFP transgene was less efficient in inducing silencing when compared with the siRNAs targeting the 5' and middle region of the GFP. Moreover, sRNA sequencing of locally silenced leaves showed that the amount but not the profile of secondary RNAs is shaped by the occupancy of the primary siRNA triggers on the target RNA. Our findings suggest that RDR6-mediated dsRNA synthesis is not primed by primary siRNAs and that dsRNA synthesis appears to be generally initiated at the 3'-end of the target RNA.
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Affiliation(s)
- Veli Vural Uslu
- AlPlanta-Institute for Plant Research, RLP AgroScience GmbH, Neustadt an der Weinstraße, Germany
| | - Athanasios Dalakouras
- Institute of Industrial and Forage Crops, Hellenic Agricultural Organization ELGO-DEMETER, Larissa, Greece
| | - Victor A Steffens
- AlPlanta-Institute for Plant Research, RLP AgroScience GmbH, Neustadt an der Weinstraße, Germany
| | - Gabi Krczal
- AlPlanta-Institute for Plant Research, RLP AgroScience GmbH, Neustadt an der Weinstraße, Germany
| | - Michael Wassenegger
- AlPlanta-Institute for Plant Research, RLP AgroScience GmbH, Neustadt an der Weinstraße, Germany
- Centre for Organismal Studies Heidelberg, University of Heidelberg, Heidelberg, Germany
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11
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Iwakawa HO, Tomari Y. Life of RISC: Formation, action, and degradation of RNA-induced silencing complex. Mol Cell 2021; 82:30-43. [PMID: 34942118 DOI: 10.1016/j.molcel.2021.11.026] [Citation(s) in RCA: 99] [Impact Index Per Article: 33.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2021] [Revised: 11/23/2021] [Accepted: 11/23/2021] [Indexed: 01/12/2023]
Abstract
Small RNAs regulate a wide variety of biological processes by repressing the expression of target genes at the transcriptional and post-transcriptional levels. To achieve these functions, small RNAs form RNA-induced silencing complex (RISC) together with a member of the Argonaute (AGO) protein family. RISC is directed by its bound small RNA to target complementary RNAs and represses their expression through mRNA cleavage, degradation, and/or translational repression. Many different factors fine-tune RISC activity and stability-from guide-target RNA complementarity to the recruitment of other protein partners to post-translational modifications of RISC itself. Here, we review recent progress in understanding RISC formation, action, and degradation, and discuss new, intriguing questions in the field.
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Affiliation(s)
- Hiro-Oki Iwakawa
- Laboratory of RNA Function, Institute for Quantitative Biosciences, The University of Tokyo, Bunkyo-ku, Tokyo 113-0032, Japan.
| | - Yukihide Tomari
- Laboratory of RNA Function, 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.
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12
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Lidak T, Baloghova N, Korinek V, Sedlacek R, Balounova J, Kasparek P, Cermak L. CRL4-DCAF12 Ubiquitin Ligase Controls MOV10 RNA Helicase during Spermatogenesis and T Cell Activation. Int J Mol Sci 2021; 22:5394. [PMID: 34065512 PMCID: PMC8161014 DOI: 10.3390/ijms22105394] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2021] [Revised: 05/12/2021] [Accepted: 05/16/2021] [Indexed: 12/27/2022] Open
Abstract
Multisubunit cullin-RING ubiquitin ligase 4 (CRL4)-DCAF12 recognizes the C-terminal degron containing acidic amino acid residues. However, its physiological roles and substrates are largely unknown. Purification of CRL4-DCAF12 complexes revealed a wide range of potential substrates, including MOV10, an "ancient" RNA-induced silencing complex (RISC) complex RNA helicase. We show that DCAF12 controls the MOV10 protein level via its C-terminal motif in a proteasome- and CRL-dependent manner. Next, we generated Dcaf12 knockout mice and demonstrated that the DCAF12-mediated degradation of MOV10 is conserved in mice and humans. Detailed analysis of Dcaf12-deficient mice revealed that their testes produce fewer mature sperms, phenotype accompanied by elevated MOV10 and imbalance in meiotic markers SCP3 and γ-H2AX. Additionally, the percentages of splenic CD4+ T and natural killer T (NKT) cell populations were significantly altered. In vitro, activated Dcaf12-deficient T cells displayed inappropriately stabilized MOV10 and increased levels of activated caspases. In summary, we identified MOV10 as a novel substrate of CRL4-DCAF12 and demonstrated the biological relevance of the DCAF12-MOV10 pathway in spermatogenesis and T cell activation.
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Affiliation(s)
- Tomas Lidak
- Laboratory of Cancer Biology, Institute of Molecular Genetics of the Czech Academy of Sciences, 252 42 Vestec, Czech Republic; (T.L.); (N.B.); (V.K.)
- Faculty of Science, Charles University, 128 00 Prague, Czech Republic
| | - Nikol Baloghova
- Laboratory of Cancer Biology, Institute of Molecular Genetics of the Czech Academy of Sciences, 252 42 Vestec, Czech Republic; (T.L.); (N.B.); (V.K.)
| | - Vladimir Korinek
- Laboratory of Cancer Biology, Institute of Molecular Genetics of the Czech Academy of Sciences, 252 42 Vestec, Czech Republic; (T.L.); (N.B.); (V.K.)
- Laboratory of Cell and Developmental Biology, Institute of Molecular Genetics of the Czech Academy of Sciences, 252 42 Vestec, Czech Republic
| | - Radislav Sedlacek
- Czech Centre for Phenogenomics, Institute of Molecular Genetics of the Czech Academy of Sciences, 252 50 Vestec, Czech Republic; (R.S.); (J.B.); (P.K.)
| | - Jana Balounova
- Czech Centre for Phenogenomics, Institute of Molecular Genetics of the Czech Academy of Sciences, 252 50 Vestec, Czech Republic; (R.S.); (J.B.); (P.K.)
| | - Petr Kasparek
- Czech Centre for Phenogenomics, Institute of Molecular Genetics of the Czech Academy of Sciences, 252 50 Vestec, Czech Republic; (R.S.); (J.B.); (P.K.)
| | - Lukas Cermak
- Laboratory of Cancer Biology, Institute of Molecular Genetics of the Czech Academy of Sciences, 252 42 Vestec, Czech Republic; (T.L.); (N.B.); (V.K.)
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13
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Jullien PE, Grob S, Marchais A, Pumplin N, Chevalier C, Bonnet DMV, Otto C, Schott G, Voinnet O. Functional characterization of Arabidopsis ARGONAUTE 3 in reproductive tissues. Plant J 2020; 103:1796-1809. [PMID: 32506562 DOI: 10.1111/tpj.14868] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/08/2019] [Revised: 04/08/2020] [Accepted: 05/20/2020] [Indexed: 05/03/2023]
Abstract
Arabidopsis encodes 10 ARGONAUTE (AGO) effectors of RNA silencing, canonically loaded with either 21-22 nucleotide (nt) long small RNAs (sRNAs) to mediate post-transcriptional gene silencing (PTGS) or 24 nt sRNAs to promote RNA-directed DNA methylation. Using full-locus constructs, we characterized the expression, biochemical properties and possible modes of action of AGO3. Although AGO3 arose from a recent duplication at the AGO2 locus, their expression patterns differ drastically, with AGO2 being expressed in both male and female gametes whereas AGO3 accumulates in aerial vascular terminations and specifically in chalazal seed integuments. Accordingly, AGO3 downregulation alters gene expression in siliques. Similar to AGO2, AGO3 binds sRNAs with a strong 5' adenosine bias, but unlike Arabidopsis AGO2, it binds 24 nt sRNAs most efficiently. AGO3 immunoprecipitation experiments in siliques revealed that these sRNAs mostly correspond to genes and intergenic regions in a manner reflecting their respective accumulation from their loci of origin. AGO3 localizes to the cytoplasm and co-fractionates with polysomes to possibly mediate PTGS via translation inhibition.
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Affiliation(s)
- Pauline E Jullien
- Institute of Molecular Plant Biology, Swiss Federal Institute of Technology Zurich (ETH Zurich), Universitätstrasse 2, Zurich, 8092, Switzerland
- Institute of Plant Sciences, University of Bern, Altenbergrain 21, Bern, 3013, Switzerland
| | - Stefan Grob
- Department of Plant and Microbial Biology, University of Zurich and Zurich-Basel Plant Science Center, University of Zurich, Zollikerstrasse 107, Zurich, 8008, Switzerland
| | - Antonin Marchais
- Institute of Molecular Plant Biology, Swiss Federal Institute of Technology Zurich (ETH Zurich), Universitätstrasse 2, Zurich, 8092, Switzerland
| | - Nathan Pumplin
- Institute of Molecular Plant Biology, Swiss Federal Institute of Technology Zurich (ETH Zurich), Universitätstrasse 2, Zurich, 8092, Switzerland
| | - Clement Chevalier
- Institute of Molecular Plant Biology, Swiss Federal Institute of Technology Zurich (ETH Zurich), Universitätstrasse 2, Zurich, 8092, Switzerland
| | - Diane M V Bonnet
- Institute of Plant Sciences, University of Bern, Altenbergrain 21, Bern, 3013, Switzerland
| | - Caroline Otto
- Institute of Molecular Plant Biology, Swiss Federal Institute of Technology Zurich (ETH Zurich), Universitätstrasse 2, Zurich, 8092, Switzerland
| | - Gregory Schott
- Institute of Molecular Plant Biology, Swiss Federal Institute of Technology Zurich (ETH Zurich), Universitätstrasse 2, Zurich, 8092, Switzerland
| | - Olivier Voinnet
- Institute of Molecular Plant Biology, Swiss Federal Institute of Technology Zurich (ETH Zurich), Universitätstrasse 2, Zurich, 8092, Switzerland
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14
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Devers EA, Brosnan CA, Sarazin A, Albertini D, Amsler AC, Brioudes F, Jullien PE, Lim P, Schott G, Voinnet O. Movement and differential consumption of short interfering RNA duplexes underlie mobile RNA interference. Nat Plants 2020; 6:789-799. [PMID: 32632272 DOI: 10.1038/s41477-020-0687-2] [Citation(s) in RCA: 39] [Impact Index Per Article: 9.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/22/2019] [Accepted: 05/06/2020] [Indexed: 05/19/2023]
Abstract
In RNA interference (RNAi), the RNase III Dicer processes long double-stranded RNA (dsRNA) into short interfering RNA (siRNA), which, when loaded into ARGONAUTE (AGO) family proteins, execute gene silencing1. Remarkably, RNAi can act non-cell autonomously2,3: it is graft transmissible4-7, and plasmodesmata-associated proteins modulate its cell-to-cell spread8,9. Nonetheless, the molecular mechanisms involved remain ill defined, probably reflecting a disparity of experimental settings. Among other caveats, these almost invariably cause artificially enhanced movement via transitivity, whereby primary RNAi-target transcripts are converted into further dsRNA sources of secondary siRNA5,10,11. Whether siRNA mobility naturally requires transitivity and whether it entails the same or distinct signals for cell-to-cell versus long-distance movement remains unclear, as does the identity of the mobile signalling molecules themselves. Movement of long single-stranded RNA, dsRNA, free/AGO-bound secondary siRNA or primary siRNA have all been advocated12-15; however, an entity necessary and sufficient for all known manifestations of plant mobile RNAi remains to be ascertained. Here, we show that the same primary RNAi signal endows both vasculature-to-epidermis and long-distance silencing movement from three distinct RNAi sources. The mobile entities are AGO-free primary siRNA duplexes spreading length and sequence independently. However, their movement is accompanied by selective siRNA depletion reflecting the AGO repertoires of traversed cell types. Coupling movement with this AGO-mediated consumption process creates qualitatively distinct silencing territories, potentially enabling unlimited spatial gene regulation patterns well beyond those granted by mere gradients.
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Affiliation(s)
| | - Christopher A Brosnan
- Department of Biology, ETH Zürich, Zurich, Switzerland
- Queensland Alliance for Agriculture and Food Innovation, The University of Queensland, Brisbane, Australia
| | | | | | | | | | - Pauline E Jullien
- Department of Biology, ETH Zürich, Zurich, Switzerland
- Institute of Plant Sciences, University of Bern, Bern, Switzerland
| | - Peiqi Lim
- Department of Biology, ETH Zürich, Zurich, Switzerland
- QIAGEN Singapore, Singapore, Singapore
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15
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Abstract
RNA granules are dynamic cellular foci that are widely spread in eukaryotic cells and play essential roles in cell growth and development, and immune and stress responses. Different types of granules can be distinguished, each with a specific function and playing a role in, for example, RNA transcription, modification, processing, decay, translation, and arrest. By means of communication and exchange of (shared) components, they form a large regulatory network in cells. Viruses have been reported to interact with one or more of these either cytoplasmic or nuclear granules, and act either proviral, to enable and support viral infection and facilitate viral movement, or antiviral, protecting or clearing hosts from viral infection. This review describes an overview and recent progress on cytoplasmic and nuclear RNA granules and their interplay with virus infection, first in animal systems and as a prelude to the status and current developments on plant viruses, which have been less well studied on this thus far.
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Affiliation(s)
- Min Xu
- Key Laboratory of Integrated Management of Crop Diseases and Pests, Ministry of Education, Department of Plant Pathology, Nanjing Agricultural University, Nanjing 210095, China
- Laboratory of Virology, Department of Plant Sciences, Wageningen University & Research, Droevendaalsesteeg 1, 6708PB Wageningen, The Netherlands
| | - Magdalena J Mazur
- Laboratory of Virology, Department of Plant Sciences, Wageningen University & Research, Droevendaalsesteeg 1, 6708PB Wageningen, The Netherlands
| | - Xiaorong Tao
- Key Laboratory of Integrated Management of Crop Diseases and Pests, Ministry of Education, Department of Plant Pathology, Nanjing Agricultural University, Nanjing 210095, China
| | - Richard Kormelink
- Laboratory of Virology, Department of Plant Sciences, Wageningen University & Research, Droevendaalsesteeg 1, 6708PB Wageningen, The Netherlands
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16
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Han Q, Bartels A, Cheng X, Meyer A, An YQC, Hsieh TF, Xiao W. Epigenetics Regulates Reproductive Development in Plants. Plants (Basel) 2019; 8:plants8120564. [PMID: 31810261 PMCID: PMC6963493 DOI: 10.3390/plants8120564] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/26/2019] [Revised: 11/23/2019] [Accepted: 11/27/2019] [Indexed: 12/20/2022]
Abstract
Seed, resulting from reproductive development, is the main nutrient source for human beings, and reproduction has been intensively studied through genetic, molecular, and epigenetic approaches. However, how different epigenetic pathways crosstalk and integrate to regulate seed development remains unknown. Here, we review the recent progress of epigenetic changes that affect chromatin structure, such as DNA methylation, polycomb group proteins, histone modifications, and small RNA pathways in regulating plant reproduction. In gametogenesis of flowering plants, epigenetics is dynamic between the companion cell and gametes. Cytosine DNA methylation occurs in CG, CHG, CHH contexts (H = A, C, or T) of genes and transposable elements, and undergoes dynamic changes during reproduction. Cytosine methylation in the CHH context increases significantly during embryogenesis, reaches the highest levels in mature embryos, and decreases as the seed germinates. Polycomb group proteins are important transcriptional regulators during seed development. Histone modifications and small RNA pathways add another layer of complexity in regulating seed development. In summary, multiple epigenetic pathways are pivotal in regulating seed development. It remains to be elucidated how these epigenetic pathways interplay to affect dynamic chromatin structure and control reproduction.
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Affiliation(s)
- Qiang Han
- Department of Biology, Saint Louis University, St. Louis, MO 63103, USA (A.B.); (X.C.)
| | - Arthur Bartels
- Department of Biology, Saint Louis University, St. Louis, MO 63103, USA (A.B.); (X.C.)
| | - Xi Cheng
- Department of Biology, Saint Louis University, St. Louis, MO 63103, USA (A.B.); (X.C.)
| | - Angela Meyer
- Department of Biology, Saint Louis University, St. Louis, MO 63103, USA (A.B.); (X.C.)
- Department of Biochemistry, Purdue University, West Lafayette, IN 47907, USA
| | - Yong-Qiang Charles An
- US Department of Agriculture, Agricultural Research Service, Midwest Area, Plant Genetics Research Unit, Donald Danforth Plant Science Center, MO 63132, USA;
| | - Tzung-Fu Hsieh
- Department of Plant and Microbial Biology, North Carolina State University, Raleigh, NC 27695, USA;
- Plants for Human Health Institute, North Carolina State University, North Carolina Research Campus, Kannapolis, NC 28081, USA
| | - Wenyan Xiao
- Department of Biology, Saint Louis University, St. Louis, MO 63103, USA (A.B.); (X.C.)
- Correspondence: ; Tel.: +1-314-977-2547
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17
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Gaffar FY, Koch A. Catch Me If You Can! RNA Silencing-Based Improvement of Antiviral Plant Immunity. Viruses 2019; 11:E673. [PMID: 31340474 DOI: 10.3390/v11070673] [Citation(s) in RCA: 43] [Impact Index Per Article: 8.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2019] [Revised: 07/11/2019] [Accepted: 07/17/2019] [Indexed: 12/27/2022] Open
Abstract
Viruses are obligate parasites which cause a range of severe plant diseases that affect farm productivity around the world, resulting in immense annual losses of yield. Therefore, control of viral pathogens continues to be an agronomic and scientific challenge requiring innovative and ground-breaking strategies to meet the demands of a growing world population. Over the last decade, RNA silencing has been employed to develop plants with an improved resistance to biotic stresses based on their function to provide protection from invasion by foreign nucleic acids, such as viruses. This natural phenomenon can be exploited to control agronomically relevant plant diseases. Recent evidence argues that this biotechnological method, called host-induced gene silencing, is effective against sucking insects, nematodes, and pathogenic fungi, as well as bacteria and viruses on their plant hosts. Here, we review recent studies which reveal the enormous potential that RNA-silencing strategies hold for providing an environmentally friendly mechanism to protect crop plants from viral diseases.
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18
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Diao P, Zhang Q, Sun H, Ma W, Cao A, Yu R, Wang J, Niu Y, Wuriyanghan H. miR403a and SA Are Involved in NbAGO2 Mediated Antiviral Defenses Against TMV Infection in Nicotiana benthamiana. Genes (Basel) 2019; 10:E526. [PMID: 31336929 PMCID: PMC6679004 DOI: 10.3390/genes10070526] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2019] [Revised: 07/06/2019] [Accepted: 07/09/2019] [Indexed: 11/18/2022] Open
Abstract
RNAi (RNA interference) is an important defense response against virus infection in plants. The core machinery of the RNAi pathway in plants include DCL (Dicer Like), AGO (Argonaute) and RdRp (RNA dependent RNA polymerase). Although involvement of these RNAi components in virus infection responses was demonstrated in Arabidopsis thaliana, their contribution to antiviral immunity in Nicotiana benthamiana, a model plant for plant-pathogen interaction studies, is not well understood. In this study, we investigated the role of N. benthamiana NbAGO2 gene against TMV (Tomato mosaic virus) infection. Silencing of NbAGO2 by transient expression of an hpRNA construct recovered GFP (Green fluorescent protein) expression in GFP-silenced plant, demonstrating that NbAGO2 participated in RNAi process in N. benthamiana. Expression of NbAGO2 was transcriptionally induced by both MeSA (Methylsalicylate acid) treatment and TMV infection. Down-regulation of NbAGO2 gene by amiR-NbAGO2 transient expression compromised plant resistance against TMV infection. Inhibition of endogenous miR403a, a predicted regulatory microRNA of NbAGO2, reduced TMV infection. Our study provides evidence for the antiviral role of NbAGO2 against a Tobamovirus family virus TMV in N. benthamiana, and SA (Salicylic acid) mediates this by induction of NbAGO2 expression upon TMV infection. Our data also highlighted that miR403a was involved in TMV defense by regulation of target NbAGO2 gene in N. Benthamiana.
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Affiliation(s)
- Pengfei Diao
- Key Laboratory of Forage and Endemic Crop Biotechnology, Ministry of Education, School of Life Sciences, Inner Mongolia University, Hohhot 010070, China
| | - Qimeng Zhang
- Key Laboratory of Forage and Endemic Crop Biotechnology, Ministry of Education, School of Life Sciences, Inner Mongolia University, Hohhot 010070, China
| | - Hongyu Sun
- Key Laboratory of Forage and Endemic Crop Biotechnology, Ministry of Education, School of Life Sciences, Inner Mongolia University, Hohhot 010070, China
| | - Wenjie Ma
- Key Laboratory of Forage and Endemic Crop Biotechnology, Ministry of Education, School of Life Sciences, Inner Mongolia University, Hohhot 010070, China
| | - Aiping Cao
- Key Laboratory of Forage and Endemic Crop Biotechnology, Ministry of Education, School of Life Sciences, Inner Mongolia University, Hohhot 010070, China
| | - Ruonan Yu
- Key Laboratory of Forage and Endemic Crop Biotechnology, Ministry of Education, School of Life Sciences, Inner Mongolia University, Hohhot 010070, China
| | - Jiaojiao Wang
- Key Laboratory of Forage and Endemic Crop Biotechnology, Ministry of Education, School of Life Sciences, Inner Mongolia University, Hohhot 010070, China
| | - Yiding Niu
- Key Laboratory of Forage and Endemic Crop Biotechnology, Ministry of Education, School of Life Sciences, Inner Mongolia University, Hohhot 010070, China.
| | - Hada Wuriyanghan
- Key Laboratory of Forage and Endemic Crop Biotechnology, Ministry of Education, School of Life Sciences, Inner Mongolia University, Hohhot 010070, China.
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19
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Pontier D, Picart C, El Baidouri M, Roudier F, Xu T, Lahmy S, Llauro C, Azevedo J, Laudié M, Attina A, Hirtz C, Carpentier MC, Shen L, Lagrange T. The m 6A pathway protects the transcriptome integrity by restricting RNA chimera formation in plants. Life Sci Alliance 2019; 2:2/3/e201900393. [PMID: 31142640 PMCID: PMC6545605 DOI: 10.26508/lsa.201900393] [Citation(s) in RCA: 35] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2019] [Revised: 05/20/2019] [Accepted: 05/20/2019] [Indexed: 11/24/2022] Open
Abstract
This study reveals that an m6A-assisted polyadenylation pathway comprising conserved m6A writer proteins and a plant-specific m6A reader contributes to transcriptome integrity in Arabidopsis thaliana by restricting RNA chimera formation at rearranged loci. Global, segmental, and gene duplication–related processes are driving genome size and complexity in plants. Despite their evolutionary potentials, those processes can also have adverse effects on genome regulation, thus implying the existence of specialized corrective mechanisms. Here, we report that an N6-methyladenosine (m6A)–assisted polyadenylation (m-ASP) pathway ensures transcriptome integrity in Arabidopsis thaliana. Efficient m-ASP pathway activity requires the m6A methyltransferase-associated factor FIP37 and CPSF30L, an m6A reader corresponding to an YT512-B Homology Domain-containing protein (YTHDC)-type domain containing isoform of the 30-kD subunit of cleavage and polyadenylation specificity factor. Targets of the m-ASP pathway are enriched in recently rearranged gene pairs, displayed an atypical chromatin signature, and showed transcriptional readthrough and mRNA chimera formation in FIP37- and CPSF30L-deficient plants. Furthermore, we showed that the m-ASP pathway can also restrict the formation of chimeric gene/transposable-element transcript, suggesting a possible implication of this pathway in the control of transposable elements at specific locus. Taken together, our results point to selective recognition of 3′-UTR m6A as a safeguard mechanism ensuring transcriptome integrity at rearranged genomic loci in plants.
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Affiliation(s)
- Dominique Pontier
- Centre National de la Recherche Scientifique, Laboratoire Génome et Développement des Plantes, UMR 5096, Perpignan, France.,Univ. Perpignan Via Domitia, Laboratoire Génome et Développement des Plantes, Unité Mixte de Recherche 5096, Perpignan, France
| | - Claire Picart
- Centre National de la Recherche Scientifique, Laboratoire Génome et Développement des Plantes, UMR 5096, Perpignan, France.,Univ. Perpignan Via Domitia, Laboratoire Génome et Développement des Plantes, Unité Mixte de Recherche 5096, Perpignan, France
| | - Moaine El Baidouri
- Centre National de la Recherche Scientifique, Laboratoire Génome et Développement des Plantes, UMR 5096, Perpignan, France.,Univ. Perpignan Via Domitia, Laboratoire Génome et Développement des Plantes, Unité Mixte de Recherche 5096, Perpignan, France
| | - François Roudier
- Laboratoire Reproduction et Développement des Plantes, Univ Lyon, Ecole Normale Supérieure de Lyon, Université Claude Bernard Lyon1, Centre National de la Recherche Scientifique, Institut National de la Recherche Agronomique, Lyon, France
| | - Tao Xu
- Department of Biological Sciences, National University of Singapore, Singapore
| | - Sylvie Lahmy
- Centre National de la Recherche Scientifique, Laboratoire Génome et Développement des Plantes, UMR 5096, Perpignan, France.,Univ. Perpignan Via Domitia, Laboratoire Génome et Développement des Plantes, Unité Mixte de Recherche 5096, Perpignan, France
| | - Christel Llauro
- Centre National de la Recherche Scientifique, Laboratoire Génome et Développement des Plantes, UMR 5096, Perpignan, France.,Univ. Perpignan Via Domitia, Laboratoire Génome et Développement des Plantes, Unité Mixte de Recherche 5096, Perpignan, France
| | - Jacinthe Azevedo
- Centre National de la Recherche Scientifique, Laboratoire Génome et Développement des Plantes, UMR 5096, Perpignan, France.,Univ. Perpignan Via Domitia, Laboratoire Génome et Développement des Plantes, Unité Mixte de Recherche 5096, Perpignan, France
| | - Michèle Laudié
- Centre National de la Recherche Scientifique, Laboratoire Génome et Développement des Plantes, UMR 5096, Perpignan, France.,Univ. Perpignan Via Domitia, Laboratoire Génome et Développement des Plantes, Unité Mixte de Recherche 5096, Perpignan, France
| | - Aurore Attina
- Platform SMART/Laboratoire de Biochimie et Protéomique Clinique/Plateforme de Protéomique Clinique, University of Montpellier, Institut de Médecine Régénérative et de Biothérapie , Centre Hospitalier Universitaire Montpellier, Institut national de la santé et de la Recherche Médicale, Montpeller, France
| | - Christophe Hirtz
- Platform SMART/Laboratoire de Biochimie et Protéomique Clinique/Plateforme de Protéomique Clinique, University of Montpellier, Institut de Médecine Régénérative et de Biothérapie , Centre Hospitalier Universitaire Montpellier, Institut national de la santé et de la Recherche Médicale, Montpeller, France
| | - Marie-Christine Carpentier
- Centre National de la Recherche Scientifique, Laboratoire Génome et Développement des Plantes, UMR 5096, Perpignan, France.,Univ. Perpignan Via Domitia, Laboratoire Génome et Développement des Plantes, Unité Mixte de Recherche 5096, Perpignan, France
| | - Lisha Shen
- Temasek Life Sciences Laboratory, 1 Research Link, NUS, Singapore
| | - Thierry Lagrange
- Centre National de la Recherche Scientifique, Laboratoire Génome et Développement des Plantes, UMR 5096, Perpignan, France .,Univ. Perpignan Via Domitia, Laboratoire Génome et Développement des Plantes, Unité Mixte de Recherche 5096, Perpignan, France
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20
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Šečić E, Zanini S, Kogel KH. Further Elucidation of the Argonaute and Dicer Protein Families in the Model Grass Species Brachypodium distachyon. Front Plant Sci 2019; 10:1332. [PMID: 31708948 PMCID: PMC6822278 DOI: 10.3389/fpls.2019.01332] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/13/2019] [Accepted: 09/25/2019] [Indexed: 05/08/2023]
Abstract
RNA interference (RNAi) is a biological process in which small RNAs regulate gene silencing at the transcriptional or posttranscriptional level. The trigger for gene silencing is double-stranded RNA generated from an endogenous genomic locus or a foreign source, such as a transgene or virus. In addition to regulating endogenous gene expression, RNAi provides the mechanistic basis for small RNA-mediated communication between plant hosts and interacting pathogenic microbes, known as cross-kingdom RNAi. Two core protein components, Argonaute (AGO) and Dicer (DCL), are central to the RNAi machinery of eukaryotes. Plants encode for several copies of AGO and DCL genes; in Arabidopsis thaliana, the AGO protein family contains 10 members, and the DCL family contains four. Little is known about the conservation and specific roles of these proteins in monocotyledonous plants, which account for the most important food staples. Here, we utilized in silico tools to investigate the structure and related functions of AGO and DCL proteins from the model grass Brachypodium distachyon. Based on the presence of characteristic domains, 16 BdAGO- and 6 BdDCL-predicted proteins were identified. Phylogenetic analysis showed that both protein families were expanded in Brachypodium as compared with Arabidopsis. For BdDCL proteins, both plant species contain a single copy of DCL1 and DCL4; however, Brachypodium contains two copies each of DCL2 and DCL3. Members of the BdAGO family were placed in all three functional clades of AGO proteins previously described in Arabidopsis. The greatest expansion occurred in the AtAGO1/5/10 clade, which contains nine BdAGOs (BdAGO5/6/7/9/10/11/12/15/16). The catalytic tetrad of the AGO P-element-induced wimpy testis domain (PIWI), which is required for endonuclease activity, is conserved in most BdAGOs, with the exception of BdAGO1, which lacks the last D/H residue. Three-dimensional modeling of BdAGO proteins using tertiary structure prediction software supported the phylogenetic classification. We also predicted a provisional interactome network for BdAGOs, their localization within the cell, and organ/tissue-specific expression. Exploring the specifics of RNAi machinery proteins in a model grass species can serve as a proxy for agronomically important cereals such as barley and wheat, where the development of RNAi-based plant protection strategies is of great interest.
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21
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Abstract
Plant growth and productivity are greatly impacted by environmental stresses. Therefore, plants have evolved mechanisms which allow them to adapt to abiotic stresses through alterations in gene expression and metabolism. In recent years, studies have investigated the role of long noncoding RNA (lncRNA) in regulating gene expression in plants and characterized their involvement in various biological functions through their regulation of DNA methylation, DNA structural modifications, histone modifications, and RNA-RNA interactions. Genome-wide transcriptome analyses have identified various types of noncoding RNAs (ncRNAs) that respond to abiotic stress. These ncRNAs are in addition to the well-known housekeeping ncRNAs, such as rRNAs, tRNAs, snoRNAs, and snRNAs. In this review, recent research pertaining to the role of lncRNAs in the response of plants to abiotic stress is summarized and discussed.
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Affiliation(s)
- Akihiro Matsui
- Plant Genomic Network Research Team, RIKEN Center for Sustainable Resource Science, Yokohama, Kanagawa, Japan.
- Plant Epigenome Regulation Laboratory, RIKEN Cluster for Pioneering Research, Wako, Saitama, Japan.
| | - Motoaki Seki
- Plant Genomic Network Research Team, RIKEN Center for Sustainable Resource Science, Yokohama, Kanagawa, Japan.
- Plant Epigenome Regulation Laboratory, RIKEN Cluster for Pioneering Research, Wako, Saitama, Japan.
- Kihara Institute for Biological Research, Yokohama City University, Yokohama, Kanagawa, Japan.
- Core Research for Evolutional Science and Technology, Japan Science and Technology, Kawaguchi, Saitama, Japan.
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22
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Incarbone M, Ritzenthaler C, Dunoyer P. Peroxisomal Targeting as a Sensitive Tool to Detect Protein-Small RNA Interactions through in Vivo Piggybacking. Front Plant Sci 2018; 9:135. [PMID: 29479364 PMCID: PMC5812032 DOI: 10.3389/fpls.2018.00135] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/02/2017] [Accepted: 01/24/2018] [Indexed: 05/09/2023]
Abstract
Peroxisomes are organelles that play key roles in eukaryotic metabolism. Their protein complement is entirely imported from the cytoplasm thanks to a unique pathway that is able to translocate folded proteins and protein complexes across the peroxisomal membrane. The import of molecules bound to a protein targeted to peroxisomes is an active process known as 'piggybacking' and we have recently shown that P15, a virus-encoded protein possessing a peroxisomal targeting sequence, is able to piggyback siRNAs into peroxisomes. Here, we extend this observation by analyzing the small RNA repertoire found in peroxisomes of P15-expressing plants. A direct comparison with the P15-associated small RNA retrieved during immunoprecipitation (IP) experiments, revealed that in vivo piggybacking coupled to peroxisome isolation could be a more sensitive means to determine the various small RNA species bound by a given protein. This increased sensitivity of peroxisome isolation as opposed to IP experiments was also striking when we analyzed the small RNA population bound by the Tomato bushy stunt virus-encoded P19, one of the best characterized viral suppressors of RNA silencing (VSR), artificially targeted to peroxisomes. These results support that peroxisomal targeting should be considered as a novel/alternative experimental approach to assess in vivo interactions that allows detection of labile binding events. The advantages and limitations of this approach are discussed.
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23
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Barghetti A, Sjögren L, Floris M, Paredes EB, Wenkel S, Brodersen P. Heat-shock protein 40 is the key farnesylation target in meristem size control, abscisic acid signaling, and drought resistance. Genes Dev 2017; 31:2282-2295. [PMID: 29269486 PMCID: PMC5769771 DOI: 10.1101/gad.301242.117] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2017] [Accepted: 11/20/2017] [Indexed: 12/11/2022]
Abstract
In this study, Barghetti et al. investigate the functions of protein farnesylation in plants. They show that defective farnesylation of a single factor—heat-shock protein 40 (HSP40), encoded by the J2 and J3 genes—is sufficient to confer ABA hypersensitivity, drought resistance, late flowering, and enlarged meristems, indicating that altered function of chaperone client proteins underlies most farnesyl transferase mutant phenotypes. Protein farnesylation is central to molecular cell biology. In plants, protein farnesyl transferase mutants are pleiotropic and exhibit defective meristem organization, hypersensitivity to the hormone abscisic acid, and increased drought resistance. The precise functions of protein farnesylation in plants remain incompletely understood because few relevant farnesylated targets have been identified. Here, we show that defective farnesylation of a single factor—heat-shock protein 40 (HSP40), encoded by the J2 and J3 genes—is sufficient to confer ABA hypersensitivity, drought resistance, late flowering, and enlarged meristems, indicating that altered function of chaperone client proteins underlies most farnesyl transferase mutant phenotypes. We also show that expression of an abiotic stress-related microRNA (miRNA) regulon controlled by the transcription factor SPL7 requires HSP40 farnesylation. Expression of a truncated SPL7 form mimicking its activated proteolysis fragment of the membrane-bound SPL7 precursor partially restores accumulation of SPL7-dependent miRNAs in farnesyl transferase mutants. These results implicate the pathway directing SPL7 activation from its membrane-bound precursor as an important target of farnesylated HSP40, consistent with our demonstration that HSP40 farnesylation facilitates its membrane association. The results also suggest that altered gene regulation via select miRNAs contributes to abiotic stress-related phenotypes of farnesyl transferase mutants.
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Affiliation(s)
- Andrea Barghetti
- Department of Biology, University of Copenhagen, DK-2200 Copenhagen N, Denmark.,Copenhagen Plant Science Center, University of Copenhagen, 1871 Frederiksberg C, Denmark
| | - Lars Sjögren
- Department of Biology, University of Copenhagen, DK-2200 Copenhagen N, Denmark.,Copenhagen Plant Science Center, University of Copenhagen, 1871 Frederiksberg C, Denmark
| | - Maïna Floris
- Department of Biology, University of Copenhagen, DK-2200 Copenhagen N, Denmark.,Copenhagen Plant Science Center, University of Copenhagen, 1871 Frederiksberg C, Denmark
| | - Esther Botterweg Paredes
- Copenhagen Plant Science Center, University of Copenhagen, 1871 Frederiksberg C, Denmark.,Department of Plant and Environmental Sciences, University of Copenhagen, DK-1871 Frederiksberg C, Denmark
| | - Stephan Wenkel
- Copenhagen Plant Science Center, University of Copenhagen, 1871 Frederiksberg C, Denmark.,Department of Plant and Environmental Sciences, University of Copenhagen, DK-1871 Frederiksberg C, Denmark
| | - Peter Brodersen
- Department of Biology, University of Copenhagen, DK-2200 Copenhagen N, Denmark.,Copenhagen Plant Science Center, University of Copenhagen, 1871 Frederiksberg C, Denmark
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24
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Córdoba-Cañero D, Cognat V, Ariza RR, Roldán Arjona T, Molinier J. Dual control of ROS1-mediated active DNA demethylation by DNA damage-binding protein 2 (DDB2). Plant J 2017; 92:1170-1181. [PMID: 29078035 DOI: 10.1111/tpj.13753] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/13/2017] [Revised: 10/10/2017] [Accepted: 10/17/2017] [Indexed: 06/07/2023]
Abstract
By controlling gene expression, DNA methylation contributes to key regulatory processes during plant development. Genomic methylation patterns are dynamic and must be properly maintained and/or re-established upon DNA replication and active removal, and therefore require sophisticated control mechanisms. Here we identify direct interplay between the DNA repair factor DNA damage-binding protein 2 (DDB2) and the ROS1-mediated active DNA demethylation pathway in Arabidopsis thaliana. We show that DDB2 forms a complex with ROS1 and AGO4 and that they act at the ROS1 locus to modulate levels of DNA methylation and therefore ROS1 expression. We found that DDB2 represses enzymatic activity of ROS1. DNA demethylation intermediates generated by ROS1 are processed by the DNA 3'-phosphatase ZDP and the apurinic/apyrimidinic endonuclease APE1L, and we also show that DDB2 interacts with both enzymes and stimulates their activities. Taken together, our results indicate that DDB2 acts as a critical regulator of ROS1-mediated active DNA demethylation.
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Affiliation(s)
- Dolores Córdoba-Cañero
- Maimónides Biomedical Research Institute of Córdoba (IMIBIC), Av. Menéndez Pidal, 14004, Córdoba, Spain
- University of Córdoba, Campus de Rabanales, Edif. C5, 14071, Córdoba, Spain
- Reina Sofia University Hospital, Av. Menéndez Pidal, 14004, Córdoba, Spain
| | - Valérie Cognat
- Institut de Biologie Moléculaire des Plantes, 12 Rue du Général Zimmer, 67000, Strasbourg, France
| | - Rafael R Ariza
- Maimónides Biomedical Research Institute of Córdoba (IMIBIC), Av. Menéndez Pidal, 14004, Córdoba, Spain
- University of Córdoba, Campus de Rabanales, Edif. C5, 14071, Córdoba, Spain
- Reina Sofia University Hospital, Av. Menéndez Pidal, 14004, Córdoba, Spain
| | - Teresa Roldán Arjona
- Maimónides Biomedical Research Institute of Córdoba (IMIBIC), Av. Menéndez Pidal, 14004, Córdoba, Spain
- University of Córdoba, Campus de Rabanales, Edif. C5, 14071, Córdoba, Spain
- Reina Sofia University Hospital, Av. Menéndez Pidal, 14004, Córdoba, Spain
| | - Jean Molinier
- Institut de Biologie Moléculaire des Plantes, 12 Rue du Général Zimmer, 67000, Strasbourg, France
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25
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Incarbone M, Zimmermann A, Hammann P, Erhardt M, Michel F, Dunoyer P. Neutralization of mobile antiviral small RNA through peroxisomal import. Nat Plants 2017; 3:17094. [PMID: 28628079 DOI: 10.1038/nplants.2017.94] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/09/2016] [Accepted: 05/18/2017] [Indexed: 05/10/2023]
Abstract
In animals, certain viral proteins are targeted to peroxisomes to dampen the antiviral immune response mediated by these organelles1-3. In plants, RNA interference (RNAi) mediated by small interfering (si)RNA is the main antiviral defence mechanism. To protect themselves against the cell- and non-cell autonomous effects of RNAi, viruses produce viral suppressors of RNA silencing (VSR)4, whose study is crucial to properly understand the biological cycle of plant viruses and potentially find new solutions to control these pathogens. By combining biochemical approaches, cell-specific inhibition of RNAi movement and peroxisome isolation, we show here that one such VSR, the peanut clump virus (PCV)-encoded P15, isolates siRNA from the symplasm by delivering them into the peroxisomal matrix. Infection with PCV lacking this ability reveals that piggybacking of these VSR-bound nucleic acids into peroxisomes potentiates viral systemic movement by preventing the spread of antiviral siRNA. Collectively, these results highlight organellar confinement of antiviral molecules as a novel pathogenic strategy that may have its direct counterpart in other plant and animal viruses.
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Affiliation(s)
- M Incarbone
- Institut de Biologie Moléculaire des Plantes du CNRS, UPR2357, Université de Strasbourg, F-67000 Strasbourg, France
| | - A Zimmermann
- Institut de Biologie Moléculaire des Plantes du CNRS, UPR2357, Université de Strasbourg, F-67000 Strasbourg, France
| | - P Hammann
- Institut de Biologie Moléculaire et Cellulaire du CNRS, Plateforme Protéomique Strasbourg - Esplanade, FRC1589, F-67000 Strasbourg, France
| | - M Erhardt
- Institut de Biologie Moléculaire des Plantes du CNRS, UPR2357, Université de Strasbourg, F-67000 Strasbourg, France
| | - F Michel
- Institut de Biologie Moléculaire des Plantes du CNRS, UPR2357, Université de Strasbourg, F-67000 Strasbourg, France
| | - P Dunoyer
- Institut de Biologie Moléculaire des Plantes du CNRS, UPR2357, Université de Strasbourg, F-67000 Strasbourg, France
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26
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Butel N, Le Masson I, Bouteiller N, Vaucheret H, Elmayan T. sgs1: a neomorphic nac52 allele impairing post-transcriptional gene silencing through SGS3 downregulation. Plant J 2017; 90:505-519. [PMID: 28207953 DOI: 10.1111/tpj.13508] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/05/2016] [Accepted: 02/01/2017] [Indexed: 06/06/2023]
Abstract
Post-transcriptional gene silencing (PTGS) is a defense mechanism that targets invading nucleic acids from endogenous (transposons) or exogenous (pathogens, transgenes) sources. Genetic screens based on the reactivation of silenced transgenes have long been used to identify cellular components and regulators of PTGS. Here we show that the first isolated PTGS-deficient mutant, sgs1, is impaired in the transcription factor NAC52. This mutant exhibits striking similarities to a mutant impaired in the H3K4me3 demethylase JMJ14 isolated from the same genetic screen. These similarities include increased transgene promoter DNA methylation, reduced H3K4me3 and H3K36me3 levels, reduced PolII occupancy and reduced transgene mRNA accumulation. It is likely that increased DNA methylation is the cause of reduced transcription because the effect of jmj14 and sgs1 on transgene transcription is suppressed by drm2, a mutation that compromises de novo DNA methylation, suggesting that the JMJ14-NAC52 module promotes transgene transcription by preventing DNA methylation. Remarkably, sgs1 has a stronger effect than jmj14 and nac52 null alleles on PTGS systems requiring siRNA amplification, and this is due to reduced SGS3 mRNA levels in sgs1. Given that the sgs1 mutation changes a conserved amino acid of the NAC proteins involved in homodimerization, we propose that sgs1 corresponds to a neomorphic nac52 allele encoding a mutant protein that lacks wild-type NAC52 activity but promotes SGS3 downregulation. Together, these results indicate that impairment of PTGS in sgs1 is due to its dual effect on transgene transcription and SGS3 transcription, thus compromising siRNA amplification.
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Affiliation(s)
- Nicolas Butel
- Institut Jean-Pierre Bourgin, UMR 1318, INRA AgroParisTech CNRS, Université Paris-Saclay, 78000, Versailles, France
- Université Paris-Sud, Université Paris-Saclay, 91405, Orsay, France
| | - Ivan Le Masson
- Institut Jean-Pierre Bourgin, UMR 1318, INRA AgroParisTech CNRS, Université Paris-Saclay, 78000, Versailles, France
| | - Nathalie Bouteiller
- Institut Jean-Pierre Bourgin, UMR 1318, INRA AgroParisTech CNRS, Université Paris-Saclay, 78000, Versailles, France
| | - Hervé Vaucheret
- Institut Jean-Pierre Bourgin, UMR 1318, INRA AgroParisTech CNRS, Université Paris-Saclay, 78000, Versailles, France
| | - Taline Elmayan
- Institut Jean-Pierre Bourgin, UMR 1318, INRA AgroParisTech CNRS, Université Paris-Saclay, 78000, Versailles, France
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27
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Upadhyay U, Srivastava S, Khatri I, Nanda JS, Subramanian S, Arora A, Singh J. Ablation of RNA interference and retrotransposons accompany acquisition and evolution of transposases to heterochromatin protein CENPB. Mol Biol Cell 2017; 28:1132-1146. [PMID: 28228545 PMCID: PMC5391189 DOI: 10.1091/mbc.e16-07-0485] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2016] [Revised: 01/19/2017] [Accepted: 02/14/2017] [Indexed: 02/02/2023] Open
Abstract
Fission yeast have adapted to retrotransposon invasion by RNAi-mediated silencing, which has coevolved into a mechanism involving CENPB-mediated heterochromatinization together with ablation of RNAi components via accumulation of recombinogenic repeats in recently diverged species of Schizosaccharomyces. Similar trends are seen in the metazoans. Inactivation of retrotransposons is accompanied by the emergence of centromere-binding protein-B (CENPB) in Schizosaccharomyces, as well as in metazoans. The RNA interference (RNAi)-induced transcriptional silencing (RITS) complex, comprising chromodomain protein-1 (Chp1), Tas3 (protein with unknown function), and Argonaute (Ago1), plays an important role in RNAi-mediated heterochromatinization. We find that whereas the Ago1 subunit of the RITS complex is highly conserved, Tas3 is lost and Chp1 is truncated in Schizosaccharomyces cryophilus and Schizosaccharomyces octosporus. We show that truncated Chp1 loses the property of heterochromatin localization and silencing when transformed in Schizosaccharomyces pombe. Furthermore, multiple copies of CENPB, related to Tc1/mariner and Tc5 transposons, occur in all Schizosaccharomyces species, as well as in humans, but with loss of transposase function (except Schizosaccharomyces japonicus). We propose that acquisition of Tc1/mariner and Tc5 elements by horizontal transfer in S. pombe (and humans) is accompanied by alteration of their function from a transposase/endonuclease to a heterochromatin protein, designed to suppress transposon expression and recombination. The resulting redundancy of RITS may have eased the selection pressure, resulting in progressive loss or truncation of tas3 and chp1 genes in S. octosporus and S. cryophilus and triggered similar evolutionary dynamics in the metazoan orthologues.
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Affiliation(s)
- Udita Upadhyay
- Department of Anesthesiology, Miller School of Medicine, University of Miami, Miami, FL 33136
| | - Suchita Srivastava
- Yeast Epigenetic Regulation Laboratory, Council of Scientific and Industrial Research, Chandigarh 160036, India
| | - Indu Khatri
- Department of Medicine and Biology, Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, MA 02215
| | - Jagpreet Singh Nanda
- Department of Pharmacology, Case Western Reserve University, Cleveland, OH 44106
| | - Srikrishna Subramanian
- Protein Evolution Laboratory, Council of Scientific and Industrial Research, Chandigarh 160036, India
| | - Amit Arora
- Microbial Type Culture Collection, Institute of Microbial Technology, Council of Scientific and Industrial Research, Chandigarh 160036, India
| | - Jagmohan Singh
- Yeast Epigenetic Regulation Laboratory, Council of Scientific and Industrial Research, Chandigarh 160036, India
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28
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Abstract
Small RNA-directed DNA methylation (RdDM) has been extensively studied in plants, resulting in a deep understanding of a major 'canonical RdDM' mechanism. However, current models of canonical RdDM cannot explain how this self-perpetuating mechanism is initiated. Recent investigations into the initiation of epigenetic silencing have determined that there are several alternative 'non-canonical RdDM' pathways that function through distinct mechanisms to modify chromatin. This Review aims to illustrate the diversity of non-canonical RdDM mechanisms described to date, recognize common themes within this dizzying array of interconnected pathways, and identify the key unanswered questions remaining in this field.
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Affiliation(s)
- Diego Cuerda-Gil
- Department of Molecular Genetics, The Ohio State University, 500 Aronoff Laboratory, 318 West Twelfth Avenue, Columbus, Ohio 43210, USA
| | - R Keith Slotkin
- Department of Molecular Genetics, The Ohio State University, 500 Aronoff Laboratory, 318 West Twelfth Avenue, Columbus, Ohio 43210, USA
- Center for RNA Biology, The Ohio State University, 105 Biological Sciences Building, 484 West Twelfth Avenue, Columbus, Ohio 43210, USA
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29
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Bejerman N, Mann KS, Dietzgen RG. Alfalfa dwarf cytorhabdovirus P protein is a local and systemic RNA silencing supressor which inhibits programmed RISC activity and prevents transitive amplification of RNA silencing. Virus Res 2016; 224:19-28. [PMID: 27543392 DOI: 10.1016/j.virusres.2016.08.008] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2016] [Revised: 08/09/2016] [Accepted: 08/14/2016] [Indexed: 11/16/2022]
Abstract
Plants employ RNA silencing as an innate defense mechanism against viruses. As a counter-defense, plant viruses have evolved to express RNA silencing suppressor proteins (RSS), which target one or more steps of the silencing pathway. In this study, we show that the phosphoprotein (P) encoded by the negative-sense RNA virus alfalfa dwarf virus (ADV), a species of the genus Cytorhabdovirus, family Rhabdoviridae, is a suppressor of RNA silencing. ADV P has a relatively weak local RSS activity, and does not prevent siRNA accumulation. On the other hand, ADV P strongly suppresses systemic RNA silencing, but does not interfere with the short-distance spread of silencing, which is consistent with its lack of inhibition of siRNA accumulation. The mechanism of suppression appears to involve ADV P binding to RNA-induced silencing complex proteins AGO1 and AGO4 as shown in protein-protein interaction assays when ectopically expressed. In planta, we demonstrate that ADV P likely functions by inhibiting miRNA-guided AGO1 cleavage and prevents transitive amplification by repressing the production of secondary siRNAs. As recently described for lettuce necrotic yellows cytorhabdovirus P, but in contrast to other viral RSS known to disrupt AGO activity, ADV P sequence does not contain any recognizable GW/WG or F-box motifs, which suggests that cytorhabdovirus P proteins may use alternative motifs to bind to AGO proteins.
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Affiliation(s)
- Nicolás Bejerman
- Queensland Alliance for Agriculture and Food Innovation, The University of Queensland, St. Lucia, QLD 4072, Australia.
| | - Krin S Mann
- Queensland Alliance for Agriculture and Food Innovation, The University of Queensland, St. Lucia, QLD 4072, Australia.
| | - Ralf G Dietzgen
- Queensland Alliance for Agriculture and Food Innovation, The University of Queensland, St. Lucia, QLD 4072, Australia.
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30
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Panda K, Ji L, Neumann DA, Daron J, Schmitz RJ, Slotkin RK. Full-length autonomous transposable elements are preferentially targeted by expression-dependent forms of RNA-directed DNA methylation. Genome Biol 2016; 17:170. [PMID: 27506905 PMCID: PMC4977677 DOI: 10.1186/s13059-016-1032-y] [Citation(s) in RCA: 84] [Impact Index Per Article: 10.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2016] [Accepted: 07/26/2016] [Indexed: 01/06/2023] Open
Abstract
Background Chromatin modifications such as DNA methylation are targeted to transposable elements by small RNAs in a process termed RNA-directed DNA methylation (RdDM). In plants, canonical RdDM functions through RNA polymerase IV to reinforce pre-existing transposable element silencing. Recent investigations have identified a “non-canonical” form of RdDM dependent on RNA polymerase II expression to initiate and re-establish silencing of active transposable elements. This expression-dependent RdDM mechanism functions through RNAi degradation of transposable element mRNAs into small RNAs guided by the RNA-dependent RNA polymerase 6 (RDR6) protein and is therefore referred to as RDR6-RdDM. Results We performed whole-genome MethylC-seq in 20 mutants that distinguish RdDM mechanisms when transposable elements are either transcriptionally silent or active. We identified a new mechanism of expression-dependent RdDM, which functions through DICER-LIKE3 (DCL3) but bypasses the requirement of both RNA polymerase IV and RDR6 (termed DCL3-RdDM). We found that RNA polymerase II expression-dependent forms of RdDM function on over 20 % of transcribed transposable elements, including the majority of full-length elements with all of the domains required for autonomous transposition. Lastly, we find that RDR6-RdDM preferentially targets long transposable elements due to the specificity of primary small RNAs to cleave full-length mRNAs. Conclusions Expression-dependent forms of RdDM function to critically target DNA methylation to full-length and transcriptionally active transposable elements, suggesting that these pathways are key to suppressing mobilization. This targeting specificity is initiated on the mRNA cleavage-level, yet manifested as chromatin-level silencing that in plants is epigenetically inherited from generation to generation. Electronic supplementary material The online version of this article (doi:10.1186/s13059-016-1032-y) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Kaushik Panda
- Department of Molecular Genetics, The Ohio State University, Columbus, OH, USA
| | - Lexiang Ji
- Institute of Bioinformatics, University of Georgia, Athens, GA, USA
| | | | - Josquin Daron
- Department of Molecular Genetics, The Ohio State University, Columbus, OH, USA
| | | | - R Keith Slotkin
- Department of Molecular Genetics, The Ohio State University, Columbus, OH, USA.
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31
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Abstract
RNA guided ribonuclease complexes play central role in RNA interference. Members of the evolutionarily conserved Argonaute protein family form the catalytic cores of these complexes. Unlike a number of other plant Argonautes, the role of AGO2 has been obscure until recently. Newer data, however, have indicated its involvement in various biotic and abiotic stress responses. Despite its suggested importance, there is no detailed characterization of this protein to date. Here we report cloning and molecular characterization of the AGO2 protein of the virological model plant Nicotiana benthamiana. We show that AGO2 can directly repress translation via various miRNA target site constellations (ORF, 3' UTR). Interestingly, although AGO2 seems to be able to silence gene expression in a slicing independent fashion, its catalytic activity is still a prerequisite for efficient translational repression. Additionally, mismatches between the 3' end of the miRNA guide strand and the 5' end of the target site enhance gene silencing by AGO2. Several functionally important amino acid residues of AGO2 have been identified that affect its small RNA loading, cleavage activity, translational repression potential and antiviral activity. The data presented here help us to understand how AGO2 aids plants to deal with stress.
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Affiliation(s)
- Károly Fátyol
- Agricultural Biotechnology Institute, National Agricultural Research and Innovation Centre Szent-Györgyi Albert u. 4. Gödöllő 2100, Hungary
| | - Márta Ludman
- Agricultural Biotechnology Institute, National Agricultural Research and Innovation Centre Szent-Györgyi Albert u. 4. Gödöllő 2100, Hungary
| | - József Burgyán
- Agricultural Biotechnology Institute, National Agricultural Research and Innovation Centre Szent-Györgyi Albert u. 4. Gödöllő 2100, Hungary
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Abstract
Argonaute (AGO) family proteins are effectors of RNAi in eukaryotes. AGOs bind small RNAs and use them as guides to silence target genes or transposable elements at the transcriptional or posttranscriptional level. Eukaryotic AGO proteins share common structural and biochemical properties and function through conserved core mechanisms in RNAi pathways, yet plant AGOs have evolved specialized and diversified functions. This Review covers the general features of AGO proteins and highlights recent progress toward our understanding of the mechanisms and functions of plant AGOs.
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Affiliation(s)
- Xiaofeng Fang
- Center for Plant Biology, School of Life Sciences, Tsinghua University, Beijing 100084, China Tsinghua-Peking Center for Life Sciences, Beijing 100084, China
| | - Yijun Qi
- Center for Plant Biology, School of Life Sciences, Tsinghua University, Beijing 100084, China Tsinghua-Peking Center for Life Sciences, Beijing 100084, China
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Wang J, Qi M, Liu J, Zhang Y. CARMO: a comprehensive annotation platform for functional exploration of rice multi-omics data. Plant J 2015; 83:359-74. [PMID: 26040787 DOI: 10.1111/tpj.12894] [Citation(s) in RCA: 36] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/13/2015] [Revised: 05/14/2015] [Accepted: 05/19/2015] [Indexed: 05/05/2023]
Abstract
High-throughput technology is gradually becoming a powerful tool for routine research in rice. Interpretation of biological significance from the huge amount of data is a critical but non-trivial task, especially for rice, for which gene annotations rely heavily on sequence similarity rather than direct experimental evidence. Here we describe the annotation platform for comprehensive annotation of rice multi-omics data (CARMO), which provides multiple web-based analysis tools for in-depth data mining and visualization. The central idea involves systematic integration of 1819 samples from omics studies and diverse sources of functional evidence (15 401 terms), which are further organized into gene sets and higher-level gene modules. In this way, the high-throughput data may easily be compared across studies and platforms, and integration of multiple types of evidence allows biological interpretation from the level of gene functional modules with high confidence. In addition, the functions and pathways for thousands of genes lacking description or validation may be deduced based on concerted expression of genes within the constructed co-expression networks or gene modules. Overall, CARMO provides comprehensive annotations for transcriptomic datasets, epi-genomic modification sites, single nucleotide polymorphisms identified from genome re-sequencing, and the large gene lists derived from these omics studies. Well-organized results, as well as multiple tools for interactive visualization, are available through a user-friendly web interface. Finally, we illustrate how CARMO enables biological insights using four examples, demonstrating that CARMO is a highly useful resource for intensive data mining and hypothesis generation based on rice multi-omics data. CARMO is freely available online (http://bioinfo.sibs.ac.cn/carmo).
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Affiliation(s)
- Jiawei Wang
- National Laboratory of Plant Molecular Genetics, Shanghai Institute of Plant Physiology and Ecology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, 300 Fenglin Road, Shanghai, 200032, China
| | - Meifang Qi
- National Laboratory of Plant Molecular Genetics, Shanghai Institute of Plant Physiology and Ecology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, 300 Fenglin Road, Shanghai, 200032, China
| | - Jian Liu
- National Laboratory of Plant Molecular Genetics, Shanghai Institute of Plant Physiology and Ecology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, 300 Fenglin Road, Shanghai, 200032, China
| | - Yijing Zhang
- National Laboratory of Plant Molecular Genetics, Shanghai Institute of Plant Physiology and Ecology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, 300 Fenglin Road, Shanghai, 200032, China
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34
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Abstract
A broad range of parasites rely on the functions of effector proteins to subvert host immune response and facilitate disease development. The notorious Phytophthora pathogens evolved effectors with RNA silencing suppression activity to promote infection in plant hosts. Here we report that the Phytophthora Suppressor of RNA Silencing 1 (PSR1) can bind to an evolutionarily conserved nuclear protein containing the aspartate-glutamate-alanine-histidine-box RNA helicase domain in plants. This protein, designated PSR1-Interacting Protein 1 (PINP1), regulates the accumulation of both microRNAs and endogenous small interfering RNAs in Arabidopsis. A null mutation of PINP1 causes embryonic lethality, and silencing of PINP1 leads to developmental defects and hypersusceptibility to Phytophthora infection. These phenotypes are reminiscent of transgenic plants expressing PSR1, supporting PINP1 as a direct virulence target of PSR1. We further demonstrate that the localization of the Dicer-like 1 protein complex is impaired in the nucleus of PINP1-silenced or PSR1-expressing cells, indicating that PINP1 may facilitate small RNA processing by affecting the assembly of dicing complexes. A similar function of PINP1 homologous genes in development and immunity was also observed in Nicotiana benthamiana. These findings highlight PINP1 as a previously unidentified component of RNA silencing that regulates distinct classes of small RNAs in plants. Importantly, Phytophthora has evolved effectors to target PINP1 in order to promote infection.
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Affiliation(s)
- Yongli Qiao
- Department of Plant Pathology and Microbiology and Center for Plant Cell Biology, University of California, Riverside, CA 92521; and National Key Facility for Crop Gene Resources and Genetic Improvement, Institute of Crop Science, Chinese Academy of Agricultural Sciences, Beijing 100081, China
| | - Jinxia Shi
- Department of Plant Pathology and Microbiology and Center for Plant Cell Biology, University of California, Riverside, CA 92521; and
| | - Yi Zhai
- Department of Plant Pathology and Microbiology and
| | - Yingnan Hou
- Department of Plant Pathology and Microbiology and Center for Plant Cell Biology, University of California, Riverside, CA 92521; and
| | - Wenbo Ma
- Department of Plant Pathology and Microbiology and Center for Plant Cell Biology, University of California, Riverside, CA 92521; and
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35
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Abstract
DNA cytosine methylationis an important epigenetic process that is correlated with transgene silencing, transposon suppression, and gene imprinting. In plants, small interfering RNAs (siRNAs) can trigger DNA methylation at loci containing their homolog sequences through a process called RNA-directed DNA methylation (RdDM). In canonical RdDM, 24 nucleotide (nt) siRNAs (ra-siRNAs) will be loaded into their effector protein called ARGONAUTE 4 (AGO4) and subsequently targeted to RdDM loci through base-pairing with the non-coding transcripts produced by DNA-directed RNA Polymerase V. Then, the AGO4-ra-siRNA will recruit the DNA methyltransferase to catalyze de novo DNA methylation. Recent studies also identified non-canonical RdDM pathways that involve microRNAs or 21 nt siRNAs. These RdDM pathways are biologically important since they control responses biotic and abiotic stresses, maintain genome stability and regulate development. Here, we summarize recent pro-gresses of mechanisms governing canonical and non-canonical RdDM pathways.
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Affiliation(s)
- Meng Xie
- Center for Plant Science Innovation & School of Biological Sciences, University of Nebraska-Lincoln, Lincoln, Nebraska 68588-0660, USA
| | - Bin Yu
- Center for Plant Science Innovation & School of Biological Sciences, University of Nebraska-Lincoln, Lincoln, Nebraska 68588-0660, USA
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36
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Phetrungnapha A, Kondo H, Hirono I, Panyim S, Ongvarrasopone C. Molecular cloning and characterization of Mj-mov-10, a putative RNA helicase involved in RNAi of kuruma shrimp. Fish Shellfish Immunol 2015; 44:241-247. [PMID: 25724627 DOI: 10.1016/j.fsi.2015.02.028] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/27/2014] [Revised: 02/15/2015] [Accepted: 02/16/2015] [Indexed: 06/04/2023]
Abstract
Identification and characterization of the RNAi-related genes is the key to understanding RNAi mechanism in shrimp. In this study, we have identified and characterized a novel putative RNA helicase gene, Mj-mov-10 from the kuruma shrimp, Marsupenaeus japonicus and its implication in shrimp RNAi was demonstrated. The full-length Mj-mov-10 gene contained 3536bp, including 239 bp of 5'UTR, 2895 bp of the open reading frame (ORF) and 402bp of 3'UTR, respectively. An ORF of Mj-mov-10 could be translated to a 109-kDa protein which consists of a single helicase core domain containing seven signature motifs of the RNA helicase superfamily-1. Mj-MOV-10 protein shared 47% and 40% identity with mammalian MOV-10 and plant SDE3, respectively. Expression of Mj-mov-10 gene was significantly up-regulated upon dsRNA and white spot syndrome virus (WSSV) challenge. In vivo gene knockdown of Mj-mov-10 resulted in an increase of a susceptibility of shrimp to WSSV infection. Our results implied the functional significance of Mj-MOV-10 in dsRNA-mediated gene silencing and antiviral defense mechanism in shrimp.
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Affiliation(s)
- Amnat Phetrungnapha
- Department of Biochemistry, Faculty of Medical Science, Naresuan University, Phitsanulok 65000, Thailand
| | - Hidehiro Kondo
- Laboratory of Genome Science, Graduate School of Tokyo University of Marine Science and Technology, Minato, Tokyo, Japan
| | - Ikuo Hirono
- Laboratory of Genome Science, Graduate School of Tokyo University of Marine Science and Technology, Minato, Tokyo, Japan
| | - Sakol Panyim
- Institute of Molecular Biosciences, Mahidol University, Phutthamonthon 4 Road, Salaya, Nakhon Pathom 73170, Thailand; Department of Biochemistry, Faculty of Science, Mahidol University, Rama VI Road, Phayathai, Bangkok 10400, Thailand
| | - Chalermporn Ongvarrasopone
- Institute of Molecular Biosciences, Mahidol University, Phutthamonthon 4 Road, Salaya, Nakhon Pathom 73170, Thailand.
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Csorba T, Kontra L, Burgyán J. viral silencing suppressors: Tools forged to fine-tune host-pathogen coexistence. Virology 2015; 479-480:85-103. [DOI: 10.1016/j.virol.2015.02.028] [Citation(s) in RCA: 368] [Impact Index Per Article: 40.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2014] [Revised: 01/31/2015] [Accepted: 02/16/2015] [Indexed: 12/27/2022]
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Klein-Cosson C, Chambrier P, Rogowsky PM, Vernoud V. Regulation of a maize HD-ZIP IV transcription factor by a non-conventional RDR2-dependent small RNA. Plant J 2015; 81:747-758. [PMID: 25619590 DOI: 10.1111/tpj.12771] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/18/2014] [Revised: 12/22/2014] [Accepted: 01/07/2015] [Indexed: 06/04/2023]
Abstract
Small non-coding RNAs are versatile riboregulators that control gene expression at the transcriptional or post-transcriptional level, governing many facets of plant development. Here we present evidence for the existence of a 24 nt small RNA (named small1) that is complementary to the 3' UTR of OCL1 (Outer Cell Layer1), the founding member of the maize HD-ZIP IV gene family encoding plant-specific transcription factors that are mainly involved in epidermis differentiation and specialization. The biogenesis of small1 depends on DICER-like 3 (DCL3), RNA-dependent RNA polymerase 2 (RDR2) and RNA polymerase IV, components that are usually required for RNA-dependent DNA-methylation. Unexpectedly, GFP sensor experiments in transient and stable transformation systems revealed that small1 may regulate its target at the post-transcriptional level, mainly through translational repression. This translational repression is attenuated in an rdr2 mutant background in which small1 does not accumulate. Our experiments further showed the possible involvement of a secondary stem-loop structure present in the 3' UTR of OCL1 for efficient target repression, suggesting the existence of several regulatory mechanisms affecting OCL1 mRNA stability and translation.
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Affiliation(s)
- Catherine Klein-Cosson
- Unité Reproduction et Développement des Plantes, Université de Lyon, Ecole Normale Supérieure de Lyon, Université Lyon 1, F-69364, Lyon, France; Institut National de la Recherche Agronomique, UMR879 Reproduction et Développement des Plantes, F-69364, Lyon, France; Centre National de la Recherche Scientifique, UMR5667 Reproduction et Développement des Plantes, F-69364, Lyon, France
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Pirovano W, Miozzi L, Boetzer M, Pantaleo V. Bioinformatics approaches for viral metagenomics in plants using short RNAs: model case of study and application to a Cicer arietinum population. Front Microbiol 2015; 5:790. [PMID: 25674078 PMCID: PMC4307218 DOI: 10.3389/fmicb.2014.00790] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2014] [Accepted: 12/22/2014] [Indexed: 12/12/2022] Open
Abstract
Over the past years deep sequencing experiments have opened novel doors to reconstruct viral populations in a high-throughput and cost-effective manner. Currently a substantial number of studies have been performed which employ next generation sequencing techniques to either analyze known viruses by means of a reference-guided approach or to discover novel viruses using a de novo-based strategy. Taking advantage of the well-known Cymbidium ringspot virus we have carried out a comparison of different bioinformatics tools to reconstruct the viral genome based on 21–27 nt short (s)RNA sequencing with the aim to identify the most efficient pipeline. The same approach was applied to a population of plants constituting an ancient variety of Cicer arietinum with red seeds. Among the discovered viruses, we describe the presence of a Tobamovirus referring to the Tomato mottle mosaic virus (NC_022230), which was not yet observed on C. arietinum nor revealed in Europe and a viroid referring to Hop stunt viroid (NC_001351.1) never reported in chickpea. Notably, a reference sequence guided approach appeared the most efficient in such kind of investigation. Instead, the de novo assembly reached a non-appreciable coverage although the most prominent viral species could still be identified. Advantages and limitations of viral metagenomics analysis using sRNAs are discussed.
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Affiliation(s)
- Walter Pirovano
- Genome Analysis and Technology Department, BaseClear B. V. Leiden, Netherlands
| | - Laura Miozzi
- Institute for Sustainable Plant Protection of National Research Council Torino, Italy
| | - Marten Boetzer
- Genome Analysis and Technology Department, BaseClear B. V. Leiden, Netherlands
| | - Vitantonio Pantaleo
- Institute for Sustainable Plant Protection of National Research Council, Bari Research Unit Bari, Italy
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40
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Abstract
Small RNA (sRNA)-mediated gene silencing is an important gene expression regulatory mechanism conserved in eukaryotes. Such sRNAs, first discovered in plants, are involved in diverse biological processes. In plants, sRNAs participate in many growth and developmental processes, such as embryo development, seed germination, flowering, hormone synthesis and distribution, and nutrient assimilation. However, the significance of sRNA in shaping the relationship between plants and their symbiotic microbes or pathogens has been underestimated. Recent progress in profiling sRNA, especially advances in next-generation sequencing technology, has revealed its extensive and complicated involvement in interactions between plants and viruses, bacteria, and fungi. In this review, we will summarize recent findings regarding sRNA in plant-pathogen interactions.
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Affiliation(s)
- Dongdong Niu
- Department of Plant Pathology, College of Plant Protection, Nanjing Agricultural University, Xuanwu, Nanjing, Jiangsu, 210095, China
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41
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Dotto MC, Petsch KA, Aukerman MJ, Beatty M, Hammell M, Timmermans MCP. Genome-wide analysis of leafbladeless1-regulated and phased small RNAs underscores the importance of the TAS3 ta-siRNA pathway to maize development. PLoS Genet 2014; 10:e1004826. [PMID: 25503246 PMCID: PMC4263373 DOI: 10.1371/journal.pgen.1004826] [Citation(s) in RCA: 42] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2014] [Accepted: 10/15/2014] [Indexed: 01/05/2023] Open
Abstract
Maize leafbladeless1 (lbl1) encodes a key component in the trans-acting short-interfering RNA (ta-siRNA) biogenesis pathway. Correlated with a great diversity in ta-siRNAs and the targets they regulate, the phenotypes conditioned by mutants perturbing this small RNA pathway vary extensively across species. Mutations in lbl1 result in severe developmental defects, giving rise to plants with radial, abaxialized leaves. To investigate the basis for this phenotype, we compared the small RNA content between wild-type and lbl1 seedling apices. We show that LBL1 affects the accumulation of small RNAs in all major classes, and reveal unexpected crosstalk between ta-siRNA biogenesis and other small RNA pathways regulating transposons. Interestingly, in contrast to data from other plant species, we found no evidence for the existence of phased siRNAs generated via the one-hit model. Our analysis identified nine TAS loci, all belonging to the conserved TAS3 family. Information from RNA deep sequencing and PARE analyses identified the tasiR-ARFs as the major functional ta-siRNAs in the maize vegetative apex where they regulate expression of AUXIN RESPONSE FACTOR3 (ARF3) homologs. Plants expressing a tasiR-ARF insensitive arf3a transgene recapitulate the phenotype of lbl1, providing direct evidence that deregulation of ARF3 transcription factors underlies the developmental defects of maize ta-siRNA biogenesis mutants. The phenotypes of Arabidopsis and Medicago ta-siRNA mutants, while strikingly different, likewise result from misexpression of the tasiR-ARF target ARF3. Our data indicate that diversity in TAS pathways and their targets cannot fully account for the phenotypic differences conditioned by ta-siRNA biogenesis mutants across plant species. Instead, we propose that divergence in the gene networks downstream of the ARF3 transcription factors or the spatiotemporal pattern during leaf development in which these proteins act constitute key factors underlying the distinct contributions of the ta-siRNA pathway to development in maize, Arabidopsis, and possibly other plant species as well. Mutations in maize leafbladeless1 (lbl1) that disrupt ta-siRNA biogenesis give rise to plants with thread-like leaves that have lost top/bottom polarity. We used genomic approaches to identify lbl1-dependent small RNAs and their targets to determine the basis for these polarity defects. This revealed substantial diversity in small RNA pathways across plant species and identified unexpected roles for LBL1 in the regulation of repetitive elements within the maize genome. We further show that only ta-siRNA loci belonging to the TAS3 family function in the maize vegetative apex. The TAS3-derived tasiR-ARFs are the main ta-siRNA active in the apex, and misregulation of their ARF3 targets emerges as the basis for the lbl1 leaf polarity defects. Supporting this, we show that plants expressing arf3a transcripts insensitive to tasiR-ARF-directed cleavage recapitulate the phenotypes observed in lbl1. The TAS3 ta-siRNA pathway, including the regulation of ARF3 genes, is conserved throughout land plant evolution, yet the phenotypes of plants defective for ta-siRNA biogenesis are strikingly different. Our data leads us to propose that divergence in the processes regulated by the ARF3 transcription factors or the spatiotemporal pattern during development in which these proteins act, underlies the diverse developmental contributions of this small RNA pathway across plants.
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Affiliation(s)
- Marcela C. Dotto
- Cold Spring Harbor Laboratory, Cold Spring Harbor, New York, United States of America
| | - Katherine A. Petsch
- Cold Spring Harbor Laboratory, Cold Spring Harbor, New York, United States of America
| | - Milo J. Aukerman
- DuPont Crop Genetics, Wilmington, Delaware, United States of America
| | - Mary Beatty
- Pioneer-DuPont, Johnston, Iowa, United States of America
| | - Molly Hammell
- Cold Spring Harbor Laboratory, Cold Spring Harbor, New York, United States of America
| | - Marja C. P. Timmermans
- Cold Spring Harbor Laboratory, Cold Spring Harbor, New York, United States of America
- * E-mail:
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42
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Wroblewski T, Matvienko M, Piskurewicz U, Xu H, Martineau B, Wong J, Govindarajulu M, Kozik A, Michelmore RW. Distinctive profiles of small RNA couple inverted repeat-induced post-transcriptional gene silencing with endogenous RNA silencing pathways in Arabidopsis. RNA 2014; 20:1987-99. [PMID: 25344399 PMCID: PMC4238362 DOI: 10.1261/rna.046532.114] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/09/2023]
Abstract
The experimental induction of RNA silencing in plants often involves expression of transgenes encoding inverted repeat (IR) sequences to produce abundant dsRNAs that are processed into small RNAs (sRNAs). These sRNAs are key mediators of post-transcriptional gene silencing (PTGS) and determine its specificity. Despite its application in agriculture and broad utility in plant research, the mechanism of IR-PTGS is incompletely understood. We generated four sets of 60 Arabidopsis plants, each containing IR transgenes expressing different configurations of uidA and CHALCONE Synthase (At-CHS) gene fragments. Levels of PTGS were found to depend on the orientation and position of the fragment in the IR construct. Deep sequencing and mapping of sRNAs to corresponding transgene-derived and endogenous transcripts identified distinctive patterns of differential sRNA accumulation that revealed similarities among sRNAs associated with IR-PTGS and endogenous sRNAs linked to uncapped mRNA decay. Detailed analyses of poly-A cleavage products from At-CHS mRNA confirmed this hypothesis. We also found unexpected associations between sRNA accumulation and the presence of predicted open reading frames in the trigger sequence. In addition, strong IR-PTGS affected the prevalence of endogenous sRNAs, which has implications for the use of PTGS for experimental or applied purposes.
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Affiliation(s)
- Tadeusz Wroblewski
- The Genome Center, University of California, Davis, Davis, California 95616, USA
| | - Marta Matvienko
- The Genome Center, University of California, Davis, Davis, California 95616, USA
| | - Urszula Piskurewicz
- The Genome Center, University of California, Davis, Davis, California 95616, USA
| | - Huaqin Xu
- The Genome Center, University of California, Davis, Davis, California 95616, USA
| | - Belinda Martineau
- The Genome Center, University of California, Davis, Davis, California 95616, USA
| | - Joan Wong
- The Genome Center, University of California, Davis, Davis, California 95616, USA
| | | | - Alexander Kozik
- The Genome Center, University of California, Davis, Davis, California 95616, USA
| | - Richard W Michelmore
- The Genome Center, University of California, Davis, Davis, California 95616, USA Department of Plant Science, University of California, Davis, Davis, California 95616, USA Department of Molecular and Cellular Biology, University of California, Davis, Davis, California 95616, USA Department of Medical Microbiology and Immunology, University of California, Davis, Davis, California 95616, USA
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43
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Garcia D, Garcia S, Voinnet O. Nonsense-mediated decay serves as a general viral restriction mechanism in plants. Cell Host Microbe 2014; 16:391-402. [PMID: 25155460 PMCID: PMC7185767 DOI: 10.1016/j.chom.2014.08.001] [Citation(s) in RCA: 101] [Impact Index Per Article: 10.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2014] [Revised: 04/16/2014] [Accepted: 07/14/2014] [Indexed: 11/17/2022]
Abstract
(+)strand RNA viruses have to overcome various points of restriction in the host to establish successful infection. In plants, this includes RNA silencing. To uncover additional bottlenecks to RNA virus infection, we genetically attenuated the impact of RNA silencing on transgenically expressed Potato virus X (PVX), a (+)strand RNA virus that replicates in Arabidopsis. A genetic screen in this sensitized background uncovered how nonsense-mediated decay (NMD), a host RNA quality control mechanism, recognizes and eliminates PVX RNAs with internal termination codons and long 3′ UTRs. NMD also operates in natural infection contexts, and while some viruses have evolved genome expression strategies to overcome this process altogether, the virulence of NMD-activating viruses entails their ability to directly suppress NMD or to promote an NMD-unfavorable cellular state. These principles of induction, evasion, and suppression define NMD as a general viral restriction mechanism in plants that also likely operates in animals. A sensitized genetic screen for modifiers of (+)strand RNA virus accumulation in Arabidopsis The host nonsense-mediated decay (NMD) pathway restricts PVX during natural infection NMD targets viral RNAs containing internal termination codons and long 3′ UTRs Some viruses have evolved to evade NMD altogether, while others may suppress NMD actively
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Affiliation(s)
- Damien Garcia
- Institut de Biologie Moléculaire des Plantes (IBMP), Centre National de la Recherche Scientifique, UPR 2357, 67084 Strasbourg, France.
| | - Shahinez Garcia
- Institut de Biologie Moléculaire des Plantes (IBMP), Centre National de la Recherche Scientifique, UPR 2357, 67084 Strasbourg, France
| | - Olivier Voinnet
- Institut de Biologie Moléculaire des Plantes (IBMP), Centre National de la Recherche Scientifique, UPR 2357, 67084 Strasbourg, France; Swiss Federal Institute of Technology Zurich, Department of Biology, Universitätstrasse 2, 8092 Zürich, Switzerland.
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44
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Dueck A, Meister G. Assembly and function of small RNA – Argonaute protein complexes. Biol Chem 2014; 395:611-29. [DOI: 10.1515/hsz-2014-0116] [Citation(s) in RCA: 54] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2014] [Accepted: 02/28/2014] [Indexed: 01/05/2023]
Abstract
Abstract
Small RNAs such as microRNAs (miRNAs), short interfering RNAs (siRNAs) or Piwi-interacting RNAs (piRNAs) are important regulators of gene expression in various organisms. Small RNAs bind to a member of the Argonaute protein family and are incorporated into larger structures that mediate diverse gene silencing events. The loading of Argonaute proteins with small RNAs is aided by a number of auxiliary factors as well as ATP hydrolysis. This review will focus on the mechanisms of Argonaute loading in different organisms. Furthermore, we highlight the versatile functions of small RNA-Argonaute protein complexes in organisms from all three kingdoms of life.
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45
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Okano Y, Senshu H, Hashimoto M, Neriya Y, Netsu O, Minato N, Yoshida T, Maejima K, Oshima K, Komatsu K, Yamaji Y, Namba S. In Planta Recognition of a Double-Stranded RNA Synthesis Protein Complex by a Potexviral RNA Silencing Suppressor. Plant Cell 2014; 26:2168-2183. [PMID: 24879427 PMCID: PMC4079376 DOI: 10.1105/tpc.113.120535] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/07/2013] [Revised: 04/23/2014] [Accepted: 05/09/2014] [Indexed: 05/22/2023]
Abstract
RNA silencing plays an important antiviral role in plants and invertebrates. To counteract antiviral RNA silencing, most plant viruses have evolved viral suppressors of RNA silencing (VSRs). TRIPLE GENE BLOCK PROTEIN1 (TGBp1) of potexviruses is a well-characterized VSR, but the detailed mechanism by which it suppresses RNA silencing remains unclear. We demonstrate that transgenic expression of TGBp1 of plantago asiatica mosaic virus (PlAMV) induced developmental abnormalities in Arabidopsis thaliana similar to those observed in mutants of SUPPRESSOR OF GENE SILENCING3 (SGS3) and RNA-DEPENDENT RNA POLYMERASE6 (RDR6) required for the trans-acting small interfering RNA synthesis pathway. PlAMV-TGBp1 inhibits SGS3/RDR6-dependent double-stranded RNA synthesis in the trans-acting small interfering RNA pathway. TGBp1 interacts with SGS3 and RDR6 and coaggregates with SGS3/RDR6 bodies, which are normally dispersed in the cytoplasm. In addition, TGBp1 forms homooligomers, whose formation coincides with TGBp1 aggregation with SGS3/RDR6 bodies. These results reveal the detailed molecular function of TGBp1 as a VSR and shed new light on the SGS3/RDR6-dependent double-stranded RNA synthesis pathway as another general target of VSRs.
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Affiliation(s)
- Yukari Okano
- Laboratory of Plant Pathology, Graduate School of Agricultural and Life Sciences, The University of Tokyo, Bunkyo-ku, Tokyo 113-8657, Japan
| | - Hiroko Senshu
- Laboratory of Plant Pathology, Graduate School of Agricultural and Life Sciences, The University of Tokyo, Bunkyo-ku, Tokyo 113-8657, Japan
| | - Masayoshi Hashimoto
- Laboratory of Plant Pathology, Graduate School of Agricultural and Life Sciences, The University of Tokyo, Bunkyo-ku, Tokyo 113-8657, Japan
| | - Yutaro Neriya
- Laboratory of Plant Pathology, Graduate School of Agricultural and Life Sciences, The University of Tokyo, Bunkyo-ku, Tokyo 113-8657, Japan
| | - Osamu Netsu
- Laboratory of Plant Pathology, Graduate School of Agricultural and Life Sciences, The University of Tokyo, Bunkyo-ku, Tokyo 113-8657, Japan
| | - Nami Minato
- Laboratory of Plant Pathology, Graduate School of Agricultural and Life Sciences, The University of Tokyo, Bunkyo-ku, Tokyo 113-8657, Japan
| | - Tetsuya Yoshida
- Laboratory of Plant Pathology, Graduate School of Agricultural and Life Sciences, The University of Tokyo, Bunkyo-ku, Tokyo 113-8657, Japan
| | - Kensaku Maejima
- Laboratory of Plant Pathology, Graduate School of Agricultural and Life Sciences, The University of Tokyo, Bunkyo-ku, Tokyo 113-8657, Japan
| | - Kenro Oshima
- Laboratory of Plant Pathology, Graduate School of Agricultural and Life Sciences, The University of Tokyo, Bunkyo-ku, Tokyo 113-8657, Japan
| | - Ken Komatsu
- Laboratory of Plant Pathology, Graduate School of Agricultural and Life Sciences, The University of Tokyo, Bunkyo-ku, Tokyo 113-8657, Japan
| | - Yasuyuki Yamaji
- Laboratory of Plant Pathology, Graduate School of Agricultural and Life Sciences, The University of Tokyo, Bunkyo-ku, Tokyo 113-8657, Japan
| | - Shigetou Namba
- Laboratory of Plant Pathology, Graduate School of Agricultural and Life Sciences, The University of Tokyo, Bunkyo-ku, Tokyo 113-8657, Japan
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46
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Abstract
In eukaryotic RNA silencing, RNase-III classes of enzymes in the Dicer family process double-stranded RNA of cellular or exogenous origin into small-RNA (sRNA) molecules. sRNAs are then loaded into effector proteins known as ARGONAUTEs (AGOs), which, as part of RNA-induced silencing complexes, target complementary RNA or DNA for silencing. Plants have evolved a large variety of pathways over the Dicer-AGO consortium, which most likely underpins part of their phenotypic plasticity. Dicer-like proteins produce all known classes of plant silencing sRNAs, which are invariably stabilized via 2'-O-methylation mediated by HUA ENHANCER 1 (HEN1), potentially amplified by the action of several RNA-dependent RNA polymerases, and function through a variety of AGO proteins. Here, we review the known characteristics and biochemical properties of the core silencing factors found in the model plant Arabidopsis thaliana. We also describe how interactions between these core factors and more specialized proteins allow the production of a plethora of silencing sRNAs involved in a large array of biological functions. We emphasize in particular the biogenesis and activities of silencing sRNAs of endogenous origin.
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Affiliation(s)
- Nicolas G Bologna
- Department of Biology, Swiss Federal Institute of Technology (ETH-Z), 8093 Zurich, Switzerland;
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47
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Vargason JM, Burch CJ, Wilson JW. Identification and RNA binding characterization of plant virus RNA silencing suppressor proteins. Methods 2013; 64:88-93. [PMID: 23981361 DOI: 10.1016/j.ymeth.2013.08.016] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2013] [Revised: 08/06/2013] [Accepted: 08/13/2013] [Indexed: 10/26/2022] Open
Abstract
Suppression is a common mechanism employed by viruses to evade the antiviral effects of the host's RNA silencing pathway. The activity of suppression has commonly been localized to gene products in the virus, but the variety of mechanisms used in suppression by these viral proteins spans nearly the complete biochemical pathway of RNA silencing in the host. This review describes the agrofiltration assay and a slightly modified version of the agro-infiltration assay called co-infiltration, which are common methods used to observe RNA silencing and identify viral silencing suppressor proteins in plants, respectively. In addition, this review will provide an overview of two methods, electrophoretic mobility shift assay and fluorescence polarization, used to assess the binding of a suppressor protein to siRNA which has been shown to be a general mechanism to suppress RNA silencing by plant viruses.
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Affiliation(s)
- Jeffrey M Vargason
- Department of Biology and Chemistry, George Fox University, 414 North Meridian Street, Newberg, OR 97132, USA.
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48
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Martínez de Alba AE, Elvira-Matelot E, Vaucheret H. Gene silencing in plants: a diversity of pathways. Biochim Biophys Acta 2013; 1829:1300-8. [PMID: 24185199 DOI: 10.1016/j.bbagrm.2013.10.005] [Citation(s) in RCA: 90] [Impact Index Per Article: 8.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Received: 05/06/2013] [Revised: 10/22/2013] [Accepted: 10/24/2013] [Indexed: 10/26/2022]
Abstract
Eukaryotic organisms have evolved a variety of gene silencing pathways in which small RNAs, 20- to 30-nucleotides in length, repress the expression of sequence homologous genes at the transcriptional or post-transcriptional levels. In plants, RNA silencing pathways play important roles in regulating development and response to both biotic and abiotic stresses. The molecular basis of these complex and interconnected pathways has emerged only in recent years with the identification of many of the genes necessary for the biogenesis and action of small RNAs. This review covers the diversity of RNA silencing pathways identified in plants.
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49
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Duc C, Sherstnev A, Cole C, Barton GJ, Simpson GG. Transcription termination and chimeric RNA formation controlled by Arabidopsis thaliana FPA. PLoS Genet 2013; 9:e1003867. [PMID: 24204292 PMCID: PMC3814327 DOI: 10.1371/journal.pgen.1003867] [Citation(s) in RCA: 53] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2013] [Accepted: 08/22/2013] [Indexed: 11/18/2022] Open
Abstract
Alternative cleavage and polyadenylation influence the coding and regulatory potential of mRNAs and where transcription termination occurs. Although widespread, few regulators of this process are known. The Arabidopsis thaliana protein FPA is a rare example of a trans-acting regulator of poly(A) site choice. Analysing fpa mutants therefore provides an opportunity to reveal generic consequences of disrupting this process. We used direct RNA sequencing to quantify shifts in RNA 3′ formation in fpa mutants. Here we show that specific chimeric RNAs formed between the exons of otherwise separate genes are a striking consequence of loss of FPA function. We define intergenic read-through transcripts resulting from defective RNA 3′ end formation in fpa mutants and detail cryptic splicing and antisense transcription associated with these read-through RNAs. We identify alternative polyadenylation within introns that is sensitive to FPA and show FPA-dependent shifts in IBM1 poly(A) site selection that differ from those recently defined in mutants defective in intragenic heterochromatin and DNA methylation. Finally, we show that defective termination at specific loci in fpa mutants is shared with dicer-like 1 (dcl1) or dcl4 mutants, leading us to develop alternative explanations for some silencing roles of these proteins. We relate our findings to the impact that altered patterns of 3′ end formation can have on gene and genome organisation. The ends of almost all eukaryotic protein-coding genes are defined by a poly(A) signal. When genes are transcribed into mRNA by RNA polymerase II, the poly(A) signal guides cleavage of the precursor mRNA at a particular site; this is accompanied by the addition of a poly(A) tail to the mRNA and termination of transcription. Many genes have more than one poly(A) signal and the regulated choice of which to select can effectively determine what the gene will code for, how the gene can be regulated and where transcription termination occurs. We discovered a rare example of a regulator of poly(A) site choice, called FPA, while studying flower development in the model plant Arabidopsis thaliana. Studying FPA therefore provides an opportunity to understand not only its roles in plant biology but also the generic consequences of disrupting alternative polyadenylation. In this study, we use a technique called direct RNA sequencing to quantify genome-wide shifts in poly(A) site selection in plants that lack FPA function. One of our most striking findings is that in the absence of FPA we detect chimeric RNAs formed between two otherwise separate and well-characterised genes.
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Affiliation(s)
- Céline Duc
- College of Life Sciences, University of Dundee, Dundee, Scotland, United Kingdom
| | - Alexander Sherstnev
- College of Life Sciences, University of Dundee, Dundee, Scotland, United Kingdom
| | - Christian Cole
- College of Life Sciences, University of Dundee, Dundee, Scotland, United Kingdom
| | - Geoffrey J. Barton
- College of Life Sciences, University of Dundee, Dundee, Scotland, United Kingdom
- * E-mail: (GJB); (GGS)
| | - Gordon G. Simpson
- College of Life Sciences, University of Dundee, Dundee, Scotland, United Kingdom
- James Hutton Institute, Invergowrie, Dundee, Scotland, United Kingdom
- * E-mail: (GJB); (GGS)
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50
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Peláez P, Sanchez F. Small RNAs in plant defense responses during viral and bacterial interactions: similarities and differences. Front Plant Sci 2013; 4:343. [PMID: 24046772 PMCID: PMC3763480 DOI: 10.3389/fpls.2013.00343] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/09/2013] [Accepted: 08/14/2013] [Indexed: 05/20/2023]
Abstract
Small non-coding RNAs constitute an important class of gene expression regulators that control different biological processes in most eukaryotes. In plants, several small RNA (sRNA) silencing pathways have evolved to produce a wide range of small RNAs with specialized functions. Evidence for the diverse mode of action of the small RNA pathways has been highlighted during plant-microbe interactions. Host sRNAs and small RNA silencing pathways have been recognized as essential components of plant immunity. One way plants respond and defend against pathogen infections is through the small RNA silencing immune system. To deal with plant defense responses, pathogens have evolved sophisticated mechanisms to avoid and counterattack this defense strategy. The relevance of the small RNA-mediated plant defense responses during viral infections has been well-established. Recent evidence points out its importance also during plant-bacteria interactions. Herein, this review discusses recent findings, similarities and differences about the small RNA-mediated arms race between plants and these two groups of microbes, including the small RNA silencing pathway components that contribute to plant immune responses, the pathogen-responsive endogenous sRNAs and the pathogen-delivered effector proteins.
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Affiliation(s)
| | - Federico Sanchez
- *Correspondence: Federico Sanchez, Departamento de Biología Molecular de Plantas, Instituto de Biotecnología, Universidad Nacional Autónoma de México, Avenida Universidad 2001, 62210 Cuernavaca, Morelos, México e-mail:
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