101
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Brandão BB, Guerra BA, Mori MA. Shortcuts to a functional adipose tissue: The role of small non-coding RNAs. Redox Biol 2017; 12:82-102. [PMID: 28214707 PMCID: PMC5312655 DOI: 10.1016/j.redox.2017.01.020] [Citation(s) in RCA: 41] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2017] [Accepted: 01/30/2017] [Indexed: 12/20/2022] Open
Abstract
Metabolic diseases such as type 2 diabetes are a major public health issue worldwide. These diseases are often linked to a dysfunctional adipose tissue. Fat is a large, heterogenic, pleiotropic and rather complex tissue. It is found in virtually all cavities of the human body, shows unique plasticity among tissues, and harbors many cell types in addition to its main functional unit - the adipocyte. Adipose tissue function varies depending on the localization of the fat depot, the cell composition of the tissue and the energy status of the organism. While the white adipose tissue (WAT) serves as the main site for triglyceride storage and acts as an important endocrine organ, the brown adipose tissue (BAT) is responsible for thermogenesis. Beige adipocytes can also appear in WAT depots to sustain heat production upon certain conditions, and it is becoming clear that adipose tissue depots can switch phenotypes depending on cell autonomous and non-autonomous stimuli. To maintain such degree of plasticity and respond adequately to changes in the energy balance, three basic processes need to be properly functioning in the adipose tissue: i) adipogenesis and adipocyte turnover, ii) metabolism, and iii) signaling. Here we review the fundamental role of small non-coding RNAs (sncRNAs) in these processes, with focus on microRNAs, and demonstrate their importance in adipose tissue function and whole body metabolic control in mammals.
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Affiliation(s)
- Bruna B Brandão
- Program in Molecular Biology, Universidade Federal de São Paulo, São Paulo, Brazil; Department of Biochemistry and Tissue Biology, Universidade Estadual de Campinas, Campinas, Brazil
| | - Beatriz A Guerra
- Program in Molecular Biology, Universidade Federal de São Paulo, São Paulo, Brazil; Department of Biochemistry and Tissue Biology, Universidade Estadual de Campinas, Campinas, Brazil
| | - Marcelo A Mori
- Program in Molecular Biology, Universidade Federal de São Paulo, São Paulo, Brazil; Department of Biochemistry and Tissue Biology, Universidade Estadual de Campinas, Campinas, Brazil; Program in Genetics and Molecular Biology, Universidade Estadual de Campinas, Campinas, Brazil.
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102
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Zhou X, Chen X, Wang Y, Feng X, Guang S. A new layer of rRNA regulation by small interference RNAs and the nuclear RNAi pathway. RNA Biol 2017. [PMID: 28640690 DOI: 10.1080/15476286.2017.1341034] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/19/2022] Open
Abstract
Ribosome biogenesis drives cell growth and proliferation, but mechanisms that modulate this process remain poorly understood. For a long time, small rRNA sequences have been widely treated as non-specific degradation products and neglected as garbage sequences. Recently, we identified a new class of antisense ribosomal siRNAs (risiRNAs) that downregulate pre-rRNA through the nuclear RNAi pathway in C. elegans. risiRNAs exhibit sequence characteristics similar to 22G RNA while complement to 18S and 26S rRNA. risiRNAs elicit the translocation of the nuclear Argonaute protein NRDE-3 from the cytoplasm to nucleus and nucleolus, in which the risiRNA/NRDE complex binds to pre-rRNA and silences rRNA expression. Interestingly, when C. elegans is exposed to environmental stimuli, such as cold shock and ultraviolet illumination, risiRNAs accumulate and further turn on the nuclear RNAi-mediated gene silencing pathway. risiRNA may act in a quality control mechanism of rRNA homeostasis. When the exoribonuclease SUSI-1(ceDis3L2) is mutated, risiRNAs are dramatically increased. In this Point of View article, we will summarize our understanding of the small antisense ribosomal siRNAs in a variety of organisms, especially C. elegans, and their possible roles in the quality control mechanism of rRNA homeostasis.
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Affiliation(s)
- Xufei Zhou
- a School of Life Sciences, CAS Center for Excellence in Molecular Cell Science, University of Science and Technology of China , Hefei , Anhui , P.R. China
| | - Xiangyang Chen
- a School of Life Sciences, CAS Center for Excellence in Molecular Cell Science, University of Science and Technology of China , Hefei , Anhui , P.R. China
| | - Yun Wang
- a School of Life Sciences, CAS Center for Excellence in Molecular Cell Science, University of Science and Technology of China , Hefei , Anhui , P.R. China
| | - Xuezhu Feng
- a School of Life Sciences, CAS Center for Excellence in Molecular Cell Science, University of Science and Technology of China , Hefei , Anhui , P.R. China
| | - Shouhong Guang
- a School of Life Sciences, CAS Center for Excellence in Molecular Cell Science, University of Science and Technology of China , Hefei , Anhui , P.R. China
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103
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Guo S, Hsueh YC, Tucker-Kellogg G, Wong SM. Differential expression of novel microRNAs in response to the infection of a TMV mutant with an internal poly(A) tract in N. benthamiana. Virus Res 2017; 239:143-171. [PMID: 28668702 DOI: 10.1016/j.virusres.2017.06.001] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2017] [Revised: 05/15/2017] [Accepted: 06/01/2017] [Indexed: 11/17/2022]
Abstract
We first constructed small RNA libraries of TMV- and TMV-43A-infected N. benthamiana for high throughput sequencing. A total number of 181 novel microRNAs (miRNAs) were identified through an improved miRNAs analysis pipeline. We were able to identify consistent miRNA expression changes induced in TMV and TMV-43A-infected plants, as well as differences associated with the UPD substitution in the TMV-43A viral genome. Virally induced miRNAs are associated with distinct processes and functions of predicted mRNA targets, including relation to host target defense. This study suggests an approach for functional genomics miRNAs in incompletely assembled genomes. These findings provide valuable information for further characterization of miRNAs by two genomic similar viruses, and provide clues to the study of TMV-UPD to find potential defense-related host genes targeted by miRNAs (126 words).
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Affiliation(s)
- Song Guo
- Department of Biological Sciences, National University of Singapore, Republic of Singapore
| | | | - Greg Tucker-Kellogg
- Department of Biological Sciences, National University of Singapore, Republic of Singapore
| | - Sek-Man Wong
- Department of Biological Sciences, National University of Singapore, Republic of Singapore; Temasek Life Sciences Laboratory, Singapore, Republic of Singapore; National University of Singapore Research Institute in Suzhou, Jiangsu, PR China.
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104
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Guo Y, Jia MA, Yang Y, Zhan L, Cheng X, Cai J, Zhang J, Yang J, Liu T, Fu Q, Zhao J, Shamsi IH. Integrated analysis of tobacco miRNA and mRNA expression profiles under PVY infection provids insight into tobacco-PVY interactions. Sci Rep 2017; 7:4895. [PMID: 28687775 PMCID: PMC5501784 DOI: 10.1038/s41598-017-05155-w] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2017] [Accepted: 05/24/2017] [Indexed: 02/02/2023] Open
Abstract
Potato virus Y (PVY) is a globally and economically important pathogen of potato, tobacco, tomato and other staple crops and caused significant yield losses and reductions in quality.To explore the molecular PVY-host interactions, we analysed changes in the miRNA and mRNA profiles of tobacco in response to PVY infection. A total of 81 differentially expressed miRNAs belonging to 29 families and 8133 mRNAs were identified. The Gene Ontology (GO) enrichment analyses showed that genes encoding the DNA/RNA binding, catalytic activity and signalling molecules were all significantly enriched. Moreover, 88 miRNA-mRNA interaction pairs were identified through a combined analysis of the two datasets. We also found evidence showing that the virus-derived siRNAs (vsiRNAs) from the PVY genome target tobacco translationally controlled tumor protein (NtTCTP) mRNA and mediate plant resistance to PVY. Together, our findings revealed that both miRNA and mRNA expression patterns can be changed in response to PVY infection and novel vsiRNA-plant interactions that may regulate plant resistance to PVY. Both provide fresh insights into the virus-plant interactions.
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MESH Headings
- Biomarkers, Tumor/antagonists & inhibitors
- Biomarkers, Tumor/genetics
- Biomarkers, Tumor/immunology
- Biomarkers, Tumor/metabolism
- Disease Resistance/genetics
- Gene Ontology
- Gene Regulatory Networks
- Host-Pathogen Interactions
- MicroRNAs/genetics
- MicroRNAs/immunology
- MicroRNAs/metabolism
- Molecular Sequence Annotation
- Plant Diseases/genetics
- Plant Diseases/immunology
- Plant Diseases/virology
- Plant Proteins/genetics
- Plant Proteins/immunology
- Plant Proteins/metabolism
- Potyvirus/genetics
- Potyvirus/metabolism
- Potyvirus/pathogenicity
- RNA, Messenger/genetics
- RNA, Messenger/immunology
- RNA, Messenger/metabolism
- RNA, Plant/genetics
- RNA, Plant/immunology
- RNA, Plant/metabolism
- RNA, Small Interfering/genetics
- RNA, Small Interfering/metabolism
- RNA, Viral/genetics
- RNA, Viral/metabolism
- Nicotiana/genetics
- Nicotiana/immunology
- Nicotiana/virology
- Tumor Protein, Translationally-Controlled 1
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Affiliation(s)
- Yushuang Guo
- Key Laboratory of Molecular Genetics, China National Tobacco Corporation, Guizhou Institute of Tobacco Science, Guiyang, Guizhou, 550083, P. R. China
| | - Meng-Ao Jia
- Key Laboratory of Molecular Genetics, China National Tobacco Corporation, Guizhou Institute of Tobacco Science, Guiyang, Guizhou, 550083, P. R. China.
| | - Yumei Yang
- Annoroad Gene Technology (Beijing) Co., Ltd, Beijing, 101100, P. R. China
| | - Linlin Zhan
- College of Agriculture and Food Science, Zhejiang Agriculture and Forestry University, Hangzhou, Zhejiang, 311300, P. R. China
| | - Xiaofei Cheng
- School of Life and Environmental science, Hangzhou Normal University, Hangzhou, Zhejiang, 311121, P. R. China
| | - Jianyu Cai
- College of Agriculture and Food Science, Zhejiang Agriculture and Forestry University, Hangzhou, Zhejiang, 311300, P. R. China
| | - Jie Zhang
- Key Laboratory of Molecular Genetics, China National Tobacco Corporation, Guizhou Institute of Tobacco Science, Guiyang, Guizhou, 550083, P. R. China
| | - Jie Yang
- Annoroad Gene Technology (Beijing) Co., Ltd, Beijing, 101100, P. R. China
| | - Tao Liu
- Annoroad Gene Technology (Beijing) Co., Ltd, Beijing, 101100, P. R. China
| | - Qiang Fu
- Key Laboratory of Molecular Genetics, China National Tobacco Corporation, Guizhou Institute of Tobacco Science, Guiyang, Guizhou, 550083, P. R. China
| | - Jiehong Zhao
- Key Laboratory of Molecular Genetics, China National Tobacco Corporation, Guizhou Institute of Tobacco Science, Guiyang, Guizhou, 550083, P. R. China
| | - Imran Haider Shamsi
- Department of Agronomy, College of Agriculture and Biotechnology, Zhejiang University, Hangzhou, Zhejiang, 310058, P. R. China.
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105
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Paces J, Nic M, Novotny T, Svoboda P. Literature review of baseline information to support the risk assessment of RNAi‐based GM plants. ACTA ACUST UNITED AC 2017. [PMCID: PMC7163844 DOI: 10.2903/sp.efsa.2017.en-1246] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Affiliation(s)
- Jan Paces
- Institute of Molecular Genetics of the Academy of Sciences of the Czech Republic (IMG)
| | | | | | - Petr Svoboda
- Institute of Molecular Genetics of the Academy of Sciences of the Czech Republic (IMG)
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106
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Wu YY, Hou BH, Lee WC, Lu SH, Yang CJ, Vaucheret H, Chen HM. DCL2- and RDR6-dependent transitive silencing of SMXL4 and SMXL5 in Arabidopsis dcl4 mutants causes defective phloem transport and carbohydrate over-accumulation. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2017; 90:1064-1078. [PMID: 28267232 DOI: 10.1111/tpj.13528] [Citation(s) in RCA: 36] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/10/2016] [Revised: 02/02/2017] [Accepted: 02/28/2017] [Indexed: 05/25/2023]
Abstract
DICER-LIKE (DCL) enzymes process double-stranded RNA into small RNAs that act as regulators of gene expression. Arabidopsis DCL4 and DCL2 each allow the post-transcriptional gene silencing (PTGS) of viruses and transgenes, but primary PTGS-prone DCL4 outcompetes transitive PTGS-prone DCL2 in wild-type plants. This hierarchy likely prevents DCL2 having any detrimental effects on endogenous genes. Indeed, dcl4 mutants exhibit developmental defects and increased sensitivity to genotoxic stress. In this study, the mechanism underlying dcl4 defects was investigated using genetic, biochemical and high-throughput sequencing approaches. We show that the purple phenotype of dcl4 leaves correlates with carbohydrate over-accumulation and defective phloem transport, and depends on the activity of SUPPRESSOR OF GENE SILENCING 3, RNA-DEPENDENT RNA POLYMERASE 6 (RDR6) and DCL2. This phenotype correlates with the downregulation of two genes expressed in the apex and the vasculature, SMAX1-LIKE 4 (SMXL4) and SMXL5, and the accumulation of DCL2- and RDR6-dependent small interfering RNAs derived from these two genes. Supporting a causal effect, smxl4 smxl5 double mutants exhibit leaf pigmentation, enhanced starch accumulation and defective phloem transport, similar to dcl4 plants. Overall, this study elucidates the detrimental action of DCL2 when DCL4 is absent, and indicates that DCL4 outcompeting DCL2 in wild-type plants is crucial to prevent the degradation of endogenous transcripts by DCL2- and RDR6-dependent transitive PTGS.
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Affiliation(s)
- Yu-Yi Wu
- Agricultural Biotechnology Research Center, Academia Sinica, Taipei, 11529, Taiwan
| | - Bo-Han Hou
- Agricultural Biotechnology Research Center, Academia Sinica, Taipei, 11529, Taiwan
| | - Wen-Chi Lee
- Agricultural Biotechnology Research Center, Academia Sinica, Taipei, 11529, Taiwan
| | - Shin-Hua Lu
- Agricultural Biotechnology Research Center, Academia Sinica, Taipei, 11529, Taiwan
| | - Chen-Jui Yang
- Agricultural Biotechnology Research Center, Academia Sinica, Taipei, 11529, Taiwan
| | - Hervé Vaucheret
- Institut Jean-Pierre Bourgin, UMR 1318, INRA, SPS Saclay Plant Sciences, Versailles, France
| | - Ho-Ming Chen
- Agricultural Biotechnology Research Center, Academia Sinica, Taipei, 11529, Taiwan
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107
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Tsuzuki M, Motomura K, Kumakura N, Takeda A. Interconnections between mRNA degradation and RDR-dependent siRNA production in mRNA turnover in plants. JOURNAL OF PLANT RESEARCH 2017; 130:211-226. [PMID: 28197782 DOI: 10.1007/s10265-017-0906-8] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/24/2016] [Accepted: 12/08/2016] [Indexed: 06/06/2023]
Abstract
Accumulation of an mRNA species is determined by the balance between the synthesis and the degradation of the mRNA. Individual mRNA molecules are selectively and actively degraded through RNA degradation pathways, which include 5'-3' mRNA degradation pathway, 3'-5' mRNA degradation pathway, and RNA-dependent RNA polymerase-mediated mRNA degradation pathway. Recent studies have revealed that these RNA degradation pathways compete with each other in mRNA turnover in plants and that plants have a hidden layer of non-coding small-interfering RNA production from a set of mRNAs. In this review, we summarize the current information about plant mRNA degradation pathways in mRNA turnover and discuss the potential roles of a novel class of the endogenous siRNAs derived from plant mRNAs.
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Affiliation(s)
- Masayuki Tsuzuki
- Department of Life Sciences, Graduate School of Arts and Sciences, The University of Tokyo, Tokyo, 153-8902, Japan
- Department of Molecular, Cellular and Developmental Biology, University of Michigan, Ann Arbor, MI, 48109, USA
| | - Kazuki Motomura
- Institute of Transformative Bio-Molecules, Nagoya University, Furo-cho, Chikusa-ku, Nagoya, Aichi, 464-8601, Japan
| | - Naoyoshi Kumakura
- Center for Sustainable Resource Science, RIKEN, Suehiro-cho 1-7-22, Tsurumi-ku, Yokohama, Kanagawa, 230-0045, Japan
| | - Atsushi Takeda
- Department of Biotechnology, Graduate School of Life Sciences, Ritsumeikan University, Shiga, 525-8577, Japan.
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108
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Si H, Cao Y, Zhu H, Li D, Lv Z, Sheng Q, Nie Z. Transposable Element Bm1645 is a Source of BmAGO2-associated Small RNAs that affect its expression in Bombyx mori. BMC Genomics 2017; 18:201. [PMID: 28231766 PMCID: PMC5324241 DOI: 10.1186/s12864-017-3598-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2016] [Accepted: 02/21/2017] [Indexed: 12/04/2022] Open
Abstract
Background A transposable element (TE) is a DNA fragment that can change its position within a genome. Transposable elements play important roles in maintaining the stability and diversity of organisms by transposition. Recent studies have shown that approximately half of the genes in Bombyx mori are TEs. Results We systematically identified and analyzed the BmAGO2-associated TEs, which exceed 100 in the B. mori genome. Additionally, we also mapped the small RNAs associated with BmAGO2 in B.mori. The transposon Bm1645 is the most abundant TE associated with BmAGO2, and Bm1645-derived small RNAs represent a small RNA pool. We determined the expression patterns of several Bm1645-derived small RNAs by northern blotting, and the results showed there was differential expression of multiple small RNAs in normal and BmNPV-infected BmN cells and silkworms from various developmental stages. We confirmed that four TE-siRNAs could bind to BmAGO2 using EMSA and also validated the recognition sites of these four TE-siRNAs in Bm1645 by dual-luciferase reporter assays. Furthermore, qRT-PCR analysis revealed the overexpression of the four TE-siRNAs could downregulate the expression of Bm1645 in BmN cells, and the transcription of Bm1645 was upregulated by the downregulation of BmAGO2. Conclusions Our results suggest Bm1645 functions as a source of small RNAs pool and this pool can produce many BmAGO2-associated small RNAs that regulate TE’s expression. Electronic supplementary material The online version of this article (doi:10.1186/s12864-017-3598-5) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Hongqiang Si
- College of Life Sciences, Zhejiang Sci-Tech University, Hangzhou, Zhejiang, China.,Zhejiang Provincial Key Laboratory of Silkworm Bioreactor and Biomedicine, Hangzhou, Zhejiang, China
| | - Yunjie Cao
- College of Life Sciences, Zhejiang Sci-Tech University, Hangzhou, Zhejiang, China.,Zhejiang Provincial Key Laboratory of Silkworm Bioreactor and Biomedicine, Hangzhou, Zhejiang, China
| | - Honglin Zhu
- College of Life Sciences, Zhejiang Sci-Tech University, Hangzhou, Zhejiang, China.,Zhejiang Provincial Key Laboratory of Silkworm Bioreactor and Biomedicine, Hangzhou, Zhejiang, China
| | - Dan Li
- College of Life Sciences, Zhejiang Sci-Tech University, Hangzhou, Zhejiang, China.,Zhejiang Provincial Key Laboratory of Silkworm Bioreactor and Biomedicine, Hangzhou, Zhejiang, China
| | - Zhengbing Lv
- College of Life Sciences, Zhejiang Sci-Tech University, Hangzhou, Zhejiang, China.,Zhejiang Provincial Key Laboratory of Silkworm Bioreactor and Biomedicine, Hangzhou, Zhejiang, China
| | - Qing Sheng
- College of Life Sciences, Zhejiang Sci-Tech University, Hangzhou, Zhejiang, China.,Zhejiang Provincial Key Laboratory of Silkworm Bioreactor and Biomedicine, Hangzhou, Zhejiang, China
| | - Zuoming Nie
- College of Life Sciences, Zhejiang Sci-Tech University, Hangzhou, Zhejiang, China. .,Zhejiang Provincial Key Laboratory of Silkworm Bioreactor and Biomedicine, Hangzhou, Zhejiang, China.
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109
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Koonin EV. Evolution of RNA- and DNA-guided antivirus defense systems in prokaryotes and eukaryotes: common ancestry vs convergence. Biol Direct 2017; 12:5. [PMID: 28187792 PMCID: PMC5303251 DOI: 10.1186/s13062-017-0177-2] [Citation(s) in RCA: 65] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2016] [Accepted: 02/06/2017] [Indexed: 12/18/2022] Open
Abstract
Abstract Complementarity between nucleic acid molecules is central to biological information transfer processes. Apart from the basal processes of replication, transcription and translation, complementarity is also employed by multiple defense and regulatory systems. All cellular life forms possess defense systems against viruses and mobile genetic elements, and in most of them some of the defense mechanisms involve small guide RNAs or DNAs that recognize parasite genomes and trigger their inactivation. The nucleic acid-guided defense systems include prokaryotic Argonaute (pAgo)-centered innate immunity and CRISPR-Cas adaptive immunity as well as diverse branches of RNA interference (RNAi) in eukaryotes. The archaeal pAgo machinery is the direct ancestor of eukaryotic RNAi that, however, acquired additional components, such as Dicer, and enormously diversified through multiple duplications. In contrast, eukaryotes lack any heritage of the CRISPR-Cas systems, conceivably, due to the cellular toxicity of some Cas proteins that would get activated as a result of operon disruption in eukaryotes. The adaptive immunity function in eukaryotes is taken over partly by the PIWI RNA branch of RNAi and partly by protein-based immunity. In this review, I briefly discuss the interplay between homology and analogy in the evolution of RNA- and DNA-guided immunity, and attempt to formulate some general evolutionary principles for this ancient class of defense systems. Reviewers This article was reviewed by Mikhail Gelfand and Bojan Zagrovic.
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Affiliation(s)
- Eugene V Koonin
- National Center for Biotechnology Information, National Library of Medicine, Bethesda, MD, 20894, USA.
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110
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Zhou X, Feng X, Mao H, Li M, Xu F, Hu K, Guang S. RdRP-synthesized antisense ribosomal siRNAs silence pre-rRNA via the nuclear RNAi pathway. Nat Struct Mol Biol 2017; 24:258-269. [DOI: 10.1038/nsmb.3376] [Citation(s) in RCA: 39] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2016] [Accepted: 01/10/2017] [Indexed: 12/27/2022]
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111
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Lipid flippases promote antiviral silencing and the biogenesis of viral and host siRNAs in Arabidopsis. Proc Natl Acad Sci U S A 2017; 114:1377-1382. [PMID: 28123063 DOI: 10.1073/pnas.1614204114] [Citation(s) in RCA: 42] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022] Open
Abstract
Dicer-mediated processing of virus-specific dsRNA into short interfering RNAs (siRNAs) in plants and animals initiates a specific antiviral defense by RNA interference (RNAi). In this study, we developed a forward genetic screen for the identification of host factors required for antiviral RNAi in Arabidopsis thaliana Using whole-genome sequencing and a computational pipeline, we identified aminophospholipid transporting ATPase 2 (ALA2) and the related ALA1 in the type IV subfamily of P-type ATPases as key components of antiviral RNAi. ALA1 and ALA2 are flippases, which are transmembrane lipid transporter proteins that transport phospholipids across cellular membranes. We found that the ala1/ala2 single- and double-mutant plants exhibited enhanced disease susceptibility to cucumber mosaic virus when the virus-encoded function to suppress RNAi was disrupted. Notably, the antiviral activity of both ALA1 and ALA2 was abolished by a single amino acid substitution known to inactivate the flippase activity. Genetic analysis revealed that ALA1 and ALA2 acted to enhance the amplification of the viral siRNAs by RNA-dependent RNA polymerase (RdRP) 1 (RDR1) and RDR6 and of the endogenous virus-activated siRNAs by RDR1. RNA virus replication by plant viral RdRPs occurs inside vesicle-like membrane invaginations induced by the recruitment of the viral RdRP and host factors to subcellular membrane microdomains enriched with specific phospholipids. Our results suggest that the phospholipid transporter activity of ALA1/ALA2 may be necessary for the formation of similar invaginations for the synthesis of dsRNA precursors of highly abundant viral and host siRNAs by the cellular RdRPs.
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112
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Zhu B, Gao H, Xu G, Wu D, Song S, Jiang H, Zhu S, Qi T, Xie D. Arabidopsis ALA1 and ALA2 Mediate RNAi-Based Antiviral Immunity. FRONTIERS IN PLANT SCIENCE 2017; 8:422. [PMID: 28439275 PMCID: PMC5383662 DOI: 10.3389/fpls.2017.00422] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/28/2016] [Accepted: 03/13/2017] [Indexed: 05/22/2023]
Abstract
RNA intereferencing (RNAi) pathway regulates antiviral immunity and mediates plant growth and development. Despite considerable research efforts, a few components in RNAi pathway have been revealed, including ARGONAUTEs (AGOs), DICER-LIKEs (DCLs), RNA-dependent RNA polymerase 1 and 6 (RDR1/6), and ALTERED MERISTEM PROGRAM 1 (AMP1). In this study, we performed a forward genetic screening for enhancers of rdr6 via inoculation of CMV2aTΔ2b, a 2b-deficient Cucumber Mosaic Virus that is unable to suppress RNAi-mediated antiviral immunity. We uncover that the membrane-localized flippase Aminophospholipid ATPase 1 (ALA1) cooperates with RDR6 and RDR1 to promote antiviral immunity and regulate fertility in Arabidopsis. Moreover, we find that ALA2, a homolog of ALA1, also participates in antiviral immunity. Our findings suggest that ALA1 and ALA2 act as novel components in the RNAi pathway and function additively with RDR1 and RDR6 to mediate RNAi-based antiviral immunity and plant development.
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Affiliation(s)
- Biyun Zhu
- Tsinghua-Peking Joint Center for Life Sciences, and MOE Key Laboratory of Bioinformatics, School of Life Sciences, Tsinghua UniversityBeijing, China
| | - Hua Gao
- Tsinghua-Peking Joint Center for Life Sciences, and MOE Key Laboratory of Bioinformatics, School of Life Sciences, Tsinghua UniversityBeijing, China
| | - Gang Xu
- Tsinghua-Peking Joint Center for Life Sciences, and MOE Key Laboratory of Bioinformatics, School of Life Sciences, Tsinghua UniversityBeijing, China
| | - Dewei Wu
- Tsinghua-Peking Joint Center for Life Sciences, and MOE Key Laboratory of Bioinformatics, School of Life Sciences, Tsinghua UniversityBeijing, China
| | - Susheng Song
- Beijing Key Laboratory of Plant Gene Resources and Biotechnology for Carbon Reduction and Environmental Improvement, College of Life Sciences, Capital Normal UniversityBeijing, China
| | - Hongshan Jiang
- The Institute of Plant Quarantine, Chinese Academy of Inspection and QuarantineBeijing, China
| | - Shuifang Zhu
- The Institute of Plant Quarantine, Chinese Academy of Inspection and QuarantineBeijing, China
| | - Tiancong Qi
- Tsinghua-Peking Joint Center for Life Sciences, and MOE Key Laboratory of Bioinformatics, School of Life Sciences, Tsinghua UniversityBeijing, China
- *Correspondence: Daoxin Xie, Tiancong Qi,
| | - Daoxin Xie
- Tsinghua-Peking Joint Center for Life Sciences, and MOE Key Laboratory of Bioinformatics, School of Life Sciences, Tsinghua UniversityBeijing, China
- *Correspondence: Daoxin Xie, Tiancong Qi,
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113
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Rabiger DS, Taylor JM, Spriggs A, Hand ML, Henderson ST, Johnson SD, Oelkers K, Hrmova M, Saito K, Suzuki G, Mukai Y, Carroll BJ, Koltunow AMG. Generation of an integrated Hieracium genomic and transcriptomic resource enables exploration of small RNA pathways during apomixis initiation. BMC Biol 2016; 14:86. [PMID: 27716180 PMCID: PMC5054587 DOI: 10.1186/s12915-016-0311-0] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2016] [Accepted: 09/21/2016] [Indexed: 11/23/2022] Open
Abstract
Background Application of apomixis, or asexual seed formation, in crop breeding would allow rapid fixation of complex traits, economizing improved crop delivery. Identification of apomixis genes is confounded by the polyploid nature, high genome complexity and lack of genomic sequence integration with reproductive tissue transcriptomes in most apomicts. Results A genomic and transcriptomic resource was developed for Hieracium subgenus Pilosella (Asteraceae) which incorporates characterized sexual, apomictic and mutant apomict plants exhibiting reversion to sexual reproduction. Apomicts develop additional female gametogenic cells that suppress the sexual pathway in ovules. Disrupting small RNA pathways in sexual Arabidopsis also induces extra female gametogenic cells; therefore, the resource was used to examine if changes in small RNA pathways correlate with apomixis initiation. An initial characterization of small RNA pathway genes within Hieracium was undertaken, and ovary-expressed ARGONAUTE genes were identified and cloned. Comparisons of whole ovary transcriptomes from mutant apomicts, relative to the parental apomict, revealed that differentially expressed genes were enriched for processes involved in small RNA biogenesis and chromatin silencing. Small RNA profiles within mutant ovaries did not reveal large-scale alterations in composition or length distributions; however, a small number of differentially expressed, putative small RNA targets were identified. Conclusions The established Hieracium resource represents a substantial contribution towards the investigation of early sexual and apomictic female gamete development, and the generation of new candidate genes and markers. Observed changes in small RNA targets and biogenesis pathways within sexual and apomictic ovaries will underlie future functional research into apomixis initiation in Hieracium. Electronic supplementary material The online version of this article (doi:10.1186/s12915-016-0311-0) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- David S Rabiger
- Commonwealth Scientific and Industrial Research Organisation Agriculture and Food, Private Bag 2, Glen Osmond, South Australia, 5064, Australia
| | - Jennifer M Taylor
- Commonwealth Scientific and Industrial Research Organisation Agriculture and Food, Bellenden Street, Crace, Australian Capital Territory, 2911, Australia
| | - Andrew Spriggs
- Commonwealth Scientific and Industrial Research Organisation Agriculture and Food, Bellenden Street, Crace, Australian Capital Territory, 2911, Australia
| | - Melanie L Hand
- Commonwealth Scientific and Industrial Research Organisation Agriculture and Food, Private Bag 2, Glen Osmond, South Australia, 5064, Australia
| | - Steven T Henderson
- Commonwealth Scientific and Industrial Research Organisation Agriculture and Food, Private Bag 2, Glen Osmond, South Australia, 5064, Australia
| | - Susan D Johnson
- Commonwealth Scientific and Industrial Research Organisation Agriculture and Food, Private Bag 2, Glen Osmond, South Australia, 5064, Australia
| | - Karsten Oelkers
- Commonwealth Scientific and Industrial Research Organisation Agriculture and Food, Private Bag 2, Glen Osmond, South Australia, 5064, Australia
| | - Maria Hrmova
- Australian Centre for Plant Functional Genomics, University of Adelaide PMB 1, Glen Osmond, South Australia, 5064, Australia
| | - Keisuke Saito
- Division of Natural Science, Osaka Kyoiku University, Osaka, 582-8582, Japan
| | - Go Suzuki
- Division of Natural Science, Osaka Kyoiku University, Osaka, 582-8582, Japan
| | - Yasuhiko Mukai
- Division of Natural Science, Osaka Kyoiku University, Osaka, 582-8582, Japan
| | - Bernard J Carroll
- School of Chemistry and Molecular Biosciences, University of Queensland, St. Lucia, Queensland, 4072, Australia
| | - Anna M G Koltunow
- Commonwealth Scientific and Industrial Research Organisation Agriculture and Food, Private Bag 2, Glen Osmond, South Australia, 5064, Australia.
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Castellano M, Martinez G, Marques MC, Moreno-Romero J, Köhler C, Pallas V, Gomez G. Changes in the DNA methylation pattern of the host male gametophyte of viroid-infected cucumber plants. JOURNAL OF EXPERIMENTAL BOTANY 2016; 67:5857-5868. [PMID: 27697787 PMCID: PMC5066502 DOI: 10.1093/jxb/erw353] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/22/2023]
Abstract
Eukaryotic organisms exposed to adverse conditions are required to show a certain degree of transcriptional plasticity in order to cope successfully with stress. Epigenetic regulation of the genome is a key regulatory mechanism allowing dynamic changes of the transcriptional status of the plant in response to stress. The Hop stunt viroid (HSVd) induces the demethylation of ribosomal RNA (rRNA) in cucumber (Cucumis sativus) leaves, leading to increasing transcription rates of rRNA. In addition to the clear alterations observed in vegetative tissues, HSVd infection is also associated with drastic changes in gametophyte development. To examine the basis of viroid-induced alterations in reproductive tissues, we analysed the cellular and molecular consequences of HSVd infection in the male gametophyte of cucumber plants. Our results indicate that in the pollen grain, accumulation of HSVd RNA induces a decondensation of the generative nucleus that correlates with a dynamic demethylation of repetitive regions in the cucumber genome that include rRNA genes and transposable elements (TEs). We therefore propose that HSVd infection impairs the epigenetic control of rRNA genes and TEs in gametic cells of cucumber, a phenomenon thus far unknown to occur in this reproductive tissue as a consequence of pathogen infection.
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Affiliation(s)
- Mayte Castellano
- Instituto de Biología Molecular y Celular de Plantas (IBMCP), Consejo Superior de Investigaciones Científicas (CSIC)-Universidad Politecnica de Valencia (UPV), CPI, Edificio 8 E, Av. de los Naranjos s/n, 46022 Valencia, Spain
| | - German Martinez
- Department of Plant Biology, Swedish University of Agricultural Sciences and Linnean Center for Plant Biology, SE-750 07 Uppsala, Sweden
| | - Maria Carmen Marques
- Instituto de Biología Molecular y Celular de Plantas (IBMCP), Consejo Superior de Investigaciones Científicas (CSIC)-Universidad Politecnica de Valencia (UPV), CPI, Edificio 8 E, Av. de los Naranjos s/n, 46022 Valencia, Spain
| | - Jordi Moreno-Romero
- Department of Plant Biology, Swedish University of Agricultural Sciences and Linnean Center for Plant Biology, SE-750 07 Uppsala, Sweden
| | - Claudia Köhler
- Department of Plant Biology, Swedish University of Agricultural Sciences and Linnean Center for Plant Biology, SE-750 07 Uppsala, Sweden
| | - Vicente Pallas
- Instituto de Biología Molecular y Celular de Plantas (IBMCP), Consejo Superior de Investigaciones Científicas (CSIC)-Universidad Politecnica de Valencia (UPV), CPI, Edificio 8 E, Av. de los Naranjos s/n, 46022 Valencia, Spain
| | - Gustavo Gomez
- Instituto de Biología Molecular y Celular de Plantas (IBMCP), Consejo Superior de Investigaciones Científicas (CSIC)-Universidad Politecnica de Valencia (UPV), CPI, Edificio 8 E, Av. de los Naranjos s/n, 46022 Valencia, Spain
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115
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Screening for plant viruses by next generation sequencing using a modified double strand RNA extraction protocol with an internal amplification control. J Virol Methods 2016; 236:35-40. [PMID: 27387642 DOI: 10.1016/j.jviromet.2016.07.001] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2015] [Revised: 05/30/2016] [Accepted: 07/03/2016] [Indexed: 11/21/2022]
Abstract
The majority of plant viruses contain RNA genomes. Detection of viral RNA genomes in infected plant material by next generation sequencing (NGS) is possible through the extraction and sequencing of total RNA, total RNA devoid of ribosomal RNA, small RNA interference (RNAi) molecules, or double stranded RNA (dsRNA). Plants do not typically produce high molecular weight dsRNA, therefore the presence of dsRNA makes it an attractive target for plant virus diagnostics. The sensitivity of NGS as a diagnostic method demands an effective dsRNA protocol that is both representative of the sample and minimizes sample cross contamination. We have developed a modified dsRNA extraction protocol that is more efficient compared to traditional protocols, requiring reduced amounts of starting material, that is less prone to sample cross contamination. This was accomplished by using bead based homogenization of plant material in closed, disposable 50ml tubes. To assess the quality of extraction, we also developed an internal control by designing a real-time (quantitative) PCR (qPCR) assay that targets endornaviruses present in Phaseolus vulgaris cultivar Black Turtle Soup (BTS).
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116
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Liu L, Chen X. RNA Quality Control as a Key to Suppressing RNA Silencing of Endogenous Genes in Plants. MOLECULAR PLANT 2016; 9:826-36. [PMID: 27045817 PMCID: PMC5123867 DOI: 10.1016/j.molp.2016.03.011] [Citation(s) in RCA: 66] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/17/2016] [Revised: 03/10/2016] [Accepted: 03/14/2016] [Indexed: 05/19/2023]
Abstract
RNA quality control of endogenous RNAs is an integral part of eukaryotic gene expression and often relies on exonucleolytic degradation to eliminate dysfunctional transcripts. In parallel, exogenous and selected endogenous RNAs are degraded through RNA silencing, which is a genome defense mechanism used by many eukaryotes. In plants, RNA silencing is triggered by the production of double-stranded RNAs (dsRNAs) by RNA-DEPENDENT RNA POLYMERASEs (RDRs) and proceeds through small interfering (si) RNA-directed, ARGONAUTE (AGO)-mediated cleavage of homologous transcripts. Many studies revealed that plants avert inappropriate posttranscriptional gene silencing of endogenous coding genes by using RNA surveillance mechanisms as a safeguard to protect their transcriptome profiles. The tug of war between RNA surveillance and RNA silencing ensures the appropriate partitioning of endogenous RNA substrates among these degradation pathways. Here we review recent advances on RNA quality control and its role in the suppression of RNA silencing at endogenous genes and discuss the mechanisms underlying the crosstalk among these pathways.
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Affiliation(s)
- Lin Liu
- Guangdong Provincial Key Laboratory for Plant Epigenetics, College of Life Sciences and Oceanography, Shenzhen University, Shenzhen 518060, P.R. China; Department of Botany and Plant Sciences, Institute of Integrative Genome Biology, University of California, Riverside, CA 92521, USA
| | - Xuemei Chen
- Guangdong Provincial Key Laboratory for Plant Epigenetics, College of Life Sciences and Oceanography, Shenzhen University, Shenzhen 518060, P.R. China; Department of Botany and Plant Sciences, Institute of Integrative Genome Biology, University of California, Riverside, CA 92521, USA; Howard Hughes Medical Institute, University of California, Riverside, CA 92521, USA.
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117
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Kuan T, Zhai Y, Ma W. Small RNAs regulate plant responses to filamentous pathogens. Semin Cell Dev Biol 2016; 56:190-200. [PMID: 27208726 DOI: 10.1016/j.semcdb.2016.05.013] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2016] [Revised: 05/10/2016] [Accepted: 05/17/2016] [Indexed: 01/04/2023]
Abstract
Small RNAs are central players of RNA silencing in eukaryotes. These short RNA molecules (20-25 nucleotides in length) repress target gene expression based on sequence complementarity. While small RNAs are well-known for their essential function in regulating growth and development, recent research has revealed that they also influence plant immunity. Extensive changes in small RNA accumulation have been observed during infection. This review focuses on specific small RNA changes that are involved in plant responses to filamentous eukaryotic pathogens including fungi and oomycetes. We describe how changes in small RNA accumulation influence plant immunity and summarize the cellular processes affected by these small RNAs. In particular, we discuss secondary small interfering RNAs that directly modulate the expression of defense-related genes.
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Affiliation(s)
- Tung Kuan
- Department of Plant Pathology and Microbiology, University of California, Riverside, CA 92521, USA; Center for Plant Cell Biology, University of California, Riverside, CA 92521, USA
| | - Yi Zhai
- Department of Plant Pathology and Microbiology, University of California, Riverside, CA 92521, USA; Center for Plant Cell Biology, University of California, Riverside, CA 92521, USA
| | - Wenbo Ma
- Department of Plant Pathology and Microbiology, University of California, Riverside, CA 92521, USA; Center for Plant Cell Biology, University of California, Riverside, CA 92521, USA.
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118
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Garcia-Ruiz H, Ruiz MTG, Peralta SMG, Gabriel CBM, El-Mounadi K. Mechanisms, applications, and perspectives of antiviral RNA silencing in plants. ACTA ACUST UNITED AC 2016; 34. [PMID: 28890589 DOI: 10.18781/r.mex.fit.1606-8] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022]
Abstract
Viral diseases of plants cause important economic losses due to reduction in crop quality and quantity to the point of threatening food security in some countries. Given the reduced availability of natural sources, genetic resistance to viruses has been successfully engineered for some plant-virus combinations. A sound understanding of the basic mechanisms governing plant-virus interactions, including antiviral RNA silencing, is the foundation to design better management strategies and biotechnological approaches to engineer and implement antiviral resistance in plants. In this review, we present current molecular models to explain antiviral RNA silencing and its application in basic plant research, biotechnology and genetic engineering.
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Affiliation(s)
- Hernan Garcia-Ruiz
- Department of Plant Pathology, Nebraska Center for Virology, University of Nebraska-Lincoln, Lincoln, NE 68583 USA
| | | | | | | | - Kautar El-Mounadi
- Department of Biology, Kuztown University of Pennsylvania, Kuztown, PA 19530 USA
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119
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Wang H, Jiao X, Kong X, Hamera S, Wu Y, Chen X, Fang R, Yan Y. A Signaling Cascade from miR444 to RDR1 in Rice Antiviral RNA Silencing Pathway. PLANT PHYSIOLOGY 2016; 170:2365-77. [PMID: 26858364 PMCID: PMC4825140 DOI: 10.1104/pp.15.01283] [Citation(s) in RCA: 86] [Impact Index Per Article: 10.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/14/2015] [Accepted: 02/06/2016] [Indexed: 05/19/2023]
Abstract
Plant RNA-DEPENDENT RNA POLYMERASE1 (RDR1) is a key component of the antiviral RNA-silencing pathway, contributing to the biogenesis of virus-derived small interfering RNAs. This enzyme also is responsible for producing virus-activated endogenous small interfering RNAs to stimulate the broad-spectrum antiviral activity through silencing host genes. The expression of RDR1 orthologs in various plants is usually induced by virus infection. However, the molecular mechanisms of activation of RDR1 expression in response to virus infection remain unknown. Here, we show that a monocot-specific microRNA, miR444, is a key factor in relaying the antiviral signaling from virus infection to OsRDR1 expression. The expression of miR444 is enhanced by infection with Rice stripe virus (RSV), and overexpression of miR444 improves rice (Oryza sativa) resistance against RSV infection accompanied by the up-regulation of OsRDR1 expression. We further show that three miR444 targets, the MIKC(C)-type MADS box proteins OsMADS23, OsMADS27a, and OsMADS57, form homodimers and heterodimers between them to repress the expression of OsRDR1 by directly binding to the CArG motifs of its promoter. Consequently, an increased level of miR444 diminishes the repressive roles of OsMADS23, OsMADS27a, and OsMADS57 on OsRDR1 transcription, thus activating the OsRDR1-dependent antiviral RNA-silencing pathway. We also show that overexpression of miR444-resistant OsMADS57 reduced OsRDR1 expression and rice resistance against RSV infection, and knockout of OsRDR1 reduced rice resistance against RSV infection. In conclusion, our results reveal a molecular cascade in the rice antiviral pathway in which miR444 and its MADS box targets directly control OsRDR1 transcription.
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Affiliation(s)
- Huacai Wang
- State Key Laboratory of Plant Genomics, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, China (H.W., X.J., X.K., Y.W., X.C., R.F., Y.Y.);National Plant Gene Research Center, Beijing 100101, China (H.W., X.J., X.K., X.C., R.F., Y.Y.);University of the Chinese Academy of Sciences, Beijing 100049, China (H.W., X.K.); andDepartment of Biology, Syed Babar Ali (SBA) School of Science and Engineering, Lahore University of Management Sciences, Defence Housing Authority (DHA), Lahore 54792, Pakistan (S.H.)
| | - Xiaoming Jiao
- State Key Laboratory of Plant Genomics, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, China (H.W., X.J., X.K., Y.W., X.C., R.F., Y.Y.);National Plant Gene Research Center, Beijing 100101, China (H.W., X.J., X.K., X.C., R.F., Y.Y.);University of the Chinese Academy of Sciences, Beijing 100049, China (H.W., X.K.); andDepartment of Biology, Syed Babar Ali (SBA) School of Science and Engineering, Lahore University of Management Sciences, Defence Housing Authority (DHA), Lahore 54792, Pakistan (S.H.)
| | - Xiaoyu Kong
- State Key Laboratory of Plant Genomics, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, China (H.W., X.J., X.K., Y.W., X.C., R.F., Y.Y.);National Plant Gene Research Center, Beijing 100101, China (H.W., X.J., X.K., X.C., R.F., Y.Y.);University of the Chinese Academy of Sciences, Beijing 100049, China (H.W., X.K.); andDepartment of Biology, Syed Babar Ali (SBA) School of Science and Engineering, Lahore University of Management Sciences, Defence Housing Authority (DHA), Lahore 54792, Pakistan (S.H.)
| | - Sadia Hamera
- State Key Laboratory of Plant Genomics, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, China (H.W., X.J., X.K., Y.W., X.C., R.F., Y.Y.);National Plant Gene Research Center, Beijing 100101, China (H.W., X.J., X.K., X.C., R.F., Y.Y.);University of the Chinese Academy of Sciences, Beijing 100049, China (H.W., X.K.); andDepartment of Biology, Syed Babar Ali (SBA) School of Science and Engineering, Lahore University of Management Sciences, Defence Housing Authority (DHA), Lahore 54792, Pakistan (S.H.)
| | - Yao Wu
- State Key Laboratory of Plant Genomics, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, China (H.W., X.J., X.K., Y.W., X.C., R.F., Y.Y.);National Plant Gene Research Center, Beijing 100101, China (H.W., X.J., X.K., X.C., R.F., Y.Y.);University of the Chinese Academy of Sciences, Beijing 100049, China (H.W., X.K.); andDepartment of Biology, Syed Babar Ali (SBA) School of Science and Engineering, Lahore University of Management Sciences, Defence Housing Authority (DHA), Lahore 54792, Pakistan (S.H.)
| | - Xiaoying Chen
- State Key Laboratory of Plant Genomics, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, China (H.W., X.J., X.K., Y.W., X.C., R.F., Y.Y.);National Plant Gene Research Center, Beijing 100101, China (H.W., X.J., X.K., X.C., R.F., Y.Y.);University of the Chinese Academy of Sciences, Beijing 100049, China (H.W., X.K.); andDepartment of Biology, Syed Babar Ali (SBA) School of Science and Engineering, Lahore University of Management Sciences, Defence Housing Authority (DHA), Lahore 54792, Pakistan (S.H.)
| | - Rongxiang Fang
- State Key Laboratory of Plant Genomics, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, China (H.W., X.J., X.K., Y.W., X.C., R.F., Y.Y.);National Plant Gene Research Center, Beijing 100101, China (H.W., X.J., X.K., X.C., R.F., Y.Y.);University of the Chinese Academy of Sciences, Beijing 100049, China (H.W., X.K.); andDepartment of Biology, Syed Babar Ali (SBA) School of Science and Engineering, Lahore University of Management Sciences, Defence Housing Authority (DHA), Lahore 54792, Pakistan (S.H.)
| | - Yongsheng Yan
- State Key Laboratory of Plant Genomics, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, China (H.W., X.J., X.K., Y.W., X.C., R.F., Y.Y.);National Plant Gene Research Center, Beijing 100101, China (H.W., X.J., X.K., X.C., R.F., Y.Y.);University of the Chinese Academy of Sciences, Beijing 100049, China (H.W., X.K.); andDepartment of Biology, Syed Babar Ali (SBA) School of Science and Engineering, Lahore University of Management Sciences, Defence Housing Authority (DHA), Lahore 54792, Pakistan (S.H.)
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Zhao JH, Hua CL, Fang YY, Guo HS. The dual edge of RNA silencing suppressors in the virus–host interactions. Curr Opin Virol 2016; 17:39-44. [DOI: 10.1016/j.coviro.2015.12.002] [Citation(s) in RCA: 36] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2015] [Revised: 12/19/2015] [Accepted: 12/28/2015] [Indexed: 02/02/2023]
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121
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Omarov RT, Ciomperlik J, Scholthof HB. An in vitro reprogrammable antiviral RISC with size-preferential ribonuclease activity. Virology 2016; 490:41-8. [PMID: 26812224 DOI: 10.1016/j.virol.2015.12.017] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2015] [Revised: 12/22/2015] [Accepted: 12/23/2015] [Indexed: 01/29/2023]
Abstract
Infection of Nicotiana benthamiana plants with Tomato bushy stunt virus (TBSV) mutants compromised for silencing suppression induces formation of an antiviral RISC (vRISC) that can be isolated using chromatography procedures. The isolated vRISC sequence-specifically degrades TBSV RNA in vitro, its activity can be down-regulated by removing siRNAs, and re-stimulated by exogenous supply of siRNAs. vRISC is most effective at hydrolyzing the ~4.8kb genomic RNA, but less so for a ~2.2kb TBSV subgenomic mRNA (sgRNA1), while the 3' co-terminal sgRNA2 of ~0.9kb appears insensitive to vRISC cleavage. Moreover, experiments with in vitro generated 5' co-terminal viral transcripts show that RNAs of ~2.7kb are efficiently cleaved while those of ~1.1kb or shorter are unaffected. The isolated antiviral ribonuclease complex fails to degrade ~0.4kb defective interfering RNAs (DIs) in vitro, agreeing with findings that in plants DIs are not targeted by silencing.
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Affiliation(s)
- Rustem T Omarov
- Department of Plant Pathology and Microbiology, Texas A&M University, 2132 TAMU, College Station, TX 77843, United States
| | - Jessica Ciomperlik
- Department of Plant Pathology and Microbiology, Texas A&M University, 2132 TAMU, College Station, TX 77843, United States
| | - Herman B Scholthof
- Department of Plant Pathology and Microbiology, Texas A&M University, 2132 TAMU, College Station, TX 77843, United States.
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122
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Fátyol K, Ludman M, Burgyán J. Functional dissection of a plant Argonaute. Nucleic Acids Res 2016; 44:1384-97. [PMID: 26673719 PMCID: PMC4756824 DOI: 10.1093/nar/gkv1371] [Citation(s) in RCA: 48] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2015] [Revised: 11/24/2015] [Accepted: 11/25/2015] [Indexed: 12/21/2022] Open
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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123
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Elvira-Matelot E, Hachet M, Shamandi N, Comella P, Sáez-Vásquez J, Zytnicki M, Vaucheret H. Arabidopsis RNASE THREE LIKE2 Modulates the Expression of Protein-Coding Genes via 24-Nucleotide Small Interfering RNA-Directed DNA Methylation. THE PLANT CELL 2016; 28:406-25. [PMID: 26764378 PMCID: PMC4790866 DOI: 10.1105/tpc.15.00540] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/16/2015] [Accepted: 01/12/2016] [Indexed: 05/08/2023]
Abstract
RNaseIII enzymes catalyze the cleavage of double-stranded RNA (dsRNA) and have diverse functions in RNA maturation. Arabidopsis thaliana RNASE THREE LIKE2 (RTL2), which carries one RNaseIII and two dsRNA binding (DRB) domains, is a unique Arabidopsis RNaseIII enzyme resembling the budding yeast small interfering RNA (siRNA)-producing Dcr1 enzyme. Here, we show that RTL2 modulates the production of a subset of small RNAs and that this activity depends on both its RNaseIII and DRB domains. However, the mode of action of RTL2 differs from that of Dcr1. Whereas Dcr1 directly cleaves dsRNAs into 23-nucleotide siRNAs, RTL2 likely cleaves dsRNAs into longer molecules, which are subsequently processed into small RNAs by the DICER-LIKE enzymes. Depending on the dsRNA considered, RTL2-mediated maturation either improves (RTL2-dependent loci) or reduces (RTL2-sensitive loci) the production of small RNAs. Because the vast majority of RTL2-regulated loci correspond to transposons and intergenic regions producing 24-nucleotide siRNAs that guide DNA methylation, RTL2 depletion modifies DNA methylation in these regions. Nevertheless, 13% of RTL2-regulated loci correspond to protein-coding genes. We show that changes in 24-nucleotide siRNA levels also affect DNA methylation levels at such loci and inversely correlate with mRNA steady state levels, thus implicating RTL2 in the regulation of protein-coding gene expression.
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Affiliation(s)
- Emilie Elvira-Matelot
- Institut Jean-Pierre Bourgin, UMR 1318, INRA AgroParisTech CNRS, Université Paris-Saclay, 78000 Versailles, France
| | | | - Nahid Shamandi
- Institut Jean-Pierre Bourgin, UMR 1318, INRA AgroParisTech CNRS, Université Paris-Saclay, 78000 Versailles, France Université Paris-Sud, Université Paris-Saclay, 91405 Orsay, France
| | - Pascale Comella
- CNRS, UMR 5096, LGDP, 66860 Perpignan, France Université de Perpignan Via Domitia, UMR 5096, LGDP, 66860 Perpignan, France
| | - Julio Sáez-Vásquez
- CNRS, UMR 5096, LGDP, 66860 Perpignan, France Université de Perpignan Via Domitia, UMR 5096, LGDP, 66860 Perpignan, France
| | | | - Hervé Vaucheret
- Institut Jean-Pierre Bourgin, UMR 1318, INRA AgroParisTech CNRS, Université Paris-Saclay, 78000 Versailles, France
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124
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Post-transcriptional gene silencing in plants: a double-edged sword. SCIENCE CHINA-LIFE SCIENCES 2015; 59:271-6. [PMID: 26718356 DOI: 10.1007/s11427-015-4972-7] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/18/2015] [Accepted: 09/08/2015] [Indexed: 01/08/2023]
Abstract
In plants, post-transcriptional gene silencing (PTGS) protects the genome from foreign genes and restricts the expression of certain endogenous genes for proper development. Here, we review the recent progress about how the unwanted PTGS is avoided in plants. As a decision-making step of PTGS, aberrant transcripts from most endogenous coding genes are strictly sorted to the bidirectional RNA decay pathways in cytoplasm but not to the short interference RNA (siRNA)-mediated PTGS, with the exception of a few development-relevant endogenous siRNA-producing genes. We also discuss a finely balanced PTGS threshold model that plants fully take advantage of the power of PTGS without self-harm.
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125
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Zhang C, Wu Z, Li Y, Wu J. Biogenesis, Function, and Applications of Virus-Derived Small RNAs in Plants. Front Microbiol 2015; 6:1237. [PMID: 26617580 PMCID: PMC4637412 DOI: 10.3389/fmicb.2015.01237] [Citation(s) in RCA: 80] [Impact Index Per Article: 8.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2015] [Accepted: 10/26/2015] [Indexed: 11/13/2022] Open
Abstract
RNA silencing, an evolutionarily conserved and sequence-specific gene-inactivation system, has a pivotal role in antiviral defense in most eukaryotic organisms. In plants, a class of exogenous small RNAs (sRNAs) originating from the infecting virus called virus-derived small interfering RNAs (vsiRNAs) are predominantly responsible for RNA silencing-mediated antiviral immunity. Nowadays, the process of vsiRNA formation and the role of vsiRNAs in plant viral defense have been revealed through deep sequencing of sRNAs and diverse genetic analysis. The biogenesis of vsiRNAs is analogous to that of endogenous sRNAs, which require diverse essential components including dicer-like (DCL), argonaute (AGO), and RNA-dependent RNA polymerase (RDR) proteins. vsiRNAs trigger antiviral defense through post-transcriptional gene silencing (PTGS) or transcriptional gene silencing (TGS) of viral RNA, and they hijack the host RNA silencing system to target complementary host transcripts. Additionally, several applications that take advantage of the current knowledge of vsiRNAs research are being used, such as breeding antiviral plants through genetic engineering technology, reconstructing of viral genomes, and surveying viral ecology and populations. Here, we will provide an overview of vsiRNA pathways, with a primary focus on the advances in vsiRNA biogenesis and function, and discuss their potential applications as well as the future challenges in vsiRNAs research.
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Affiliation(s)
- Chao Zhang
- Key Laboratory of Plant Virology of Fujian Province, Institute of Plant Virology, Fujian Agriculture and Forestry University Fuzhou, China
| | - Zujian Wu
- Key Laboratory of Plant Virology of Fujian Province, Institute of Plant Virology, Fujian Agriculture and Forestry University Fuzhou, China
| | - Yi Li
- Peking-Yale Joint Center for Plant Molecular Genetics and Agrobiotechnology, The National Laboratory of Protein Engineering and Plant Genetic Engineering, College of Life Sciences, Peking University Beijing, China
| | - Jianguo Wu
- Key Laboratory of Plant Virology of Fujian Province, Institute of Plant Virology, Fujian Agriculture and Forestry University Fuzhou, China ; Peking-Yale Joint Center for Plant Molecular Genetics and Agrobiotechnology, The National Laboratory of Protein Engineering and Plant Genetic Engineering, College of Life Sciences, Peking University Beijing, China
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Abstract
Plant genomes encode various small RNAs that function in distinct, yet overlapping, genetic and epigenetic silencing pathways. However, the abundance and diversity of small-RNA classes varies among plant species, suggesting coevolution between environmental adaptations and gene-silencing mechanisms. Biogenesis of small RNAs in plants is well understood, but we are just beginning to uncover their intricate regulation and activity. Here, we discuss the biogenesis of plant small RNAs, such as microRNAs, secondary siRNAs and heterochromatic siRNAs, and their diverse cellular and developmental functions, including in reproductive transitions, genomic imprinting and paramutation. We also discuss the diversification of small-RNA-directed silencing pathways through the expansion of RNA-dependent RNA polymerases, DICER proteins and ARGONAUTE proteins.
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127
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Branscheid A, Marchais A, Schott G, Lange H, Gagliardi D, Andersen SU, Voinnet O, Brodersen P. SKI2 mediates degradation of RISC 5'-cleavage fragments and prevents secondary siRNA production from miRNA targets in Arabidopsis. Nucleic Acids Res 2015; 43:10975-88. [PMID: 26464441 PMCID: PMC4678812 DOI: 10.1093/nar/gkv1014] [Citation(s) in RCA: 59] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2015] [Accepted: 09/24/2015] [Indexed: 12/19/2022] Open
Abstract
Small regulatory RNAs are fundamental in eukaryotic and prokaryotic gene regulation. In plants, an important element of post-transcriptional control is effected by 20–24 nt microRNAs (miRNAs) and short interfering RNAs (siRNAs) bound to the ARGONAUTE1 (AGO1) protein in an RNA induced silencing complex (RISC). AGO1 may cleave target mRNAs with small RNA complementarity, but the fate of the resulting cleavage fragments remains incompletely understood. Here, we show that SKI2, SKI3 and SKI8, subunits of a cytoplasmic cofactor of the RNA exosome, are required for degradation of RISC 5′, but not 3′-cleavage fragments in Arabidopsis. In the absence of SKI2 activity, many miRNA targets produce siRNAs via the RNA-dependent RNA polymerase 6 (RDR6) pathway. These siRNAs are low-abundant, and map close to the cleavage site. In most cases, siRNAs were produced 5′ to the cleavage site, but several examples of 3′-spreading were also identified. These observations suggest that siRNAs do not simply derive from RDR6 action on stable 5′-cleavage fragments and hence that SKI2 has a direct role in limiting secondary siRNA production in addition to its function in mediating degradation of 5′-cleavage fragments.
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Affiliation(s)
- Anja Branscheid
- Department of Biology, University of Copenhagen, Ole Maaløes Vej 5, DK-2200 Copenhagen N, Denmark
| | - Antonin Marchais
- Swiss Federal Institute of Technology (ETH) Zürich, Department of Biology, LFW D17/D18, Universitätsstrasse 2, CH-8092 Zürich, Switzerland
| | - Gregory Schott
- Swiss Federal Institute of Technology (ETH) Zürich, Department of Biology, LFW D17/D18, Universitätsstrasse 2, CH-8092 Zürich, Switzerland
| | - Heike Lange
- Institut de Biologie Moléculaire des Plantes du CNRS, 12 Rue du Général Zimmer, F-67084 Strasbourg Cedex, France
| | - Dominique Gagliardi
- Institut de Biologie Moléculaire des Plantes du CNRS, 12 Rue du Général Zimmer, F-67084 Strasbourg Cedex, France
| | - Stig Uggerhøj Andersen
- Department of Molecular Biology, University of Aarhus, Gustav Wieds Vej 10, DK-8000 Aarhus C, Denmark
| | - Olivier Voinnet
- Swiss Federal Institute of Technology (ETH) Zürich, Department of Biology, LFW D17/D18, Universitätsstrasse 2, CH-8092 Zürich, Switzerland
| | - Peter Brodersen
- Department of Biology, University of Copenhagen, Ole Maaløes Vej 5, DK-2200 Copenhagen N, Denmark
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128
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Margaria P, Miozzi L, Rosa C, Axtell MJ, Pappu HR, Turina M. Small RNA profiles of wild-type and silencing suppressor-deficient tomato spotted wilt virus infected Nicotiana benthamiana. Virus Res 2015; 208:30-8. [PMID: 26047586 DOI: 10.1016/j.virusres.2015.05.021] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2015] [Revised: 05/25/2015] [Accepted: 05/25/2015] [Indexed: 01/01/2023]
Abstract
Tospoviruses are plant-infecting viruses belonging to the family Bunyaviridae. We used a collection of wild-type, phylogenetically distinct tomato spotted wilt virus isolates and related silencing-suppressor defective mutants to study the effects on the small RNA (sRNA) accumulation during infection of Nicotiana benthamiana. Our data showed that absence of a functional silencing suppressor determined a marked increase of the total amount of viral sRNAs (vsRNAs), and specifically of the 21 nt class. We observed a common under-representation of vsRNAs mapping to the intergenic region of S and M genomic segments, and preferential mapping of the reads against the viral sense open reading frames, with the exception of the NSs gene. The NSs-mutant strains showed enrichment of NSm-derived vsRNA compared to the expected amount based on gene size. Analysis of 5' terminal nucleotide preference evidenced a significant enrichment in U for the 21 nt- and in A for 24 nt-long endogenous sRNAs in all the samples. Hotspot analysis revealed a common abundant accumulation of reads at the 5' end of the L segment, mostly in the antiviral sense, for the NSs-defective isolates, suggesting that absence of the silencing suppressor can influence preferential targeting of the viral genome.
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Affiliation(s)
- Paolo Margaria
- Istituto per la Protezione Sostenibile delle Piante, CNR, Strada delle Cacce 73, 10135 Torino, Italy; Department of Plant Pathology and Environmental Microbiology, Pennsylvania State University, University Park, PA 16802, USA
| | - Laura Miozzi
- Istituto per la Protezione Sostenibile delle Piante, CNR, Strada delle Cacce 73, 10135 Torino, Italy
| | - Cristina Rosa
- Department of Plant Pathology and Environmental Microbiology, Pennsylvania State University, University Park, PA 16802, USA
| | - Michael J Axtell
- Department of Biology, and The Huck Institutes of the Life Sciences, Pennsylvania State University, University Park, PA 16802, USA
| | - Hanu R Pappu
- Department of Plant Pathology, Washington State University, PO Box 646430, Pullman, WA 99164, USA
| | - Massimo Turina
- Istituto per la Protezione Sostenibile delle Piante, CNR, Strada delle Cacce 73, 10135 Torino, Italy.
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129
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Carbonell A, Carrington JC. Antiviral roles of plant ARGONAUTES. CURRENT OPINION IN PLANT BIOLOGY 2015; 27:111-7. [PMID: 26190744 PMCID: PMC4618181 DOI: 10.1016/j.pbi.2015.06.013] [Citation(s) in RCA: 181] [Impact Index Per Article: 20.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/21/2015] [Revised: 06/11/2015] [Accepted: 06/19/2015] [Indexed: 05/20/2023]
Abstract
ARGONAUTES (AGOs) are the effector proteins functioning in eukaryotic RNA silencing pathways. AGOs associate with small RNAs and are programmed to target complementary RNA or DNA. Plant viruses induce a potent and specific antiviral RNA silencing host response in which AGOs play a central role. Antiviral AGOs associate with virus-derived small RNAs to repress complementary viral RNAs or DNAs, or with endogenous small RNAs to regulate host gene expression and promote antiviral defense. Here, we review recent progress towards understanding the roles of plant AGOs in antiviral defense. We also discuss the strategies that viruses have evolved to modulate, attenuate or suppress AGO antiviral functions.
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Affiliation(s)
- Alberto Carbonell
- Donald Danforth Plant Science Center, St. Louis, Missouri 63132, USA
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130
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Chiba S, Suzuki N. Highly activated RNA silencing via strong induction of dicer by one virus can interfere with the replication of an unrelated virus. Proc Natl Acad Sci U S A 2015; 112:E4911-8. [PMID: 26283371 PMCID: PMC4568273 DOI: 10.1073/pnas.1509151112] [Citation(s) in RCA: 57] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Viruses often coinfect single host organisms in nature. Depending on the combination of viruses in such coinfections, the interplay between them may be synergistic, apparently neutral with no effect on each other, or antagonistic. RNA silencing is responsible for many cases of interference or cross-protection between viruses, but such antagonistic interactions are usually restricted to closely related strains of the same viral species. In this study, we present an unprecedented example of RNA silencing-mediated one-way interference between unrelated viruses in a filamentous model fungus, Cryphonectria parasitica. The replication of Rosellinia necatrix victorivirus 1 (RnVV1; Totiviridae) was strongly impaired by coinfection with the prototypic member of the genus Mycoreovirus (MyRV1) or a mutant of the prototype hypovirus (Cryphonectria hypovirus 1, CHV1) lacking the RNA silencing suppressor (CHV1-Δp69). This interference was associated with marked transcriptional induction of key genes in antiviral RNA silencing, dicer-like 2 (dcl2) and argonaute-like 2 (agl2), following MyRV1 or CHV1-Δp69 infection. Interestingly, the inhibition of RnVV1 replication was reproduced when the levels of dcl2 and agl2 transcripts were elevated by transgenic expression of a hairpin construct of an endogenous C. parasitica gene. Disruption of dcl2 completely abolished the interference, whereas that of agl2 did not always lead to its abolishment, suggesting more crucial roles of dcl2 in antiviral defense. Taken altogether, these results demonstrated the susceptible nature of RnVV1 to the antiviral silencing in C. parasitica activated by distinct viruses or transgene-derived double-stranded RNAs and provide insight into the potential for broad-spectrum virus control mediated by RNA silencing.
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Affiliation(s)
- Sotaro Chiba
- Institute of Plant Science and Resources, Okayama University, Kurashiki, Okayama 710-0046, Japan
| | - Nobuhiro Suzuki
- Institute of Plant Science and Resources, Okayama University, Kurashiki, Okayama 710-0046, Japan
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131
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Hong W, Qian D, Sun R, Jiang L, Wang Y, Wei C, Zhang Z, Li Y. OsRDR6 plays role in host defense against double-stranded RNA virus, Rice Dwarf Phytoreovirus. Sci Rep 2015; 5:11324. [PMID: 26165755 PMCID: PMC4499934 DOI: 10.1038/srep11324] [Citation(s) in RCA: 38] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2015] [Accepted: 05/13/2015] [Indexed: 11/29/2022] Open
Abstract
RNAi is a major antiviral defense response in plant and animal model systems. RNA-dependent RNA polymerase 6 (RDR6) is an essential component of RNAi, which plays an important role in the resistance against viruses in the model plants. We found previously that rice RDR6 (OsRDR6) functioned in the defense against Rice stripe virus (RSV), and Rice Dwarf Phytoreovirus (RDV) infection resulted in down-regulation of expression of RDR6. Here we report our new findings on the function of OsRDR6 against RDV. Our result showed that down-regulation of OsRDR6 through the antisense (OsRDR6AS) strategy increased rice susceptibility to RDV infection while over-expression of OsRDR6 had no effect on RDV infection. The accumulation of RDV vsiRNAs was reduced in the OsRDR6AS plants. In the OsRDR6 over-expressed plants, the levels of OsRDR6 RNA transcript and protein were much higher than that in the control plants. Interestingly, the accumulation level of OsRDR6 protein became undetectable after RDV infection. This finding indicated that the translation and/or stability of OsRDR6 protein were negatively impacted upon RDV infection. This new finding provides a new light on the function of RDR6 in plant defense response and the cross-talking between factors encoded by host plant and double-stranded RNA viruses.
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Affiliation(s)
- Wei Hong
- State Key Laboratory of Protein and Plant Gene Research, College of Life Sciences, Peking University, Beijing 100871, China
| | - Dan Qian
- State Key Laboratory of Protein and Plant Gene Research, College of Life Sciences, Peking University, Beijing 100871, China
| | - Runhong Sun
- 1] State Key Laboratory of Protein and Plant Gene Research, College of Life Sciences, Peking University, Beijing 100871, China [2] Institute of Plant Protection, Henan Academy of Agricultural Sciences, Henan Key Laboratory of Crop Pest Control, Zhengzhou 450002, China
| | - Lin Jiang
- State Key Laboratory of Protein and Plant Gene Research, College of Life Sciences, Peking University, Beijing 100871, China
| | - Yu Wang
- State Key Laboratory of Protein and Plant Gene Research, College of Life Sciences, Peking University, Beijing 100871, China
| | - Chunhong Wei
- State Key Laboratory of Protein and Plant Gene Research, College of Life Sciences, Peking University, Beijing 100871, China
| | - Zhongkai Zhang
- Ministry of Agriculture Key Lab of Southwestern Crop Gene Resources and Germplasm Innovation, Yunnan Provincial Key Lab of Agricultural Biotechnology, Biotechnology and Germplasm Resources Institute, Yunnan Academy of Agricultural Sciences, Kunming 650223, China
| | - Yi Li
- State Key Laboratory of Protein and Plant Gene Research, College of Life Sciences, Peking University, Beijing 100871, China
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132
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Aguiar ERGR, Olmo RP, Paro S, Ferreira FV, de Faria IJDS, Todjro YMH, Lobo FP, Kroon EG, Meignin C, Gatherer D, Imler JL, Marques JT. Sequence-independent characterization of viruses based on the pattern of viral small RNAs produced by the host. Nucleic Acids Res 2015; 43:6191-206. [PMID: 26040701 PMCID: PMC4513865 DOI: 10.1093/nar/gkv587] [Citation(s) in RCA: 80] [Impact Index Per Article: 8.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2015] [Accepted: 05/24/2015] [Indexed: 12/20/2022] Open
Abstract
Virus surveillance in vector insects is potentially of great benefit to public health. Large-scale sequencing of small and long RNAs has previously been used to detect viruses, but without any formal comparison of different strategies. Furthermore, the identification of viral sequences largely depends on similarity searches against reference databases. Here, we developed a sequence-independent strategy based on virus-derived small RNAs produced by the host response, such as the RNA interference pathway. In insects, we compared sequences of small and long RNAs, demonstrating that viral sequences are enriched in the small RNA fraction. We also noted that the small RNA size profile is a unique signature for each virus and can be used to identify novel viral sequences without known relatives in reference databases. Using this strategy, we characterized six novel viruses in the viromes of laboratory fruit flies and wild populations of two insect vectors: mosquitoes and sandflies. We also show that the small RNA profile could be used to infer viral tropism for ovaries among other aspects of virus biology. Additionally, our results suggest that virus detection utilizing small RNAs can also be applied to vertebrates, although not as efficiently as to plants and insects.
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Affiliation(s)
- Eric Roberto Guimarães Rocha Aguiar
- Department of Biochemistry and Immunology, Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais, Belo Horizonte, Minas Gerais, CEP 30270-901, Brazil CNRS-UPR9022, Institut de Biologie Moléculaire et Cellulaire, 67084 Strasbourg Cedex, France
| | - Roenick Proveti Olmo
- Department of Biochemistry and Immunology, Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais, Belo Horizonte, Minas Gerais, CEP 30270-901, Brazil CNRS-UPR9022, Institut de Biologie Moléculaire et Cellulaire, 67084 Strasbourg Cedex, France
| | - Simona Paro
- CNRS-UPR9022, Institut de Biologie Moléculaire et Cellulaire, 67084 Strasbourg Cedex, France
| | - Flavia Viana Ferreira
- Department of Microbiology, Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais, Belo Horizonte, Minas Gerais, CEP 30270-901, Brazil
| | - Isaque João da Silva de Faria
- Department of Biochemistry and Immunology, Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais, Belo Horizonte, Minas Gerais, CEP 30270-901, Brazil
| | - Yaovi Mathias Honore Todjro
- Department of Biochemistry and Immunology, Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais, Belo Horizonte, Minas Gerais, CEP 30270-901, Brazil
| | - Francisco Pereira Lobo
- Laboratório Multiusuário de Bioinformática, Embrapa Informática Agropecuária, Campinas, São Paulo, CEP 13083-886, Brazil
| | - Erna Geessien Kroon
- Department of Microbiology, Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais, Belo Horizonte, Minas Gerais, CEP 30270-901, Brazil
| | - Carine Meignin
- CNRS-UPR9022, Institut de Biologie Moléculaire et Cellulaire, 67084 Strasbourg Cedex, France Faculté des Sciences de la Vie, Université de Strasbourg, 67083 Strasbourg Cedex, France
| | - Derek Gatherer
- Division of Biomedical and Life Sciences, Faculty of Health and Medicine, Lancaster University, Lancaster, Lancashire, LA1 4YQ, UK
| | - Jean-Luc Imler
- CNRS-UPR9022, Institut de Biologie Moléculaire et Cellulaire, 67084 Strasbourg Cedex, France Faculté des Sciences de la Vie, Université de Strasbourg, 67083 Strasbourg Cedex, France Institut d'Etudes Avancées de l'Université de Strasbourg (USIAS), 67084 Strasbourg Cedex, France
| | - João Trindade Marques
- Department of Biochemistry and Immunology, Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais, Belo Horizonte, Minas Gerais, CEP 30270-901, Brazil
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133
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Symptom recovery in virus-infected plants: Revisiting the role of RNA silencing mechanisms. Virology 2015; 479-480:167-79. [DOI: 10.1016/j.virol.2015.01.008] [Citation(s) in RCA: 100] [Impact Index Per Article: 11.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2014] [Revised: 01/02/2015] [Accepted: 01/08/2015] [Indexed: 01/11/2023]
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134
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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] [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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135
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Viral factors involved in plant pathogenesis. Curr Opin Virol 2015; 11:21-30. [DOI: 10.1016/j.coviro.2015.01.001] [Citation(s) in RCA: 67] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2014] [Accepted: 01/06/2015] [Indexed: 12/31/2022]
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136
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Garcia-Ruiz H, Carbonell A, Hoyer JS, Fahlgren N, Gilbert KB, Takeda A, Giampetruzzi A, Garcia Ruiz MT, McGinn MG, Lowery N, Martinez Baladejo MT, Carrington JC. Roles and programming of Arabidopsis ARGONAUTE proteins during Turnip mosaic virus infection. PLoS Pathog 2015; 11:e1004755. [PMID: 25806948 PMCID: PMC4373807 DOI: 10.1371/journal.ppat.1004755] [Citation(s) in RCA: 132] [Impact Index Per Article: 14.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2014] [Accepted: 02/19/2015] [Indexed: 11/24/2022] Open
Abstract
In eukaryotes, ARGONAUTE proteins (AGOs) associate with microRNAs (miRNAs), short interfering RNAs (siRNAs), and other classes of small RNAs to regulate target RNA or target loci. Viral infection in plants induces a potent and highly specific antiviral RNA silencing response characterized by the formation of virus-derived siRNAs. Arabidopsis thaliana has ten AGO genes of which AGO1, AGO2, and AGO7 have been shown to play roles in antiviral defense. A genetic analysis was used to identify and characterize the roles of AGO proteins in antiviral defense against Turnip mosaic virus (TuMV) in Arabidopsis. AGO1, AGO2 and AGO10 promoted anti-TuMV defense in a modular way in various organs, with AGO2 providing a prominent antiviral role in leaves. AGO5, AGO7 and AGO10 had minor effects in leaves. AGO1 and AGO10 had overlapping antiviral functions in inflorescence tissues after systemic movement of the virus, although the roles of AGO1 and AGO10 accounted for only a minor amount of the overall antiviral activity. By combining AGO protein immunoprecipitation with high-throughput sequencing of associated small RNAs, AGO2, AGO10, and to a lesser extent AGO1 were shown to associate with siRNAs derived from silencing suppressor (HC-Pro)-deficient TuMV-AS9, but not with siRNAs derived from wild-type TuMV. Co-immunoprecipitation and small RNA sequencing revealed that viral siRNAs broadly associated with wild-type HC-Pro during TuMV infection. These results support the hypothesis that suppression of antiviral silencing during TuMV infection, at least in part, occurs through sequestration of virus-derived siRNAs away from antiviral AGO proteins by HC-Pro. These findings indicate that distinct AGO proteins function as antiviral modules, and provide a molecular explanation for the silencing suppressor activity of HC-Pro. RNA silencing is a primary, adaptive defense system against viruses in plants. Viruses have evolved counter-defensive mechanisms that inhibit RNA silencing through the activity of silencing suppressor proteins. Understanding how antiviral silencing is controlled, and how suppressor proteins function, is essential for understanding how plants normally resist viruses, why some viruses are highly virulent in different hosts, and how sustainable antiviral resistance strategies can be deployed in agricultural settings. We used a mutant version of Turnip mosaic virus lacking a functional silencing suppressor (HC-Pro) to understand the genetic requirements for resistance in the model plant Arabidopsis thaliana. We focused on ARGONAUTE proteins, which have long been hypothesized to bind short interfering RNAs (siRNAs) derived from virus genomes for use as sequence-specific guides to recognize and target viral RNA for degradation or repression. We demonstrated specialized antiviral roles for specific ARGONAUTES and showed that several can bind viral siRNAs from across the entire viral genome. However, ARGONAUTE proteins are only loaded with virus-derived siRNAs in the absence of HC-Pro, which we showed binds siRNAs from the viral genome. This indicates that several AGO proteins, which collectively are necessary for full anti-TuMV defense, need to properly load virus-derived siRNAs to execute their antiviral roles.
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Affiliation(s)
- Hernan Garcia-Ruiz
- Donald Danforth Plant Science Center, St. Louis, Missouri, United States of America
- Center for Genome Research and Biocomputing, Department of Botany and Plant Pathology, Oregon State University, Corvallis, Oregon, United States of America
| | - Alberto Carbonell
- Donald Danforth Plant Science Center, St. Louis, Missouri, United States of America
- Center for Genome Research and Biocomputing, Department of Botany and Plant Pathology, Oregon State University, Corvallis, Oregon, United States of America
| | - J. Steen Hoyer
- Donald Danforth Plant Science Center, St. Louis, Missouri, United States of America
- Center for Genome Research and Biocomputing, Department of Botany and Plant Pathology, Oregon State University, Corvallis, Oregon, United States of America
- Computational and Systems Biology Program, Washington University in St. Louis, St. Louis, Missouri, United States of America
| | - Noah Fahlgren
- Donald Danforth Plant Science Center, St. Louis, Missouri, United States of America
- Center for Genome Research and Biocomputing, Department of Botany and Plant Pathology, Oregon State University, Corvallis, Oregon, United States of America
| | - Kerrigan B. Gilbert
- Donald Danforth Plant Science Center, St. Louis, Missouri, United States of America
| | - Atsushi Takeda
- Center for Genome Research and Biocomputing, Department of Botany and Plant Pathology, Oregon State University, Corvallis, Oregon, United States of America
| | - Annalisa Giampetruzzi
- Center for Genome Research and Biocomputing, Department of Botany and Plant Pathology, Oregon State University, Corvallis, Oregon, United States of America
| | - Mayra T. Garcia Ruiz
- Donald Danforth Plant Science Center, St. Louis, Missouri, United States of America
| | - Michaela G. McGinn
- Donald Danforth Plant Science Center, St. Louis, Missouri, United States of America
| | - Nicholas Lowery
- Center for Genome Research and Biocomputing, Department of Botany and Plant Pathology, Oregon State University, Corvallis, Oregon, United States of America
| | | | - James C. Carrington
- Donald Danforth Plant Science Center, St. Louis, Missouri, United States of America
- Center for Genome Research and Biocomputing, Department of Botany and Plant Pathology, Oregon State University, Corvallis, Oregon, United States of America
- * E-mail:
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137
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Martínez de Alba AE, Moreno AB, Gabriel M, Mallory AC, Christ A, Bounon R, Balzergue S, Aubourg S, Gautheret D, Crespi MD, Vaucheret H, Maizel A. In plants, decapping prevents RDR6-dependent production of small interfering RNAs from endogenous mRNAs. Nucleic Acids Res 2015; 43:2902-13. [PMID: 25694514 PMCID: PMC4357720 DOI: 10.1093/nar/gkv119] [Citation(s) in RCA: 86] [Impact Index Per Article: 9.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2014] [Revised: 01/16/2015] [Accepted: 02/04/2015] [Indexed: 01/24/2023] Open
Abstract
Cytoplasmic degradation of endogenous RNAs is an integral part of RNA quality control (RQC) and often relies on the removal of the 5' cap structure and their subsequent 5' to 3' degradation in cytoplasmic processing (P-)bodies. In parallel, many eukaryotes degrade exogenous and selected endogenous RNAs through post-transcriptional gene silencing (PTGS). In plants, PTGS depends on small interfering (si)RNAs produced after the conversion of single-stranded RNAs to double-stranded RNAs by the cellular RNA-dependent RNA polymerase 6 (RDR6) in cytoplasmic siRNA-bodies. PTGS and RQC compete for transgene-derived RNAs, but it is unknown whether this competition also occurs for endogenous transcripts. We show that the lethality of decapping mutants is suppressed by impairing RDR6 activity. We establish that upon decapping impairment hundreds of endogenous mRNAs give rise to a new class of rqc-siRNAs, that over-accumulate when RQC processes are impaired, a subset of which depending on RDR6 for their production. We observe that P- and siRNA-bodies often are dynamically juxtaposed, potentially allowing for cross-talk of the two machineries. Our results suggest that the decapping of endogenous RNA limits their entry into the PTGS pathway. We anticipate that the rqc-siRNAs identified in decapping mutants represent a subset of a larger ensemble of endogenous siRNAs.
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MESH Headings
- Arabidopsis/genetics
- Arabidopsis/metabolism
- Arabidopsis Proteins/genetics
- Arabidopsis Proteins/metabolism
- Endoribonucleases/genetics
- Endoribonucleases/metabolism
- Gene Expression Regulation, Plant
- Mutation
- Oligonucleotide Array Sequence Analysis
- Plants, Genetically Modified
- RNA Caps/genetics
- RNA Caps/metabolism
- RNA Interference
- RNA, Messenger/genetics
- RNA, Messenger/metabolism
- RNA, Plant/genetics
- RNA, Plant/metabolism
- RNA, Small Interfering/genetics
- RNA, Small Interfering/metabolism
- RNA, Small Untranslated/genetics
- RNA, Small Untranslated/metabolism
- RNA-Dependent RNA Polymerase/genetics
- RNA-Dependent RNA Polymerase/metabolism
- Transcriptome
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Affiliation(s)
| | - Ana Beatriz Moreno
- Institut des Sciences du Végétal, CNRS UPR 2355, SPS Saclay Plant Sciences, Gif-sur-Yvette, France
| | - Marc Gabriel
- Institute for Integrative Biology of the Cell, UMR 9198 - Universite Paris-Sud, Gif-sur-Yvette, France
| | - Allison C Mallory
- Institut Jean-Pierre Bourgin UMR 1318, INRA, SPS Saclay Plant Sciences, Versailles, France
| | - Aurélie Christ
- Institut des Sciences du Végétal, CNRS UPR 2355, SPS Saclay Plant Sciences, Gif-sur-Yvette, France
| | - Rémi Bounon
- Unité de Recherche en Génomique Végétale, UMR INRA 1165-CNRS 8114-UEVE, Evry, France
| | - Sandrine Balzergue
- Unité de Recherche en Génomique Végétale, UMR INRA 1165-CNRS 8114-UEVE, Evry, France
| | - Sebastien Aubourg
- Unité de Recherche en Génomique Végétale, UMR INRA 1165-CNRS 8114-UEVE, Evry, France
| | - Daniel Gautheret
- Institute for Integrative Biology of the Cell, UMR 9198 - Universite Paris-Sud, Gif-sur-Yvette, France
| | - Martin D Crespi
- Institut des Sciences du Végétal, CNRS UPR 2355, SPS Saclay Plant Sciences, Gif-sur-Yvette, France
| | - Hervé Vaucheret
- Institut Jean-Pierre Bourgin UMR 1318, INRA, SPS Saclay Plant Sciences, Versailles, France
| | - Alexis Maizel
- Institut des Sciences du Végétal, CNRS UPR 2355, SPS Saclay Plant Sciences, Gif-sur-Yvette, France Center for Organismal Studies, University of Heidelberg, Germany
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138
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Dalakouras A, Dadami E, Wassenegger M. Engineering viroid resistance. Viruses 2015; 7:634-46. [PMID: 25674769 PMCID: PMC4353907 DOI: 10.3390/v7020634] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2015] [Accepted: 01/30/2015] [Indexed: 12/31/2022] Open
Abstract
Viroids are non-encapsidated, non-coding, circular, single-stranded RNAs (ssRNAs). They are classified into the families Pospiviroidae and Avsunviroidae, whose members replicate in the nucleus and chloroplast of plant cells, respectively. Viroids have a wide host range, including crop and ornamental plants, and can cause devastating diseases with significant economic losses. Thus, several viroids are world-wide, classified as quarantine pathogens and, hence, there is an urgent need for the development of robust antiviroid strategies. RNA silencing-based technologies seem to be a promising tool in this direction. Here, we review the recent advances concerning the complex interaction of viroids with the host's RNA silencing machinery, evaluate past and present antiviroid approaches, and finally suggest alternative strategies that could potentially be employed in the future in order to achieve transgenic and non-transgenic viroid-free plants.
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Affiliation(s)
- Athanasios Dalakouras
- RLP AgroScience GmbH, AIPlanta-Institute for Plant Research, Neustadt, 67435, Germany.
| | - Elena Dadami
- RLP AgroScience GmbH, AIPlanta-Institute for Plant Research, Neustadt, 67435, Germany.
| | - Michael Wassenegger
- RLP AgroScience GmbH, AIPlanta-Institute for Plant Research, Neustadt, Germany and Centre for Organisational Studies (COS) Heidelberg, University of Heidelberg, Heidelberg, 69120, Germany.
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139
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Naidu RA, Maree HJ, Burger JT. Grapevine leafroll disease and associated viruses: a unique pathosystem. ANNUAL REVIEW OF PHYTOPATHOLOGY 2015; 53:613-34. [PMID: 26243729 DOI: 10.1146/annurev-phyto-102313-045946] [Citation(s) in RCA: 44] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/26/2023]
Abstract
Grapevine leafroll is the most complex and intriguing viral disease of grapevine (Vitis spp.). Several monopartite closteroviruses (family Closteroviridae) from grapevines have been molecularly characterized, yet their role in disease etiology is not completely resolved. Hence, these viruses are currently designated under the umbrella term of Grapevine leafroll-associated viruses (GLRaVs). This review examines our current understanding of the genetically divergent GLRaVs and highlights the emerging picture of several unique aspects of the leafroll disease pathosystem. A systems biology approach using contemporary technologies in molecular biology, -omics, and cell biology aids in exploring the comparative molecular biology of GLRaVs and deciphering the complex network of host-virus-vector interactions to bridge the gap between genomics and phenomics of leafroll disease. In addition, grapevine-infecting closteroviruses have a great potential as designer viruses to pursue functional genomics and for the rational design of novel disease intervention strategies in this agriculturally important perennial fruit crop.
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Affiliation(s)
- Rayapati A Naidu
- Department of Plant Pathology, Irrigated Agriculture Research and Extension Center, Washington State University, Prosser, Washington 99350;
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