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Deng Y, Yarur-Thys A, Baulcombe DC. Virus-induced overexpression of heterologous FLOWERING LOCUS T for efficient speed breeding in tomato. J Exp Bot 2024; 75:36-44. [PMID: 37788568 PMCID: PMC10735598 DOI: 10.1093/jxb/erad369] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/13/2023] [Accepted: 10/02/2023] [Indexed: 10/05/2023]
Abstract
Potato virus X (PVX) vectors expressing the Arabidopsis thaliana FLOWERING LOCUS T (FT) or tomato FT ortholog SINGLE-FLOWER TRUSS (SFT) shortened the generation time in tomato due to accelerated tomato flowering and ripening by 14-21 d, and caused a 2-3-fold increase in the number of flowers and fruits, compared with non-infected or empty vector-infected plants. The Arabidopsis FT was more effective than the tomato orthologue SFT and there was no alteration of the flower or fruit morphology. The virus was not transmitted to the next generation; therefore viral vectors with expression of a heterologous FT will be a useful approach to speed breeding in tomato and other species.
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Affiliation(s)
- Yingtian Deng
- Department of Plant Sciences, University of Cambridge, Downing Street, Cambridge CB2 3EA, UK
- National Key Laboratory for Germplasm Innovation and Utilization for Fruit and Vegetable Horticultural Crops, College of Horticulture and Forestry Sciences, Huazhong Agricultural University, Wuhan, 430070, China
| | - Antonia Yarur-Thys
- Department of Plant Sciences, University of Cambridge, Downing Street, Cambridge CB2 3EA, UK
| | - David C Baulcombe
- Department of Plant Sciences, University of Cambridge, Downing Street, Cambridge CB2 3EA, UK
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2
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Abstract
My research career started with an ambition to work out how genes are regulated in plants. I tried out various experimental systems-artichoke tissue culture in Edinburgh; soybean root nodules in Montreal; soybean hypocotyls in Athens, Georgia; and cereal aleurones in Cambridge-but eventually I discovered plant viruses. Viral satellite RNAs were my first interest, but I then explored transgenic and natural disease resistance and was led by curiosity into topics beyond virology, including RNA silencing, epigenetics, and more recently, genome evolution. On the way, I have learned about approaches to research, finding tractable systems, and taking academic research into the real world. I have always tried to consider the broader significance of our work, and my current projects address the definition of epigenetics, the arms race concept of disease resistance, and Darwin's abominable mystery.
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Affiliation(s)
- David C Baulcombe
- Department of Plant Sciences, University of Cambridge, Cambridge, United Kingdom;
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3
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Abstract
Adaptive antiviral immunity in plants is an RNA-based mechanism in which small RNAs derived from both strands of the viral RNA are guides for an Argonaute (AGO) nuclease. The primed AGO specifically targets and silences the viral RNA. In plants this system has diversified to involve mobile small interfering RNAs (siRNAs), an amplification system involving secondary siRNAs and targeting mechanisms involving DNA methylation. Most, if not all, plant viruses encode multifunctional proteins that are suppressors of RNA silencing that may also influence the innate immune system and fine-tune the virus-host interaction. Animal viruses similarly trigger RNA silencing, although it may be masked in differentiated cells by the interferon system and by the action of the virus-encoded suppressor proteins. There is huge potential for RNA silencing to combat viral disease in crops, farm animals, and people, although there are complications associated with the various strategies for siRNA delivery including transgenesis. Alternative approaches could include using breeding or small molecule treatment to enhance the inherent antiviral capacity of infected cells.
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Affiliation(s)
- David C Baulcombe
- Department of Plant Sciences, University of Cambridge, Cambridge, United Kingdom;
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4
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Wang Z, Wang XY, Martinho C, Baulcombe DC. Post-transcriptional Gene Silencing Using Virus-Induced Gene Silencing to Study Plant Gametogenesis in Tomato. Methods Mol Biol 2022; 2484:201-212. [PMID: 35461454 DOI: 10.1007/978-1-0716-2253-7_15] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/14/2023]
Abstract
Loss-of-function analyses are essential to dissect the complex nature of biological processes, including gametogenesis. Virus-induced gene silencing (VIGS) has been widely used in crop species as an amenable and rapid way to generate gene knockdowns. As a transient assay, VIGS circumvents the generation of stable transgenic lines through laborious and time-consuming tissue culture techniques. VIGS involves inoculating plants during early development with genetically manipulated viral constructs carrying an endogenous gene target sequence. The viral infection triggers the host plant gene silencing machinery to process the viral genomic RNA into small RNAs (sRNAs) including the gene complementary region. The sRNAs with complementary sequences to the endogenous gene mediate posttranscriptional gene silencing of the targeted gene. Here, we provide a simple and reproducible VIGS protocol employing the tobacco rattle virus (TRV) in tomato (Solanum lycopersicum cv. M82). As it is stable at later developmental stages this approach is suitable for many traits in tomato including gametogenesis and it can be adapted to other crop species.
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Affiliation(s)
- Zhengming Wang
- Department of Plant Sciences, University of Cambridge, Cambridge, UK.
- Key Laboratory of Horticulture Biology, Ministry of Education, College of Horticulture and Forestry Sciences, Huazhong Agricultural University, Wuhan, Hubei, China.
| | - Xiao Yu Wang
- Department of Plant Sciences, University of Cambridge, Cambridge, UK
| | - Claudia Martinho
- Department of Plant Sciences, University of Cambridge, Cambridge, UK
| | - David C Baulcombe
- Department of Plant Sciences, University of Cambridge, Cambridge, UK
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5
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Abstract
Small (s)RNAs play crucial roles in the regulation of gene expression and genome stability across eukaryotes where they direct epigenetic modifications, post-transcriptional gene silencing, and defense against both endogenous and exogenous viruses. It is known that Chlamydomonas reinhardtii, a well-studied unicellular green algae species, possesses sRNA-based mechanisms that are distinct from those of land plants. However, definition of sRNA loci and further systematic classification is not yet available for this or any other algae. Here, using data-driven machine learning approaches including Multiple Correspondence Analysis (MCA) and clustering, we have generated a comprehensively annotated and classified sRNA locus map for C. reinhardtii. This map shows some common characteristics with higher plants and animals, but it also reveals distinct features. These results are consistent with the idea that there was diversification in sRNA mechanisms after the evolutionary divergence of algae from higher plant lineages.
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Affiliation(s)
- Sebastian Y. Müller
- Department of Plant Sciences, University of Cambridge, Cambridge, United Kingdom
| | - Nicholas E. Matthews
- Department of Plant Sciences, University of Cambridge, Cambridge, United Kingdom
| | - Adrian A. Valli
- Department of Plant Sciences, University of Cambridge, Cambridge, United Kingdom
| | - David C. Baulcombe
- Department of Plant Sciences, University of Cambridge, Cambridge, United Kingdom
- * E-mail:
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6
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Corrêa RL, Sanz-Carbonell A, Kogej Z, Müller SY, Ambrós S, López-Gomollón S, Gómez G, Baulcombe DC, Elena SF. Viral Fitness Determines the Magnitude of Transcriptomic and Epigenomic Reprograming of Defense Responses in Plants. Mol Biol Evol 2020; 37:1866-1881. [DOI: 10.1093/molbev/msaa091] [Citation(s) in RCA: 20] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022] Open
Abstract
Abstract
Although epigenetic factors may influence the expression of defense genes in plants, their role in antiviral responses and the impact of viral adaptation and evolution in shaping these interactions are still poorly explored. We used two isolates of turnip mosaic potyvirus with varying degrees of adaptation to Arabidopsis thaliana to address these issues. One of the isolates was experimentally evolved in the plant and presented increased load and virulence relative to the ancestral isolate. The magnitude of the transcriptomic responses was larger for the evolved isolate and indicated a role of innate immunity systems triggered by molecular patterns and effectors in the infection process. Several transposable elements located in different chromatin contexts and epigenetic-related genes were also affected. Correspondingly, mutant plants having loss or gain of repressive marks were, respectively, more tolerant and susceptible to turnip mosaic potyvirus, with a more efficient response against the ancestral isolate. In wild-type plants, both isolates induced similar levels of cytosine methylation changes, including in and around transposable elements and stress-related genes. Results collectively suggested that apart from RNA silencing and basal immunity systems, DNA methylation and histone modification pathways may also be required for mounting proper antiviral defenses and that the effectiveness of this type of regulation strongly depends on the degree of viral adaptation to the host.
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Affiliation(s)
- Régis L Corrêa
- Instituto de Biología Integrativa de Sistemas (I2SysBio), Consejo Superior de Investigaciones Científicas (CSIC)—Universitat de València, Paterna, Valencia, Spain
- Department of Genetics, Federal University of Rio de Janeiro (UFRJ), Rio de Janeiro, Brazil
- Department of Plant Sciences, University of Cambridge, Cambridge, United Kingdom
| | - Alejandro Sanz-Carbonell
- Instituto de Biología Integrativa de Sistemas (I2SysBio), Consejo Superior de Investigaciones Científicas (CSIC)—Universitat de València, Paterna, Valencia, Spain
| | - Zala Kogej
- Department of Biotechnology and Systems Biology, National Institute of Biology, Ljubljana, Slovenia
- Instituto de Biología Integrativa de Sistemas (I2SysBio), Consejo Superior de Investigaciones Científicas (CSIC)—Universitat de València, Paterna, Valencia, Spain
| | - Sebastian Y Müller
- Department of Plant Sciences, University of Cambridge, Cambridge, United Kingdom
| | - Silvia Ambrós
- Instituto de Biología Integrativa de Sistemas (I2SysBio), Consejo Superior de Investigaciones Científicas (CSIC)—Universitat de València, Paterna, Valencia, Spain
| | - Sara López-Gomollón
- Department of Plant Sciences, University of Cambridge, Cambridge, United Kingdom
| | - Gustavo Gómez
- Instituto de Biología Integrativa de Sistemas (I2SysBio), Consejo Superior de Investigaciones Científicas (CSIC)—Universitat de València, Paterna, Valencia, Spain
| | - David C Baulcombe
- Department of Plant Sciences, University of Cambridge, Cambridge, United Kingdom
| | - Santiago F Elena
- Instituto de Biología Integrativa de Sistemas (I2SysBio), Consejo Superior de Investigaciones Científicas (CSIC)—Universitat de València, Paterna, Valencia, Spain
- The Santa Fe Institute, Santa Fe, NM
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7
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Abstract
Silencing of transposable elements (TEs) is established by small RNA-directed DNA methylation (RdDM). Maintenance of silencing is then based on a combination of RdDM and RNA-independent mechanisms involving DNA methyltransferase MET1 and chromodomain DNA methyltransferases (CMTs). Involvement of RdDM, according to this model should decrease with TE age but here we show a different pattern in tomato and Arabidopsis. In these species the CMTs silence long terminal repeat (LTR) transposons in the distal chromatin that are younger than those affected by RdDM. To account for these findings we propose that, after establishment of primary RdDM as in the original model, there is an RNA-independent maintenance phase involving CMTs followed by secondary RdDM. This progression of epigenetic silencing in the gene-rich distal chromatin is likely to influence the transcriptome either in cis or in trans depending on whether the mechanisms are RNA-dependent or -independent. RNA-directed DNA methylation (RdDM) is thought to silence newly inserted transposable elements (TEs) with RNA-independent mechanisms becoming more prominent as TEs age. Here, the authors show that RdDM continues to silence the oldest intact distal TEs in tomato and Arabidopsis suggesting a second, later phase of RdDM.
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Affiliation(s)
- Zhengming Wang
- Department of Plant Sciences, University of Cambridge, Cambridge, CB2 3EA, UK
| | - David C Baulcombe
- Department of Plant Sciences, University of Cambridge, Cambridge, CB2 3EA, UK.
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8
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Chung BYW, Valli A, Deery MJ, Navarro FJ, Brown K, Hnatova S, Howard J, Molnar A, Baulcombe DC. Distinct roles of Argonaute in the green alga Chlamydomonas reveal evolutionary conserved mode of miRNA-mediated gene expression. Sci Rep 2019; 9:11091. [PMID: 31366981 PMCID: PMC6668577 DOI: 10.1038/s41598-019-47415-x] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2019] [Accepted: 07/11/2019] [Indexed: 12/20/2022] Open
Abstract
The unicellular green alga Chlamydomonas reinhardtii is evolutionarily divergent from higher plants, but has a fully functional silencing machinery including microRNA (miRNA)-mediated translation repression and mRNA turnover. However, distinct from the metazoan machinery, repression of gene expression is primarily associated with target sites within coding sequences instead of 3′UTRs. This feature indicates that the miRNA-Argonaute (AGO) machinery is ancient and the primary function is for post transcriptional gene repression and intermediate between the mechanisms in the rest of the plant and animal kingdoms. Here, we characterize AGO2 and 3 in Chlamydomonas, and show that cytoplasmically enriched Cr-AGO3 is responsible for endogenous miRNA-mediated gene repression. Under steady state, mid-log phase conditions, Cr-AGO3 binds predominantly miR-C89, which we previously identified as the predominant miRNA with effects on both translation repression and mRNA turnover. In contrast, the paralogue Cr-AGO2 is nuclear enriched and exclusively binds to 21-nt siRNAs. Further analysis of the highly similar Cr-AGO2 and Cr-AGO 3 sequences (90% amino acid identity) revealed a glycine-arginine rich N-terminal extension of ~100 amino acids that, given previous work on unicellular protists, may associate AGO with the translation machinery. Phylogenetic analysis revealed that this glycine-arginine rich N-terminal extension is present outside the animal kingdom and is highly conserved, consistent with our previous proposal that miRNA-mediated CDS-targeting operates in this green alga.
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Affiliation(s)
- Betty Y-W Chung
- Department of Plant Sciences, University of Cambridge, Cambridge, CB2 3EA, United Kingdom. .,Department of Pathology, University of Cambridge, Cambridge, CB2 1QP, United Kingdom.
| | - Adrian Valli
- Department of Plant Sciences, University of Cambridge, Cambridge, CB2 3EA, United Kingdom.,Department of Plant Molecular Genetics, Spanish National Centre for Biotechnology, Madrid, 28049, Spain
| | - Michael J Deery
- Cambridge System Biology Centre and Department of Biochemistry, University of Cambridge, Cambridge, CB2 1GA, United Kingdom
| | - Francisco J Navarro
- Department of Plant Sciences, University of Cambridge, Cambridge, CB2 3EA, United Kingdom
| | - Katherine Brown
- Department of Pathology, University of Cambridge, Cambridge, CB2 1QP, United Kingdom
| | - Silvia Hnatova
- Department of Plant Sciences, University of Cambridge, Cambridge, CB2 3EA, United Kingdom
| | - Julie Howard
- Cambridge System Biology Centre and Department of Biochemistry, University of Cambridge, Cambridge, CB2 1GA, United Kingdom
| | - Attila Molnar
- Institute of Molecular Plant Sciences, University of Edinburgh, Edinburgh, EH9 3BF, United Kingdom
| | - David C Baulcombe
- Department of Plant Sciences, University of Cambridge, Cambridge, CB2 3EA, United Kingdom.
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9
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Affiliation(s)
- David C Baulcombe
- Department of Plant Science University of CambridgeCambridge CB2 3EA, United Kingdom
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10
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Abstract
MicroRNAs (miRNAs), small RNA molecules of 20-24 nts, have many features that make them useful tools for gene expression regulation-small size, flexible design, target predictability, and action at a late stage of the gene expression pipeline. In addition, their role in fine-tuning gene expression can be harnessed to increase robustness of synthetic gene networks. In this work, we apply a synthetic biology approach to characterize miRNA-mediated gene expression regulation in the unicellular green alga Chlamydomonas reinhardtii. This characterization is then used to build tools based on miRNAs, such as synthetic miRNAs, miRNA-responsive 3'UTRs, miRNA decoys, and self-regulatory loops. These tools will facilitate the engineering of gene expression for new applications and improved traits in this alga.
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Affiliation(s)
- Francisco J. Navarro
- Department of Plant Sciences, University of Cambridge, Cambridge CB2 3EA, United Kingdom
| | - David C. Baulcombe
- Department of Plant Sciences, University of Cambridge, Cambridge CB2 3EA, United Kingdom
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11
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Crozet P, Navarro FJ, Willmund F, Mehrshahi P, Bakowski K, Lauersen KJ, Pérez-Pérez ME, Auroy P, Gorchs Rovira A, Sauret-Gueto S, Niemeyer J, Spaniol B, Theis J, Trösch R, Westrich LD, Vavitsas K, Baier T, Hübner W, de Carpentier F, Cassarini M, Danon A, Henri J, Marchand CH, de Mia M, Sarkissian K, Baulcombe DC, Peltier G, Crespo JL, Kruse O, Jensen PE, Schroda M, Smith AG, Lemaire SD. Birth of a Photosynthetic Chassis: A MoClo Toolkit Enabling Synthetic Biology in the Microalga Chlamydomonas reinhardtii. ACS Synth Biol 2018; 7:2074-2086. [PMID: 30165733 DOI: 10.1021/acssynbio.8b00251] [Citation(s) in RCA: 122] [Impact Index Per Article: 20.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
Microalgae are regarded as promising organisms to develop innovative concepts based on their photosynthetic capacity that offers more sustainable production than heterotrophic hosts. However, to realize their potential as green cell factories, a major challenge is to make microalgae easier to engineer. A promising approach for rapid and predictable genetic manipulation is to use standardized synthetic biology tools and workflows. To this end we have developed a Modular Cloning toolkit for the green microalga Chlamydomonas reinhardtii. It is based on Golden Gate cloning with standard syntax, and comprises 119 openly distributed genetic parts, most of which have been functionally validated in several strains. It contains promoters, UTRs, terminators, tags, reporters, antibiotic resistance genes, and introns cloned in various positions to allow maximum modularity. The toolkit enables rapid building of engineered cells for both fundamental research and algal biotechnology. This work will make Chlamydomonas the next chassis for sustainable synthetic biology.
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Affiliation(s)
- Pierre Crozet
- Institut de Biologie Physico-Chimique, UMR 8226, CNRS, Sorbonne Université, Paris, France
| | | | - Felix Willmund
- Department of Biology, Technische Universität Kaiserslautern, Kaiserslautern, 67663, Germany
| | - Payam Mehrshahi
- Department of Plant Sciences, University of Cambridge, Cambridge, CB2 3EA, U.K
| | - Kamil Bakowski
- Copenhagen Plant Science Centre, Department of Plant and Environmental Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Kyle J. Lauersen
- Faculty of Biology, Center for Biotechnology (CeBiTec), Bielefeld University, Bielefeld, 33615, Germany
| | - Maria-Esther Pérez-Pérez
- Instituto de Bioquímica Vegetal y Fotosíntesis, CSIC-Universidad de Sevilla, Sevilla, 41092, Spain
| | - Pascaline Auroy
- Laboratoire de Bioénergétique et Biotechnologie des Bactéries et Microalgues Cadarache, Aix Marseille University, CEA, CNRS, BIAM, Saint Paul-Lez-Durance, France
| | - Aleix Gorchs Rovira
- Department of Plant Sciences, University of Cambridge, Cambridge, CB2 3EA, U.K
| | - Susana Sauret-Gueto
- Department of Plant Sciences, University of Cambridge, Cambridge, CB2 3EA, U.K
| | - Justus Niemeyer
- Department of Biology, Technische Universität Kaiserslautern, Kaiserslautern, 67663, Germany
| | - Benjamin Spaniol
- Department of Biology, Technische Universität Kaiserslautern, Kaiserslautern, 67663, Germany
| | - Jasmine Theis
- Department of Biology, Technische Universität Kaiserslautern, Kaiserslautern, 67663, Germany
| | - Raphael Trösch
- Department of Biology, Technische Universität Kaiserslautern, Kaiserslautern, 67663, Germany
| | - Lisa-Desiree Westrich
- Department of Biology, Technische Universität Kaiserslautern, Kaiserslautern, 67663, Germany
| | - Konstantinos Vavitsas
- Copenhagen Plant Science Centre, Department of Plant and Environmental Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Thomas Baier
- Faculty of Biology, Center for Biotechnology (CeBiTec), Bielefeld University, Bielefeld, 33615, Germany
| | - Wolfgang Hübner
- Biomolecular Photonics, Department of Physics, Bielefeld University, Bielefeld, 33615, Germany
| | - Felix de Carpentier
- Institut de Biologie Physico-Chimique, UMR 8226, CNRS, Sorbonne Université, Paris, France
| | - Mathieu Cassarini
- Institut de Biologie Physico-Chimique, UMR 8226, CNRS, Sorbonne Université, Paris, France
| | - Antoine Danon
- Institut de Biologie Physico-Chimique, UMR 8226, CNRS, Sorbonne Université, Paris, France
| | - Julien Henri
- Institut de Biologie Physico-Chimique, UMR 8226, CNRS, Sorbonne Université, Paris, France
| | - Christophe H. Marchand
- Institut de Biologie Physico-Chimique, UMR 8226, CNRS, Sorbonne Université, Paris, France
| | - Marcello de Mia
- Institut de Biologie Physico-Chimique, UMR 8226, CNRS, Sorbonne Université, Paris, France
| | - Kevin Sarkissian
- Institut de Biologie Physico-Chimique, UMR 8226, CNRS, Sorbonne Université, Paris, France
| | - David C. Baulcombe
- Department of Plant Sciences, University of Cambridge, Cambridge, CB2 3EA, U.K
| | - Gilles Peltier
- Laboratoire de Bioénergétique et Biotechnologie des Bactéries et Microalgues Cadarache, Aix Marseille University, CEA, CNRS, BIAM, Saint Paul-Lez-Durance, France
| | - José-Luis Crespo
- Instituto de Bioquímica Vegetal y Fotosíntesis, CSIC-Universidad de Sevilla, Sevilla, 41092, Spain
| | - Olaf Kruse
- Faculty of Biology, Center for Biotechnology (CeBiTec), Bielefeld University, Bielefeld, 33615, Germany
| | - Poul-Erik Jensen
- Copenhagen Plant Science Centre, Department of Plant and Environmental Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Michael Schroda
- Department of Biology, Technische Universität Kaiserslautern, Kaiserslautern, 67663, Germany
| | - Alison G. Smith
- Department of Plant Sciences, University of Cambridge, Cambridge, CB2 3EA, U.K
| | - Stéphane D. Lemaire
- Institut de Biologie Physico-Chimique, UMR 8226, CNRS, Sorbonne Université, Paris, France
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12
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Wang Z, Hardcastle TJ, Canto Pastor A, Yip WH, Tang S, Baulcombe DC. A novel DCL2-dependent miRNA pathway in tomato affects susceptibility to RNA viruses. Genes Dev 2018; 32:1155-1160. [PMID: 30150254 PMCID: PMC6120711 DOI: 10.1101/gad.313601.118] [Citation(s) in RCA: 36] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2018] [Accepted: 06/27/2018] [Indexed: 12/19/2022]
Abstract
Wang et al. show that Dicer-like 2 (DCL2) is the major Dicer in tomato defense against tobacco mosaic virus (TMV) and potato virus X (PVX) and that it is involved in the biogenesis of endogenous 22-nt sRNA. Tomato Dicer-like2 (slDCL2) is a key component of resistance pathways against potato virus X (PVX) and tobacco mosaic virus (TMV). It is also required for production of endogenous small RNAs, including miR6026 and other noncanonical microRNAs (miRNAs). The slDCL2 mRNAs are targets of these slDCL2-dependent RNAs in a feedback loop that was disrupted by target mimic RNAs of miR6026. In lines expressing these RNAs, there was correspondingly enhanced resistance against PVX and TMV. These findings illustrate a novel miRNA pathway in plants and a crop protection strategy in which miRNA target mimicry elevates expression of defense-related mRNAs.
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Affiliation(s)
- Zhengming Wang
- Department of Plant Sciences, University of Cambridge, Cambridge, CB2 3EA, United Kingdom
| | - Thomas J Hardcastle
- Department of Plant Sciences, University of Cambridge, Cambridge, CB2 3EA, United Kingdom
| | - Alex Canto Pastor
- Department of Plant Sciences, University of Cambridge, Cambridge, CB2 3EA, United Kingdom
| | - Wing Hin Yip
- Department of Biomedical Sciences, City University of Hong Kong, Hong Kong
| | - Shuoya Tang
- Department of Plant Sciences, University of Cambridge, Cambridge, CB2 3EA, United Kingdom
| | - David C Baulcombe
- Department of Plant Sciences, University of Cambridge, Cambridge, CB2 3EA, United Kingdom
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13
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Abstract
Background Freakish and rare or the tip of the iceberg? Both phrases have been used to refer to paramutation, an epigenetic drive that contravenes Mendel’s first law of segregation. Although its underlying mechanisms are beginning to unravel, its understanding relies only on a few examples that may involve transgenes or artificially generated epialleles. Results By using DNA methylation of introgression lines as an indication of past paramutation, we reveal that the paramutation-like properties of the H06 locus in hybrids of Solanum lycopersicum and a range of tomato relatives and cultivars depend on the timing of sRNA production and conform to an RNA-directed mechanism. In addition, by scanning the methylomes of tomato introgression lines for shared regions of differential methylation that are absent in the S. lycopersicum parent, we identify thousands of candidate regions for paramutation-like behaviour. The methylation patterns for a subset of these regions segregate with non Mendelian ratios, consistent with secondary paramutation-like interactions to variable extents depending on the locus. Conclusion Together these results demonstrate that paramutation-like epigenetic interactions are common for natural epialleles in tomato, but vary in timing and penetrance. Electronic supplementary material The online version of this article (10.1186/s12864-018-4590-4) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Quentin Gouil
- Present address: Walter and Eliza Hall Institute of Medical Research, 1G Royal Parade, Parkville, 3052, Australia. .,Department of Plant Sciences, University of Cambridge, Downing Site, Cambridge, CB2 3EA, UK.
| | - David C Baulcombe
- Department of Plant Sciences, University of Cambridge, Downing Site, Cambridge, CB2 3EA, UK.
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14
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Braidwood L, Quito-Avila DF, Cabanas D, Bressan A, Wangai A, Baulcombe DC. Maize chlorotic mottle virus exhibits low divergence between differentiated regional sub-populations. Sci Rep 2018; 8:1173. [PMID: 29352173 PMCID: PMC5775324 DOI: 10.1038/s41598-018-19607-4] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2017] [Accepted: 12/29/2017] [Indexed: 12/01/2022] Open
Abstract
Maize chlorotic mottle virus has been rapidly spreading around the globe over the past decade. The interactions of maize chlorotic mottle virus with Potyviridae viruses causes an aggressive synergistic viral condition - maize lethal necrosis, which can cause total yield loss. Maize production in sub-Saharan Africa, where it is the most important cereal, is threatened by the arrival of maize lethal necrosis. We obtained maize chlorotic mottle virus genome sequences from across East Africa and for the first time from Ecuador and Hawaii, and constructed a phylogeny which highlights the similarity of Chinese to African isolates, and Ecuadorian to Hawaiian isolates. We used a measure of clustering, the adjusted Rand index, to extract region-specific SNPs and coding variation that can be used for diagnostics. The population genetics analysis we performed shows that the majority of sequence diversity is partitioned between populations, with diversity extremely low within China and East Africa.
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Affiliation(s)
- Luke Braidwood
- University of Cambridge, Plant Sciences, Cambridge, CB2 3EA, United Kingdom.
| | - Diego F Quito-Avila
- Centro de Investigaciones Biotecnologicas del Ecuador, Facultad de Ciencias de la Vida, Escuela Superior Politecnica del Litoral, ESPOL, Guayaquil, Ecuador
| | - Darlene Cabanas
- Department of Molecular Biosciences and Bioengineering, University of Hawaii, 3050 Maile Way, Gilmore Hall 310, Honolulu, Hawaii, USA
| | - Alberto Bressan
- Department of Plant and Environmental Protection Sciences, University of Hawaii, 3050 Maile Way, Gilmore Hall 310, Honolulu, Hawaii, USA
- Bayer CropScience LP, R&D Trait Research, 3500 Paramount Parkway, Morrisville, USA
| | - Anne Wangai
- Kenya Agricultural and Livestock Research Organization (KALRO), Nairobi, Kenya
| | - David C Baulcombe
- University of Cambridge, Plant Sciences, Cambridge, CB2 3EA, United Kingdom
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15
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Chung BYW, Deery MJ, Groen AJ, Howard J, Baulcombe DC. Endogenous miRNA in the green alga Chlamydomonas regulates gene expression through CDS-targeting. Nat Plants 2017; 3:787-794. [PMID: 28970560 PMCID: PMC5662147 DOI: 10.1038/s41477-017-0024-6] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/14/2017] [Accepted: 08/31/2017] [Indexed: 05/29/2023]
Abstract
MicroRNAs (miRNAs) are 21-24-nucleotide RNAs present in many eukaryotes that regulate gene expression as part of the RNA-induced silencing complex. The sequence identity of the miRNA provides the specificity to guide the silencing effector Argonaute (AGO) protein to target mRNAs via a base-pairing process 1 . The AGO complex promotes translation repression and/or accelerated decay of this target mRNA 2 . There is overwhelming evidence both in vivo and in vitro that translation repression plays a major role 3-7 . However, there has been controversy about which of these three mechanisms is more significant in vivo, especially when effects of miRNA on endogenous genes cannot be faithfully represented by reporter systems in which, at least in metazoans, the observed repression vastly exceeds that typically observed for endogenous mRNAs 8,9 . Here, we provide a comprehensive global analysis of the evolutionarily distant unicellular green alga Chlamydomonas reinhardtii to quantify the effects of miRNA on protein synthesis and RNA abundance. We show that, similar to metazoan steady-state systems, endogenous miRNAs in Chlamydomonas can regulate gene expression both by destabilization of the mRNA and by translational repression. However, unlike metazoan miRNA where target site utilization localizes mainly to 3' UTRs, in Chlamydomonas utilized target sites lie predominantly within coding regions. These results demonstrate the evolutionarily conserved mode of action for miRNAs, but details of the mechanism diverge between the plant and metazoan kingdoms.
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Affiliation(s)
- Betty Y-W Chung
- Department of Plant Sciences, University of Cambridge, Cambridge, CB2 3EA, UK.
| | - Michael J Deery
- Cambridge System Biology Centre and Department of Biochemistry, University of Cambridge, Cambridge, CB2 1GA, UK
| | - Arnoud J Groen
- Cambridge System Biology Centre and Department of Biochemistry, University of Cambridge, Cambridge, CB2 1GA, UK
| | - Julie Howard
- Cambridge System Biology Centre and Department of Biochemistry, University of Cambridge, Cambridge, CB2 1GA, UK
| | - David C Baulcombe
- Department of Plant Sciences, University of Cambridge, Cambridge, CB2 3EA, UK.
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16
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Harris CJ, Baulcombe DC, Molnar A. Improved Denaturation of Small RNA Duplexes and Its Application for Northern Blotting. Methods Mol Biol 2017; 1580:1-6. [PMID: 28439822 DOI: 10.1007/978-1-4939-6866-4_1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/07/2023]
Abstract
Small RNAs (sRNAs) are short (18-30 nucleotide) noncoding RNA molecules, which control gene expression and pathogen response in eukaryotes. They are associated with and guide nucleases to target nucleic acids by nucleotide base pairing. We found that current techniques for small RNA detection are adversely affected by the presence of complementary RNA. Thus we established FDF-PAGE (fully denaturing formaldehyde polyacrylamide gel electrophoresis), which dramatically improves denaturation efficiency and subsequently the detection of sequestered sRNAs.
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Affiliation(s)
- C Jake Harris
- Department of Plant Sciences, University of Cambridge, Cambridge, UK
| | - David C Baulcombe
- Department of Plant Sciences, University of Cambridge, Cambridge, UK
| | - Attila Molnar
- School of Biological Sciences, University of Edinburgh, Edinburgh, UK.
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17
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Abstract
DNA methylation in plants is traditionally partitioned into CG, CHG and CHH contexts (with H any nucleotide but G). By investigating DNA methylation patterns in trinucleotide contexts in four angiosperm species, we show that such a representation hides spatial and functional partitioning of different methylation pathways and is incomplete. CG methylation (mCG) is largely context-independent whereas, at CHG motifs, there is under-representation of mCCG in pericentric regions of A. thaliana and tomato and throughout the chromosomes of maize and rice. In A. thaliana the biased representation of mCCG in heterochromatin is related to specificities of H3K9 methyltransferase SUVH family members. At CHH motifs there is an over-representation of different variant forms of mCHH that, similarly to mCCG hypomethylation, is partitioned into the pericentric regions of the two dicots but dispersed in the monocot chromosomes. The over-represented mCHH motifs in A. thaliana associate with specific types of transposon including both class I and II elements. At mCHH the contextual bias is due to the involvement of various chromomethyltransferases whereas the context-independent CHH methylation in A. thaliana and tomato is mediated by the RNA-directed DNA methylation process that is most active in the gene-rich euchromatin. This analysis therefore reveals that the sequence context of the methylome of plant genomes is informative about the mechanisms associated with maintenance of methylation and the overlying chromatin structure. Dense cytosine DNA methylation (mC) in eukaryotes is associated with closed chromatin and gene silencing. In plants it is well known that the sequence context of the mC (either mCG, mCHG or mCHH) provides a clue as to which of several mechanisms is involved but now, based on detailed analyses of the DNA methylome in wild type and mutants of four plant species, we reveal that there is additional information in the mC sequence context. Low mCCG and over-representation of mCAA and mCTA or mCAT in A. thaliana and tomato differentiates regions of the chromosomes near the centromere where methylation is dominated by chromomethyltransferases from the chromosome arms in which mCHH is context-independent and predominantly RNA-directed. Rice and maize have similar sequence context-dependent DNA methylation but the corresponding chromosome domains are not spatially separate as in the dicots. The discovery of the subcomponents of plant methylomes based on sequence context will allow greater resolution in past and future analyses of plant methylomes.
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Affiliation(s)
- Quentin Gouil
- Department of Plant Sciences, University of Cambridge, Cambridge, United Kingdom
| | - David C. Baulcombe
- Department of Plant Sciences, University of Cambridge, Cambridge, United Kingdom
- * E-mail:
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18
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Voinnet O, Vain P, Angell S, Baulcombe DC. Systemic Spread of Sequence-Specific Transgene RNA Degradation in Plants Is Initiated by Localized Introduction of Ectopic Promoterless DNA. Cell 2016; 166:779. [PMID: 27471968 DOI: 10.1016/j.cell.2016.07.014] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [What about the content of this article? (0)] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/21/2022]
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19
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20
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Abstract
The sulfurea (sulf) allele is a silent epigenetic variant of a tomato (Solanum lycopersicum) gene affecting pigment production. It is homozygous lethal but, in a heterozygote sulf/+, the wild-type (wt) allele undergoes silencing so that the plants exhibit chlorotic sectors. This transfer of the silenced state between alleles is termed paramutation and is best characterized in maize. To understand the mechanism of paramutation we mapped SULF to the orthologue SLTAB2 of an Arabidopsis gene that, consistent with the pigment deficiency, is involved in the translation of photosystem I. Paramutation of SLTAB2 is linked to an increase in DNA methylation and the production of small interfering RNAs at its promoter. Virus-induced gene silencing of SLTAB2 phenocopies sulf, consistent with the possibility that siRNAs mediate the paramutation of SULFUREA Unlike the maize systems, the paramutagenicity of sulf is not, however, associated with repeated sequences at the region of siRNA production or DNA methylation.
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Affiliation(s)
- Quentin Gouil
- Department of Plant Sciences, University of Cambridge, Cambridge, UK
| | - Ondřej Novák
- Laboratory of Growth Regulators, Centre of the Region Haná for Biotechnological and Agricultural Research, Institute of Experimental Botany AS CR and Faculty of Science of Palacký University, CZ-78371 Olomouc, Czech Republic
| | - David C Baulcombe
- Department of Plant Sciences, University of Cambridge, Cambridge, UK
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21
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Valli AA, Santos BACM, Hnatova S, Bassett AR, Molnar A, Chung BY, Baulcombe DC. Most microRNAs in the single-cell alga Chlamydomonas reinhardtii are produced by Dicer-like 3-mediated cleavage of introns and untranslated regions of coding RNAs. Genome Res 2016; 26:519-29. [PMID: 26968199 PMCID: PMC4817775 DOI: 10.1101/gr.199703.115] [Citation(s) in RCA: 37] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2015] [Accepted: 02/10/2016] [Indexed: 01/20/2023]
Abstract
We describe here a forward genetic screen to investigate the biogenesis, mode of action, and biological function of miRNA-mediated RNA silencing in the model algal species, Chlamydomonas reinhardtii. Among the mutants from this screen, there were three at Dicer-like 3 that failed to produce both miRNAs and siRNAs and others affecting diverse post-biogenesis stages of miRNA-mediated silencing. The DCL3-dependent siRNAs fell into several classes including transposon- and repeat-derived siRNAs as in higher plants. The DCL3-dependent miRNAs differ from those of higher plants, however, in that many of them are derived from mRNAs or from the introns of pre-mRNAs. Transcriptome analysis of the wild-type and dcl3 mutant strains revealed a further difference from higher plants in that the sRNAs are rarely negative switches of mRNA accumulation. The few transcripts that were more abundant in dcl3 mutant strains than in wild-type cells were not due to sRNA-targeted RNA degradation but to direct DCL3 cleavage of miRNA and siRNA precursor structures embedded in the untranslated (and translated) regions of the mRNAs. Our analysis reveals that the miRNA-mediated RNA silencing in C. reinhardtii differs from that of higher plants and informs about the evolution and function of this pathway in eukaryotes.
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Affiliation(s)
- Adrian A Valli
- Department of Plant Sciences, University of Cambridge CB2 3EA, Cambridge CB2 3EA, United Kingdom
| | - Bruno A C M Santos
- Department of Plant Sciences, University of Cambridge CB2 3EA, Cambridge CB2 3EA, United Kingdom
| | - Silvia Hnatova
- Department of Plant Sciences, University of Cambridge CB2 3EA, Cambridge CB2 3EA, United Kingdom
| | - Andrew R Bassett
- Department of Plant Sciences, University of Cambridge CB2 3EA, Cambridge CB2 3EA, United Kingdom
| | - Attila Molnar
- Department of Plant Sciences, University of Cambridge CB2 3EA, Cambridge CB2 3EA, United Kingdom
| | - Betty Y Chung
- Department of Plant Sciences, University of Cambridge CB2 3EA, Cambridge CB2 3EA, United Kingdom
| | - David C Baulcombe
- Department of Plant Sciences, University of Cambridge CB2 3EA, Cambridge CB2 3EA, United Kingdom
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22
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Mingot A, Valli A, Rodamilans B, San León D, Baulcombe DC, García JA, López-Moya JJ. The P1N-PISPO trans-Frame Gene of Sweet Potato Feathery Mottle Potyvirus Is Produced during Virus Infection and Functions as an RNA Silencing Suppressor. J Virol 2016; 90:3543-57. [PMID: 26792740 PMCID: PMC4794657 DOI: 10.1128/jvi.02360-15] [Citation(s) in RCA: 45] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2015] [Accepted: 01/07/2016] [Indexed: 12/31/2022] Open
Abstract
UNLABELLED The positive-sense RNA genome of Sweet potato feathery mottle virus (SPFMV) (genus Potyvirus, family Potyviridae) contains a large open reading frame (ORF) of 3,494 codons translatable as a polyprotein and two embedded shorter ORFs in the -1 frame: PISPO, of 230 codons, and PIPO, of 66 codons, located in the P1 and P3 regions, respectively. PISPO is specific to some sweet potato-infecting potyviruses, while PIPO is present in all potyvirids. In SPFMV these two extra ORFs are preceded by conserved G2A6 motifs. We have shown recently that a polymerase slippage mechanism at these sites could produce transcripts bringing these ORFs in frame with the upstream polyprotein, thus leading to P1N-PISPO and P3N-PIPO products (B. Rodamilans, A. Valli, A. Mingot, D. San Leon, D. B. Baulcombe, J. J. Lopez-Moya, and J.A. Garcia, J Virol 89:6965-6967, 2015, doi:10.1128/JVI.00337-15). Here, we demonstrate by liquid chromatography coupled to mass spectrometry that both P1 and P1N-PISPO are produced during viral infection and coexist in SPFMV-infected Ipomoea batatas plants. Interestingly, transient expression of SPFMV gene products coagroinfiltrated with a reporter gene in Nicotiana benthamiana revealed that P1N-PISPO acts as an RNA silencing suppressor, a role normally associated with HCPro in other potyviruses. Moreover, mutation of WG/GW motifs present in P1N-PISPO abolished its silencing suppression activity, suggesting that the function might require interaction with Argonaute components of the silencing machinery, as was shown for other viral suppressors. Altogether, our results reveal a further layer of complexity of the RNA silencing suppression activity within the Potyviridae family. IMPORTANCE Gene products of potyviruses include P1, HCPro, P3, 6K1, CI, 6K2, VPg/NIaPro, NIb, and CP, all derived from the proteolytic processing of a large polyprotein, and an additional P3N-PIPO product, with the PIPO segment encoded in a different frame within the P3 cistron. In sweet potato feathery mottle virus (SPFMV), another out-of-frame element (PISPO) was predicted within the P1 region. We have shown recently that a polymerase slippage mechanism can generate the transcript variants with extra nucleotides that could be translated into P1N-PISPO and P3N-PIPO. Now, we demonstrate by mass spectrometry analysis that P1N-PISPO is indeed produced in SPFMV-infected plants, in addition to P1. Interestingly, while in other potyviruses the suppressor of RNA silencing is HCPro, we show here that P1N-PISPO exhibited this activity in SPFMV, revealing how the complexity of the gene content could contribute to supply this essential function in members of the Potyviridae family.
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Affiliation(s)
- Ares Mingot
- Center for Research in Agricultural Genomics, CSIC-IRTA-UAB-UB, Cerdanyola del Vallès, Barcelona, Spain
| | - Adrián Valli
- Department of Plant Sciences, University of Cambridge, Cambridge, United Kingdom
| | | | - David San León
- Centro Nacional de Biotecnología CNB, CSIC, Madrid, Spain
| | - David C Baulcombe
- Department of Plant Sciences, University of Cambridge, Cambridge, United Kingdom
| | | | - Juan José López-Moya
- Center for Research in Agricultural Genomics, CSIC-IRTA-UAB-UB, Cerdanyola del Vallès, Barcelona, Spain
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23
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Harris CJ, Baulcombe DC. Chlorophyll Content Assay to Quantify the Level of Necrosis Induced by Different R Gene/Elicitor Combinations after Transient Expression. Bio Protoc 2015; 5:e1670. [PMID: 28748201 DOI: 10.21769/bioprotoc.1670] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/02/2022] Open
Abstract
This assay can be used to rapidly and accurately quantify levels of leaf necrosis induced after transient expression of R genes and elicitor combinations (Harris et al., 2013). It is based on the inverse correlation between level of necrosis and chlorophyll content in leaf tissue. It is adapted from the calculations described by (Strain et al., 1971).
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Affiliation(s)
- C Jake Harris
- Plant Sciences Department, Cambridge University, Cambridge, UK
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24
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Brigneti G, Voinnet O, Li WX, Ji LH, Ding SW, Baulcombe DC. Retraction: 'Viral pathogenicity determinants are suppressors of transgene silencing in Nicotiana benthamiana'. EMBO J 2015; 34:2595. [PMID: 26286615 DOI: 10.15252/embj.201570030] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022] Open
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25
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Chung BY, Hardcastle TJ, Jones JD, Irigoyen N, Firth AE, Baulcombe DC, Brierley I. The use of duplex-specific nuclease in ribosome profiling and a user-friendly software package for Ribo-seq data analysis. RNA 2015; 21:1731-45. [PMID: 26286745 PMCID: PMC4574750 DOI: 10.1261/rna.052548.115] [Citation(s) in RCA: 81] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/15/2015] [Accepted: 06/23/2015] [Indexed: 05/19/2023]
Abstract
Ribosome profiling is a technique that permits genome-wide, quantitative analysis of translation and has found broad application in recent years. Here we describe a modified profiling protocol and software package designed to benefit more broadly the translation community in terms of simplicity and utility. The protocol, applicable to diverse organisms, including organelles, is based largely on previously published profiling methodologies, but uses duplex-specific nuclease (DSN) as a convenient, species-independent way to reduce rRNA contamination. We show that DSN-based depletion compares favorably with other commonly used rRNA depletion strategies and introduces little bias. The profiling protocol typically produces high levels of triplet periodicity, facilitating the detection of coding sequences, including upstream, downstream, and overlapping open reading frames (ORFs) and an alternative ribosome conformation evident during termination of protein synthesis. In addition, we provide a software package that presents a set of methods for parsing ribosomal profiling data from multiple samples, aligning reads to coding sequences, inferring alternative ORFs, and plotting average and transcript-specific aspects of the data. Methods are also provided for extracting the data in a form suitable for differential analysis of translation and translational efficiency.
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Affiliation(s)
- Betty Y Chung
- Department of Plant Sciences, University of Cambridge, Cambridge CB2 3EA, United Kingdom
| | - Thomas J Hardcastle
- Department of Plant Sciences, University of Cambridge, Cambridge CB2 3EA, United Kingdom
| | - Joshua D Jones
- Division of Virology, Department of Pathology, University of Cambridge, Cambridge CB2 1QP, United Kingdom
| | - Nerea Irigoyen
- Division of Virology, Department of Pathology, University of Cambridge, Cambridge CB2 1QP, United Kingdom
| | - Andrew E Firth
- Division of Virology, Department of Pathology, University of Cambridge, Cambridge CB2 1QP, United Kingdom
| | - David C Baulcombe
- Department of Plant Sciences, University of Cambridge, Cambridge CB2 3EA, United Kingdom
| | - Ian Brierley
- Division of Virology, Department of Pathology, University of Cambridge, Cambridge CB2 1QP, United Kingdom
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26
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Patron NJ, Orzaez D, Marillonnet S, Warzecha H, Matthewman C, Youles M, Raitskin O, Leveau A, Farré G, Rogers C, Smith A, Hibberd J, Webb AAR, Locke J, Schornack S, Ajioka J, Baulcombe DC, Zipfel C, Kamoun S, Jones JDG, Kuhn H, Robatzek S, Van Esse HP, Sanders D, Oldroyd G, Martin C, Field R, O'Connor S, Fox S, Wulff B, Miller B, Breakspear A, Radhakrishnan G, Delaux PM, Loqué D, Granell A, Tissier A, Shih P, Brutnell TP, Quick WP, Rischer H, Fraser PD, Aharoni A, Raines C, South PF, Ané JM, Hamberger BR, Langdale J, Stougaard J, Bouwmeester H, Udvardi M, Murray JAH, Ntoukakis V, Schäfer P, Denby K, Edwards KJ, Osbourn A, Haseloff J. Standards for plant synthetic biology: a common syntax for exchange of DNA parts. New Phytol 2015; 208:13-9. [PMID: 26171760 DOI: 10.1111/nph.13532] [Citation(s) in RCA: 159] [Impact Index Per Article: 17.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/02/2023]
Abstract
Inventors in the field of mechanical and electronic engineering can access multitudes of components and, thanks to standardization, parts from different manufacturers can be used in combination with each other. The introduction of BioBrick standards for the assembly of characterized DNA sequences was a landmark in microbial engineering, shaping the field of synthetic biology. Here, we describe a standard for Type IIS restriction endonuclease-mediated assembly, defining a common syntax of 12 fusion sites to enable the facile assembly of eukaryotic transcriptional units. This standard has been developed and agreed by representatives and leaders of the international plant science and synthetic biology communities, including inventors, developers and adopters of Type IIS cloning methods. Our vision is of an extensive catalogue of standardized, characterized DNA parts that will accelerate plant bioengineering.
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Affiliation(s)
- Nicola J Patron
- The Sainsbury Laboratory, Norwich Research Park, Norwich, NR4 7RG, UK
- OpenPlant Consortium: The University of Cambridge, The John Innes Centre and The Sainsbury Laboratory, Norwich, NR4 7UH, UK
| | - Diego Orzaez
- Instituto de Biología Molecular y Celular de Plantas (IBMCP), Consejo Superior de Investigaciones Científicas, Universidad Politécnica de Valencia, Avda Tarongers SN, Valencia, Spain
| | | | - Heribert Warzecha
- Plant Biotechnology and Metabolic Engineering, Technische Universität Darmstadt, Schnittspahnstrasse 4, Darmstadt 64287, Germany
| | - Colette Matthewman
- OpenPlant Consortium: The University of Cambridge, The John Innes Centre and The Sainsbury Laboratory, Norwich, NR4 7UH, UK
- The John Innes Centre, Norwich Research Park, Norwich, NR4 7UH, UK
| | - Mark Youles
- The Sainsbury Laboratory, Norwich Research Park, Norwich, NR4 7RG, UK
| | - Oleg Raitskin
- The Sainsbury Laboratory, Norwich Research Park, Norwich, NR4 7RG, UK
- OpenPlant Consortium: The University of Cambridge, The John Innes Centre and The Sainsbury Laboratory, Norwich, NR4 7UH, UK
| | - Aymeric Leveau
- The John Innes Centre, Norwich Research Park, Norwich, NR4 7UH, UK
| | - Gemma Farré
- The John Innes Centre, Norwich Research Park, Norwich, NR4 7UH, UK
| | - Christian Rogers
- The John Innes Centre, Norwich Research Park, Norwich, NR4 7UH, UK
| | - Alison Smith
- OpenPlant Consortium: The University of Cambridge, The John Innes Centre and The Sainsbury Laboratory, Norwich, NR4 7UH, UK
- Department of Plant Sciences, University of Cambridge, Downing Street, Cambridge, CB2 3EA, UK
| | - Julian Hibberd
- OpenPlant Consortium: The University of Cambridge, The John Innes Centre and The Sainsbury Laboratory, Norwich, NR4 7UH, UK
- Department of Plant Sciences, University of Cambridge, Downing Street, Cambridge, CB2 3EA, UK
| | - Alex A R Webb
- OpenPlant Consortium: The University of Cambridge, The John Innes Centre and The Sainsbury Laboratory, Norwich, NR4 7UH, UK
- Department of Plant Sciences, University of Cambridge, Downing Street, Cambridge, CB2 3EA, UK
| | - James Locke
- OpenPlant Consortium: The University of Cambridge, The John Innes Centre and The Sainsbury Laboratory, Norwich, NR4 7UH, UK
- The Sainsbury Laboratory, Cambridge University, Bateman Street, Cambridge, CB2 1LR, UK
| | - Sebastian Schornack
- OpenPlant Consortium: The University of Cambridge, The John Innes Centre and The Sainsbury Laboratory, Norwich, NR4 7UH, UK
- The Sainsbury Laboratory, Cambridge University, Bateman Street, Cambridge, CB2 1LR, UK
| | - Jim Ajioka
- OpenPlant Consortium: The University of Cambridge, The John Innes Centre and The Sainsbury Laboratory, Norwich, NR4 7UH, UK
- Department of Pathology, University of Cambridge, Tennis Court Road, Cambridge, CB2 1QP, UK
| | - David C Baulcombe
- OpenPlant Consortium: The University of Cambridge, The John Innes Centre and The Sainsbury Laboratory, Norwich, NR4 7UH, UK
- Department of Plant Sciences, University of Cambridge, Downing Street, Cambridge, CB2 3EA, UK
| | - Cyril Zipfel
- The Sainsbury Laboratory, Norwich Research Park, Norwich, NR4 7RG, UK
| | - Sophien Kamoun
- The Sainsbury Laboratory, Norwich Research Park, Norwich, NR4 7RG, UK
| | | | - Hannah Kuhn
- The Sainsbury Laboratory, Norwich Research Park, Norwich, NR4 7RG, UK
| | - Silke Robatzek
- The Sainsbury Laboratory, Norwich Research Park, Norwich, NR4 7RG, UK
| | - H Peter Van Esse
- The Sainsbury Laboratory, Norwich Research Park, Norwich, NR4 7RG, UK
| | - Dale Sanders
- OpenPlant Consortium: The University of Cambridge, The John Innes Centre and The Sainsbury Laboratory, Norwich, NR4 7UH, UK
- The John Innes Centre, Norwich Research Park, Norwich, NR4 7UH, UK
| | - Giles Oldroyd
- OpenPlant Consortium: The University of Cambridge, The John Innes Centre and The Sainsbury Laboratory, Norwich, NR4 7UH, UK
- The John Innes Centre, Norwich Research Park, Norwich, NR4 7UH, UK
| | - Cathie Martin
- OpenPlant Consortium: The University of Cambridge, The John Innes Centre and The Sainsbury Laboratory, Norwich, NR4 7UH, UK
- The John Innes Centre, Norwich Research Park, Norwich, NR4 7UH, UK
| | - Rob Field
- OpenPlant Consortium: The University of Cambridge, The John Innes Centre and The Sainsbury Laboratory, Norwich, NR4 7UH, UK
- The John Innes Centre, Norwich Research Park, Norwich, NR4 7UH, UK
| | - Sarah O'Connor
- OpenPlant Consortium: The University of Cambridge, The John Innes Centre and The Sainsbury Laboratory, Norwich, NR4 7UH, UK
- The John Innes Centre, Norwich Research Park, Norwich, NR4 7UH, UK
| | - Samantha Fox
- The John Innes Centre, Norwich Research Park, Norwich, NR4 7UH, UK
| | - Brande Wulff
- The John Innes Centre, Norwich Research Park, Norwich, NR4 7UH, UK
| | - Ben Miller
- The John Innes Centre, Norwich Research Park, Norwich, NR4 7UH, UK
| | - Andy Breakspear
- The John Innes Centre, Norwich Research Park, Norwich, NR4 7UH, UK
| | | | | | - Dominique Loqué
- Physical Biosciences Division, Lawrence Berkeley National Laboratory, Berkeley, CA, 94720, USA
- Joint BioEnergy Institute, EmeryStation East, 5885 Hollis St, 4th Floor, Emeryville, CA, 94608, USA
| | - Antonio Granell
- Instituto de Biología Molecular y Celular de Plantas (IBMCP), Consejo Superior de Investigaciones Científicas, Universidad Politécnica de Valencia, Avda Tarongers SN, Valencia, Spain
| | - Alain Tissier
- Leibniz-Institut für Pflanzenbiochemie, Weinberg 3, 06120, Halle (Saale), Germany
| | - Patrick Shih
- Physical Biosciences Division, Lawrence Berkeley National Laboratory, Berkeley, CA, 94720, USA
| | | | - W Paul Quick
- Department of Animal and Plant Sciences, University of Sheffield, Sheffield, S10 2TN, UK
| | - Heiko Rischer
- VTT Technical Research Centre of Finland, Espoo 02044, Finland
| | - Paul D Fraser
- School of Biological Sciences, Royal Holloway, University of London, Egham Hill, Egham, TW20 0EX, UK
| | - Asaph Aharoni
- Department of Plant Sciences, Weizmann Institute of Science, Rehovot 76100, Israel
| | - Christine Raines
- School of Biological Sciences, University of Essex, Colchester, CO4 3SQ, UK
| | - Paul F South
- United States Department of Agriculture, Global Change and Photosynthesis Research Unit, ARS 1206 West Gregory Drive, Urbana, IL 61801, USA
| | - Jean-Michel Ané
- Departments of Bacteriology and Agronomy, University of Wisconsin, 1575 Linden Drive, Madison, WI, 53706, USA
| | - Björn R Hamberger
- Biochemistry Laboratory, Department of Plant and Environmental Sciences, University of Copenhagen, Thorvaldsensvej 40, Frederiksberg C, Denmark
| | - Jane Langdale
- Department of Plant Sciences, University of Oxford, Oxford, OX1 3RB, UK
| | - Jens Stougaard
- Centre for Carbohydrate Recognition and Signalling, Department of Molecular Biology and Genetics, Aarhus University, Gustav Wieds Vej 10C, Aarhus, Denmark
| | - Harro Bouwmeester
- Wageningen UR, Wageningen University, Wageningen 6700 AA, the Netherlands
| | - Michael Udvardi
- Plant Biology Division, The Samuel Roberts Noble Foundation, 2510 Sam Noble Parkway, Ardmore, OK 73401, USA
| | - James A H Murray
- School of Biosciences, Sir Martin Evans Building, Cardiff University, Museum Avenue, Cardiff, CF10 3AX, UK
| | - Vardis Ntoukakis
- Warwick Integrative Synthetic Biology Centre and School of Life Sciences, University of Warwick, Coventry, CV4 7AL, UK
| | - Patrick Schäfer
- Warwick Integrative Synthetic Biology Centre and School of Life Sciences, University of Warwick, Coventry, CV4 7AL, UK
| | - Katherine Denby
- Warwick Integrative Synthetic Biology Centre and School of Life Sciences, University of Warwick, Coventry, CV4 7AL, UK
| | - Keith J Edwards
- BrisSynBio, Life Sciences Building, University of Bristol, Tyndall Avenue, Bristol, BS8 1TQ, UK
| | - Anne Osbourn
- OpenPlant Consortium: The University of Cambridge, The John Innes Centre and The Sainsbury Laboratory, Norwich, NR4 7UH, UK
- The John Innes Centre, Norwich Research Park, Norwich, NR4 7UH, UK
| | - Jim Haseloff
- OpenPlant Consortium: The University of Cambridge, The John Innes Centre and The Sainsbury Laboratory, Norwich, NR4 7UH, UK
- Department of Plant Sciences, University of Cambridge, Downing Street, Cambridge, CB2 3EA, UK
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Harris CJ, Molnar A, Müller SY, Baulcombe DC. FDF-PAGE: a powerful technique revealing previously undetected small RNAs sequestered by complementary transcripts. Nucleic Acids Res 2015; 43:7590-9. [PMID: 26071954 PMCID: PMC4551911 DOI: 10.1093/nar/gkv604] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/29/2014] [Revised: 05/22/2015] [Accepted: 05/27/2015] [Indexed: 12/16/2022] Open
Abstract
Small RNAs, between 18nt and 30nt in length, are a diverse class of non-coding RNAs that mediate a range of cellular processes, from gene regulation to pathogen defense. They guide ribonucleoprotein complexes to their target nucleic acids by Watson-Crick base pairing. We report here that current techniques for small RNA detection and library generation are biased by formation of RNA duplexes. To address this problem, we established FDF-PAGE (fully-denaturing formaldehyde polyacrylamide gel electrophoresis) to prevent annealing of sRNAs to their complement. By applying FDF-PAGE, we provide evidence that both strands of viral small RNA are present in near equimolar ratios, indicating that the predominant precursor is a long double-stranded RNA. Comparing non-denaturing conditions to FDF-PAGE uncovered extensive sequestration of miRNAs in model organisms and allowed us to identify candidate small RNAs under the control of competing endogenous RNAs (ceRNAs). By revealing the full repertoire of small RNAs, we can begin to create a better understanding of small RNA mediated interactions.
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Affiliation(s)
- C Jake Harris
- Plant Sciences Department, Cambridge University, Cambridge, CB2 3EA, UK
| | - Attila Molnar
- Plant Sciences Department, Cambridge University, Cambridge, CB2 3EA, UK School of Biological Sciences, Edinburgh University, Edinburgh, EH9 3JH, UK
| | | | - David C Baulcombe
- Plant Sciences Department, Cambridge University, Cambridge, CB2 3EA, UK
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28
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Baulcombe DC. VIGS, HIGS and FIGS: small RNA silencing in the interactions of viruses or filamentous organisms with their plant hosts. Curr Opin Plant Biol 2015; 26:141-6. [PMID: 26247121 DOI: 10.1016/j.pbi.2015.06.007] [Citation(s) in RCA: 78] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/05/2015] [Revised: 05/28/2015] [Accepted: 06/06/2015] [Indexed: 05/21/2023]
Abstract
Recent evidence indicates two-way traffic of silencing RNA between filamentous organisms and their plant hosts. There are also indications that suppressors of RNA silencing are transferred from filamentous organisms into host plant cells where they influence the innate immune system. Here I use virus disease as a template for interpretation of RNA silencing in connection with filamentous organisms and infected plant cells. I propose that host plant interactions of these organisms are influenced by RNA silencing networks in which there are: small interfering RNAs from the host that are transported into the filamentous organism and vice versa; silencing suppressors from the organism that are transported into the host; endogenous small interfering RNAs and micro RNAs that target components of the innate immune system or endogenous suppressors of the innate immune system.
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Affiliation(s)
- David C Baulcombe
- Department of Plant Sciences, University of Cambridge, Downing Street, Cambridge CB2 3EA, UK.
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29
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Abstract
In this article, we review environmentally mediated epigenetic regulation in plants using two case histories. One of these, vernalization, mediates adaptation of plants to different environments and it exemplifies processes that are reset in each generation. The other, virus-induced silencing, involves transgenerationally inherited epigenetic modifications. Heritable epigenetic marks may result in heritable phenotypic variation, influencing fitness, and so be subject to natural selection. However, unlike genetic inheritance, the epigenetic modifications show instability and are influenced by the environment. These two case histories are then compared with other phenomena in plant biology that are likely to represent epigenetic regulation in response to the environment.
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Affiliation(s)
- David C Baulcombe
- Department of Plant Science, University of Cambridge, Cambridge CB2 3EA, United Kingdom
| | - Caroline Dean
- Department of Cell and Developmental Biology, John Innes Centre, Norwich NR4 7UH, United Kingdom
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30
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Du Z, Chen A, Chen W, Westwood JH, Baulcombe DC, Carr JP. Using a viral vector to reveal the role of microRNA159 in disease symptom induction by a severe strain of Cucumber mosaic virus. Plant Physiol 2014; 164:1378-88. [PMID: 24492335 PMCID: PMC3938627 DOI: 10.1104/pp.113.232090] [Citation(s) in RCA: 37] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/05/2013] [Accepted: 01/30/2014] [Indexed: 05/20/2023]
Abstract
In transgenic Arabidopsis (Arabidopsis thaliana), expression of the Cucumber mosaic virus (CMV) 2b silencing suppressor protein from the severe subgroup IA strain Fny disrupted microRNA (miRNA)-regulated development but orthologs from mild subgroup II strains (Q and LS) did not, explaining strain-specific differences in symptom severity. However, it is unknown which miRNAs affected by Fny2b critically affect viral symptoms. Observations that Fny2b-transgenic plants phenocopy microRNA159ab (mir159ab) mutant plants and that Fny2b altered miR159ab-regulated transcript levels suggested a role for miR159ab in elicitation of severe symptoms by Fny-CMV. Using restoration of the normal phenotype in transgenic plants expressing an artificial miRNA as a proof of concept, we developed a LS-CMV-based vector to express sequences mimicking miRNA targets. Expressing a miR159 target mimic sequence using LS-CMV depleted miR159 and induced symptoms resembling those of Fny-CMV. Suppression of Fny-CMV-induced symptoms in plants harboring mutant alleles for the miR159ab targets MYB domain protein33 (MYB33) and MYB65 confirmed the importance of this miRNA in pathogenesis. This study demonstrates the utility of a viral vector to express miRNA target mimics to facilitate functional studies of miRNAs in plants.
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31
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Abstract
Genes encoding plant nucleotide-binding leucine-rich repeat (NB-LRR) proteins confer dominant resistance to diverse pathogens. The wild-type potato NB-LRR protein Rx confers resistance against a single strain of potato virus X (PVX), whereas LRR mutants protect against both a second PVX strain and the distantly related poplar mosaic virus (PopMV). In one of the Rx mutants there was a cost to the broad-spectrum resistance because the response to PopMV was transformed from a mild disease on plants carrying wild-type Rx to a trailing necrosis that killed the plant. To explore the use of secondary mutagenesis to eliminate this cost of broad-spectrum resistance, we performed random mutagenesis of the N-terminal domains of this broad-recognition version of Rx and isolated four mutants with a stronger response against the PopMV coat protein due to enhanced activation sensitivity. These mutations are located close to the nucleotide-binding pocket, a highly conserved structure that likely controls the "switch" between active and inactive NB-LRR conformations. Stable transgenic plants expressing one of these versions of Rx are resistant to the strains of PVX and the PopMV that previously caused trailing necrosis. We conclude from this work that artificial evolution of NB-LRR disease resistance genes in crops can be enhanced by modification of both activation and recognition phases, to both accentuate the positive and eliminate the negative aspects of disease resistance.
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Affiliation(s)
- C. Jake Harris
- Department of Plant Sciences, University of Cambridge, Cambridge CB2 3EA, United Kingdom; and
| | - Erik J. Slootweg
- Laboratory of Nematology, Department of Plant Sciences, Wageningen University, 6708 PB, Wageningen, The Netherlands
| | - Aska Goverse
- Laboratory of Nematology, Department of Plant Sciences, Wageningen University, 6708 PB, Wageningen, The Netherlands
| | - David C. Baulcombe
- Department of Plant Sciences, University of Cambridge, Cambridge CB2 3EA, United Kingdom; and
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32
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Havecker ER, Wallbridge LM, Fedito P, Hardcastle TJ, Baulcombe DC. Metastable differentially methylated regions within Arabidopsis inbred populations are associated with modified expression of non-coding transcripts. PLoS One 2012; 7:e45242. [PMID: 23028873 PMCID: PMC3447930 DOI: 10.1371/journal.pone.0045242] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2012] [Accepted: 08/17/2012] [Indexed: 01/26/2023] Open
Abstract
Individual plants within a population may vary at both genetic and epigenetic levels. The rate of genetic divergence and its underlying mechanisms is well understood. Less is known about the factors contributing to epigenetic divergence among isogenic populations except that, despite the presence of mechanisms that faithfully maintain epigenetic marks, epigenetic differences are more frequent than genetic variation. Epigenetically divergent stretches of isogenic DNA sequence are called epialleles. Currently, it is not clear why certain regions exhibit variable epigenetic status. We identified and characterised two long RNA transcripts with altered expression and DNA methylation in an ago5 mutant. However, further investigation revealed that these changes were not dependent upon AGO5. Rather, the variable transcription of these loci in Arabidopsis mutant and wild-type populations corresponds to spontaneous differential methylated regions (DMRs) or epialleles. These two DMRs are delineated by RNAs which are highly expressed when the DMR is hypomethylated. Furthermore, they control the expression of 5′ transcriptional start site mRNA variants of nearby protein coding genes. Our data support the recent observations that meiotically stable DMRs exist within inbred populations. We further demonstrate that DMR boundaries can be defined by putative non-coding promoter-associated transcripts.
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Affiliation(s)
- Ericka R. Havecker
- Department of Plant Sciences, University of Cambridge, Cambridge, United Kingdom
| | - Laura M. Wallbridge
- Department of Plant Sciences, University of Cambridge, Cambridge, United Kingdom
| | - Paola Fedito
- BIOMAA, University Mediterranea of Reggio Calabria, Reggio Calabria, Italy
| | - Thomas J. Hardcastle
- Department of Plant Sciences, University of Cambridge, Cambridge, United Kingdom
| | - David C. Baulcombe
- Department of Plant Sciences, University of Cambridge, Cambridge, United Kingdom
- * E-mail:
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33
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Shivaprasad PV, Chen HM, Patel K, Bond DM, Santos BA, Baulcombe DC. A microRNA superfamily regulates nucleotide binding site-leucine-rich repeats and other mRNAs. Plant Cell 2012; 24:859-74. [PMID: 22408077 PMCID: PMC3336131 DOI: 10.1105/tpc.111.095380] [Citation(s) in RCA: 461] [Impact Index Per Article: 38.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/29/2011] [Revised: 02/16/2012] [Accepted: 02/22/2012] [Indexed: 05/18/2023]
Abstract
Analysis of tomato (Solanum lycopersicum) small RNA data sets revealed the presence of a regulatory cascade affecting disease resistance. The initiators of the cascade are microRNA members of an unusually diverse superfamily in which miR482 and miR2118 are prominent members. Members of this superfamily are variable in sequence and abundance in different species, but all variants target the coding sequence for the P-loop motif in the mRNA sequences for disease resistance proteins with nucleotide binding site (NBS) and leucine-rich repeat (LRR) motifs. We confirm, using transient expression in Nicotiana benthamiana, that miR482 targets mRNAs for NBS-LRR disease resistance proteins with coiled-coil domains at their N terminus. The targeting causes mRNA decay and production of secondary siRNAs in a manner that depends on RNA-dependent RNA polymerase 6. At least one of these secondary siRNAs targets other mRNAs of a defense-related protein. The miR482-mediated silencing cascade is suppressed in plants infected with viruses or bacteria so that expression of mRNAs with miR482 or secondary siRNA target sequences is increased. We propose that this process allows pathogen-inducible expression of NBS-LRR proteins and that it contributes to a novel layer of defense against pathogen attack.
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34
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Shivaprasad PV, Dunn RM, Santos BA, Bassett A, Baulcombe DC. Extraordinary transgressive phenotypes of hybrid tomato are influenced by epigenetics and small silencing RNAs. EMBO J 2011; 31:257-66. [PMID: 22179699 DOI: 10.1038/emboj.2011.458] [Citation(s) in RCA: 137] [Impact Index Per Article: 10.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2011] [Accepted: 11/16/2011] [Indexed: 01/06/2023] Open
Abstract
Hybrid organisms may fail to develop, be sterile or they may be more vigorous than either of the parents. Examples of hybrid vigour or hybrid necrosis in the F1 are often not inherited stably in subsequent generations if they are associated with overdominance. There can also be transgressive phenotypes that are inherited stably in these later generations, but the underlying mechanisms are not well understood. Here we have investigated the possibility that stable transgressive phenotypes in the progeny of crosses between cultivated tomato (Solanum lycopersicum cv. M82) and a wild relative (Solanum pennellii, accession LA716) are associated with micro or small interfering(si) RNAs. We identified loci from which these small(s)RNAs were more abundant in hybrids than in either parent and we show that accumulation of such transgressive sRNAs correlated with suppression of the corresponding target genes. In one instance this effect was associated with hypermethylation of the corresponding genomic DNA. Our results illustrate a potential role of transgressive sRNAs in plant breeding and in natural evolution with wild plants.
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35
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Abstract
MOTIVATION Small interfering RNAs (siRNAs) are produced from much longer sequences of double-stranded RNA precursors through cleavage by Dicer or a Dicer-like protein. These small RNAs play a key role in genetic and epigenetic regulation; however, a full understanding of the mechanisms by which they operate depends on the characterization of the precursors from which they are derived. RESULTS High-throughput sequencing of small RNA populations allows the locations of the double-stranded RNA precursors to be inferred. We have developed methods to analyse small RNA sequencing data from multiple biological sources, taking into account replicate information, to identify robust sets of siRNA precursors. Our methods show good performance on both a set of small RNA sequencing data in Arabidopsis thaliana and simulated datasets. AVAILABILITY Our methods are available as the Bioconductor (www.bioconductor.org) package segmentSeq (version 1.5.6 and above).
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Affiliation(s)
- Thomas J Hardcastle
- Department of Plant Sciences, University of Cambridge, Cambridge CB2 3EA, UK.
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36
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Mosher RA, Tan EH, Shin J, Fischer RL, Pikaard CS, Baulcombe DC. An atypical epigenetic mechanism affects uniparental expression of Pol IV-dependent siRNAs. PLoS One 2011; 6:e25756. [PMID: 22003406 PMCID: PMC3189211 DOI: 10.1371/journal.pone.0025756] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2011] [Accepted: 09/11/2011] [Indexed: 12/29/2022] Open
Abstract
Background Small RNAs generated by RNA polymerase IV (Pol IV) are the most abundant class of small RNAs in flowering plants. In Arabidopsis thaliana Pol IV-dependent short interfering (p4-si)RNAs are imprinted and accumulate specifically from maternal chromosomes in the developing seeds. Imprinted expression of protein-coding genes is controlled by differential DNA or histone methylation placed in gametes. To identify epigenetic factors required for maternal-specific expression of p4-siRNAs we analyzed the effect of a series of candidate mutations, including those required for genomic imprinting of protein-coding genes, on uniparental expression of a representative p4-siRNA locus. Results Paternal alleles of imprinted genes are marked by DNA or histone methylation placed by DNA METHYLTRANSFERASE 1 or the Polycomb Repressive Complex 2. Here we demonstrate that repression of paternal p4-siRNA expression at locus 08002 is not controlled by either of these mechanisms. Similarly, loss of several chromatin modification enzymes, including a histone acetyltransferase, a histone methyltransferase, and two nucleosome remodeling proteins, does not affect maternal expression of locus 08002. Maternal alleles of imprinted genes are hypomethylated by DEMETER DNA glycosylase, yet expression of p4-siRNAs occurs irrespective of demethylation by DEMETER or related glycosylases. Conclusions Differential DNA methylation and other chromatin modifications associated with epigenetic silencing are not required for maternal-specific expression of p4-siRNAs at locus 08002. These data indicate that there is an as yet unknown epigenetic mechanism causing maternal-specific p4-siRNA expression that is distinct from the well-characterized mechanisms associated with DNA methylation or the Polycomb Repressive Complex 2.
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Affiliation(s)
- Rebecca A Mosher
- Department of Plant Sciences, University of Cambridge, Cambridge, United Kingdom.
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37
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Melnyk CW, Molnar A, Bassett A, Baulcombe DC. Mobile 24 nt small RNAs direct transcriptional gene silencing in the root meristems of Arabidopsis thaliana. Curr Biol 2011; 21:1678-83. [PMID: 21962713 DOI: 10.1016/j.cub.2011.08.065] [Citation(s) in RCA: 97] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2011] [Revised: 08/01/2011] [Accepted: 08/31/2011] [Indexed: 12/12/2022]
Abstract
RNA silencing in flowering plants generates a signal that moves between cells and through the phloem [1, 2]. Nucleotide sequence specificity of the signal is conferred by 21, 22, and 24 nucleotide (nt) sRNAs that are generated by Dicer-like (DCL) proteins [3]. In the recipient cells these sRNAs bind to Argonaute (AGO) effectors of silencing and the 21 nt sRNAs mediate posttranscriptional regulation (PTGS) via mRNA cleavage [4] whereas the 24 nt sRNAs are associated with RNA-dependent DNA methylation (RdDM) [5] that may underlie transcriptional gene silencing (TGS). Intriguingly, genes involved in TGS are required for graft-transmissible gene silencing associated with PTGS [6]. However, some of the same genes were also required for spread of a PTGS silencing signal out of the veins of Arabidopsis [7], and grafting tests failed to demonstrate direct transmission of TGS signals [8-10]. It seemed likely, therefore, that mobile silencing is associated only with PTGS. To address this possibility, we grafted TGS-inducing wild-type Arabidopsis and a mutant that is compromised in 24 nt sRNA production onto a wild-type reporter line. The 21-24 nt sRNAs from the TGS construct were transmitted across a graft union but only the 24 nt sRNAs directed RdDM and TGS of a transgene promoter in meristematic cells. These data extend the significance of an RNA silencing signal to embrace epigenetics and transcriptional gene silencing and support the hypothesis that these signals transmit information to meristematic cells where they initiate persistent epigenetic changes that may influence growth, development, and heritable phenotypes.
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Affiliation(s)
- Charles W Melnyk
- Department of Plant Sciences, University of Cambridge, Cambridge CB2 3EA, UK
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38
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Melnyk CW, Molnar A, Baulcombe DC. Intercellular and systemic movement of RNA silencing signals. EMBO J 2011; 30:3553-63. [PMID: 21878996 DOI: 10.1038/emboj.2011.274] [Citation(s) in RCA: 204] [Impact Index Per Article: 15.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2011] [Accepted: 07/19/2011] [Indexed: 12/17/2022] Open
Abstract
In most eukaryotes, double-stranded RNA is processed into small RNAs that are potent regulators of gene expression. This gene silencing process is known as RNA silencing or RNA interference (RNAi) and, in plants and nematodes, it is associated with the production of a mobile signal that can travel from cell-to-cell and over long distances. The sequence-specific nature of systemic RNA silencing indicates that a nucleic acid is a component of the signalling complex. Recent work has shed light on the mobile RNA species, the genes involved in the production and transport of the signal. This review discusses the advances in systemic RNAi and presents the current challenges and questions in this rapidly evolving field.
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Abstract
BACKGROUND Argonaute (AGO) proteins bind to small-interfering (si)RNAs and micro (mi)RNAs to target RNA silencing against viruses, transgenes and in regulation of mRNAs. Plants encode multiple AGO proteins but, in Arabidopsis, only AGO1 is known to have an antiviral role. METHODOLOGY/PRINCIPAL FINDINGS To uncover the roles of specific AGOs in limiting virus accumulation we inoculated turnip crinkle virus (TCV) to Arabidopsis plants that were mutant for each of the ten AGO genes. The viral symptoms on most of the plants were the same as on wild type plants although the ago2 mutants were markedly hyper-susceptible to this virus. ago2 plants were also hyper-susceptible to cucumber mosaic virus (CMV), confirming that the antiviral role of AGO2 is not specific to a single virus. For both viruses, this phenotype was associated with transient increase in virus accumulation. In wild type plants the AGO2 protein was induced by TCV and CMV infection. CONCLUSIONS/SIGNIFICANCE Based on these results we propose that there are multiple layers to RNA-mediated defense and counter-defense in the interactions between plants and their viruses. AGO1 represents a first layer. With some viruses, including TCV and CMV, this layer is overcome by viral suppressors of silencing that can target AGO1 and a second layer involving AGO2 limits virus accumulation. The second layer is activated when the first layer is suppressed because AGO2 is repressed by AGO1 via miR403. The activation of the second layer is therefore a direct consequence of the loss of the first layer of defense.
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Affiliation(s)
- Jagger J. W. Harvey
- Department of Plant Sciences, University of Cambridge, Cambridge, United Kingdom
| | - Mathew G. Lewsey
- Department of Plant Sciences, University of Cambridge, Cambridge, United Kingdom
| | - Kanu Patel
- Department of Plant Sciences, University of Cambridge, Cambridge, United Kingdom
| | - Jack Westwood
- Department of Plant Sciences, University of Cambridge, Cambridge, United Kingdom
| | - Susanne Heimstädt
- Department of Plant Sciences, University of Cambridge, Cambridge, United Kingdom
| | - John P. Carr
- Department of Plant Sciences, University of Cambridge, Cambridge, United Kingdom
| | - David C. Baulcombe
- Department of Plant Sciences, University of Cambridge, Cambridge, United Kingdom
- * E-mail:
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40
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Abstract
Recent research shows that short RNA molecules act as mobile signals that direct mRNA cleavage and DNA methylation in recipient cells.
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Affiliation(s)
- Attila Molnar
- Department of Plant Sciences, University of Cambridge, Cambridge CB2 3EA, UK.
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41
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Molnar A, Melnyk C, Baulcombe DC. Silencing signals in plants: a long journey for small RNAs. Genome Biol 2011. [PMID: 21235831 DOI: 10.1186/gb-2010-ll-12-219] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/07/2023] Open
Abstract
Recent research shows that short RNA molecules act as mobile signals that direct mRNA cleavage and DNA methylation in recipient cells.
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Affiliation(s)
- Attila Molnar
- Department of Plant Sciences, University of Cambridge, Cambridge CB2 3EA, UK.
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42
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Chiu MH, Chen IH, Baulcombe DC, Tsai CH. The silencing suppressor P25 of Potato virus X interacts with Argonaute1 and mediates its degradation through the proteasome pathway. Mol Plant Pathol 2010; 11:641-9. [PMID: 20696002 PMCID: PMC6640501 DOI: 10.1111/j.1364-3703.2010.00634.x] [Citation(s) in RCA: 90] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/18/2023]
Abstract
Previous evidence has indicated that the P25 protein encoded by Potato virus X (PVX) inhibits either the assembly or function of the effector complexes in the RNA silencing-based antiviral defence system (Bayne et al., Cell-to-cell movement of Potato Potexvirus X is dependent on suppression of RNA silencing. Plant J.44, 471-482). This finding prompted us to investigate the possibility that P25 targets the Argonaute (AGO) effector nuclease of RNA silencing. Co-immunoprecipitation and Western blot analysis indicated that there is a strong interaction between P25 and AGO1 of Arabidopsis when these proteins are transiently co-expressed in Nicotiana benthamiana. P25 also interacts with AGO1, AGO2, AGO3 and AGO4, but not with AGO5 and AGO9. As an effective suppressor, the amount of AGO1 accumulated in the presence of P25 was dramatically lower than that infiltrated with HcPro, but was restored when treated with a proteasome inhibitor MG132. These findings are consistent with the idea that RNA silencing is an antiviral defence mechanism and that the counter-defence role of P25 is through the degradation of AGO proteins via the proteasome pathway. Further support for this idea is provided by the observation that plants treated with MG132 are less susceptible to PVX and its relative Bamboo mosaic virus.
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Affiliation(s)
- Meng-Hsuen Chiu
- Graduate Institute of Biotechnology, National Chung Hsing University, Taichung, Taiwan
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43
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Abstract
The effect of RNA silencing in plants can be amplified if the production of secondary small interfering RNAs (siRNAs) is triggered by the interaction of microRNAs (miRNAs) or siRNAs with a long target RNA. miRNA and siRNA interactions are not all equivalent, however; most of them do not trigger secondary siRNA production. Here we use bioinformatics to show that the secondary siRNA triggers are miRNAs and transacting siRNAs of 22 nt, rather than the more typical 21-nt length. Agrobacterium-mediated transient expression in Nicotiana benthamiana confirms that the siRNA-initiating miRNAs, miR173 and miR828, are effective as triggers only if expressed in a 22-nt form and, conversely, that increasing the length of miR319 from 21 to 22 nt converts it to an siRNA trigger. We also predicted and validated that the 22-nt miR771 is a secondary siRNA trigger. Our data demonstrate that the function of small RNAs is influenced by size, and that a length of 22 nt facilitates the triggering of secondary siRNA production.
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Affiliation(s)
- Ho-Ming Chen
- Institute of Plant and Microbial Biology, Academia Sinica, Taipei 11529, Taiwan; and
| | - Li-Teh Chen
- Institute of Plant and Microbial Biology, Academia Sinica, Taipei 11529, Taiwan; and
| | - Kanu Patel
- Department of Plant Science, University of Cambridge, Cambridge CB2 3EA, United Kingdom
| | - Yi-Hang Li
- Institute of Plant and Microbial Biology, Academia Sinica, Taipei 11529, Taiwan; and
| | - David C. Baulcombe
- Department of Plant Science, University of Cambridge, Cambridge CB2 3EA, United Kingdom
| | - Shu-Hsing Wu
- Institute of Plant and Microbial Biology, Academia Sinica, Taipei 11529, Taiwan; and
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44
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Searle IR, Pontes O, Melnyk CW, Smith LM, Baulcombe DC. JMJ14, a JmjC domain protein, is required for RNA silencing and cell-to-cell movement of an RNA silencing signal in Arabidopsis. Genes Dev 2010; 24:986-91. [PMID: 20478993 DOI: 10.1101/gad.579910] [Citation(s) in RCA: 87] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
Abstract
JMJ14 is a histone H3 Lys4 (H3K4) trimethyl demethylase that affects mobile RNA silencing in an Arabidopsis transgene system. It also influences CHH DNA methylation, abundance of endogenous transposon transcripts, and flowering time. JMJ14 acts at a point in RNA silencing pathways that is downstream from RNA-dependent RNA polymerase 2 (RDR2) and Argonaute 4 (AGO4). Our results illustrate a link between RNA silencing and demethylation of histone H3 trimethylysine. We propose that JMJ14 acts downstream from the Argonaute effector complex to demethylate histone H3K4 at the target of RNA silencing.
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Affiliation(s)
- Iain R Searle
- Plant Sciences Department, Cambridge University, Cambridge, United Kingdom
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45
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Molnar A, Melnyk CW, Bassett A, Hardcastle TJ, Dunn R, Baulcombe DC. Small silencing RNAs in plants are mobile and direct epigenetic modification in recipient cells. Science 2010; 328:872-5. [PMID: 20413459 DOI: 10.1126/science.1187959] [Citation(s) in RCA: 469] [Impact Index Per Article: 33.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
A silencing signal in plants with an RNA specificity determinant moves through plasmodesmata and the phloem. To identify the mobile RNA, we grafted Arabidopsis thaliana shoots to roots that would be a recipient for the silencing signal. Using mutants that block small RNA (sRNA) biogenesis in either source or recipient tissue, we found that transgene-derived sRNA as well as a substantial proportion of the endogenous sRNA had moved across the graft union, and we provide evidence that 24-nucleotide mobile sRNAs direct epigenetic modifications in the genome of the recipient cells. Mobile sRNA thus represents a mechanism for transmitting the specification of epigenetic modification and could affect genome defense and responses to external stimuli that have persistent effects in plants.
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Affiliation(s)
- Attila Molnar
- Department of Plant Sciences, University of Cambridge, Cambridge CB2 3EA, UK
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MacLean D, Elina N, Havecker ER, Heimstaedt SB, Studholme DJ, Baulcombe DC. Evidence for large complex networks of plant short silencing RNAs. PLoS One 2010; 5:e9901. [PMID: 20360863 PMCID: PMC2845630 DOI: 10.1371/journal.pone.0009901] [Citation(s) in RCA: 35] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2009] [Accepted: 02/26/2010] [Indexed: 11/19/2022] Open
Abstract
BACKGROUND In plants and animals there are many classes of short RNAs that carry out a wide range of functions within the cell; short silencing RNAs (ssRNAs) of 21-25 nucleotides in length are produced from double-stranded RNA precursors by the protein Dicer and guide nucleases and other proteins to their RNA targets through base pairing interactions. The consequence of this process is degradation of the targeted RNA, suppression of its translation or initiation of secondary ssRNA production. The secondary ssRNAs in turn could then initiate further layers of ssRNA production to form extensive cascades and networks of interacting RNA [1]. Previous empirical analysis in plants established the existence of small secondary ssRNA cascade [2], in which a single instance of this event occurred but it was not known whether there are other more extensive networks of secondary sRNA production. METHODOLOGY/PRINCIPAL FINDINGS We generated a network by predicting targets of ssRNA populations obtained from high-throughput sequencing experiments. The topology of the network shows it to have power law connectivity distribution, to be dissortative, highly clustered and composed of multiple components. We also identify protein families, PPR and ULP1, that act as hubs within the network. Comparison of the repetition of genomic sub-sequences of ssRNA length between Arabidopsis and E.coli suggest that the network structure is made possible by the underlying repetitiveness in the genome sequence. CONCLUSIONS/SIGNIFICANCE Together our results provide good evidence for the existence of a large, robust ssRNA interaction network with distinct regulatory function. Such a network could have a massive effect on the regulation of gene expression via mediation of transcript levels.
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Affiliation(s)
- Daniel MacLean
- The Sainsbury Laboratory, John Innes Centre, Norwich, United Kingdom.
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Havecker ER, Wallbridge LM, Hardcastle TJ, Bush MS, Kelly KA, Dunn RM, Schwach F, Doonan JH, Baulcombe DC. The Arabidopsis RNA-directed DNA methylation argonautes functionally diverge based on their expression and interaction with target loci. Plant Cell 2010; 22:321-34. [PMID: 20173091 PMCID: PMC2845420 DOI: 10.1105/tpc.109.072199] [Citation(s) in RCA: 255] [Impact Index Per Article: 18.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/14/2009] [Revised: 12/31/2009] [Accepted: 01/29/2010] [Indexed: 05/18/2023]
Abstract
Argonaute (AGO) effectors of RNA silencing bind small RNA (sRNA) molecules and mediate mRNA cleavage, translational repression, or epigenetic DNA modification. In many organisms, these targeting mechanisms are devolved to different products of AGO multigene families. To investigate the basis of AGO functional diversification, we characterized three closely related Arabidopsis thaliana AGOs (AGO4, AGO6, and AGO9) implicated in RNA-directed DNA methylation. All three AGOs bound 5' adenosine 24-nucleotide sRNAs, but each exhibited different preferences for sRNAs from different heterochromatin-associated loci. This difference was reduced when AGO6 and AGO9 were expressed from the AGO4 promoter, indicating that the functional diversification was partially due to differential expression of the corresponding genes. However, the AGO4-directed pattern of sRNA accumulation and DNA methylation was not fully recapitulated with AGO6 or AGO9 expressed from the AGO4 promoter. Here, we show that sRNA length and 5' nucleotide do not account for the observed functional diversification of these AGOs. Instead, the selectivity of sRNA binding is determined by the coincident expression of the AGO and sRNA-generating loci, and epigenetic modification is influenced by interactions between the AGO protein and the different target loci. These findings highlight the importance of tissue specificity and AGO-associated proteins in influencing epigenetic modifications.
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Affiliation(s)
- Ericka R. Havecker
- Department of Plant Sciences, University of Cambridge, Cambridge CB2 3EA, United Kingdom
| | - Laura M. Wallbridge
- Department of Plant Sciences, University of Cambridge, Cambridge CB2 3EA, United Kingdom
| | - Thomas J. Hardcastle
- Department of Plant Sciences, University of Cambridge, Cambridge CB2 3EA, United Kingdom
| | - Maxwell S. Bush
- Cell and Developmental Biology, John Innes Centre, Norwich NR4 7UH, United Kingdom
| | - Krystyna A. Kelly
- Department of Plant Sciences, University of Cambridge, Cambridge CB2 3EA, United Kingdom
| | - Ruth M. Dunn
- Department of Plant Sciences, University of Cambridge, Cambridge CB2 3EA, United Kingdom
| | - Frank Schwach
- Computing Sciences, University of East Anglia, Norwich NR4 7TJ, United Kingdom
| | - John H. Doonan
- Cell and Developmental Biology, John Innes Centre, Norwich NR4 7UH, United Kingdom
| | - David C. Baulcombe
- Department of Plant Sciences, University of Cambridge, Cambridge CB2 3EA, United Kingdom
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Djupedal I, Kos-Braun IC, Mosher RA, Söderholm N, Simmer F, Hardcastle TJ, Fender A, Heidrich N, Kagansky A, Bayne E, Wagner EGH, Baulcombe DC, Allshire RC, Ekwall K. Analysis of small RNA in fission yeast; centromeric siRNAs are potentially generated through a structured RNA. EMBO J 2010; 28:3832-44. [PMID: 19942857 DOI: 10.1038/emboj.2009.351] [Citation(s) in RCA: 64] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2009] [Accepted: 11/05/2009] [Indexed: 11/09/2022] Open
Abstract
The formation of heterochromatin at the centromeres in fission yeast depends on transcription of the outer repeats. These transcripts are processed into siRNAs that target homologous loci for heterochromatin formation. Here, high throughput sequencing of small RNA provides a comprehensive analysis of centromere-derived small RNAs. We found that the centromeric small RNAs are Dcr1 dependent, carry 5'-monophosphates and are associated with Ago1. The majority of centromeric small RNAs originate from two remarkably well-conserved sequences that are present in all centromeres. The high degree of similarity suggests that this non-coding sequence in itself may be of importance. Consistent with this, secondary structure-probing experiments indicate that this centromeric RNA is partially double-stranded and is processed by Dicer in vitro. We further demonstrate the existence of small centromeric RNA in rdp1Delta cells. Our data suggest a pathway for siRNA generation that is distinct from the well-documented model involving RITS/RDRC. We propose that primary transcripts fold into hairpin-like structures that may be processed by Dcr1 into siRNAs, and that these siRNAs may initiate heterochromatin formation independent of RDRC activity.
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Affiliation(s)
- Ingela Djupedal
- Department of Biosciences and Nutrition, Center for Biosciences, Karolinska Institutet, Sweden/School of Life Sciences, University College Sodertorn, NOVUM, Huddinge, Sweden
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Mosher RA, Melnyk CW, Kelly KA, Dunn RM, Studholme DJ, Baulcombe DC. Uniparental expression of PolIV-dependent siRNAs in developing endosperm of Arabidopsis. Nature 2009; 460:283-6. [PMID: 19494814 DOI: 10.1038/nature08084] [Citation(s) in RCA: 221] [Impact Index Per Article: 14.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2009] [Accepted: 04/21/2009] [Indexed: 11/09/2022]
Abstract
Most eukaryotes produce small RNA (sRNA) mediators of gene silencing that bind to Argonaute proteins and guide them, by base pairing, to an RNA target. MicroRNAs (miRNAs) that normally target messenger RNAs for degradation or translational arrest are the best-understood class of sRNAs. However, in Arabidopsis thaliana flowers, miRNAs account for only 5% of the sRNA mass and less than 0.1% of the sequence complexity. The remaining sRNAs form a complex population of more than 100,000 different small interfering RNAs (siRNAs) transcribed from thousands of loci. The biogenesis of most of the siRNAs in Arabidopsis are dependent on RNA polymerase IV (PolIV), a homologue of DNA-dependent RNA polymerase II. A subset of these PolIV-dependent (p4)-siRNAs are involved in stress responses, and others are associated with epigenetic modifications to DNA or chromatin; however, the biological role is not known for most of them. Here we show that the predominant phase of p4-siRNA accumulation is initiated in the maternal gametophyte and continues during seed development. Expression of p4-siRNAs in developing endosperm is specifically from maternal chromosomes. Our results provide the first evidence for a link between genomic imprinting and RNA silencing in plants.
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Affiliation(s)
- Rebecca A Mosher
- Department of Plant Sciences, University of Cambridge, Downing Street, Cambridge CB2 3EA, UK
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50
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Preuss SB, Costa-Nunes P, Tucker S, Pontes O, Lawrence RJ, Mosher R, Kasschau KD, Carrington JC, Baulcombe DC, Viegas W, Pikaard CS. Multimegabase silencing in nucleolar dominance involves siRNA-directed DNA methylation and specific methylcytosine-binding proteins. Mol Cell 2009; 32:673-84. [PMID: 19061642 DOI: 10.1016/j.molcel.2008.11.009] [Citation(s) in RCA: 117] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2008] [Revised: 10/31/2008] [Accepted: 11/07/2008] [Indexed: 01/01/2023]
Abstract
In genetic hybrids, the silencing of nucleolar rRNA genes inherited from one progenitor is the epigenetic phenomenon known as nucleolar dominance. An RNAi knockdown screen identified the Arabidopsis de novo cytosine methyltransferase, DRM2, and the methylcytosine binding domain proteins, MBD6 and MBD10, as activities required for nucleolar dominance. MBD10 localizes throughout the nucleus, but MBD6 preferentially associates with silenced rRNA genes and does so in a DRM2-dependent manner. DRM2 methylation is thought to be guided by siRNAs whose biogenesis requires RNA-DEPENDENT RNA POLYMERASE 2 (RDR2) and DICER-LIKE 3 (DCL3). Consistent with this hypothesis, knockdown of DCL3 or RDR2 disrupts nucleolar dominance. Collectively, these results indicate that in addition to directing the silencing of retrotransposons and noncoding repeats, siRNAs specify de novo cytosine methylation patterns that are recognized by MBD6 and MBD10 in the large-scale silencing of rRNA gene loci.
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Affiliation(s)
- Sasha B Preuss
- Biology Department, Washington University, St. Louis, MO 63130, USA
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