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Miloro F, Kis A, Havelda Z, Dalmadi Á. Barley AGO4 proteins show overlapping functionality with distinct small RNA-binding properties in heterologous complementation. PLANT CELL REPORTS 2024; 43:96. [PMID: 38480545 PMCID: PMC10937801 DOI: 10.1007/s00299-024-03177-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 01/08/2024] [Accepted: 02/15/2024] [Indexed: 03/17/2024]
Abstract
KEY MESSAGE Barley AGO4 proteins complement expressional changes of epigenetically regulated genes in Arabidopsis ago4-3 mutant and show a distinct affinity for the 5' terminal nucleotide of small RNAs, demonstrating functional conservation and divergence. The function of Argonaute 4 (AGO4) in Arabidopsis thaliana has been extensively characterized; however, its role in monocots, which have large genomes abundantly supplemented with transposable elements (TEs), remains elusive. The study of barley AGO4 proteins can provide insights into the conserved aspects of RNA-directed DNA methylation (RdDM) and could also have further applications in the field of epigenetics or crop improvement. Bioinformatic analysis of RNA sequencing data identified two active AGO4 genes in barley, HvAGO4a and HvAGO4b. These genes function similar to AtAGO4 in an Arabidopsis heterologous complementation system, primarily binding to 24-nucleotide long small RNAs (sRNAs) and triggering methylation at specific target loci. Like AtAGO4, HvAGO4B exhibits a preference for binding sRNAs with 5' adenine residue, while also accepting 5' guanine, uracil, and cytosine residues. In contrast, HvAGO4A selectively binds only sRNAs with a 5' adenine residue. The diverse binding capacity of barley AGO4 proteins is reflected in TE-derived sRNAs and in their varying abundance. Both barley AGO4 proteins effectively restore the levels of extrachromosomal DNA and transcript abundancy of the heat-activated ONSEN retrotransposon to those observed in wild-type Arabidopsis plants. Our study provides insight into the distinct binding specificities and involvement in TE regulation of barley AGO4 proteins in Arabidopsis by heterologous complementation.
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Affiliation(s)
- Fabio Miloro
- Hungarian University of Agriculture and Life Sciences (MATE), Institute of Genetics and Biotechnology, Gödöllő, Hungary
- Agribiotechnology and Precision Breeding for Food Security National Laboratory, Plant Biotechnology Section, Gödöllő, Hungary
| | - András Kis
- Hungarian University of Agriculture and Life Sciences (MATE), Institute of Genetics and Biotechnology, Gödöllő, Hungary
| | - Zoltán Havelda
- Hungarian University of Agriculture and Life Sciences (MATE), Institute of Genetics and Biotechnology, Gödöllő, Hungary
- Agribiotechnology and Precision Breeding for Food Security National Laboratory, Plant Biotechnology Section, Gödöllő, Hungary
| | - Ágnes Dalmadi
- Hungarian University of Agriculture and Life Sciences (MATE), Institute of Genetics and Biotechnology, Gödöllő, Hungary.
- Agribiotechnology and Precision Breeding for Food Security National Laboratory, Plant Biotechnology Section, Gödöllő, Hungary.
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Larson ER, Armstrong EM, Harper H, Knapp S, Edwards KJ, Grierson D, Poppy G, Chase MW, Jones JDG, Bastow R, Jellis G, Barnes S, Temple P, Clarke M, Oldroyd G, Grierson CS. One hundred important questions for plant science - reflecting on a decade of plant research. THE NEW PHYTOLOGIST 2023; 238:464-469. [PMID: 36924326 DOI: 10.1111/nph.18663] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/27/2022] [Accepted: 11/14/2022] [Indexed: 06/18/2023]
Affiliation(s)
- Emily R Larson
- School of Biological Sciences, Bristol University, 24 Tyndall Avenue, Bristol, BS8 1TQ, UK
| | - Emily May Armstrong
- School of Biological Sciences, Bristol University, 24 Tyndall Avenue, Bristol, BS8 1TQ, UK
| | - Helen Harper
- School of Biological Sciences, Bristol University, 24 Tyndall Avenue, Bristol, BS8 1TQ, UK
| | - Sandra Knapp
- Natural History Museum, Cromwell Road, London, SW7 5BD, UK
| | - Keith J Edwards
- School of Biological Sciences, Bristol University, 24 Tyndall Avenue, Bristol, BS8 1TQ, UK
| | - Don Grierson
- School of Biosciences, University of Nottingham, Sutton Bonington Campus, nr Loughborough, LE12 5RD, UK
| | - Guy Poppy
- Biological Sciences, University of Southampton, University Road, Southampton, SO17 1BJ, UK
| | - Mark W Chase
- Department of Environment and Agriculture, Curtin University, Perth, WA, 6845, Australia
- Royal Botanic Gardens Kew, Richmond, London, TW9 3AE, UK
| | | | - Ruth Bastow
- Crop Health and Protection Ltd, York Biotech Campus, Sand Hutton, York, YO41 1LZ, UK
| | - Graham Jellis
- Agrifood Charities Partnership, The Bullock Building, University Way, Cranfield, Bedford, MK43 OGH, UK
| | | | - Paul Temple
- Wold Farm, Driffield, East Yorkshire, YO25 3BB, UK
| | - Matthew Clarke
- Bayer - Crop Science, Monsanto UK Ltd, 230 Science Park, Cambridge, CB4 0WB, UK
| | - Giles Oldroyd
- Crop Science Centre, Lawrence Weaver Road, Cambridge, CB3 0LE, UK
| | - Claire S Grierson
- School of Biological Sciences, Bristol University, 24 Tyndall Avenue, Bristol, BS8 1TQ, UK
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Guzmán-Benito I, Achkar NP, Bologna N, Ursache R. CRISPR/Cas-mediated inplanta gene targeting: current advances and challenges. JOURNAL OF EXPERIMENTAL BOTANY 2023:erad072. [PMID: 36861321 DOI: 10.1093/jxb/erad072] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/13/2022] [Indexed: 06/18/2023]
Abstract
We can use gene targeting (GT) to make modifications at a specific region in a plant's genome and create high-precision tools for plant biotechnology and breeding. However, its low efficiency is a major barrier to its use in plants. The discovery of CRISPR (Clustered Regularly Interspaced Short Palindromic Repeats)-Cas-based site-specific nucleases capable of inducing double-strand breaks in desired loci resulted in the development of novel approaches for plant GT. Several studies have recently demonstrated improvements in GT efficiency through cell-type-specific expression of Cas nucleases, the use of self-amplified GT-vector DNA, or manipulation of RNA silencing and DNA repair pathways. In this review, we summarize recent advances in CRISPR/Cas-mediated GT in plants and discuss potential efficiency improvements. Increasing the efficiency of GT technology will help us pave the way for increased crop yields and food safety in environmentally friendly agriculture.
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Affiliation(s)
- Irene Guzmán-Benito
- The Department of Plant Molecular Biology, University of Lausanne, 1015 Lausanne, Switzerland
| | - Natalia Patricia Achkar
- Centre for Research in Agricultural Genomics (CRAG), CSIC-IRTA-UAB-UB, Bellaterra, Barcelona 08193, Spain
| | - Nicolas Bologna
- Centre for Research in Agricultural Genomics (CRAG), CSIC-IRTA-UAB-UB, Bellaterra, Barcelona 08193, Spain
| | - Robertas Ursache
- Centre for Research in Agricultural Genomics (CRAG), CSIC-IRTA-UAB-UB, Bellaterra, Barcelona 08193, Spain
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4
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Orchid fleck dichorhavirus movement protein shows RNA silencing suppressor activity. J Gen Virol 2022; 103. [DOI: 10.1099/jgv.0.001805] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022] Open
Abstract
To counteract RNA interference-mediated antiviral defence, virus genomes evolved to express proteins that inhibit this plant defence mechanism. Using six independent biological approaches, we show that orchid fleck dichorhavirus citrus strain (OFV-citrus) movement protein (MP) may act as a viral suppressor of RNA silencing (VSR). By using the alfalfa mosaic virus (AMV) RNA 3 expression vector, it was observed that the MP triggered necrosis response in transgenic tobacco leaves and increased the viral RNA (vRNA) accumulation. The use of the potato virus X (PVX) expression system revealed that the cis expression of MP increased both the severity of the PVX infection and the accumulation of PVX RNAs, further supporting that MP could act as an RNA silencing suppressor (RSS). From the analysis of the RSS-defective turnip crinkle virus (TCV), we do not find local RSS activity for MP, suggesting a link between MP suppressor activity and the prevention of systemic silencing. In the analysis of local suppressive activity using the GFP-based agroinfiltration assay in Nicotiana benthamiana (16 c line), we do not identify local RSS activity for the five OFV RNA1-encoded proteins. However, when evaluating the small interfering RNA (siRNA) accumulation, we find that the expression of MP significantly reduces the accumulation of GFP-derived siRNA. Finally, we examine whether the MP can prevent systemic silencing in 16c plants. Our findings show that MP inhibits the long-distance spread of RNA silencing, but does not affect the short-distance spread. Together, our findings indicate that MP is part of OFV’s counter-defence mechanism, acting mainly in the prevention of systemic long-distance silencing. This work presents the first report of a VSR for a member of the genus Dichorhavirus.
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Wise JC, Wise AG, Rakotondravelo M, Vandervoort C, Seeve C, Fabbri B. Trunk injection delivery of dsRNA for RNAi-based pest control in apple trees. PEST MANAGEMENT SCIENCE 2022; 78:3528-3533. [PMID: 35578562 PMCID: PMC9541757 DOI: 10.1002/ps.6993] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/07/2022] [Revised: 05/13/2022] [Accepted: 05/16/2022] [Indexed: 06/15/2023]
Abstract
BACKGROUND RNA interference (RNAi) is a promising new approach for controlling insect pests without the use of synthetic pesticides. Trunk injection is a delivery system for woody plants that harnesses the vascular system of the tree to transport materials to the tree canopy. Full size apple trees were injected with double-stranded RNA (dsRNA), and season-long leaf samples were taken to measure the vascular mobility and temporal persistence of dsRNA, using quantitative reverse transcription polymerase chain reaction (qRT-PCR). RESULTS The qRT-PCR results revealed that the quantities of dsRNA in the apple leaves of treated trees were significantly greater than those in the leaves of untreated trees for both 2019 and 2020 studies. The peak dsRNA concentration in 2019 was 242 pg/30 mg of leaf tissue, and in 2020 was 16.4 pg/30 mg. The persistence of dsRNA in the apple tree canopy in 2019 was at least 84 days, and in 2020 was at least 141 days. CONCLUSIONS The highest mean measurement of dsRNA on a single date in 2019 was 242 pg, which is approximately equivalent to 8 ng/1 g leaf tissue. The projection using the highest replicate concentration from the same date is approximately equivalent to 27 ng/1 g leaf tissue, which may be sufficient to be considered biologically active. © 2022 The Authors. Pest Management Science published by John Wiley & Sons Ltd on behalf of Society of Chemical Industry.
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Affiliation(s)
- John C Wise
- Department of EntomologyMichigan State UniversityEast LansingMIUSA
| | - Annabel G Wise
- Veterinary Diagnostic LaboratoryMichigan State UniversityEast LansingMIUSA
| | | | - Christine Vandervoort
- Department of Plant, Soil and Microbial SciencesMichigan State UniversityEast LansingMIUSA
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Yan Y, Ham BK. The Mobile Small RNAs: Important Messengers for Long-Distance Communication in Plants. FRONTIERS IN PLANT SCIENCE 2022; 13:928729. [PMID: 35783973 PMCID: PMC9247610 DOI: 10.3389/fpls.2022.928729] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/26/2022] [Accepted: 05/25/2022] [Indexed: 06/06/2023]
Abstract
Various species of small RNAs (sRNAs), notably microRNAs and small interfering RNAs (siRNAs), have been characterized as the major effectors of RNA interference in plants. Growing evidence supports a model in which sRNAs move, intercellularly, systemically, and between cross-species. These non-coding sRNAs can traffic cell-to-cell through plasmodesmata (PD), in a symplasmic manner, as well as from source to sink tissues, via the phloem, to trigger gene silencing in their target cells. Such mobile sRNAs function in non-cell-autonomous communication pathways, to regulate various biological processes, such as plant development, reproduction, and plant defense. In this review, we summarize recent progress supporting the roles of mobile sRNA in plants, and discuss mechanisms of sRNA transport, signal amplification, and the plant's response, in terms of RNAi activity, within the recipient tissues. We also discuss potential research directions and their likely impact on engineering of crops with traits for achieving food security.
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Affiliation(s)
- Yan Yan
- Department of Biochemistry and Biophysics, Texas A&M University, College Station, TX, United States
| | - Byung-Kook Ham
- Global Institute for Food Security, University of Saskatchewan, Saskatoon, SK, Canada
- Department of Biology, University of Saskatchewan, Saskatoon, SK, Canada
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Interspecific hybridization in tomato influences endogenous viral sRNAs and alters gene expression. Genome Biol 2022; 23:120. [PMID: 35597968 PMCID: PMC9124383 DOI: 10.1186/s13059-022-02685-z] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2021] [Accepted: 05/09/2022] [Indexed: 11/23/2022] Open
Abstract
Background Hybridization is associated with the activation of transposable elements and changes in the patterns of gene expression leading to phenotypic changes. However, the underlying mechanisms are not well understood. Results Here, we describe the changes to the gene expression in interspecific Solanum hybrids that are associated with small RNAs derived from endogenous (para)retroviruses (EPRV). There were prominent changes to sRNA profiles in these hybrids involving 22-nt species produced in the DCL2 biogenesis pathway, and the hybridization-induced changes to the gene expression were similar to those in a dcl2 mutant. Conclusions These findings indicate that hybridization leads to activation of EPRV, perturbation of small RNA profiles, and, consequently, changes in the gene expression. Such hybridization-induced variation in the gene expression could increase the natural phenotypic variation in natural evolution or in breeding for agriculture. Supplementary Information The online version contains supplementary material available at 10.1186/s13059-022-02685-z.
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Cisneros AE, de la Torre‐Montaña A, Carbonell A. Systemic silencing of an endogenous plant gene by two classes of mobile 21-nucleotide artificial small RNAs. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2022; 110:1166-1181. [PMID: 35277899 PMCID: PMC9310713 DOI: 10.1111/tpj.15730] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 12/07/2021] [Revised: 03/02/2022] [Accepted: 03/03/2022] [Indexed: 06/14/2023]
Abstract
Artificial small RNAs (art-sRNAs) are 21-nucleotide small RNAs (sRNAs) computationally designed to silence plant genes or pathogenic RNAs with high efficacy and specificity. They are typically produced in transgenic plants to induce silencing at the whole-organism level, although their expression in selected tissues for inactivating genes in distal tissues has not been reported. Here, art-sRNAs designed against the magnesium chelatase subunit CHLI-encoding SULFUR gene (NbSu) were agroinfiltrated in Nicotiana benthamiana leaves, and the induction of local and systemic silencing was analyzed phenotypically by monitoring the appearance of the characteristic bleached phenotype, as well as molecularly by analyzing art-sRNA processing, accumulation and targeting activity and efficacy. We found that the two classes of art-sRNAs, artificial microRNAs (amiRNAs) and synthetic trans-acting small interfering RNAs (syn-tasiRNAs), are able to induce systemic silencing of NbSu, which requires high art-sRNA expression in the vicinity of the leaf petiole but is independent on the production of secondary sRNAs from NbSu mRNAs. Moreover, we revealed that 21-nucleotide amiRNA and syn-tasiRNA duplexes, and not their precursors, are the molecules moving between cells and through the phloem to systemically silence NbSu in upper leaves. In sum, our results indicate that 21-nucleotide art-sRNAs can move throughout the plant to silence plant genes in tissues different from where they are produced. This highlights the biotechnological potential of art-sRNAs, which might be applied locally for triggering whole-plant and highly specific silencing to regulate gene expression or induce resistance against pathogenic RNAs in next-generation crops. The present study demonstrates that artificial small RNAs, such as artificial microRNAs and synthetic trans-acting small interfering RNAs, can move long distances in plants as 21-nucleotide duplexes, specifically silencing endogenous genes in tissues different from where they are applied. This highlights the biotechnological potential of artificial small RNAs, which might be applied locally for triggering whole-plant, highly specific silencing to regulate gene expression or induce resistance against pathogenic RNAs in next-generation crops.
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Affiliation(s)
- Adriana E. Cisneros
- Instituto de Biología Molecular y Celular de Plantas (Consejo Superior de Investigaciones Científicas – Universitat Politècnica de València)46022ValenciaSpain
| | - Ainhoa de la Torre‐Montaña
- Instituto de Biología Molecular y Celular de Plantas (Consejo Superior de Investigaciones Científicas – Universitat Politècnica de València)46022ValenciaSpain
| | - Alberto Carbonell
- Instituto de Biología Molecular y Celular de Plantas (Consejo Superior de Investigaciones Científicas – Universitat Politècnica de València)46022ValenciaSpain
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Han H, Zhou Y. Function and Regulation of microRNA171 in Plant Stem Cell Homeostasis and Developmental Programing. Int J Mol Sci 2022; 23:2544. [PMID: 35269685 PMCID: PMC8910752 DOI: 10.3390/ijms23052544] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2022] [Revised: 02/21/2022] [Accepted: 02/22/2022] [Indexed: 12/17/2022] Open
Abstract
MicroRNA171 (miR171), a group of 21-nucleotide single-strand small RNAs, is one ancient and conserved microRNA family in land plants. This review focuses on the recent progress in understanding the role of miR171 in plant stem cell homeostasis and developmental patterning, and the regulation of miR171 by developmental cues and environmental signals. Specifically, miR171 regulates shoot meristem activity and phase transition through repressing the HAIRYMERISTEM (HAM) family genes. In the model species Arabidopsis, miR171 serves as a short-range mobile signal, which initiates in the epidermal layer of shoot meristems and moves downwards within a limited distance, to pattern the apical-basal polarity of gene expression and drive stem cell dynamics. miR171 levels are regulated by light and various abiotic stresses, suggesting miR171 may serve as a linkage between environmental factors and cell fate decisions. Furthermore, miR171 family members also demonstrate both conserved and lineage-specific functions in land plants, which are summarized and discussed here.
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Affiliation(s)
- Han Han
- Department of Botany and Plant Pathology, Purdue University, West Lafayette, IN 47907, USA;
- Purdue Center for Plant Biology, Purdue University, West Lafayette, IN 47907, USA
| | - Yun Zhou
- Department of Botany and Plant Pathology, Purdue University, West Lafayette, IN 47907, USA;
- Purdue Center for Plant Biology, Purdue University, West Lafayette, IN 47907, USA
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Rubio B, Stammitti L, Cookson SJ, Teyssier E, Gallusci P. Small RNA populations reflect the complex dialogue established between heterograft partners in grapevine. HORTICULTURE RESEARCH 2022; 9:uhab067. [PMID: 35048109 PMCID: PMC8935936 DOI: 10.1093/hr/uhab067] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 07/12/2021] [Revised: 10/24/2021] [Accepted: 11/27/2021] [Indexed: 06/14/2023]
Abstract
Grafting is an ancient method that has been intensively used for the clonal propagation of vegetables and woody trees. Despite its importance in agriculture the physiological and molecular mechanisms underlying phenotypic changes of plants following grafting are still poorly understood. In the present study, we analyse the populations of small RNAs in homo and heterografts and take advantage of the sequence differences in the genomes of heterograft partners to analyse the possible exchange of small RNAs. We demonstrate that the type of grafting per se dramatically influences the small RNA populations independently of genotypes but also show genotype specific effects. In addition, we demonstrate that bilateral exchanges of small RNAs, mainly short interfering RNAs, may occur in heterograft with the preferential transfer of small RNAs from the scion to the rootstock. Altogether, the results suggest that small RNAs may have an important role in the phenotype modifications observed in heterografts.
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Affiliation(s)
- Bernadette Rubio
- EGFV, University Bordeaux, Bordeaux Sciences Agro, INRAE, ISVV, F-33882, Villenave d’Ornon, France
| | - Linda Stammitti
- EGFV, University Bordeaux, Bordeaux Sciences Agro, INRAE, ISVV, F-33882, Villenave d’Ornon, France
| | - Sarah Jane Cookson
- EGFV, University Bordeaux, Bordeaux Sciences Agro, INRAE, ISVV, F-33882, Villenave d’Ornon, France
| | - Emeline Teyssier
- EGFV, University Bordeaux, Bordeaux Sciences Agro, INRAE, ISVV, F-33882, Villenave d’Ornon, France
| | - Philippe Gallusci
- EGFV, University Bordeaux, Bordeaux Sciences Agro, INRAE, ISVV, F-33882, Villenave d’Ornon, France
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11
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Harnessing epigenetic variability for crop improvement: current status and future prospects. Genes Genomics 2021; 44:259-266. [PMID: 34807374 DOI: 10.1007/s13258-021-01189-7] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2021] [Accepted: 11/07/2021] [Indexed: 10/19/2022]
Abstract
BACKGROUND The epigenetic mechanisms play critical roles in a vast diversity of biological processes of plants, including development and response to environmental challenges. Particularly, DNA methylation is a stable epigenetic signature that supplements the genetics-based view of complex life phenomena. In crop breeding, the decrease in genetic diversity due to artificial selection of conventional breeding methods has been a long-standing concern. Therefore, the epigenetic diversity has been proposed as a new resource for future crop breeding, which will be hereinafter referred to as epibreeding. DISCUSSION The induction of methylome changes has been performed in plants by several methods including chemical drugs treatment and tissue culture. Target-specific epigenetic engineering has been also attempted by exogenous RNAi mediated by virus-induced gene silencing and grafting. Importantly, the new and innovative techniques including the CRISPR-Cas9 system have recently been adopted in epigenetic engineering of plant genomes, facilitating the efforts for epibreeding. CONCLUSION In this review, we introduce several examples of natural and induced epigenetic changes impacting on agronomic traits and discuss the methods for generating epigenomic diversity and site-specific epigenetic engineering.
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12
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Betti F, Ladera-Carmona MJ, Weits DA, Ferri G, Iacopino S, Novi G, Svezia B, Kunkowska AB, Santaniello A, Piaggesi A, Loreti E, Perata P. Exogenous miRNAs induce post-transcriptional gene silencing in plants. NATURE PLANTS 2021; 7:1379-1388. [PMID: 34650259 PMCID: PMC8516643 DOI: 10.1038/s41477-021-01005-w] [Citation(s) in RCA: 42] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/12/2021] [Accepted: 08/25/2021] [Indexed: 05/04/2023]
Abstract
Plants seem to take up exogenous RNA that was artificially designed to target specific genes, followed by activation of the RNA interference (RNAi) machinery. It is, however, not known whether plants use RNAs themselves as signalling molecules in plant-to-plant communication, other than evidence that an exchange of small RNAs occurs between parasitic plants and their hosts. Exogenous RNAs from the environment, if taken up by some living organisms, can indeed induce RNAi. This phenomenon has been observed in nematodes and insects, and host Arabidopsis cells secrete exosome-like extracellular vesicles to deliver plant small RNAs into Botrytis cinerea. Here we show that micro-RNAs (miRNAs) produced by plants act as signalling molecules affecting gene expression in other, nearby plants. Exogenous miRNAs, such as miR156 and miR399, trigger RNAi via a mechanism requiring both AGO1 and RDR6. This emphasizes that the production of secondary small interfering RNAs is required. This evidence highlights the existence of a mechanism in which miRNAs represent signalling molecules that enable communication between plants.
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Affiliation(s)
- Federico Betti
- PlantLab, Institute of Life Sciences, Sant'Anna School of Advanced Studies, Pisa, Italy
| | | | - Daan A Weits
- PlantLab, Institute of Life Sciences, Sant'Anna School of Advanced Studies, Pisa, Italy
| | | | | | - Giacomo Novi
- PlantLab, Institute of Life Sciences, Sant'Anna School of Advanced Studies, Pisa, Italy
| | - Benedetta Svezia
- PlantLab, Institute of Life Sciences, Sant'Anna School of Advanced Studies, Pisa, Italy
| | - Alicja B Kunkowska
- PlantLab, Institute of Life Sciences, Sant'Anna School of Advanced Studies, Pisa, Italy
| | | | | | - Elena Loreti
- Institute of Agricultural Biology and Biotechnology, National Research Council, Pisa, Italy.
| | - Pierdomenico Perata
- PlantLab, Institute of Life Sciences, Sant'Anna School of Advanced Studies, Pisa, Italy.
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Wicaksono A, Dobránszki J, Teixeira da Silva JA. The term "caline" in plant developmental biology. Biol Futur 2021; 72:299-306. [PMID: 34554550 DOI: 10.1007/s42977-021-00076-2] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2020] [Accepted: 02/10/2021] [Indexed: 11/28/2022]
Abstract
In the 1930s, Frits Warmolt Went conducted a number of seminal studies on pea seedlings that had been germinated in the dark and assessed their growth when either the apical parts, cotyledons, or roots were cut off or grafted, to assess whether coplant growth factors assisted auxin in the development of these organs. Went assigned the term "calines" to all auxin-assisting substances, specifically rhizocaline, caulocaline, and phyllocaline in root, shoot (and axillary buds) and leaf development, respectively. Those experiments were based exclusively on growth assays, and no supplementary biochemical or physiological analyses were ever conducted, and additional proof was only provided by Went using pea or tomato. The lack of independent reproducibility by other groups, combined with the fact that the hormonal control of these developmental events in plants is now fairly well-studied event, even at the molecular level, suggests that these growth factors that Went observed 80 years ago either do not exist or are known by some other term in modern plant development. The terms related to "calines" should thus no longer be used in plant developmental biology.
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Affiliation(s)
- Adhityo Wicaksono
- Division of Biotechnology, Generasi Biologi Indonesia (Genbinesia) Foundation, Jl. Swadaya Barat No. 4, Gresik Regency, 61171, Indonesia.
| | - Judit Dobránszki
- Research Institute of Nyíregyháza, IAREF, University of Debrecen, P.O. Box 12, Nyíregyháza, 4400, Hungary.
| | - Jaime A Teixeira da Silva
- Research Institute of Nyíregyháza, IAREF, University of Debrecen, P.O. Box 12, Nyíregyháza, 4400, Hungary. .,Independent Researcher, Kagawa-ken, Japan.
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14
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Reinvigoration/Rejuvenation Induced through Micrografting of Tree Species: Signaling through Graft Union. PLANTS 2021; 10:plants10061197. [PMID: 34208406 PMCID: PMC8231136 DOI: 10.3390/plants10061197] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/04/2021] [Revised: 06/01/2021] [Accepted: 06/09/2021] [Indexed: 02/05/2023]
Abstract
Trees have a distinctive and generally long juvenile period during which vegetative growth rate is rapid and floral organs do not differentiate. Among trees, the juvenile period can range from 1 year to 15–20 years, although with some forest tree species, it can be longer. Vegetative propagation of trees is usually much easier during the juvenile phase than with mature phase materials. Therefore, reversal of maturity is often necessary in order to obtain materials in which rooting ability has been restored. Micrografting has been developed for trees to address reinvigoration/rejuvenation of elite selections to facilitate vegetative propagation. Generally, shoots obtained after serial grafting have increased rooting competence and develop juvenile traits; in some cases, graft-derived shoots show enhanced in vitro proliferation. Recent advances in graft signaling have shown that several factors, e.g., plant hormones, proteins, and different types of RNA, could be responsible for changes in the scion. The focus of this review includes (1) a discussion of the differences between the juvenile and mature growth phases in trees, (2) successful restoration of juvenile traits through micrografting, and (3) the nature of the different signals passing through the graft union.
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15
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Liu L, Wang T. Male gametophyte development in flowering plants: A story of quarantine and sacrifice. JOURNAL OF PLANT PHYSIOLOGY 2021; 258-259:153365. [PMID: 33548696 DOI: 10.1016/j.jplph.2021.153365] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/26/2020] [Revised: 01/06/2021] [Accepted: 01/06/2021] [Indexed: 05/19/2023]
Abstract
Over 160 years ago, scientists made the first microscopic observations of angiosperm pollen. Unlike in animals, male meiosis in angiosperms produces a haploid microspore that undergoes one asymmetric division to form a vegetative cell and a generative cell. These two cells have distinct fates: the vegetative cell exits the cell cycle and elongates to form a tip-growing pollen tube; the generative cell divides once more in the pollen grain or within the growing pollen tube to form a pair of sperm cells. The concept that male germ cells are less active than the vegetative cell came from biochemical analyses and pollen structure anatomy early in the last century and is supported by the pollen transcriptome data of the last decade. However, the mechanism of how and when the transcriptional repression in male germ cells occurs is still not fully understood. In this review, we provide a brief account of the cytological and metabolic differentiation between the vegetative cell and male germ cells, with emphasis on the role of temporary callose walls, dynamic nuclear pore density, transcription repression, and histone variants. We further discuss the intercellular movement of small interfering RNA (siRNA) derived from transposable elements (TEs) and reexamine the function of TE expression in male germ cells.
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Affiliation(s)
- Lingtong Liu
- Key Laboratory of Plant Molecular Physiology, Institute of Botany, Chinese Academy of Sciences, Beijing 100093, China.
| | - Tai Wang
- Key Laboratory of Plant Molecular Physiology, Institute of Botany, Chinese Academy of Sciences, Beijing 100093, China; College of Life Science, University of Chinese Academy of Sciences, Beijing 100049, China; Innovative Academy of Seed Design, Chinese Academy of Sciences, Beijing 100093, China.
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16
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Fei Y, Nyikó T, Molnar A. Non-perfectly matching small RNAs can induce stable and heritable epigenetic modifications and can be used as molecular markers to trace the origin and fate of silencing RNAs. Nucleic Acids Res 2021; 49:1900-1913. [PMID: 33524108 PMCID: PMC7913690 DOI: 10.1093/nar/gkab023] [Citation(s) in RCA: 20] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2020] [Revised: 01/04/2021] [Accepted: 01/08/2021] [Indexed: 02/06/2023] Open
Abstract
Short non-coding RNA molecules (sRNAs) play a fundamental role in gene regulation and development in higher organisms. They act as molecular postcodes and guide AGO proteins to target nucleic acids. In plants, sRNA-targeted mRNAs are degraded, reducing gene expression. In contrast, sRNA-targeted DNA sequences undergo cytosine methylation referred to as RNA-directed DNA methylation (RdDM). Cytosine methylation can suppress transcription, thus sRNAs are potent regulators of gene expression. sRNA-mediated RdDM is involved in genome stability through transposon silencing, mobile signalling for epigenetic gene control and hybrid vigour. Since cytosine methylation can be passed on to subsequent generations, RdDM contributes to transgenerational inheritance of the epigenome. Using a novel approach, which can differentiate between primary (inducer) and secondary (amplified) sRNAs, we show that initiation of heritable RdDM does not require complete sequence complementarity between the sRNAs and their nuclear target sequences. sRNAs with up to four regularly interspaced mismatches are potent inducers of RdDM, however, the number and disruptive nature of nucleotide polymorphisms negatively correlate with their efficacy. Our findings contribute to understanding how sRNA can directly shape the epigenome and may be used in designing the next generation of RNA silencing constructs.
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Affiliation(s)
- Yue Fei
- University of Edinburgh, Institute of Molecular Plant Sciences, Max Born Crescent, Edinburgh EH9 3BF, UK
| | - Tünde Nyikó
- Agricultural Biotechnology Institute, Szent-Györgyi A. 4., Gödöllő 2100, Hungary
| | - Attila Molnar
- University of Edinburgh, Institute of Molecular Plant Sciences, Max Born Crescent, Edinburgh EH9 3BF, UK
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17
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Tsaballa A, Xanthopoulou A, Madesis P, Tsaftaris A, Nianiou-Obeidat I. Vegetable Grafting From a Molecular Point of View: The Involvement of Epigenetics in Rootstock-Scion Interactions. FRONTIERS IN PLANT SCIENCE 2021; 11:621999. [PMID: 33488662 PMCID: PMC7817540 DOI: 10.3389/fpls.2020.621999] [Citation(s) in RCA: 18] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/27/2020] [Accepted: 12/07/2020] [Indexed: 05/25/2023]
Abstract
Vegetable grafting is extensively used today in agricultural production to control soil-borne pathogens, abiotic and biotic stresses and to improve phenotypic characteristics of the scion. Commercial vegetable grafting is currently practiced in tomato, watermelon, melon, eggplant, cucumber, and pepper. It is also regarded as a rapid alternative to the relatively slow approach of breeding for increased environmental-stress tolerance of fruit vegetables. However, even though grafting has been used for centuries, until today, there are still many issues that have not been elucidated. This review will emphasize on the important mechanisms taking place during grafting, especially the genomic interactions between grafting partners and the impact of rootstocks in scion's performance. Special emphasis will be drawn on the relation between vegetable grafting, epigenetics, and the changes in morphology and quality of the products. Recent advances in plant science such as next-generation sequencing provide new information regarding the molecular interactions between rootstock and scion. It is now evidenced that genetic exchange is happening across grafting junctions between rootstock and scion, potentially affecting grafting-mediated effects already recorded in grafted plants. Furthermore, significant changes in DNA methylation are recorded in grafted scions, suggesting that these epigenetic mechanisms could be implicated in grafting effects. In this aspect, we also discuss the process and the molecular aspects of rootstock scion communication. Finally, we provide with an extensive overview of gene expression changes recorded in grafted plants and how these are related to the phenotypic changes observed. Τhis review finally seeks to elucidate the dynamics of rootstock-scion interactions and thus stimulate more research on grafting in the future. In a future where sustainable agricultural production is the way forward, grafting could play an important role to develop products of higher yield and quality in a safe and "green" way.
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Affiliation(s)
- Aphrodite Tsaballa
- Institute of Plant Breeding and Genetic Resources, Hellenic Agricultural Organization (ELGO-Dimitra), Thessaloniki, Greece
| | - Aliki Xanthopoulou
- Institute of Plant Breeding and Genetic Resources, Hellenic Agricultural Organization (ELGO-Dimitra), Thessaloniki, Greece
| | - Panagiotis Madesis
- Laboratory of Molecular Biology of Plants, School of Agricultural Sciences, University of Thessaly, Volos, Greece
- Institute of Applied Biosciences, Centre for Research & Technology Hellas, Thessaloniki, Greece
| | - Athanasios Tsaftaris
- Perrotis College, American Farm School, Thessaloniki, Greece
- Laboratory of Genetics and Plant Breeding, School of Agriculture, Forestry and Natural Environment, Aristotle University of Thessaloniki, Thessaloniki, Greece
| | - Irini Nianiou-Obeidat
- Laboratory of Genetics and Plant Breeding, School of Agriculture, Forestry and Natural Environment, Aristotle University of Thessaloniki, Thessaloniki, Greece
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18
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Affiliation(s)
- Quentin Gouil
- La Trobe Institute for Agriculture and Food, Department of Animal, Plant and Soil Sciences, School of Life Sciences, La Trobe University, Bundoora, Victoria, Australia.
- Epigenetics and Development Division, Walter and Eliza Hall Institute of Medical Research, Parkville, Victoria, Australia.
- Department of Medical Biology, University of Melbourne, Parkville, Victoria, Australia.
| | - Mathew G Lewsey
- La Trobe Institute for Agriculture and Food, Department of Animal, Plant and Soil Sciences, School of Life Sciences, La Trobe University, Bundoora, Victoria, Australia.
- Australian Research Council Research Hub for Medicinal Agriculture, La Trobe University, Bundoora, Victoria, Australia.
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19
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Dutta TK, Papolu PK, Singh D, Sreevathsa R, Rao U. Expression interference of a number of Heterodera avenae conserved genes perturbs nematode parasitic success in Triticum aestivum. PLANT SCIENCE : AN INTERNATIONAL JOURNAL OF EXPERIMENTAL PLANT BIOLOGY 2020; 301:110670. [PMID: 33218636 DOI: 10.1016/j.plantsci.2020.110670] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/22/2020] [Revised: 09/01/2020] [Accepted: 09/06/2020] [Indexed: 05/26/2023]
Abstract
The cereal cyst nematode, Heterodera avenae is distributed worldwide and causes substantial damage in bread wheat, Triticum aestivum. This nematode is extremely difficult to manage because of its prolonged persistence as unhatched eggs encased in cysts. Due to its sustainable and target-specific nature, RNA interference (RNAi)-based strategy has gained unprecedented importance for pest control. To date, RNAi strategy has not been exploited to manage H. avenae in wheat. In the present study, 40 H. avenae target genes with different molecular function were rationally selected for in vitro soaking analysis in order to assess their susceptibility to RNAi. In contrast to target-specific downregulation of 18 genes, 7 genes were upregulated and 15 genes showed unaltered expression (although combinatorial soaking showed some of these genes are RNAi susceptible), suggesting that a few of the target genes were refractory or recalcitrant to RNAi. However, RNAi of 37 of these genes negatively altered nematode behavior in terms of reduced penetration, development and reproduction in wheat. Subsequently, wheat plants were transformed with seven H. avenae target genes (that showed greatest abrogation of nematode parasitic success) for host-induced gene silencing (HIGS) analysis. Transformed plants were molecularly characterized by PCR, RT-qPCR and Southern hybridization. Production of target gene-specific double- and single-stranded RNA (dsRNA/siRNA) was detected in transformed plants. Transgenic expression of galectin, cathepsin L, vap1, serpin, flp12, RanBPM and chitinase genes conferred 33.24-72.4 % reduction in H. avenae multiplication in T1 events with single copy ones exhibiting greatest reduction. A similar degree of resistance observed in T2 plants indicated the consistent HIGS effect in the subsequent generations. Intriguingly, cysts isolated from RNAi plants were of smaller size with translucent cuticle compared to normal size, dark brown control cysts, suggesting H. avenae developmental retardation due to HIGS. Our study reinforces the potential of HIGS to manage nematode problems in crop plant.
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Affiliation(s)
- Tushar K Dutta
- Division of Nematology, ICAR-Indian Agricultural Research Institute, New Delhi, 110012, India
| | - Pradeep K Papolu
- Division of Nematology, ICAR-Indian Agricultural Research Institute, New Delhi, 110012, India
| | - Divya Singh
- Division of Nematology, ICAR-Indian Agricultural Research Institute, New Delhi, 110012, India
| | - Rohini Sreevathsa
- ICAR-National Institute for Plant Biotechnology, New Delhi, 110012, India.
| | - Uma Rao
- Division of Nematology, ICAR-Indian Agricultural Research Institute, New Delhi, 110012, India.
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20
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Chen JR, Ou SL, Nieh TI, Lu CY, Ku HM. Molecular Dissection of Cucumis metuliferus Resistance against Papaya Ringspot Virus by Grafting. PLANTS (BASEL, SWITZERLAND) 2020; 9:E1666. [PMID: 33261122 PMCID: PMC7759848 DOI: 10.3390/plants9121666] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/29/2020] [Revised: 11/25/2020] [Accepted: 11/25/2020] [Indexed: 12/30/2022]
Abstract
Vegetable crops of the genus Cucumis are very popular worldwide and have great market value. However, their fruit quality and yield are hindered by viral diseases. C. metuliferus is considered a wild species with resistance to viral diseases that is lacking in cultivated crops of the Cucumis genus, such as melon. The C. metuliferus line L37 shows extreme resistance against Papaya ringspot virus (PRSV-HA), whereas line L35 is a susceptible line. In this study, reciprocal grafting experiments between L35 and L37 were performed, and the PRSV-HA strain was pre-inoculated in the rootstock leaves. The results revealed that the resistance signal in the L37 rootstock could transmit and provide resistance to the L35 scion. Subsequently, double sandwich grafting was performed using the pre-inoculated L35 as the rootstock, which was then grafted onto the L37 intermediate and the L35 scion. The results showed that PRSV-HA RNA accumulated in the L35 rootstock leaf, petiole, and stem tissues, whereas PRSV-HA RNA accumulated in some intermediate and scion petiole and stem tissues. No HCPro RNA was detected in the L35 scion leaves. The results showed that the suppression of the virus occurred in the leaves, and the resistance effect spread from the rootstock in the scion direction. Hence, this study has demonstrated that RNA silencing of systemic signals is responsible for L37 resistance against PRSV. C. metuliferus L37 could provide a valuable resistance source for crops of the Cucumis species against viral diseases through grafting.
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Affiliation(s)
- Jen-Ren Chen
- Section of Biotechnology, Taiwan Seed Improvement and Propagation Station, Taichung City 426, Taiwan
- Department of Agronomy, National Chung Hsing University, Taichung City 402, Taiwan
| | - Shang-Ling Ou
- Department of Agronomy, National Chung Hsing University, Taichung City 402, Taiwan
| | - Ting-Iun Nieh
- Department of Agronomy, National Chung Hsing University, Taichung City 402, Taiwan
| | - Chih-Yu Lu
- Department of Agronomy, National Chung Hsing University, Taichung City 402, Taiwan
| | - Hsin-Mei Ku
- Department of Agronomy, National Chung Hsing University, Taichung City 402, Taiwan
- Advanced Plant Biotechnology Center, National Chung Hsing University, Taichung City 402, Taiwan
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21
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Spanò R, Ferrara M, Gallitelli D, Mascia T. The Role of Grafting in the Resistance of Tomato to Viruses. PLANTS (BASEL, SWITZERLAND) 2020; 9:E1042. [PMID: 32824316 PMCID: PMC7463508 DOI: 10.3390/plants9081042] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/01/2020] [Revised: 08/07/2020] [Accepted: 08/12/2020] [Indexed: 12/14/2022]
Abstract
Grafting is routinely implemented in modern agriculture to manage soilborne pathogens such as fungi, oomycetes, bacteria, and viruses of solanaceous crops in a sustainable and environmentally friendly approach. Some rootstock/scion combinations use specific genetic resistance mechanisms to impact also some foliar and airborne pathogens, including arthropod or contact-transmitted viruses. These approaches resulted in poor efficiency in the management of plant viruses with superior virulence such as the strains of tomato spotted wilt virus breaking the Sw5 resistance, strains of cucumber mosaic virus carrying necrogenic satellite RNAs, and necrogenic strains of potato virus Y. Three different studies from our lab documented that suitable levels of resistance/tolerance can be obtained by grafting commercial tomato varieties onto the tomato ecotype Manduria (Ma) rescued in the framework of an Apulian (southern Italy) regional program on biodiversity. Here we review the main approaches, methods, and results of the three case studies and propose some mechanisms leading to the tolerance/resistance observed in susceptible tomato varieties grafted onto Ma as well as in self-grafted plants. The proposed mechanisms include virus movement in plants, RNA interference, genes involved in graft wound response, resilience, and tolerance to virus infection.
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Affiliation(s)
- Roberta Spanò
- Department of Soil, Plant and Food Sciences, University of Bari “Aldo Moro”, 70126 Bari, Italy; (D.G.); (T.M.)
| | - Massimo Ferrara
- Institute of Sciences of Food Production (ISPA)—CNR, 70126 Bari, Italy;
| | - Donato Gallitelli
- Department of Soil, Plant and Food Sciences, University of Bari “Aldo Moro”, 70126 Bari, Italy; (D.G.); (T.M.)
| | - Tiziana Mascia
- Department of Soil, Plant and Food Sciences, University of Bari “Aldo Moro”, 70126 Bari, Italy; (D.G.); (T.M.)
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22
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Zhao D, Zhong GY, Song GQ. Transfer of endogenous small RNAs between branches of scions and rootstocks in grafted sweet cherry trees. PLoS One 2020; 15:e0236376. [PMID: 32722723 PMCID: PMC7386610 DOI: 10.1371/journal.pone.0236376] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2020] [Accepted: 07/03/2020] [Indexed: 11/29/2022] Open
Abstract
Grafting is a well-established agricultural practice in cherry production for clonal propagation, altered plant vigor and architecture, increased tolerance to biotic and abiotic stresses, precocity, and higher yield. Mobile molecules, such as water, hormones, nutrients, DNAs, RNAs, and proteins play essential roles in rootstock-scion interactions. Small RNAs (sRNAs) are 19 to 30-nucleotides (nt) RNA molecules that are a group of mobile signals in plants. Rootstock-to-scion transfer of transgene-derived small interfering RNAs enabled virus resistance in nontransgenic sweet cherry scion. To determine whether there was long-distance scion-to-rootstock transfer of endogenous sRNAs, we compared sRNAs profiles in bud tissues of an ungrafted 'Gisela 6' rootstock, two sweet cherry 'Emperor Francis' scions as well as their 'Gisela 6' rootstocks. Over two million sRNAs were detected in each sweet cherry scion, where 21-nt sRNA (56.1% and 55.8%) being the most abundant, followed by 24-nt sRNAs (13.1% and 12.5%). Furthermore, we identified over three thousand sRNAs that were potentially transferred from the sweet cherry scions to their corresponding rootstocks. In contrast to the sRNAs in scions, among the transferred sRNAs in rootstocks, the most abundant were 24-nt sRNAs (46.3% and 34.8%) followed by 21-nt sRNAs (14.6% and 19.3%). In other words, 21-nt sRNAs had the least transferred proportion out of the total sRNAs in sources (scions) while 24-nt had the largest proportion. The transferred sRNAs were from 574 cherry transcripts, of which 350 had a match from the Arabidopsis thaliana standard protein set. The finding that "DNA or RNA binding activity" was enriched in the transcripts producing transferred sRNAs indicated that they may affect the biological processes of the rootstocks at different regulatory levels. Overall, the profiles of the transported sRNAs and their annotations revealed in this study facilitate a better understanding of the role of the long-distance transported sRNAs in sweet cherry rootstock-scion interactions as well as in branch-to-branch interactions in a tree.
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Affiliation(s)
- Dongyan Zhao
- Plant Biotechnology Resource and Outreach Center, Department of Horticulture, Michigan State University, East Lansing, MI, United States of America
- Biotechnology Center, Cornell University, Ithaca, NY, United States of America
| | - Gan-yuan Zhong
- Grape Genetics Research Unit, USDA-ARS, Geneva, NY, United States of America
| | - Guo-qing Song
- Plant Biotechnology Resource and Outreach Center, Department of Horticulture, Michigan State University, East Lansing, MI, United States of America
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23
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Taning CN, Arpaia S, Christiaens O, Dietz-Pfeilstetter A, Jones H, Mezzetti B, Sabbadini S, Sorteberg HG, Sweet J, Ventura V, Smagghe G. RNA-based biocontrol compounds: current status and perspectives to reach the market. PEST MANAGEMENT SCIENCE 2020. [PMID: 31743573 DOI: 10.1007/s10340-020-01238-2] [Citation(s) in RCA: 49] [Impact Index Per Article: 12.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/06/2023]
Abstract
Facing current climate challenges and drastically reduced chemical options for plant protection, the exploitation of RNA interference (RNAi) as an agricultural biotechnology tool has unveiled possible new solutions to the global problems of agricultural losses caused by pests and other biotic and abiotic stresses. While the use of RNAi as a tool in agriculture is still limited to a few transgenic crops, and only adopted in restricted parts of the world, scientists and industry are already seeking innovations in leveraging and exploiting the potential of RNAi in the form of RNA-based biocontrol compounds for external applications. Here, we highlight the expanding research and development pipeline, commercial landscape and regulatory environment surrounding the pursuit of RNA-based biocontrol compounds with improved environmental profiles. The commitments of well-established agrochemical companies to invest in research endeavours and the role of start-up companies are crucial for the successful development of practical applications for these compounds. Additionally, the availability of standardized guidelines to tackle regulatory ambiguities surrounding RNA-based biocontrol compounds will help to facilitate the entire commercialization process. Finally, communication to create awareness and public acceptance will be key to the deployment of these compounds. © 2019 Society of Chemical Industry.
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Affiliation(s)
- Clauvis Nt Taning
- Laboratory of Agrozoology, Department of Plants and Crops, Faculty of Bioscience Engineering, Ghent University, Ghent, Belgium
| | - Salvatore Arpaia
- Italian National Agency for New Technologies, Energy and Sustainable Economic Development (ENEA), DTE-BBC, Rotondella, Italy
| | - Olivier Christiaens
- Laboratory of Agrozoology, Department of Plants and Crops, Faculty of Bioscience Engineering, Ghent University, Ghent, Belgium
| | - Antje Dietz-Pfeilstetter
- Julius Kühn-Institut (JKI), Federal Research Centre for Cultivated Plants, Institute for Biosafety in Plant Biotechnology, Braunschweig, Germany
| | - Huw Jones
- IBERS, Aberystwyth University, Aberystwyth, Wales, UK
| | - Bruno Mezzetti
- Department of Agricultural, Food and Environmental Sciences, Università Politecnica delle Marche (UPM), Ancona, Italy
| | - Silvia Sabbadini
- Department of Agricultural, Food and Environmental Sciences, Università Politecnica delle Marche (UPM), Ancona, Italy
| | | | | | - Vera Ventura
- Department of Environmental Science and Policy, Università degli Studi di Milano, Milan, Italy
| | - Guy Smagghe
- Laboratory of Agrozoology, Department of Plants and Crops, Faculty of Bioscience Engineering, Ghent University, Ghent, Belgium
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24
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Baskara-Yhuellou I, Tost J. The impact of microRNAs on alterations of gene regulatory networks in allergic diseases. ADVANCES IN PROTEIN CHEMISTRY AND STRUCTURAL BIOLOGY 2020; 120:237-312. [PMID: 32085883 DOI: 10.1016/bs.apcsb.2019.11.006] [Citation(s) in RCA: 24] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
Allergic diseases including asthma are worldwide on the rise and contribute significantly to health expenditures. Allergic diseases are prototypic diseases with a strong gene by environment interaction component and epigenetic mechanisms might mediate the effects of the environment on the disease phenotype. MicroRNAs, small non-coding RNAs (miRNAs), regulate gene expression post-transcriptionally. Functional single-stranded miRNAs are generated in multiple steps of enzymatic processing from their precursors and mature miRNAs are included into the RNA-induced silencing complex (RISC). They imperfectly base-pair with the 3'UTR region of targeted genes leading to translational repression or mRNA decay. The cellular context and microenvironment as well the isoform of the mRNA control the dynamics and complexity of the regulatory circuits induced by miRNAs that regulate cell fate decisions and function. MiR-21, miR-146a/b and miR-155 are among the best understood miRNAs of the immune system and implicated in different diseases including allergic diseases. MiRNAs are implicated in the induction of the allergy reinforcing the Th2 phenotype (miR-19a, miR-24, miR-27), while other miRNAs promote regulatory T cells associated with allergen tolerance or unresponsiveness. In the current chapter we describe in detail the biogenesis and regulatory function of miRNAs and summarize current knowledge on miRNAs in allergic diseases and allergy relevant cell fate decisions focusing mainly on immune cells. Furthermore, we evoke the principles of regulatory loops and feedback mechanisms involving miRNAs on examples with relevance for allergic diseases. Finally, we show the potential of miRNAs and exosomes containing miRNAs present in several biological fluids that can be exploited with non-invasive procedures for diagnostic and potentially therapeutic purposes.
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Affiliation(s)
- Indoumady Baskara-Yhuellou
- Laboratory for Epigenetics & Environment, Centre National de Recherche en Génomique Humaine, CEA-Institut de Biologie François Jacob, Evry, France
| | - Jörg Tost
- Laboratory for Epigenetics & Environment, Centre National de Recherche en Génomique Humaine, CEA-Institut de Biologie François Jacob, Evry, France
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25
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Kobayashi CR, Castillo-González C, Survotseva Y, Canal E, Nelson ADL, Shippen DE. Recent emergence and extinction of the protection of telomeres 1c gene in Arabidopsis thaliana. PLANT CELL REPORTS 2019; 38:1081-1097. [PMID: 31134349 PMCID: PMC6708462 DOI: 10.1007/s00299-019-02427-9] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/17/2019] [Accepted: 03/27/2019] [Indexed: 05/20/2023]
Abstract
Duplicate POT1 genes must rapidly diverge or be inactivated. Protection of telomeres 1 (POT1) encodes a conserved telomere binding protein implicated in both chromosome end protection and telomere length maintenance. Most organisms harbor a single POT1 gene, but in the few lineages where the POT1 family has expanded, the duplicate genes have diversified. Arabidopsis thaliana bears three POT1-like loci, POT1a, POT1b and POT1c. POT1a retains the ancestral function of telomerase regulation, while POT1b is implicated in chromosome end protection. Here we examine the function and evolution of the third POT1 paralog, POT1c. POT1c is a new gene, unique to A. thaliana, and was derived from a duplication event involving the POT1a locus and a neighboring gene encoding ribosomal protein S17. The duplicate S17 locus (dS17) is highly conserved across A. thaliana accessions, while POT1c is highly divergent, harboring multiple deletions within the gene body and two transposable elements within the promoter. The POT1c locus is transcribed at very low to non-detectable levels under standard growth conditions. In addition, no discernable molecular or developmental defects are associated with plants bearing a CRISPR mutation in the POT1c locus. However, forced expression of POT1c leads to decreased telomerase enzyme activity and shortened telomeres. Evolutionary reconstruction indicates that transposons invaded the POT1c promoter soon after the locus was formed, permanently silencing the gene. Altogether, these findings argue that POT1 dosage is critically important for viability and duplicate gene copies are retained only upon functional divergence.
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Affiliation(s)
- Callie R Kobayashi
- Biochemistry and Biophysics, Texas A&M University, College Station, Texas, USA
| | | | - Yulia Survotseva
- Yale Center for Molecular Discovery, Yale University, New Haven, Connecticut, USA
| | - Elijah Canal
- Biochemistry and Biophysics, Texas A&M University, College Station, Texas, USA
| | - Andrew D L Nelson
- The School of Plant Sciences, University of Arizona, Tucson, Arizona, USA
| | - Dorothy E Shippen
- Biochemistry and Biophysics, Texas A&M University, College Station, Texas, USA.
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26
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Müller LM, Harrison MJ. Phytohormones, miRNAs, and peptide signals integrate plant phosphorus status with arbuscular mycorrhizal symbiosis. CURRENT OPINION IN PLANT BIOLOGY 2019; 50:132-139. [PMID: 31212139 DOI: 10.1016/j.pbi.2019.05.004] [Citation(s) in RCA: 50] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/28/2019] [Revised: 04/24/2019] [Accepted: 05/15/2019] [Indexed: 05/21/2023]
Abstract
Most land plant species engage in a beneficial interaction with arbuscular mycorrhizal fungi in order to increase mineral nutrient acquisition, in particular the major macronutrient phosphorus (P). Initiation, development, and maintenance of the symbiosis are largely under the control of the host plant and strongly influenced by the plants' P status. Recent advances reveal that phytohormones, microRNAs, and secreted peptides all regulate and integrate development of arbuscular mycorrhizal (AM) symbiosis with the P status of the plant. This occurs through a complex, multi-layered signaling network with crosstalk between phosphate (Pi) starvation signaling pathways and AM symbiosis signaling, and also via direct effects on the AM fungal symbiont. Multiple checkpoints allow the plant to fine-tune symbiosis based on its P status.
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Affiliation(s)
- Lena M Müller
- Boyce Thompson Institute, 533 Tower Road, Ithaca, NY 14853, USA
| | - Maria J Harrison
- Boyce Thompson Institute, 533 Tower Road, Ithaca, NY 14853, USA.
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27
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Sabbadini S, Ricci A, Limera C, Baldoni D, Capriotti L, Mezzetti B. Factors Affecting the Regeneration, via Organogenesis, and the Selection of Transgenic Calli in the Peach Rootstock Hansen 536 ( Prunus persica × Prunus amygdalus) to Express an RNAi Construct against PPV Virus. PLANTS (BASEL, SWITZERLAND) 2019; 8:E178. [PMID: 31213013 PMCID: PMC6631258 DOI: 10.3390/plants8060178] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/31/2019] [Revised: 06/13/2019] [Accepted: 06/15/2019] [Indexed: 01/27/2023]
Abstract
Prunus spp. is one of the most recalcitrant fruit tree species in terms of in vitro regeneration and transformation, mostly when mature tissues are used as explants. The present study describes the in vitro regeneration via indirect organogenesis, and Agrobacterium tumefaciens-mediated transformation of the peach rootstock Hansen 536 (Prunus persica × Prunus amygdalus) through the use of meristematic bulks (MBs) as starting explants. Efficient adventitious shoot regeneration was obtained when Hansen 536 MBs were cultured on an optimized medium consisting of modified McCown Woody Plant medium (WPM) enriched with 4.4 M 6-Benzyladenine (BA), 0.1 M 1-Naphthaleneacetic acid (NAA) and 6.0 g L-1 plant agar S1000 (B&V). MB slices were used later as starting explants for Agrobacterium-mediated transformation to introduce an RNAi construct "ihp35S-PPV194" against PPV virus. Transgenic events were identified by both green fluorescent protein (GFP) screening and kanamycin selection at different concentrations (0, 17 or 42 M). GFP-fluorescent proliferating callus lines were selected and confirmed to stably express the ihp35S-PPV194::eGFP gene construct by molecular analysis. Although shoot regeneration from these transgenic calli has not been obtained yet, this represents one of the few examples of successful attempts in peach genetic transformation from somatic tissues, and also serves as a useful in vitro system for future gene functional analysis in peach.
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Affiliation(s)
- Silvia Sabbadini
- Department of Agricultural, Food and Environmental Sciences, Marche Polytechnic University, 60131 Ancona, Italy.
| | - Angela Ricci
- Department of Agricultural, Food and Environmental Sciences, Marche Polytechnic University, 60131 Ancona, Italy.
| | - Cecilia Limera
- Department of Agricultural, Food and Environmental Sciences, Marche Polytechnic University, 60131 Ancona, Italy.
| | - Dania Baldoni
- Department of Agricultural, Food and Environmental Sciences, Marche Polytechnic University, 60131 Ancona, Italy.
| | - Luca Capriotti
- Department of Agricultural, Food and Environmental Sciences, Marche Polytechnic University, 60131 Ancona, Italy.
| | - Bruno Mezzetti
- Department of Agricultural, Food and Environmental Sciences, Marche Polytechnic University, 60131 Ancona, Italy.
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Molecular basis of transitivity in plant RNA silencing. Mol Biol Rep 2019; 46:4645-4660. [DOI: 10.1007/s11033-019-04866-9] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2018] [Accepted: 05/09/2019] [Indexed: 12/11/2022]
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Suzuki T, Ikeda S, Kasai A, Taneda A, Fujibayashi M, Sugawara K, Okuta M, Maeda H, Sano T. RNAi-Mediated Down-Regulation of Dicer-Like 2 and 4 Changes the Response of 'Moneymaker' Tomato to Potato Spindle Tuber Viroid Infection from Tolerance to Lethal Systemic Necrosis, Accompanied by Up-Regulation of miR398, 398a-3p and Production of Excessive Amount of Reactive Oxygen Species. Viruses 2019; 11:v11040344. [PMID: 31013904 PMCID: PMC6521110 DOI: 10.3390/v11040344] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2019] [Revised: 04/08/2019] [Accepted: 04/10/2019] [Indexed: 12/14/2022] Open
Abstract
To examine the role of RNA silencing in plant defenses against viroids, a Dicer-like 2 and 4 (DCL2&4)–double knockdown transgenic tomato plant line, 72E, was created. The expression of endogenous SlDCL2s and SlDCL4 in line 72E decreased to about a half that of the empty cassette line, EC. When challenged with potato spindle tuber viroid (PSTVd), line 72E showed significantly higher levels of PSTVd accumulation early in the course of the infection and lethal systemic necrosis late in the infection. The size distribution of PSTVd-derived small RNAs was significantly different with the number of RNAs of 21 and 22 nucleotides (nt) in line 72E, at approximately 66.7% and 5% of those in line EC, respectively. Conversely, the numbers of 24 nt species increased by 1100%. Furthermore, expression of the stress-responsive microRNA species miR398 and miR398a-3p increased 770% and 868% in the PSTVd-infected line 72E compared with the PSTVd-infected EC. At the same time, the expression of cytosolic and chloroplast-localized Cu/Zn-superoxide dismutase 1 and 2 (SOD1 and SOD2) and the copper chaperon for SOD (CCS1) mRNAs, potential targets of miR398 or 398a-3p, decreased significantly in the PSTVd-infected line 72E leaves, showing necrosis. In concert with miR398 and 398a-3p, SODs control the detoxification of reactive oxygen species (ROS) generated in cells. Since high levels of ROS production were observed in PSTVd-infected line 72E plants, it is likely that the lack of full dicer-likes (DCL) activity in these plants made them unable to control excessive ROS production after PSTVd infection, as disruption in the ability of miR398 and miR398a-3p to regulate SODs resulted in the development of lethal systemic necrosis.
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Affiliation(s)
- Takahiro Suzuki
- Faculty of Agriculture and Life Science, Hirosaki University, Bunkyo-cho 3, Hirosaki 036-8561, Japan.
- Union Graduate School of Agricultural Sciences, Iwate University, 3-18-8 Ueda, Morioka, Iwate 020-8550, Japan.
| | - Sho Ikeda
- Faculty of Agriculture and Life Science, Hirosaki University, Bunkyo-cho 3, Hirosaki 036-8561, Japan.
| | - Atsushi Kasai
- Faculty of Agriculture and Life Science, Hirosaki University, Bunkyo-cho 3, Hirosaki 036-8561, Japan.
| | - Akito Taneda
- Graduate School of Science and Technology, Hirosaki University, Bunkyo-cho 3, Hirosaki 036-8561, Japan.
| | - Misato Fujibayashi
- Faculty of Agriculture and Life Science, Hirosaki University, Bunkyo-cho 3, Hirosaki 036-8561, Japan.
| | - Kohei Sugawara
- Faculty of Agriculture and Life Science, Hirosaki University, Bunkyo-cho 3, Hirosaki 036-8561, Japan.
| | - Maki Okuta
- Faculty of Agriculture and Life Science, Hirosaki University, Bunkyo-cho 3, Hirosaki 036-8561, Japan.
| | - Hayato Maeda
- Faculty of Agriculture and Life Science, Hirosaki University, Bunkyo-cho 3, Hirosaki 036-8561, Japan.
| | - Teruo Sano
- Faculty of Agriculture and Life Science, Hirosaki University, Bunkyo-cho 3, Hirosaki 036-8561, Japan.
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Zhang H, Demirer GS, Zhang H, Ye T, Goh NS, Aditham AJ, Cunningham FJ, Fan C, Landry MP. DNA nanostructures coordinate gene silencing in mature plants. Proc Natl Acad Sci U S A 2019; 116:7543-7548. [PMID: 30910954 PMCID: PMC6462094 DOI: 10.1073/pnas.1818290116] [Citation(s) in RCA: 127] [Impact Index Per Article: 25.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022] Open
Abstract
Delivery of biomolecules to plants relies on Agrobacterium infection or biolistic particle delivery, the former of which is amenable only to DNA delivery. The difficulty in delivering functional biomolecules such as RNA to plant cells is due to the plant cell wall, which is absent in mammalian cells and poses the dominant physical barrier to biomolecule delivery in plants. DNA nanostructure-mediated biomolecule delivery is an effective strategy to deliver cargoes across the lipid bilayer of mammalian cells; however, nanoparticle-mediated delivery without external mechanical aid remains unexplored for biomolecule delivery across the cell wall in plants. Herein, we report a systematic assessment of different DNA nanostructures for their ability to internalize into cells of mature plants, deliver siRNAs, and effectively silence a constitutively expressed gene in Nicotiana benthamiana leaves. We show that nanostructure internalization into plant cells and corresponding gene silencing efficiency depends on the DNA nanostructure size, shape, compactness, stiffness, and location of the siRNA attachment locus on the nanostructure. We further confirm that the internalization efficiency of DNA nanostructures correlates with their respective gene silencing efficiencies but that the endogenous gene silencing pathway depends on the siRNA attachment locus. Our work establishes the feasibility of biomolecule delivery to plants with DNA nanostructures and both details the design parameters of importance for plant cell internalization and also assesses the impact of DNA nanostructure geometry for gene silencing mechanisms.
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Affiliation(s)
- Huan Zhang
- Department of Chemical and Biomolecular Engineering, University of California, Berkeley, CA 94720
| | - Gozde S Demirer
- Department of Chemical and Biomolecular Engineering, University of California, Berkeley, CA 94720
| | - Honglu Zhang
- Department of Molecular and Cell Biology, University of California, Berkeley, CA 94720
| | - Tianzheng Ye
- Department of Chemical and Biomolecular Engineering, University of California, Berkeley, CA 94720
| | - Natalie S Goh
- Department of Chemical and Biomolecular Engineering, University of California, Berkeley, CA 94720
| | - Abhishek J Aditham
- Department of Chemical and Biomolecular Engineering, University of California, Berkeley, CA 94720
| | - Francis J Cunningham
- Department of Chemical and Biomolecular Engineering, University of California, Berkeley, CA 94720
| | - Chunhai Fan
- Division of Physical Biology & Bioimaging Center, Shanghai Synchrotron Radiation Facility, Chinese Academy of Sciences Key Laboratory of Interfacial Physics and Technology, Shanghai Institute of Applied Physics, Chinese Academy of Sciences, Shanghai 201800, China
- School of Chemistry and Chemical Engineering, Shanghai Jiao Tong University, Shanghai 200240, China
| | - Markita P Landry
- Department of Chemical and Biomolecular Engineering, University of California, Berkeley, CA 94720;
- Innovative Genomics Institute, Berkeley, CA 94720
- California Institute for Quantitative Biosciences (QB3), University of California, Berkeley, CA 94720
- Chan-Zuckerberg Biohub, San Francisco, CA 94158
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31
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Mewalal R, Yin H, Hu R, Jawdy S, Vion P, Tuskan GA, Le Tacon F, Labbé JL, Yang X. Identification of Populus Small RNAs Responsive to Mutualistic Interactions With Mycorrhizal Fungi, Laccaria bicolor and Rhizophagus irregularis. Front Microbiol 2019; 10:515. [PMID: 30936859 PMCID: PMC6431645 DOI: 10.3389/fmicb.2019.00515] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2018] [Accepted: 02/28/2019] [Indexed: 12/02/2022] Open
Abstract
Ecto- and endo-mycorrhizal colonization of Populus roots have a positive impact on the overall tree health and growth. A complete molecular understanding of these interactions will have important implications for increasing agricultural or forestry sustainability using plant:microbe-based strategies. These beneficial associations entail extensive morphological changes orchestrated by the genetic reprogramming in both organisms. In this study, we performed a comparative analysis of two Populus species (Populus deltoides and P. trichocarpa) that were colonized by either an arbuscular mycorrhizal fungus (AmF), Rhizophagus irregularis or an ectomycorrhizal fungus (EmF), Laccaria bicolor, to describe the small RNA (sRNA) landscape including small open reading frames (sORFs) and micro RNAs (miRNAs) involved in these mutualistic interactions. We identified differential expression of sRNAs that were, to a large extent, (1) within the genomic regions lacking annotated genes in the Populus genome and (2) distinct for each fungal interaction. These sRNAs may be a source of novel sORFs within a genome, and in this regard, we identified potential sORFs encoded by the sRNAs. We predicted a higher number of differentially-expressed miRNAs in P. trichocarpa (4 times more) than in P. deltoides (conserved and novel). In addition, 44 miRNAs were common in P. trichocarpa between the EmF and AmF treatments, and only 4 miRNAs were common in P. deltoides between the treatments. Root colonization by either fungus was more effective in P. trichocarpa than in P. deltoides, thus the relatively few differentially-expressed miRNAs predicted in P. deltoides might reflect the extent of the symbiosis. Finally, we predicted several genes targets for the plant miRNAs identified here, including potential fungal gene targets. Our findings shed light on additional molecular tiers with a role in Populus-fungal mutualistic associations and provides a set of potential molecular targets for future enhancement.
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Affiliation(s)
- Ritesh Mewalal
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN, United States
| | - Hengfu Yin
- State Key Laboratory of Tree Genetics and Breeding, Research Institute of Subtropical Forestry, Chinese Academy of Forestry, Fuyang, China
| | - Rongbin Hu
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN, United States
| | - Sara Jawdy
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN, United States
| | - Patrice Vion
- INRA, UMR 1136 INRA-University of Lorraine, Interactions Arbres/Microorganismes, Laboratory of Excellence ARBRE, INRA-Nancy, VandIJuvre-lès-Nancy, France
| | - Gerald A. Tuskan
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN, United States
| | - François Le Tacon
- INRA, UMR 1136 INRA-University of Lorraine, Interactions Arbres/Microorganismes, Laboratory of Excellence ARBRE, INRA-Nancy, VandIJuvre-lès-Nancy, France
| | - Jessy L. Labbé
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN, United States
| | - Xiaohan Yang
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN, United States
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32
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Cagliari D, Dias NP, Galdeano DM, dos Santos EÁ, Smagghe G, Zotti MJ. Management of Pest Insects and Plant Diseases by Non-Transformative RNAi. FRONTIERS IN PLANT SCIENCE 2019; 10:1319. [PMID: 31708946 PMCID: PMC6823229 DOI: 10.3389/fpls.2019.01319] [Citation(s) in RCA: 88] [Impact Index Per Article: 17.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/05/2019] [Accepted: 09/23/2019] [Indexed: 05/17/2023]
Abstract
Since the discovery of RNA interference (RNAi), scientists have made significant progress towards the development of this unique technology for crop protection. The RNAi mechanism works at the mRNA level by exploiting a sequence-dependent mode of action with high target specificity due to the design of complementary dsRNA molecules, allowing growers to target pests more precisely compared to conventional agrochemicals. The delivery of RNAi through transgenic plants is now a reality with some products currently in the market. Conversely, it is also expected that more RNA-based products reach the market as non-transformative alternatives. For instance, topically applied dsRNA/siRNA (SIGS - Spray Induced Gene Silencing) has attracted attention due to its feasibility and low cost compared to transgenic plants. Once on the leaf surface, dsRNAs can move directly to target pest cells (e.g., insects or pathogens) or can be taken up indirectly by plant cells to then be transferred into the pest cells. Water-soluble formulations containing pesticidal dsRNA provide alternatives, especially in some cases where plant transformation is not possible or takes years and cost millions to be developed (e.g., perennial crops). The ever-growing understanding of the RNAi mechanism and its limitations has allowed scientists to develop non-transgenic approaches such as trunk injection, soaking, and irrigation. While the technology has been considered promising for pest management, some issues such as RNAi efficiency, dsRNA degradation, environmental risk assessments, and resistance evolution still need to be addressed. Here, our main goal is to review some possible strategies for non-transgenic delivery systems, addressing important issues related to the use of this technology.
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Affiliation(s)
- Deise Cagliari
- Laboratory of Molecular Entomology, Department of Crop Protection, Federal University of Pelotas, Pelotas, Brazil
- *Correspondence: Deise Cagliari, ; Guy Smagghe, ; Moisés João Zotti,
| | - Naymã P. Dias
- Laboratory of Molecular Entomology, Department of Crop Protection, Federal University of Pelotas, Pelotas, Brazil
| | | | - Ericmar Ávila dos Santos
- Laboratory of Molecular Entomology, Department of Crop Protection, Federal University of Pelotas, Pelotas, Brazil
| | - Guy Smagghe
- Department of Plants and Crops, Ghent University, Ghent, Belgium
- *Correspondence: Deise Cagliari, ; Guy Smagghe, ; Moisés João Zotti,
| | - Moisés João Zotti
- Laboratory of Molecular Entomology, Department of Crop Protection, Federal University of Pelotas, Pelotas, Brazil
- *Correspondence: Deise Cagliari, ; Guy Smagghe, ; Moisés João Zotti,
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33
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Liu L, Chen X. Intercellular and systemic trafficking of RNAs in plants. NATURE PLANTS 2018; 4:869-878. [PMID: 30390090 PMCID: PMC7155933 DOI: 10.1038/s41477-018-0288-5] [Citation(s) in RCA: 87] [Impact Index Per Article: 14.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/21/2016] [Accepted: 09/21/2018] [Indexed: 05/14/2023]
Abstract
Plants have evolved dynamic and complex networks of cell-to-cell communication to coordinate and adapt their growth and development to a variety of environmental changes. In addition to small molecules, such as metabolites and phytohormones, macromolecules such as proteins and RNAs also act as signalling agents in plants. As information molecules, RNAs can move locally between cells through plasmodesmata, and over long distances through phloem. Non-cell-autonomous RNAs may act as mobile signals to regulate plant development, nutrient allocation, gene silencing, antiviral defence, stress responses and many other physiological processes in plants. Recent work has shed light on mobile RNAs and, in some cases, uncovered their roles in intercellular and systemic signalling networks. This review summarizes the current knowledge of local and systemic RNA movement, and discusses the potential regulatory mechanisms and biological significance of RNA trafficking in plants.
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Affiliation(s)
- Lin Liu
- Guangdong Provincial Key Laboratory for Plant Epigenetics, College of Life Sciences and Oceanography, Shenzhen University, Shenzhen, China
- Longhua Bioindustry and Innovation Research Institute, Shenzhen University, Shenzhen, China
| | - Xuemei Chen
- Department of Botany and Plant Sciences, Institute of Integrative Genome Biology, University of California, Riverside, CA, USA.
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34
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Tucker MR, Lou H, Aubert MK, Wilkinson LG, Little A, Houston K, Pinto SC, Shirley NJ. Exploring the Role of Cell Wall-Related Genes and Polysaccharides during Plant Development. PLANTS (BASEL, SWITZERLAND) 2018; 7:E42. [PMID: 29857498 PMCID: PMC6028917 DOI: 10.3390/plants7020042] [Citation(s) in RCA: 41] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/29/2018] [Revised: 05/28/2018] [Accepted: 05/29/2018] [Indexed: 12/17/2022]
Abstract
The majority of organs in plants are not established until after germination, when pluripotent stem cells in the growing apices give rise to daughter cells that proliferate and subsequently differentiate into new tissues and organ primordia. This remarkable capacity is not only restricted to the meristem, since maturing cells in many organs can also rapidly alter their identity depending on the cues they receive. One general feature of plant cell differentiation is a change in cell wall composition at the cell surface. Historically, this has been viewed as a downstream response to primary cues controlling differentiation, but a closer inspection of the wall suggests that it may play a much more active role. Specific polymers within the wall can act as substrates for modifications that impact receptor binding, signal mobility, and cell flexibility. Therefore, far from being a static barrier, the cell wall and its constituent polysaccharides can dictate signal transmission and perception, and directly contribute to a cell's capacity to differentiate. In this review, we re-visit the role of plant cell wall-related genes and polysaccharides during various stages of development, with a particular focus on how changes in cell wall machinery accompany the exit of cells from the stem cell niche.
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Affiliation(s)
- Matthew R Tucker
- School of Agriculture, Food and Wine, Waite Research Institute, The University of Adelaide, Glen Osmond, SA 5062, Australia.
| | - Haoyu Lou
- School of Agriculture, Food and Wine, Waite Research Institute, The University of Adelaide, Glen Osmond, SA 5062, Australia.
- Australian Research Council Centre of Excellence in Plant Cell Walls, The University of Adelaide, Glen Osmond, SA 5062, Australia.
| | - Matthew K Aubert
- School of Agriculture, Food and Wine, Waite Research Institute, The University of Adelaide, Glen Osmond, SA 5062, Australia.
- Australian Research Council Centre of Excellence in Plant Cell Walls, The University of Adelaide, Glen Osmond, SA 5062, Australia.
| | - Laura G Wilkinson
- School of Agriculture, Food and Wine, Waite Research Institute, The University of Adelaide, Glen Osmond, SA 5062, Australia.
- Australian Research Council Centre of Excellence in Plant Cell Walls, The University of Adelaide, Glen Osmond, SA 5062, Australia.
| | - Alan Little
- School of Agriculture, Food and Wine, Waite Research Institute, The University of Adelaide, Glen Osmond, SA 5062, Australia.
| | - Kelly Houston
- Cell and Molecular Sciences, The James Hutton Institute, Dundee DD2 5DA, UK.
| | - Sara C Pinto
- Departamento de Biologia, Faculdade de Ciências da Universidade do Porto, 4169-007 Porto, Portugal.
| | - Neil J Shirley
- School of Agriculture, Food and Wine, Waite Research Institute, The University of Adelaide, Glen Osmond, SA 5062, Australia.
- Australian Research Council Centre of Excellence in Plant Cell Walls, The University of Adelaide, Glen Osmond, SA 5062, Australia.
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35
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Faustinelli PC, Power IL, Arias RS. Detection of exogenous double-stranded RNA movement in in vitro peanut plants. PLANT BIOLOGY (STUTTGART, GERMANY) 2018; 20:444-449. [PMID: 29405546 DOI: 10.1111/plb.12703] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/29/2017] [Accepted: 01/30/2018] [Indexed: 06/07/2023]
Abstract
New technologies are needed to eliminate mycotoxins and/or fungal pathogens from agricultural products. RNA interference (RNAi) has shown potential to control fungi associated with crops. In RNAi, double-stranded RNA (dsRNA) targets homologous mRNA for cleavage, and can reach the mRNA of pathogens in contact with the plant. The key element in this process is the movement of RNA signals cell-to-cell and over long distances within the plant, and between host plants and parasites. In this study, we selected a regulatory gene in the aflatoxin biosynthesis pathway, aflS/aflR, necessary for the production of aflatoxins in Aspergillus spp. We designed a Dicer-substrate RNA (DsiRNA) to study the movement and stability of the duplex over time in in vitro peanut plants using stem-loop primers and RT-PCR for DsiRNA detection. The preliminary results demonstrated that DsiRNA was absorbed and moved away from the point of application, spread systemically and was transported rapidly, most likely through the phloem of the shoot, to the sink tissues, such as new auxiliary shoots, flowers and newly formed pegs. The DsiRNA remained detectable for at least 30 days after treatment. This is the first time that movement of exogenous DsiRNA in in vitro peanut plants has been described. Since DsiRNA was detectable in the pegs 15 days after treatment, aflatoxin reduction may be possible if the duplexes containing part of the aflatoxin biosynthesis pathogen gene induce silencing in the peanut seeds colonised by Aspergillus spp. The application of small RNAs could be a non-transformative option for mycotoxin contamination control.
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Affiliation(s)
- P C Faustinelli
- USDA-ARS National Peanut Research Laboratory, Dawson, GA, USA
| | - I L Power
- USDA-ARS National Peanut Research Laboratory, Dawson, GA, USA
| | - R S Arias
- USDA-ARS National Peanut Research Laboratory, Dawson, GA, USA
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36
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Brant EJ, Budak H. Plant Small Non-coding RNAs and Their Roles in Biotic Stresses. FRONTIERS IN PLANT SCIENCE 2018; 9:1038. [PMID: 30079074 PMCID: PMC6062887 DOI: 10.3389/fpls.2018.01038] [Citation(s) in RCA: 60] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/02/2018] [Accepted: 06/26/2018] [Indexed: 05/04/2023]
Abstract
Non-coding RNAs (ncRNAs) have emerged as critical components of gene regulatory networks across a plethora of plant species. In particular, the 20-30 nucleotide small ncRNAs (sRNAs) play important roles in mediating both developmental processes and responses to biotic stresses. Based on variation in their biogenesis pathways, a number of different sRNA classes have been identified, and their specific functions have begun to be characterized. Here, we review the current knowledge of the biogenesis of the primary sRNA classes, microRNA (miRNA) and small nuclear RNA (snRNA), and their respective secondary classes, and discuss the roles of sRNAs in plant-pathogen interactions. sRNA mobility between species is also discussed along with potential applications of sRNA-plant-pathogen interactions in crop improvement technologies.
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Srivastava S, Sharma A. Study of microRNA mediated gene regulation in Striga hermonthica through in-silico approach. ACTA ACUST UNITED AC 2017. [DOI: 10.1016/j.aggene.2017.09.004] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
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38
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Limera C, Sabbadini S, Sweet JB, Mezzetti B. New Biotechnological Tools for the Genetic Improvement of Major Woody Fruit Species. FRONTIERS IN PLANT SCIENCE 2017; 8:1418. [PMID: 28861099 PMCID: PMC5559511 DOI: 10.3389/fpls.2017.01418] [Citation(s) in RCA: 51] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/17/2017] [Accepted: 07/31/2017] [Indexed: 05/09/2023]
Abstract
The improvement of woody fruit species by traditional plant breeding techniques has several limitations mainly caused by their high degree of heterozygosity, the length of their juvenile phase and auto-incompatibility. The development of new biotechnological tools (NBTs), such as RNA interference (RNAi), trans-grafting, cisgenesis/intragenesis, and genome editing tools, like zinc-finger and CRISPR/Cas9, has introduced the possibility of more precise and faster genetic modifications of plants. This aspect is of particular importance for the introduction or modification of specific traits in woody fruit species while maintaining unchanged general characteristics of a selected cultivar. Moreover, some of these new tools give the possibility to obtain transgene-free modified fruit tree genomes, which should increase consumer's acceptance. Over the decades biotechnological tools have undergone rapid development and there is a continuous addition of new and valuable techniques for plant breeders. This makes it possible to create desirable woody fruit varieties in a fast and more efficient way to meet the demand for sustainable agricultural productivity. Although, NBTs have a common goal i.e., precise, fast, and efficient crop improvement, individually they are markedly different in approach and characteristics from each other. In this review we describe in detail their mechanisms and applications for the improvement of fruit trees and consider the relationship between these biotechnological tools and the EU biosafety regulations applied to the plants and products obtained through these techniques.
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Affiliation(s)
- Cecilia Limera
- Department of Agricultural, Food and Environmental Sciences, Università Politecnica delle MarcheAncona, Italy
| | - Silvia Sabbadini
- Department of Agricultural, Food and Environmental Sciences, Università Politecnica delle MarcheAncona, Italy
| | - Jeremy B. Sweet
- J. T. Environmental Consultants LtdCambridge, United Kingdom
| | - Bruno Mezzetti
- Department of Agricultural, Food and Environmental Sciences, Università Politecnica delle MarcheAncona, Italy
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Dubey NK, Eizenberg H, Leibman D, Wolf D, Edelstein M, Abu-Nassar J, Marzouk S, Gal-On A, Aly R. Enhanced Host-Parasite Resistance Based on Down-Regulation of Phelipanche aegyptiaca Target Genes Is Likely by Mobile Small RNA. FRONTIERS IN PLANT SCIENCE 2017; 8:1574. [PMID: 28955363 PMCID: PMC5601039 DOI: 10.3389/fpls.2017.01574] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/27/2016] [Accepted: 08/28/2017] [Indexed: 05/06/2023]
Abstract
RNA silencing refers to diverse mechanisms that control gene expression at transcriptional and post-transcriptional levels which can also be used in parasitic pathogens of plants that Broomrapes (Orobanche/Phelipanche spp.) are holoparasitic plants that subsist on the roots of a variety of agricultural crops and cause severe negative effects on the yield and yield quality of those crops. Effective methods for controlling parasitic weeds are scarce, with only a few known cases of genetic resistance. In the current study, we suggest an improved strategy for the control of parasitic weeds based on trans-specific gene-silencing of three parasite genes at once. We used two strategies to express dsRNA containing selected sequences of three Phelipanche aegyptiaca genes PaACS, PaM6PR, and PaPrx1 (pma): transient expression using Tobacco rattle virus (TRV:pma) as a virus-induced gene-silencing vector and stable expression in transgenic tomato Solanum lycopersicum (Mill.) plants harboring a hairpin construct (pBINPLUS35:pma). siRNA-mediated transgene-silencing (20-24 nt) was detected in the host plants. Our results demonstrate that the quantities of PaACS and PaM6PR transcripts from P. aegyptiaca tubercles grown on transgenic tomato or on TRV-infected Nicotiana benthamiana plants were significantly reduced. However, only partial reductions in the quantity of PaPrx1 transcripts were observed in the parasite tubercles grown on tomato and on N. benthamiana plants. Concomitant with the suppression of the target genes, there were significant decreases in the number and weight of the parasite tubercles that grew on the host plants, in both the transient and the stable experimental systems. The results of the work carried out using both strategies point to the movement of mobile exogenous siRNA from the host to the parasite, leading to the impaired expression of essential parasite target genes.
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Affiliation(s)
- Neeraj K. Dubey
- Department of Plant Pathology and Weed Research, Newe Ya’ar Research Center, Agricultural Research Organization, Volcani CenterRamat Yishay, Israel
| | - Hanan Eizenberg
- Department of Plant Pathology and Weed Research, Newe Ya’ar Research Center, Agricultural Research Organization, Volcani CenterRamat Yishay, Israel
| | - Diana Leibman
- Department of Plant Pathology and Weed Research, Agricultural Research Organization, Volcani CenterRishon LeZion, Israel
| | - Dalia Wolf
- Department of Plant Science, Agricultural Research Organization, Volcani CenterRishon LeZion, Israel
| | - Menahem Edelstein
- Department of Plant Science, Agricultural Research Organization, Volcani CenterRishon LeZion, Israel
| | - Jackline Abu-Nassar
- Department of Plant Pathology and Weed Research, Newe Ya’ar Research Center, Agricultural Research Organization, Volcani CenterRamat Yishay, Israel
| | - Sally Marzouk
- Department of Plant Pathology and Weed Research, Newe Ya’ar Research Center, Agricultural Research Organization, Volcani CenterRamat Yishay, Israel
| | - Amit Gal-On
- Department of Plant Pathology and Weed Research, Agricultural Research Organization, Volcani CenterRishon LeZion, Israel
| | - Radi Aly
- Department of Plant Pathology and Weed Research, Newe Ya’ar Research Center, Agricultural Research Organization, Volcani CenterRamat Yishay, Israel
- *Correspondence: Radi Aly,
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Hamera S, Yan Y, Song X, Chaudhary SU, Murtaza I, Su L, Tariq M, Chen X, Fang R. Expression of Cucumber mosaic virus suppressor 2b alters FWA methylation and its siRNA accumulation in Arabidopsis thaliana. Biol Open 2016; 5:1727-1734. [PMID: 27659688 PMCID: PMC5155521 DOI: 10.1242/bio.017244] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022] Open
Abstract
The Cucumber mosaic virus (CMV) suppressor 2b co-localizes with AGO4 in cytoplasmic and nuclear fractions of Arabidopsis thaliana Biochemical fractionation of A. thaliana cellular extracts revealed that 2b and AGO4 coexist in multiple size exclusions. 2b transgenic A. thaliana exhibited an enhanced accumulation of 24nt siRNAs from flowering wageningen (FWA) and other heterochromatic loci. These plants also exhibited hypo-methylation of an endogenous- as well as transgene-FWA promoter at non-CG sites. In corroboration, both transgenic 2b and CMV infection affected the regulation of transposons which mimics the ago4 phenotype. In conclusion, 2b perturbs plant defense by interfering with AGO4-regulated transcriptional gene silencing.
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Affiliation(s)
- Sadia Hamera
- SBA School of Science and Engineering, Lahore University of Management Sciences (LUMS), DHA, Lahore 54792, Pakistan .,State Key Laboratory of Plant Genomics and National Center for Plant Gene Research, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, China
| | - Youngsheng Yan
- State Key Laboratory of Plant Genomics and National Center for Plant Gene Research, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, China
| | - Xiaoguang Song
- State Key Laboratory of Plant Genomics and National Center for Plant Gene Research, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, China
| | - Safee Ullah Chaudhary
- SBA School of Science and Engineering, Lahore University of Management Sciences (LUMS), DHA, Lahore 54792, Pakistan
| | - Iram Murtaza
- Department of Biochemistry, Quaid i Azam University, Islamabad 54320, Pakistan
| | - Lei Su
- State Key Laboratory of Plant Genomics and National Center for Plant Gene Research, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, China
| | - Muhammad Tariq
- SBA School of Science and Engineering, Lahore University of Management Sciences (LUMS), DHA, Lahore 54792, Pakistan
| | - Xiaoying Chen
- State Key Laboratory of Plant Genomics and National Center for Plant Gene Research, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, China
| | - Rongxiang Fang
- State Key Laboratory of Plant Genomics and National Center for Plant Gene Research, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, China
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Kontra L, Csorba T, Tavazza M, Lucioli A, Tavazza R, Moxon S, Tisza V, Medzihradszky A, Turina M, Burgyán J. Distinct Effects of p19 RNA Silencing Suppressor on Small RNA Mediated Pathways in Plants. PLoS Pathog 2016; 12:e1005935. [PMID: 27711201 PMCID: PMC5053613 DOI: 10.1371/journal.ppat.1005935] [Citation(s) in RCA: 55] [Impact Index Per Article: 6.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2016] [Accepted: 09/13/2016] [Indexed: 12/30/2022] Open
Abstract
RNA silencing is one of the main defense mechanisms employed by plants to fight viruses. In change, viruses have evolved silencing suppressor proteins to neutralize antiviral silencing. Since the endogenous and antiviral functions of RNA silencing pathway rely on common components, it was suggested that viral suppressors interfere with endogenous silencing pathway contributing to viral symptom development. In this work, we aimed to understand the effects of the tombusviral p19 suppressor on endogenous and antiviral silencing during genuine virus infection. We showed that ectopically expressed p19 sequesters endogenous small RNAs (sRNAs) in the absence, but not in the presence of virus infection. Our presented data question the generalized model in which the sequestration of endogenous sRNAs by the viral suppressor contributes to the viral symptom development. We further showed that p19 preferentially binds the perfectly paired ds-viral small interfering RNAs (vsiRNAs) but does not select based on their sequence or the type of the 5' nucleotide. Finally, co-immunoprecipitation of sRNAs with AGO1 or AGO2 from virus-infected plants revealed that p19 specifically impairs vsiRNA loading into AGO1 but not AGO2. Our findings, coupled with the fact that p19-expressing wild type Cymbidium ringspot virus (CymRSV) overcomes the Nicotiana benthamiana silencing based defense killing the host, suggest that AGO1 is the main effector of antiviral silencing in this host-virus combination.
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Affiliation(s)
- Levente Kontra
- National Agricultural Research and Innovation Centre, Agricultural Biotechnology Institute, Gödöllő, Hungary
- Szent István University, Gödöllő, Hungary
| | - Tibor Csorba
- National Agricultural Research and Innovation Centre, Agricultural Biotechnology Institute, Gödöllő, Hungary
| | - Mario Tavazza
- Italian National Agency for New Technologies, Energy and Sustainable Economic Development (ENEA), C.R. Casaccia, Rome, Italy
| | - Alessandra Lucioli
- Italian National Agency for New Technologies, Energy and Sustainable Economic Development (ENEA), C.R. Casaccia, Rome, Italy
| | - Raffaela Tavazza
- Italian National Agency for New Technologies, Energy and Sustainable Economic Development (ENEA), C.R. Casaccia, Rome, Italy
| | - Simon Moxon
- School of Biological Sciences, University of East Anglia, Norwich, Norfolk, United Kingdom
| | - Viktória Tisza
- National Agricultural Research and Innovation Centre, Agricultural Biotechnology Institute, Gödöllő, Hungary
| | - Anna Medzihradszky
- National Agricultural Research and Innovation Centre, Agricultural Biotechnology Institute, Gödöllő, Hungary
| | - Massimo Turina
- National Research Council, Institute for Sustainable Plant Protection, Torino, Italy
| | - József Burgyán
- National Agricultural Research and Innovation Centre, Agricultural Biotechnology Institute, Gödöllő, Hungary
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Liu L, Chen X. RNA Quality Control as a Key to Suppressing RNA Silencing of Endogenous Genes in Plants. MOLECULAR PLANT 2016; 9:826-36. [PMID: 27045817 PMCID: PMC5123867 DOI: 10.1016/j.molp.2016.03.011] [Citation(s) in RCA: 66] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/17/2016] [Revised: 03/10/2016] [Accepted: 03/14/2016] [Indexed: 05/19/2023]
Abstract
RNA quality control of endogenous RNAs is an integral part of eukaryotic gene expression and often relies on exonucleolytic degradation to eliminate dysfunctional transcripts. In parallel, exogenous and selected endogenous RNAs are degraded through RNA silencing, which is a genome defense mechanism used by many eukaryotes. In plants, RNA silencing is triggered by the production of double-stranded RNAs (dsRNAs) by RNA-DEPENDENT RNA POLYMERASEs (RDRs) and proceeds through small interfering (si) RNA-directed, ARGONAUTE (AGO)-mediated cleavage of homologous transcripts. Many studies revealed that plants avert inappropriate posttranscriptional gene silencing of endogenous coding genes by using RNA surveillance mechanisms as a safeguard to protect their transcriptome profiles. The tug of war between RNA surveillance and RNA silencing ensures the appropriate partitioning of endogenous RNA substrates among these degradation pathways. Here we review recent advances on RNA quality control and its role in the suppression of RNA silencing at endogenous genes and discuss the mechanisms underlying the crosstalk among these pathways.
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Affiliation(s)
- Lin Liu
- Guangdong Provincial Key Laboratory for Plant Epigenetics, College of Life Sciences and Oceanography, Shenzhen University, Shenzhen 518060, P.R. China; Department of Botany and Plant Sciences, Institute of Integrative Genome Biology, University of California, Riverside, CA 92521, USA
| | - Xuemei Chen
- Guangdong Provincial Key Laboratory for Plant Epigenetics, College of Life Sciences and Oceanography, Shenzhen University, Shenzhen 518060, P.R. China; Department of Botany and Plant Sciences, Institute of Integrative Genome Biology, University of California, Riverside, CA 92521, USA; Howard Hughes Medical Institute, University of California, Riverside, CA 92521, USA.
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43
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Syller J, Grupa A. Antagonistic within-host interactions between plant viruses: molecular basis and impact on viral and host fitness. MOLECULAR PLANT PATHOLOGY 2016; 17:769-82. [PMID: 26416204 PMCID: PMC6638324 DOI: 10.1111/mpp.12322] [Citation(s) in RCA: 69] [Impact Index Per Article: 8.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/21/2023]
Abstract
Double infections of related or unrelated viruses frequently occur in single plants, the viral agents being inoculated into the host plant simultaneously (co-infection) or sequentially (super-infection). Plants attacked by viruses activate sophisticated defence pathways which operate at different levels, often at significant fitness costs, resulting in yield reduction in crop plants. The occurrence and severity of the negative effects depend on the type of within-host interaction between the infecting viruses. Unrelated viruses generally interact with each other in a synergistic manner, whereas interactions between related viruses are mostly antagonistic. These can incur substantial fitness costs to one or both of the competitors. A relatively well-known antagonistic interaction is cross-protection, also referred to as super-infection exclusion. This type of interaction occurs when a previous infection with one virus prevents or interferes with subsequent infection by a homologous second virus. The current knowledge on why and how one virus variant excludes or restricts another is scant. Super-infection exclusion between viruses has predominantly been attributed to the induction of RNA silencing, which is a major antiviral defence mechanism in plants. There are, however, presumptions that various mechanisms are involved in this phenomenon. This review outlines the current state of knowledge concerning the molecular mechanisms behind antagonistic interactions between plant viruses. Harmful or beneficial effects of these interactions on viral and host plant fitness are also characterized. Moreover, the review briefly outlines the past and present attempts to utilize antagonistic interactions among viruses to protect crop plants against destructive diseases.
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Affiliation(s)
- Jerzy Syller
- Plant Breeding and Acclimatization Institute-National Research Institute, Laboratory of Phytopathology, Centre Młochów, 05-831, Młochów, Poland
| | - Anna Grupa
- Plant Breeding and Acclimatization Institute-National Research Institute, Laboratory of Phytopathology, Centre Młochów, 05-831, Młochów, Poland
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44
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Kubota K, Ng JCK. Lettuce chlorosis virus P23 Suppresses RNA Silencing and Induces Local Necrosis with Increased Severity at Raised Temperatures. PHYTOPATHOLOGY 2016; 106:653-62. [PMID: 26828232 DOI: 10.1094/phyto-09-15-0219-r] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/05/2023]
Abstract
RNA silencing functions as an antivirus defense strategy in plants, one that plant viruses counter by producing viral suppressors of RNA silencing (VSRs). VSRs have been identified in three members of the genus Crinivirus but they do not all share identical suppression mechanisms. Here, we used Agrobacterium co-infiltration assays to investigate the suppressor activity of proteins encoded by Lettuce chlorosis virus (LCV). Of 7 LCV proteins (1b, P23, HSP70 homolog, P60, CP, CPm, and P27) tested for the suppression of silencing of green fluorescent protein (GFP) expression in wild-type Nicotiana benthamiana plants, only P23 suppressed the onset of local silencing. Small-interfering (si)RNA accumulation was reduced in leaves co-infiltrated with P23, suggesting that P23 inhibited the accumulation or enhanced the degradation of siRNA. P23 also inhibited the cell-to-cell and systemic movement of RNA silencing in GFP-expressing transgenic N. benthamiana plants. Expression of P23 via agroinfiltration of N. benthamiana leaves induced local necrosis that increased in severity at elevated temperatures, a novelty given that a direct temperature effect on necrosis severity has not been reported for the other crinivirus VSRs. These results further affirm the sophistication of crinivirus VSRs in mediating the evasion of host's antiviral defenses and in symptom modulation.
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Affiliation(s)
- Kenji Kubota
- First author: NARO Agricultural Research Center, Kannondai, Tsukuba, Ibaraki 305-8666, Japan, and Department of Plant Pathology and Microbiology, University of California, Riverside 92521; second author: Department of Plant Pathology and Microbiology, University of California, Riverside 92521
| | - James C K Ng
- First author: NARO Agricultural Research Center, Kannondai, Tsukuba, Ibaraki 305-8666, Japan, and Department of Plant Pathology and Microbiology, University of California, Riverside 92521; second author: Department of Plant Pathology and Microbiology, University of California, Riverside 92521
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45
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Huang J, Yang M, Zhang X. The function of small RNAs in plant biotic stress response. JOURNAL OF INTEGRATIVE PLANT BIOLOGY 2016; 58:312-27. [PMID: 26748943 DOI: 10.1111/jipb.12463] [Citation(s) in RCA: 53] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/09/2015] [Accepted: 01/07/2016] [Indexed: 05/18/2023]
Abstract
Small RNAs (sRNAs) play essential roles in plants upon biotic stress. Plants utilize RNA silencing machinery to facilitate pathogen-associated molecular pattern-triggered immunity and effector-triggered immunity to defend against pathogen attack or to facilitate defense against insect herbivores. Pathogens, on the other hand, are also able to generate effectors and sRNAs to counter the host immune response. The arms race between plants and pathogens/insect herbivores has triggered the evolution of sRNAs, RNA silencing machinery and pathogen effectors. A great number of studies have been performed to investigate the roles of sRNAs in plant defense, bringing in the opportunity to utilize sRNAs in plant protection. Transgenic plants with pathogen-derived resistance ability or transgenerational defense have been generated, which show promising potential as solutions for pathogen/insect herbivore problems in the field. Here we summarize the recent progress on the function of sRNAs in response to biotic stress, mainly in plant-pathogen/insect herbivore interaction, and the application of sRNAs in disease and insect herbivore control.
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Affiliation(s)
- Juan Huang
- State Key Laboratory of Integrated Management of Pest Insects and Rodents, Institute of Zoology, Chinese Academy of Sciences, Beijing, China
| | - Meiling Yang
- State Key Laboratory of Integrated Management of Pest Insects and Rodents, Institute of Zoology, Chinese Academy of Sciences, Beijing, China
| | - Xiaoming Zhang
- State Key Laboratory of Integrated Management of Pest Insects and Rodents, Institute of Zoology, Chinese Academy of Sciences, Beijing, China
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Kotakis C. Non-coding RNAs' partitioning in the evolution of photosynthetic organisms via energy transduction and redox signaling. RNA Biol 2015; 12:101-4. [PMID: 25826417 DOI: 10.1080/15476286.2015.1017201] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/23/2022] Open
Abstract
Ars longa, vita brevis -Hippocrates Chloroplasts and mitochondria are genetically semi-autonomous organelles inside the plant cell. These constructions formed after endosymbiosis and keep evolving throughout the history of life. Experimental evidence is provided for active non-coding RNAs (ncRNAs) in these prokaryote-like structures, and a possible functional imprinting on cellular electrophysiology by those RNA entities is described. Furthermore, updated knowledge on RNA metabolism of organellar genomes uncovers novel inter-communication bridges with the nucleus. This class of RNA molecules is considered as a unique ontogeny which transforms their biological role as a genetic rheostat into a synchronous biochemical one that can affect the energetic charge and redox homeostasis inside cells. A hypothesis is proposed where such modulation by non-coding RNAs is integrated with genetic signals regulating gene transfer. The implications of this working hypothesis are discussed, with particular reference to ncRNAs involvement in the organellar and nuclear genomes evolution since their integrity is functionally coupled with redox signals in photosynthetic organisms.
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Affiliation(s)
- Christos Kotakis
- a Agro-environmental cooperative BioNet West Hellas ; Gastouni Ileias, Hellas , Greece
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47
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Time-delayed model of immune response in plants. J Theor Biol 2015; 389:28-39. [PMID: 26551159 DOI: 10.1016/j.jtbi.2015.10.020] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2015] [Revised: 10/01/2015] [Accepted: 10/28/2015] [Indexed: 11/21/2022]
Abstract
In the studies of plant infections, the plant immune response is known to play an essential role. In this paper we derive and analyse a new mathematical model of plant immune response with particular account for post-transcriptional gene silencing (PTGS). Besides biologically accurate representation of the PTGS dynamics, the model explicitly includes two time delays to represent the maturation time of the growing plant tissue and the non-instantaneous nature of the PTGS. Through analytical and numerical analysis of stability of the steady states of the model we identify parameter regions associated with recovery and resistant phenotypes, as well as possible chronic infections. Dynamics of the system in these regimes is illustrated by numerical simulations of the model.
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48
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Grafting on a Non-Transgenic Tolerant Tomato Variety Confers Resistance to the Infection of a Sw5-Breaking Strain of Tomato spotted wilt virus via RNA Silencing. PLoS One 2015. [PMID: 26496695 DOI: 10.1371/journal.pone.0141319.] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
RNA silencing controls endogenous gene expression and drives defensive reactions against invasive nucleic acids like viruses. In plants, it has been demonstrated that RNA silencing can be transmitted through grafting between scions and silenced rootstocks to attenuate virus and viroid accumulation in the scions. This has been obtained mostly using transgenic plants, which may be a drawback in current agriculture. In the present study, we examined the dynamics of infection of a resistance-breaking strain of Tomato spotted wilt virus (RB-TSWV) through the graft between an old Apulian (southern Italy) tomato variety, denoted Sl-Ma, used as a rootstock and commercial tomato varieties used as scions. In tests with non-grafted plants, Sl-Ma showed resistance to the RB-TSWV infection as viral RNA accumulated at low levels and plants recovered from disease symptoms by 21 days post inoculation. The resistance trait was transmitted to the otherwise highly susceptible tomato genotypes grafted onto Sl-Ma. The results from the analysis of small RNAs hallmark genes involved in RNA silencing and virus-induced gene silencing suggest that RNA silencing is involved in the resistance showed by Sl-Ma against RB-TSWV and in scions grafted on this rootstock. The results from self-grafted susceptible tomato varieties suggest also that RNA silencing is enhanced by the graft itself. We can foresee interesting practical implications of the approach described in this paper.
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49
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Spanò R, Mascia T, Kormelink R, Gallitelli D. Grafting on a Non-Transgenic Tolerant Tomato Variety Confers Resistance to the Infection of a Sw5-Breaking Strain of Tomato spotted wilt virus via RNA Silencing. PLoS One 2015; 10:e0141319. [PMID: 26496695 PMCID: PMC4619829 DOI: 10.1371/journal.pone.0141319] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2014] [Accepted: 10/07/2015] [Indexed: 02/03/2023] Open
Abstract
RNA silencing controls endogenous gene expression and drives defensive reactions against invasive nucleic acids like viruses. In plants, it has been demonstrated that RNA silencing can be transmitted through grafting between scions and silenced rootstocks to attenuate virus and viroid accumulation in the scions. This has been obtained mostly using transgenic plants, which may be a drawback in current agriculture. In the present study, we examined the dynamics of infection of a resistance-breaking strain of Tomato spotted wilt virus (RB-TSWV) through the graft between an old Apulian (southern Italy) tomato variety, denoted Sl-Ma, used as a rootstock and commercial tomato varieties used as scions. In tests with non-grafted plants, Sl-Ma showed resistance to the RB-TSWV infection as viral RNA accumulated at low levels and plants recovered from disease symptoms by 21 days post inoculation. The resistance trait was transmitted to the otherwise highly susceptible tomato genotypes grafted onto Sl-Ma. The results from the analysis of small RNAs hallmark genes involved in RNA silencing and virus-induced gene silencing suggest that RNA silencing is involved in the resistance showed by Sl-Ma against RB-TSWV and in scions grafted on this rootstock. The results from self-grafted susceptible tomato varieties suggest also that RNA silencing is enhanced by the graft itself. We can foresee interesting practical implications of the approach described in this paper.
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Affiliation(s)
- Roberta Spanò
- Dipartimento di Scienze del Suolo della Pianta e Degli Alimenti, Università degli Studi di Bari Aldo Moro, Via Amendola 165/A, Bari, Italy
- Istituto di Virologia vegetale del CNR, Unità Operativa di Supporto di Bari, Via Amendola 165/A, Bari, Italy
| | - Tiziana Mascia
- Dipartimento di Scienze del Suolo della Pianta e Degli Alimenti, Università degli Studi di Bari Aldo Moro, Via Amendola 165/A, Bari, Italy
- Istituto di Virologia vegetale del CNR, Unità Operativa di Supporto di Bari, Via Amendola 165/A, Bari, Italy
- * E-mail:
| | - Richard Kormelink
- Laboratory of Virology, Wageningen University, Droevendaalsesteeg 1, Wageningen, The Netherlands
| | - Donato Gallitelli
- Dipartimento di Scienze del Suolo della Pianta e Degli Alimenti, Università degli Studi di Bari Aldo Moro, Via Amendola 165/A, Bari, Italy
- Istituto di Virologia vegetale del CNR, Unità Operativa di Supporto di Bari, Via Amendola 165/A, Bari, Italy
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50
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Chaves SS, Fernandes-Brum CN, Silva GFF, Ferrara-Barbosa BC, Paiva LV, Nogueira FTS, Cardoso TCS, Amaral LR, de Souza Gomes M, Chalfun-Junior A. New Insights on Coffea miRNAs: Features and Evolutionary Conservation. Appl Biochem Biotechnol 2015; 177:879-908. [PMID: 26277190 DOI: 10.1007/s12010-015-1785-x] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2015] [Accepted: 07/27/2015] [Indexed: 12/31/2022]
Abstract
Small RNAs influence the gene expression at the post-transcriptional level by guiding messenger RNA (mRNA) cleavage, translational repression, and chromatin modifications. In addition to model plants, the microRNAs (miRNAs) have been identified in different crop species. In this work, we developed a specific pipeline to search for coffee miRNA homologs on expressed sequence tags (ESTs) and genome survey sequences (GSS) databases. As a result, 36 microRNAs were identified and a total of 616 and 362 potential targets for Coffea arabica and Coffea canephora, respectively. The evolutionary analyses of these molecules were performed by comparing the primary and secondary structures of precursors and mature miRNAs with their orthologs. Moreover, using a stem-loop RT-PCR assay, we evaluated the accumulation of mature miRNAs in genomes with different ploidy levels, detecting an increase in the miRNAs accumulation according to the ploidy raising. Finally, a 5' RACE (Rapid Amplification of cDNA Ends) assay was performed to verify the regulation of auxin responsive factor 8 (ARF8) by MIR167 in coffee plants. The great variety of target genes indicates the functional plasticity of these molecules and reinforces the importance of understanding the RNAi-dependent regulatory mechanisms. Our results expand the study of miRNAs and their target genes in this crop, providing new challenges to understand the biology of these species.
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Affiliation(s)
- S S Chaves
- Plant Molecular Physiology Laboratory, Biology Department, Federal University of Lavras (UFLA), s/n - Cx., Lavras, Minas Gerais, P 3037, Brazil
| | - C N Fernandes-Brum
- Plant Molecular Physiology Laboratory, Biology Department, Federal University of Lavras (UFLA), s/n - Cx., Lavras, Minas Gerais, P 3037, Brazil
| | - G F F Silva
- Agricultural Biotechnology Center, Agriculture College "Luiz de Queiroz" (ESALQ)/USP, Piracicaba, SP, Brazil
| | - B C Ferrara-Barbosa
- Plant Molecular Physiology Laboratory, Biology Department, Federal University of Lavras (UFLA), s/n - Cx., Lavras, Minas Gerais, P 3037, Brazil
| | - L V Paiva
- Central Laboratory of Molecular Biology (LCBM), Chemistry Department, Federal University of Lavras (UFLA), Lavras, Minas Gerais, Brazil
| | - F T S Nogueira
- Agricultural Biotechnology Center, Agriculture College "Luiz de Queiroz" (ESALQ)/USP, Piracicaba, SP, Brazil
| | - T C S Cardoso
- Laboratory of Bioinformatics and Molecular Analysis-INGEB/FACOM, Federal University of Uberlandia, Campus Patos de Minas, Patos de Minas, MG, Brazil
| | - L R Amaral
- Laboratory of Bioinformatics and Molecular Analysis-INGEB/FACOM, Federal University of Uberlandia, Campus Patos de Minas, Patos de Minas, MG, Brazil
| | - M de Souza Gomes
- Laboratory of Bioinformatics and Molecular Analysis-INGEB/FACOM, Federal University of Uberlandia, Campus Patos de Minas, Patos de Minas, MG, Brazil
| | - A Chalfun-Junior
- Plant Molecular Physiology Laboratory, Biology Department, Federal University of Lavras (UFLA), s/n - Cx., Lavras, Minas Gerais, P 3037, Brazil.
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