1
|
Kallemi P, Verret F, Andronis C, Ioannidis N, Glampedakis N, Kotzabasis K, Kalantidis K. Stress-related transcriptomic changes associated with GFP transgene expression and active transgene silencing in plants. Sci Rep 2024; 14:13314. [PMID: 38858413 PMCID: PMC11164987 DOI: 10.1038/s41598-024-63527-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2023] [Accepted: 05/29/2024] [Indexed: 06/12/2024] Open
Abstract
Plants respond to biotic and abiotic stress by activating and interacting with multiple defense pathways, allowing for an efficient global defense response. RNA silencing is a conserved mechanism of regulation of gene expression directed by small RNAs important in acquired plant immunity and especially virus and transgene repression. Several RNA silencing pathways in plants are crucial to control developmental processes and provide protection against abiotic and biotic stresses as well as invasive nucleic acids such as viruses and transposable elements. Various notable studies have shed light on the genes, small RNAs, and mechanisms involved in plant RNA silencing. However, published research on the potential interactions between RNA silencing and other plant stress responses is limited. In the present study, we tested the hypothesis that spreading and maintenance of systemic post-transcriptional gene silencing (PTGS) of a GFP transgene are associated with transcriptional changes that pertain to non-RNA silencing-based stress responses. To this end, we analyzed the structure and function of the photosynthetic apparatus and conducted whole transcriptome analysis in a transgenic line of Nicotiana benthamiana that spontaneously initiates transgene silencing, at different stages of systemic GFP-PTGS. In vivo analysis of chlorophyll a fluorescence yield and expression levels of key photosynthetic genes indicates that photosynthetic activity remains unaffected by systemic GFP-PTGS. However, transcriptomic analysis reveals that spreading and maintenance of GFP-PTGS are associated with transcriptional reprogramming of genes that are involved in abiotic stress responses and pattern- or effector-triggered immunity-based stress responses. These findings suggest that systemic PTGS may affect non-RNA-silencing-based defense pathways in N. benthamiana, providing new insights into the complex interplay between different plant stress responses.
Collapse
Affiliation(s)
- Paraskevi Kallemi
- Department of Biology, University of Crete, 70013, Heraklion, Greece
| | - Frederic Verret
- Institute of Molecular Biology and Biotechnology, Foundation for Research and Technology-Hellas, 70013, Heraklion, Greece
| | - Christos Andronis
- Institute of Molecular Biology and Biotechnology, Foundation for Research and Technology-Hellas, 70013, Heraklion, Greece
| | | | | | | | - Kriton Kalantidis
- Department of Biology, University of Crete, 70013, Heraklion, Greece.
- Institute of Molecular Biology and Biotechnology, Foundation for Research and Technology-Hellas, 70013, Heraklion, Greece.
| |
Collapse
|
2
|
Hasan MN, Mosharaf MP, Uddin KS, Das KR, Sultana N, Noorunnahar M, Naim D, Mollah MNH. Genome-Wide Identification and Characterization of Major RNAi Genes Highlighting Their Associated Factors in Cowpea ( Vigna unguiculata (L.) Walp.). BIOMED RESEARCH INTERNATIONAL 2023; 2023:8832406. [PMID: 38046903 PMCID: PMC10691899 DOI: 10.1155/2023/8832406] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 06/06/2023] [Revised: 09/07/2023] [Accepted: 10/30/2023] [Indexed: 12/05/2023]
Abstract
In different regions of the world, cowpea (Vigna unguiculata (L.) Walp.) is an important vegetable and an excellent source of protein. It lessens the malnutrition of the underprivileged in developing nations and has some positive effects on health, such as a reduction in the prevalence of cancer and cardiovascular disease. However, occasionally, certain biotic and abiotic stresses caused a sharp fall in cowpea yield. Major RNA interference (RNAi) genes like Dicer-like (DCL), Argonaute (AGO), and RNA-dependent RNA polymerase (RDR) are essential for the synthesis of their associated factors like domain, small RNAs (sRNAs), transcription factors, micro-RNAs, and cis-acting factors that shield plants from biotic and abiotic stresses. In this study, applying BLASTP search and phylogenetic tree analysis with reference to the Arabidopsis RNAi (AtRNAi) genes, we discovered 28 VuRNAi genes, including 7 VuDCL, 14 VuAGO, and 7 VuRDR genes in cowpea. We looked at the domains, motifs, gene structures, chromosomal locations, subcellular locations, gene ontology (GO) terms, and regulatory factors (transcription factors, micro-RNAs, and cis-acting elements (CAEs)) to characterize the VuRNAi genes and proteins in cowpea in response to stresses. Predicted VuDCL1, VuDCL2(a, b), VuAGO7, VuAGO10, and VuRDR6 genes might have an impact on cowpea growth, development of the vegetative and flowering stages, and antiviral defense. The VuRNAi gene regulatory features miR395 and miR396 might contribute to grain quality improvement, immunity boosting, and pathogen infection resistance under salinity and drought conditions. Predicted CAEs from the VuRNAi genes might play a role in plant growth and development, improving grain quality and production and protecting plants from biotic and abiotic stresses. Therefore, our study provides crucial information about the functional roles of VuRNAi genes and their associated components, which would aid in the development of future cowpeas that are more resilient to biotic and abiotic stress. The manuscript is available as a preprint at this link: doi:10.1101/2023.02.15.528631v1.
Collapse
Affiliation(s)
- Mohammad Nazmol Hasan
- Department of Statistics, Bangabandhu Sheikh Mujibur Rahman Agricultural University, Gazipur 1706, Bangladesh
| | - Md Parvez Mosharaf
- School of Business, Faculty of Business, Education, Law and Arts, University of Southern Queensland, Toowoomba, QLD 4350, Australia
| | - Khandoker Saif Uddin
- Department of Quantitative Science (Statistics), International University of Business Agriculture and Technology (IUBAT), Uttara, Bangladesh
| | - Keya Rani Das
- Department of Statistics, Bangabandhu Sheikh Mujibur Rahman Agricultural University, Gazipur 1706, Bangladesh
| | - Nasrin Sultana
- Department of Statistics, Bangabandhu Sheikh Mujibur Rahman Agricultural University, Gazipur 1706, Bangladesh
| | - Mst. Noorunnahar
- Department of Statistics, Bangabandhu Sheikh Mujibur Rahman Agricultural University, Gazipur 1706, Bangladesh
| | - Darun Naim
- Department of Botany, Faculty of Biological Sciences, University of Rajshahi, Rajshahi 6205, Bangladesh
- Bioinformatics Lab, Department of Statistics, Faculty of Science, University of Rajshahi, Rajshahi 6205, Bangladesh
| | - Md. Nurul Haque Mollah
- Bioinformatics Lab, Department of Statistics, Faculty of Science, University of Rajshahi, Rajshahi 6205, Bangladesh
| |
Collapse
|
3
|
Calvo‐Baltanás V, De Jaeger‐Braet J, Cher WY, Schönbeck N, Chae E, Schnittger A, Wijnker E. Knock-down of gene expression throughout meiosis and pollen formation by virus-induced gene silencing in Arabidopsis thaliana. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2022; 111:19-37. [PMID: 35340073 PMCID: PMC9543169 DOI: 10.1111/tpj.15733] [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: 04/22/2021] [Revised: 02/16/2022] [Accepted: 02/18/2022] [Indexed: 06/14/2023]
Abstract
Through the inactivation of genes that act during meiosis it is possible to direct the genetic make-up of plants in subsequent generations and optimize breeding schemes. Offspring may show higher recombination of parental alleles resulting from elevated crossover (CO) incidence, or by omission of meiotic divisions, offspring may become polyploid. However, stable mutations in genes essential for recombination, or for either one of the two meiotic divisions, can have pleiotropic effects on plant morphology and line stability, for instance by causing lower fertility. Therefore, it is often favorable to temporarily change gene expression during meiosis rather than relying on stable null mutants. It was previously shown that virus-induced gene silencing (VIGS) can be used to transiently reduce CO frequencies. We asked if VIGS could also be used to modify other processes throughout meiosis and during pollen formation in Arabidopsis thaliana. Here, we show that VIGS-mediated knock-down of FIGL1, RECQ4A/B, OSD1 and QRT2 can induce (i) an increase in chiasma numbers, (ii) unreduced gametes and (iii) pollen tetrads. We further show that VIGS can target both sexes and different genetic backgrounds and can simultaneously silence different gene copies. The successful knock-down of these genes in A. thaliana suggests that VIGS can be exploited to manipulate any process during or shortly after meiosis. Hence, the transient induction of changes in inheritance patterns can be used as a powerful tool for applied research and biotechnological applications.
Collapse
Affiliation(s)
- Vanesa Calvo‐Baltanás
- Laboratory of GeneticsWageningen University & ResearchDroevendaalsesteeg 1Wageningen6700 AAthe Netherlands
- Department of Developmental Biology, Institut für Pflanzenwissenschaften und MikrobiologieUniversity of HamburgOhnhorststrasse 18Hamburg22609Germany
- Department of Biological SciencesNational University of Singapore14 Science Drive 4Singapore117543Singapore
| | - Joke De Jaeger‐Braet
- Department of Developmental Biology, Institut für Pflanzenwissenschaften und MikrobiologieUniversity of HamburgOhnhorststrasse 18Hamburg22609Germany
| | - Wei Yuan Cher
- A*STAR, Institute of Molecular and Cell Biology (IMCB)61 Biopolis DriveProteos138673Singapore
| | - Nils Schönbeck
- Department of Developmental Biology, Institut für Pflanzenwissenschaften und MikrobiologieUniversity of HamburgOhnhorststrasse 18Hamburg22609Germany
- UKEMartinistrasse 5220251HamburgGermany
| | - Eunyoung Chae
- Department of Biological SciencesNational University of Singapore14 Science Drive 4Singapore117543Singapore
| | - Arp Schnittger
- Department of Developmental Biology, Institut für Pflanzenwissenschaften und MikrobiologieUniversity of HamburgOhnhorststrasse 18Hamburg22609Germany
| | - Erik Wijnker
- Laboratory of GeneticsWageningen University & ResearchDroevendaalsesteeg 1Wageningen6700 AAthe Netherlands
| |
Collapse
|
4
|
Plastid Transformation of Micro-Tom Tomato with a Hemipteran Double-Stranded RNA Results in RNA Interference in Multiple Insect Species. Int J Mol Sci 2022; 23:ijms23073918. [PMID: 35409279 PMCID: PMC8999928 DOI: 10.3390/ijms23073918] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2022] [Revised: 03/29/2022] [Accepted: 03/31/2022] [Indexed: 01/27/2023] Open
Abstract
Plant-mediated RNA interference (RNAi) holds great promise for insect pest control, as plants can be transformed to produce double-stranded RNA (dsRNA) to selectively down-regulate insect genes essential for survival. For optimum potency, dsRNA can be produced in plant plastids, enabling the accumulation of unprocessed dsRNAs. However, the relative effectiveness of this strategy in inducing an RNAi response in insects using different feeding mechanisms is understudied. To investigate this, we first tested an in vitro-synthesized 189 bp dsRNA matching a highly conserved region of the v-ATPaseA gene from cotton mealybug (Phenacoccus solenopsis) on three insect species from two different orders that use leaf-chewing, lacerate-and-flush, or sap-sucking mechanisms to feed, and showed that the dsRNA significantly down-regulated the target gene. We then developed transplastomic Micro-tom tomato plants to produce the dsRNA in plant plastids and showed that the dsRNA is produced in leaf, flower, green fruit, red fruit, and roots, with the highest dsRNA levels found in the leaf. The plastid-produced dsRNA induced a significant gene down-regulation in insects using leaf-chewing and lacerate-and-flush feeding mechanisms, while sap-sucking insects were unaffected. Our results suggest that plastid-produced dsRNA can be used to control leaf-chewing and lacerate-and-flush feeding insects, but may not be useful for sap-sucking insects.
Collapse
|
5
|
Exploring the Effectiveness and Durability of Trans-Kingdom Silencing of Fungal Genes in the Vascular Pathogen Verticillium dahliae. Int J Mol Sci 2022; 23:ijms23052742. [PMID: 35269884 PMCID: PMC8910871 DOI: 10.3390/ijms23052742] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/11/2022] [Revised: 02/25/2022] [Accepted: 02/26/2022] [Indexed: 02/04/2023] Open
Abstract
Host-induced gene silencing (HIGS) based on trans-kingdom RNA interference (RNAi) has been successfully exploited to engineer host resistance to pests and pathogens, including fungi and oomycetes. However, revealing the mechanisms underlying trans-kingdom RNAi between hosts and pathogens lags behind applications. The effectiveness and durability of trans-kingdom silencing of pathogenic genes are uncharacterized. In this study, using our transgenic 35S-VdH1i cotton plants in which dsVdH1-derived small RNAs (siVdH1) accumulated, small RNA sequencing analysis revealed that siVdH1s exclusively occur within the double-stranded (ds)VdH1 region, and no transitive siRNAs were produced beyond this region in recovered hyphae of Verticillium dahliae (V. dahliae). Accordingly, we found that VdH1 silencing was reduced over time in recovered hyphae cultured in vitro, inferring that once the fungus got rid of the 35S-VdH1i cotton plants would gradually regain their pathogenicity. To explore whether continually exporting dsRNAs/siRNAs from transgenic plants into recipient fungal cells guaranteed the effectiveness and stability of HIGS, we created GFP/RFP double-labeled V. dahliae and transgenic Arabidopsis expressing dsGFP (35S-GFPi plants). Confocal images visually demonstrate the efficient silencing of GFP in V. dahliae that colonized host vascular tissues. Taken together, our results demonstrate that HIGS effectively triggers long-lasting trans-kingdom RNAi during plant vasculature V. dahliae interactions, despite no amplification or transitivity of RNAi being noted in this soil-borne fungal pathogen.
Collapse
|
6
|
Hajieghrari B, Farrokhi N. Plant RNA-mediated gene regulatory network. Genomics 2021; 114:409-442. [PMID: 34954000 DOI: 10.1016/j.ygeno.2021.12.020] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2020] [Revised: 07/21/2021] [Accepted: 12/20/2021] [Indexed: 11/26/2022]
Abstract
Not all transcribed RNAs are protein-coding RNAs. Many of them are non-protein-coding RNAs in diverse eukaryotes. However, some of them seem to be non-functional and are resulted from spurious transcription. A lot of non-protein-coding transcripts have a significant function in the translation process. Gene expressions depend on complex networks of diverse gene regulatory pathways. Several non-protein-coding RNAs regulate gene expression in a sequence-specific system either at the transcriptional level or post-transcriptional level. They include a significant part of the gene expression regulatory network. RNA-mediated gene regulation machinery is evolutionarily ancient. They well-evolved during the evolutionary time and are becoming much more complex than had been expected. In this review, we are trying to summarizing the current knowledge in the field of RNA-mediated gene silencing.
Collapse
Affiliation(s)
- Behzad Hajieghrari
- Department of Agricultural Biotechnology, College of Agriculture, Jahrom University, Jahrom, Iran.
| | - Naser Farrokhi
- Department of Cell, Molecular Biology Faculty of Life Sciences, Biotechnology, Shahid Beheshti University, G. C Evin, Tehran, Iran.
| |
Collapse
|
7
|
Hendrix B, Hoffer P, Sanders R, Schwartz S, Zheng W, Eads B, Taylor D, Deikman J. Systemic GFP silencing is associated with high transgene expression in Nicotiana benthamiana. PLoS One 2021; 16:e0245422. [PMID: 33720987 PMCID: PMC7959375 DOI: 10.1371/journal.pone.0245422] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/29/2020] [Accepted: 02/21/2021] [Indexed: 12/28/2022] Open
Abstract
Gene silencing in plants using topical dsRNA is a new approach that has the potential to be a sustainable component of the agricultural production systems of the future. However, more research is needed to enable this technology as an economical and efficacious supplement to current crop protection practices. Systemic gene silencing is one key enabling aspect. The objective of this research was to better understand topically-induced, systemic transgene silencing in Nicotiana benthamiana. A previous report details sequencing of the integration site of the Green Fluorescent Protein (GFP) transgene in the well-known N. benthamiana GFP16C event. This investigation revealed an inadvertent co-integration of part of a bacterial transposase in this line. To determine the effect of this transgene configuration on systemic silencing, new GFP transgenic lines with or without the transposase sequences were produced. GFP expression levels in the 19 single-copy events and three hemizygous GFP16C lines produced for this study ranged from 50-72% of the homozygous GFP16C line. GFP expression was equivalent to GFP16C in a two-copy event. Local GFP silencing was observed in all transgenic and GFP16C hemizygous lines after topical application of carbon dot-based formulations containing a GFP targeting dsRNA. The GFP16C-like systemic silencing phenotype was only observed in the two-copy line. The partial transposase had no impact on transgene expression level, local GFP silencing, small RNA abundance and distribution, or systemic GFP silencing in the transgenic lines. We conclude that high transgene expression level is a key enabler of topically-induced, systemic transgene silencing in N. benthamiana.
Collapse
Affiliation(s)
- Bill Hendrix
- Bayer Crop Science, Woodland, California, United States of America
| | - Paul Hoffer
- Bayer Crop Science, Woodland, California, United States of America
| | - Rick Sanders
- Bayer Crop Science, Woodland, California, United States of America
| | - Steve Schwartz
- Bayer Crop Science, Woodland, California, United States of America
| | - Wei Zheng
- Bayer Crop Science, Woodland, California, United States of America
| | - Brian Eads
- Bayer Crop Science, Chesterfield Parkway, St. Louis, Missouri, United States of America
| | - Danielle Taylor
- Bayer Crop Science, Chesterfield Parkway, St. Louis, Missouri, United States of America
| | - Jill Deikman
- Bayer Crop Science, Woodland, California, United States of America
| |
Collapse
|
8
|
Santos D, Remans S, Van den Brande S, Vanden Broeck J. RNAs on the Go: Extracellular Transfer in Insects with Promising Prospects for Pest Management. PLANTS (BASEL, SWITZERLAND) 2021; 10:484. [PMID: 33806650 PMCID: PMC8001424 DOI: 10.3390/plants10030484] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 01/31/2021] [Revised: 02/28/2021] [Accepted: 03/01/2021] [Indexed: 01/16/2023]
Abstract
RNA-mediated pathways form an important regulatory layer of myriad biological processes. In the last decade, the potential of RNA molecules to contribute to the control of agricultural pests has not been disregarded, specifically via the RNA interference (RNAi) mechanism. In fact, several proofs-of-concept have been made in this scope. Furthermore, a novel research field regarding extracellular RNAs and RNA-based intercellular/interorganismal communication is booming. In this article, we review key discoveries concerning extracellular RNAs in insects, insect RNA-based cell-to-cell communication, and plant-insect transfer of RNA. In addition, we overview the molecular mechanisms implicated in this form of communication and discuss future biotechnological prospects, namely from the insect pest-control perspective.
Collapse
Affiliation(s)
- Dulce Santos
- Research Group of Molecular Developmental Physiology and Signal Transduction, Division of Animal Physiology and Neurobiology, Department of Biology, KU Leuven, Naamsestraat 59, 3000 Leuven, Belgium; (S.R.); (S.V.d.B.); (J.V.B.)
| | | | | | | |
Collapse
|
9
|
Degradome sequencing-based identification of phasiRNAs biogenesis pathways in Oryza sativa. BMC Genomics 2021; 22:93. [PMID: 33516199 PMCID: PMC7847607 DOI: 10.1186/s12864-021-07406-7] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2020] [Accepted: 01/25/2021] [Indexed: 01/07/2023] Open
Abstract
BACKGROUND The microRNAs(miRNA)-derived secondary phased small interfering RNAs (phasiRNAs) participate in post-transcriptional gene silencing and play important roles in various bio-processes in plants. In rice, two miRNAs, miR2118 and miR2275, were mainly responsible for triggering of 21-nt and 24-nt phasiRNAs biogenesis, respectively. However, relative fewer phasiRNA biogenesis pathways have been discovered in rice compared to other plant species, which limits the comprehensive understanding of phasiRNA biogenesis and the miRNA-derived regulatory network. RESULTS In this study, we performed a systematical searching for phasiRNA biogenesis pathways in rice. As a result, five novel 21-nt phasiRNA biogenesis pathways and five novel 24-nt phasiRNA biogenesis pathways were identified. Further investigation of their regulatory function revealed that eleven novel phasiRNAs in 21-nt length recognized forty-one target genes. Most of these genes were involved in the growth and development of rice. In addition, five novel 24-nt phasiRNAs targeted to the promoter of an OsCKI1 gene and thereafter resulted in higher level of methylation in panicle, which implied their regulatory function in transcription of OsCKI1,which acted as a regulator of rice development. CONCLUSIONS These results substantially extended the information of phasiRNA biogenesis pathways and their regulatory function in rice.
Collapse
|
10
|
Sanan-Mishra N, Abdul Kader Jailani A, Mandal B, Mukherjee SK. Secondary siRNAs in Plants: Biosynthesis, Various Functions, and Applications in Virology. FRONTIERS IN PLANT SCIENCE 2021; 12:610283. [PMID: 33737942 PMCID: PMC7960677 DOI: 10.3389/fpls.2021.610283] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/25/2020] [Accepted: 01/18/2021] [Indexed: 05/13/2023]
Abstract
The major components of RNA silencing include both transitive and systemic small RNAs, which are technically called secondary sRNAs. Double-stranded RNAs trigger systemic silencing pathways to negatively regulate gene expression. The secondary siRNAs generated as a result of transitive silencing also play a substantial role in gene silencing especially in antiviral defense. In this review, we first describe the discovery and pathways of transitivity with emphasis on RNA-dependent RNA polymerases followed by description on the short range and systemic spread of silencing. We also provide an in-depth view on the various size classes of secondary siRNAs and their different roles in RNA silencing including their categorization based on their biogenesis. The other regulatory roles of secondary siRNAs in transgene silencing, virus-induced gene silencing, transitivity, and trans-species transfer have also been detailed. The possible implications and applications of systemic silencing and the different gene silencing tools developed are also described. The details on mobility and roles of secondary siRNAs derived from viral genome in plant defense against the respective viruses are presented. This entails the description of other compatible plant-virus interactions and the corresponding small RNAs that determine recovery from disease symptoms, exclusion of viruses from shoot meristems, and natural resistance. The last section presents an overview on the usefulness of RNA silencing for management of viral infections in crop plants.
Collapse
Affiliation(s)
- Neeti Sanan-Mishra
- Plant RNAi Biology Group, International Centre for Genetic Engineering and Biotechnology, New Delhi, India
| | - A. Abdul Kader Jailani
- Plant RNAi Biology Group, International Centre for Genetic Engineering and Biotechnology, New Delhi, India
- Advanced Center for Plant Virology, Division of Plant Pathology, Indian Agricultural Research Institute, New Delhi, India
| | - Bikash Mandal
- Advanced Center for Plant Virology, Division of Plant Pathology, Indian Agricultural Research Institute, New Delhi, India
| | - Sunil K. Mukherjee
- Advanced Center for Plant Virology, Division of Plant Pathology, Indian Agricultural Research Institute, New Delhi, India
- *Correspondence: Sunil K. Mukherjee,
| |
Collapse
|
11
|
Mimulus sRNAs Are Wound Responsive and Associated with Transgenerationally Plastic Genes but Rarely Both. Int J Mol Sci 2020; 21:ijms21207552. [PMID: 33066159 PMCID: PMC7589798 DOI: 10.3390/ijms21207552] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2020] [Revised: 10/07/2020] [Accepted: 10/10/2020] [Indexed: 12/25/2022] Open
Abstract
Organisms alter development in response to environmental cues. Recent studies demonstrate that they can transmit this plasticity to progeny. While the phenotypic and transcriptomic evidence for this “transgenerational plasticity” has accumulated, genetic and developmental mechanisms remain unclear. Plant defenses, gene expression and DNA methylation are modified as an outcome of parental wounding in Mimulus guttatus. Here, we sequenced M. guttatus small RNAs (sRNA) to test their possible role in mediating transgenerational plasticity. We sequenced sRNA populations of leaf-wounded and control plants at 1 h and 72 h after damage and from progeny of wounded and control parents. This allowed us to test three components of an a priori model of sRNA mediated transgenerational plasticity—(1) A subset of sRNAs will be differentially expressed in response to wounding, (2) these will be associated with previously identified differentially expressed genes and differentially methylated regions and (3) changes in sRNA abundance in wounded plants will be predictive of sRNA abundance, DNA methylation, and/or gene expression shifts in the following generation. Supporting (1) and (2), we found significantly different sRNA abundances in wounded leaves; the majority were associated with tRNA fragments (tRFs) rather than small-interfering RNAs (siRNA). However, siRNAs responding to leaf wounding point to Jasmonic Acid mediated responses in this system. We found that different sRNA classes were associated with regions of the genome previously found to be differentially expressed or methylated in progeny of wounded plants. Evidence for (3) was mixed. We found that non-dicer sRNAs with increased abundance in response to wounding tended to be nearby genes with decreased expression in the next generation. Counter to expectations, we did not find that siRNA responses to wounding were associated with gene expression or methylation changes in the next generation and within plant and transgenerational sRNA plasticity were negatively correlated.
Collapse
|
12
|
Abstract
RNA-directed DNA methylation (RdDM) is a biological process in which non-coding RNA molecules direct the addition of DNA methylation to specific DNA sequences. The RdDM pathway is unique to plants, although other mechanisms of RNA-directed chromatin modification have also been described in fungi and animals. To date, the RdDM pathway is best characterized within angiosperms (flowering plants), and particularly within the model plant Arabidopsis thaliana. However, conserved RdDM pathway components and associated small RNAs (sRNAs) have also been found in other groups of plants, such as gymnosperms and ferns. The RdDM pathway closely resembles other sRNA pathways, particularly the highly conserved RNAi pathway found in fungi, plants, and animals. Both the RdDM and RNAi pathways produce sRNAs and involve conserved Argonaute, Dicer and RNA-dependent RNA polymerase proteins. RdDM has been implicated in a number of regulatory processes in plants. The DNA methylation added by RdDM is generally associated with transcriptional repression of the genetic sequences targeted by the pathway. Since DNA methylation patterns in plants are heritable, these changes can often be stably transmitted to progeny. As a result, one prominent role of RdDM is the stable, transgenerational suppression of transposable element (TE) activity. RdDM has also been linked to pathogen defense, abiotic stress responses, and the regulation of several key developmental transitions. Although the RdDM pathway has a number of important functions, RdDM-defective mutants in Arabidopsis thaliana are viable and can reproduce, which has enabled detailed genetic studies of the pathway. However, RdDM mutants can have a range of defects in different plant species, including lethality, altered reproductive phenotypes, TE upregulation and genome instability, and increased pathogen sensitivity. Overall, RdDM is an important pathway in plants that regulates a number of processes by establishing and reinforcing specific DNA methylation patterns, which can lead to transgenerational epigenetic effects on gene expression and phenotype.
Collapse
|
13
|
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: 9] [Impact Index Per Article: 2.3] [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.
Collapse
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.)
| |
Collapse
|
14
|
Das PR, Sherif SM. Application of Exogenous dsRNAs-induced RNAi in Agriculture: Challenges and Triumphs. FRONTIERS IN PLANT SCIENCE 2020; 11:946. [PMID: 32670336 PMCID: PMC7330088 DOI: 10.3389/fpls.2020.00946] [Citation(s) in RCA: 69] [Impact Index Per Article: 17.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/14/2020] [Accepted: 06/10/2020] [Indexed: 05/05/2023]
Abstract
In recent years, RNA interference (RNAi) machinery has widely been explored by plant biologists for its potential applications in disease management, plant development, and germplasm improvement. RNAi-based technologies have mainly been applied in the form of transgenic plant generation and host-induced-gene-silencing (HIGS). However, the approval of RNAi-based transgenic plants has always been challenging due to the proclaimed concerns surrounding their impacts on human health and the environment. Lately, exogenous applications of double-stranded RNAs (dsRNAs), short interfering RNAs (siRNAs), and hairpin RNAs (hpRNAs) has emerged as another technology that could be regarded as more eco-friendly, sustainable, and publicly acceptable than genetic transformation. Inside the plant cell, dsRNAs can undergo several steps of processing, which not only triggers RNAi machinery but may also involve transitive and systemic silencing, as well as epigenetic modifications. Therefore, along with the considerations of proper exogenous applications of dsRNAs, defining their final destination into plant cells is highly relevant. In this review, we highlighted the significance of several factors that affect dsRNA-induced gene silencing, the fate of exogenous dsRNAs in the plant cell, and the challenges surrounding production technologies, cost-effectiveness, and dsRNAs stability under open-field conditions. This review also provided insights into the potential applications of exogenous dsRNAs in plant protection and crop improvement.
Collapse
Affiliation(s)
| | - Sherif M. Sherif
- Alson H. Smith Jr. Agricultural Research and Extension Center, School of Plant and Environmental Sciences, Virginia Polytechnic Institute and State University, Winchester, VA, United States
| |
Collapse
|
15
|
Tzean Y, Chang HH, Tu TC, Hou BH, Chen HM, Chiu YS, Chou WY, Chang L, Yeh HH. Engineering Plant Resistance to Tomato Yellow Leaf Curl Thailand Virus Using a Phloem-Specific Promoter Expressing Hairpin RNA. MOLECULAR PLANT-MICROBE INTERACTIONS : MPMI 2020; 33:87-97. [PMID: 31638467 DOI: 10.1094/mpmi-06-19-0158-r] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/19/2023]
Abstract
Transgenic approaches employing RNA interference (RNAi) strategies have been successfully applied to generate desired traits in plants; however, variations between RNAi transgenic siblings and the ability to quickly apply RNAi resistance to diverse cultivars remain challenging. In this study, we assessed the promoter activity of a cauliflower mosaic virus 35S promoter (35S) and a phloem-specific promoter derived from rice tungro bacilliform virus (RTBV) and their efficacy to drive RNAi against the endogenous glutamate-1-semialdehyde aminotransferase gene (GSA) that acts as a RNAi marker, through chlorophyll synthesis inhibition, and against tomato yellow leaf curl Thailand virus (TYLCTHV), a begomovirus (family Geminiviridae) reported to be the prevalent cause of tomato yellow leaf curl disease (TYLCD) in Taiwan. Transgenic Nicotiana benthamiana expressing hairpin RNA of GSA driven by either the 35S or RTBV promoter revealed that RTBV::hpGSA induced stronger silencing along the vein and more uniformed silencing phenotype among its siblings than 35S::hpGSA. Analysis of transgenic N. benthamiana, 35S::hpTYLCTHV, and RTBV::hpTYLCTHV revealed that, although 35S::hpTYLCTHV generated a higher abundance of small RNA than RTBV::hpTYLCTHV, RTBV::hpTYLCTHV transgenic plants conferred better TYLCTHV resistance than 35S::hpTYLCTHV. Grafting of wild-type (WT) scions to TYLCTHV RNAi rootstocks allowed transferable TYLCTHV resistance to the scion. A TYLCTHV-inoculation assay showed that noninfected WT scions were only observed when grafted to RTBV::hpTYLCTHV rootstocks but not 35S::hpTYLCTHV nor WT rootstocks. Together, our findings demonstrate an approach that may be widely applied to efficiently confer TYLCD resistance.
Collapse
Affiliation(s)
- Yuh Tzean
- Agricultural Biotechnology Research Center, Academia Sinica, No. 128, Sec. 2, Academia Road, Nankang District, Taipei 11529, Taiwan
| | - Ho-Hsiung Chang
- Agricultural Biotechnology Research Center, Academia Sinica, No. 128, Sec. 2, Academia Road, Nankang District, Taipei 11529, Taiwan
| | - Tsui-Chin Tu
- Agricultural Biotechnology Research Center, Academia Sinica, No. 128, Sec. 2, Academia Road, Nankang District, Taipei 11529, Taiwan
| | - Bo-Han Hou
- Agricultural Biotechnology Research Center, Academia Sinica, No. 128, Sec. 2, Academia Road, Nankang District, Taipei 11529, Taiwan
| | - Ho-Ming Chen
- Agricultural Biotechnology Research Center, Academia Sinica, No. 128, Sec. 2, Academia Road, Nankang District, Taipei 11529, Taiwan
| | - Yi-Shu Chiu
- Agricultural Biotechnology Research Center, Academia Sinica, No. 128, Sec. 2, Academia Road, Nankang District, Taipei 11529, Taiwan
| | - Wei-Yi Chou
- Agricultural Biotechnology Research Center, Academia Sinica, No. 128, Sec. 2, Academia Road, Nankang District, Taipei 11529, Taiwan
| | - Li Chang
- Agricultural Biotechnology Research Center, Academia Sinica, No. 128, Sec. 2, Academia Road, Nankang District, Taipei 11529, Taiwan
| | - Hsin-Hung Yeh
- Agricultural Biotechnology Research Center, Academia Sinica, No. 128, Sec. 2, Academia Road, Nankang District, Taipei 11529, Taiwan
- Department of Plant Pathology and Microbiology, National Taiwan University, No. 1, Sec. 4, Roosevelt Rd, Da'an District, Taipei 10617, Taiwan
| |
Collapse
|
16
|
Goodfellow S, Zhang D, Wang MB, Zhang R. Bacterium-Mediated RNA Interference: Potential Application in Plant Protection. PLANTS (BASEL, SWITZERLAND) 2019; 8:E572. [PMID: 31817412 PMCID: PMC6963952 DOI: 10.3390/plants8120572] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/01/2019] [Revised: 11/26/2019] [Accepted: 11/27/2019] [Indexed: 01/10/2023]
Abstract
RNAi has emerged as a promising tool for targeting agricultural pests and pathogens and could provide an environmentally friendly alternative to traditional means of control. However, the deployment of this technology is still limited by a lack of suitable exogenous- or externally applied delivery mechanisms. Numerous means of overcoming this limitation are being explored. One such method, bacterium-mediated RNA interference, or bmRNAi, has been explored in other systems and shows great potential for application to agriculture. Here, we review the current state of bmRNAi, examine the technical limitations and possible improvements, and discuss its potential applications in crop protection.
Collapse
Affiliation(s)
- Simon Goodfellow
- School of Chemistry and Molecular Bioscience, University of Wollongong, NSW 2522, Australia
- CSIRO Agriculture and Food, Canberra, ACT 2601, Australia
| | - Daai Zhang
- School of Chemistry and Molecular Bioscience, University of Wollongong, NSW 2522, Australia
- CSIRO Agriculture and Food, Canberra, ACT 2601, Australia
| | - Ming-Bo Wang
- CSIRO Agriculture and Food, Canberra, ACT 2601, Australia
| | - Ren Zhang
- School of Chemistry and Molecular Bioscience, University of Wollongong, NSW 2522, Australia
| |
Collapse
|
17
|
Orfanidou CG, Mathioudakis MM, Katsarou K, Livieratos I, Katis N, Maliogka VI. Cucurbit chlorotic yellows virus p22 is a suppressor of local RNA silencing. Arch Virol 2019; 164:2747-2759. [PMID: 31502079 DOI: 10.1007/s00705-019-04391-x] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2019] [Accepted: 08/04/2019] [Indexed: 01/20/2023]
Abstract
RNA silencing is a major antiviral mechanism in plants, which is counteracted by virus-encoded proteins with silencing suppression activity. ORFs encoding putative silencing suppressor proteins that share no structural or sequence homology have been identified in the genomes of four criniviruses. In this study, we investigated the RNA silencing suppression activity of several proteins encoded by the RNA1 (RdRp, p22) and RNA2 (CP, CPm and p26) of cucurbit chlorotic yellows virus (CCYV) using co-agroinfiltration assays on Nicotiana benthamiana plants. Our results indicate that p22 is a suppressor of local RNA silencing that does not interfere with cell-to-cell movement of the RNA silencing signal or with systemic silencing. Furthermore, comparisons of the suppression activity of CCYV p22 with that of two other well-known crinivirus suppressors (CYSDV p25 and ToCV p22) revealed that CCYV p22 is a weaker suppressor of local RNA silencing than the other two proteins. Finally, a comparative sequence analysis of the p22 genes of seven Greek CCYV isolates was performed, revealing a high level of conservation. Taken together, our research advances our knowledge about plant-virus interactions of criniviruses, an emergent group of pathogens that threatens global agriculture.
Collapse
Affiliation(s)
- Chrysoula G Orfanidou
- Plant Pathology Laboratory, Faculty of Agriculture, Forestry and Natural Environment, School of Agriculture, Aristotle University of Thessaloniki, 54 124, Thessaloniki, Greece
| | - Matthaios M Mathioudakis
- Department of Sustainable Agriculture, Mediterranean Agronomic Institute of Chania, Alsylio Agrokepio, 73100, Chania, Greece
- Institute for Olive tree, Subtropical crops and Viticulture, Plant Pathology Laboratory, Hellenic Agricultural Organization-"DEMETER", Karamanlis Ave. 167, 73134, Chania, Greece
| | | | - Ioannis Livieratos
- Department of Sustainable Agriculture, Mediterranean Agronomic Institute of Chania, Alsylio Agrokepio, 73100, Chania, Greece
| | - Nikolaos Katis
- Plant Pathology Laboratory, Faculty of Agriculture, Forestry and Natural Environment, School of Agriculture, Aristotle University of Thessaloniki, 54 124, Thessaloniki, Greece
| | - Varvara I Maliogka
- Plant Pathology Laboratory, Faculty of Agriculture, Forestry and Natural Environment, School of Agriculture, Aristotle University of Thessaloniki, 54 124, Thessaloniki, Greece.
| |
Collapse
|
18
|
Gaut BS, Miller AJ, Seymour DK. Living with Two Genomes: Grafting and Its Implications for Plant Genome-to-Genome Interactions, Phenotypic Variation, and Evolution. Annu Rev Genet 2019; 53:195-215. [PMID: 31424971 DOI: 10.1146/annurev-genet-112618-043545] [Citation(s) in RCA: 28] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
Plant genomes interact when genetically distinct individuals join, or are joined, together. Individuals can fuse in three contexts: artificial grafts, natural grafts, and host-parasite interactions. Artificial grafts have been studied for decades and are important platforms for studying the movement of RNA, DNA, and protein. Yet several mysteries about artificial grafts remain, including the factors that contribute to graft incompatibility, the prevalence of genetic and epigenetic modifications caused by exchanges between graft partners, and the long-term effects of these modifications on phenotype. Host-parasite interactions also lead to the exchange of materials, and RNA exchange actively contributes to an ongoing arms race between parasite virulence and host resistance. Little is known about natural grafts except that they can be frequent and may provide opportunities for evolutionary innovation through genome exchange. In this review, we survey our current understanding about these three mechanisms of contact, the genomic interactions that result, and the potential evolutionary implications.
Collapse
Affiliation(s)
- Brandon S Gaut
- Department of Ecology and Evolutionary Biology, University of California, Irvine, California 92697, USA;
| | - Allison J Miller
- Department of Biology, Saint Louis University, Saint Louis, Missouri 63103, USA.,Donald Danforth Plant Science Center, St. Louis, Missouri 63132, USA
| | - Danelle K Seymour
- Department of Botany and Plant Sciences, University of California, Riverside, California 92521, USA
| |
Collapse
|
19
|
Dubrovina AS, Kiselev KV. Exogenous RNAs for Gene Regulation and Plant Resistance. Int J Mol Sci 2019; 20:E2282. [PMID: 31072065 PMCID: PMC6539981 DOI: 10.3390/ijms20092282] [Citation(s) in RCA: 91] [Impact Index Per Article: 18.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2019] [Revised: 05/05/2019] [Accepted: 05/06/2019] [Indexed: 01/08/2023] Open
Abstract
Recent investigations documented that plants can uptake and process externally applied double-stranded RNAs (dsRNAs), hairpin RNAs (hpRNAs), and small interfering RNAs (siRNAs) designed to silence important genes of plant pathogenic viruses, fungi, or insects. The exogenously applied RNAs spread locally and systemically, move into the pathogens, and induce RNA interference-mediated plant pathogen resistance. Recent findings also provided examples of plant transgene and endogene post-transcriptional down-regulation by complementary dsRNAs or siRNAs applied onto the plant surfaces. Understanding the plant perception and processing of exogenous RNAs could result in the development of novel biotechnological approaches for crop protection. This review summarizes and discusses the emerging studies reporting on exogenous RNA applications for down-regulation of essential fungal and insect genes, targeting of plant viruses, or suppression of plant transgenes and endogenes for increased resistance and changed phenotypes. We also analyze the current understanding of dsRNA uptake mechanisms and dsRNA stability in plant environments.
Collapse
Affiliation(s)
- Alexandra S Dubrovina
- Laboratory of Biotechnology, Federal Scientific Center of the East Asia Terrestrial Biodiversity, Far Eastern Branch of the Russian Academy of Sciences, 690022 Vladivostok, Russia.
| | - Konstantin V Kiselev
- Laboratory of Biotechnology, Federal Scientific Center of the East Asia Terrestrial Biodiversity, Far Eastern Branch of the Russian Academy of Sciences, 690022 Vladivostok, Russia.
- Far Eastern Federal University, The School of Natural Sciences, 690090 Vladivostok, Russia.
| |
Collapse
|
20
|
Kryovrysanaki N, Alexiadis A, Grigoriadou AM, Katsarou K, Kalantidis K. SERRATE, a miRNA biogenesis factor, affects viroid infection in Nicotiana benthamiana and Nicotiana tabacum. Virology 2019; 528:164-175. [PMID: 30599275 DOI: 10.1016/j.virol.2018.12.011] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2018] [Revised: 12/14/2018] [Accepted: 12/15/2018] [Indexed: 12/14/2022]
Abstract
Viroids are plant infecting, non - coding RNA molecules of economic importance. Potato spindle tuber viroid (PSTVd), the type species of Pospiviroidae family, has been shown to be affected by specific RNA silencing pathways. Dicer like 1 (DCL1), a key player in micro RNA (miRNA) pathway has been previously linked with PSTVd infectivity. In this report we aim to further dissect the interaction between the miRNA pathway and Pospiviroid virulence. We mainly focused on the Zinc-finger protein SERRATE (SE) a co-factor of DCL1 and core component of miRNA pathway. We generated Nicotiana tabacum and Nicotiana benthamiana SE knock-down plants exhibiting considerable miRNA reduction and strong phenotypic abnormalities. PSTVd infection of SE suppressed plants resulted in a significant viroid reduction, especially at the initial infection stages. This positive correlation between SE levels and viroid infectivity underlines its role in PSTVd life cycle and reveals the importance of the miRNA pathway upon viroid infection.
Collapse
Affiliation(s)
- Nikoleta Kryovrysanaki
- Institute of Molecular Biology and Biotechnology, Foundation for Research and Technology, GR-7110 Heraklion, Crete, Greece; Department of Biology, University of Crete, Vassilika Vouton, GR-71409 Heraklion, Crete, Greece.
| | - Anastasios Alexiadis
- Institute of Molecular Biology and Biotechnology, Foundation for Research and Technology, GR-7110 Heraklion, Crete, Greece; Department of Biology, University of Crete, Vassilika Vouton, GR-71409 Heraklion, Crete, Greece
| | - Alexandra M Grigoriadou
- Department of Biology, University of Crete, Vassilika Vouton, GR-71409 Heraklion, Crete, Greece
| | - Konstantina Katsarou
- Institute of Molecular Biology and Biotechnology, Foundation for Research and Technology, GR-7110 Heraklion, Crete, Greece
| | - Kriton Kalantidis
- Institute of Molecular Biology and Biotechnology, Foundation for Research and Technology, GR-7110 Heraklion, Crete, Greece; Department of Biology, University of Crete, Vassilika Vouton, GR-71409 Heraklion, Crete, Greece.
| |
Collapse
|
21
|
Li C, Yamagishi N, Yoshikawa N. RNA Silencing-Mediated Apple Latent Spherical Virus Vaccine in Plants. Methods Mol Biol 2019; 2028:273-288. [PMID: 31228121 DOI: 10.1007/978-1-4939-9635-3_16] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
The apple latent spherical virus (ALSV), originally isolated from an apple tree in Japan, is a small spherical virus with a diameter of 25 nm and comprises a bisegmented, single-stranded RNA genome (RNA1 and RNA2) and three different capsid proteins (Vp25, Vp20, and Vp24). The virus can experimentally infect a broad range of plants including, not only model plants (Arabidopsis thaliana and Nicotiana species) but also economically important crops such as cucumber, soybean, tomato, fruit trees, and flowers. ALSV has been used as an effective plant virus vector for virus-induced gene silencing (VIGS) to assess gene functions because the virus infects most of the host plants without showing any symptoms and induces a uniform knockout phenotype in infected plants. Moreover, the VIGS persists throughout plant growth in infected plants. Here, we show that genetically engineered ALSV vectors (ALSV vaccines) containing a partial genome sequence of pathogenic viruses display a high degree of cross-protection against the challenge inoculation of the corresponding pathogenic viruses. Treatment effects can also be expected in virus-infected plants by subsequent inoculation with ALSV vaccine.
Collapse
Affiliation(s)
- Chunjiang Li
- Faculty of Agriculture, Iwate University, Morioka, Japan
| | - Noriko Yamagishi
- Faculty of Agriculture, Iwate University, Morioka, Japan.,Agri-Innovation Center, Iwate University, Morioka, Japan
| | - Nobuyuki Yoshikawa
- Faculty of Agriculture, Iwate University, Morioka, Japan. .,Agri-Innovation Center, Iwate University, Morioka, Japan.
| |
Collapse
|
22
|
Bally J, Jung H, Mortimer C, Naim F, Philips JG, Hellens R, Bombarely A, Goodin MM, Waterhouse PM. The Rise and Rise of Nicotiana benthamiana: A Plant for All Reasons. ANNUAL REVIEW OF PHYTOPATHOLOGY 2018; 56:405-426. [PMID: 30149789 DOI: 10.1146/annurev-phyto-080417-050141] [Citation(s) in RCA: 138] [Impact Index Per Article: 23.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/21/2023]
Abstract
A decade ago, the value of Nicotiana benthamiana as a tool for plant molecular biologists was beginning to be appreciated. Scientists were using it to study plant-microbe and protein-protein interactions, and it was the species of choice with which to activate plasmid-encoded viruses, screen for gene functions with virus-induced gene silencing (VIGS), and transiently express genes by leaf agroinfiltration. However, little information about the species' origin, diversity, genetics, and genomics was available, and biologists were asking the question of whether N. benthamiana is a second fiddle or virtuoso. In this review, we look at the increased knowledge about the species and its applications over the past decade. Although N. benthamiana may still be the sidekick to Arabidopsis, it shines ever more brightly with realized and yet-to-be-exploited potential.
Collapse
Affiliation(s)
- Julia Bally
- Centre for Tropical Crops and Biocommodities, Queensland University of Technology, 4001 Brisbane, Queensland, Australia;
| | - Hyungtaek Jung
- Centre for Tropical Crops and Biocommodities, Queensland University of Technology, 4001 Brisbane, Queensland, Australia;
| | - Cara Mortimer
- Centre for Tropical Crops and Biocommodities, Queensland University of Technology, 4001 Brisbane, Queensland, Australia;
| | - Fatima Naim
- Centre for Tropical Crops and Biocommodities, Queensland University of Technology, 4001 Brisbane, Queensland, Australia;
| | - Joshua G Philips
- Centre for Tropical Crops and Biocommodities, Queensland University of Technology, 4001 Brisbane, Queensland, Australia;
| | - Roger Hellens
- Centre for Tropical Crops and Biocommodities, Queensland University of Technology, 4001 Brisbane, Queensland, Australia;
| | - Aureliano Bombarely
- Department of Horticulture, Virginia Polytechnic Institute and State University, Blacksburg, Virginia 24061-0002, USA
| | - Michael M Goodin
- Department of Plant Pathology, University of Kentucky, Lexington, Kentucky 40546, USA;
| | - Peter M Waterhouse
- Centre for Tropical Crops and Biocommodities, Queensland University of Technology, 4001 Brisbane, Queensland, Australia;
| |
Collapse
|
23
|
Cai Q, He B, Kogel KH, Jin H. Cross-kingdom RNA trafficking and environmental RNAi-nature's blueprint for modern crop protection strategies. Curr Opin Microbiol 2018; 46:58-64. [PMID: 29549797 PMCID: PMC6499079 DOI: 10.1016/j.mib.2018.02.003] [Citation(s) in RCA: 105] [Impact Index Per Article: 17.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2018] [Revised: 01/29/2018] [Accepted: 02/02/2018] [Indexed: 10/17/2022]
Abstract
In plants, small RNA (sRNA)-mediated RNA interference (RNAi) is critical for regulating host immunity against bacteria, fungi, oomycetes, viruses, and pests. Similarly, sRNAs from pathogens and pests also play an important role in modulating their virulence. Strikingly, recent evidence supports that some sRNAs can travel between interacting organisms and induce gene silencing in the counter party, a mechanism termed cross-kingdom RNAi. Exploiting this new knowledge, host-induced gene silencing (HIGS) by transgenic expression of pathogen gene-targeting double-stranded (ds)RNA has the potential to become an important disease-control method. To circumvent transgenic approaches, direct application of dsRNAs or sRNAs (environmental RNAi) onto host plants or post-harvest products leads to silencing of the target microbe/pest gene (referred to spray-induced gene silencing, SIGS) and confers efficient disease control. This review summarizes the current understanding of cross-kingdom RNA trafficking and environmental RNAi and how these findings can be developed into novel effective strategies to fight diseases caused by microbial pathogens and pests.
Collapse
Affiliation(s)
- Qiang Cai
- Department of Microbiology and Plant Pathology, Center for Plant Cell Biology, Institute for Integrative Genome Biology, University of California, Riverside, CA 92521, USA
| | - Baoye He
- Department of Microbiology and Plant Pathology, Center for Plant Cell Biology, Institute for Integrative Genome Biology, University of California, Riverside, CA 92521, USA
| | - Karl-Heinz Kogel
- Department of Phytopathology, Interdisciplinary Research Center for Biosystems, Land Use and Nutrition, Justus Liebig University Giessen, Germany
| | - Hailing Jin
- Department of Microbiology and Plant Pathology, Center for Plant Cell Biology, Institute for Integrative Genome Biology, University of California, Riverside, CA 92521, USA.
| |
Collapse
|
24
|
Islam W, Qasim M, Noman A, Adnan M, Tayyab M, Farooq TH, Wei H, Wang L. Plant microRNAs: Front line players against invading pathogens. Microb Pathog 2018. [PMID: 29524548 DOI: 10.1016/j.micpath.2018.03.008] [Citation(s) in RCA: 35] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022]
Abstract
Plants are attacked by a large number of pathogens. To defend against these pathogens, plants activate or repress a vast array of genes. For genetic expression and reprogramming, host endogenous small RNAs (sRNAs) are the key factors. Among these sRNAs, microRNAs (miRNAs) mediate gene regulation through RNA silencing at the post-transcriptional level and play an essential role in the defense responses to biotic and abiotic stress. In the recent years, high-throughput sequencing has enabled the researchers to uncover the role of plant miRNAs during pathogen invasion. So here we have reviewed the recent research findings illustrating the plant miRNAs active involvement in various defense processes during fungal, bacterial, viral and nematode infections. However, rapid validation of direct targets of miRNAs is the dire need of time, which can be very helpful in improving the plant resistance against various pathogenic diseases.
Collapse
Affiliation(s)
- Waqar Islam
- College of Plant Protection, Fujian Agriculture and Forestry University, Fuzhou, 350002, China; Govt. of Punjab, Agriculture Department, Lahore, Pakistan.
| | - Muhammad Qasim
- College of Plant Protection, Fujian Agriculture and Forestry University, Fuzhou, 350002, China; State Key Laboratory of Ecological Pest Control for Fujian and Taiwan Crops, Fujian Agriculture and Forestry University, Fuzhou, 350002, China; Key Laboratory of Integrated Pest Management for Fujian-Taiwan Crops, Ministry of Agriculture, Fuzhou, 350002, China
| | - Ali Noman
- College of Crop Sciences, Fujian Agriculture and Forestry University, Fuzhou, 350002, China; Department of Botany, Govt. College University, Faisalabad, Pakistan
| | - Muhammad Adnan
- College of Plant Protection, Fujian Agriculture and Forestry University, Fuzhou, 350002, China; State Key Laboratory of Ecological Pest Control for Fujian and Taiwan Crops, Fujian Agriculture and Forestry University, Fuzhou, 350002, China
| | - Muhammad Tayyab
- College of Crop Sciences, Fujian Agriculture and Forestry University, Fuzhou, 350002, China
| | - Taimoor Hassan Farooq
- College of Forestry, Fujian Agriculture and Forestry University, Fuzhou, 350002, China
| | - Huang Wei
- College of Plant Protection, Fujian Agriculture and Forestry University, Fuzhou, 350002, China
| | - Liande Wang
- College of Plant Protection, Fujian Agriculture and Forestry University, Fuzhou, 350002, China; State Key Laboratory of Ecological Pest Control for Fujian and Taiwan Crops, Fujian Agriculture and Forestry University, Fuzhou, 350002, China; Key Laboratory of Integrated Pest Management for Fujian-Taiwan Crops, Ministry of Agriculture, Fuzhou, 350002, China.
| |
Collapse
|
25
|
Hua C, Zhao JH, Guo HS. Trans-Kingdom RNA Silencing in Plant-Fungal Pathogen Interactions. MOLECULAR PLANT 2018; 11:235-244. [PMID: 29229568 DOI: 10.1016/j.molp.2017.12.001] [Citation(s) in RCA: 69] [Impact Index Per Article: 11.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/21/2017] [Revised: 10/31/2017] [Accepted: 12/01/2017] [Indexed: 05/02/2023]
Abstract
Fungal pathogens represent a major group of plant invaders that are the causative agents of many notorious plant diseases. Large quantities of RNAs, especially small RNAs involved in gene silencing, have been found to transmit bidirectionally between fungal pathogens and their hosts. Although host-induced gene silencing (HIGS) technology has been developed and applied to protect crops from fungal infections, the mechanisms of RNA transmission, especially small RNAs regulating trans-kingdom RNA silencing in plant immunity, are largely unknown. In this review, we summarize and discuss recent important findings regarding trans-kingdom sRNAs and RNA silencing in plant-fungal pathogen interactions compared with the well-known RNAi mechanisms in plants and fungi. We focus on the interactions between plant and fungal pathogens with broad hosts, represented by the vascular pathogen Verticillium dahliae and non-vascular pathogen Botrytis cinerea, and discuss the known instances of natural RNAi transmission between fungal pathogens and host plants. Given that HIGS has been developed and recently applied in controlling Verticillium wilt diseases, we propose an ideal research system exploiting plant vasculature-Verticillium interaction to further study trans-kingdom RNA silencing.
Collapse
Affiliation(s)
- Chenlei Hua
- State Key Laboratory of Plant Genomics, Institute of Microbiology, Chinese Academy of Sciences, 100101 Beijing, China
| | - Jian-Hua Zhao
- State Key Laboratory of Plant Genomics, Institute of Microbiology, Chinese Academy of Sciences, 100101 Beijing, China
| | - Hui-Shan Guo
- State Key Laboratory of Plant Genomics, Institute of Microbiology, Chinese Academy of Sciences, 100101 Beijing, China; College of Life Science, University of the Chinese Academy of Sciences, 100049 Beijing, China.
| |
Collapse
|
26
|
Yan H, Shi S, Ma N, Cao X, Zhang H, Qiu X, Wang Q, Jian H, Zhou N, Zhang Z, Tang K. Graft-accelerated virus-induced gene silencing facilitates functional genomics in rose flowers. JOURNAL OF INTEGRATIVE PLANT BIOLOGY 2018; 60:34-44. [PMID: 28895654 DOI: 10.1111/jipb.12599] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/11/2017] [Accepted: 09/10/2017] [Indexed: 05/02/2023]
Abstract
Rose has emerged as a model ornamental plant for studies of flower development, senescence, and morphology, as well as the metabolism of floral fragrances and colors. Virus-induced gene silencing (VIGS) has long been used in functional genomics studies of rose by vacuum infiltration of cuttings or seedlings with an Agrobacterium suspension carrying TRV-derived vectors. However, VIGS in rose flowers remains a challenge because of its low efficiency and long time to establish silencing. Here we present a novel and rapid VIGS method that can be used to analyze gene function in rose, called 'graft-accelerated VIGS', where axillary sprouts are cut from the rose plant and vacuum infiltrated with Agrobacterium. The inoculated scions are then grafted back onto the plants to flower and silencing phenotypes can be observed within 5 weeks, post-infiltration. Using this new method, we successfully silenced expression of the RhDFR1, RhAG, and RhNUDX1 in rose flowers, and affected their color, petal number, as well as fragrance, respectively. This grafting method will facilitate high-throughput functional analysis of genes in rose flowers. Importantly, it may also be applied to other woody species that are not currently amenable to VIGS by conventional leaf or plantlet/seedling infiltration methods.
Collapse
Affiliation(s)
- Huijun Yan
- Flower Research Institute of Yunnan Academy of Agricultural Sciences, 650205 Kunming, China
| | - Shaochuan Shi
- Beijing Key Laboratory of Development and Quality Control of Ornamental Crops, Department of Ornamental Horticulture, China Agricultural University, 100193 Beijing, China
| | - Nan Ma
- Beijing Key Laboratory of Development and Quality Control of Ornamental Crops, Department of Ornamental Horticulture, China Agricultural University, 100193 Beijing, China
| | - Xiaoqian Cao
- Beijing Key Laboratory of Development and Quality Control of Ornamental Crops, Department of Ornamental Horticulture, China Agricultural University, 100193 Beijing, China
| | - Hao Zhang
- Flower Research Institute of Yunnan Academy of Agricultural Sciences, 650205 Kunming, China
| | - Xianqin Qiu
- Flower Research Institute of Yunnan Academy of Agricultural Sciences, 650205 Kunming, China
| | - Qigang Wang
- Flower Research Institute of Yunnan Academy of Agricultural Sciences, 650205 Kunming, China
| | - Hongying Jian
- Flower Research Institute of Yunnan Academy of Agricultural Sciences, 650205 Kunming, China
| | - Ningning Zhou
- Flower Research Institute of Yunnan Academy of Agricultural Sciences, 650205 Kunming, China
| | - Zhao Zhang
- Beijing Key Laboratory of Development and Quality Control of Ornamental Crops, Department of Ornamental Horticulture, China Agricultural University, 100193 Beijing, China
| | - Kaixue Tang
- Flower Research Institute of Yunnan Academy of Agricultural Sciences, 650205 Kunming, China
| |
Collapse
|
27
|
Tamiru M, Hardcastle TJ, Lewsey MG. Regulation of genome-wide DNA methylation by mobile small RNAs. THE NEW PHYTOLOGIST 2018; 217:540-546. [PMID: 29105762 DOI: 10.1111/nph.14874] [Citation(s) in RCA: 25] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/19/2017] [Accepted: 09/20/2017] [Indexed: 05/20/2023]
Abstract
Contents Summary 540 I. Introduction 540 II. There are different types of sRNA mobility 541 III. Mechanisms of sRNA movement 541 IV. Long-distance, shoot-root, mobile siRNAs influence DNA methylation in recipient tissues 541 V. Classes of interactions between shoot-root mobile siRNAs and DNA methylation 542 VI. Loci targeted directly and indirectly by shoot-root mobile siRNAs are associated with different histone modifications 543 VII. Is mobile siRNA-regulated DNA methylation important in specific tissues or under specific conditions? 543 VIII. Mobile sRNAs can be used to modify plant traits 544 IX. Conclusions 544 Acknowledgements 544 References 544 SUMMARY: RNA-directed DNA methylation (RdDM) at cytosine residues regulates gene expression, silences transposable elements and influences genome stability. The mechanisms responsible for RdDM are guided to target loci by small RNAs (sRNAs) that can move within plants cell to cell and long distance. Here we discuss recent advances in the understanding of interactions between mobile sRNAs and DNA methylation. We describe the mechanisms of sRNA movement, the differences between known classes of mobile sRNA-DNA methylation interactions and the limits of current knowledge. Finally, we discuss potential applications of mobile sRNAs in modifying plant traits.
Collapse
Affiliation(s)
- Muluneh Tamiru
- Centre for AgriBioscience, Department of Animal, Plant and Soil Science, School of Life Science, La Trobe University, Bundoora, Vic., 3086, Australia
| | - Thomas J Hardcastle
- Department of Plant Sciences, University of Cambridge, Downing Street, Cambridge, CB2 3EA, UK
| | - Mathew G Lewsey
- Centre for AgriBioscience, Department of Animal, Plant and Soil Science, School of Life Science, La Trobe University, Bundoora, Vic., 3086, Australia
| |
Collapse
|
28
|
Cordero T, Cerdán L, Carbonell A, Katsarou K, Kalantidis K, Daròs JA. Dicer-Like 4 Is Involved in Restricting the Systemic Movement of Zucchini yellow mosaic virus in Nicotiana benthamiana. MOLECULAR PLANT-MICROBE INTERACTIONS : MPMI 2017; 30:63-71. [PMID: 27958768 DOI: 10.1094/mpmi-11-16-0239-r] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/06/2023]
Abstract
Zucchini yellow mosaic virus (ZYMV) induces serious diseases in cucurbits. To create a tool to screen for resistance genes, we cloned a wild ZYMV isolate and inserted the visual marker Rosea1 to obtain recombinant clone ZYMV-Ros1. While in some plant-virus combinations Rosea1 induces accumulation of anthocyanins in infected tissues, ZYMV-Ros1 infection of cucurbits did not lead to detectable anthocyanin accumulation. However, the recombinant virus did induce dark red pigmentation in infected tissues of the model plant Nicotiana benthamiana. In this species, ZYMV-Ros1 multiplied efficiently in local inoculated tissue but only a few progeny particles established infection foci in upper leaves. We used this system to analyze the roles of Dicer-like (DCL) genes, core components of plant antiviral RNA silencing pathways, in ZYMV infection. ZYMV-Ros1 local replication was not significantly affected in single DCL knockdown lines nor in double DCL2/4 and triple DCL2/3/4 knockdown lines. ZYMV-Ros1 systemic accumulation was not affected in knockdown lines DCL1, DCL2, and DCL3. However in DCL4 and also in DCL2/4 and DCL2/3/4 knockdown lines, ZYMV-Ros1 systemic accumulation dramatically increased, which highlights the key role of DCL4 in restricting virus systemic movement. The effect of DCL4 on ZYMV systemic movement was confirmed with a wild-type version of the virus.
Collapse
Affiliation(s)
- Teresa Cordero
- 1 Instituto de Biología Molecular y Celular de Plantas (Consejo Superior de Investigaciones Científicas-Universidad Politécnica de Valencia), 46022 Valencia, Spain; and
| | - Lidia Cerdán
- 1 Instituto de Biología Molecular y Celular de Plantas (Consejo Superior de Investigaciones Científicas-Universidad Politécnica de Valencia), 46022 Valencia, Spain; and
| | - Alberto Carbonell
- 1 Instituto de Biología Molecular y Celular de Plantas (Consejo Superior de Investigaciones Científicas-Universidad Politécnica de Valencia), 46022 Valencia, Spain; and
| | - Konstantina Katsarou
- 2 Institute of Molecular Biology and Biotechnology, Foundation for Research and Technology; and Department of Biology, University of Crete, Heraklion, Crete, Greece
| | - Kriton Kalantidis
- 2 Institute of Molecular Biology and Biotechnology, Foundation for Research and Technology; and Department of Biology, University of Crete, Heraklion, Crete, Greece
| | - José-Antonio Daròs
- 1 Instituto de Biología Molecular y Celular de Plantas (Consejo Superior de Investigaciones Científicas-Universidad Politécnica de Valencia), 46022 Valencia, Spain; and
| |
Collapse
|
29
|
Flobinus A, Hleibieh K, Klein E, Ratti C, Bouzoubaa S, Gilmer D. A Viral Noncoding RNA Complements a Weakened Viral RNA Silencing Suppressor and Promotes Efficient Systemic Host Infection. Viruses 2016; 8:E272. [PMID: 27782046 PMCID: PMC5086608 DOI: 10.3390/v8100272] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2016] [Accepted: 09/27/2016] [Indexed: 12/24/2022] Open
Abstract
Systemic movement of beet necrotic yellow vein virus (BNYVV) in Beta macrocarpa depends on viral RNA3, whereas in Nicotiana benthamiana this RNA is dispensable. RNA3 contains a coremin motif of 20 nucleotides essential for the stabilization of noncoding RNA3 (ncRNA3) and for long-distance movement in Beta species. Coremin mutants that are unable to accumulate ncRNA3 also do not achieve systemic movement in Beta species. A mutant virus carrying a mutation in the p14 viral suppressor of RNA silencing (VSR), unable to move long distances, can be complemented with the ncRNA3 in the lesion phenotype, viral RNA accumulation, and systemic spread. Analyses of the BNYVV VSR mechanism of action led to the identification of the RNA-dependent RNA polymerase 6 (RDR6) pathway as a target of the virus VSR and the assignment of a VSR function to the ncRNA3.
Collapse
Affiliation(s)
- Alyssa Flobinus
- Institut de Biologie Moléculaire des Plantes, Integrative Virology, CNRS UPR2367, Université de Strasbourg, 12 rue du Général Zimmer, 67084 Strasbourg, France.
| | - Kamal Hleibieh
- Institut de Biologie Moléculaire des Plantes, Integrative Virology, CNRS UPR2367, Université de Strasbourg, 12 rue du Général Zimmer, 67084 Strasbourg, France.
| | - Elodie Klein
- Institut de Biologie Moléculaire des Plantes, Integrative Virology, CNRS UPR2367, Université de Strasbourg, 12 rue du Général Zimmer, 67084 Strasbourg, France.
- SESVanderHave, Industriepark soldatenplein, Z2nr15, Tienen B3300, Belgium.
| | - Claudio Ratti
- Dipartimento di Scienze Agrarie, Area Patologia Vegetale, Università di Bologna, Viale Fanin 40, 40127 Bologna, Italy.
| | - Salah Bouzoubaa
- Institut de Biologie Moléculaire des Plantes, Integrative Virology, CNRS UPR2367, Université de Strasbourg, 12 rue du Général Zimmer, 67084 Strasbourg, France.
| | - David Gilmer
- Institut de Biologie Moléculaire des Plantes, Integrative Virology, CNRS UPR2367, Université de Strasbourg, 12 rue du Général Zimmer, 67084 Strasbourg, France.
| |
Collapse
|
30
|
Intracellular and extracellular microRNA: An update on localization and biological role. ACTA ACUST UNITED AC 2016; 51:33-49. [PMID: 27396686 DOI: 10.1016/j.proghi.2016.06.001] [Citation(s) in RCA: 153] [Impact Index Per Article: 19.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2016] [Revised: 06/24/2016] [Accepted: 06/24/2016] [Indexed: 12/12/2022]
Abstract
MicroRNA (miRNA) is a class of small non-coding RNAs which mediate post-transcriptional gene silencing (PTGS) by sequence-specific inhibition of target mRNAs translation and/or lowering their half-lives in the cytoplasm. Together with their binding partners, Argonaute (AGO) proteins, miRNAs form cores of RNA-induced silencing complexes (RISC). Despite a substantial progress in understanding RISC structure, until recently little was known about its localization in the cell. This review is aimed to provide an overview of the emerging picture of miRNA and RISC localization and function both in the intracellular space and outside of the cell. In contrast to the common assumption that PTGS occurs in the cytoplasm, it was found to operate mainly on the membranes of the endoplasmic reticulum (ER). Besides ER membranes miRNAs were found in all main cellular compartments including nucleus, nucleolus and mitochondria where they regulate various processes including transcription, translation, alternative splicing and DNA repair. Moreover, a certain pool of miRNAs may not be associated with RISC and carry completely different functions. Finally, the discovery of cell-free miRNAs in all biological fluids suggests that miRNAs might also act as signaling molecules outside the cell, and may be utilized as biomarkers for a variety of diseases. In this review we discuss miRNA secretion mechanisms and possible pathways of cell-cell communication via miRNA-containing exosomes in vivo.
Collapse
|
31
|
Affiliation(s)
- Hailing Jin
- Director of Genetics, Genomics and Bioinformatics Graduate Program, Center for Plant Cell Biology, Institute for Integrative Genome Biology, University of California, Riverside, USA
| |
Collapse
|
32
|
Saplaoura E, Kragler F. Mobile Transcripts and Intercellular Communication in Plants. DEVELOPMENTAL SIGNALING IN PLANTS 2016; 40:1-29. [DOI: 10.1016/bs.enz.2016.07.001] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
|