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Nivedha M, Harish S, Angappan K, Karthikeyan G, Kumar KK, Murugan M, Infant Richard J. Profiling of Groundnut bud necrosis orthotospovirus-responsive microRNA and their targets in tomato based on deep sequencing. J Virol Methods 2024; 327:114924. [PMID: 38574773 DOI: 10.1016/j.jviromet.2024.114924] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2023] [Revised: 03/26/2024] [Accepted: 04/01/2024] [Indexed: 04/06/2024]
Abstract
Tomato, an extensively cultivated vegetable crop produces miRNAs in response to infection with Groundnut bud necrosis orthotospovirus, a viral pathogen causing significant economic losses. High-throughput miRNA sequencing was performed on tomato leaves inoculated with GBNV and mock-inoculated leaves as controls. Analysis revealed 73 known miRNAs belonging to 24 miRNA families, with variable expression levels. Interestingly, 39 miRNAs were upregulated, and 34 were downregulated in response to GBNV infection. Stem-loop quantitative reverse transcription PCR validated the differential expression of selected miRNAs. Additionally, 30 miRNA encoded proteins were identified to be involved in disease resistance and susceptibility. The miRNA-target interactions were found to play significant roles in cellular and metabolic activities, as well as modulating signaling pathways during the plant-virus interaction. The findings shed light on the intricate regulatory network of miRNAs in tomato response to viral infection and may contribute to developing strategies for improving crop protection against viral diseases.
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Affiliation(s)
- M Nivedha
- Department of Plant Pathology, Tamil Nadu Agricultural University, Coimbatore, Tamil Nadu 641 003, India
| | - S Harish
- Department of Plant Pathology, Tamil Nadu Agricultural University, Coimbatore, Tamil Nadu 641 003, India.
| | - K Angappan
- Department of Plant Pathology, Tamil Nadu Agricultural University, Coimbatore, Tamil Nadu 641 003, India
| | - G Karthikeyan
- Department of Plant Pathology, Tamil Nadu Agricultural University, Coimbatore, Tamil Nadu 641 003, India
| | - K K Kumar
- Department of Plant Biotechnology, Centre for Plant Molecular Biology and Biotechnology, Tamil Nadu Agricultural University, Coimbatore, Tamil Nadu 641 003, India
| | - M Murugan
- Department of Agricultural Entomology, Tamil Nadu Agricultural University, Coimbatore, Tamil Nadu 641 003, India
| | - J Infant Richard
- Department of Plant Molecular Biology and Bioinformatics, Centre for Plant Molecular Biology and Biotechnology, Tamil Nadu Agricultural University, Coimbatore, Tamil Nadu 641 003, India
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Rotunno S, Leonetti P, Szittya G, Pantaleo V. Distribution of Small RNAs Along Transposable Elements in Vitis vinifera During Somatic Embryogenesis. Methods Mol Biol 2024; 2732:279-286. [PMID: 38060132 DOI: 10.1007/978-1-0716-3515-5_19] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/08/2023]
Abstract
Metaviridae is a family of reverse-transcribing viruses, closely related to retroviruses; they exist within their host's DNA as transposable elements. Transposable element study requires the use of specialized tools, in part because of their repetitive nature. By combining data from transcript RNA-Seq, small RNA-Seq, and parallel analysis of RNA ends-Seq from grapevine somatic embryos, we set up a bioinformatics flowchart that could be able to assemble and identify transposable elements.
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Affiliation(s)
- Silvia Rotunno
- Institute for Sustainable Plant Protection, National Research Council, Torino, Italy
| | - Paola Leonetti
- Institute for Sustainable Plant Protection, National Research Council, Bari, Italy
| | - György Szittya
- Institute of Genetics and Biotechnology, Hungarian University of Agricultural and Life Sciences, Gödöllő, Hungary
| | - Vitantonio Pantaleo
- Institute for Sustainable Plant Protection, National Research Council, Bari, Italy.
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Guan Y, Wei Z, Song P, Zhou L, Hu H, Hu P, Li C. MicroRNA Expression Profiles in Response to Phytophthora infestans and Oidium neolycopersici and Functional Identification of sly-miR397 in Tomato. PHYTOPATHOLOGY 2023; 113:497-507. [PMID: 36346372 DOI: 10.1094/phyto-04-22-0117-r] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/16/2023]
Abstract
Late blight and powdery mildew are two widespread tomato diseases caused by Phytophthora infestans and Oidium neolycopersici, respectively, which reduce the quantity and quality of tomato. MicroRNAs (miRNAs) play critical roles in tomato resistance to various pathogens. Investigating the function of miRNAs is of great significance in controlling tomato diseases. To identify potential miRNAs involved in the interaction of tomato with P. infestans or O. neolycopersici, we analyzed the expression profiles of small RNAs in tomato leaves infected with these two pathogens using RNA-seq technology. A total of 330 and 288 miRNAs exhibited differences in expression levels after exposure to P. infestans and O. neolycopersici, respectively. One hundred and forty-six commonly differentially expressed (DE) miRNAs responsive to P. infestans and O. neolycopersici infestation were detected, including 10 commonly known conserved DE miRNAs and 136 novel miRNAs. Among these known DE miRNAs, sly-miR397 was strongly downregulated in response to P. infestans or O. neolycopersici infection. Silencing of sly-miR397 resulted in enhanced tolerance to the pathogens, whereas overexpression of sly-miR397 showed increased susceptibility. Furthermore, changes in sly-miR397 expression could also affect expression levels of pathogenesis-related genes and reactive oxygen species-scavenging genes, leading to altered necrotic cells and H2O2 levels. In addition, the number of lateral branches significantly changed in transgenic plants. Taken together, our results provide potential miRNA resources for further research of miRNA-disease associations and indicates that sly-miR397 acts as a negative regulator of disease resistance and influences lateral branch development in tomato.
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Affiliation(s)
- Yuanyuan Guan
- College of Life Science and Technology, Henan Engineering Research Center of Crop Genome Editing, Henan Institute of Science and Technology, Xinxiang 453000, China
| | - Zhiyuan Wei
- College of Life Science and Technology, Henan Engineering Research Center of Crop Genome Editing, Henan Institute of Science and Technology, Xinxiang 453000, China
| | - Puwen Song
- College of Life Science and Technology, Henan Engineering Research Center of Crop Genome Editing, Henan Institute of Science and Technology, Xinxiang 453000, China
| | - Luyi Zhou
- College of Life Science and Technology, Henan Engineering Research Center of Crop Genome Editing, Henan Institute of Science and Technology, Xinxiang 453000, China
| | - Haiyan Hu
- College of Life Science and Technology, Henan Engineering Research Center of Crop Genome Editing, Henan Institute of Science and Technology, Xinxiang 453000, China
| | - Ping Hu
- College of Life Science and Technology, Henan Engineering Research Center of Crop Genome Editing, Henan Institute of Science and Technology, Xinxiang 453000, China
| | - Chengwei Li
- College of Biological Engineering, Henan University of Technology, Zhengzhou 450001, China
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Dey S, Sarkar A, Chowdhury S, Singh R, Mukherjee A, Ghosh Z, Kundu P. Heightened miR6024-NLR interactions facilitate necrotrophic pathogenesis in tomato. PLANT MOLECULAR BIOLOGY 2022; 109:717-739. [PMID: 35499677 DOI: 10.1007/s11103-022-01270-z] [Citation(s) in RCA: 15] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/14/2021] [Accepted: 03/27/2022] [Indexed: 06/14/2023]
Abstract
miR6024 acts as a negative regulator of R genes, hence of Tomato plant immunity, and facilitates disease by the necrotrophic pathogen A. solani. Plant resistance genes or Nucleotide-binding leucine-rich repeat (NLR) genes, integral components of plant disease stress-signaling are targeted by variable groups of miRNAs. However, the significance of miRNA-mediated regulation of NLRs during a pathogen stress response, specifically for necrotrophic fungus, is poorly understood. A thorough examination of Tomato NLRs and miRNAs could map substantial interactions of which half the annotated NLRs were targets of Solanaceae-specific and conserved miRNAs, at the NB subdomain. The Solanaceae-specific miR6024 and its NLR targets analysed in different phytopathogenic stresses revealed differential and mutually antagonistic regulation. Interestingly, miR6024-targeted cleavage of a target NLR also triggered the generation of secondary phased siRNAs which could potentially amplify the defense signal. RNA-seq analysis of leaf tissues from miR6024 overexpressing Tomato plants evidenced a perturbation in the defense transcriptome with the transgenics showing unwarranted immune response-related genes' expression with or without infection with necrotrophic Alternaria solani, though no adverse effect could be observed in the growth and development of the transgenic plants. Transgenic plants exhibited constitutive downregulation of the target NLRs, aggravated disease phenotype with an enhanced lesion, greater ROS generation and hypersusceptibility to A. solani infection, thus establishing that miR6024 negatively impacts plant immune response during necrotrophic pathogenesis. Limited knowledge about the outcome of NLR-miRNA interaction during necrotrophic pathogenesis is a hindrance to the deployment of miRNAs in crop improvement programs. With the elucidation of the necrotrophic disease-synergistic role played by miR6024, it becomes a potent candidate for biotechnological manipulation for the rapid development of pathogen-tolerant solanaceous plants.
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Affiliation(s)
- Sayani Dey
- Division of Plant Biology, Unified Academic Campus, Bose Institute, EN 80, Bidhan Nagar, Kolkata, West Bengal, 700091, India
| | - Arijita Sarkar
- Division of Bioinformatics, Unified Academic Campus, Bose Institute, EN 80, Bidhan Nagar, Kolkata, West Bengal, 700091, India
| | - Shreya Chowdhury
- Division of Plant Biology, Unified Academic Campus, Bose Institute, EN 80, Bidhan Nagar, Kolkata, West Bengal, 700091, India
| | - Raghuvir Singh
- Division of Plant Biology, Unified Academic Campus, Bose Institute, EN 80, Bidhan Nagar, Kolkata, West Bengal, 700091, India
| | - Ananya Mukherjee
- Division of Plant Biology, Unified Academic Campus, Bose Institute, EN 80, Bidhan Nagar, Kolkata, West Bengal, 700091, India
| | - Zhumur Ghosh
- Division of Bioinformatics, Unified Academic Campus, Bose Institute, EN 80, Bidhan Nagar, Kolkata, West Bengal, 700091, India
| | - Pallob Kundu
- Division of Plant Biology, Unified Academic Campus, Bose Institute, EN 80, Bidhan Nagar, Kolkata, West Bengal, 700091, India.
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Wang C, Jiang F, Zhu S. Complex Small RNA-mediated Regulatory Networks between Viruses/Viroids/Satellites and Host Plants. Virus Res 2022; 311:198704. [DOI: 10.1016/j.virusres.2022.198704] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2021] [Revised: 01/16/2022] [Accepted: 01/29/2022] [Indexed: 12/26/2022]
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Leonetti P, Stuttmann J, Pantaleo V. Regulation of plant antiviral defense genes via host RNA-silencing mechanisms. Virol J 2021; 18:194. [PMID: 34565394 PMCID: PMC8474839 DOI: 10.1186/s12985-021-01664-3] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2021] [Accepted: 09/14/2021] [Indexed: 12/23/2022] Open
Abstract
Background Plants in nature or crops in the field interact with a multitude of beneficial or parasitic organisms, including bacteria, fungi and viruses. Viruses are highly specialized to infect a limited range of host plants, leading in extreme cases to the full invasion of the host and a diseased phenotype. Resistance to viruses can be mediated by various passive or active mechanisms, including the RNA-silencing machinery and the innate immune system. Main text RNA-silencing mechanisms may inhibit viral replication, while viral components can elicit the innate immune system. Viruses that successfully enter the plant cell can elicit pattern-triggered immunity (PTI), albeit by yet unknown mechanisms. As a counter defense, viruses suppress PTI. Furthermore, viral Avirulence proteins (Avr) may be detected by intracellular immune receptors (Resistance proteins) to elicit effector-triggered immunity (ETI). ETI often culminates in a localized programmed cell death reaction, the hypersensitive response (HR), and is accompanied by a potent systemic defense response. In a dichotomous view, RNA silencing and innate immunity are seen as two separate mechanisms of resistance. Here, we review the intricate connections and similarities between these two regulatory systems, which are collectively required to ensure plant fitness and resilience. Conclusions The detailed understanding of immune regulation at the transcriptional level provides novel opportunities for enhancing plant resistance to viruses by RNA-based technologies. However, extensive use of RNA technologies requires a thorough understanding of the molecular mechanisms of RNA gene regulation. We describe the main examples of host RNA-mediated regulation of virus resistance.
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Affiliation(s)
- Paola Leonetti
- Department of Biology, Agricultural and Food Sciences, Institute for Sustainable Plant Protection, Research Unit of Bari, CNR, 70126, Bari, Italy
| | - Johannes Stuttmann
- Institute of Biology, Department of Plant Genetics, Martin Luther University, Halle-Wittenberg, 06120, Halle (Saale), Germany
| | - Vitantonio Pantaleo
- Department of Biology, Agricultural and Food Sciences, Institute for Sustainable Plant Protection, Research Unit of Bari, CNR, 70126, Bari, Italy. .,Institute of Biochemistry and Biotechnology, Martin Luther University, Halle-Wittenberg, 06120, Halle (Saale), Germany.
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Leonetti P, Ghasemzadeh A, Consiglio A, Gursinsky T, Behrens S, Pantaleo V. Endogenous activated small interfering RNAs in virus-infected Brassicaceae crops show a common host gene-silencing pattern affecting photosynthesis and stress response. THE NEW PHYTOLOGIST 2021; 229:1650-1664. [PMID: 32945560 PMCID: PMC7821159 DOI: 10.1111/nph.16932] [Citation(s) in RCA: 20] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/27/2020] [Accepted: 09/04/2020] [Indexed: 05/14/2023]
Abstract
Viral infections are accompanied by a massive production of small interfering RNAs (siRNAs) of plant origin, such as virus-activated (va)siRNAs, which drive the widespread silencing of host gene expression, and whose effects in plant pathogen interactions remain unknown. By combining phenotyping and molecular analyses, we characterized vasiRNAs that are associated with typical mosaic symptoms of cauliflower mosaic virus infection in two crops, turnip (Brassica rapa) and oilseed rape (Brassica napus), and the reference plant Arabidopsis thaliana. We identified 15 loci in the three infected plant species, whose transcripts originate vasiRNAs. These loci appear to be generally affected by virus infections in Brassicaceae and encode factors that are centrally involved in photosynthesis and stress response, such as Rubisco activase (RCA), senescence-associated protein, heat shock protein HSP70, light harvesting complex, and membrane-related protein CP5. During infection, the expression of these factors is significantly downregulated, suggesting that their silencing is a central component of the plant's response to virus infections. Further findings indicate an important role for 22 nt long vasiRNAs in the plant's endogenous RNA silencing response. Our study considerably enhances knowledge about the new class of vasiRNAs that are triggered in virus-infected plants and will help to advance strategies for the engineering of gene clusters involved in the development of crop diseases.
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Affiliation(s)
- Paola Leonetti
- Department of Biology, Agricultural and Food SciencesInstitute for Sustainable Plant ProtectionBari UnitCNRBari70126Italy
| | - Aysan Ghasemzadeh
- Department of Biology, Agricultural and Food SciencesInstitute for Sustainable Plant ProtectionBari UnitCNRBari70126Italy
- Department of Plant PathologyFaculty of AgricultureTarbiat Modares UniversityTehran14115‐111Iran
- Institute of Biochemistry and Biotechnology (NFI)Section Microbial BiotechnologyMartin Luther University Halle‐WittenbergHalle/SaaleD‐06120Germany
| | - Arianna Consiglio
- Department of Biomedical SciencesInstitute for Biomedical TechnologiesBari UnitCNRBari70126Italy
| | - Torsten Gursinsky
- Institute of Biochemistry and Biotechnology (NFI)Section Microbial BiotechnologyMartin Luther University Halle‐WittenbergHalle/SaaleD‐06120Germany
| | - Sven‐Erik Behrens
- Institute of Biochemistry and Biotechnology (NFI)Section Microbial BiotechnologyMartin Luther University Halle‐WittenbergHalle/SaaleD‐06120Germany
| | - Vitantonio Pantaleo
- Department of Biology, Agricultural and Food SciencesInstitute for Sustainable Plant ProtectionBari UnitCNRBari70126Italy
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8
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Chakraborty J, Ghosh P. Advancement of research on plant NLRs evolution, biochemical activity, structural association, and engineering. PLANTA 2020; 252:101. [PMID: 33180185 DOI: 10.1007/s00425-020-03512-0] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/22/2020] [Accepted: 11/03/2020] [Indexed: 06/11/2023]
Abstract
In this review, we have included evolution of plant intracellular immune receptors, oligomeric complex formation, enzymatic action, engineering, and mechanisms of immune inspection for appropriate defense outcomes. NLR (Nucleotide binding oligomerization domain containing leucine-rich repeat) proteins are the intracellular immune receptors that recognize pathogen-derived virulence factors to confer effector-triggered immunity (ETI). Activation of plant defense by the NLRs are often conveyed through N-terminal Toll-like/ IL-1 receptor (TIR) or non-TIR (coiled-coils or CC) domains. Homodimerization or self-association property of CC/ TIR domains of plant NLRs contribute to their auto-activity and induction of in planta ectopic cell death. High resolution crystal structures of Arabidopsis thaliana RPS4TIR, L6TIR, SNC1TIR, RPP1TIR and Muscadinia rotundifolia RPV1TIR showed that interaction is mediated through one or two distinct interfaces i.e., αA and αE helices comprise AE interface and αD and αE helices were found to form DE interface. By contrast, conserved helical regions were determined for CC domains of plant NLRs. Evolutionary history of NLRs diversification has shown that paired forms were originated from NLR singletons. Plant TIRs executed NAD+ hydrolysis activity for cell death promotion. Plant NLRs were found to form large oligomeric complexes as observed in animal inflammasomes. We have also discussed different protein engineering methods includes domain shuffling, and decoy modification that increase effector recognition spectrum of plant NLRs. In summary, our review highlights structural basis of perception of the virulence factors by NLRs or NLR pairs to design novel classes of plant immune receptors.
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Affiliation(s)
| | - Prithwi Ghosh
- Department of Botany, Narajole Raj College, Narajole, Paschim Medinipur, 721211, West Bengal, India
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Islam S, Bhor SA, Tanaka K, Sakamoto H, Yaeno T, Kaya H, Kobayashi K. Impaired Expression of Chloroplast HSP90C Chaperone Activates Plant Defense Responses with a Possible Link to a Disease-Symptom-Like Phenotype. Int J Mol Sci 2020; 21:E4202. [PMID: 32545608 PMCID: PMC7352560 DOI: 10.3390/ijms21124202] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2020] [Revised: 06/10/2020] [Accepted: 06/11/2020] [Indexed: 12/13/2022] Open
Abstract
RNA-seq analysis of a transgenic tobacco plant, i-hpHSP90C, in which chloroplast HSP90C genes can be silenced in an artificially inducible manner resulting in the development of chlorosis, revealed the up- and downregulation of 2746 and 3490 genes, respectively. Gene ontology analysis of these differentially expressed genes indicated the upregulation of ROS-responsive genes; the activation of the innate immunity and cell death pathways; and the downregulation of genes involved in photosynthesis, plastid organization, and cell cycle. Cell death was confirmed by trypan blue staining and electrolyte leakage assay, and the H2O2 production was confirmed by diaminobenzidine staining. The results collectively suggest that the reduced levels of HSP90C chaperone lead the plant to develop chlorosis primarily through the global downregulation of chloroplast- and photosynthesis-related genes and additionally through the light-dependent production of ROS, followed by the activation of immune responses, including cell death.
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Affiliation(s)
- Shaikhul Islam
- The United Graduate School of Agricultural Sciences, Ehime University, Matsuyama, Ehime 790-8566, Japan; (S.I.); (S.A.B.); (T.Y.); (H.K.)
| | - Sachin Ashok Bhor
- The United Graduate School of Agricultural Sciences, Ehime University, Matsuyama, Ehime 790-8566, Japan; (S.I.); (S.A.B.); (T.Y.); (H.K.)
| | - Keisuke Tanaka
- NODAI Genome Research Center, Tokyo University of Agriculture, Setagaya, Tokyo 156-8502, Japan;
| | - Hikaru Sakamoto
- Faculty of Bio-Industry, Tokyo University of Agriculture, Abashiri, Hokkaido 099-2493, Japan;
| | - Takashi Yaeno
- The United Graduate School of Agricultural Sciences, Ehime University, Matsuyama, Ehime 790-8566, Japan; (S.I.); (S.A.B.); (T.Y.); (H.K.)
- Graduate School of Agriculture, Ehime University, Matsuyama, Ehime 790-8566, Japan
- Research Unit for Citromics, Ehime University, Matsuyama, Ehime 790-8566, Japan
| | - Hidetaka Kaya
- The United Graduate School of Agricultural Sciences, Ehime University, Matsuyama, Ehime 790-8566, Japan; (S.I.); (S.A.B.); (T.Y.); (H.K.)
- Graduate School of Agriculture, Ehime University, Matsuyama, Ehime 790-8566, Japan
- Research Unit for Citromics, Ehime University, Matsuyama, Ehime 790-8566, Japan
| | - Kappei Kobayashi
- The United Graduate School of Agricultural Sciences, Ehime University, Matsuyama, Ehime 790-8566, Japan; (S.I.); (S.A.B.); (T.Y.); (H.K.)
- Graduate School of Agriculture, Ehime University, Matsuyama, Ehime 790-8566, Japan
- Research Unit for Citromics, Ehime University, Matsuyama, Ehime 790-8566, Japan
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Leonetti P, Miesen P, van Rij RP, Pantaleo V. Viral and subviral derived small RNAs as pathogenic determinants in plants and insects. Adv Virus Res 2020; 107:1-36. [PMID: 32711727 DOI: 10.1016/bs.aivir.2020.04.001] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/21/2023]
Abstract
The phenotypic manifestations of disease induced by viruses and subviral infectious entities are the result of complex molecular interactions between host and viral factors. The viral determinants of the diseased phenotype have traditionally been sought at the level of structural or non-structural proteins. However, the discovery of RNA silencing mechanisms has led to speculations that determinants of the diseased phenotype are caused by viral nucleic acid sequences in addition to proteins. RNA silencing is a gene regulation mechanism conserved within eukaryotic kingdoms (with the exception of some yeast species), and in plants and insects it also functions as an antiviral mechanism. Non-coding RNAs of viral origin, ranging in size from 21 to 24 nucleotides (viral small interfering RNAs, vsiRNAs) accumulate in virus-infected tissues and organs, in some cases to comparable levels as the entire complement of host-encoded small interfering RNAs. Upon incorporation into RNA-induced silencing complexes, vsiRNAs can mediate cleavage or induce translational inhibition of nucleic acid targets in a sequence-specific manner. This review focuses on recent findings that suggest an increased complexity of small RNA-based interactions between virus and host. We mainly address plant viruses, but where applicable discuss insect viruses as well. Prominence is given to studies that have indisputably demonstrated that vsiRNAs determine diseased phenotype by either carrying sequence determinants or, indirectly, by altering host-gene regulatory pathways. Results from these studies suggest biotechnological applications, which are also discussed.
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Affiliation(s)
- Paola Leonetti
- Department of Biology, Agricultural and Food Sciences, Institute for Sustainable Plant Protection, CNR, Bari, Italy
| | - Pascal Miesen
- Department of Medical Microbiology, Radboud Institute for Molecular Life Sciences, Radboud University Medical Center, Nijmegen, The Netherlands
| | - Ronald P van Rij
- Department of Medical Microbiology, Radboud Institute for Molecular Life Sciences, Radboud University Medical Center, Nijmegen, The Netherlands.
| | - Vitantonio Pantaleo
- Department of Biology, Agricultural and Food Sciences, Institute for Sustainable Plant Protection, CNR, Bari, Italy..
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Prigigallo MI, Križnik M, De Paola D, Catalano D, Gruden K, Finetti-Sialer MM, Cillo F. Potato Virus Y Infection Alters Small RNA Metabolism and Immune Response in Tomato. Viruses 2019; 11:v11121100. [PMID: 31783643 PMCID: PMC6950276 DOI: 10.3390/v11121100] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2019] [Revised: 11/19/2019] [Accepted: 11/24/2019] [Indexed: 12/17/2022] Open
Abstract
Potato virus Y (PVY) isolate PVYC-to induces growth reduction and foliar symptoms in tomato, but new vegetation displays symptom recovery at a later stage. In order to investigate the role of micro(mi)RNA and secondary small(s)RNA-regulated mechanisms in tomato defenses against PVY, we performed sRNA sequencing from healthy and PVYC-to infected tomato plants at 21 and 30 days post-inoculation (dpi). A total of 792 miRNA sequences were obtained, among which were 123 canonical miRNA sequences, many isomiR variants, and 30 novel miRNAs. MiRNAs were mostly overexpressed in infected vs. healthy plants, whereas only a few miRNAs were underexpressed. Increased accumulation of isomiRs was correlated with viral infection. Among miRNA targets, enriched functional categories included resistance (R) gene families, transcription and hormone factors, and RNA silencing genes. Several 22-nt miRNAs were shown to target R genes and trigger the production of 21-nt phased sRNAs (phasiRNAs). Next, 500 phasiRNA-generating loci were identified, and were shown to be mostly active in PVY-infected tissues and at 21 dpi. These data demonstrate that sRNA-regulated host responses, encompassing miRNA alteration, diversification within miRNA families, and phasiRNA accumulation, regulate R and disease-responsive genes. The dynamic regulation of miRNAs and secondary sRNAs over time suggests a functional role of sRNA-mediated defenses in the recovery phenotype.
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Affiliation(s)
- Maria I. Prigigallo
- Consiglio Nazionale delle Ricerche, Istituto per la Protezione Sostenibile delle Piante, G. Via Amendola 122/D, 70126 Bari, Italy;
| | - Maja Križnik
- National Institute of Biology, Department of Biotechnology and Systems Biology, Večna pot 111, 1000 Ljubljana, Slovenia; (M.K.); (K.G.)
| | - Domenico De Paola
- Consiglio Nazionale delle Ricerche, Istituto di Bioscienze e BioRisorse, Via G. Amendola 165/A, 70126 Bari, Italy;
| | - Domenico Catalano
- Consiglio Nazionale delle Ricerche, Istituto di Tecnologie Biomediche, Via G. Amendola 122/D, 70126 Bari, Italy;
| | - Kristina Gruden
- National Institute of Biology, Department of Biotechnology and Systems Biology, Večna pot 111, 1000 Ljubljana, Slovenia; (M.K.); (K.G.)
| | - Mariella M. Finetti-Sialer
- Consiglio Nazionale delle Ricerche, Istituto di Bioscienze e BioRisorse, Via G. Amendola 165/A, 70126 Bari, Italy;
- Correspondence: (M.M.F.-S.); (F.C.); Tel.: +39-080-55583400 (ext. 213) (M.M.F.-S.); +39-080-5443109 (F.C.)
| | - Fabrizio Cillo
- Consiglio Nazionale delle Ricerche, Istituto per la Protezione Sostenibile delle Piante, G. Via Amendola 122/D, 70126 Bari, Italy;
- Correspondence: (M.M.F.-S.); (F.C.); Tel.: +39-080-55583400 (ext. 213) (M.M.F.-S.); +39-080-5443109 (F.C.)
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