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Zavallo D, Cara N, Leone M, Crescente JM, Marfil C, Masuelli R, Asurmendi S. Assessing small RNA profiles in potato diploid hybrid and its resynthesized allopolyploid reveals conserved abundance with distinct genomic distribution. PLANT CELL REPORTS 2024; 43:85. [PMID: 38453711 DOI: 10.1007/s00299-024-03170-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/31/2023] [Accepted: 02/07/2024] [Indexed: 03/09/2024]
Abstract
KEY MESSAGE The shock produced by the allopolyploidization process on a potato interspecific diploid hybrid displays a non-random remobilization of the small RNAs profile on a variety of genomic features. Allopolyploidy, a complex process involving interspecific hybridization and whole genome duplication, significantly impacts plant evolution, leading to the emergence of novel phenotypes. Polyploids often present phenotypic nuances that enhance adaptability, enabling them to compete better and occasionally to colonize new habitats. Whole-genome duplication represents a genomic "shock" that can trigger genetic and epigenetic changes that yield novel expression patterns. In this work, we investigate the polyploidization effect on a diploid interspecific hybrid obtained through the cross between the cultivated potato Solanum tuberosum and the wild potato Solanum kurtzianum, by assessing the small RNAs (sRNAs) profile of the parental diploid hybrid and its derived allopolyploid. Small RNAs are key components of the epigenetic mechanisms involved in silencing by RNA-directed DNA Methylation (RdDM). A sRNA sequencing (sRNA-Seq) analysis was performed to individually profile the 21 to 22 nucleotide (21 to 22-nt) and 24-nt sRNA size classes due to their unique mechanism of biogenesis and mode of function. The composition and distribution of different genomic features and differentially accumulated (DA) sRNAs were evaluated throughout the potato genome. We selected a subset of genes associated with DA sRNAs for messenger RNA (mRNA) expression analysis to assess potential impacts on the transcriptome. Interestingly, we noted that 24-nt DA sRNAs that exclusively mapped to exons were correlated with differentially expressed mRNAs between genotypes, while this behavior was not observed when 24-nt DA sRNAs were mapped to intronic regions. These findings collectively emphasize the nonstochastic nature of sRNA remobilization in response to the genomic shock induced by allopolyploidization.
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Affiliation(s)
- Diego Zavallo
- Instituto de Agrobiotecnología y Biología Molecular (IABIMO), CICVyA - Instituto Nacional de Tecnología Agropecuaria (INTA), Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Los Reseros y Nicolás Repetto, 1686, Hurlingham, CP, Argentina
| | - Nicolas Cara
- Instituto de Biología Agrícola de Mendoza (IBAM), Facultad de Ciencias Agrarias (FCA), CONICET-UNCuyo, Almirante Brown 500, M5528AHB, Chacras de Coria, Mendoza, Argentina
| | - Melisa Leone
- Universidad Nacional de Hurlingham, Instituto de Biotecnología, Av. Vergara 2222 (B1688GEZ), Villa Tesei, Buenos Aires, Argentina
| | - Juan Manuel Crescente
- Grupo Biotecnología y Recursos Genéticos, EEA INTA Marcos Juárez, Ruta 12 Km 3, 2580, Marcos Juárez, Argentina
| | - Carlos Marfil
- Estación Experimental Agropecuaria Mendoza, Instituto Nacional de Tecnología Agropecuaria (EEA-Mendoza-INTA), San Martín 3853, Luján de Cuyo, 5534, Mendoza, Argentina
| | - Ricardo Masuelli
- Instituto de Biología Agrícola de Mendoza (IBAM), Facultad de Ciencias Agrarias (FCA), CONICET-UNCuyo, Almirante Brown 500, M5528AHB, Chacras de Coria, Mendoza, Argentina
| | - Sebastián Asurmendi
- Instituto de Agrobiotecnología y Biología Molecular (IABIMO), CICVyA - Instituto Nacional de Tecnología Agropecuaria (INTA), Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Los Reseros y Nicolás Repetto, 1686, Hurlingham, CP, Argentina.
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Caro MDP, Venturuzzi AL, Moschen S, Salazar SM, Díaz-Ricci JC, Asurmendi S. A fungal protease named AsES triggers antiviral immune responses and effectively restricts virus infection in arabidopsis and Nicotiana benthamiana plants. ANNALS OF BOTANY 2022; 129:593-606. [PMID: 35134835 PMCID: PMC9007096 DOI: 10.1093/aob/mcac013] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/13/2022] [Accepted: 01/29/2022] [Indexed: 06/14/2023]
Abstract
BACKGROUND AND AIMS Plants have evolved complex mechanisms to fight against pathogens. Among these mechanisms, pattern-triggered immunity (PTI) relies on the recognition of conserved microbe- or pathogen-associated molecular patterns (MAMPs or PAMPs, respectively) by membrane-bound receptors. Indeed, PTI restricts virus infection in plants and, in addition, BRI1-associated kinase 1 (BAK1), a central regulator of PTI, plays a role in antiviral resistance. However, the compounds that trigger antiviral defences, along with their molecular mechanisms of action, remain mostly elusive. Herein, we explore the role of a fungal extracellular subtilase named AsES in its capacity to trigger antiviral responses. METHODS In this study, we obtained AsES by recombinant expression, and evaluated and characterized its capacity to trigger antiviral responses against Tobacco mosaic virus (TMV) by performing time course experiments, analysing gene expression, virus movement and callose deposition. KEY RESULTS The results of this study provide direct evidence that exogenous treatment with recombinant AsES increases a state of resistance against TMV infection, in both arabidopsis and Nicotiana benthamiana plants. Also, the antiviral PTI response exhibited by AsES in arabidopsis is mediated by the BAK1/SERK3 and BKK1/SERK4 co-receptors. Moreover, AsES requires a fully active salicylic acid (SA) signalling pathway to restrict the TMV movement by inducing callose deposition. Additionally, treatment with PSP1, a biostimulant based on AsES as the active compound, showed an increased resistance against TMV in N. benthamiana and tobacco plants. CONCLUSIONS AsES is a fungal serine protease which triggers antiviral responses relying on a conserved mechanism by means of the SA signalling pathway and could be exploited as an effective and sustainable biotechnology strategy for viral disease management in plants.
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Affiliation(s)
- Maria Del Pilar Caro
- Instituto de Agrobiotecnología y Biología Molecular (IABIMO), CICVyA, Instituto Nacional de Tecnología Agropecuaria (INTA), Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), De los Reseros y N. Repetto s/n, Hurlingham B1686IGC, Argentina
- Estación Experimental Agropecuaria Famaillá, Instituto Nacional de Tecnología Agropecuaria (INTA), Ruta Provincial 301 Km 32, Tucumán, Argentina
- Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Argentina
| | - Andrea Laura Venturuzzi
- Instituto de Agrobiotecnología y Biología Molecular (IABIMO), CICVyA, Instituto Nacional de Tecnología Agropecuaria (INTA), Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), De los Reseros y N. Repetto s/n, Hurlingham B1686IGC, Argentina
| | - Sebastian Moschen
- Estación Experimental Agropecuaria Famaillá, Instituto Nacional de Tecnología Agropecuaria (INTA), Ruta Provincial 301 Km 32, Tucumán, Argentina
- Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Argentina
| | - Sergio Miguel Salazar
- Estación Experimental Agropecuaria Famaillá, Instituto Nacional de Tecnología Agropecuaria (INTA), Ruta Provincial 301 Km 32, Tucumán, Argentina
| | - Juan Carlos Díaz-Ricci
- Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Argentina
- Instituto Superior de Investigaciones Biológicas (INSIBIO), CONICET-UNT, and Instituto de Química Biológica ‘Dr. Bernabé Bloj’, Facultad de Bioquímica, Química y Farmacia, UNT, San Miguel de Tucumán, Argentina
| | - Sebastian Asurmendi
- Instituto de Agrobiotecnología y Biología Molecular (IABIMO), CICVyA, Instituto Nacional de Tecnología Agropecuaria (INTA), Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), De los Reseros y N. Repetto s/n, Hurlingham B1686IGC, Argentina
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3
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Dang T, Lavagi-Craddock I, Bodaghi S, Vidalakis G. Next-Generation Sequencing Identification and Characterization of MicroRNAs in Dwarfed Citrus Trees Infected With Citrus Dwarfing Viroid in High-Density Plantings. Front Microbiol 2021; 12:646273. [PMID: 33995303 PMCID: PMC8121382 DOI: 10.3389/fmicb.2021.646273] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2021] [Accepted: 04/06/2021] [Indexed: 11/19/2022] Open
Abstract
Citrus dwarfing viroid (CDVd) induces stunting on sweet orange trees [Citrus sinensis (L.) Osbeck], propagated on trifoliate orange rootstock [Citrus trifoliata (L.), syn. Poncirus trifoliata (L.) Raf.]. MicroRNAs (miRNAs) are a class of non-coding small RNAs (sRNAs) that play important roles in the regulation of tree gene expression. To identify miRNAs in dwarfed citrus trees, grown in high-density plantings, and their response to CDVd infection, sRNA next-generation sequencing was performed on CDVd-infected and non-infected controls. A total of 1,290 and 628 miRNAs were identified in stem and root tissues, respectively, and among those, 60 were conserved in each of these two tissue types. Three conserved miRNAs (csi-miR479, csi-miR171b, and csi-miR156) were significantly downregulated (adjusted p-value < 0.05) in the stems of CDVd-infected trees compared to the non-infected controls. The three stem downregulated miRNAs are known to be involved in various physiological and developmental processes some of which may be related to the characteristic dwarfed phenotype displayed by CDVd-infected C. sinensis on C. trifoliata rootstock field trees. Only one miRNA (csi-miR535) was significantly downregulated in CDVd-infected roots and it was predicted to target genes controlling a wide range of cellular functions. Reverse transcription quantitative polymerase chain reaction analysis performed on selected miRNA targets validated the negative correlation between the expression levels of these targets and their corresponding miRNAs in CDVd-infected trees. Our results indicate that CDVd-responsive plant miRNAs play a role in regulating important citrus growth and developmental processes that may participate in the cellular changes leading to the observed citrus dwarf phenotype.
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Affiliation(s)
- Tyler Dang
- Department of Microbiology and Plant Pathology, University of California, Riverside, Riverside, CA, United States
| | - Irene Lavagi-Craddock
- Department of Microbiology and Plant Pathology, University of California, Riverside, Riverside, CA, United States
| | - Sohrab Bodaghi
- Department of Microbiology and Plant Pathology, University of California, Riverside, Riverside, CA, United States
| | - Georgios Vidalakis
- Department of Microbiology and Plant Pathology, University of California, Riverside, Riverside, CA, United States
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Leone M, Zavallo D, Venturuzzi A, Asurmendi S. RdDM pathway components differentially modulate Tobamovirus symptom development. PLANT MOLECULAR BIOLOGY 2020; 104:467-481. [PMID: 32813230 DOI: 10.1007/s11103-020-01051-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/08/2020] [Accepted: 08/11/2020] [Indexed: 06/11/2023]
Abstract
The crop yield losses induced by phytoviruses are mainly associated with the symptoms of the disease. DNA modifications as methylation can modulate the information coded by the sequence, process named epigenetics. Viral infection can change the expression patterns of different genes linked to defenses and symptoms. This work represents the initial step to expose the role of epigenetic process, in the production of symptoms associated with plants-virus interactions. Small RNAs (sRNAs) are important molecules for gene regulation in plants and play an essential role in plant-pathogen interactions. Researchers have evaluated the relationship between viral infections as well as the endogenous accumulation of sRNAs and the transcriptional changes associated with the production of symptoms, but little is known about a possible direct role of epigenetics, mediated by 24-nt sRNAs, in the induction of these symptoms. Using different RNA directed DNA methylation (RdDM) pathway mutants and a triple demethylase mutant; here we demonstrate that the disruption of RdDM pathway during viral infection produce alterations in the plant transcriptome and in consequence changes in plant symptoms. This study represents the initial step in exposing that DNA methylation directed by endogenous sRNAs has an important role, uncoupled to defense, in the production of symptoms associated with plant-virus interactions.
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Affiliation(s)
- Melisa Leone
- Instituto de Agrobiotecnología y Biología Molecular (IABIMO), Instituto Nacional de Tecnología Agropecuaria (INTA), Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), De Los Reseros y N. Repetto S/N, Hurlingham, B1686IGC, Buenos Aires, Argentina
- Agencia Nacional de Promoción Científica y Tecnológica (ANPCyT), Buenos Aires, Argentina
| | - Diego Zavallo
- Instituto de Agrobiotecnología y Biología Molecular (IABIMO), Instituto Nacional de Tecnología Agropecuaria (INTA), Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), De Los Reseros y N. Repetto S/N, Hurlingham, B1686IGC, Buenos Aires, Argentina
| | - Andrea Venturuzzi
- Instituto de Agrobiotecnología y Biología Molecular (IABIMO), Instituto Nacional de Tecnología Agropecuaria (INTA), Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), De Los Reseros y N. Repetto S/N, Hurlingham, B1686IGC, Buenos Aires, Argentina
| | - Sebastián Asurmendi
- Instituto de Agrobiotecnología y Biología Molecular (IABIMO), Instituto Nacional de Tecnología Agropecuaria (INTA), Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), De Los Reseros y N. Repetto S/N, Hurlingham, B1686IGC, Buenos Aires, Argentina.
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Sheng Y, Yang L, Li C, Wang Y, Guo H. Transcriptomic changes in Nicotiana tabacum leaves during mosaic virus infection. 3 Biotech 2019; 9:220. [PMID: 31114744 DOI: 10.1007/s13205-019-1740-6] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2018] [Accepted: 05/08/2019] [Indexed: 02/04/2023] Open
Abstract
To provide a detailed insight into the early biological process of tobacco mosaic disease, transcriptomic changes in tobacco leaves were surveyed at 1, 3 and 5 days after mono-infected by Tobacco mosaic virus (TMV) and co-infected by Cucumber mosaic virus (CMV) and TMV. At the three different stages, there were 2372, 3168 and 2045 differentially expressed genes (DEGs) in mono-infected leaves, and 2388, 3281 and 3417 DEGs were identified in co-infected leaves. There were 836, 1538 and 1185 common DEGs between the mono-infection and co-infection at the three time points, respectively. These common DEGs were enriched in the pathways, such as photosynthesis, biosynthesis of secondary metabolites, plant-pathogen interaction, porphyrin and chlorophyll metabolism, phenylalanine metabolism and phenylpropanoid biosynthesis. Photosynthesis pathway was observably down-regulated, and defense response pathways were markedly up-regulated. These pathways have been found to be related to tobacco mosaic disease. Of these common DEGs, the changes in expression of argonaute proteins, thioredoxins and peroxidases showed that the activation of RNA silencing and the destruction of redox balance can be induced by tobacco mosaic virus infection, resulting in the reset of biology process and damage in tobacco plants. Additionally, the occurrence of symptoms in co-infected tobacco plants was more early and serious than mono-infection, indicating that there is synergy between TMV and CMV in co-infected tobacco plants. The timely usage of antiviral agents and plant resistance inducers can decrease the incidence of tobacco mosaic disease through changing the expression of some DEGs, indicating that these genes can be used to screen novel plant resistance inducers and antiviral agents. Overall, our results were helpful in clarifying the mechanism of tobacco mosaic disease and provided novel strategies for the prevention of tobacco mosaic disease.
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Affiliation(s)
- Yangyang Sheng
- 1College of Life Sciences, Henan Agricultural University, Zhengzhou, 450002 Henan China
| | - Lijun Yang
- Zhumadian Branch of Henan Province Tobacco Company, Zhumadian, 463000 Henan China
| | - Chunfu Li
- 1College of Life Sciences, Henan Agricultural University, Zhengzhou, 450002 Henan China
| | - Yuping Wang
- 1College of Life Sciences, Henan Agricultural University, Zhengzhou, 450002 Henan China
| | - Hongxiang Guo
- 1College of Life Sciences, Henan Agricultural University, Zhengzhou, 450002 Henan China
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Cambiagno DA, Nota F, Zavallo D, Rius S, Casati P, Asurmendi S, Alvarez ME. Immune receptor genes and pericentromeric transposons as targets of common epigenetic regulatory elements. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2018; 96:1178-1190. [PMID: 30238536 DOI: 10.1111/tpj.14098] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/18/2018] [Revised: 08/24/2018] [Accepted: 09/03/2018] [Indexed: 05/04/2023]
Abstract
Pattern recognition receptors (PRR) and nucleotide-binding leucine-rich repeat proteins (NLR) are major components of the plant immune system responsible for pathogen detection. To date, the transcriptional regulation of PRR/NLR genes is poorly understood. Some PRR/NLR genes are affected by epigenetic changes of neighboring transposable elements (TEs) (cis regulation). We analyzed whether these genes can also respond to changes in the epigenetic marks of distal pericentromeric TEs (trans regulation). We found that Arabidopsis tissues infected with Pseudomonas syringae pv. tomato (Pst) initially induced the expression of pericentromeric TEs, and then repressed it by RNA-directed DNA methylation (RdDM). The latter response was accompanied by the accumulation of small RNAs (sRNAs) mapping to the TEs. Curiously these sRNAs also mapped to distal PRR/NLR genes, which were controlled by RdDM but remained induced in the infected tissues. Then, we used non-infected mom1 (Morpheus' molecule 1) mutants that expressed pericentromeric TEs to test if they lose repression of PRR/NLR genes. mom1 plants activated several PRR/NLR genes that were unlinked to MOM1-targeted TEs, and showed enhanced resistance to Pst. Remarkably, the increased defenses of mom1 were abolished when MOM1/RdDM-mediated pericentromeric TEs silencing was re-established. Therefore, common sRNAs could control PRR/NLR genes and distal pericentromeric TEs and preferentially silence TEs when they are activated.
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Affiliation(s)
- Damián A Cambiagno
- CONICET, Universidad Nacional de Córdoba, Centro de Investigaciones en Química Biológica de Córdoba (CIQUIBIC), Córdoba, Argentina
- Departamento de Química Biológica Ranwel Caputto, Universidad Nacional de Córdoba, Facultad de Ciencias Químicas, Córdoba, Argentina
| | - Florencia Nota
- CONICET, Universidad Nacional de Córdoba, Centro de Investigaciones en Química Biológica de Córdoba (CIQUIBIC), Córdoba, Argentina
- Departamento de Química Biológica Ranwel Caputto, Universidad Nacional de Córdoba, Facultad de Ciencias Químicas, Córdoba, Argentina
| | - Diego Zavallo
- Instituto de Biotecnología, CICVyA, INTA, Hurlingham, Argentina
| | - Sebastián Rius
- Centro de Estudios Fotosintéticos y Bioquímicos, Universidad Nacional de Rosario, Rosario, Argentina
| | - Paula Casati
- Centro de Estudios Fotosintéticos y Bioquímicos, Universidad Nacional de Rosario, Rosario, Argentina
| | - Sebastián Asurmendi
- Instituto de Biotecnología, CICVyA, INTA, Hurlingham, Argentina
- CONICET, Buenos Aires, Argentina
| | - María E Alvarez
- CONICET, Universidad Nacional de Córdoba, Centro de Investigaciones en Química Biológica de Córdoba (CIQUIBIC), Córdoba, Argentina
- Departamento de Química Biológica Ranwel Caputto, Universidad Nacional de Córdoba, Facultad de Ciencias Químicas, Córdoba, Argentina
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Manacorda CA, Asurmendi S. Arabidopsis phenotyping through geometric morphometrics. Gigascience 2018; 7:5039702. [PMID: 29917076 PMCID: PMC6041757 DOI: 10.1093/gigascience/giy073] [Citation(s) in RCA: 15] [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: 10/26/2017] [Revised: 02/07/2018] [Accepted: 06/11/2018] [Indexed: 12/18/2022] Open
Abstract
Background Recently, great technical progress has been achieved in the field of plant phenotyping. High-throughput platforms and the development of improved algorithms for rosette image segmentation make it possible to extract shape and size parameters for genetic, physiological, and environmental studies on a large scale. The development of low-cost phenotyping platforms and freeware resources make it possible to widely expand phenotypic analysis tools for Arabidopsis. However, objective descriptors of shape parameters that could be used independently of the platform and segmentation software used are still lacking, and shape descriptions still rely on ad hoc or even contradictory descriptors, which could make comparisons difficult and perhaps inaccurate. Modern geometric morphometrics is a family of methods in quantitative biology proposed to be the main source of data and analytical tools in the emerging field of phenomics studies. Based on the location of landmarks (corresponding points) over imaged specimens and by combining geometry, multivariate analysis, and powerful statistical techniques, these tools offer the possibility to reproducibly and accurately account for shape variations among groups and measure them in shape distance units. Results Here, a particular scheme of landmark placement on Arabidopsis rosette images is proposed to study shape variation in viral infection processes. Shape differences between controls and infected plants are quantified throughout the infectious process and visualized. Quantitative comparisons between two unrelated ssRNA+ viruses are shown, and reproducibility issues are assessed. Conclusions Combined with the newest automated platforms and plant segmentation procedures, geometric morphometric tools could boost phenotypic features extraction and processing in an objective, reproducible manner.
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Affiliation(s)
- Carlos A Manacorda
- Instituto de Biotecnología, CICVyA, INTA, Nicolas Repetto y de los Reseros s/n, Hurlingham, (1686) Buenos Aires, Argentina
| | - Sebastian Asurmendi
- Instituto de Biotecnología, CICVyA, INTA, Nicolas Repetto y de los Reseros s/n, Hurlingham, (1686) Buenos Aires, Argentina
- CONICET, Nicolas Repetto y de los Reseros s/n, Hurlingham, (1686) Buenos Aires, Argentina
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Malpica-López N, Rajeswaran R, Beknazariants D, Seguin J, Golyaev V, Farinelli L, Pooggin MM. Revisiting the Roles of Tobamovirus Replicase Complex Proteins in Viral Replication and Silencing Suppression. MOLECULAR PLANT-MICROBE INTERACTIONS : MPMI 2018; 31:125-144. [PMID: 29140168 DOI: 10.1094/mpmi-07-17-0164-r] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/07/2023]
Abstract
Tobamoviral replicase possesses an RNA-dependent RNA polymerase (RDR) domain and is translated from genomic (g)RNA via a stop codon readthrough mechanism at a one-to-ten ratio relative to a shorter protein lacking the RDR domain. The two proteins share methyltransferase and helicase domains and form a heterodimer implicated in gRNA replication. The shorter protein is also implicated in suppressing RNA silencing-based antiviral defenses. Using a stop codon mutant of Oilseed rape mosaic tobamovirus (ORMV), we demonstrate that the readthrough replicase (p182) is sufficient for gRNA replication and for subgenomic RNA transcription during systemic infection in Nicotiana benthamiana and Arabidopsis thaliana. However, the mutant virus displays milder symptoms and does not interfere with HEN1-mediated methylation of viral short interfering (si)RNAs or plant small (s)RNAs. The mutant virus tends to revert the stop codon, thereby restoring expression of the shorter protein (p125), even in the absence of plant Dicer-like activities that generate viral siRNAs. Plant RDR activities that generate endogenous siRNA precursors do not prevent replication or movement of the mutant virus, and double-stranded precursors of viral siRNAs representing the entire virus genome are likely synthesized by p182. Transgenic expression of p125 partially recapitulates the ORMV disease symptoms associated with overaccumulation of plant sRNAs. Taken together, the readthrough replicase p182 is sufficient for viral replication and transcription but not for silencing suppression. By contrast, the shorter p125 protein suppresses silencing, provokes severe disease symptoms, causes overaccumulation of unmethylated viral and plant sRNAs but it is not an essential component of the viral replicase complex.
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Affiliation(s)
| | | | - Daria Beknazariants
- 1 University of Basel, Department of Environmental Sciences, Basel, Switzerland
| | - Jonathan Seguin
- 1 University of Basel, Department of Environmental Sciences, Basel, Switzerland
| | - Victor Golyaev
- 1 University of Basel, Department of Environmental Sciences, Basel, Switzerland
| | | | - Mikhail M Pooggin
- 1 University of Basel, Department of Environmental Sciences, Basel, Switzerland
- 3 INRA, UMR BGPI, Montpellier, France
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Matsumura EE, Coletta-Filho HD, Nouri S, Falk BW, Nerva L, Oliveira TS, Dorta SO, Machado MA. Deep Sequencing Analysis of RNAs from Citrus Plants Grown in a Citrus Sudden Death-Affected Area Reveals Diverse Known and Putative Novel Viruses. Viruses 2017; 9:E92. [PMID: 28441782 PMCID: PMC5408698 DOI: 10.3390/v9040092] [Citation(s) in RCA: 38] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2017] [Revised: 04/18/2017] [Accepted: 04/20/2017] [Indexed: 01/07/2023] Open
Abstract
Citrus sudden death (CSD) has caused the death of approximately four million orange trees in a very important citrus region in Brazil. Although its etiology is still not completely clear, symptoms and distribution of affected plants indicate a viral disease. In a search for viruses associated with CSD, we have performed a comparative high-throughput sequencing analysis of the transcriptome and small RNAs from CSD-symptomatic and -asymptomatic plants using the Illumina platform. The data revealed mixed infections that included Citrus tristeza virus (CTV) as the most predominant virus, followed by the Citrus sudden death-associated virus (CSDaV), Citrus endogenous pararetrovirus (CitPRV) and two putative novel viruses tentatively named Citrus jingmen-like virus (CJLV), and Citrus virga-like virus (CVLV). The deep sequencing analyses were sensitive enough to differentiate two genotypes of both viruses previously associated with CSD-affected plants: CTV and CSDaV. Our data also showed a putative association of the CSD-symptomatic plants with a specific CSDaV genotype and a likely association with CitPRV as well, whereas the two putative novel viruses showed to be more associated with CSD-asymptomatic plants. This is the first high-throughput sequencing-based study of the viral sequences present in CSD-affected citrus plants, and generated valuable information for further CSD studies.
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Affiliation(s)
- Emilyn E Matsumura
- Instituto de Biociências da Universidade Estadual Paulista (Unesp), Botucatu, SP, 18615-689, Brazil.
- Centro de Citricultura Sylvio Moreira, Instituto Agronômico de Campinas, Cordeirópolis, SP, 13490-970, Brazil.
| | - Helvecio D Coletta-Filho
- Centro de Citricultura Sylvio Moreira, Instituto Agronômico de Campinas, Cordeirópolis, SP, 13490-970, Brazil.
| | - Shahideh Nouri
- Department of Plant Pathology, University of California, Davis, CA 9561608751, USA.
| | - Bryce W Falk
- Department of Plant Pathology, University of California, Davis, CA 9561608751, USA.
| | - Luca Nerva
- Institute for Sustainable Plant Protection (IPSP), CNR, Turin, 10135, Italy.
| | - Tiago S Oliveira
- Centro de Citricultura Sylvio Moreira, Instituto Agronômico de Campinas, Cordeirópolis, SP, 13490-970, Brazil.
| | - Silvia O Dorta
- Centro de Citricultura Sylvio Moreira, Instituto Agronômico de Campinas, Cordeirópolis, SP, 13490-970, Brazil.
| | - Marcos A Machado
- Centro de Citricultura Sylvio Moreira, Instituto Agronômico de Campinas, Cordeirópolis, SP, 13490-970, Brazil.
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Conti G, Zavallo D, Venturuzzi AL, Rodriguez MC, Crespi M, Asurmendi S. TMV induces RNA decay pathways to modulate gene silencing and disease symptoms. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2017; 89:73-84. [PMID: 27599263 DOI: 10.1111/tpj.13323] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/05/2016] [Revised: 08/23/2016] [Accepted: 08/31/2016] [Indexed: 06/06/2023]
Abstract
RNA decay pathways comprise a combination of RNA degradation mechanisms that are implicated in gene expression, development and defense responses in eukaryotes. These mechanisms are known as the RNA Quality Control or RQC pathways. In plants, another important RNA degradation mechanism is the post-transcriptional gene silencing (PTGS) mediated by small RNAs (siRNAs). Notably, the RQC pathway antagonizes PTGS by preventing the entry of dysfunctional mRNAs into the silencing pathway to avoid global degradation of mRNA by siRNAs. Viral transcripts must evade RNA degrading mechanisms, thus viruses encode PTGS suppressor proteins to counteract viral RNA silencing. Here, we demonstrate that tobacco plants infected with TMV and transgenic lines expressing TMV MP and CP (coat protein) proteins (which are not linked to the suppression of silencing) display increased transcriptional levels of RNA decay genes. These plants also showed accumulation of cytoplasmic RNA granules with altered structure, increased rates of RNA decay for transgenes and defective transgene PTGS amplification. Furthermore, knockdown of RRP41 or RRP43 RNA exosome components led to lower levels of TMV accumulation with milder symptoms after infection, several developmental defects and miRNA deregulation. Thus, we propose that TMV proteins induce RNA decay pathways (in particular exosome components) to impair antiviral PTGS and this defensive mechanism would constitute an additional counter-defense strategy that lead to disease symptoms.
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Affiliation(s)
- Gabriela Conti
- Instituto de Biotecnología, CICVyA, INTA, Hurlingham, Argentina
- CONICET, Hurlingham, Argentina
| | - Diego Zavallo
- Instituto de Biotecnología, CICVyA, INTA, Hurlingham, Argentina
| | - Andrea L Venturuzzi
- Instituto de Biotecnología, CICVyA, INTA, Hurlingham, Argentina
- CONICET, Hurlingham, Argentina
| | | | - Martin Crespi
- Institute of Plant Sciences Paris-Saclay, IPS2, CNRS, INRA, University Paris-Sud, Orsay, France
| | - Sebastian Asurmendi
- Instituto de Biotecnología, CICVyA, INTA, Hurlingham, Argentina
- CONICET, Hurlingham, Argentina
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Mishra AK, Duraisamy GS, Matoušek J, Radisek S, Javornik B, Jakse J. Identification and characterization of microRNAs in Humulus lupulus using high-throughput sequencing and their response to Citrus bark cracking viroid (CBCVd) infection. BMC Genomics 2016; 17:919. [PMID: 27846797 PMCID: PMC5109749 DOI: 10.1186/s12864-016-3271-4] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2016] [Accepted: 11/05/2016] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Hop (Humulus lupulus L.) plants are grown primarily for the brewing industry and have been used as a traditional medicinal herb for a long time. Severe hop stunt disease caused by the recently discovered Citrus bark cracking viroid (CBCVd) is one of the most devastating diseases among other viroid infections in hop. MicroRNAs (miRNAs) are a class of non-coding small RNAs that play important roles in gene expression regulation. To identify miRNAs in hop and their response to CBCVd-infection, two small RNA (sRNA) libraries were prepared from healthy and CBCVd-infected hop plants and were investigated by high throughput sequencing. RESULTS A total of 67 conserved and 49 novel miRNAs were identified. Among them, 36 conserved and 37 novel miRNAs were found to be differentially recovered in response to CBCVd-infection. A total of 311 potential targets was predicted for conserved and novel miRNAs based on a sequence homology search using hop transcriptome data. The majority of predicted targets significantly belonged to transcriptional factors that may regulate hop leaf, root and cone growth and development. In addition, the identified miRNAs might also play an important roles in other cellular and metabolic processes, such as signal transduction, stress response and other physiological processes, including prenylflavonoid biosynthesis pathways. Quantitative real time PCR analysis of selected targets revealed their negative correlation with their corresponding CBCVd-responsive miRNAs. CONCLUSIONS Based on the results, we concluded that CBCVd-responsive miRNAs modulate several hormone pathways and transcriptional factors that play important roles in the regulation of metabolism, growth and development. These results provide a framework for further analysis of regulatory roles of sRNAs in plant defense mechanism including other hop infecting viroids in particular.
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Affiliation(s)
- Ajay Kumar Mishra
- Biology Centre ASCR v.v.i, Department of Molecular Genetics, Institute of Plant Molecular Biology, Branišovská 31, České Budějovice, 37005, Czech Republic
| | - Ganesh Selvaraj Duraisamy
- Biology Centre ASCR v.v.i, Department of Molecular Genetics, Institute of Plant Molecular Biology, Branišovská 31, České Budějovice, 37005, Czech Republic
| | - Jaroslav Matoušek
- Biology Centre ASCR v.v.i, Department of Molecular Genetics, Institute of Plant Molecular Biology, Branišovská 31, České Budějovice, 37005, Czech Republic
| | - Sebastjan Radisek
- Slovenian Institute of Hop Research and Brewing, Plant Protection Department, Cesta Zalskega tabora 2, Žalec, SI-3310, Slovenia
| | - Branka Javornik
- Department of Agronomy, Biotechnical Faculty, University of Ljubljana, Jamnikarjeva 101, Ljubljana, SI-1000, Slovenia
| | - Jernej Jakse
- Department of Agronomy, Biotechnical Faculty, University of Ljubljana, Jamnikarjeva 101, Ljubljana, SI-1000, Slovenia.
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