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Philips JG, Naim F, Lorenc MT, Dudley KJ, Hellens RP, Waterhouse PM. The widely used Nicotiana benthamiana 16c line has an unusual T-DNA integration pattern including a transposon sequence. PLoS One 2017; 12:e0171311. [PMID: 28231340 PMCID: PMC5322946 DOI: 10.1371/journal.pone.0171311] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2016] [Accepted: 01/19/2017] [Indexed: 11/29/2022] Open
Abstract
Nicotiana benthamiana is employed around the world for many types of research and one transgenic line has been used more extensively than any other. This line, 16c, expresses the Aequorea victoria green fluorescent protein (GFP), highly and constitutively, and has been a major resource for visualising the mobility and actions of small RNAs. Insights into the mechanisms studied at a molecular level in N. benthamiana 16c are likely to be deeper and more accurate with a greater knowledge of the GFP gene integration site. Therefore, using next generation sequencing, genome mapping and local alignment, we identified the location and characteristics of the integrated T-DNA. As suggested from previous molecular hybridisation and inheritance data, the transgenic line contains a single GFP-expressing locus. However, the GFP coding sequence differs from that originally reported. Furthermore, a 3.2 kb portion of a transposon, appears to have co-integrated with the T-DNA. The location of the integration mapped to a region of the genome represented by Nbv0.5scaffold4905 in the www.benthgenome.com assembly, and with less integrity to Niben101Scf03641 in the www.solgenomics.net assembly. The transposon is not endogenous to laboratory strains of N. benthamiana or Agrobacterium tumefaciens strain GV3101 (MP90), which was reportedly used in the generation of line 16c. However, it is present in the popular LBA4404 strain. The integrated transposon sequence includes its 5' terminal repeat and a transposase gene, and is immediately adjacent to the GFP gene. This unexpected genetic arrangement may contribute to the characteristics that have made the 16c line such a popular research tool and alerts researchers, taking transgenic plants to commercial release, to be aware of this genomic hitchhiker.
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Affiliation(s)
- Joshua G. Philips
- Centre for Tropical Crops and Biocommodities, Queensland University of Technology, Brisbane, Australia
| | - Fatima Naim
- Centre for Tropical Crops and Biocommodities, Queensland University of Technology, Brisbane, Australia
| | - Michał T. Lorenc
- Centre for Tropical Crops and Biocommodities, Queensland University of Technology, Brisbane, Australia
| | - Kevin J. Dudley
- Institute for Future Environments, Central Analytical Research Facility, Queensland University of Technology, Brisbane, Australia
| | - Roger P. Hellens
- Centre for Tropical Crops and Biocommodities, Queensland University of Technology, Brisbane, Australia
- Institute for Future Environments, Queensland University of Technology, Brisbane, Australia
| | - Peter M. Waterhouse
- Centre for Tropical Crops and Biocommodities, Queensland University of Technology, Brisbane, Australia
- Institute for Future Environments, Queensland University of Technology, Brisbane, Australia
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52
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Machado JPB, Calil IP, Santos AA, Fontes EPB. Translational control in plant antiviral immunity. Genet Mol Biol 2017; 40:292-304. [PMID: 28199446 PMCID: PMC5452134 DOI: 10.1590/1678-4685-gmb-2016-0092] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2016] [Accepted: 09/27/2016] [Indexed: 01/11/2023] Open
Abstract
Due to the limited coding capacity of viral genomes, plant viruses depend extensively on the host cell machinery to support the viral life cycle and, thereby, interact with a large number of host proteins during infection. Within this context, as plant viruses do not harbor translation-required components, they have developed several strategies to subvert the host protein synthesis machinery to produce rapidly and efficiently the viral proteins. As a countermeasure against infection, plants have evolved defense mechanisms that impair viral infections. Among them, the host-mediated translational suppression has been characterized as an efficient mean to restrict infection. To specifically suppress translation of viral mRNAs, plants can deploy susceptible recessive resistance genes, which encode translation initiation factors from the eIF4E and eIF4G family and are required for viral mRNA translation and multiplication. Additionally, recent evidence has demonstrated that, alternatively to the cleavage of viral RNA targets, host cells can suppress viral protein translation to silence viral RNA. Finally, a novel strategy of plant antiviral defense based on suppression of host global translation, which is mediated by the transmembrane immune receptor NIK1 (nuclear shuttle protein (NSP)-Interacting Kinase1), is discussed in this review.
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Affiliation(s)
- João Paulo B Machado
- Department of Biochemistry and Molecular Biology, BIOAGRO, National Institute of Science and Technology in Plant-Pest Interactions, Universidade Federal de Viçosa, 36571.000, Viçosa, MG, Brazil
| | - Iara P Calil
- Department of Biochemistry and Molecular Biology, BIOAGRO, National Institute of Science and Technology in Plant-Pest Interactions, Universidade Federal de Viçosa, 36571.000, Viçosa, MG, Brazil
| | - Anésia A Santos
- Department of General Biology, Universidade Federal de Viçosa, 36571.000, Viçosa, MG, Brazil
| | - Elizabeth P B Fontes
- Department of Biochemistry and Molecular Biology, BIOAGRO, National Institute of Science and Technology in Plant-Pest Interactions, Universidade Federal de Viçosa, 36571.000, Viçosa, MG, Brazil
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Nummert G, Sõmera M, Uffert G, Abner E, Truve E. P1-independent replication and local movement of Rice yellow mottle virus in host and non-host plant species. Virology 2017; 502:28-32. [PMID: 27960111 DOI: 10.1016/j.virol.2016.12.007] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2016] [Revised: 12/04/2016] [Accepted: 12/06/2016] [Indexed: 11/18/2022]
Abstract
Sobemovirus P1 protein, characterized previously as a suppressor of posttranscriptional gene silencing, is required for systemic virus spread and infection in plants. Mutations in the ORF1 initiation codon do not affect viral replication indicating P1 is not necessary for this process. Wild type, recombinant and P1 deletion mutants of Cocksfoot mottle virus and Rice yellow mottle virus were used to infect oat, rice, wheat, barley, Arabidopsis thaliana and Nicotiana benthamiana plants. Wild type RYMV, RYMV without P1 and RYMV with CfMV P1 were detected in inoculated leaves of all tested plant species. We found that RYMV does not need P1 for replication and for local movement neither in host nor non-host species tested in this study. However, it is crucial for successful systemic spread of the virus in its host plant rice. Moreover, adding CfMV P1 into RYMV genome did not help it to overcome restriction to the inoculated leaf.
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Affiliation(s)
- Grete Nummert
- Department of Gene Technology, Tallinn University of Technology, Akadeemia tee 15, 12618 Tallinn, Estonia.
| | - Merike Sõmera
- Department of Gene Technology, Tallinn University of Technology, Akadeemia tee 15, 12618 Tallinn, Estonia
| | - Gabriela Uffert
- Department of Gene Technology, Tallinn University of Technology, Akadeemia tee 15, 12618 Tallinn, Estonia
| | - Erik Abner
- Department of Gene Technology, Tallinn University of Technology, Akadeemia tee 15, 12618 Tallinn, Estonia
| | - Erkki Truve
- Department of Gene Technology, Tallinn University of Technology, Akadeemia tee 15, 12618 Tallinn, Estonia
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54
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Murota K, Shimura H, Takeshita M, Masuta C. Interaction between Cucumber mosaic virus 2b protein and plant catalase induces a specific necrosis in association with proteasome activity. PLANT CELL REPORTS 2017; 36:37-47. [PMID: 27659495 PMCID: PMC5206265 DOI: 10.1007/s00299-016-2055-2] [Citation(s) in RCA: 31] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/12/2016] [Accepted: 09/06/2016] [Indexed: 05/20/2023]
Abstract
Cucumber mosaic virus (CMV) can induce a specific necrosis on Arabidopsis through the interaction between the CMV 2b protein and host catalase, in which the ubiquitin-proteasome pathway may be involved. We previously reported that the CMV 2b protein, the viral RNA silencing suppressor, interacted with the H2O2 scavenger catalase (CAT3), leading to necrosis on CMV-inoculated Arabidopsis leaves. We here confirmed that CMV could more abundantly accumulate in the CAT3-knockout mutant (cat3), and that CAT3 makes host plants a little more tolerant to CMV. We also found that the necrosis severity is not simply explained by a high level of H2O2 given by the lack of CAT3, because the recombinant CMV, CMV-N, induced much milder necrosis in cat3 than in the wild type, suggesting some specific mechanism for the necrosis induction. To further characterize the 2b-inducing necrosis in relation to its binding to CAT3, we conducted the agroinfiltration experiments to overexpress CAT3 and 2b in N. benthamiana leaves. The accumulation levels of CAT3 were higher when co-expressed with the CMV-N 2b (N2b) than with CMV-Y 2b (Y2b). We infer that N2b made a more stable complex with CAT3 than Y2b did, and the longevity of the 2b-CAT3 complex seemed to be important to induce necrosis. By immunoprecipitation (IP) with an anti-ubiquitin antibody followed by the detection with anti-CAT3 antibodies, we detected a higher molecular-weight smear and several breakdown products of CAT3 among the IP-proteins. In addition, the proteasome inhibitor MG132 treatment could actually increase the accumulation levels of CAT3. This study suggests that the host proteasome pathway is, at least partially, responsible for the degradation of CAT3, which is manifested in CMV-infected tissues.
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Affiliation(s)
- Katsunori Murota
- Research Faculty of Agriculture, Hokkaido University, Kita-ku kita 9, Nishi 9, Sapporo, 060-8589, Japan
| | - Hanako Shimura
- Research Faculty of Agriculture, Hokkaido University, Kita-ku kita 9, Nishi 9, Sapporo, 060-8589, Japan.
| | - Minoru Takeshita
- Laboratory of Plant Pathology, Faculty of Agriculture, University of Miyazaki, Miyazaki, 889-2192, Japan
| | - Chikara Masuta
- Research Faculty of Agriculture, Hokkaido University, Kita-ku kita 9, Nishi 9, Sapporo, 060-8589, Japan.
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55
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Plant Virus Infection and the Ubiquitin Proteasome Machinery: Arms Race along the Endoplasmic Reticulum. Viruses 2016; 8:v8110314. [PMID: 27869775 PMCID: PMC5127028 DOI: 10.3390/v8110314] [Citation(s) in RCA: 35] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2016] [Revised: 09/29/2016] [Accepted: 11/08/2016] [Indexed: 12/24/2022] Open
Abstract
The endoplasmic reticulum (ER) is central to plant virus replication, translation, maturation, and egress. Ubiquitin modification of ER associated cellular and viral proteins, alongside the actions of the 26S proteasome, are vital for the regulation of infection. Viruses can arrogate ER associated ubiquitination as well as cytosolic ubiquitin ligases with the purpose of directing the ubiquitin proteasome system (UPS) to new targets. Such targets include necessary modification of viral proteins which may stabilize certain complexes, or modification of Argonaute to suppress gene silencing. The UPS machinery also contributes to the regulation of effector triggered immunity pattern recognition receptor immunity. Combining the results of unrelated studies, many positive strand RNA plant viruses appear to interact with cytosolic Ub-ligases to provide novel avenues for controlling the deleterious consequences of disease. Viral interactions with the UPS serve to regulate virus infection in a manner that promotes replication and movement, but also modulates the levels of RNA accumulation to ensure successful biotrophic interactions. In other instances, the UPS plays a central role in cellular immunity. These opposing roles are made evident by contrasting studies where knockout mutations in the UPS can either hamper viruses or lead to more aggressive diseases. Understanding how viruses manipulate ER associated post-translational machineries to better manage virus–host interactions will provide new targets for crop improvement.
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56
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Bejerman N, Mann KS, Dietzgen RG. Alfalfa dwarf cytorhabdovirus P protein is a local and systemic RNA silencing supressor which inhibits programmed RISC activity and prevents transitive amplification of RNA silencing. Virus Res 2016; 224:19-28. [PMID: 27543392 DOI: 10.1016/j.virusres.2016.08.008] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2016] [Revised: 08/09/2016] [Accepted: 08/14/2016] [Indexed: 11/16/2022]
Abstract
Plants employ RNA silencing as an innate defense mechanism against viruses. As a counter-defense, plant viruses have evolved to express RNA silencing suppressor proteins (RSS), which target one or more steps of the silencing pathway. In this study, we show that the phosphoprotein (P) encoded by the negative-sense RNA virus alfalfa dwarf virus (ADV), a species of the genus Cytorhabdovirus, family Rhabdoviridae, is a suppressor of RNA silencing. ADV P has a relatively weak local RSS activity, and does not prevent siRNA accumulation. On the other hand, ADV P strongly suppresses systemic RNA silencing, but does not interfere with the short-distance spread of silencing, which is consistent with its lack of inhibition of siRNA accumulation. The mechanism of suppression appears to involve ADV P binding to RNA-induced silencing complex proteins AGO1 and AGO4 as shown in protein-protein interaction assays when ectopically expressed. In planta, we demonstrate that ADV P likely functions by inhibiting miRNA-guided AGO1 cleavage and prevents transitive amplification by repressing the production of secondary siRNAs. As recently described for lettuce necrotic yellows cytorhabdovirus P, but in contrast to other viral RSS known to disrupt AGO activity, ADV P sequence does not contain any recognizable GW/WG or F-box motifs, which suggests that cytorhabdovirus P proteins may use alternative motifs to bind to AGO proteins.
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Affiliation(s)
- Nicolás Bejerman
- Queensland Alliance for Agriculture and Food Innovation, The University of Queensland, St. Lucia, QLD 4072, Australia.
| | - Krin S Mann
- Queensland Alliance for Agriculture and Food Innovation, The University of Queensland, St. Lucia, QLD 4072, Australia.
| | - Ralf G Dietzgen
- Queensland Alliance for Agriculture and Food Innovation, The University of Queensland, St. Lucia, QLD 4072, Australia.
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57
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Cho SK, Ryu MY, Shah P, Poulsen CP, Yang SW. Post-Translational Regulation of miRNA Pathway Components, AGO1 and HYL1, in Plants. Mol Cells 2016; 39:581-6. [PMID: 27440184 PMCID: PMC4990749 DOI: 10.14348/molcells.2016.0085] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2016] [Revised: 06/09/2016] [Accepted: 06/10/2016] [Indexed: 01/27/2023] Open
Abstract
Post-translational modifications (PTMs) of proteins are essential to increase the functional diversity of the proteome. By adding chemical groups to proteins, or degrading entire proteins by phosphorylation, glycosylation, ubiquitination, neddylation, acetylation, lipidation, and proteolysis, the complexity of the proteome increases, and this then influences most biological processes. Although small RNAs are crucial regulatory elements for gene expression in most eukaryotes, PTMs of small RNA microprocessor and RNA silencing components have not been extensively investigated in plants. To date, several studies have shown that the proteolytic regulation of AGOs is important for host-pathogen interactions. DRB4 is regulated by the ubiquitin-proteasome system, and the degradation of HYL1 is modulated by a de-etiolation repressor, COP1, and an unknown cytoplasmic protease. Here, we discuss current findings on the PTMs of microprocessor and RNA silencing components in plants.
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Affiliation(s)
- Seok Keun Cho
- Department of Systems Biology, College of Life Science and Biotechnology, Yonsei University 03722,
Korea
| | - Moon Young Ryu
- Department of Systems Biology, College of Life Science and Biotechnology, Yonsei University 03722,
Korea
| | - Pratik Shah
- Department of Biomedical Engineering, University of California Irvine, 92697, CA,
USA
| | | | - Seong Wook Yang
- Department of Systems Biology, College of Life Science and Biotechnology, Yonsei University 03722,
Korea
- Department of Plant and Environmental Sciences, Center for UNIK Synthetic Biology, Faculty of Science, University of Copenhagen, Thorvaldsensvej 40, DK-1871 Frederiksberg,
Denmark
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58
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Li Y, Alonso-Peral M, Wong G, Wang MB, Millar AA. Ubiquitous miR159 repression of MYB33/65 in Arabidopsis rosettes is robust and is not perturbed by a wide range of stresses. BMC PLANT BIOLOGY 2016; 16:179. [PMID: 27542984 PMCID: PMC4992245 DOI: 10.1186/s12870-016-0867-4] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/15/2015] [Accepted: 08/05/2016] [Indexed: 05/03/2023]
Abstract
BACKGROUND The microR159 (miR159) - GAMYB pathway is conserved in higher plants, where GAMYB, expression promotes programmed cell death in seeds (aleurone) and anthers (tapetum). In cereals, restriction of GAMYB expression to seeds and anthers is mainly achieved transcriptionally, whereas in Arabidopsis this is achieved post-transcriptionally, as miR159 silences GAMYB (MYB33 and MYB65) in vegetative tissues, but not in seeds and anthers. However, we cannot rule out a role for miR159-MYB33/65 pathway in Arabidopsis vegetative tissues; a loss-of-function mir159 Arabidopsis mutant displays strong pleiotropic defects and numerous reports have documented changes in miR159 abundance during stress and hormone treatments. Hence, we have investigated the functional role of this pathway in vegetative tissues. RESULTS It was found that the miR159-MYB33/65 pathway was ubiquitously present throughout rosette development. However, miR159 appears to continuously repress MYB33/MYB65 expression to levels that have no major impact on rosette development. Inducible inhibition of miR159 resulted in MYB33/65 de-repression and associated phenotypic defects, indicating that a potential role in vegetative development is only possible through MYB33 and MYB65 if miR159 levels decrease. However, miR159 silencing of MYB33/65 appeared extremely robust; no tested abiotic stress resulted in strong miR159 repression. Consistent with this, the stress responses of an Arabidopsis mutant lacking the miR159-MYB33/65 pathway were indistinguishable from wild-type. Moreover, expression of viral silencing suppressors, either via transgenesis or viral infection, was unable to prevent miR159 repression of MYB33/65, highlighting the robustness of miR159-mediated silencing. CONCLUSIONS Despite being ubiquitously present, molecular, genetic and physiological analysis failed to find a major functional role for the miR159-MYB33/65 pathway in Arabidopsis rosette development or stress response. Although it is likely that this pathway is important for a stress not tested here or in different plant species, our findings argue against the miR159-MYB33/65 pathway playing a major conserved role in general stress response. Finally, in light of the robustness of miR159-mediated repression of MYB33/65, it appears unlikely that low fold-level changes of miR159 abundance in response to stress would have any major physiological impact in Arabidopsis.
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Affiliation(s)
- Yanjiao Li
- Plant Science Division, Research School of Biology, Australian National University, Canberra, 2601 ACT Australia
| | - Maria Alonso-Peral
- Plant Science Division, Research School of Biology, Australian National University, Canberra, 2601 ACT Australia
| | - Gigi Wong
- Plant Science Division, Research School of Biology, Australian National University, Canberra, 2601 ACT Australia
| | - Ming-Bo Wang
- CSIRO, Agriculture, Canberra, 2601 ACT Australia
| | - Anthony A Millar
- Plant Science Division, Research School of Biology, Australian National University, Canberra, 2601 ACT Australia
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59
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Hedil M, Kormelink R. Viral RNA Silencing Suppression: The Enigma of Bunyavirus NSs Proteins. Viruses 2016; 8:v8070208. [PMID: 27455310 PMCID: PMC4974542 DOI: 10.3390/v8070208] [Citation(s) in RCA: 35] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2016] [Revised: 07/18/2016] [Accepted: 07/19/2016] [Indexed: 12/21/2022] Open
Abstract
The Bunyaviridae is a family of arboviruses including both plant- and vertebrate-infecting representatives. The Tospovirus genus accommodates plant-infecting bunyaviruses, which not only replicate in their plant host, but also in their insect thrips vector during persistent propagative transmission. For this reason, they are generally assumed to encounter antiviral RNA silencing in plants and insects. Here we present an overview on how tospovirus nonstructural NSs protein counteracts antiviral RNA silencing in plants and what is known so far in insects. Like tospoviruses, members of the related vertebrate-infecting bunyaviruses classified in the genera Orthobunyavirus, Hantavirus and Phlebovirus also code for a NSs protein. However, for none of them RNA silencing suppressor activity has been unambiguously demonstrated in neither vertebrate host nor arthropod vector. The second part of this review will briefly describe the role of these NSs proteins in modulation of innate immune responses in mammals and elaborate on a hypothetical scenario to explain if and how NSs proteins from vertebrate-infecting bunyaviruses affect RNA silencing. If so, why this discovery has been hampered so far.
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Affiliation(s)
- Marcio Hedil
- Laboratory of Virology, Department of Plant Sciences, Wageningen University, Wageningen, 6708PB, The Netherlands.
| | - Richard Kormelink
- Laboratory of Virology, Department of Plant Sciences, Wageningen University, Wageningen, 6708PB, The Netherlands.
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60
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Naim F, Shrestha P, Singh SP, Waterhouse PM, Wood CC. Stable expression of silencing-suppressor protein enhances the performance and longevity of an engineered metabolic pathway. PLANT BIOTECHNOLOGY JOURNAL 2016; 14:1418-26. [PMID: 26628000 PMCID: PMC5063197 DOI: 10.1111/pbi.12506] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/21/2015] [Revised: 10/11/2015] [Accepted: 11/02/2015] [Indexed: 05/27/2023]
Abstract
Transgenic engineering of plants is important in both basic and applied research. However, the expression of a transgene can dwindle over time as the plant's small (s)RNA-guided silencing pathways shut it down. The silencing pathways have evolved as antiviral defence mechanisms, and viruses have co-evolved viral silencing-suppressor proteins (VSPs) to block them. Therefore, VSPs have been routinely used alongside desired transgene constructs to enhance their expression in transient assays. However, constitutive, stable expression of a VSP in a plant usually causes pronounced developmental abnormalities, as their actions interfere with endogenous microRNA-regulated processes, and has largely precluded the use of VSPs as an aid to stable transgene expression. In an attempt to avoid the deleterious effects but obtain the enhancing effect, a number of different VSPs were expressed exclusively in the seeds of Arabidopsis thaliana alongside a three-step transgenic pathway for the synthesis of arachidonic acid (AA), an ω-6 long chain polyunsaturated fatty acid. Results from independent transgenic events, maintained for four generations, showed that the VSP-AA-transformed plants were developmentally normal, apart from minor phenotypes at the cotyledon stage, and could produce 40% more AA than plants transformed with the AA transgene cassette alone. Intriguingly, a geminivirus VSP, V2, was constitutively expressed without causing developmental defects, as it acts on the siRNA amplification step that is not part of the miRNA pathway, and gave strong transgene enhancement. These results demonstrate that VSP expression can be used to protect and enhance stable transgene performance and has significant biotechnological application.
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Affiliation(s)
- Fatima Naim
- CSIRO Agriculture, Canberra, ACT, Australia
- School of Biological Sciences, The University of Sydney, Sydney, NSW, Australia
| | | | | | - Peter M Waterhouse
- CSIRO Agriculture, Canberra, ACT, Australia
- School of Biological Sciences, The University of Sydney, Sydney, NSW, Australia
- School of Molecular Bioscience, The University of Sydney, Sydney, NSW, Australia
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61
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Bejerman N, Giolitti F, Trucco V, de Breuil S, Dietzgen RG, Lenardon S. Complete genome sequence of a new enamovirus from Argentina infecting alfalfa plants showing dwarfism symptoms. Arch Virol 2016; 161:2029-32. [PMID: 27068164 DOI: 10.1007/s00705-016-2854-3] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/07/2016] [Accepted: 03/30/2016] [Indexed: 11/27/2022]
Abstract
Alfalfa dwarf disease, probably caused by synergistic interactions of mixed virus infections, is a major and emergent disease that threatens alfalfa production in Argentina. Deep sequencing of diseased alfalfa plant samples from the central region of Argentina resulted in the identification of a new virus genome resembling enamoviruses in sequence and genome structure. Phylogenetic analysis suggests that it is a new member of the genus Enamovirus, family Luteoviridae. The virus is tentatively named "alfalfa enamovirus 1" (AEV-1). The availability of the AEV-1 genome sequence will make it possible to assess the genetic variability of this virus and to construct an infectious clone to investigate its role in alfalfa dwarfism disease.
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Affiliation(s)
- Nicolás Bejerman
- IPAVE-CIAP-INTA, Av. 11 de Septiembre 4755, Córdoba, 5020, Argentina. .,Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Godoy Cruz 2290 (1425 FBQ) CABA, Buenos Aires, Argentina.
| | - Fabián Giolitti
- IPAVE-CIAP-INTA, Av. 11 de Septiembre 4755, Córdoba, 5020, Argentina
| | - Verónica Trucco
- IPAVE-CIAP-INTA, Av. 11 de Septiembre 4755, Córdoba, 5020, Argentina
| | - Soledad de Breuil
- IPAVE-CIAP-INTA, Av. 11 de Septiembre 4755, Córdoba, 5020, Argentina.,Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Godoy Cruz 2290 (1425 FBQ) CABA, Buenos Aires, Argentina
| | - Ralf G Dietzgen
- Queensland Alliance for Agriculture and Food Innovation, The University of Queensland, St Lucia, QLD, 4072, Australia
| | - Sergio Lenardon
- IPAVE-CIAP-INTA, Av. 11 de Septiembre 4755, Córdoba, 5020, Argentina
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62
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Mann KS, Johnson KN, Carroll BJ, Dietzgen RG. Cytorhabdovirus P protein suppresses RISC-mediated cleavage and RNA silencing amplification in planta. Virology 2016; 490:27-40. [PMID: 26808923 DOI: 10.1016/j.virol.2016.01.003] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2015] [Revised: 01/05/2016] [Accepted: 01/09/2016] [Indexed: 11/16/2022]
Abstract
Plant viruses have evolved to undermine the RNA silencing pathway by expressing suppressor protein(s) that interfere with one or more key components of this antiviral defense. Here we show that the recently identified RNA silencing suppressor (RSS) of lettuce necrotic yellows virus (LNYV), phosphoprotein P, binds to RNA silencing machinery proteins AGO1, AGO2, AGO4, RDR6 and SGS3 in protein-protein interaction assays when transiently expressed. In planta, we demonstrate that LNYV P inhibits miRNA-guided AGO1 cleavage and translational repression, and RDR6/SGS3-dependent amplification of silencing. Analysis of LNYV P deletion mutants identified a C-terminal protein domain essential for both local RNA silencing suppression and interaction with AGO1, AGO2, AGO4, RDR6 and SGS3. In contrast to other viral RSS known to disrupt AGO activity, LNYV P sequence does not contain any recognizable GW/WG or F-box motifs. This suggests that LNYV P may represent a new class of AGO binding proteins.
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Affiliation(s)
- Krin S Mann
- Queensland Alliance for Agriculture and Food Innovation, The University of Queensland, St Lucia, QLD 4072, Australia
| | - Karyn N Johnson
- School of Biological Sciences, The University of Queensland, St Lucia, QLD 4072, Australia
| | - Bernard J Carroll
- School of Chemistry and Molecular Biosciences, The University of Queensland, St Lucia, QLD 4072, Australia
| | - Ralf G Dietzgen
- Queensland Alliance for Agriculture and Food Innovation, The University of Queensland, St Lucia, QLD 4072, Australia; School of Chemistry and Molecular Biosciences, The University of Queensland, St Lucia, QLD 4072, Australia.
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63
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Bally J, Nakasugi K, Jia F, Jung H, Ho SYW, Wong M, Paul CM, Naim F, Wood CC, Crowhurst RN, Hellens RP, Dale JL, Waterhouse PM. The extremophile Nicotiana benthamiana has traded viral defence for early vigour. NATURE PLANTS 2015; 1:15165. [PMID: 27251536 DOI: 10.1038/nplants.2015.165] [Citation(s) in RCA: 79] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/19/2015] [Accepted: 10/01/2015] [Indexed: 05/03/2023]
Abstract
A single lineage of Nicotiana benthamiana is widely used as a model plant(1) and has been instrumental in making revolutionary discoveries about RNA interference (RNAi), viral defence and vaccine production. It is peerless in its susceptibility to viruses and its amenability in transiently expressing transgenes(2,3). These unparalleled characteristics have been associated both positively and negatively with a disruptive insertion in the RNA-dependent RNA polymerase 1 gene, Rdr1(4-6). For a plant so routinely used in research, the origin, diversity and evolution of the species, and the basis of its unusual abilities, have been relatively unexplored. Here, by comparison with wild accessions from across the spectrum of the species' natural distribution, we show that the laboratory strain of N. benthamiana is an extremophile originating from a population that has retained a mutation in Rdr1 for ∼0.8 Myr and thereby traded its defence capacity for early vigour and survival in the extreme habitat of central Australia. Reconstituting Rdr1 activity in this isolate provided protection. Silencing the functional allele in a wild strain rendered it hypersusceptible and was associated with a doubling of seed size and enhanced early growth rate. These findings open the way to a deeper understanding of the delicate balance between protection and vigour.
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Affiliation(s)
- Julia Bally
- Centre for Tropical Crops and Biocommodities, Queensland University of Technology, Brisbane, Queensland 4001, Australia
- School of Molecular Biology, The University of Sydney, Sydney, New South Wales 2006, Australia
| | - Kenlee Nakasugi
- School of Molecular Biology, The University of Sydney, Sydney, New South Wales 2006, Australia
| | - Fangzhi Jia
- School of Biological Sciences, The University of Sydney, Sydney, New South Wales 2006, Australia
| | - Hyungtaek Jung
- Centre for Tropical Crops and Biocommodities, Queensland University of Technology, Brisbane, Queensland 4001, Australia
| | - Simon Y W Ho
- School of Biological Sciences, The University of Sydney, Sydney, New South Wales 2006, Australia
| | - Mei Wong
- School of Molecular Biology, The University of Sydney, Sydney, New South Wales 2006, Australia
| | - Chloe M Paul
- School of Molecular Biology, The University of Sydney, Sydney, New South Wales 2006, Australia
| | - Fatima Naim
- Centre for Tropical Crops and Biocommodities, Queensland University of Technology, Brisbane, Queensland 4001, Australia
- School of Biological Sciences, The University of Sydney, Sydney, New South Wales 2006, Australia
| | - Craig C Wood
- Commonwealth Scientific and Industrial Research Organisation-Plant Industry, Canberra, Australia
| | - Ross N Crowhurst
- Mount Albert Research Centre, Plant and Food Research, Auckland, New Zealand
| | - Roger P Hellens
- Centre for Tropical Crops and Biocommodities, Queensland University of Technology, Brisbane, Queensland 4001, Australia
- Mount Albert Research Centre, Plant and Food Research, Auckland, New Zealand
| | - James L Dale
- Centre for Tropical Crops and Biocommodities, Queensland University of Technology, Brisbane, Queensland 4001, Australia
| | - Peter M Waterhouse
- Centre for Tropical Crops and Biocommodities, Queensland University of Technology, Brisbane, Queensland 4001, Australia
- School of Molecular Biology, The University of Sydney, Sydney, New South Wales 2006, Australia
- School of Biological Sciences, The University of Sydney, Sydney, New South Wales 2006, Australia
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64
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Almasi R, Miller WA, Ziegler-Graff V. Mild and severe cereal yellow dwarf viruses differ in silencing suppressor efficiency of the P0 protein. Virus Res 2015; 208:199-206. [PMID: 26116275 DOI: 10.1016/j.virusres.2015.06.020] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2015] [Revised: 06/18/2015] [Accepted: 06/20/2015] [Indexed: 10/23/2022]
Abstract
Viral pathogenicity has often been correlated to the expression of the viral encoded-RNA silencing suppressor protein (SSP). The silencing suppressor activity of the P0 protein encoded by cereal yellow dwarf virus-RPV (CYDV-RPV) and -RPS (CYDV-RPS), two poleroviruses differing in their symptomatology was investigated. CYDV-RPV displays milder symptoms in oat and wheat whereas CYDV-RPS is responsible for more severe disease. We showed that both P0 proteins (P0(CY-RPV) and P0(CY-RPS)) were able to suppress local RNA silencing induced by either sense or inverted repeat transgenes in an Agrobacterium tumefaciens-mediated expression assay in Nicotiana benthamiana. P0(CY-RPS) displayed slightly higher activity. Systemic spread of the silencing signal was not impaired. Analysis of short-interfering RNA (siRNA) abundance revealed that accumulation of primary siRNA was not affected, but secondary siRNA levels were reduced by both CYDV P0 proteins, suggesting that they act downstream of siRNA production. Correlated with this finding we showed that both P0 proteins partially destabilized ARGONAUTE1. Finally both P0(CY-RPV) and P0(CY-RPS) interacted in yeast cells with ASK2, a component of an E3-ubiquitin ligase, with distinct affinities.
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Affiliation(s)
- Reza Almasi
- Institut de Biologie Moléculaire des Plantes CNRS-UPR 2357, associée à l'Université de Strasbourg, 12 rue du Général Zimmer, 67084 Strasbourg, France; Plant Virology Research Center, College of Agriculture, Shiraz University, Iran
| | - W Allen Miller
- Institut de Biologie Moléculaire des Plantes CNRS-UPR 2357, associée à l'Université de Strasbourg, 12 rue du Général Zimmer, 67084 Strasbourg, France; Department of Plant Pathology and Microbiology, Iowa State University, Ames, IA 50011, USA
| | - Véronique Ziegler-Graff
- Institut de Biologie Moléculaire des Plantes CNRS-UPR 2357, associée à l'Université de Strasbourg, 12 rue du Général Zimmer, 67084 Strasbourg, France.
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65
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Carbonell A, Carrington JC. Antiviral roles of plant ARGONAUTES. CURRENT OPINION IN PLANT BIOLOGY 2015; 27:111-7. [PMID: 26190744 PMCID: PMC4618181 DOI: 10.1016/j.pbi.2015.06.013] [Citation(s) in RCA: 182] [Impact Index Per Article: 20.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/21/2015] [Revised: 06/11/2015] [Accepted: 06/19/2015] [Indexed: 05/20/2023]
Abstract
ARGONAUTES (AGOs) are the effector proteins functioning in eukaryotic RNA silencing pathways. AGOs associate with small RNAs and are programmed to target complementary RNA or DNA. Plant viruses induce a potent and specific antiviral RNA silencing host response in which AGOs play a central role. Antiviral AGOs associate with virus-derived small RNAs to repress complementary viral RNAs or DNAs, or with endogenous small RNAs to regulate host gene expression and promote antiviral defense. Here, we review recent progress towards understanding the roles of plant AGOs in antiviral defense. We also discuss the strategies that viruses have evolved to modulate, attenuate or suppress AGO antiviral functions.
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Affiliation(s)
- Alberto Carbonell
- Donald Danforth Plant Science Center, St. Louis, Missouri 63132, USA
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66
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Luo H. Interplay between the virus and the ubiquitin-proteasome system: molecular mechanism of viral pathogenesis. Curr Opin Virol 2015; 17:1-10. [PMID: 26426962 PMCID: PMC7102833 DOI: 10.1016/j.coviro.2015.09.005] [Citation(s) in RCA: 107] [Impact Index Per Article: 11.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2015] [Revised: 09/08/2015] [Accepted: 09/15/2015] [Indexed: 01/24/2023]
Abstract
Many viruses have evolved to utilize the host UPS for their own benefit. Viruses subvert the UPS to maintain optimal level/function of viral proteins. Viruses exploit the UPS to degrade host proteins which impede viral growth. The UPS serves as an important host anti-viral defense mechanism. The UPS is inhibited by some viruses to prevent viral clearance.
The ubiquitin–proteasome system (UPS) plays a central role in a wide range of fundamental cellular functions by ensuring protein quality control and through maintaining a critical level of important regulatory proteins. Viruses subvert or manipulate this cellular machinery to favor viral propagation and to evade host immune response. The UPS serves as a double-edged sword in viral pathogenesis: on the one hand, the UPS is utilized by many viruses to maintain proper function and level of viral proteins; while on the other hand, the UPS constitutes a host defense mechanism to eliminate viral components. To combat this host anti-viral machinery, viruses have evolved to employ the UPS to degrade or inactivate cellular proteins that limit viral growth. This review will highlight our current knowledge pertaining to the different roles for the UPS in viral pathogenesis.
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Affiliation(s)
- Honglin Luo
- Centre for Heart Lung Innovation, St. Paul's Hospital, Vancouver, BC, Canada; Department of Pathology and Laboratory Medicine, University of British Columbia, Vancouver, BC, Canada.
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67
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A long downstream probe-based platform for multiplex target capture. Anal Biochem 2015; 491:4-9. [PMID: 26344895 DOI: 10.1016/j.ab.2015.08.029] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/04/2015] [Revised: 08/25/2015] [Accepted: 08/27/2015] [Indexed: 11/20/2022]
Abstract
A simple and rapid detection platform was established for multiplex target capture through generating single-strand long downstream probe (ssLDP), which was integrated with the ligase detection reaction (LDR) method for the purpose of multiplicity and high specificity. To increase sensitivity, the ladder-like polymerase chain reaction (PCR) amplicons were generated by using universal primers that complement ligated products. Each of the amplicons contained a stuffer sequence with a defined yet variable length. Thus, the length of the amplicon is an index of the specific suppressor, allowing its identification via electrophoresis. The multiplexed diagnostic platform was optimized using standard plasmids and validated by using potato virus suppressors as a detection model. This technique can detect down to 1.2 × 10(3) copies for single or two mixed target plasmids. When compared with microarray results, the electrophoresis showed 98.73-100% concordance rates for the seven suppressors in the 79 field samples. This strategy could be applied to detect a large number of targets in field and clinical surveillance.
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68
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Cascardo RS, Arantes ILG, Silva TF, Sachetto-Martins G, Vaslin MFS, Corrêa RL. Function and diversity of P0 proteins among cotton leafroll dwarf virus isolates. Virol J 2015; 12:123. [PMID: 26260343 PMCID: PMC4531488 DOI: 10.1186/s12985-015-0356-7] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2015] [Accepted: 08/04/2015] [Indexed: 11/23/2022] Open
Abstract
Background The RNA silencing pathway is an important anti-viral defense mechanism in plants. As a counter defense, some members of the viral family Luteoviridae are able to evade host immunity by encoding the P0 RNA silencing suppressor protein. Here we explored the functional diversity of P0 proteins among eight cotton leafroll dwarf virus (CLRDV) isolates, a virus associated with a worldwide cotton disease known as cotton blue disease (CBD). Methods CLRDV-infected cotton plants of different varieties were collected from five growing fields in Brazil and their P0 sequences compared to three previously obtained isolates. P0’s silencing suppression activities were scored based on transient expression experiments in Nicotiana benthamiana leaves. Results High sequence diversity was observed among CLRDV P0 proteins, indicating that some isolates found in cotton varieties formerly resistant to CLRDV should be regarded as new genotypes within the species. All tested proteins were able to suppress local and systemic silencing, but with significantly variable degrees. All P0 proteins were able to mediate the decay of ARGONAUTE proteins, a key component of the RNA silencing machinery. Conclusions The sequence diversity observed in CLRDV P0s is also reflected in their silencing suppression capabilities. However, the strength of local and systemic silencing suppression was not correlated for some proteins. Electronic supplementary material The online version of this article (doi:10.1186/s12985-015-0356-7) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Renan S Cascardo
- Department of Genetics, Federal University of Rio de Janeiro, Rio de Janeiro, Rio de Janeiro, Brazil.
| | - Ighor L G Arantes
- Department of Genetics, Federal University of Rio de Janeiro, Rio de Janeiro, Rio de Janeiro, Brazil.
| | - Tatiane F Silva
- Department of Virology, Federal University of Rio de Janeiro, Rio de Janeiro, Rio de Janeiro, Brazil. .,Present address: Departamento de Biotecnologia, Escola de Engenharia de Lorena, Universidade de São Paulo, Lorena, São Paulo, Brazil.
| | - Gilberto Sachetto-Martins
- Department of Genetics, Federal University of Rio de Janeiro, Rio de Janeiro, Rio de Janeiro, Brazil.
| | - Maité F S Vaslin
- Department of Virology, Federal University of Rio de Janeiro, Rio de Janeiro, Rio de Janeiro, Brazil.
| | - Régis L Corrêa
- Department of Genetics, Federal University of Rio de Janeiro, Rio de Janeiro, Rio de Janeiro, Brazil.
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69
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Sõmera M, Sarmiento C, Truve E. Overview on Sobemoviruses and a Proposal for the Creation of the Family Sobemoviridae. Viruses 2015; 7:3076-115. [PMID: 26083319 PMCID: PMC4488728 DOI: 10.3390/v7062761] [Citation(s) in RCA: 48] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2015] [Revised: 05/18/2015] [Accepted: 06/02/2015] [Indexed: 12/26/2022] Open
Abstract
The genus Sobemovirus, unassigned to any family, consists of viruses with single-stranded plus-oriented single-component RNA genomes and small icosahedral particles. Currently, 14 species within the genus have been recognized by the International Committee on Taxonomy of Viruses (ICTV) but several new species are to be recognized in the near future. Sobemovirus genomes are compact with a conserved structure of open reading frames and with short untranslated regions. Several sobemoviruses are important pathogens. Moreover, over the last decade sobemoviruses have become important model systems to study plant virus evolution. In the current review we give an overview of the structure and expression of sobemovirus genomes, processing and functions of individual proteins, particle structure, pathology and phylogenesis of sobemoviruses as well as of satellite RNAs present together with these viruses. Based on a phylogenetic analysis we propose that a new family Sobemoviridae should be recognized including the genera Sobemovirus and Polemovirus. Finally, we outline the future perspectives and needs for the research focusing on sobemoviruses.
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Affiliation(s)
- Merike Sõmera
- Department of Gene Technology, Tallinn University of Technology, Akadeemia tee 15, 12618 Tallinn, Estonia.
| | - Cecilia Sarmiento
- Department of Gene Technology, Tallinn University of Technology, Akadeemia tee 15, 12618 Tallinn, Estonia.
| | - Erkki Truve
- Department of Gene Technology, Tallinn University of Technology, Akadeemia tee 15, 12618 Tallinn, Estonia.
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70
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Soler N, Fagoaga C, López C, Moreno P, Navarro L, Flores R, Peña L. Symptoms induced by transgenic expression of p23 from Citrus tristeza virus in phloem-associated cells of Mexican lime mimic virus infection without the aberrations accompanying constitutive expression. MOLECULAR PLANT PATHOLOGY 2015; 16:388-99. [PMID: 25171669 PMCID: PMC6638416 DOI: 10.1111/mpp.12188] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/19/2023]
Abstract
Citrus tristeza virus (CTV) is phloem restricted in natural citrus hosts. The 23-kDa protein (p23) encoded by the virus is an RNA silencing suppressor and a pathogenicity determinant. The expression of p23, or its N-terminal 157-amino-acid fragment comprising the zinc finger and flanking basic motifs, driven by the constitutive 35S promoter of cauliflower mosaic virus, induces CTV-like symptoms and other aberrations in transgenic citrus. To better define the role of p23 in CTV pathogenesis, we compared the phenotypes of Mexican lime transformed with p23-derived transgenes from the severe T36 and mild T317 CTV isolates under the control of the phloem-specific promoter from Commelina yellow mottle virus (CoYMV) or the 35S promoter. Expression of the constructs restricted to the phloem induced a phenotype resembling CTV-specific symptoms (vein clearing and necrosis, and stem pitting), but not the non-specific aberrations (such as mature leaf epinasty and yellow pinpoints, growth cessation and apical necrosis) observed when p23 was ectopically expressed. Furthermore, vein necrosis and stem pitting in Mexican lime appeared to be specifically associated with p23 from T36. Phloem-specific accumulation of the p23Δ158-209(T36) fragment was sufficient to induce the same anomalies, indicating that the region comprising the N-terminal 157 amino acids of p23 is responsible (at least in part) for the vein clearing, stem pitting and, possibly, vein corking in this host.
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Affiliation(s)
- Nuria Soler
- Centro de Protección Vegetal y Biotecnología, Instituto Valenciano de Investigaciones Agrarias (IVIA), Apdo. Oficial, Moncada, Valencia, 46113, Spain
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71
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Deng XG, Peng XJ, Zhu F, Chen YJ, Zhu T, Qin SB, Xi DH, Lin HH. A critical domain of Sweet potato chlorotic fleck virus nucleotide-binding protein (NaBp) for RNA silencing suppression, nuclear localization and viral pathogenesis. MOLECULAR PLANT PATHOLOGY 2015; 16:365-75. [PMID: 25138489 PMCID: PMC6638403 DOI: 10.1111/mpp.12186] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/08/2023]
Abstract
RNA silencing is an important mechanism of antiviral defence in plants. To counteract this resistance mechanism, many viruses have evolved RNA silencing suppressors. In this study, we analysed five proteins encoded by Sweet potato chlorotic fleck virus (SPCFV) for their abilities to suppress RNA silencing using a green fluorescent protein (GFP)-based transient expression assay in Nicotiana benthamiana line 16c plants. Our results showed that a putative nucleotide-binding protein (NaBp), but not other proteins encoded by the virus, could efficiently suppress local and systemic RNA silencing induced by either sense or double-stranded RNA (dsRNA) molecules. Deletion mutation analysis of NaBp demonstrated that the basic motif (an arginine-rich region) was critical for its RNA silencing suppression activity. Using confocal laser scanning microscopy imaging of transfected protoplasts expressing NaBp fused to GFP, we showed that NaBp accumulated predominantly in the nucleus. Mutational analysis of NaBp demonstrated that the basic motif represented part of the nuclear localization signal. In addition, we demonstrated that the basic motif in NaBp was a pathogenicity determinant in the Potato virus X (PVX) heterogeneous system. Overall, our results demonstrate that the basic motif of SPCFV NaBp plays a critical role in RNA silencing suppression, nuclear localization and viral pathogenesis.
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Affiliation(s)
- Xing-Guang Deng
- Ministry of Education Key Laboratory for Bio-Resource and Eco-Environment, College of Life Science, State Key Laboratory of Hydraulics and Mountain River Engineering, Sichuan University, Chengdu, Sichuan, 610064, China
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72
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Csorba T, Kontra L, Burgyán J. viral silencing suppressors: Tools forged to fine-tune host-pathogen coexistence. Virology 2015; 479-480:85-103. [DOI: 10.1016/j.virol.2015.02.028] [Citation(s) in RCA: 368] [Impact Index Per Article: 40.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2014] [Revised: 01/31/2015] [Accepted: 02/16/2015] [Indexed: 12/27/2022]
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73
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da Silva AKF, Romanel E, Silva TDF, Castilhos Y, Schrago CG, Galbieri R, Bélot JL, Vaslin MFS. Complete genome sequences of two new virus isolates associated with cotton blue disease resistance breaking in Brazil. Arch Virol 2015; 160:1371-4. [PMID: 25772571 DOI: 10.1007/s00705-015-2380-8] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2014] [Accepted: 02/21/2015] [Indexed: 11/26/2022]
Abstract
Since 2006, Brazilian cotton (Gossypium hirsutum) crops planted with cultivars that are resistant to cotton blue disease have developed a new disease termed "atypical" cotton blue disease or atypical vein mosaic disease. Here, we describe the complete genomes of two virus isolates associated with this disease. The new virus isolates, called CLRDV-Acr3 and CLRDV-IMA2, were found to have a high degree of nucleotide and amino acid sequence similarity to previously described isolates of cotton leafroll dwarf virus, the causal agent of cotton blue disease. However, their P0 proteins were 86.1 % identical. These results show that this new disease is caused by a new CLRDV genotype that seems to have acquired the ability to overcome cotton blue disease resistance.
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Affiliation(s)
- Anna Karoline Fausto da Silva
- Depto. Virologia, Lab. Virologia Molecular Vegetal, IMPPG, Universidade Federal do Rio de Janeiro, UFRJ, Rio de Janeiro, RJ, Brasil
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74
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Dey KK, Borth WB, Melzer MJ, Wang ML, Hu JS. Analysis of pineapple mealybug wilt associated virus -1 and -2 for potential RNA silencing suppressors and pathogenicity factors. Viruses 2015; 7:969-95. [PMID: 25751306 PMCID: PMC4379557 DOI: 10.3390/v7030969] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2014] [Revised: 02/05/2015] [Accepted: 02/15/2015] [Indexed: 01/02/2023] Open
Abstract
Higher plants use RNA silencing to defend against viral infections. As a counter defense, plant viruses have evolved proteins that suppress RNA silencing. Mealybug wilt of pineapple (MWP), an important disease of pineapple, has been associated with at least three distinct viruses, Pineapple mealybug wilt associated virus -1, -2, and -3 (PMWaV-1, -2, and -3). Selected open reading frames (ORFs) of PMWaV-1 and PMWaV-2 were screened for their local and systemic suppressor activities in Agrobacterium-mediated transient assays using green fluorescent protein (GFP) in Nicotiana benthamiana. Results indicate that PMWaV-2 utilizes a multiple-component RNA silencing suppression mechanism. Two proteins, p20 and CP, target both local and systemic silencing in N. benthamiana, while the p22 and CPd proteins target only systemic silencing. In the related virus PMWaV-1, we found that only one of the encoded proteins, p61, had only systemic suppressor activity. Of all the proteins tested from both viruses, only the PMWaV-2 p20 protein suppressed local silencing induced by double-stranded RNA (dsRNA), but only when low levels of inducing dsRNA were used. None of the proteins analyzed could interfere with the short distance spread of silencing. We examined the mechanism of systemic suppression activity by investigating the effect of PMWaV-2-encoded p20 and CP proteins on secondary siRNAs. Our results suggest that the PMWaV-2 p20 and CP proteins block the systemic silencing signal by repressing production of secondary siRNAs. We also demonstrate that the PMWaV-2 p20 and p22 proteins enhanced the pathogenicity of Potato virus X in N. benthamiana.
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Affiliation(s)
- Kishore K Dey
- Department of Plant and Environmental Protection Sciences, University of Hawaii, 3190 Maile Way, Honolulu, HI 96822, USA.
| | - Wayne B Borth
- Department of Plant and Environmental Protection Sciences, University of Hawaii, 3190 Maile Way, Honolulu, HI 96822, USA.
| | - Michael J Melzer
- Department of Plant and Environmental Protection Sciences, University of Hawaii, 3190 Maile Way, Honolulu, HI 96822, USA.
| | - Ming-Li Wang
- Hawaii Agricultural Research Center, Kunia, Honolulu, HI 96797, USA.
| | - John S Hu
- Department of Plant and Environmental Protection Sciences, University of Hawaii, 3190 Maile Way, Honolulu, HI 96822, USA.
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75
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Mann KS, Johnson KN, Dietzgen RG. Cytorhabdovirus phosphoprotein shows RNA silencing suppressor activity in plants, but not in insect cells. Virology 2015; 476:413-418. [PMID: 25591176 DOI: 10.1016/j.virol.2014.12.023] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2014] [Revised: 11/16/2014] [Accepted: 12/14/2014] [Indexed: 01/01/2023]
Abstract
RNA silencing in plants and insects provides an antiviral defense and as a countermeasure most viruses encode RNA silencing suppressors (RSS). For the family Rhabdoviridae, no detailed functional RSS studies have been reported in plant hosts and insect vectors. In agroinfiltrated Nicotiana benthamiana leaves we show for the first time for a cytorhabdovirus, lettuce necrotic yellows virus (LNYV), that one of the nucleocapsid core proteins, phosphoprotein (P) has relatively weak local RSS activity and delays systemic silencing of a GFP reporter. Analysis of GFP small RNAs indicated that the P protein did not prevent siRNA accumulation. To explore RSS activity in insects, we used a Flock House virus replicon system in Drosophila S2 cells. In contrast to the plant host, LNYV P protein did not exhibit RSS activity in the insect cells. Taken together our results suggest that P protein may target plant-specific components of RNA silencing post siRNA biogenesis.
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Affiliation(s)
- Krin S Mann
- Queensland Alliance for Agriculture and Food Innovation, The University of Queensland, St Lucia, Qld 4072, Australia
| | - Karyn N Johnson
- School of Biological Sciences, The University of Queensland, St Lucia, Qld 4072, Australia
| | - Ralf G Dietzgen
- Queensland Alliance for Agriculture and Food Innovation, The University of Queensland, St Lucia, Qld 4072, Australia.
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76
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Sõmera M, Truve E. Rottboellia yellow mottle virus is a distinct species within the genus Sobemovirus. Arch Virol 2015; 160:857-63. [PMID: 25613163 DOI: 10.1007/s00705-015-2336-z] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2014] [Accepted: 01/08/2015] [Indexed: 11/28/2022]
Abstract
Once considered a tentative member of the genus Sobemovirus, rottboellia yellow mottle virus (RoMoV) was excluded from the latest species list of the ICTV after the discovery of imperata yellow mottle virus (IYMV), which resembles RoMoV in host range and geographic origin. Here, sequence analysis of the complete genome of RoMoV suggested that it should be considered a distinct species within the genus Sobemovirus. It has the highest sequence identity (55 %) to ryegrass mottle virus (RGMoV), whereas its sequence identity to IYMV is lower (44 %). In a phylogenetic tree, RoMoV clusters together with RGMoV and artemisia virus A (ArtVA), a dicot-infecting sobemovirus.
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Affiliation(s)
- Merike Sõmera
- Department of Gene Technology, Tallinn University of Technology, Akadeemia tee 15, 12618, Tallinn, Estonia,
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77
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Masson P, Hulo C, de Castro E, Foulger R, Poux S, Bridge A, Lomax J, Bougueleret L, Xenarios I, Le Mercier P. An integrated ontology resource to explore and study host-virus relationships. PLoS One 2014; 9:e108075. [PMID: 25233094 PMCID: PMC4169452 DOI: 10.1371/journal.pone.0108075] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2014] [Accepted: 08/25/2014] [Indexed: 11/17/2022] Open
Abstract
Our growing knowledge of viruses reveals how these pathogens manage to evade innate host defenses. A global scheme emerges in which many viruses usurp key cellular defense mechanisms and often inhibit the same components of antiviral signaling. To accurately describe these processes, we have generated a comprehensive dictionary for eukaryotic host-virus interactions. This controlled vocabulary has been detailed in 57 ViralZone resource web pages which contain a global description of all molecular processes. In order to annotate viral gene products with this vocabulary, an ontology has been built in a hierarchy of UniProt Knowledgebase (UniProtKB) keyword terms and corresponding Gene Ontology (GO) terms have been developed in parallel. The results are 65 UniProtKB keywords related to 57 GO terms, which have been used in 14,390 manual annotations; 908,723 automatic annotations and propagated to an estimation of 922,941 GO annotations. ViralZone pages, UniProtKB keywords and GO terms provide complementary tools to users, and the three resources have been linked to each other through host-virus vocabulary.
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Affiliation(s)
- Patrick Masson
- SIB Swiss Institute of Bioinformatics, CMU, University of Geneva Medical School, Geneva, Switzerland
| | - Chantal Hulo
- SIB Swiss Institute of Bioinformatics, CMU, University of Geneva Medical School, Geneva, Switzerland
| | - Edouard de Castro
- SIB Swiss Institute of Bioinformatics, CMU, University of Geneva Medical School, Geneva, Switzerland
| | - Rebecca Foulger
- European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Trust Genome Campus, Hinxton, United Kingdom
| | - Sylvain Poux
- SIB Swiss Institute of Bioinformatics, CMU, University of Geneva Medical School, Geneva, Switzerland
| | - Alan Bridge
- SIB Swiss Institute of Bioinformatics, CMU, University of Geneva Medical School, Geneva, Switzerland
| | - Jane Lomax
- European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Trust Genome Campus, Hinxton, United Kingdom
| | - Lydie Bougueleret
- SIB Swiss Institute of Bioinformatics, CMU, University of Geneva Medical School, Geneva, Switzerland
| | - Ioannis Xenarios
- SIB Swiss Institute of Bioinformatics, CMU, University of Geneva Medical School, Geneva, Switzerland
| | - Philippe Le Mercier
- SIB Swiss Institute of Bioinformatics, CMU, University of Geneva Medical School, Geneva, Switzerland
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78
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Zhuo T, Li YY, Xiang HY, Wu ZY, Wang XB, Wang Y, Zhang YL, Li DW, Yu JL, Han CG. Amino acid sequence motifs essential for P0-mediated suppression of RNA silencing in an isolate of potato leafroll virus from Inner Mongolia. MOLECULAR PLANT-MICROBE INTERACTIONS : MPMI 2014; 27:515-27. [PMID: 24450775 DOI: 10.1094/mpmi-08-13-0231-r] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/19/2023]
Abstract
Polerovirus P0 suppressors of host gene silencing contain a consensus F-box-like motif with Leu/Pro (L/P) requirements for suppressor activity. The Inner Mongolian Potato leafroll virus (PLRV) P0 protein (P0(PL-IM)) has an unusual F-box-like motif that contains a Trp/Gly (W/G) sequence and an additional GW/WG-like motif (G139/W140/G141) that is lacking in other P0 proteins. We used Agrobacterium infiltration-mediated RNA silencing assays to establish that P0(PL-IM) has a strong suppressor activity. Mutagenesis experiments demonstrated that the P0(PL-IM) F-box-like motif encompasses amino acids 76-LPRHLHYECLEWGLLCG THP-95, and that the suppressor activity is abolished by L76A, W87A, or G88A substitution. The suppressor activity is also weakened substantially by mutations within the G139/W140/G141 region and is eliminated by a mutation (F220R) in a C-terminal conserved sequence of P0(PL-IM). As has been observed with other P0 proteins, P0(PL-IM) suppression is correlated with reduced accumulation of the host AGO1-silencing complex protein. However, P0(PL-IM) fails to bind SKP1, which functions in a proteasome pathway that may be involved in AGO1 degradation. These results suggest that P0(PL-IM) may suppress RNA silencing by using an alternative pathway to target AGO1 for degradation. Our results help improve our understanding of the molecular mechanisms involved in PLRV infection.
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79
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Verchot J. The ER quality control and ER associated degradation machineries are vital for viral pathogenesis. FRONTIERS IN PLANT SCIENCE 2014; 5:66. [PMID: 24653727 DOI: 10.3389/fpls.2014.00066/abstract] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Received: 12/11/2013] [Accepted: 02/07/2014] [Indexed: 05/24/2023]
Abstract
The endoplasmic reticulum (ER) is central to protein production and membrane lipid synthesis. The unfolded protein response (UPR) supports cellular metabolism by ensuring protein quality control in the ER. Most positive strand RNA viruses cause extensive remodeling of membranes and require active membrane synthesis to promote infection. How viruses interact with the cellular machinery controlling membrane metabolism is largely unknown. Furthermore, there is mounting data pointing to the importance of the UPR and ER associated degradation (ERAD) machineries in viral pathogenesis in eukaryotes emerging topic. For many viruses, the UPR is an early event that is essential for persistent infection and benefits virus replication. In addition, many viruses are reported to commandeer ER resident chaperones to contribute to virus replication and intercellular movement. In particular, calreticulin, the ubiquitin machinery, and the 26S proteasome are most commonly identified components of the UPR and ERAD machinery that also regulate virus infection. In addition, researchers have noted a link between UPR and autophagy. It is well accepted that positive strand RNA viruses use autophagic membranes as scaffolds to support replication and assembly. However this topic has yet to be explored using plant viruses. The goal of research on this topic is to uncover how viruses interact with this ER-related machinery and to use this information for designing novel strategies to boost immune responses to virus infection.
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Affiliation(s)
- Jeanmarie Verchot
- Department of Entomology and Plant Pathology, Oklahoma State University Stillwater, OK, USA
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80
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Delfosse VC, Agrofoglio YC, Casse MF, Kresic IB, Hopp HE, Ziegler-Graff V, Distéfano AJ. The P0 protein encoded by cotton leafroll dwarf virus (CLRDV) inhibits local but not systemic RNA silencing. Virus Res 2014; 180:70-5. [PMID: 24370867 DOI: 10.1016/j.virusres.2013.12.018] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2013] [Revised: 12/08/2013] [Accepted: 12/13/2013] [Indexed: 11/28/2022]
Abstract
Plants employ RNA silencing as a natural defense mechanism against viruses. As a counter-defense, viruses encode silencing suppressor proteins (SSPs) that suppress RNA silencing. Most, but not all, the P0 proteins encoded by poleroviruses have been identified as SSP. In this study, we demonstrated that cotton leafroll dwarf virus (CLRDV, genus Polerovirus) P0 protein suppressed local silencing that was induced by sense or inverted repeat transgenes in Agrobacterium co-infiltration assay in Nicotiana benthamiana plants. A CLRDV full-length infectious cDNA clone that is able to infect N. benthamiana through Agrobacterium-mediated inoculation also inhibited local silencing in co-infiltration assays, suggesting that the P0 protein exhibits similar RNA silencing suppression activity when expressed from the full-length viral genome. On the other hand, the P0 protein did not efficiently inhibit the spread of systemic silencing signals. Moreover, Northern blotting indicated that the P0 protein inhibits the generation of secondary but not primary small interfering RNAs. The study of CLRDV P0 suppression activity may contribute to understanding the molecular mechanisms involved in the induction of cotton blue disease by CLRDV infection.
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Affiliation(s)
| | | | | | | | - H Esteban Hopp
- Instituto de Biotecnología, CICVyA, CNIA, INTA, Buenos Aires, Argentina; Facultad de Ciencias Exactas y Naturales, UBA, Buenos Aires, Argentina.
| | - Véronique Ziegler-Graff
- Institut de Biologie Moléculaire des Plantes, laboratoire propre du CNRS conventionné avec l'Université de Strasbourg, Strasbourg, France.
| | - Ana J Distéfano
- Instituto de Biotecnología, CICVyA, CNIA, INTA, Buenos Aires, Argentina; Facultad de Ciencias Exactas y Naturales, UBA, Buenos Aires, Argentina.
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81
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Verchot J. The ER quality control and ER associated degradation machineries are vital for viral pathogenesis. FRONTIERS IN PLANT SCIENCE 2014; 5:66. [PMID: 24653727 PMCID: PMC3949406 DOI: 10.3389/fpls.2014.00066] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/11/2013] [Accepted: 02/07/2014] [Indexed: 05/19/2023]
Abstract
The endoplasmic reticulum (ER) is central to protein production and membrane lipid synthesis. The unfolded protein response (UPR) supports cellular metabolism by ensuring protein quality control in the ER. Most positive strand RNA viruses cause extensive remodeling of membranes and require active membrane synthesis to promote infection. How viruses interact with the cellular machinery controlling membrane metabolism is largely unknown. Furthermore, there is mounting data pointing to the importance of the UPR and ER associated degradation (ERAD) machineries in viral pathogenesis in eukaryotes emerging topic. For many viruses, the UPR is an early event that is essential for persistent infection and benefits virus replication. In addition, many viruses are reported to commandeer ER resident chaperones to contribute to virus replication and intercellular movement. In particular, calreticulin, the ubiquitin machinery, and the 26S proteasome are most commonly identified components of the UPR and ERAD machinery that also regulate virus infection. In addition, researchers have noted a link between UPR and autophagy. It is well accepted that positive strand RNA viruses use autophagic membranes as scaffolds to support replication and assembly. However this topic has yet to be explored using plant viruses. The goal of research on this topic is to uncover how viruses interact with this ER-related machinery and to use this information for designing novel strategies to boost immune responses to virus infection.
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Affiliation(s)
- Jeanmarie Verchot
- *Correspondence: Jeanmarie Verchot, Department of Entomology and Plant Pathology, Oklahoma State University, 127 Noble Research Center, Stillwater, OK 74078, USA e-mail:
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82
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Derrien B, Genschik P. When RNA and protein degradation pathways meet. FRONTIERS IN PLANT SCIENCE 2014; 5:161. [PMID: 24795741 PMCID: PMC4006050 DOI: 10.3389/fpls.2014.00161] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/26/2014] [Accepted: 04/07/2014] [Indexed: 05/07/2023]
Abstract
RNA silencing has become a major focus of molecular and biomedical research in the last decade. This mechanism, which is conserved in most eukaryotes, has been extensively studied and is associated to various pathways implicated in the regulation of development, in the control of transposition events, heterochromatin maintenance and also playing a role in defense against viruses. Despite of its importance, the regulation of the RNA silencing machinery itself remains still poorly explored. Recently several reports in both plants and metazoans revealed that key components of RNA silencing, such as RNA-induced silencing complex component ARGONAUTE proteins, but also the endonuclease Dicer are subjected to proteasomal and autophagic pathways. Here we will review these post-translational proteolytic regulations with a special emphasis on plant research and also discuss their functional relevance.
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Affiliation(s)
- Benoît Derrien
- Centre National de la Recherche Scientifique, Institut de Biologie Moléculaire des Plantes, Unité Propre de Recherche 2357, Conventionné avec l’Université de StrasbourgStrasbourg, France
| | - Pascal Genschik
- Centre National de la Recherche Scientifique, Institut de Biologie Moléculaire des Plantes, Unité Propre de Recherche 2357, Conventionné avec l’Université de StrasbourgStrasbourg, France
- Laboratoire de Biochimie et Physiologie Moléculaire des Plantes, Institut de Biologie Intégrative des Plantes ’Claude Grignon’, UMR CNRS/INRA/SupAgro/UM2, Montpellier CedexFrance
- *Correspondence: Pascal Genschik, Centre National de la Recherche Scientifique, Institut de Biologie Moléculaire des Plantes, Unité Propre de Recherche 2357, Conventionné avec l’Université de Strasbourg, 67084 Strasbourg, France e-mail:
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83
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Vives MC, Velázquez K, Pina JA, Moreno P, Guerri J, Navarro L. Identification of a new enamovirus associated with citrus vein enation disease by deep sequencing of small RNAs. PHYTOPATHOLOGY 2013; 103:1077-86. [PMID: 23718835 DOI: 10.1094/phyto-03-13-0068-r] [Citation(s) in RCA: 37] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/05/2023]
Abstract
To identify the causal agent of citrus vein enation disease, we examined by deep sequencing (Solexa-Illumina) the small RNA (sRNA) fraction from infected and healthy Etrog citron plants. Our results showed that virus-derived sRNAs (vsRNAs): (i) represent about 14.21% of the total sRNA population, (ii) are predominantly of 21 and 24 nucleotides with a biased distribution of their 5' nucleotide and with a clear prevalence of those of (+) polarity, and (iii) derive from all the viral genome, although a prominent hotspot is present at a 5'-proximal region. Contigs assembled from vsRNAs showed similarity with luteovirus sequences, particularly with Pea enation mosaic virus, the type member of the genus Enamovirus. The genomic RNA (gRNA) sequence of a new virus, provisionally named Citrus vein enation virus (CVEV), was completed and characterized. The CVEV gRNA was found to be single-stranded, positive-sense, with a size of 5,983 nucleotides and five open reading frames. Phylogenetic comparisons based on amino acid signatures of the RNA polymerase and the coat protein clearly classifies CVEV within the genus Enamovirus. Dot-blot hybridization and reverse transcription-polymerase chain reaction tests were developed to detect CVEV in plants affected by vein enation disease. CVEV detection by these methods has already been adopted for use in the Spanish citrus quarantine, sanitation, and certification programs.
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84
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Krueger EN, Beckett RJ, Gray SM, Miller WA. The complete nucleotide sequence of the genome of Barley yellow dwarf virus-RMV reveals it to be a new Polerovirus distantly related to other yellow dwarf viruses. Front Microbiol 2013; 4:205. [PMID: 23888156 PMCID: PMC3719023 DOI: 10.3389/fmicb.2013.00205] [Citation(s) in RCA: 36] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2013] [Accepted: 07/01/2013] [Indexed: 11/13/2022] Open
Abstract
The yellow dwarf viruses (YDVs) of the Luteoviridae family represent the most widespread group of cereal viruses worldwide. They include the Barley yellow dwarf viruses (BYDVs) of genus Luteovirus, the Cereal yellow dwarf viruses (CYDVs) and Wheat yellow dwarf virus (WYDV) of genus Polerovirus. All of these viruses are obligately aphid transmitted and phloem-limited. The first described YDVs (initially all called BYDV) were classified by their most efficient vector. One of these viruses, BYDV-RMV, is transmitted most efficiently by the corn leaf aphid, Rhopalosiphum maidis. Here we report the complete 5612 nucleotide sequence of the genomic RNA of a Montana isolate of BYDV-RMV (isolate RMV MTFE87, Genbank accession no. KC921392). The sequence revealed that BYDV-RMV is a polerovirus, but it is quite distantly related to the CYDVs or WYDV, which are very closely related to each other. Nor is BYDV-RMV closely related to any other particular polerovirus. Depending on the gene that is compared, different poleroviruses (none of them a YDV) share the most sequence similarity to BYDV-RMV. Because of its distant relationship to other YDVs, and because it commonly infects maize via its vector, R. maidis, we propose that BYDV-RMV be renamed Maize yellow dwarf virus-RMV (MYDV-RMV).
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Affiliation(s)
| | - Randy J. Beckett
- Plant Pathology and Microbiology Department, Iowa State UniversityAmes, IA, USA
| | - Stewart M. Gray
- USDA/ARS and Plant Pathology Department, Cornell UniversityIthaca, NY, USA
| | - W. Allen Miller
- Plant Pathology and Microbiology Department, Iowa State UniversityAmes, IA, USA
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85
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Delfosse VC, Casse MF, Agrofoglio YC, Kresic IB, Hopp HE, Ziegler-Graff V, Distéfano AJ. Agroinoculation of a full-length cDNA clone of cotton leafroll dwarf virus (CLRDV) results in systemic infection in cotton and the model plant Nicotiana benthamiana. Virus Res 2013; 175:64-70. [PMID: 23623981 DOI: 10.1016/j.virusres.2013.04.007] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2013] [Revised: 04/11/2013] [Accepted: 04/17/2013] [Indexed: 10/26/2022]
Abstract
Cotton blue disease is the most important viral disease of cotton in the southern part of South America. Its etiological agent, cotton leafroll dwarf virus (CLRDV), is specifically transmitted to host plants by the aphid vector (Aphis gossypii) and any attempt to perform mechanical inoculations of this virus into its host has failed. This limitation has held back the study of this virus and the disease it causes. In this study, a full-length cDNA of CLRDV was constructed and expressed in vivo under the control of cauliflower mosaic virus 35S promoter. An agrobacterium-mediated inoculation system for the cloned cDNA construct of CLRDV was developed. Northern and immunoblot analyses showed that after several weeks the replicon of CLRDV delivered by Agrobacterium tumefaciens in Gossypium hirsutum plants gave rise to a systemic infection and typical blue disease symptoms correlated to the presence of viral RNA and P3 capsid protein. We also demonstrated that the virus that accumulated in the agroinfected plants was transmissible by the vector A. gossypii. This result confirms the production of biologically active transmissible virions. In addition, the clone was infectious in Nicotiana benthamiana plants which developed interveinal chlorosis three weeks postinoculation and CLRDV was detected both in the inoculated and systemic leaves. Attempts to agroinfect Arabidopsis thaliana plants were irregularly successful. Although no symptoms were observed, the P3 capsid protein as well as the genomic and subgenomic RNAs were irregularly detected in systemic leaves of some agroinfiltrated plants. The inefficient infection rate infers that A. thaliana is a poor host for CLRDV. This is the first report on the construction of a biologically-active infectious full-length clone of a cotton RNA virus showing successful agroinfection of host and non-host plants. The system herein developed will be useful to study CLRDV viral functions and plant-virus interactions using a reverse genetic approach.
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86
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Incarbone M, Dunoyer P. RNA silencing and its suppression: novel insights from in planta analyses. TRENDS IN PLANT SCIENCE 2013; 18:382-92. [PMID: 23684690 DOI: 10.1016/j.tplants.2013.04.001] [Citation(s) in RCA: 111] [Impact Index Per Article: 10.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/14/2013] [Revised: 03/25/2013] [Accepted: 04/04/2013] [Indexed: 05/19/2023]
Abstract
Plants employ multiple layers of innate immunity to fight pathogens. For both RNA and DNA viruses, RNA silencing plays a critical role in plant resistance. To escape this antiviral silencing-based immune response, viruses have evolved various counterdefense strategies, the most widespread being production of viral suppressors of RNA silencing (VSRs) that target various stages of the silencing mechanisms. Recent findings from in planta analyses have provided new insights into the mode of action of VSRs and revealed that plants react to the perturbation of the silencing pathways brought by viral infection by deploying a battery of counter-counterdefense measures. As well as discussing which experimental approaches have been most effective in delivering clear and unambiguous results, this review provides a detailed account of the surprising variety of offensive and defensive strategies set forth by both viruses and hosts in their struggle for survival.
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Affiliation(s)
- Marco Incarbone
- IBMP-CNRS, 12 rue du General Zimmer, 67084 Strasbourg Cedex, France
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87
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Hwang YT, Kalischuk M, Fusaro AF, Waterhouse PM, Kawchuk L. Small RNA sequencing of Potato leafroll virus-infected plants reveals an additional subgenomic RNA encoding a sequence-specific RNA-binding protein. Virology 2013; 438:61-9. [DOI: 10.1016/j.virol.2012.12.012] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2012] [Revised: 10/28/2012] [Accepted: 12/25/2012] [Indexed: 10/27/2022]
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88
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Correa RL, Bruckner FP, de Souza Cascardo R, Alfenas-Zerbini P. The Role of F-Box Proteins during Viral Infection. Int J Mol Sci 2013; 14:4030-49. [PMID: 23429191 PMCID: PMC3588083 DOI: 10.3390/ijms14024030] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/23/2012] [Revised: 12/14/2012] [Accepted: 01/17/2013] [Indexed: 01/10/2023] Open
Abstract
The F-box domain is a protein structural motif of about 50 amino acids that mediates protein–protein interactions. The F-box protein is one of the four components of the SCF (SKp1, Cullin, F-box protein) complex, which mediates ubiquitination of proteins targeted for degradation by the proteasome, playing an essential role in many cellular processes. Several discoveries have been made on the use of the ubiquitin–proteasome system by viruses of several families to complete their infection cycle. On the other hand, F-box proteins can be used in the defense response by the host. This review describes the role of F-box proteins and the use of the ubiquitin–proteasome system in virus–host interactions.
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Affiliation(s)
- Régis Lopes Correa
- Department of Genetics, Federal University of Rio de Janeiro, Rio de Janeiro, RJ 21944-970, Brazil; E-Mails: (R.L.C.); (R.S.C.)
| | - Fernanda Prieto Bruckner
- Department of Microbiology/BIOAGRO, Federal University of Viçosa, Viçosa, MG 36570-000, Brazil; E-Mail:
| | - Renan de Souza Cascardo
- Department of Genetics, Federal University of Rio de Janeiro, Rio de Janeiro, RJ 21944-970, Brazil; E-Mails: (R.L.C.); (R.S.C.)
- Department of Microbiology/BIOAGRO, Federal University of Viçosa, Viçosa, MG 36570-000, Brazil; E-Mail:
| | - Poliane Alfenas-Zerbini
- Department of Microbiology/BIOAGRO, Federal University of Viçosa, Viçosa, MG 36570-000, Brazil; E-Mail:
- Author to whom correspondence should be addressed; E-Mail: ; Tel.: +55-31-3899-2955; Fax: +55-31-3899-2864
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89
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Szittya G, Burgyán J. RNA Interference-Mediated Intrinsic Antiviral Immunity in Plants. Curr Top Microbiol Immunol 2013; 371:153-81. [DOI: 10.1007/978-3-642-37765-5_6] [Citation(s) in RCA: 65] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
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90
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Naim F, Nakasugi K, Crowhurst RN, Hilario E, Zwart AB, Hellens RP, Taylor JM, Waterhouse PM, Wood CC. Advanced engineering of lipid metabolism in Nicotiana benthamiana using a draft genome and the V2 viral silencing-suppressor protein. PLoS One 2012; 7:e52717. [PMID: 23300750 PMCID: PMC3530501 DOI: 10.1371/journal.pone.0052717] [Citation(s) in RCA: 68] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2012] [Accepted: 11/20/2012] [Indexed: 01/05/2023] Open
Abstract
The transient leaf assay in Nicotiana benthamiana is widely used in plant sciences, with one application being the rapid assembly of complex multigene pathways that produce new fatty acid profiles. This rapid and facile assay would be further improved if it were possible to simultaneously overexpress transgenes while accurately silencing endogenes. Here, we report a draft genome resource for N. benthamiana spanning over 75% of the 3.1 Gb haploid genome. This resource revealed a two-member NbFAD2 family, NbFAD2.1 and NbFAD2.2, and quantitative RT-PCR (qRT-PCR) confirmed their expression in leaves. FAD2 activities were silenced using hairpin RNAi as monitored by qRT-PCR and biochemical assays. Silencing of endogenous FAD2 activities was combined with overexpression of transgenes via the use of the alternative viral silencing-suppressor protein, V2, from Tomato yellow leaf curl virus. We show that V2 permits maximal overexpression of transgenes but, crucially, also allows hairpin RNAi to operate unimpeded. To illustrate the efficacy of the V2-based leaf assay system, endogenous lipids were shunted from the desaturation of 18∶1 to elongation reactions beginning with 18∶1 as substrate. These V2-based leaf assays produced ∼50% more elongated fatty acid products than p19-based assays. Analyses of small RNA populations generated from hairpin RNAi against NbFAD2 confirm that the siRNA population is dominated by 21 and 22 nt species derived from the hairpin. Collectively, these new tools expand the range of uses and possibilities for metabolic engineering in transient leaf assays.
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Affiliation(s)
- Fatima Naim
- Plant Industry, The Commonwealth Scientific and Industrial Research Organisation, Canberra, Australian Capital Territory, Australia
- School of Biological Sciences, University of Sydney, Sydney, New South Wales, Australia
| | - Kenlee Nakasugi
- School of Biological Sciences, University of Sydney, Sydney, New South Wales, Australia
| | - Ross N. Crowhurst
- Breeding and Genomics, The New Zealand Institute for Plant and Food Research Limited, Mt Albert, Auckland, New Zealand
| | - Elena Hilario
- Breeding and Genomics, The New Zealand Institute for Plant and Food Research Limited, Mt Albert, Auckland, New Zealand
| | - Alexander B. Zwart
- Mathematics, Informatics and Statistics, The Commonwealth Scientific and Industrial Research Organisation, Canberra, Australian Capital Territory, Australia
| | - Roger P. Hellens
- Breeding and Genomics, The New Zealand Institute for Plant and Food Research Limited, Mt Albert, Auckland, New Zealand
| | - Jennifer M. Taylor
- Plant Industry, The Commonwealth Scientific and Industrial Research Organisation, Canberra, Australian Capital Territory, Australia
| | - Peter M. Waterhouse
- Plant Industry, The Commonwealth Scientific and Industrial Research Organisation, Canberra, Australian Capital Territory, Australia
- School of Molecular Bioscience, School of Biological Sciences, University of Sydney, Sydney, New South Wales, Australia
| | - Craig C. Wood
- Plant Industry, The Commonwealth Scientific and Industrial Research Organisation, Canberra, Australian Capital Territory, Australia
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91
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Romanel E, Silva TF, Corrêa RL, Farinelli L, Hawkins JS, Schrago CEG, Vaslin MFS. Global alteration of microRNAs and transposon-derived small RNAs in cotton (Gossypium hirsutum) during Cotton leafroll dwarf polerovirus (CLRDV) infection. PLANT MOLECULAR BIOLOGY 2012; 80:443-60. [PMID: 22987114 DOI: 10.1007/s11103-012-9959-1] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/15/2012] [Accepted: 08/22/2012] [Indexed: 05/13/2023]
Abstract
Small RNAs (sRNAs) are a class of non-coding RNAs ranging from 20- to 40-nucleotides (nts) that are present in most eukaryotic organisms. In plants, sRNAs are involved in the regulation of development, the maintenance of genome stability and the antiviral response. Viruses, however, can interfere with and exploit the silencing-based regulatory networks, causing the deregulation of sRNAs, including small interfering RNAs (siRNAs) and microRNAs (miRNAs). To understand the impact of viral infection on the plant sRNA pathway, we deep sequenced the sRNAs in cotton leaves infected with Cotton leafroll dwarf virus (CLRDV), which is a member of the economically important virus family Luteoviridae. A total of 60 putative conserved cotton miRNAs were identified, including 19 new miRNA families that had not been previously described in cotton. Some of these miRNAs were clearly misregulated during viral infection, and their possible role in symptom development and disease progression is discussed. Furthermore, we found that the 24-nt heterochromatin-associated siRNAs were quantitatively and qualitatively altered in the infected plant, leading to the reactivation of at least one cotton transposable element. This is the first study to explore the global alterations of sRNAs in virus-infected cotton plants. Our results indicate that some CLRDV-induced symptoms may be correlated with the deregulation of miRNA and/or epigenetic networks.
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Affiliation(s)
- Elisson Romanel
- Departamento de Genética, Instituto de Biologia, Universidade Federal do Rio de Janeiro, Rio de Janeiro, Brazil.
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92
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Alcaide-Loridan C, Jupin I. Ubiquitin and plant viruses, let's play together! PLANT PHYSIOLOGY 2012; 160:72-82. [PMID: 22802610 PMCID: PMC3440231 DOI: 10.1104/pp.112.201905] [Citation(s) in RCA: 90] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/05/2023]
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