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Wang MB, Smith NA. Satellite RNA pathogens of plants: impacts and origins-an RNA silencing perspective. WILEY INTERDISCIPLINARY REVIEWS-RNA 2015; 7:5-16. [PMID: 26481458 DOI: 10.1002/wrna.1311] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/03/2015] [Revised: 09/15/2015] [Accepted: 09/16/2015] [Indexed: 11/09/2022]
Abstract
Viral satellite RNAs (satRNAs) are among the smallest RNA pathogens in plants. They have little or no protein-coding capacity but can have a major impact on the host plants through trilateral interactions with helper viruses and host plants. Studies around the 1980s revealed much of what we know about satRNAs: they can affect helper virus accumulation, modulate helper virus-induced disease symptoms, and induce their own symptoms with the assistance of helper viruses which depend on specific nucleotide sequences of their genome and host species. The molecular basis of these satRNA-caused impacts and the origin of satRNAs have yet to be fully understood and revealed, but recent understanding of the antiviral RNA silencing pathways and advancement in RNA and DNA sequencing technologies have provided new avenues and opportunities to examine these unanswered questions. These RNA silencing-based studies have revealed the existence of cross silencing between some satRNAs and helper viruses, the downregulation of helper virus-encoded suppressor (VSR) of RNA silencing or inhibition/enhancement of VSR activity by satRNAs, the silencing of host-encoded genes by satRNA-derived small interfering RNA (siRNAs), and the presence of satRNA-like small RNAs in uninfected host plants. These findings have provided alternative RNA silencing-based models to explain the pathogenicity and origin of satRNAs. WIREs RNA 2016, 7:5-16. doi: 10.1002/wrna.1311 For further resources related to this article, please visit the WIREs website.
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Affiliation(s)
- Ming-Bo Wang
- Commonwealth Scientific and Industrial Research Organisation (CSIRO) Agriculture Flagship, Canberra, ACT 2601, Australia
| | - Neil A Smith
- Commonwealth Scientific and Industrial Research Organisation (CSIRO) Agriculture Flagship, Canberra, ACT 2601, Australia
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Zhu H, Guo H. The role of virus-derived small interfering RNAs in RNA silencing in plants. SCIENCE CHINA-LIFE SCIENCES 2012; 55:119-25. [DOI: 10.1007/s11427-012-4281-3] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/30/2011] [Accepted: 12/28/2011] [Indexed: 01/09/2023]
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Sturbois B, Dubrana-Ourabah MP, Gombert J, Lasseur B, Macquet A, Faure C, Bendahmane A, Baurès I, Candresse T. Identification and characterization of tomato mutants affected in the Rx-mediated resistance to PVX isolates. MOLECULAR PLANT-MICROBE INTERACTIONS : MPMI 2012; 25:341-54. [PMID: 22088194 DOI: 10.1094/mpmi-07-11-0181] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/23/2023]
Abstract
Five tomato mutants affected in the Rx-mediated resistance against Potato virus X (PVX) were identified by screening a mutagenized population derived from a transgenic, Rx1-expressing 'Micro-Tom' line. Contrary to their parental line, they failed to develop lethal systemic necrosis upon infection with the virulent PVX-KH2 isolate. Sequence analysis and quantitative reverse-transcription polymerase chain reaction experiments indicated that the mutants are not affected in the Rx1 transgene or in the Hsp90, RanGap1 and RanGap2, Rar1 and Sgt1 genes. Inoculation with the PVX-CP4 avirulent isolate demonstrated that the Rx1 resistance was still effective in the mutants. In contrast, the virulent PVX-KH2 isolate accumulation was readily detectable in all mutants, which could further be separated in two groups depending on their ability to restrict the accumulation of PVX-RR, a mutant affected at two key positions for Rx1 elicitor activity. Finally, transient expression of the viral capsid protein elicitor indicated that the various mutants have retained the ability to mount an Rx1-mediated hypersensitive response. Taken together, the results obtained are consistent with a modification of the specificity or intensity of the Rx1-mediated response. The five Micro-Tom mutants should provide very valuable resources for the identification of novel tomato genes affecting the functioning of the Rx gene.
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Affiliation(s)
- Bénédicte Sturbois
- URGV, Unité de Recherche en Génomique Végétale, Université d'Evry d'Essonne, INRA, France.
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Navarro B, Gisel A, Rodio ME, Delgado S, Flores R, Di Serio F. Viroids: how to infect a host and cause disease without encoding proteins. Biochimie 2012; 94:1474-80. [PMID: 22738729 DOI: 10.1016/j.biochi.2012.02.020] [Citation(s) in RCA: 58] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2011] [Accepted: 02/16/2012] [Indexed: 10/28/2022]
Abstract
Despite being composed by a single-stranded, circular, non-protein-coding RNA of just 246-401 nucleotides (nt), viroids can incite in their host plants symptoms similar to those caused by DNA and RNA viruses, which have genomes at least 20-fold bigger and encode proteins. On the other hand, certain non-protein-coding plant satellite RNAs display structural similarities with viroids but for replication and transmission they need to parasitize specific helper viruses (modifying concomitantly the symptoms they induce). While phenotypic alterations accompanying infection by viruses may partly result from expressing the proteins they code for, how the non-protein-coding viroids (and satellite RNAs) cause disease remains a conundrum. Initial ideas on viroid pathogenesis focused on a direct interaction of the genomic RNA with host proteins resulting in their malfunction. With the advent of RNA silencing, it was alternatively proposed that symptoms could be produced by viroid-derived small RNAs (vd-sRNAs) -generated by the host defensive machinery- targeting specific host mRNA or DNA sequences for post-transcriptional or transcriptional gene silencing, respectively, a hypothesis that could also explain pathogenesis of non-protein-coding satellite RNAs. Evidence sustaining this view has been circumstantial, but recent data provide support for it in two cases: i) the yellow symptoms associated with a specific satellite RNA result from a 22-nt small RNA (derived from the 24-nt fragment of the satellite genome harboring the pathogenic determinant), which is complementary to a segment of the mRNA of the chlorophyll biosynthetic gene CHLI and targets it for cleavage by the RNA silencing machinery, and ii) two 21-nt vd-sRNAS containing the pathogenic determinant of the albino phenotype induced by a chloroplast-replicating viroid target for cleavage the mRNA coding for the chloroplastic heat-shock protein 90 via RNA silencing too. This evidence, which is compelling for the satellite RNA, does not exclude alternative mechanisms.
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Affiliation(s)
- Beatriz Navarro
- Istituto di Virologia Vegetale (CNR), Unità Organizzativa di Bari, Via Amendola 165/A, 70126 Bari, Italy
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Hou WN, Duan CG, Fang RX, Zhou XY, Guo HS. Satellite RNA reduces expression of the 2b suppressor protein resulting in the attenuation of symptoms caused by Cucumber mosaic virus infection. MOLECULAR PLANT PATHOLOGY 2011; 12:595-605. [PMID: 21722297 PMCID: PMC6640352 DOI: 10.1111/j.1364-3703.2010.00696.x] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/05/2023]
Abstract
Satellite RNAs (satRNAs) depend on cognate helper viruses for replication, encapsidation, movement and transmission. Many satRNAs with different symptom modulation effects have been reported. The pathogenicity of satRNAs is thought to be the result of a direct interaction among the satRNA, helper viruses and host factors by unknown mechanisms. To understand the effect of satRNA of Cucumber mosaic virus (a severe field ShanDong strain, SD-CMV) on pathogenicity, and the possible involvement of host RNA silencing pathways in pathogenicity, we constructed biologically active CMV cDNA clones and a CMV-Δ2b mutant lacking the open reading frame of 2b, a silencing suppressor protein, in order to infect Nicotiana benthamiana and Arabidopsis with or without SD-satRNA. We found that SD-satRNA reduced the accumulation of the 2b protein and its coding RNA4A and attenuated the yellowing caused by SD-CMV infection. Small RNA analysis indicated that the 2b protein interfered with RNA silencing, specifically in the synthesis of CMV RNA3-derived small interfering RNAs (R3-siRNAs). The accumulation of R3-siRNAs in CMV-Δ2b infection was reduced in the presence of satRNA, for which greater accumulation of satRNA-derived siRNAs (satsiRNAs) was detected. Our results suggest that abundant SD-satRNA serving as target for RNA silencing may play a role in protecting helper CMV RNA, especially, subgenomic RNA4, from being targeted by RNA silencing. This compensates for the increase in RNA silencing resulting from the reduction in expression of the 2b suppressor in the presence of satRNA. Our data provide evidence that a plant silencing mechanism is involved in the pathogenicity of satRNA.
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Affiliation(s)
- Wei-Na Hou
- State Key Laboratory of Plant Genomics and National Center for Plant Gene Research (Beijing), Institute of Microbiology, Chinese Academy of Sciences, China
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Smith NA, Eamens AL, Wang MB. Viral small interfering RNAs target host genes to mediate disease symptoms in plants. PLoS Pathog 2011; 7:e1002022. [PMID: 21573142 PMCID: PMC3088724 DOI: 10.1371/journal.ppat.1002022] [Citation(s) in RCA: 193] [Impact Index Per Article: 14.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2010] [Accepted: 02/15/2011] [Indexed: 12/25/2022] Open
Abstract
The Cucumber mosaic virus (CMV) Y-satellite RNA (Y-Sat) has a small non-protein-coding RNA genome that induces yellowing symptoms in infected Nicotiana tabacum (tobacco). How this RNA pathogen induces such symptoms has been a longstanding question. We show that the yellowing symptoms are a result of small interfering RNA (siRNA)-directed RNA silencing of the chlorophyll biosynthetic gene, CHLI. The CHLI mRNA contains a 22-nucleotide (nt) complementary sequence to the Y-Sat genome, and in Y-Sat-infected plants, CHLI expression is dramatically down-regulated. Small RNA sequencing and 5' RACE analyses confirmed that this 22-nt sequence was targeted for mRNA cleavage by Y-Sat-derived siRNAs. Transformation of tobacco with a RNA interference (RNAi) vector targeting CHLI induced Y-Sat-like symptoms. In addition, the symptoms of Y-Sat infection can be completely prevented by transforming tobacco with a silencing-resistant variant of the CHLI gene. These results suggest that siRNA-directed silencing of CHLI is solely responsible for the Y-Sat-induced symptoms. Furthermore, we demonstrate that two Nicotiana species, which do not develop yellowing symptoms upon Y-Sat infection, contain a single nucleotide polymorphism within the siRNA-targeted CHLI sequence. This suggests that the previously observed species specificity of Y-Sat-induced symptoms is due to natural sequence variation in the CHLI gene, preventing CHLI silencing in species with a mismatch to the Y-Sat siRNA. Taken together, these findings provide the first demonstration of small RNA-mediated viral disease symptom production and offer an explanation of the species specificity of the viral disease.
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MESH Headings
- Agrobacterium tumefaciens/genetics
- Amino Acid Sequence
- Down-Regulation
- Gene Silencing
- High-Throughput Nucleotide Sequencing
- Host-Pathogen Interactions
- Lyases/genetics
- Molecular Sequence Data
- Plant Diseases/genetics
- Plant Diseases/virology
- Plant Viruses/physiology
- Plants, Genetically Modified/enzymology
- Plants, Genetically Modified/genetics
- Plants, Genetically Modified/virology
- Plasmids
- RNA, Messenger/genetics
- RNA, Messenger/metabolism
- RNA, Satellite/genetics
- RNA, Satellite/metabolism
- RNA, Small Interfering/genetics
- RNA, Small Interfering/metabolism
- RNA, Viral/genetics
- RNA, Viral/metabolism
- Nicotiana/enzymology
- Nicotiana/genetics
- Nicotiana/virology
- Virus Replication
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Shimura H, Pantaleo V, Ishihara T, Myojo N, Inaba JI, Sueda K, Burgyán J, Masuta C. A viral satellite RNA induces yellow symptoms on tobacco by targeting a gene involved in chlorophyll biosynthesis using the RNA silencing machinery. PLoS Pathog 2011; 7:e1002021. [PMID: 21573143 PMCID: PMC3088725 DOI: 10.1371/journal.ppat.1002021] [Citation(s) in RCA: 214] [Impact Index Per Article: 16.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2010] [Accepted: 02/23/2011] [Indexed: 12/25/2022] Open
Abstract
Symptoms on virus-infected plants are often very specific to the given virus. The molecular mechanisms involved in viral symptom induction have been extensively studied, but are still poorly understood. Cucumber mosaic virus (CMV) Y satellite RNA (Y-sat) is a non-coding subviral RNA and modifies the typical symptom induced by CMV in specific hosts; Y-sat causes a bright yellow mosaic on its natural host Nicotiana tabacum. The Y-sat-induced yellow mosaic failed to develop in the infected Arabidopsis and tomato plants suggesting a very specific interaction between Y-sat and its host. In this study, we revealed that Y-sat produces specific short interfering RNAs (siRNAs), which interfere with a host gene, thus inducing the specific symptom. We found that the mRNA of tobacco magnesium protoporphyrin chelatase subunit I (ChlI, the key gene involved in chlorophyll synthesis) had a 22-nt sequence that was complementary to the Y-sat sequence, including four G-U pairs, and that the Y-sat-derived siRNAs in the virus-infected plant downregulate the mRNA of ChlI by targeting the complementary sequence. ChlI mRNA was also downregulated in the transgenic lines that express Y-sat inverted repeats. Strikingly, modifying the Y-sat sequence in order to restore the 22-nt complementarity to Arabidopsis and tomato ChlI mRNA resulted in yellowing symptoms in Y-sat-infected Arabidopsis and tomato, respectively. In 5'-RACE experiments, the ChlI transcript was cleaved at the expected middle position of the 22-nt complementary sequence. In GFP sensor experiments using agroinfiltration, we further demonstrated that Y-sat specifically targeted the sensor mRNA containing the 22-nt complementary sequence of ChlI. Our findings provide direct evidence that the identified siRNAs derived from viral satellite RNA directly modulate the viral disease symptom by RNA silencing-based regulation of a host gene.
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MESH Headings
- Arabidopsis/genetics
- Arabidopsis/virology
- Base Sequence
- Capsicum/genetics
- Capsicum/virology
- Chlorophyll/biosynthesis
- Chlorophyll/genetics
- Cucumber Mosaic Virus Satellite/genetics
- Cucumber Mosaic Virus Satellite/metabolism
- Cucumovirus/metabolism
- Cucumovirus/pathogenicity
- Down-Regulation
- Gene Expression Regulation, Plant
- Genes, Plant
- Host-Pathogen Interactions
- Lyases/genetics
- Lyases/metabolism
- Solanum lycopersicum/genetics
- Solanum lycopersicum/virology
- Molecular Sequence Data
- Phenotype
- Plant Diseases/genetics
- Plant Diseases/virology
- Plants, Genetically Modified/enzymology
- Plants, Genetically Modified/genetics
- Plants, Genetically Modified/virology
- RNA Interference
- RNA, Messenger/genetics
- RNA, Messenger/metabolism
- RNA, Small Interfering/genetics
- RNA, Small Interfering/metabolism
- RNA, Viral/genetics
- RNA, Viral/metabolism
- Nicotiana/enzymology
- Nicotiana/genetics
- Nicotiana/virology
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Affiliation(s)
- Hanako Shimura
- Research Faculty of Agriculture, Hokkaido
University, Kita-ku, Sapporo, Japan
| | | | - Takeaki Ishihara
- Research Faculty of Agriculture, Hokkaido
University, Kita-ku, Sapporo, Japan
| | - Nobutoshi Myojo
- Research Faculty of Agriculture, Hokkaido
University, Kita-ku, Sapporo, Japan
| | - Jun-ichi Inaba
- Research Faculty of Agriculture, Hokkaido
University, Kita-ku, Sapporo, Japan
| | - Kae Sueda
- Research Faculty of Agriculture, Hokkaido
University, Kita-ku, Sapporo, Japan
| | | | - Chikara Masuta
- Research Faculty of Agriculture, Hokkaido
University, Kita-ku, Sapporo, Japan
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8
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Abstract
Cross-protection is a phenomenon in which infection of a plant with a mild virus or viroid strain protects it from disease resulting from a subsequent encounter with a severe strain of the same virus or viroid. In this chapter, we review the history of cross-protection with regard to the development of ideas concerning its likely mechanisms, including RNA silencing and exclusion, and its influence on the early development of genetically engineered virus resistance. We also examine examples of the practical use of cross-protection in averting crop losses due to viruses, as well as the use of satellite RNAs to ameliorate the impact of virus-induced diseases. We also discuss the potential of cross-protection to contribute in future to the maintenance of crop health in the face of emerging virus diseases and related threats to agricultural production.
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Baurès I, Candresse T, Leveau A, Bendahmane A, Sturbois B. The Rx gene confers resistance to a range of potexviruses in transgenic Nicotiana plants. MOLECULAR PLANT-MICROBE INTERACTIONS : MPMI 2008; 21:1154-64. [PMID: 18700820 DOI: 10.1094/mpmi-21-9-1154] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/18/2023]
Abstract
Rx-mediated resistance was analyzed in Rx-expressing transgenic Nicotiana plants. The infection outcome of nine Potato virus X isolates mutated at amino acid positions 121 and 127 of the coat protein (CP) confirmed the key role of these amino acids but provided a more complex picture than previously reported. In particular, in Rx-expressing Nicotiana spp., eliciting activity modulated by amino acid 121 was conditioned by the nature of amino acid 127. These results suggest that the specificity of recognition might be modulated by host factors that are somehow subtly modified between Rx-expressing potato and Rx-expressing transgenic Nicotiana plants. Moreover, the CP of three Potexviruses, Narcissus mosaic virus (NMV), White clover mosaic virus (WClMV), and Cymbidium mosaic virus (CymMV), are all recognized by the Rx-based machinery and able to trigger an Rx-dependant hypersensitive response. A smaller elicitor of 90 amino acids was identified in the CP of NMV and WClMV, which contains the previously identified key positions 121 and 127. This elicitor is only weakly conserved (approximately 40% identity) among the CP of the various recognized viruses, suggesting that the Rx molecular machinery targets a conserved structural element of the Potexvirus CP rather than a conserved amino acid motif.
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10
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Baulcombe DC. Short silencing RNA: the dark matter of genetics? COLD SPRING HARBOR SYMPOSIA ON QUANTITATIVE BIOLOGY 2007; 71:13-20. [PMID: 17381275 DOI: 10.1101/sqb.2006.71.052] [Citation(s) in RCA: 33] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
Abstract
Plants and animals have single-stranded silencing RNAs (sRNAs) of 21-25 nucleotides in length that are derived from a double-stranded (ds)RNA precursor by Dicer (DCL) processing. These RNAs are the guide RNA for nucleases of the AGO class that cleave targeted RNA in a nucleotide sequence-specific manner. The cleaved RNAs are then degraded further or they are the template for an RNA-dependent RNA polymerase (RDR) that generates a dsRNA. In this paper, I discuss the possibility that this RDR-generated dsRNA initiates a cascade in which there are multiple rounds of secondary sRNA production. I propose that these secondary sRNAs feature in mechanisms that can either buffer mRNA populations against change or, in certain circumstances, mediate extensive changes in mRNA populations. The RNA cascades may also have RNA-mediated epigenetic characteristics in addition to the DNA and chromatin transcriptional silencing potential that has been previously linked with RNA silencing.
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11
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Yamaguchi N, Seshimo Y, Yoshimoto E, Ahn HI, Ryu KH, Choi JK, Masuta C. Genetic mapping of the compatibility between a lily isolate of Cucumber mosaic virus and a satellite RNA. J Gen Virol 2005; 86:2359-2369. [PMID: 16033984 DOI: 10.1099/vir.0.81059-0] [Citation(s) in RCA: 17] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Five isolates of Cucumber mosaic virus (CMV) from Lilium sp. (lily), which were isolated from specimens in Japan, Korea and Taiwan, were unable to support satellite RNA (satRNA) accumulation. In order to map the CMV sequences that are involved in satRNA support, HL-CMV (Japanese lily isolate), Y-CMV (ordinary strain) and Y-satellite RNA (Y-sat) were used as the source material. The pseudorecombinants between Y-CMV and HL-CMV revealed that RNA1 was essential for satRNA replication in lily. The results of chimeric constructs and various mutations showed that two amino acid residues (at positions 876 and 891) in the 1a protein were the determinants for the inability of HL-CMV to support a satRNA. Specifically, Thr at position 876 had a more pronounced effect than Met at position 891. Specific changes in RNA sequence were also detected in the 3' terminus of Y-sat and these particular alterations allowed it to be supported by HL-CMV. It is believed that, through evolution, the adaptation of CMV to lily resulted in the introduction of amino acid changes in the 1a protein, changes that coincidentally affected the ability of lily CMV to support satRNAs.
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Affiliation(s)
- Naoya Yamaguchi
- Graduate School of Agriculture, Hokkaido University, Sapporo 060-8589, Japan
| | - Yuko Seshimo
- Graduate School of Agriculture, Hokkaido University, Sapporo 060-8589, Japan
| | - Eri Yoshimoto
- Graduate School of Agriculture, Hokkaido University, Sapporo 060-8589, Japan
| | - Hong Il Ahn
- Graduate School of Biotechnology, Korea University, Seoul 139-774, Korea
| | - Ki Hyun Ryu
- Plant Virus GenBank, Division of Environmental and Life Sciences, Seoul Women's University, Seoul, 139-774, Korea
| | - Jang Kyung Choi
- Division of Biological Environment, Kangwon National University, Chunchon 200-701, Korea
| | - Chikara Masuta
- Graduate School of Agriculture, Hokkaido University, Sapporo 060-8589, Japan
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12
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Abstract
Research on the molecular biology of cucumoviruses and their plant-virus interactions has been very extensive in the last decade. Cucumovirus genome structures have been analyzed, giving new insights into their genetic variability, evolution, and taxonomy. A new viral gene has been discovered, and its role in promoting virus infection has been delineated. The localization and various functions of each viral-encoded gene product have been established. The particle structures of Cucumber mosaic virus (CMV) and Tomato aspermy virus have been determined. Pathogenicity domains have been mapped, and barriers to virus infection have been localized. The movement pathways of the viruses in some hosts have been discerned, and viral mutants affecting the movement processes have been identified. Host responses to viral infection have been characterized, both temporally and spatially. Progress has been made in determining the mechanisms of replication, gene expression, and transmission of CMV. The pathogenicity determinants of various satellite RNAs have been characterized, and the importance of secondary structure in satellite RNA-mediated interactions has been recognized. Novel plant genes specifying resistance to infection by CMV have been identified. In some cases, these genes have been mapped, and one resistance gene to CMV has been isolated and characterized. Pathogen-derived resistance has been demonstrated against CMV using various segments of the CMV genome, and the mechanisms of some of these forms of resistances have been analyzed. Finally, the nature of synergistic interactions between CMV and other viruses has been characterized. This review highlights these various achievements in the context of the previous work on the biology of cucumoviruses and their interactions with plants.
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Affiliation(s)
- Peter Palukaitis
- Gene Expression Programme, Scottish Crop Research Institute, Invergowrie, Dundee, DD2 5DA, United Kingdom
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13
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García-Arenal F, Palukaitis P. Structure and functional relationships of satellite RNAs of cucumber mosaic virus. Curr Top Microbiol Immunol 1999; 239:37-63. [PMID: 9893368 DOI: 10.1007/978-3-662-09796-0_3] [Citation(s) in RCA: 41] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Affiliation(s)
- F García-Arenal
- Departamento de Biotecnología, E.T.S.I. Agrónomos, Universidad Politécnica de Madrid, Ciudad Universitaria, Spain
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14
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Tousignant ME, Kaper JM. Cucumber mosaic virus-associated RNA 5. XIII.--Opposite necrogenicities in tomato of variants with large 5' half insertion/deletion regions. RESEARCH IN VIROLOGY 1993; 144:349-60. [PMID: 8284513 DOI: 10.1016/s0923-2516(06)80050-6] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/29/2023]
Abstract
Two satellite RNA of cucumber mosaic virus (CMV) designated J876-CARNA-5 (for cucumber mosaic virus-associated RNA-5) and D27-CARNA-5 have been molecularly and biologically characterized. J876-CARNA-5 (387 nucleotides (nt)) and D27-CARNA-5 (391 nt) have nearly identical 5' half insertion/deletion regions where 120 nt replace approximately 70 nt of D-CARNA-5 (335 nt), the first variant described and sequenced. J876-CARNA-5 possesses the 15-nt conserved sequence element in its 3' half which is present in all tomato necrogenic variants and induces the same level of necrosis in tomatoes as the prototype necrogenic D-CARNA-5. D27-CARNA-5 lacks the 3' half necrosis-determining element and attenuates the CMV symptoms in tomato. Transcripts of cloned cDNA of J876-CARNA-5 were stably propagated in tomato in the presence of CMV-1. Purified J876-CARNA-5 progeny, inoculated with CMV-1 in a quantitative bioassay, induced tomato necrosis at the same dilution level as the natural satellite. Several computer-generated secondary structures of CMV satellites were examined and the possible correlation of a defined secondary structural element with necrosis induction is discussed.
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Affiliation(s)
- M E Tousignant
- Molecular Plant Pathology Laboratory, U.S. Department of Agriculture, Beltsville, Maryland 20705
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15
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Naidu RA, Collins GB, Ghabrial SA. Peanut stunt virus satellite RNA: analysis of sequences that affect symptom attenuation in tobacco. Virology 1992; 189:668-77. [PMID: 1641984 DOI: 10.1016/0042-6822(92)90590-l] [Citation(s) in RCA: 17] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Abstract
The V-satellite RNA (V-satRNA) of peanut stunt virus (PSV) has no effect on symptoms produced in tobacco by PSV. In contast, the G-satRNA induced complete or nearly complete suppression of systemic symptom development. Because G-satRNA differs from V-satRNA in only five nucleotide positions, these two satRNAs provide excellent material for investigating the molecular basis of satRNA-mediated symptom attenuation. For this purpose, we constructed transcription vectors containing full-length cDNA clones from which infectious RNA transcripts can be synthesized in vitro, and produced chimeric and mutant satRNA molecules. Although an A----C substitution at position 362 of the V-satRNA molecule delayed systemic symptom development and reduced symptom severity, changes at both nucleotide positions 226 (C----U) and 362 (A----C) of V-satRNA were required for suppression of systemic symptom development. Our results are consistent with the idea that PSV satRNAs are noncoding molecules that exert their biological activities by directly interacting with host/viral components.
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Affiliation(s)
- R A Naidu
- Department of Plant Pathology, University of Kentucky, Lexington 40546
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16
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Roossinck MJ, Sleat D, Palukaitis P. Satellite RNAs of plant viruses: structures and biological effects. Microbiol Rev 1992; 56:265-79. [PMID: 1620065 PMCID: PMC372867 DOI: 10.1128/mr.56.2.265-279.1992] [Citation(s) in RCA: 94] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
Abstract
Plant viruses often contain parasites of their own, referred to as satellites. Satellite RNAs are dependent on their associated (helper) virus for both replication and encapsidation. Satellite RNAs vary from 194 to approximately 1,500 nucleotides (nt). The larger satellites (900 to 1,500 nt) contain open reading frames and express proteins in vitro and in vivo, whereas the smaller satellites (194 to 700 nt) do not appear to produce functional proteins. The smaller satellites contain a high degree of secondary structure involving 49 to 73% of their sequences, with the circular satellites containing more base pairing than the linear satellites. Many of the smaller satellites produce multimeric forms during replication. There are various models to account for their formation and role in satellite replication. Some of these smaller satellites encode ribozymes and are able to undergo autocatalytic cleavage. The enzymology of satellite replication is poorly understood, as is the replication of their helper viruses. In many cases the coreplication of satellites suppresses the replication of the helper virus genome. This is usually paralleled by a reduction in the disease induced by the helper virus; however, there are notable exceptions in which the satellite exacerbates the pathogenicity of the helper virus, albeit on only a limited number of hosts. The ameliorative satellites are being assessed as biocontrol agents of virus-induced disease. In greenhouse studies, satellites have been known to "spontaneously" appear in virus cultures. The possible origin of satellites will be briefly considered.
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Affiliation(s)
- M J Roossinck
- Noble Foundation, Plant Biology Division, Ardmore, Oklahoma 73402
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Kaper JM. Satellite-induced viral symptom modulation in plants: a case of nested parasitic nucleic acids competing for genetic expression. RESEARCH IN VIROLOGY 1992; 143:5-10. [PMID: 1565856 DOI: 10.1016/s0923-2516(06)80070-1] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
Affiliation(s)
- J M Kaper
- Microbiology and Plant Pathology Laboratory, US Dept of Agriculture, Beltsville, MD 20705
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18
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Affiliation(s)
- P Palukaitis
- Department of Plant Pathology, Cornell University, Ithaca, New York 14853
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19
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Fraile A, García-Arenal F. Secondary structure as a constraint on the evolution of a plant viral satellite RNA. J Mol Biol 1991; 221:1065-9. [PMID: 1719213 DOI: 10.1016/0022-2836(91)90916-t] [Citation(s) in RCA: 24] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Abstract
The genetic variability and evolution of the satellite RNA (satRNA) of cucumber mosaic virus (CMV) was analyzed. Twenty-five CMV-satRNAs compared clustered into three main groups, and no correlation was found between genetic proximity and other characteristics (pathogenicity, geographical origin) of the satRNAs. Values for the number of nucleotide substitutions per site between any two satRNAs suggest that divergence is checked by functional constraints. The analysis of mutations relative to an ancestral sequence, and the number of substitutions per site at first, second and third positions of codons in putative open reading frames, show that the variation of CMV-satRNAs does not follow a pattern typical of coding sequences, and indicates that preservation of the sequence of encoded products is not a constraint to evolution. On the other hand, when the observed variation was analyzed relative to a secondary structure model proposed for CMV-satRNAs, several lines of evidence indicated that the maintenance of the secondary structure is a constraint to evolution: the number of substitutions per site, the number of point insertions and deletions and the number of base substitutions that would disrupt base-pairing were significantly higher for unpaired than for base-paired positions. Also, compensatory mutations at base-paired positions occurred more frequently than expected from random. The results suggest that CMV-satRNAs are non-coding, functional RNAs whose biology would be determined by their direct interaction with components of the host and/or the helper virus.
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Affiliation(s)
- A Fraile
- Depto. de Patología Vegetal, E.T.S.I. Agrónomos, Ciudad Universitaria, Madrid, Spain
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20
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Collmer CW, Stenzler L, Fay N, Howell SH. Nonmutant forms of the avirulent satellite D of turnip crinkle virus are produced following inoculation of plants with mutant forms synthesized in vitro. Virology 1991; 183:251-9. [PMID: 1711258 DOI: 10.1016/0042-6822(91)90137-z] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Abstract
The avirulent satellite RNA D (sat D) of turnip crinkle virus (TCV) has been cloned as a copy DNA. RNA transcripts synthesized in vitro from the cloned cDNA are infectious when coinoculated with RNA transcripts of the cloned TCV genome. Sat D is the smallest and most likely the progenitor of the other TCV satellites and, in contrast to the virulent satellite RNA C (sat C), does not intensify viral symptoms. Mutant forms of sat D including internal deletions up to 50 bases yielded sat D in infected plants. However, sat D mutants were not recovered in mutant form, but reverted to normal size and sequence in infected turnip plants. Mutations at a site with homology to the catalytic strand of self-cleaving sequences in certain viroids and satellites appeared to confer virulence on sat D in that test plants showed severe crinkling and stunting normally associated with sat C. However, sat C appeared along with a restored form of sat D in the progeny RNAs of these severely infected plants. Sat C was presumably generated by recombination between sat D and the TCV genome. In contrast, when plants were inoculated with transcripts containing the equivalent mutations in sat C, sat C was recovered from infected plants in mutant form. These findings demonstrate the tendency for mutant forms of the avirulent satellite, sat D, to revert, but raise questions about the source of information used in the reversion process.
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Affiliation(s)
- C W Collmer
- Boyce Thompson Institute, Cornell University, Ithaca, New York 14853
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21
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Ziegler-Graff V, Guilford PJ, Baulcombe DC. Tobacco rattle virus RNA-1 29K gene product potentiates viral movement and also affects symptom induction in tobacco. Virology 1991; 182:145-55. [PMID: 2024461 DOI: 10.1016/0042-6822(91)90658-x] [Citation(s) in RCA: 34] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
Abstract
In order to investigate the function of the 29K protein of tobacco rattle virus (TRV), we introduced different mutations in the 29K protein gene and analyzed the biological properties of the subsequent transcripts in tobacco plants. Although none of the mutant RNAs was able to accumulate to a detectable level, the defects in the 29K protein could be complemented by coinoculation with wild-type TRV or tobacco mosaic virus (TMV). Complementation was also achieved in transgenic plants expressing the homologous TMV 30K protein which is involved in cell-to-cell movement, but without inducing distinctive symptoms. Transcripts of chimeric TRV clones containing duplicate genes for the 29K protein initiated infections with formation of necrotic lesions and the progeny retained only one copy of the gene. These experiments demonstrate that the 29K protein is not required for viral RNA replication and, because the TRV transcripts do not encode the coat protein, that the 29K and 30K proteins act on nonencapsidated RNA. In addition to potentiating viral movement, the TRV 29K protein may also play a role in symptom induction on tobacco.
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Affiliation(s)
- V Ziegler-Graff
- Institut de Biologie Moléculaire des Plantes du CNRS, Université Louis Pasteur, Strasbourg, France
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22
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Kaper JM, Tousignant ME, Geletka LM. Cucumber-mosaic-virus-associated RNA-5. XII. Symptom-modulating effect is codetermined by the helper virus satellite replication support function. RESEARCH IN VIROLOGY 1990; 141:487-503. [PMID: 2277868 DOI: 10.1016/0923-2516(90)90082-t] [Citation(s) in RCA: 16] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
In tomato, the disease-modulating effects of a cucumber mosaic virus (CMV) satellite isolate from Belgium, here designated T-CARNA-5 (CARNA-5 = CMV-associated RNA-5), were found to be different depending on the supporting helper virus strain. With two CMV strains, T-CARNA-5 induced lethal necrosis, but with a third strain from Ixora spp. (CMV-Ix), aggravated stunting was observed. However, the primary structure of the T-CARNA-5 contained within virus isolated from tobacco or tomato infected with each of these three CMV strains, conformed to the conserved sequence profile of CARNA-5 isolates which are necrogenic in tomato. Dilution endpoint bioassay of T-CARNA-5 established a direct cause-effect relationship between it and tomato necrosis or stunting, depending on the helper virus. Total nucleic acid extracts taken at different times from tomato plants infected with the above CMV strains and T- or S-CARNA-5 (used as non-necrogenic control) showed viral RNA, ssCARNA-5 and dsCARNA-5 to be present in significant amounts, but in sometimes dissimilar proportions depending on the combination; except in CMV-Ix/S-CARNA-5 infection where neither ss-nor dsCARNA-5 was found. The experiments established that CARNA-5 biological expression studies in CMV-infected tomato have to take into account the helper virus satellite replication support function, which may be a primary codeterminant of quantitative or qualitative differences in the symptom modulation observed.
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Affiliation(s)
- J M Kaper
- Microbiology and Plant Pathology Laboratory, US Department of Agriculture, Beltsville, MD 20705
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23
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Fraile A, Moriones E, García-Arenal F. Characterization of a satellite RNA associated with strain K8 of cucumber mosaic virus. Nucleic Acids Res 1990; 18:4593. [PMID: 1697067 PMCID: PMC331286 DOI: 10.1093/nar/18.15.4593] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022] Open
Affiliation(s)
- A Fraile
- Departamento de Patología Vegetal, E.T.S.I. Agrónomos, Madrid, Spain
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24
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Kobayashi S, Okada M. Complete cDNA sequence encoding mitochondrial large ribosomal RNA of Drosophila melanogaster. Nucleic Acids Res 1990; 18:4592. [PMID: 1697066 PMCID: PMC331285 DOI: 10.1093/nar/18.15.4592] [Citation(s) in RCA: 16] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022] Open
Affiliation(s)
- S Kobayashi
- Institute of Biological Sciences, University of Tsukuba, Ibaraki, Japan
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25
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Sleat DE, Palukaitis P. Site-directed mutagenesis of a plant viral satellite RNA changes its phenotype from ameliorative to necrogenic. Proc Natl Acad Sci U S A 1990; 87:2946-50. [PMID: 1691499 PMCID: PMC53810 DOI: 10.1073/pnas.87.8.2946] [Citation(s) in RCA: 45] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022] Open
Abstract
Comparison of the nucleotide sequences of cucumber mosaic virus (CMV) satellite RNAs, which induce necrosis on tomatoes, reveals a highly conserved region within their 3' halves. The sequence of WL1 satellite (WL1-sat) RNA, which attenuates CMV symptoms on tomatoes, differs from all necrogenic satellite RNAs at three nucleotide positions within this conserved region. These nucleotides were progressively mutated to determine what sequence is required for the induction of necrosis in tomatoes. Infectious transcripts from a cDNA clone of WL1-sat RNA, and its mutated derivatives, were assayed on tomato. Three of the four mutant satellite RNAs, in which two of the three nucleotides correspond to those present in necrogenic satellite RNAs, and the rest of the molecule corresponded to WL1-sat RNA, attenuated CMV symptoms on tomatoes, and were phenotypically identical to the parental WL1-sat RNA. One other mutant satellite RNA, in which all three mutated nucleotides corresponded to the sequence of necrogenic satellite RNAs and the rest of the molecule corresponded to WL1-sat RNA, induced a lethal necrosis on tomatoes. Necrosis was also observed when the same mutant satellite RNA was associated with a second CMV strain as helper virus. These results indicate that a single nucleotide change at any of the three nucleotides examined distinguishes necrogenic from nonnecrogenic satellite RNAs. This necrosis was similar to that induced by a naturally necrogenic satellite RNA. The various mutations did not modify the effect of WL1-sat RNA on the symptoms induced by CMV on tobacco or squash.
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Affiliation(s)
- D E Sleat
- Department of Plant Pathology, Cornell University, Ithaca, NY 14853
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26
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Gadani F, Mansky LM, Medici R, Miller WA, Hill JH. Genetic engineering of plants for virus resistance. Arch Virol 1990; 115:1-21. [PMID: 2248549 DOI: 10.1007/bf01310619] [Citation(s) in RCA: 29] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
Historically, control of plant virus disease has involved numerous strategies which have often been combined to provide effective durable resistance in the field. In recent years, the dramatic advances obtained in plant molecular virology have enhanced our understanding of viral genome organizations and gene functions. Moreover, genetic engineering of plants for virus resistance has recently provided promising additional strategies for control of virus disease. At present, the most promising of these has been the expression of coat-protein coding sequences in plants transformed with a coat protein gene. Other potential methods include the expression of anti-sense viral transcripts in transgenic plants, the application of artificial anti-sense mediated gene regulation to viral systems, and the expression of viral satellite RNAs, RNAs with endoribonuclease activity, antiviral antibody genes, or human interferon genes in plants.
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Affiliation(s)
- F Gadani
- Research and Development, EniChem S.p.A., Milan, Italy
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