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Balke I, Silamikelis I, Radovica-Spalvina I, Zeltina V, Resevica G, Fridmanis D, Zeltins A. Ryegrass mottle virus complete genome determination and development of infectious cDNA by combining two methods- 3' RACE and RNA-Seq. PLoS One 2023; 18:e0287278. [PMID: 38051715 DOI: 10.1371/journal.pone.0287278] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2023] [Accepted: 11/21/2023] [Indexed: 12/07/2023] Open
Abstract
Ryegrass mottle virus (RGMoV; genus: Sobemovirus) is a single-stranded positive RNA virus with a 30 nm viral particle size. It exhibits T = 3 symmetry with 180 coat protein (CP) subunits forming a viral structure. The RGMoV genome comprises five open reading frames that encode P1, Px, a membrane-anchored 3C-like serine protease, a viral genome-linked protein, P16, an RNA-dependent RNA polymerase, and CP. The RGMoV genome size varies, ranging from 4175 nt (MW411579.1) to 4253 nt (MW411579.1) in the deposited sequences. An earlier deposited RGMoV complete genome sequence of 4212 nt length (EF091714.1) was used to develop an infectious complementary DNA (icDNA) construct for in vitro gRNA transcription from the T7 promoter. However, viral infection was not induced when the transcribed gRNA was introduced into oat plants, indicating the potential absence of certain sequences in either the 5' or 3' untranslated regions (UTR) or both. The complete sequence of the 3' UTR was determined through 3' end RACE, while the 5' UTR was identified using high-throughput sequencing (HTS)-RNA-Seq to resolve the potential absences. Only the icDNA vector containing the newly identified UTR sequences proved infectious, resulting in typical viral infection symptoms and subsequent propagation of progeny viruses, exhibiting the ability to cause repeated infections in oat plants after at least one passage. The successful generation of icDNA highlighted the synergistic potential of utilizing both methods when a single approach failed. Furthermore, this study demonstrated the reliability of HTS as a method for determining the complete genome sequence of viral genomes.
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Affiliation(s)
- Ina Balke
- Plant Virus Protein Research Group, Latvian Biomedical Research and Study Centre, Riga, Latvia
| | - Ivars Silamikelis
- Bioinformatics Core Facility, Latvian Biomedical Research and Study Centre, Riga, Latvia
| | - Ilze Radovica-Spalvina
- Genome Centre, Genotyping and Sequencing Unit, Latvian Biomedical Research and Study Centre, Riga, Latvia
| | - Vilija Zeltina
- Plant Virology Group, Latvian Biomedical Research and Study Centre, Riga, Latvia
| | - Gunta Resevica
- Plant Virology Group, Latvian Biomedical Research and Study Centre, Riga, Latvia
| | - Davids Fridmanis
- "Exotic" Site Microbiome and G-Protein Coupled Receptor Functional Research Group, Latvian Biomedical Research and Study Centre, Riga, Latvia
| | - Andris Zeltins
- Plant Virology Group, Latvian Biomedical Research and Study Centre, Riga, Latvia
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2
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Isolation of velvet tobacco mottle virus capable of replication with and without a viroid-like RNA. Virology 2008; 148:381-4. [PMID: 18640583 DOI: 10.1016/0042-6822(86)90335-1] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/1985] [Accepted: 10/01/1985] [Indexed: 11/23/2022]
Abstract
Field isolates of velvet tobacco mottle virus (VTMoV) induce severe symptoms in Nicotiana clevelandii and encapsidate viroid-like RNA reported to be essential for virus infection. An isolate of the virus producing only mild symptoms on N. clevelandii and devoid of viroid-like RNA has now been isolated from a plant inoculated by a single viruliferous Cyrtopeltis nicotianae, the mirid vector. However, after adding viroid-like RNA isolated from normal VTMoV to the inoculum, the new isolate was shown to support the synthesis of, and encapsidated the viroid-like RNA, thereby reverting to virulence characteristic of the normal isolate. This indicates that the viroid-like RNA can behave as a satellite RNA of VTMoV. The data are discussed in relation to previously published conclusions that viroid-like RNA is essential for the infectivity of VTMoV.
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3
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Morris-Krsinich BA, Forster RL. Lucerne transient streak virus RNA and its translation in rabbit reticulocyte lysate and wheat germ extract. Virology 2008; 128:176-85. [PMID: 18639026 DOI: 10.1016/0042-6822(83)90328-8] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/1982] [Accepted: 03/24/1983] [Indexed: 10/26/2022]
Abstract
Two abundant, encapsidated RNAs of lucerne transient streak virus (LTSV) are the 1.5 x 10(6) molecular weight (Mr) linear RNA-1 and both circular (RNA-2) and linear (RNA-3) forms of a 0.15 x 10(6) Mr viroid-like RNA. Two additional discrete minor RNAs, Mr 0.35 x 10(6) and 0.07 x 10(6), and a heterogeneous mixture of RNAs in the Mr range 0.05 to 1.0 x 10(6) are reported. Principal polypeptides translated from unfractionated LTSV RNA in rabbit reticulocyte lysate were of Mr 105,000 (p105), 78,000 (p78), and 33,000 (p33), the last not easily detected after translation in wheat germ extracts. All apparently are encoded in RNA-1. However, p33, which was precipitated by antibody of LTSV particles and presumably is the major capsid protein, was more readily translated from a smaller, most likely the Mr 0.35 x 10(6), RNA. Partial proteolysis and other tests indicate that p105 has a carboxyl terminal extension of p78 amino acid sequences and that neither shares sequences with p33. No translation products were attributed to RNA-2, RNA-3 or the Mr 0.07 x 10(6) RNA.
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Affiliation(s)
- B A Morris-Krsinich
- Plant Diseases Division, Department of Scientific and Industrial Research, Private Bag, Auckland, New Zealand
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4
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Keese P, Bruening G, Symons RH. Comparative sequence and structure of circular RNAs from two isolates of lucerne transient streak virus. FEBS Lett 2001. [DOI: 10.1016/0014-5793(83)80443-8] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
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5
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Tien-Po, Davies C, Hatta T, Francki R. Viroid-like RNA encapsidated in lucerne transient streak virus. FEBS Lett 2001. [DOI: 10.1016/0014-5793(81)81196-9] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
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Affiliation(s)
- T Tamm
- Institute of Chemical Physics and Biophysics and Gene Technology Centre, Tallinn Technical University, EE12618 Tallinn, Estonia
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Symons RH, Randles JW. Encapsidated circular viroid-like satellite RNAs (virusoids) of plants. Curr Top Microbiol Immunol 1999; 239:81-105. [PMID: 9893370 DOI: 10.1007/978-3-662-09796-0_5] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
MESH Headings
- Base Sequence
- Blotting, Northern
- Electrophoresis, Polyacrylamide Gel
- Microscopy, Electron
- Models, Molecular
- Molecular Sequence Data
- Plant Viruses/genetics
- Polymerase Chain Reaction
- RNA, Satellite/biosynthesis
- RNA, Satellite/isolation & purification
- RNA, Satellite/ultrastructure
- RNA, Viral/biosynthesis
- RNA, Viral/isolation & purification
- RNA, Viral/ultrastructure
- Viroids/genetics
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Affiliation(s)
- R H Symons
- Department of Plant Science, Waite Institute, University of Adelaide, Glen Osmond, Australia
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Davies C, Haseloff J, Symons RH. Structure, self-cleavage, and replication of two viroid-like satellite RNAs (virusoids) of subterranean clover mottle virus. Virology 1990; 177:216-24. [PMID: 1693803 DOI: 10.1016/0042-6822(90)90475-7] [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: 12/28/2022]
Abstract
Both the genomic and viroid-like satellite RNAs (virusoids) from four subterranean clover mottle virus isolates described by Francki et al. were analyzed in detail. Restriction endonuclease mapping of cDNAs prepared from the genomic RNAs from all isolates showed that these RNAs are closely related if not identical. The two virusoids, which can occur together in the same isolate or individually, were sequenced and shown to be able to form highly base-paired viroid-like secondary structures. The left-hand portions of these structures are almost entirely homologous but the right-hand portions show little similarity. The plus, but not the minus, virusoid RNAs contain sequences that can form the hammerhead self-cleavage structure of certain other self-cleaving viroid, virusoid, and satellite RNAs. Plus, but not minus, RNA transcripts from cDNA clones self-cleaved essentially to completion at the predicted site during transcription in vitro. Northern blot analysis of infected leaf tissue extracts revealed the presence of an oligomeric series of plus RNAs (of monomer size and greater) but minus RNAs were present only as high molecular weight species of heterogeneous size. These findings are in agreement with the lack of minus RNA self-cleavage in vitro. Hence, these virusoid RNAs appear to replicate by a rolling-circle mechanism in which only the plus RNAs self-cleave to form monomeric RNAs.
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Affiliation(s)
- C Davies
- Department of Biochemistry, University of Adelaide, South Australia
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Forster AC, Symons RH. Self-cleavage of plus and minus RNAs of a virusoid and a structural model for the active sites. Cell 1987; 49:211-20. [PMID: 2436805 DOI: 10.1016/0092-8674(87)90562-9] [Citation(s) in RCA: 545] [Impact Index Per Article: 14.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
Virusoids are circular single-stranded RNAs dependent on plant viruses for replication and encapsidation. Virusoid replication appears to involve longer-than-unit-length plus and minus RNAs, indicating that unit-length plus RNA is generated by specific cleavage reactions. Here, we synthesize plus and minus partial-length RNAs of the 324-nucleotide virusoid from lucerne transient streak virus in vitro. Both RNAs self-cleave at a unique site in the presence of magnesium ions to give 5' hydroxyl and 2',3' cyclic phosphodiester termini. Conformations other than the native structures are necessary for cleavage. Similar secondary structures with considerable sequence homology are proposed for the active sites of these and other plant pathogenic RNAs. Our results are consistent with certain rolling-circle replication models.
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Hutchins CJ, Keese P, Visvader JE, Rathjen PD, McInnes JL, Symons RH. Comparison of multimeric plus and minus forms of viroids and virusoids. PLANT MOLECULAR BIOLOGY 1985; 4:293-304. [PMID: 24310879 DOI: 10.1007/bf02418248] [Citation(s) in RCA: 71] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/02/2023]
Abstract
In order to investigate the mechanism of replication of viroids and virusoids, we have compared the replication intermediates of three members of each group in nucleic acid extracts of infected plants. Viroids were avocado sunblotch viroid (ASBV), citrus exocortis viroid (CEV) and coconut cadang cadang viroid (CCCV). Virusoids were from velvet tobacco mottle virus (VTMoV), solanum nodiflorum mottle virus (SNMV) and lucerne transient streak virus (LTSV). Analysis of intermediates was by the Northern hybridization technique with single-strand DNA and RNA probes prepared from recombinant DNA clones. The results obtained are discussed in terms of current models of viroid and virusoid replication.The plus RNA species consisted of an oligomeric series up to decamers based on the unit of full-length viroid or virusoid, which was always the major component, except for CEV where only monomer and dimer species were found. In the case of ASBV and the virusoids of VTMoV and SNMV, a minor, multimeric series of components (X-bands) was superimposed on the main oligomeric series.The complementary minus species proved more difficult to detect and characterise, with each viroid and virusoid exhibiting a unique pattern on Northern hybridization. However, they all had greater than unit-length minus species. In addition, minus species analogous to the plus X-bands were found in ASBV and CEV. The experimental difficulties encountered in this work are discussed in terms of the problem of detecting minus species by Northern analysis in the presence of excess complementary plus species.
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Affiliation(s)
- C J Hutchins
- Adelaide University Centre for Gene Technology, Department of Biochemistry, University of Adelaide, 5000, Adelaide, South Australia, Australia
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Linthorst H, Kaper J. Circular satellite-RNA molecules in satellite of tobacco ringspot virus-infected tissue. Virology 1984; 137:206-10. [DOI: 10.1016/0042-6822(84)90026-6] [Citation(s) in RCA: 21] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/1984] [Accepted: 06/02/1984] [Indexed: 11/15/2022]
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12
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Electron Microscopy for the Identification of Plant Viruses in in Vitro Preparations. ACTA ACUST UNITED AC 1984. [DOI: 10.1016/b978-0-12-470207-3.50010-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register]
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13
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Chu P, Francki R. Chemical and serological comparison of the coat proteins of velvet tobacco mottle and solanum nodiflorum mottle viruses. Virology 1983; 129:350-6. [DOI: 10.1016/0042-6822(83)90174-5] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/1983] [Accepted: 06/05/1983] [Indexed: 11/30/2022]
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14
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Maule AJ, Hull R, Donson J. The application of spot hybridization to the detection of DNA and RNA viruses in plant tissues. J Virol Methods 1983; 6:215-24. [PMID: 6863467 DOI: 10.1016/0166-0934(83)90048-4] [Citation(s) in RCA: 99] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/22/2023]
Abstract
A solid-phase nucleic acid hybridization technique for the detection of DNA and RNA viruses in plant tissues is described. The method involves spotting crude samples onto nitrocellulose and using 12P-labelled DNA hybridization probes. The limit of sensitivity is 5-20 pg virus/spot or approximately 5 micrograms/g leaf tissue. The method is quantitative for DNA viruses in crude homogenates, but not for RNA viruses. The amount of cauliflower mosaic virus in infected leaves and protoplasts was estimated. The amplitude of spot hybridization to screening plant material from glasshouses and field is discussed.
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Gould A, Francki R, Randles J. Studies on encapsidated viroid-like RNA IV. requirement for infectivity and specificity of two RNA components from velvet tobacco mottle virus. Virology 1981; 110:420-6. [DOI: 10.1016/0042-6822(81)90072-6] [Citation(s) in RCA: 21] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 10/26/1980] [Indexed: 11/16/2022]
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