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Complete Genome Sequence of Clover Yellow Mosaic Virus Isolated from White Clover in Japan. Microbiol Resour Announc 2022; 11:e0032422. [PMID: 35608357 PMCID: PMC9202368 DOI: 10.1128/mra.00324-22] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022] Open
Abstract
Clover yellow mosaic virus (ClYMV) infecting white clover was isolated in Japan, and the complete genome sequence was determined.
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Xie J, Wei D, Jiang D, Fu Y, Li G, Ghabrial S, Peng Y. Characterization of debilitation-associated mycovirus infecting the plant-pathogenic fungus Sclerotinia sclerotiorum. J Gen Virol 2006; 87:241-249. [PMID: 16361437 DOI: 10.1099/vir.0.81522-0] [Citation(s) in RCA: 120] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
It was previously reported that three dsRNA segments, designated L, M and S, were isolated from Sclerotinia sclerotiorum strain Ep-1PN and that the M dsRNA segment was coincident with hypovirulence and debilitation of the fungal host. Here, the complete nucleotide sequence of the M dsRNA of 5419 nt, excluding the poly(A) tail, was determined. Sequence analysis revealed the occurrence of a single open reading frame (nt 93-5195) encoding a protein with significant similarity to the replicases of the 'alphavirus-like' supergroup of positive-strand RNA viruses. The M dsRNA-encoded putative replicase protein contained the conserved methyl transferase, helicase and RNA-dependent RNA polymerase (RdRp) domains characteristic of the replicases of potex-like plant viruses (flexiviruses) and Botrytis virus F (BVF), a flexuous rod mycovirus infecting the phytopathogenic fungus Botrytis cinerea. Furthermore, convincing evidence is presented showing that ascospore descendents derived from the debilitated strain Ep-1PN were devoid of dsRNA and exhibited normal colony morphology. Moreover, it was demonstrated that the debilitation phenotype was transmitted from the parental debilitated strain to its normal ascospore progeny via hyphal anastomosis. These results suggest that the M dsRNA from strain Ep-1PN is derived from the genomic RNA of a positive-strand RNA virus, which we designated Sclerotinia sclerotiorum debilitation-associated RNA virus (SsDRV). Although phylogenetic analysis of the conserved RdRp motifs verified that SsDRV is closely related to BVF and to the allexiviruses in the family Flexiviridae, SsDRV is distinct from these viruses, mainly based on the lack of coat protein and movement protein.
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Affiliation(s)
- Jun Xie
- National Key Laboratory of Agriculture Microbiology, Huazhong Agricultural University, Wuhan 430070, PR China
- Plant Pathology, College of Plant Science and Technology, Huazhong Agricultural University, Wuhan 430070, PR China
| | - Dongmei Wei
- National Key Laboratory of Agriculture Microbiology, Huazhong Agricultural University, Wuhan 430070, PR China
- Plant Pathology, College of Plant Science and Technology, Huazhong Agricultural University, Wuhan 430070, PR China
| | - Daohong Jiang
- National Key Laboratory of Agriculture Microbiology, Huazhong Agricultural University, Wuhan 430070, PR China
- Plant Pathology, College of Plant Science and Technology, Huazhong Agricultural University, Wuhan 430070, PR China
| | - Yanping Fu
- Plant Pathology, College of Plant Science and Technology, Huazhong Agricultural University, Wuhan 430070, PR China
| | - Guoqing Li
- National Key Laboratory of Agriculture Microbiology, Huazhong Agricultural University, Wuhan 430070, PR China
- Plant Pathology, College of Plant Science and Technology, Huazhong Agricultural University, Wuhan 430070, PR China
| | - Said Ghabrial
- Department of Plant Pathology, University of Kentucky, 201F Plant Science Building, 1405 Veterans Drive, University of Kentucky, Lexington, KY 40546-0312, USA
| | - Youliang Peng
- Department of Plant Pathology, China Agricultural University, Beijing 100092, PR China
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Howitt RLJ, Beever RE, Pearson MN, Forster RLS. Genome characterization of a flexuous rod-shaped mycovirus, Botrytis virus X, reveals high amino acid identity to genes from plant 'potex-like' viruses. Arch Virol 2005; 151:563-79. [PMID: 16172841 DOI: 10.1007/s00705-005-0621-y] [Citation(s) in RCA: 58] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2005] [Accepted: 07/04/2005] [Indexed: 10/25/2022]
Abstract
This study reports the molecular characterization of a flexuous rod-shaped mycovirus, Botrytis virus X (BVX), infecting the plant-pathogenic fungus, Botrytis cinerea. BVX contains a ssRNA genome of 6966 nucleotides, and a poly(A) tract at or very near the 3' terminus. Computer analysis of the genomic cDNA sequence of BVX revealed five potential open reading frames (ORFs). ORF1 showed significant amino acid sequence identity to the replicase proteins of plant 'potex-like' viruses, including 73% identity to the RNA-dependent RNA polymerase (RdRp) region of the allexivirus, garlic virus A (GarV-A). The C-terminal region of ORF3 shared amino acid homology with plant 'potex-like' coat proteins. The remaining ORFs did not reveal significant homology with known protein sequences. BVX differs substantially from Botrytis virus F (BVF), another flexuous rod-shaped mycovirus characterized from the same B. Cinerea isolate. It is proposed that the mycovirus BVX belongs to a new, as yet unassigned genus in the plant 'potex-like' virus group, distinct from BVF.
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Affiliation(s)
- R L J Howitt
- School of Biological Sciences, The University of Auckland, Auckland, New Zealand.
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Pillai-Nair N, Kim KH, Hemenway C. Cis-acting regulatory elements in the potato virus X 3' non-translated region differentially affect minus-strand and plus-strand RNA accumulation. J Mol Biol 2003; 326:701-20. [PMID: 12581634 PMCID: PMC7126608 DOI: 10.1016/s0022-2836(02)01369-4] [Citation(s) in RCA: 32] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/12/2023]
Abstract
The 72nt 3' non-translated region (NTR) of potato virus X (PVX) RNA is identical in all sequenced PVX strains and contains sequences that are conserved among all potexviruses. Computer folding of the 3' NTR sequence predicted three stem-loop structures (SL1, SL2, and SL3 in the 3' to 5' direction), which generally were supported by solution structure analyses. The importance of these sequence and/or structural elements to PVX RNA accumulation was further analyzed by inoculation of Nicotiana tabacum (NT-1) protoplasts with PVX transcripts containing mutations in the 3' NTR. Analyses of RNA accumulation by S(1) nuclease protection indicated that multiple sequence elements throughout the 3' NTR were important for minus-strand RNA accumulation. Formation of SL3 was required for accumulation of minus-strand RNA, whereas SL1 and SL2 formation were less important. However, sequences within all of these predicted structures were required for minus-strand RNA accumulation, including a conserved hexanucleotide sequence element in the loop of SL3, and the CU nucleotide in a U-rich sequence within SL2. In contrast, 13 nucleotides that were predicted to reside in SL1 could be deleted without any significant reduction in minus or plus-strand RNA levels. Potential polyadenylation signals (near upstream elements; NUEs) in the 3' NTR of PVX RNA were more important for plus-strand RNA accumulation than for minus-strand RNA accumulation. In addition, one of these NUEs overlapped with other sequence required for optimal minus-strand RNA levels. These data indicate that the PVX 3' NTR contains multiple, overlapping elements that influence accumulation of both minus and plus-strand RNA.
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Affiliation(s)
- Neeta Pillai-Nair
- Department of Molecular and Structural Biochemistry, North Carolina State University, Raleigh, NC 27695-7622, USA
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Compel P, Papp I, Bibó M, Fekete C, Hornok L. Genetic interrelationships and genome organization of double-stranded RNA elements of Fusarium poae. Virus Genes 1999; 18:49-56. [PMID: 10334037 DOI: 10.1023/a:1008069318838] [Citation(s) in RCA: 48] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
Abstract
The similar sized double-stranded RNA (dsRNA) elements present in vegetatively compatible strains of Fusarium poae were always genetically related, while vegetatively incompatible strains of the fungus contained either homologous or non-homologous dsRNAs of the same size. Electron microscopic observations revealed the co-existence of encapsidated and naked dsRNA elements in the same host. A mycovirus, named FUPO-1 was purified from strain A-11 and was found to contain two kinds of dsRNA segments, dsRNA 1 and dsRNA 2. The dsRNA genome of these segments was converted to cDNA clones by reverse transcription and the clones were subjected to sequence analysis. The single long open reading frame deduced from the sequence of dsRNA 1 showed similarities to the putative coat protein genes known from other mycoviruses, while conserved motifs of an RNA-dependent RNA polymerase were identified in the predicted amino acid sequence of dsRNA 2. The genome organization and certain sequence motifs of FUPO-1 show similarities to that of the Atkinsonella hypoxylon 2H virus and the FusoV mycovirus, members of the Partitiviridae family.
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Affiliation(s)
- P Compel
- Institute for Microbiology, Slovak Academy of Sciences, Bratislava, Slovakia
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Yeh TY, Lin BY, Chang YC, Hsu YH, Lin NS. A defective RNA associated with bamboo mosaic virus and the possible common mechanisms for RNA recombination in potexviruses. Virus Genes 1999; 18:121-8. [PMID: 10403698 DOI: 10.1023/a:1008008400653] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
Abstract
A naturally occurring 1.1 kb RNA was isolated from purified virions of bamboo mosaic potexvirus isolate S (BaMV-S). This RNA is a defective RNA (D RNA) derived from a single internal deletion of the BaMV genome. A cDNA clone representing the complete nucleotide sequence of the BaMV-S D RNA was generated and its nucleotide sequence was determined. The BaMV D cDNA is 1015 nts in length [excluding the poly(A) tail] and consists of two regions corresponding to 867 nts of the 5' terminus and 148 nts of the 3' terminus of the BaMV genomic RNA. BaMV D cDNA contains a single open reading frame (ORF) encoding a putative 29.7 kDa protein comprised of a fusion of the first 258 amino acids of BaMV ORF 1 and the last 2 amino acids of coat protein. The coding capacity of D RNA was verified by in vitro translation of native BaMV-S D RNA and of 1.1 kb RNA transcribed in vitro from the full-length D cDNA. BaMV D RNA can be reproducibly generated by serial passages of BaMV-S in Nicotiana benthamiana and is the first D RNA in the potexvirus group shown to be generated de novo. Alignments of sequences surrounding the 5' and 3' junction borders of reported potexvirus D RNAs reveal a 65.2-84.6% sequence identity, suggesting that common mechanisms for viral RNA recombination are involved in the generation of potexvirus D RNAs.
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Affiliation(s)
- T Y Yeh
- Institute of Botany, Academia Sinica, Taipei, Taiwan, Republic of China
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Zhang YP, Uyemoto JK, Golino DA, Rowhani A. Nucleotide sequence and rt-PCR detection of a virus associated with grapevine rupestris stem-pitting disease. PHYTOPATHOLOGY 1998; 88:1231-1237. [PMID: 18944859 DOI: 10.1094/phyto.1998.88.11.1231] [Citation(s) in RCA: 38] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/27/2023]
Abstract
ABSTRACT Grapevine rupestris stem pitting (RSP) is a graft-transmissible disease of unknown etiology. We have characterized a virus associated with this disease. The entire genomic sequence (GenBank accession number AF026278) consisted of 8,725 nucleotides excluding a poly(A) tail. Six open reading frames (ORF) were found. ORF1 potentially encodes a polypeptide with a methyltransferase domain, a papain-like proteinase domain, a helicase domain, and a RNA-dependent RNA polymerase domain; ORF2, ORF3, and ORF4 compose a triple-gene block; ORF5 encodes a coat protein; and ORF6 is located near the 3' end with unknown function. Sequence analysis indicated that the virus is most similar to apple stem-pitting virus and may be allied with the carla- and potexviruses and grouped with other viruses that infect woody hosts. A specific reverse-transcription polymerase chain reaction (RT-PCR)-based detection method was developed. Among 62 grapevine sources known to be infected with rupestris stem-pitting disease, 60 sources tested positive by RT-PCR. Among 43 healthy vines tested, all were negative. The name grapevine rupestris stem-pitting-associated virus is proposed.
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Kim KH, Hemenway C. Mutations that alter a conserved element upstream of the potato virus X triple block and coat protein genes affect subgenomic RNA accumulation. Virology 1997; 232:187-97. [PMID: 9185602 DOI: 10.1006/viro.1997.8565] [Citation(s) in RCA: 52] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/04/2023]
Abstract
The putative subgenomic RNA (sgRNA) promoter regions upstream of the potato virus X (PVX) triple block and coat protein (CP) genes contain sequences common to other potexviruses. The importance of these sequences to PVX sgRNA accumulation was determined by inoculation of Nicotiana tabacum NT1 cell suspension protoplasts with transcripts derived from wild-type and modified PVX cDNA clones. Analyses of RNA accumulation by S1 nuclease digestion and primer extension indicated that a conserved octanucleotide sequence element and the spacing between this element and the start-site for sgRNA synthesis are critical for accumulation of the two major sgRNA species. The impact of mutations on CP sgRNA levels was also reflected in the accumulation of CP. In contrast, genomic minus- and plus-strand RNA accumulation were not significantly affected by mutations in these regions. Studies involving inoculation of tobacco plants with the modified transcripts suggested that the conserved octanucleotide element functions in sgRNA accumulation and some other aspect of the infection process.
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Affiliation(s)
- K H Kim
- Department of Biochemistry, North Carolina State University, Raleigh 27695-7622, USA
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Xu H, Leclerc D, Leung B, AbouHaidar MG. The entire nucleotide sequence and genomic organization of potato aucuba mosaic potexvirus. Arch Virol 1994; 135:461-9. [PMID: 7979982 DOI: 10.1007/bf01310031] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/28/2023]
Abstract
The entire nucleotide sequence (7057 nucleotides) of cDNA clones of potato aucuba mosaic virus (PAMV) was determined. The genome contains five major putative open reading frames (ORFs), designated from the 5' terminus as encoding putative proteins with M(r) of 187,379 (187 K), 26,326 (26 K), 12,101 (12 K), 8,183 (8 K) and 27,114 (27 K). The genomic organization of PAMV is essentially the same as that of several other potexviruses. The sizes and composition of the proteins encoded by the ORFs are generally similar to those found in other potexviruses. The genome and the capsid protein gene of PAMV, are the largest among the potexviruses sequenced to date.
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Affiliation(s)
- H Xu
- Department of Botany, University of Toronto, Ontario, Canada
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Neo KK, Wong SM, Wu M. Nucleotide sequence and in vitro translation of the coat protein gene of cymbidium mosaic virus. Virus Genes 1993; 7:157-70. [PMID: 8103614 DOI: 10.1007/bf01702396] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/28/2023]
Abstract
The nucleotide sequence of the coat protein gene of cymbidium mosaic virus (CyMV) has been determined from a cDNA clone that encompassed the 3'-region of the virus genome. The 0.75 kb coat protein open reading frame (ORF) codes for a 24kD polypeptide. The coat protein coding region was separated from the 3'-poly(A) terminal of the viral genome by an 80 base noncoding region. The derived amino acid sequence of this ORF showed considerable homology with other potexvirus coat protein sequences, notably with narcissus mosaic virus (NMV), potato virus X (PVX), and white clover mosaic virus (WClMV). In vitro expression of the CyMV coat protein gene was carried out by T7 RNA polymerase on the linearized cDNA clone template, followed by in vitro translation of the purified transcript in wheat germ extract. One of the translated products was found to comigrate with the coat protein of the virus at about 24 kD, as determined by NaDodSO4-PAGE. This translated product was also found to crossreact with antibodies raised against CyMV.
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Affiliation(s)
- K K Neo
- Department of Botany, National University of Singapore
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Forster RL, Beck DL, Guilford PJ, Voot DM, Van Dolleweerd CJ, Andersen MT. The coat protein of white clover mosaic potexvirus has a role in facilitating cell-to-cell transport in plants. Virology 1992; 191:480-4. [PMID: 1413520 DOI: 10.1016/0042-6822(92)90215-b] [Citation(s) in RCA: 73] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Abstract
Functions of the coat protein of white clover mosaic potexvirus (WCIMV) were investigated using C-terminal deletion mutants. Whereas plants inoculated with RNA transcripts of a full-length wild-type clone of WCIMV produced typical infections, plants inoculated with transcripts of each mutant did not produce symptoms, and viral RNA species were not detected by Northern analysis. The mutants were able to replicate in protoplasts, although, relative to the wild-type RNA profile, the level of genomic RNA, but not subgenomic RNA, was reduced. These results indicate a role for the coat protein in efficient cell-to-cell transport in plants. Virus-like particles were detected in protoplast extracts inoculated with transcripts of a mutant in which the coat protein was truncated by 31 amino acids. This result suggests that the lack of detectable transport in plants was not due solely to a failure of the mutants to form virus particles. Possible roles for the coat protein in transport and replication are discussed. A 6-kDa open reading frame, internal to the coat protein gene, was shown by mutational analysis not to be essential for replication or transport.
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Affiliation(s)
- R L Forster
- Plant Improvement Division, Horticulture and Food Research Institute of New Zealand Ltd., Auckland
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White KA, Bancroft JB, Mackie GA. Mutagenesis of a hexanucleotide sequence conserved in potexvirus RNAs. Virology 1992; 189:817-20. [PMID: 1641994 DOI: 10.1016/0042-6822(92)90614-u] [Citation(s) in RCA: 43] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Abstract
Biologically active in vitro transcripts were synthesized from a cloned cDNA of a defective RNA (D RNA) of clover yellow mosaic virus (CYMV) and were used to determine if a hexanucleotide motif (5'-ACUUAA) conserved in the 3' noncoding region of potexvirus RNAs is essential for accumulation of progeny D RNA in planta. Deletion of rearrangement of the entire hexanucleotide sequence in the D RNA resulted in no detectable accumulation of progeny D RNA when coinoculated with helper CYMV RNA. Single-base substitutions of the four central nucleotides of the hexanucleotide sequence revealed that viable D RNAs can tolerate single residue changes at positions 3 and 5 only. These results suggest that the hexamer motif is involved in the process of D RNA propagation. The hexanucleotide sequence was also identified in the negative strand of potexvirus RNAs in the regions proposed to represent subgenomic RNA (sgRNA) promoters. In addition, the hexamer motif is present in similar regions in carlavirus RNAs. The conservation of this hexanucleotide (in orientation and position) in potexvirus and carlavirus RNAs, which serve as templates for full-length negative-strand synthesis and sgRNA production, strongly suggests that it plays a functional role in the synthesis of viral RNAs. Taken together, our data support our previous proposal (Bancroft et al., 1991. J. Gen. Virol. 72, 2173-2181) that the hexanucleotide sequence acts as a cis element involved in synthesis of full-length negative-sense viral RNA and further implicate the sequence in a similar role in production of positive-sense sgRNA.
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Affiliation(s)
- K A White
- Department of Biochemistry, University of Western Ontario, London, Canada
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White KA, Bancroft JB, Mackie GA. Coding capacity determines in vivo accumulation of a defective RNA of clover yellow mosaic virus. J Virol 1992; 66:3069-76. [PMID: 1560537 PMCID: PMC241068 DOI: 10.1128/jvi.66.5.3069-3076.1992] [Citation(s) in RCA: 47] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022] Open
Abstract
Naturally occurring defective RNAs (D RNAs) derived from the potexvirus clover yellow mosaic virus (CYMV) contain large internal deletions yet maintain a single open reading frame (ORF) representing the in-frame fusion of 5' and 3' terminal ORFs. Capped transcripts of the prototype 1.2-kb D RNA of CYMV were synthesized in vitro and used to inoculate broad bean plants. Progeny D RNA accumulated only if synthetic D RNA transcripts were coinoculated with CYMV RNA. Several experiments showed that helper-dependent accumulation of the D RNA in vivo depended on the maintenance of its encoded fusion ORF. (i) D RNAs with six-residue deletions introduced early in the fusion ORF accumulated, whereas those with four-residue out-of-frame deletions at the same sites were nonviable. (ii) Analysis of D RNAs containing termination codons at different locations showed that only the most 3' stop codon (maintaining over 93% of the fusion ORF) was permissive for D RNA accumulation. (iii) D RNAs with small in-frame deletions and insertions in their 3' coding regions were viable. (iv) Nonviable D RNAs containing disrupted fusion ORFs could not be complemented by the presence in the infection of a D RNA encoding a complete fusion ORF. Taken together, the results indicate that the process of translation, rather than the encoded product, modulates an event(s) which influences the propagation and/or accumulation of this RNA in vivo. This represents a unique requirement among plant virus D RNAs.
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Affiliation(s)
- K A White
- Department of Biochemistry, University of Western Ontario, London, Canada
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White KA, Bancroft JB, Mackie GA. Defective RNAs of clover yellow mosaic virus encode nonstructural/coat protein fusion products. Virology 1991; 183:479-86. [PMID: 1830181 PMCID: PMC7130666 DOI: 10.1016/0042-6822(91)90977-j] [Citation(s) in RCA: 33] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
Abstract
A small group of 1.2-kb RNAs present on polyribosomes from clover yellow mosaic virus (CYMV)-infected tissue contains sequences from the genomic RNA (gRNA) of CYMV and is encapsidated by CYMV coat protein. Some features of these RNAs suggest that they are similar to defective interfering (DI) RNAs, and would be the first to be reported for the potexvirus group. The prototype 1.2-kb RNA is 1172 nucleotides in length excluding a probable poly(A) tail and is composed of two noncontiguous regions corresponding to 757 nucleotides of the 5' and 415 nucleotides of the 3' termini of CYMV's gRNA. The sequence of the prototype 1.2-kb RNA reveals that the two terminal gRNA regions present in this RNA encode a single open reading frame (ORF) joining the N-terminus of the 191-kDa nonstructural product and the C-terminus of the coat protein to form a 35-kDa 191-kDa/coat protein fusion product. The coding properties of this prototype RNA have been confirmed by translation in vitro of native and synthetic transcripts of the 1.2-kb RNAs, both of which direct the synthesis of the anticipated 35-kDa product which reacts with anti-CYMV antiserum. Three additional 1.2-kb RNA species, each of which contains a unique junction site, have been characterized. In all cases, a fusion ORF encoding a 191-kDa/coat protein fusion product is encoded on the RNA. The presence of a fusion ORF in all members of the 1.2-kb RNA species analyzed suggests that maintenance of this ORF may be important for the survival of this class of RNA within the plant. This coding strategy represents a novel property of plant virus defective RNAs.
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Affiliation(s)
- K A White
- Department of Biochemistry, University of Western Ontario, London, Canada
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Abstract
The genomic RNA of clover yellow mosaic virus (CYMV) contains at least seven open reading frames (ORFs) which are organized in a more elaborate array than in other sequenced members of the potexvirus group. We have investigated the strategy by which ORFs located in the 3' region of CYMV's genomic RNA are differentially expressed by correlating the location of the 5' termini of the two abundant viral subgenomic RNAs with their coding potential. We have mapped the 5' termini of the subgenomic RNAs precisely to the nucleotide level and have shown that both are capped. The larger 2.1-kb subgenomic RNA encodes as its 5' ORF a 25-kDa polypeptide, whose function is unknown. The smaller 1.0-kb subgenomic RNA can encode only the 23-kDa coat protein. All four ORFs in the 3' 1095 residues of CYMV are efficiently expressed in vitro, but of these only coat protein, which can be expressed from a subgenomic RNA, is detectable in CYMV infected tissue. For this reason, we believe that expression of ORFs in the 3' one-third of CYMV RNA are controlled at the transcriptional level.
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Affiliation(s)
- K A White
- Department of Biochemistry, University of Western Ontario, London, Canada
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