• Journal of Microbiology and Biotechnology
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• v.27 no.4
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• pp.834-837
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• 2017

A distinct double-stranded RNA (dsRNA) cryptic virus, named spinach cryptic virus 1 (SpCV1), was identified from spinach transcriptome datasets. The SpCV1 genome has two dsRNA genome segments. The larger dsRNA1 has an open reading frame for a conserved RNA-dependent RNA polymerase (RdRp). The smaller dsRNA2 encodes a putative coat protein (CP). The sequence identity of SpCV1 RdRp and CP to the closest cryptic virus is 81% and 60%, respectively. Phylogenetic analysis indicates that SpCV1 is a novel member of the genus Alphapartitivirus (family Partitiviridae).

• The Plant Pathology Journal
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• v.24 no.3
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• pp.289-295
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• 2008

RNA-RNA interactions and the dynamic RNA conformations are important regulators in virus replication in several RNA virus systems and may also involved in the regulation of many important virus life cycle phases, including translation, replication, assembly, and switches in these important stages. The 5' non-translated region of Potato virus X(PVX) contains multiple cis-acting elements that facilitate various viral processes. It has previously been proposed that RNA-RNA interactions between various RNA elements present in PVX RNA genome are required for PVX RNA accumulation(Hu et al., 2007; Kim and Hemenway, 1999). This model was based on the potential base-pairing between conserved sequence elements at the upstream of subgenomic RNAs(sgRNAs) and at the 5' and 3' end of RNA genome. We now provide more evidence that RNA-RNA base-pairing between elements present at the 5' end and upstream of each sgRNA is required for efficient replication of genomic and subgenomic plus-strand RNA accumulation. Site-directed mutations introduced at the 5' end of plus-strand RNA replication defective mutant(${\Delta}12$) increasing base-pairing possibility with conserved sequence elements located upstream of each sgRNAs restored genomic and subgenomic plus-strand RNA accumulation and caused symptom development in inoculated Nicotiana benthamiana plants. Serial passage of a deletion mutant(${\Delta}8$) caused more severe symptoms and restored wild type sequences and thus retained possible RNA-RNA base-pairing. Altogether, these results indicate that the RNA element located at the 5' end of PVX genome involved in RNA-RNA interactions and play a key role in high-level accumulation of plus-strand RNA in vivo.

• Korean Journal of Microbiology
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• v.29 no.4
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• pp.221-225
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• 1991

The RNA transcripts produced from in vitro transcription reaction of BTV core were analyzed on agarose-urea gel. Fast migrating abortive RNAs, in addition to full length species of RNA, were observed. Fast migrating RNAs extracted from agarose-urea gel were hybridized to all 10 segments of genomic ds RNA, while solw migrating RNAs extracted from agarose-urea gel were hybridized only to the large and medium size genomic ds RNA. These results indicate that fast migrating RNA transcripts are most likely the products of abortive transcription.

• The Plant Pathology Journal
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• v.18 no.4
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• pp.187-191
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• 2002

This paper describes the cloning and sequence analysis of the 5'-terminal region and full-length cDNA production of genomic RNA of Lily symptomless virus (LSV), a Species Of the genus Carlavirus. A sing1e DNA band about 600 bp harboring the 5'-end of genomic RNA of the virus was successfully amplified by reverse transcription-polymerase chain reaction (RT-PCR) and rapid amplification of cDNA ends (RACE), and was cloned for nucleotide sequence determination. Sequence analysis of selected RACE cDNA clones revealed that the LSV 5'non-translated region consists of 67 nucleotides long of AT rich stretch followed GC rich from the 5'-end. To produce full-length cDNA products for the viral genomic RNA, a set of LSV-specific primers could be designed based on the obtained sequence in this study and the known sequences of 3'-terminal region for the virus. Full-length cDNA copies of LSV, an 8.4 kb long, were directly amplified by the long-template RT-PCR technique from the purified viral genomic RNA samples. This full-length cDNA copies were analyzed by restriction mapping. The molecules produced in this study can be useful for the production of in vitro infectious cDNA clone, as well as, for the completion of genomic RNA sequence and genome structure for the virus.

• Journal of Life Science
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• v.12 no.2
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• pp.61-74
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• 2002

One of the major aims in studying plant viruses is to minimise the development of symptoms in infected plants. With the advent of in vitro transcript mediated research on plant viruses, substantial progress has been made. This article describes the biology of a plant specific RNA virus, Johnsongrass mosaic virus (JGMV), important to Australian sorghum and corn agriculture and, in particular, at a molecular level which of the RNA sequences in its genome that make it possible for the virus to move from cell to cell, and eventually spread systemically throughout the entire plant. The JGMV has caused considerable yield losses in maize and sorghum over a number of years in Australia. Incidents where 100% of the crop has been infected are on record. The use of this virus is convenient under laboratory conditions because it can be readily transmitted by mechanical inoculation with infected leaf sap, which obviates the need for maintaining aphid colonies. The JGMV is a single stranded positive sense RNA virus.

• Journal of Veterinary Science
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• v.23 no.2
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• pp.24.1-24.10
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• 2022

Background: Small interfering RNA technology has been considered a prospective alternative antiviral treatment using gene silencing against influenza viruses with high mutations rates. On the other hand, there are no reports on its effectiveness against the highly pathogenic avian influenza H5N1 virus isolated from Indonesia. Objectives: The main objective of this study was to improve the siRNA design based on the nucleoprotein gene (siRNA-NP) for the Indonesian H5N1 virus. Methods: The effectiveness of these siRNA-NPs (NP672, NP1433, and NP1469) was analyzed in vitro in Marbin-Darby canine kidney cells. Results: The siRNA-NP672 caused the largest decrease in viral production and gene expression at 24, 48, and 72 h post-infection compared to the other siRNA-NPs. Moreover, three serial passages of the H5N1 virus in the presence of siRNA-NP672 did not induce any mutations within the nucleoprotein gene. Conclusions: These findings suggest that siRNA-NP672 can provide better protection against the Indonesian strain of the H5N1 virus.

• The Plant Pathology Journal
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• v.20 no.3
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• pp.200-205
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• 2004

The partial nucleotide sequences of the genomic dsRNA mycovirus infecting Pleurotus ostreatus isolates ASI2223 and Suhan were determined and compared with those of mycoviruses belonging to partitiviruses and totiviruses. Partial nucleotide sequences of the purified dsRNA from ASI2223 and Suhan showed RNA-dependent RNA polymerase sequences that are closely related to those of partitiviruses, including Fusarium poae virus 1, Fusarium solani virus, Rhizoctoniasolani virus, Discula destructiva virus 2, and Oyster mushroom isometric virus 2. Specific primers were designed for RT-PCR detection of dsRNA viruses from the P. ostreatus isolate ASI2223 and Suhan. Two virus specific primer sets were found to specifically detect each virus among six sets of designed oligonucleotide primers. Collectively, these results suggest that dsRNA mycoviruses from P. ostreatus isolates ASI2223 and Suhan belong to the family Partitiviridae, although, they are not the same virus species. Our results also suggest that these virus-specific primer sets can be employed for the specific detection of each viral sequence in infected tissues.

• Proceedings of the Korean Society of Plant Pathology Conference
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• 2003.10a
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• pp.4-8
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• 2003

Cucumber mosaic virus (CMV) belongs to genus Cucumovirus. The Cucumovirus group contains three distinct members： CMV, Tomato aspermy virus (TAV), and Peanut stunt virus (PSV). The type member, CMV is the most widespread and most studied. CMV is isometric particles about 30 nm in diameter. The genome of CMV is divided into three RNAs. In addition, RNA extracted from virus particles contains a fourth RNA that is a subgenomic RNA generated from RNA3. RNA1 and RNA2 are each encapsidated in separate particles, whereas RNAs3 and 4 are coencapsidated in a third particle. Hence, inoculation by three particles, transmitted either mechanically or by the aphid vector, is required to infect plants.(중략)

• The Plant Pathology Journal
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• v.28 no.1
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• pp.81-86
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• 2012

We developed a reassortant RNA virus vector derived from $Cucumber$ $mosaic$ $virus$ (CMV), which has advantages of very wide host range and can efficiently induce gene silencing in a few model plants. Certain CMV isolates, however, show limited host ranges presumably because they naturally co-evolved with their own hosts. We used a reassortant comprised of two strains of CMV, Y-CMV and Gn-CMV, to broaden the host range and to develop a virus vector for virus-induced gene silencing (VIGS). Gn-CMV could infect chili pepper and tomato more efficiently than Y-CMV. Gn-CMV RNA1, 3 and Y-CMV RNA2-A1 vector were newly reconstructed, and the transcript mixture of RNA1 and 3 genomes of Gn-CMV and RNA2 genome of Y-CMV RNA2 containing portions of the endogenous phytoene desaturase (PDS) gene (CMV2A1::PDSs) was inoculated onto chili pepper (cv. Chung-yang), tomato (cvs. Bloody butcher, Tigerella, Silvery fir tree, and Czech bush) and $Nicotiana$ $benthamiana$. All the tested plants infected by the reassortant CMV vector showed typical photo-bleaching phenotypes and reduced expression levels of $PDS$ mRNA. These results suggest that the reassortant CMV vector would be a useful tool for the rapid induction of the RNA silencing of endogenous genes in chili pepper and tomato plants.

• The Plant Pathology Journal
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• v.19 no.4
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• pp.210-216
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• 2003

This study examined the existence of genetically diverse population of Cucumber mosaic virus (CMV), known as quasispecies, from lily, Nicotiana benthamiana and from purified virions. Based on the conserved sequences of CMV lily isolates in intergenic region (IR) on RNA3, the genetic variation of IR from three different sources was investigated by a specific restriction endonuclease hydrolysis of amplified reverse transcription-polymerase chain reaction (RT-PCR) products using virus-specific primers, and was compared with IR sequences. The IR nucleotide sequences of CMV lily isolates were highly conserved, however, quasispecies was detected from all three sources in low level, containing sub-populations of RNA3. These subpopulations of RNA3 were inoculated onto zucchini squash by in vitro transcripts from corresponding full-length cDNA clones together with Eny RNA1 and 2 transcripts. The systemic symptom of zucchini plants infected by these quasispecies was chlorotic spotting, which was milder than severe mosaic and stunt symptom caused by Eny-CMV. The severity of symptom was correlated with RNA accumulation of viruses. These results suggest that the genome of CMV lily isolates consists of quasispecies populations.