Search PubMed⌕ Search

SEARCH · Search PubMed

Results for “DsRNA”

Search indexed PubMed citations on genomics, clinical trials, systematic reviews and public health. Explore titles, authors and supplied subject terms, then open the PubMed record.

Quote a phrase for an exact phrase match. Source license links do not imply unrestricted reuse.

At least 199 records · Page 11Linked to original sources
PubMed1996

Chromosomal assignment of the gene encoding the human 58-kDa inhibitor (PRKRI) of the interferon-induced dsRNA-activated protein kinase to chromosome 13q32.

The 58-kDa inhibitor (p58) of the interferon-induced dsRNA-activated protein kinase (PKR) is a cellular protein recruited by the influenza virus to down-regulate the activity of PKR during virus infection. The inhibitor also appears to play a role in the regulation of cellular gene expression in the absence of viral infection and has oncogenic properties when overexpressed. Using fluorescence in situ hybridization, we have mapped the p58 gene (PRKRI) to human chromosome 13 band q32. Aberrations in the structure or number of chromosome 13 have been identified in a variety of human cancers, particularly in acute leukemia.

Chromosome Mapping↗
PubMed1995

RNA binding, packaging and polymerase activities of the different incomplete polymerase complex particles of dsRNA bacteriophage phi 6.

phi 6 is an enveloped dsRNA bacterial virus. Its segmented genome resides inside the virion associated polymerase complex which is formed by four proteins (P1, P2, P4 and P7) encoded by the viral L segment. Complete and incomplete polymerase complex particles can be produced using cDNA copies of this largest genome segment. We have analysed the capacity of the different purified particles to (1) package phi 6 (+) sense genomic precursors and unspecific RNA, (2) synthesize (-) and (+) strands and (3) bind phi 6 specific and unspecific RNAs. Both (-) and (+) strand synthesis polymerase activities were found to be associated with protein P2. In addition to complete particles, particles lacking protein P2 were found to package and protect genomic precursor ssRNAs. Protein P7 was needed for efficient packaging. Regulation and specificity of the packaging were found to be independent of P2. Particles composed of proteins P1 and P4 did not package or protect RNA but did bind phi 6 genomic (+) strand RNAs. The three phi 6 (+) strands bound in equal amounts to the particles when tested alone in a filter binding assay. In competition experiments they competed each other for binding, indicating that individual binding sites for the three genomic (+) strands do not exist. Differences in RNA binding competition among the four particles were observed, suggesting that packaging specificity is achieved by complex interactions of proteins and genomic (+) strand RNAs during the advancement of the packaging process after the initial binding events.

Bacteriophage phi 6↗
PubMed2000

A cellular protein with an RNA-binding activity co-purifies with viral dsRNA from mycovirus-infected Helminthosporium victoriae.

A cellular protein that co-purifies with mycoviral dsRNA was isolated from the plant pathogenic fungus Helminthosporium victoriae (telomorph: Cochliobolus victoriae) infected with two viruses, the totivirus Helminthosporium victoriae 190S virus and the chrysovirus-like Helminthosporium victoriae 145S virus (Hv145SV). The cellular protein, which was, designated Hv-p68, accumulated to higher levels in virus-infected isolates compared to virus-free ones. The majority of the Hv145S dsRNAs were found in association with Hv-p68 and not packaged in virions. Hv-p68 could also be detected as a minor component of the virus capsid. Evidence is presented that Hv-p68 occurs in vivo as an octamer and that it possesses RNA-binding activities. Based on partial amino acid sequence analysis, Hv-p68 was shown to share significant sequence identity with alcohol oxidases from methylotrophic yeasts. Hv-p68 is proposed to play a role in viral RNA packaging/replication and in regulating viral pathogenesis.

Alcohol Oxidoreductases↗
PubMed2000

Characterization of phi 13, a bacteriophage related to phi 6 and containing three dsRNA genomic segments.

The three dsRNA genomic segments of bacteriophage Phi 13 were copied as cDNA and the nucleotide sequences were determined. The organization of the genome is similar to that of Phi 6, and there is significant similarity in the amino acid sequences of the proteins of the polymerase complex and one of the membrane proteins, P6. There is little or no similarity in the nucleotide sequences. Several features of the viral proteins differ markedly from those of Phi 6. Although both phages are covered by a lipid-containing membrane, the protein compositions are different. The host attachment protein consists of two peptides rather than one and the phage attaches directly to the LPS of the host rather than to a Type IV pilus. Despite the differences in the structure of the membranes, the two viruses can successfully exchange the genes for host attachment proteins and thereby change their host specificities.

Bacteriophage phi 6↗
PubMed2001

Reverse genetics and recombination in Phi8, a dsRNA bacteriophage.

Bacteriophage Phi8 has a genome of three dsRNA segments. It is able to acquire plasmid transcripts of cDNA copies of the genomic segments as replacements of its resident chromosomes. It is also able to effect recombination between the plasmid transcripts and the resident chromosomes. Depending upon the extent of sequence identity between the plasmid transcript and the resident chromosome, the recombination can be homologous or heterologous. Homologous recombination has not previously been reported for viruses with double-stranded RNA genomes.

Base Sequence↗
PubMed1991

Cell-free translation of carnation latent virus RNA and analysis of virus-specific dsRNA.

Carnation latent virus was shown to direct the synthesis of virus-specific polypeptides in both reticulocyte lysate and wheat germ in vitro translation systems. The L-(4,5-3H)-leucine-labeled products ranged in molecular mass from Mr 190 to 33 kD. The 33 kD product, synthesized after only 15 min incubation, was the only major polypeptide that immunoprecipitated with antiserum to CarLV. Coat-protein synthesis does not occur as a result of proteolytic processing, but may arise as a result of translation of a subgenomic RNA species. Subgenomic RNA species were not detected by Northern hybridization of CarLV cDNA to either viral RNA or total nucleic acid from systemically infected plants, although CarLV-specific dsRNA species equivalent to 1.6 and 2.1 kb were detected.

Cell-Free System↗
PubMed1996

Genome analysis of the 3'-terminal part of the little cherry disease associated dsRNA reveals a monopartite clostero-like virus.

The high molecular weight dsRNA associated with little cherry disease (LCD) was extracted from infected plant tissue and cloned as cDNA. The sequence of the 3' 8337 nucleotides was determined. Computer assisted translation of the sequence portion identified six open reading frames potentially encoding proteins (from 5' to 3') with molecular masses of 70 kDa, 61 kDa, 46 kDa, 76 kDa, 21 kDa and 27 kDa respectively. A 3'-terminal non-translated region of 210 nucleotides was present. The 70 kDa protein represents a homolog of the cellular HSP70 heat shock proteins, and the 61 kDa protein showed homology to the similarly encoded products of beet yellows (BYV), citrus tristeza (CTV) and lettuce infectious yellows (LIYV) closteroviruses. The putative coat protein (CP) was found to be of 46 kDa and its diverged copy of 76 kDa. The potential coding capacity of these notably large closterovirus proteins was confirmed by their expression in vitro and immunoblotting. No proteins with significant similarity to the two C-terminal proteins were identified, but they are related in molecular mass and location to BYV. The gene arrangement as well as the alignments of the closteroviruses CPs and their diverged copies suggest that the mealybug transmissible virus associated with LCD takes an intermediate evolutionary position between the aphid- and whitefly transmissible closteroviruses.

Amino Acid Sequence↗
PubMed1999

RNA-dependent RNA polymerase activity associated with virus-like dsRNA in Eimeria maxima and E. necatrix of the domestic fowl.

RNA-dependent RNA polymerase (RDRP) activity was identified in lysates of Eimeria maxima sporozoites and E. necatrix sporozoites and merozoites. Pretreatment of cell lysates with DNase I, RNase A, proteinase K and actinomycin D prior to RDRP assay was employed to characterize RDRP activity. DNase I and actinomycin D had little effect, while proteinase K abolished RDRP activity in both species. RNase A at a concentration of 1 mg/ml also reduced the polymerase activity in E. maxima and E. necatrix sporozoite lysates to 2% and 0%, respectively. Gel electrophoresis of RDRP products revealed that while most migrated at sizes less than 3 kb, a proportion of labelled products of E. necatrix and E. maxima also migrated to the sizes of their respective putative viral genomes. The RDRP products of E. necatrix were shown to be single-stranded by digestion with RNase in both low- and high-salt solutions and by methylmercuric hydroxide treatment. Moreover, the RDRP products of E. necatrix only hybridized to the 5.6-kb dsRNA of E. necatrix but not to the 4.5-kb dsRNAs of E. necatrix or E. maxima.

Animals↗
PubMed2003

Mak5p, which is required for the maintenance of the M1 dsRNA virus, is encoded by the yeast ORF YBR142w and is involved in the biogenesis of the 60S subunit of the ribosome.

In this study, we show that the Saccharomyces cerevisiae ORF YBR142w, which encodes a putative DEAD-box RNA helicase, corresponds to MAK5. The mak5-1 allele is deficient in the maintenance of the M1 dsRNA virus, resulting in a killer minus phenotype. This allele carries two mutations, G218D in the conserved ATPase A-motif and P618S in a non-conserved region. We have separated these mutations and shown that it is the G218D mutation that is responsible for the killer minus phenotype. Mak5p is an essential nucleolar protein; depletion of the protein leads to a reduction in the level of 60S ribosomal subunits, the appearance of half-mer polysomes, and a delay in production of the mature 25S and 5.8S rRNAs. Thus, Mak5p is involved in the biogenesis of 60S ribosomal subunits.

Amino Acid Substitution↗
PubMed2007

The dsRNA-binding protein DRB4 interacts with the Dicer-like protein DCL4 in vivo and functions in the trans-acting siRNA pathway.

Arabidopsis thaliana encodes four Dicer-like (DCL) proteins and five dsRNA-binding (DRB) proteins. We have previously demonstrated that DCL4 specifically interacts with DRB4 in vitro. Here we describe the interaction between DCL4 and DRB4 in vivo. The phenotype of a mutant with a defect in DCL4 (dcl4-2) was similar to that of a mutant with a defect in DRB4 (drb4-1): both mutant plants had elongated and downwardly curled rosette leaves and over-accumulated anthocyanin. In immunoprecipitation experiments with either anti-DCL4 or anti-DRB4 antibody and crude extracts of wild-type Arabidopsis plants, co-immunoprecipitation of DCL4 and DRB4 was detected, indicating that DCL4 interacts with DRB4 in vivo. This interaction was confirmed by immunoprecipitation experiments using extracts from dcl4-2, drb4-1, or transgenic plants expressing the hemagglutinin-tagged version of DCL4 or DRB4. The results of immunoprecipitation experiments also suggest that most DCL4 is associated with DRB4, but that some DRB4 is free or associated with other proteins. Reduced accumulation of the TAS1 and TAS3 trans-acting siRNA (ta-siRNA) and over accumulation of their target mRNAs (At5g18040 and auxin response factors ARF3 and ARF4) were detected in both drb4-1 and dcl4-2 mutants. These results indicate that DRB4, together with DCL4, functions in the ta-siRNA biogenesis.

Anthocyanins↗
PubMed2004

Putative replication intermediates in endornavirus, a novel genus of plant dsRNA viruses.

Oryza sativa endornavirus (OSV) belongs to a new genus (Endornavirus) and family (Endoviridae) with members containing large double-stranded RNA (dsRNA) replicons with plasmid-like properties. Analysis of products obtained from in vitro reaction of the OSV RNA-dependent RNA polymerase revealed a rapid increase of a population of the non-coding strand RNA molecules with a head-to-tail composition. Northern hybridization of total RNA from OSV-carrier cells with riboprobes specific for the coding strand RNA, revealed two types of RNA molecules (i) with a site specific nick and (ii) full-length unnicked molecules. Quantitative analyses of these RNAs showed about 50-fold higher amounts of full-length unnicked molecules in cultured cells in which the OSV copy number increases compared with those found in the seedling cells. Both the head-to-tail linked non-coding strand and the full-length coding strand molecules were also found in wild rice and broad beans infected with other endornaviruses indicating that the presence of these unique types of RNA molecules should be considered as a characteristic feature of Endoviridae .

Base Sequence↗
PubMedDate not supplied

Detection of virus-associated dsRNA from leafroll infected grapevines.

A simple procedure is described for reproducible detection of double stranded (ds) RNAs in leafroll infected grapevines. The procedure involves the extraction of tissues by a medium which preferentially yields dsRNA. The RNA is purified by CF11 cellulose chromatography and gel electrophoresis. The dsRNAs varied in size in different vines. In the cases tested they did not cross hybridize and occurred at higher concentrations in stem cortex tissues than in leaves. They were not detectable in healthy vines, could be passaged with the disease to healthy plants by graft inoculation and removed by virus elimination procedures. These observations indicated that the dsRNAs are of viral origin and that a number of viruses are associated with the grapevine leafroll disease.

Chromatography↗
PubMed1994

Observations on polymerase chain reaction amplification of infectious bursal disease virus dsRNA.

Two methods for denaturing double stranded (ds)RNA of infectious bursal disease virus for the purpose of reverse transcribing it were compared: Heat denaturation at 65 degrees C in the presence of DMSO and in the absence of DMSO. As part of the analysis, the nature of cDNA in the two preparations was examined by polymerase chain reaction (PCR) amplification, firstly by varying the number of cycles of PCR, and secondly by re-amplification of serial dilutions of the reaction products. The results show that denaturation of dsRNA in the presence of DMSO (method 1) is superior to denaturation without DMSO (method 2) judging by the yield of a specific PCR fragment after 30 cycles, and that the products of method 2 can be re-amplified, albeit poorly, with the generation of heterologous products.

Base Sequence↗
PubMed1994

Isolation and characterization of the dsRNA virus from the yeast Endomyces magnusii.

Virus-like particles (VLPs) have been isolated from the yeast Endomyces magnusii. The VLPs measure 43 nm in diameter and contain six species of dsRNA (0.78, 0.83, 1.77, 1.84, 2.64, 4.30 kb respectively). E. magnusii produces a 'toxic' protein, which reduces the growth, and changes the colony morphology, of sensitive strains of Hansenula sp. growing on solid media. All strains of E. magnusii tested produced the 'toxin' and contained the VLPs. Current procedures of curing failed to destroy the ability to produce the 'toxin'.

Molecular Weight↗
PubMed2005

Silencing of yellow head virus replication in penaeid shrimp cells by dsRNA.

RNA interference (RNAi) has been shown to inhibit viral replication in some animals and plants. Whether the RNAi is functional in shrimp remains to be demonstrated. In vitro transcribed dsRNAs of YHV helicase, polymerase, protease, gp116, and gp64 were transfected into shrimp primary cell culture and found to inhibit YHV replication. dsRNA targeted to nonstructural genes (protease, polymerase, and helicase) effectively inhibited YHV replication. Those targeted structural genes (gp116 and gp64) were the least effective. These findings are the first evidence that RNAi-mediated gene silencing is operative in shrimp cells. This could be a powerful tool for studying gene function and to develop effective control of viral infection in shrimp.

Animals↗
PubMed2005

Loop model: mechanism to explain partial gene duplications in segmented dsRNA viruses.

Gene rearrangements in a head-to-tail fashion have been described several times for gene segments of the rota-, phytoreo-, and orbiviruses. Several mechanisms have been proposed to explain the occurrence of partial duplications, however, none of these models has been fully satisfactory to explain the occurrence of all the observed duplicated genes. Based on recently available structural data about the lambda3 RNA-dependent-RNA-polymerase of reoviruses, we propose the 'loop model' as a plausible explanation for the occurrence of partial gene duplications in dsRNA viruses.

Computer Simulation↗
PubMed2004

The nuclear dsRNA binding protein HYL1 is required for microRNA accumulation and plant development, but not posttranscriptional transgene silencing.

MicroRNAs (miRNAs) are 21-24 nucleotides long molecules processed from imperfect double-stranded RNAs (dsRNAs). They regulate gene expression by targeting complementary mRNA for cleavage or interfering with their translation. In Arabidopsis, point mutations in or short truncations of the nuclear DICER-LIKE1 (DCL1) or HEN1 protein reduce miRNA accumulation and increase uncleaved target mRNAs accumulation, resulting in developmental abnormalities. Here, we show that miRNA accumulation also depends on the activity of HYL1, a nuclear dsRNA binding protein. hyl1 mutants exhibit developmental defects overlapping with that of dcl1 and hen1 mutants, suggesting that DCL1, HEN1, and HYL1 act together in the nucleus. We validate additional target mRNAs and show that reduced miRNA accumulation in hyl1 correlates with an increased accumulation of uncleaved target mRNAs, including meristem- and auxin-related genes, providing clues for the developmental abnormalities of hyl1 and for the previous identification of hyl1 as a mutant with altered responses to phytohormones. Lastly, we show that posttranscriptional transgene silencing occurs in hyl1, suggesting that HYL1 has specialized function in the plant miRNA pathway, whereas the HYL1-related RDE-4 and R2D2 proteins associate with DICER in the cytoplasm and act in the RNAi pathway in C. elegans and Drosophila, respectively.

Arabidopsis↗
PubMed2006

Specific recognition of HIV TAR RNA by the dsRNA binding domains (dsRBD1-dsRBD2) of PKR.

PKR (double-stranded RNA-dependent protein kinase) is an important component of host defense to virus infection. Binding of dsRNA to two dsRBDs (double-stranded RNA binding domains) of PKR modulates its own kinase activation. How structural features of natural target RNAs, such as bulges and loops, have an effect on the binding to two dsRBDs of PKR still remains unclear. By using ITC and NMR, we show here that both the bulge and loop of TAR RNA are necessary for the high affinity binding to dsRBD1-dsRBD2 of PKR with 1:1 stoichiometry. The binding site for the dsRBD1-dsRBD2 spans from upper bulge to lower stem of the TAR RNA, based on chemical shift mapping. The backbone resonances in the 40 kDa TAR.dsRBD1-dsRBD2 were assigned. NMR chemical shift perturbation data suggest that the beta1-beta2 loop of the dsRBD1 interacts with the TAR RNA, whereas that of the dsRBD2 is less involved in the TAR RNA recognition. In addition, the residues of the interdomain linker between the dsRBD1 and the dsRBD2 also show large chemical perturbations indicating that the linker is involved in the recognition of TAR RNA. The results presented here provide the biophysical and spectroscopic basis for high-resolution structural studies, and show how local RNA structural features modulate recognition by dsRBDs.

Amino Acid Sequence↗