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PubMed2001

Specific inhibition of HIV-1 gene expression by double-stranded RNA.

RNA interference (RNAi) is phenomenon in which introduced double-stranded RNAs (ds-RNAs) silence gene expression through specific degradation of their cognate mRNAs. RNAi has been observed in a wide variety of organisms and is considered to be a feature of nearly all eukaryotes. The mediators of sequence specific messenger RNA degradation are 21-23 nucleotide small interfering RNAs generated by ribonucleaseIII cleavage from longer dsRNAs. To investigate the potential of dsRNA to interfere with the function of HIV-1 genes, we have designed six longer dsRNAs containing the HIV-1 gag and env genes. Double-stranded RNAs were tested for inhibitory effects using monkey COS cells. In these anti-HIV-1 activity tests, the dsRNAs targeted to the HIV-1 env sequence showed more than 90% anti-HIV-1 efficiency. Our results show that dsRNA interference can be used as a powerful method for the inhibition of HIV-1 gene expression.

Animals↗
PubMed2001

A simple and rapid system for the quantitation of RNA interference in plant cultured cells.

The phenomenon known as RNA interference (RNAi) by double-stranded RNA (dsRNA) that was reported recently in the nematode Caenorhabditis elegans has been shown to operate by a mechanism that is widely conserved among species including plant cells. No quantitative analysis of the effects of RNAi on the expression of specific genes in plant cultured cells has been reported. An RNAi effect was observed 24 h after the introduction of dsRNA expression plasmids into tobacco BY-2 cells by electroporation. The simple system for suppression of specific genes in plant cells should be useful in attempts to elucidate the roles of individual genes in plant cells.

Cell Line↗
PubMed2002

Development and application of siRNA expression vector.

RNA interference (RNAi) is a sequence-specific silencing phenomenon, which is induced by double-stranded RNA (dsRNA) and mediated through an evolutionarily conserved mechanism from plants to mammals. In mammalian cells, it has recently been reported that 21- or 22-nucleotide (nt) RNAs with 2-nt 3' overhangs (siRNA) induce RNAi without induction of the dsRNA-dependent inhibition of protein synthesis, known as the host defense system against viral infections. Moreover, we and other have developed siRNA expression systems utilizing a pol III promoter. Here we report a comparative analysis among various siRNA expression vectors and also demonstrate a regulatable RNAi in cells by using a tetracycline-controlled U6 promoter.

Genetic Vectors↗
PubMed2006

Isolation of RNA aptamers against human Toll-like receptor 3 ectodomain.

Toll-like receptor 3 (TLR3) detects double-stranded RNA (dsRNA) known as a universal viral molecular pattern and activates the antiviral immune response. While TLR3 preferentially recognizes polyriboinosine-polyribocytidylic acid (poly (I:C)), a sequence-specific dsRNA has not yet been shown to activate TLR3. To determine whether TLR3 preferentially recognizes some specific sequence that acts on the signaling pathway of TLR3, in vitro selection against human TLR3 ectodomain (TLR3 ECD) was performed. After seventh selection cycle, two major classes, Family-I and -II, were emerged from 64 clones with binding constants of about 3 nM. Although these aptamers bound to TLR3 ECD with high affinity in vitro, they did not have agonist and antagonist effects on TLR3 signaling in TLR3-transfected HEK293 cells. Further analyses of the structure/function relationship of these aptamers will be carried out by mutagenesis, RNase mapping and competition assay using poly (I:C).

Aptamers, Nucleotide↗
PubMed1999

Double-stranded RNA-activated protein kinase (PKR) fused to green fluorescent protein induces apoptosis of human embryonic kidney cells: possible role in the Fas signaling pathway.

PKR is an interferon-inducible, double-stranded (ds) RNA-activated serine/threonine protein kinase, and has been shown to play roles in viral pathogenesis, cell growth and apoptosis. We expressed PKR as a fusion protein with enhanced jellyfish green fluorescence protein (EGFP) in human embryonic kidney 293 cells to visualize the effect of PKR transfection. The EGFP-fusion construct with wild-type PKR showed both auto- and substrate-phosphorylation activities independent of dsRNA, indicating EGFP-PKR is constitutively active. The EGFP-construct with a mutant PKR with the first RNA binding domain deleted still possessed kinase activities. On the other hand, the EGFP-fusion with a catalytically inactive mutant of PKR with the substitution of K at 296 with R, which has been shown to have tumorigenic properties, did not possess kinase activities. Transfection of the constitutive active forms of EGFP-PKR constructs induced apoptosis in 293 cells without dsRNA, whereas the EGFP-fusion with the catalytically inactive mutant did not cause apoptosis but rather protected cells from Fas-induced cell death. In addition, Fas-stimulation increased endogenous PKR activities. These results constitute evidence that PKR is sufficient to induce apoptosis, and plays a role in Fas-mediated apoptosis.

Animals↗
PubMed1982

Interferon gamma-induced Ca-dependent protein kinase in mouse L cells.

Treatment of mouse L cells with mouse IFN gamma induced a cytoplasmic Ca-dependent protein kinase, which highly phosphorylated cellular enzymes such as phosphodiesterase and RNase in vitro. The kinase partially purified from IFN gamma-treated cells (100 units/ml, 12 h at 37 degrees C) was different from IFN-induced dsRNA-dependent protein kinase since it was dsRNA independent. The kinase may have played an important role in mediating IFN-induced biological effects, since cellular enzymes were found to alter enzyme activity after phosphorylation by the kinase in vitro.

Animals↗
PubMed2002

Multiple ribonuclease H-encoding genes in the Caenorhabditis elegans genome contrasts with the two typical ribonuclease H-encoding genes in the human genome.

Database searches of the Caenorhabditis elegans and human genomic DNA sequences revealed genes encoding ribonuclease H1 (RNase H1) and RNase H2 in each genome. The human genome contains a single copy of each gene, whereas C. elegans has four genes encoding RNase H1-related proteins and one gene for RNase H2. By analyzing the mRNAs produced from the C. elegans genes, examining the amino acid sequence of the predicted protein, and expressing the proteins in Esherichia coli we have identified two active RNase H1-like proteins. One is similar to other eukaryotic RNases H1, whereas the second RNase H (rnh-1.1) is unique. The rnh-1.0 gene is transcribed as a dicistronic message with three dsRNA-binding domains; the mature mRNA is transspliced with SL2 splice leader and contains only one dsRNA-binding domain. Formation of RNase H1 is further regulated by differential cis-splicing events. A single rnh-2 gene, encoding a protein similar to several other eukaryotic RNase H2L's, also has been examined. The diversity and enzymatic properties of RNase H homologues are other examples of expansion of protein families in C. elegans. The presence of two RNases H1 in C. elegans suggests that two enzymes are required in this rather simple organism to perform the functions that are accomplished by a single enzyme in more complex organisms. Phylogenetic analysis indicates that the active C. elegans RNases H1 are distantly related to one another and that the C. elegans RNase H1 is more closely related to the human RNase H1. The database searches also suggest that RNase H domains of LTR-retrotransposons in C. elegans are quite unrelated to cellular RNases H1, but numerous RNase H domains of human endogenous retroviruses are more closely related to cellular RNases H.

Amino Acid Sequence↗
PubMed2001

RNA-dependent RNA polymerase activity associated with endogenous double-stranded RNA in rice.

RNA-dependent RNA polymerase (RdRp) activity was detected in the crude microsomal fraction of rice cultured cells that contain a 14 kbp double-stranded RNA (dsRNA). RdRp activity is maximal in the presence of all four nucleotide triphosphates and Mg2+ ion and is resistant to inhibitors of DNA-dependent RNA polymerases (actinomycin D and alpha-amanitin). RdRp activity increases approximately 2.5-fold in the presence of 0.5% deoxycholate. Treatment of purified microsomal fraction with proteinase K plus deoxycholate suggests that the RdRp enzyme complex with its own 14 kb RNA template is located in vesicles. The RdRp enzyme complex was solubilized with Nonidet P-40 and purified by glycerol gradient centrifugation, then exogenous RNA templates were added. Results indicate that exogenous dsRNA reduces RNA synthesis from the endogenous 14 kb RNA template.

Cells, Cultured↗
PubMedDate not supplied

Effect of a virus on accumulation of a tissue-specific cell-surface protein of the fungus Cryphonectria (Endothia) parasitica.

Hypovirulence and decreased sporulation of the plant pathogenic fungus Cryphonectria (Endothia) parasitica is caused by double-stranded (ds)RNAs. These symptoms of dsRNA infection are correlated with down-regulation of at least nine major fungal polypeptides. One of the regulated polypeptides was purified to homogeneity and antibody to it was prepared. This polypeptide (cryparin) has a -glycine-serine-repeating sequence near the amino-terminal end that is typical of structural proteins and has properties of a lectin. Antibody-staining showed that this 18.6-kDa polypeptide is specific to aerial hyphae and fruiting bodies and that it accumulates in large amounts on hyphal cell surfaces. The dsRNA affects accumulation of this protein, both in the fugal hyphae and in the growth medium. Cryparin is similar in physical properties to those of the putative phytotoxin cerato-ulmin produced by the Dutch elm disease fungus. Toxicity of cryparin is not detectable, but the striking similarities between the physical properties and locations of accumulation of cryparin and cerato-ulmin in fungal fruiting structures suggest either conservation of structure or convergent evolution in function of these two proteins.

Amino Acid Sequence↗
PubMed2002

The occurrence of CMV-specific short Rnas in transgenic tobacco expressing virus-derived double-stranded RNA is indicative of resistance to the virus.

Expression or introduction of double-stranded (ds)RNA in eukaryotic cells can trigger sequence-specific gene silencing of transgenes, endogenes, and viruses. Transgenic plants producing dsRNAs with homology to viral sequences are likely to exhibit pathogen-derived resistance to the virus. Cucumber mosaic virus (CMV), a very widespread virus with over 1,000 host species, has the natural ability to suppress silencing in order to establish infection. Here, we report the generation of transgenic tobacco lines, where a DNA transgene containing an inverted repeat of CMV cDNA had been introduced. Expression of this DNA construct delivered an RNA transcript that is able to form an intramolecular double strand. Transgenic plants were challenged with CMV. Three categories of plants could be discriminated: susceptible plants, which typically reacted with milder symptoms than the wild-type control; a "recovery" phenotype, in which newly emerging leaves were free of symptoms; and plants that showed complete resistance. Northern analysis showed that the expression of CMV dsRNA caused, in some transgenic lines, the generation of short RNAs characteristic of posttranscriptional gene silencing. Those lines were CMV resistant. The correlation between the detection of short RNAs and virus resistance provides a molecular marker that makes it possible to predict success in attempts to engineer virus resistance by dsRNA.

Cucumovirus↗
PubMed2003

Silencing of ubiquinone biosynthesis genes extends life span in Caenorhabditis elegans.

Ubiquinone (coenzyme Q; Q) is a key factor in the mitochondria electron transport chain, but it also functions as an antioxidant and as a cofactor of mitochondrial uncoupling proteins. Furthermore, Q isoforms balance in Caenorhabditis elegans is determined by both dietary intake and endogenous biosynthesis. In the absence of synthesis, withdrawal of dietary Q8 in adulthood extends life span. Thus, Q plays an important role in the aging process and understanding its synthesis acquires a new impetus. We have identified by RNA interference (RNAi) eight genes, including clk-1, involved in ubiquinone biosynthesis in C. elegans feeding animals with dsRNA-containing Escherichia coli HT115 strains. Silenced C. elegans showed lower levels of both endogenous Q9 and Q8 provided by diet, produced less superoxide without a significant modification of mitochondrial electron chain, and extended life span compared with non-interfered animals. E. coli strains harboring dsRNA also interfered with their own Q8 biosynthesis. These findings suggest that more efficient electron transport between a lower amount of Q and electron transport capacity of the mitochondrial complexes leads to less production of reactive oxygen species that contributes to extension of life span in the nematode C. elegans.

Animals↗
PubMed2004

Functional genomic analysis of the ADP-ribosylation factor family of GTPases: phylogeny among diverse eukaryotes and function in C. elegans.

ADP-ribosylation factor (Arf) and Arf-like (Arl) proteins are a family of highly conserved 21 kDa GTPases that emerged early in the evolution of eukaryotes. These proteins serve regulatory roles in vesicular traffic, lipid metabolism, microtubule dynamics, development, and likely other cellular processes. We found evidence for the presence of 6 Arf family members in the protist Giardia lamblia and 22 members in mammals. A phylogenetic analysis was performed to delineate the evolutionary relationships among Arf family members and to attempt to organize them by both their evolutionary origins and functions in cells and/or organisms. The approximately 100 protein sequences analyzed from animals, fungi, plants, and protists clustered into 11 groups, including Arfs, nine Arls, and Sar proteins. To begin functional analyses of the family in a metazoan model organism, we examined roles for all three C. elegans Arfs (Arf-1, Arf-3, and Arf-6) and three Arls (Arl-1, Arl-2, and Arl-3) by use of RNA-mediated interference (RNAi). Injection of double-stranded RNA (dsRNA) encoding Arf-1 or Arf-3 into N2 hermaphrodites produced embryonic lethality in their offspring and, later, sterility in the injected animals themselves. Injection of Arl-2 dsRNA resulted in a disorganized germline and sterility in early offspring, with later offspring exhibiting an early embryonic arrest. Thus, of the six Arf family members examined in C. elegans, at least three are required for embryogenesis. These data represent the first analysis of the role(s) of multiple members of this family in the development of a multicellular organism.

ADP-Ribosylation Factors↗
PubMed1982

Polymorphism of the genomic RNAs among the avian reoviruses.

The genome of avian reoviruses is comprised of 10 segments of double-stranded (ds)RNA. Analysis by polyacrylamide gel electrophoresis of the genomic RNA from a small number of avian reoviruses has demonstrated a significant polymorphism in the migration pattern of the dsRNA segments among different isolates. Comparison of these patterns with that of the mammalian reovirus of serotype 1 has permitted calculation of the molecular weights of the avian dsRNA species.

Animals↗
PubMed1982

Inhibition by glucocorticosteroid hormones of interferon and prostaglandin E induction by poly(rI). Poly(rC).

We have examined the relationship between induction of interferon (IFN) and prostaglandin E (PGE) production by poly(rI).poly(rC) in cultured human foreskin fibroblasts (FS11). Hydrocortisone and dexamethasone (2 . 5 x 10(-7) M), which are known inhibitors of PGE synthesis, significantly decreased the induction of both IFN and PGE in IFN-pretreated (primed) cells. Desoxycorticosterone, progesterone and estradiol were devoid of this activity. Hydrocortisone also blocked the induction of IFN by double-stranded RNA (dsRNA), cycloheximide and actinomycin D in FS11 cells. Arachidonic acid overcame the inhibitory effect of hydrocortisone on PGE production, but failed to restore IFN production in the presence of the steroid. Moreover, the prostaglandin synthetase inhibitors, indomethacin, aspirin and flufenamic acid, did not change IFN production by dsRNA in primed FS11 cells, although prostaglandin synthesis was abolished. Although the induction of IFN and PGE by poly(rI).poly(rC) might be consequences of the same initial event in the cell, the accumulation of PGE does not seem to have a regulatory effect on the synthesis of IFN in this system.

Cells, Cultured↗
PubMed1984

The genomes of rotaviruses isolated from chronically infected immunodeficient children.

Abnormal RNA migration profiles were found in numerous rotavirus samples from two chronically infected children suffering from severe combined immunodeficiency. In both cases additional bands consisting of dsRNA were found migrating between RNA segments 1 and 7, and in one case RNA segment 11 was lost from the profile. Hybridization studies using segment-specific cloned cDNA probes indicated that some of the additional bands had sequence homologies with normal rotavirus dsRNA segments. In most cases these sequences were derived from genome segments of lower molecular weight by the formation of covalently linked concatemers.

Child, Preschool↗
PubMed1987

Genetic relatedness of Colorado tick fever virus isolates by RNA-RNA blot hybridization.

The sequence relatedness of ten isolates of the Colorado tick fever (CTF) serogroup of orbiviruses was examined by RNA-RNA blot hybridization. The 12 dsRNA genome segments of each of the isolates were electrophoresed in a 10% polyacrylamide gel, the segments were transferred electrophoretically to membranes and hybridized to radiolabelled genomic RNA from CTF Florio mouse-adapted strain (CTF FMA) or CTF SS-18. All genome segments of the ten CTF viruses exhibited cross-hybridization signals with either CTF FMA or CTF SS-18, under conditions in which greater than or equal to 74% sequence homology was required to form stable hybrids. Although the dsRNA polyacrylamide gel profiles were unique for each isolate examined, the CTF genes did not exhibit sequence divergence as has been seen among other Orbivirus serogroups. These hybridization analyses suggest that the CTF gene pool is relatively homogeneous which may be a reflection of the lack of multiple serotypes of CTF strains in neutralization tests. Nevertheless, the hybridization signals of segments 4 and 6 were lighter than those of the other genes, indicating that these two genes exhibited the highest degree of sequence variability among these isolates. These data are compared with hybridization data on other Orbivirus serogroups.

Colorado tick fever virus↗
PubMed1988

Interferon induction by viruses. XVI. 2-Aminopurine blocks selectively and reversibly an early stage in interferon induction.

A purine analogue, 2-aminopurine, reported to act as an inhibitor of protein kinase, selectively, reversibly and in a dose-dependent manner blocked a very early stage in interferon induction. With chick embryo cells and mouse L cells as hosts, and different viral inducers of interferon, maximal effects of 2-aminopurine were observed during the first 4 h of induction. At 10 mM-2-aminopurine there was a 20-fold reduction in the yield of interferon from both cell types. 2-Aminopurine and actinomycin D both prevented interferon induction with the same time course, indicating a transcriptional block to induction; however, only the action of the former was reversed upon removal of the drug. Addition of 2-aminopurine to an agarose overlay resulted in high efficiency plaque formation by vesicular stomatitis virus New Jersey (Hazelhurst) under conditions where endogenous induction of interferon and its feedback action on aged chick embryo cells normally prevented plaque formation. Two other inducible systems, representing genes involved in interferon action (both its development and activation), and those of heat shock, were not affected by 2-aminopurine. A model is presented implicating the interferon-inducible dsRNA-dependent protein kinase as an interferon induction receptor which, on interaction with dsRNA, generates an amplified signal via phosphorylation that ultimately derepresses the interferon gene(s).

2-Aminopurine↗
PubMed1988

Characterization of potentially foetotropic Palyam serogroup orbiviruses isolated in Zimbabwe.

Twelve Palyam serogroup orbiviruses isolated in Zimbabwe from aborted cattle foetuses, plus one isolated from the visceral organs of a cow and another from vulture faeces, were examined in comparison with known members of the serogroup by complement fixation, indirect immunofluorescence, fluorescent focus reduction neutralization tests and PAGE of the segmented, dsRNA genomes. The viruses were indistinguishable from known members of the serogroup by complement fixation and indirect immunofluorescence, but two novel viruses, for which the names Gweru and Marondera are proposed, and two previously described viruses, Nyabira and Abadina, were identified by neutralization tests. The dsRNA profiles of Abadina serotype isolates differed from that of the Abadina prototype virus, indicating that different electropherotypes may occur within serotypes.

Animals↗