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PubMed1992

Double-stranded RNA and interferon-alpha induce transcription through different molecular mechanisms.

Double-stranded (ds) RNA stimulates the synthesis of several mRNAs known to be induced by type I interferons (IFNs). In this report, it is shown that the IFN-alpha stimulated genes (ISGs) 15, 54, 56, and GBP are transcriptionally induced by dsRNA. Transcriptional stimulation occurred in the presence of the protein synthesis inhibitor cycloheximide (CHX), indicating that inducibility was directly mediated by dsRNA through the action of preformed proteins. ISGF-3, the protein complex mediating primary transcriptional induction of ISGs by IFN-alpha, was not activated by dsRNA in the presence of CHX. Additionally, DNA-binding activity of ISGF-2/IRF-1, a protein involved in the regulation of the IFN-beta gene and ISGs, did not correlate with dsRNA-induced transcriptional induction of ISGs. This suggests that dsRNA and IFN-alpha induce ISGs through different molecular mechanisms.

Cycloheximide↗
PubMed1998

RNA binding and modulation of PKR activity.

PKR is an RNA-dependent protein kinase that is induced in mammalian cells by interferon treatment. It is present in a latent or inactive form in mammalian cells and is activated by very low concentrations of double-stranded (ds) RNA. Activated PKR phosphorylates eIF2, an essential initiation factor of protein synthesis, as well as other substrates including histone IIA, a 90-kDa protein from rabbit reticulocytes, the inhibitor, IkappaB, of the transcription factor, NF-kappaB, and the HIV-1 Tat protein. PKR interacts with several cellular and viral products and these interactions modulate its activation by dsRNA. Here we describe methods that are used to study the activation or inhibition of PKR by RNA modulators. Specifically, we detail (1) the purification of PKR from interferon-treated mammalian cells, (2) functional assays for PKR activation and inhibition in vitro, using purified enzyme or crude cell lysates, and (3) assays allowing evaluation of the binding of dsRNA and single-stranded RNA to PKR.

Chromatography, Liquid↗
PubMed2005

The structure of the flock house virus B2 protein, a viral suppressor of RNA interference, shows a novel mode of double-stranded RNA recognition.

We report the structure of the flock house virus B2 protein, a potent suppressor of RNA interference (RNAi) in animals and plants. The B2 protein is a homodimer in solution and contains three alpha-helices per monomer. Chemical shift perturbation shows that an antiparallel arrangement of helices (alpha2/alpha2') forms an elongated binding interface with double-stranded RNA (dsRNA). This implies a novel mode of dsRNA recognition and provides insights into the mechanism of RNAi suppression by B2.

Amino Acid Sequence↗
PubMed1992

Interactions between double-stranded RNA regulators and the protein kinase DAI.

The interferon-induced protein kinase DAI, the double-stranded RNA (dsRNA)-activated inhibitor of translation, plays a key role in regulating protein synthesis in higher cells. Once activated, in a process that involves autophosphorylation, it phosphorylates the initiation factor eIF-2, leading to inhibition of polypeptide chain initiation. The activity of DAI is controlled by RNA regulators, including dsRNA activators and highly structured single-stranded RNAs which block activation by dsRNA. To elucidate the mechanism of activation, we studied the interaction of DAI with RNA duplexes of discrete sizes. Molecules shorter than 30 bp fail to bind stably and do not activate the enzyme, but at high concentrations they prevent activation by long dsRNA. Molecules longer than 30 bp bind and activate the enzyme, with an efficiency that increases with increasing chain length, reaching a maximum at about 85 bp. These dsRNAs fail to activate at high concentrations and also prevent activation by long dsRNA. Analysis of complexes between dsRNA and DAI suggests that at maximal packing the enzyme interacts with as little as a single helical turn of dsRNA (11 bp) but under conditions that allow activation the binding site protects about 80 bp of duplex. When the RNA-binding site is fully occupied with an RNA activator, the complex appears to undergo a conformational change.

Binding Sites↗
PubMed2002

Establishment of a monoclonal antibody against human Toll-like receptor 3 that blocks double-stranded RNA-mediated signaling.

A monoclonal antibody (mAb) against human Toll-like receptor (TLR) 3 was established and its effect on TLR3-mediated responses was tested using human fibroblast cell lines expressing TLR3 on the cell surface. Fibroblasts are known to produce IFN-beta upon viral infection or treatment with double-stranded RNA (dsRNA) through distinct signaling pathways. Here, we show the mAb to TLR3 suppressed poly(I):poly(C)-mediated IFN-beta production by human fibroblasts naturally expressing TLR3 on their surface. By reporter gene assay using HEK293 cells transfected with a human TLR3 expression vector, TLR3 recognized dsRNA to activate NF-kappaB and the IFN-beta promoter. TLR3 signaling was not elicited by either single-stranded RNA (ssRNA) or dsDNA. Thus, specific recognition of dsRNA by extracellular TLR3 is essential for induction of type I IFN: the interassociation between dsRNA and TLR3, regardless of direct or indirect binding, should be disrupted by mAb being attached to TLR3. The mAb against TLR3 reported herein may serve as a regulator for virus-mediated immune response via an alternative pathway involving the dsRNA-TLR3 recognition which might occur on host cells.

Animals↗
PubMed1995

Functional characterization of the RNA-binding domain and motif of the double-stranded RNA-dependent protein kinase DAI (PKR).

The double-stranded (ds) RNA-activated protein kinase, DAI (also known as PKR), contains an RNA-binding domain comprising two tandem repeats of a motif, the dsRBM, which is shared with a number of other proteins that interact with structured RNAs. We have expressed the entire domain and the first copy of the motif in Escherichia coli and purified the two proteins, p20 and p10, to apparent homogeneity in order to study their interactions with RNA and with the intact kinase enzyme. Both p20 and p10 bound preferentially to structured RNA molecules. Competition assays showed that in both cases the order of affinity is dsRNA > VA RNA > tRNA, but the isolated motif bound much less tightly than the entire domain. Measurement of the dissociation constants for dsRNA by quantitative gel mobility shift analysis gave apparent Kd values of 4 x 10(-9) M and 3.8 x 10(-7) M for p20 and p10, respectively. The binding of p20 molecules to dsRNA appeared to be cooperative. Multiple complexes were formed between the intact domain and dsRNA, saturating at a density of about one p20 molecule/11.25 base-pairs (or one turn) of duplex, whereas p10 achieved only about half of this packing density. The apparent Kd for the p20-VA RNA interaction was estimated as 3.5 x 10(-7) M and at least three complexes were detected, but no distinct complexes were visualized for the interaction between p10 and VA RNA. Both p20 and p10 inhibited autophosphorylation of intact DAI, probably by binding the dsRNA activator. Once activated, DAI could phosphorylate both p10 and p20, suggesting that intermolecular phosphorylation can occur.

Amino Acid Sequence↗
PubMed2004

A conserved siRNA-degrading RNase negatively regulates RNA interference in C. elegans.

In many organisms, introducing double-stranded RNA (dsRNA) causes the degradation of messenger RNA that is homologous to the trigger dsRNA--a process known as RNA interference. The dsRNA is cleaved into short interfering RNAs (siRNAs), which hybridize to homologous mRNAs and induce their degradation. dsRNAs vary in their ability to trigger RNA interference: many mRNA-targeting dsRNAs show weak phenotypes, and nearly all mRNAs of the Caenorhabditis elegans nervous system are refractory to RNA interference. C. elegans eri-1 was identified in a genetic screen for mutants with enhanced sensitivity to dsRNAs. Here we show that eri-1 encodes an evolutionarily conserved protein with domains homologous to nucleic-acid-binding and exonuclease proteins. After exposure to dsRNA or siRNAs, animals with eri-1 mutations accumulate more siRNAs than do wild-type animals. C. elegans ERI-1 and its human orthologue degrade siRNAs in vitro. In the nematode worm, ERI-1 is predominantly cytoplasmic and is expressed most highly in the gonad and a subset of neurons, suggesting that ERI-1 siRNase activity suppresses RNA interference more intensely in these tissues. Thus, ERI-1 is a negative regulator that may normally function to limit the duration, cell-type specificity or endogenous functions of RNA interference.

Amino Acid Sequence↗
PubMed2003

Biochemical analysis and scanning force microscopy reveal productive and nonproductive ADAR2 binding to RNA substrates.

Scanning force microscopy (SFM) can be used to image biomolecules at high resolution. Here we demonstrate that single-molecule analysis by SFM complements biochemical data on RNA protein binding and can provide information that cannot be obtained by the usual biochemical methods. We have used this method to study the interaction between the RNA editing enzyme ADAR2 and RNA transcripts containing selective and nonselective editing sites. The natural selectively edited R/G site from glutamate receptor subunit B (GluR-B) was inserted into an RNA backbone molecule consisting of a completely double-stranded (ds) central part and incompletely paired ends derived from potato spindle tuber viroid (PSTVd). This molecule was efficiently edited at the R/G site, but promiscuous editing occurred at nonselective sites in the completely double-stranded region. The construct was also used to analyze binding of ADAR2 to wild-type and modified R/G editing sites in relation to binding at other nonselectively edited sites. Editing analysis together with SFM allow us to differentiate between binding and enzymatic activity. ADAR2 has been reported to have a general affinity to dsRNA. However, we show that there is a prominent bias for stable binding at sites selectively edited over other edited sites. On the other hand, promiscuous editing at nonselective sites apparently results from transient binding of the enzyme to the substrate. Furthermore, we find distinct sites with nonproductive binding of the enzyme.

Adenosine Deaminase↗
PubMed1998

Flow cytometric fluorescence lifetime analysis of DNA-binding probes.

A new dimension has been added to multiparameter flow cytometric analysis through the recent development of techniques for rapidly measuring the fluorescence lifetime of probes bound to single cells. The lifetime measurements are made by phase-sensitive detection techniques in a flow cytometer (FCM) that also analyzes fluorescence intensity and other optical properties of stained cells. These lifetime assays have potential for elucidating the microenvironment of the interaction of fluorochrome probes and subcellular target molecules. Alterations in the lifetime of DNA probes have been observed in cells in different phases of the cell cycle, in different cell types, in differentiating cells, and in apoptotic cells with damaged chromatin. Lifetime differences noted also for intercalating dyes bound to DNA and dsRNA, indicated modifications in the modes of binding and provide the potential for analyzing both corformational states and nucleic acid metabolism. Future developments in the technology will provide multiple lifetime assays and thereby allow for detection and quantitation of selected subcellular probe-complexes with different lifetime signatures. These novel assays will expand the applications for quantitative studies on the binding of various chemical agents to DNA and other molecular targets in cells, and further improve methods for rapid screening of chemotherapeutic agents or environmentally toxic compounds.

Animals↗
PubMed1995

Double-stranded RNA adenosine deaminase binds Z-DNA in vitro.

A Z-DNA binding protein of 140,000 M(r) has been purified from chicken lungs by sedimentation through 40%(w/w) sucrose and Z-DNA affinity chromatography. Specificity of the protein for Z-DNA was confirmed by competition with polyd(CG) that had been stabilized in the Z-DNA conformer by chemical bromination and also with a supercoiled plasmid that contains a Z-DNA-forming insert. In addition to a Z-DNA binding site, the protein also has a separate binding site for double-stranded RNA. Peptide sequence of the protein shows that it has high similarity to the RNA editing enzyme double-stranded RNA adenosine deaminase (dsRAD), which deaminates adenosine in dsRNA to form inosine. The Z-DNA binding protein has this enzymatic activity, confirming its identity to dsRAD. Recombinant human dsRAD also binds to Z-DNA. Z-DNA is stabilized in a sequence-dependent manner by negative supercoiling, which occurs in actively transcribed genes upstream to RNA polymerase. It is proposed that Z-DNA links editing to transcription by localizing dsRAD to a particular region of a gene and thus determines the efficiency with which an RNA is edited. The presence of Z-DNA forming elements in many genes raises the possibility that RNA editing by dsRAD is far more prevalent than is currently thought.

Adenosine Deaminase↗
PubMed2004

Testis brain ribonucleic acid-binding protein/translin possesses both single-stranded and double-stranded ribonuclease activities.

RNA interference (RNAi) is a biological process in which animal and plant cells destroy double-stranded RNA (dsRNA) and consequently the mRNA that shares sequence homology to the dsRNA. Although it is known that the enzyme Dicer is responsible for the digestion of dsRNA into approximately 22 bp fragments, the mechanism through which these fragments are associated with the RNA-induced silencing complex (RISC) is mostly unknown. To find protein components in RISC that interact with the approximately 22 bp fragment, we synthesized a (32)P- and photoaffinity moiety-labeled 22 bp dsRNA fragment and used it as bait to fish out protein(s) directly interacting with the dsRNA fragment. One of the proteins that we discovered by mass spectrometric analysis was TB-RBP/translin. Further analysis of this DNA/RNA binding protein showed that it possesses both ssRNase and dsRNase activities but not DNase activity. The protein processes long dsRNA mainly into approximately 25 bp fragments by binding to the open ends of dsRNA and cutting it with almost no turnover due to its high affinity toward the products. The activity requires physiological ionic strength. However, with single-stranded RNA as substrate, the digestion appeared to be more complete. Both ssRNase and dsRNase activities are inhibited by high levels of common RNase inhibitors. Interestingly, both activities can be enhanced greatly by EDTA.

Amino Acid Sequence↗
PubMed1994

Double-stranded RNA-dependent protein kinase activates transcription factor NF-kappa B by phosphorylating I kappa B.

The induction of interferon (IFN) genes by viruses or double-stranded RNA (dsRNA) requires the assembly of a complex set of transcription factors on responsive DNA elements of IFN gene promoters. One of the factors necessary for regulating IFN-beta gene transcription is nuclear factor NF-kappa B, the activation of which is triggered by dsRNA. It has previously been suggested that the dsRNA-activated p68 protein kinase (PKR) may act as an inducer-receptor, transducing the signal from dsRNA to NF-kappa B through phosphorylation of the inhibitor I kappa B. We present direct evidence that PKR can phosphorylate I kappa B-alpha (MAD-3) and activate NF-kappa B DNA binding activity in vitro. We further show that dsRNA induces an unusual phosphorylated form of I kappa B-alpha. The expression of a transdominant mutant PKR is able to perturb the dsRNA-mediated signaling pathway in vivo, suggesting a role for this kinase in IFN-beta gene induction.

Animals↗
PubMed2006

The kinase complex responsible for IRF-3-mediated IFN-beta production in myeloid dendritic cells (mDC).

Type I interferons (IFN) IFN-alpha and -beta play a central role in the induction of antiviral immunity, which involves up-regulation or activation of a large number of IFN-inducible genes in host immune competent cells. Initial events in the antiviral response may occur in myeloid dendritic cells (mDCs), and the proteins expressed provoke early responses to cope with concomitant infection in the host. The participation of transcription factors IRF-3/7, AP1 and NF-kappaB in IFN-beta promoter activation in mDCs is well established. An initial trigger of this event is a viral dsRNA that is recognized by proteins with an RNA-binding motif. Toll-like receptor (TLR) 3 on membranes and RIG-Iin the cytoplasm are molecules with dsRNA-recognition ability. Our main aim in the present review is to describe how IRF-3 and/or NF-kappaB are activated through the initial recognition of dsRNA by these pattern-recognition receptors. By analogy to the trimolecular complex of IKKgamma, IKKalpha and IKKbeta, thus far, IRF-3-activated kinases have been reported to be kinase complexes with trimolecular assembly. Two kinases, TBK1 and IKKepsilon, are thought to be linked to regulatory subunit TANK or NAP1 with no kinase activity like IKKgamma. The TLR3 and RIG-I pathways converge upstream of IRF-3, possibly at NAP1, the regulatory subunit of IRF-3-activating kinase. Thus, a novel function of the regulatory subunit has emerged. These proteins are involved in the TLR3 and RIG-I pathways, and act as adapters bridging on the dsRNA-recognition unit and IRF-3-activating kinases in addition to their kinase-regulatory function. Here, we summarize the properties of regulatory subunits NAP1 and TANK, and the mode of activation of NF-kappaB and IRF-3 in conjunction with the unique properties of the TLR3 function.

Animals↗
PubMed2006

Potential role of a CD36-like class B scavenger receptor in the binding of modified low-density lipoprotein (acLDL) to the tegumental surface of Schistosoma mansoni sporocysts.

Previous studies have documented the binding of low density lipoproteins (LDLs) to the tegumental surface of the mammalian stage of the human blood fluke Schistosoma mansoni, and that such binding may be functioning in the acquisition of host lipids for nutritional and/or immune evasion purposes. To determine if the intramolluscan mother sporocyst stage of S. mansoni also possess the ability to acquire exogenous LDL, live sporocysts, derived by in vitro transformation of isolated miracidia, were treated with DiI-labeled LDL (LDL-DiI) or acetylated LDL (acLDL-DiI). Sporocysts markedly differed in their binding, exhibiting strong labeling at the tegumental surface with acLDL-DiI, and only weak binding of LDL-DiI. As scavenger receptors (SRs) are known to selectively bind modified (acetylated or oxidized) LDL and other polyanionic molecules, various potential ligands of known SRs were used in an acLDL-DiI binding inhibition assay. Significant acLDL-DiI binding inhibition was observed for fucoidan, polyinosinic acid and dextran sulfate, but not for polycytidylic acid and dextran, a binding inhibition pattern consistent with SR class A or C activity. From a S. mansoni EST sequence, we cloned a scavenger receptor homologue from sporocyst cDNA that encoded a protein with 31% amino acid sequence identity and 50% similarity to a SR class B (SRB) molecule, belonging to the CD36 superfamily. Using an RNA interference assay, treatment of miracidia with a 517bp double-stranded RNA of the S. mansoni SRB gene resulted in a significant and specific knockdown (60-70%) of SRB transcript levels in sporocysts after 6 days of dsRNA exposure and was associated with a significant reduction in acLDL-DiI binding to sporocysts at 8 and 10 days post-dsRNA incubation. There also was a time-dependent decrease in sporocyst length following dsRNA treatments. The functional linkage of acLDL binding to the cloned SRB-like S. mansoni gene using RNA interference (RNAi) suggests a possible role of the tegumental SRB-like protein as a receptor for modified LDL. Inhibition of sporocyst growth also indicates a potential involvement of this SR homologue in some aspect of larval growth and/or development.

Amino Acid Sequence↗
PubMed2001

Role of double-stranded RNA-dependent protein kinase in mediating hypersensitivity of Fanconi anemia complementation group C cells to interferon gamma, tumor necrosis factor-alpha, and double-stranded RNA.

Hematopoietic cells bearing inactivating mutations of Fanconi anemia group C (FANCC) are excessively apoptotic and demonstrate hypersensitivity not only to cross-linking agents but also to interferon gamma (IFN-gamma) and tumor necrosis factor-alpha. Seeking essential signaling pathways for this phenotype, this study quantified constitutive and induced RNA-dependent protein kinase (PKR) activation in Fanconi anemia cells of the C complementation group (FA-C). PKR was constitutively phosphorylated and exhibited an increased binding affinity for double-stranded RNA (dsRNA) in FANCC(-/-) cells. FANCC(-/-) cells were hypersensitive to both dsRNA and the combination of dsRNA and IFN-gamma in that these agents induced a higher fraction of apoptosis in FANCC(-/-) cells than in normal cells. Overexpression of wild-type PKR-sensitized FANCC(-/-) cells to apoptosis induced by IFN-gamma and dsRNA. Conversely, inhibition of PKR function by enforced expression of a dominant-negative inhibitory mutant of PKR (PKRDelta6) substantially reduced the IFN and dsRNA hypersensitivity of FANCC(-/-) cells. Two PKR target molecules, IkappaB-alpha and IRF-1, were not differentially activated in FANCC(-/-) cells, but enforced expression of a nonphosphorylatable form of eukaryotic translation initiation factor-2alpha reversed the PKR-mediated block of messenger RNA translation and partially abrogated the PKR-mediated apoptosis in FANCC(-/-) cells. Because no evidence was found of a PKR/FANCC complex in normal cells, it was concluded that an essential function of FANCC is to suppress, indirectly, the activity of PKR and that FANCC inactivation results in IFN hypersensitivity, at least in part, because this function of FANCC is abrogated.

Animals↗
PubMed2000

Interferon-alpha synergistically enhances induction of interleukin-6 by double stranded RNA in HeLa cells.

Double stranded RNA (dsRNA), an intermediate that is common during viral infection, directly induces much higher levels of expression of interleukin-6 (IL-6) mRNA than does the cytokine IL-1beta. Interferon alpha (IFNalpha) by itself does not induce expression of IL-6; nonetheless, IFNalpha pretreatment dramatically enhances IL-6 induction by dsRNA but not by IL-1beta. Mutation of either the activating transcription factor/cyclic AMP response element binding protein (ATF/CREB) or the NF-IL-6 binding element within the IL-6 promoter eliminates most responsiveness of CAT reporter constructs to either dsRNA or to IL-1beta. IFNalpha pretreatment partially restores responsiveness to dsRNA but not to IL-1beta when either the ATF/CREB site or the NF-IL-6 site is mutated, but at least one of these sites must be intact for responsiveness to be restored. Mutation of the kappaB binding site in the IL-6 promoter eliminates responsiveness to either IL-1beta or to dsRNA, and pretreatment with IFNalpha does not restore any responsiveness. Incubation with dsRNA leads to a decrease in protein translation, especially in cells that have been pretreated with IFNalpha. Nonetheless, IFNalpha pretreatment followed by dsRNA leads to very high IL-6 protein levels. These studies demonstrate that major differences exist in the induction of IL-6 at both the mRNA and protein levels by dsRNA compared to cytokines and that IFNalpha pretreatment selectively enhances IL-6 induction by dsRNA but not by IL-1beta. The high levels of IL-6 expression that result when cells encounter class I IFN prior to dsRNA suggest a mechanism for a heightened host response to viral infection with heightened production of this pleotropic cytokine.

Base Sequence↗
PubMed1994

Inhibition of DNA topoisomerase I activity by 2',5'-oligoadenylates and mismatched double-stranded RNA in uninfected and HIV-1-infected H9 cells.

2',5'-Oligoadenylates (2-5As) inhibit the type I DNA topoisomerase activity both in uninfected and HIV-1-infected human T cell line H9 as well as the purified enzyme (calf thymus). Topoisomerase I activity was determined by measuring the relaxation of negatively supercoiled pBR322 DNA. Inhibition of topoisomerase I by 2-5A depends on the chain length of the oligomer and the presence of 5'-phosphate. The 5'-triphosphate of the 2-5A hexamer was most active (almost total inhibition of DNA relaxation at 10 microM concentration); the 2-5A core trimer (at 100 microM) displayed no significant effect. In crosslinking and immunoprecipitation experiments we present evidence that 2-5A (32P-labelled 2-5A derivative, ppp(A2'p)3 A[32P]pCp) is able to bind to nuclear topoisomerase I. The mismatched dsRNA, poly(I).poly(C12U) (Ampligen), exhibited a strong anti-HIV-1 activity. However, our data show that this antiviral effect is not related to topoisomerase I inhibition. On the other hand, we did observe the production of longer oligomers of 2-5A in cells treated with poly(I).poly(C12U). It remains speculative, whether the in vivo effect could be catalyzed by this activity of poly(I).poly(C12U). In addition we could show that 2-5A also inhibits topoisomerase I activity associated with isolated HIV-1 particles.

2',5'-Oligoadenylate Synthetase↗
PubMed1999

NFkappaB activation is required for interferon regulatory factor-1-mediated interferon beta induction.

The interferon regulatory factor 1 (IRF-1) acts as a transcriptional inducer of the interferon beta (IFN-beta) gene and interferon-stimulated genes. Here we report that IRF-1-mediated IFN-beta induction depends on NFkappaB activity. IRF-1 by itself initiates NFkappaB activation by inducing a reduction in cellular MAD3/IkappaBalpha, an inhibitor of NFkappaB. After nuclear translocation, NFkappaB synergizes with IRF-1 on the cis-elements positive regulatory domain (PRD)II and PRDI/III to induce transcription of the IFN-beta gene. In contrast with IFN-beta transcription induced by dsRNA or virus, c-Jun/ATF-2 binding to PRDIV is not involved. Recombinant MAD3/IkappaBalpha is phosphorylated in vitro by extracts from IRF-1-expressing cells. IRF-1-dependent MAD3/IkappaBalpha degradation is not detectable in cells expressing a dominant negative mutant of the protein kinase PKR, suggesting that PKR mediates MAD3/IkappaBalpha degradation.

Binding Sites↗