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PubMed2005

Analysis of chitin synthase function in a plant parasitic nematode, Meloidogyne artiellia, using RNAi.

A single chitin synthase gene is responsible for chitin production in the eggshells of the plant parasitic nematode Meloidogyne artiellia. In this paper we describe a functional analysis of this gene using RNAi as well as further analysis of two similar genes from the free-living nematode Caenorhabditis elegans. The parasitic life-style of M. artiellia required the development of a novel method for delivery of dsRNA to nematode eggs that may be of utility in other experimental systems. C. elegans chitin synthase genes were silenced by feeding nematodes bacteria expressing appropriate chitin synthase dsRNA from a plasmid vector, while M. artiellia egg masses were soaked in dsRNA solution. The results obtained demonstrated that the synthesis of chitin continues to take place in nematode eggs within the egg sac in the parasitic nematode, and that the removal of this activity affects egg development in both C. elegans and M. artiellia. The method described here provides a new way of investigating gene function in plant parasitic nematodes allowing the validity of potential target genes for novel control methods to be assessed. Furthermore, since intact egg cells within the gelatinous matrix of M. artiellia are permeable to dsRNA, eggs of other nematodes may also be similarly permeable to dsRNA and therefore amenable to use with dsRNAi.

Animals↗
PubMed2005

Role of double-stranded RNA and Npro of classical swine fever virus in the activation of monocyte-derived dendritic cells.

Classical swine fever virus (CSFV) is a noncytopathogenic (ncp) positive-sense RNA virus that replicates in myeloid cells including macrophages and dendritic cells (DC). The virus does not induce type I interferon (IFN-alpha/beta), which in macrophages has been related to the presence of the viral Npro gene. In the present work, the role of viral double-stranded (ds)RNA and Npro in the virus-host cell interaction has been analyzed. Higher levels of detectable dsRNA were produced by a genetically engineered cytopathogenic (cp) CSFV compared with ncp CSFV, and cp CSFV induced IFN-alpha/beta in PK-15 cells. With DC, there was only a small difference in the levels of dsRNA between the cp and ncp viruses, and no IFN-alpha/beta was produced. However, the cp virus induced a higher degree of DC maturation, in terms of CD80/86 and MHC II expression. Npro deletion mutants induced an increase in DC maturation and IFN-alpha/beta production-for both ncp and cp viruses-despite reduced replication efficiency in the DC. Deletion of Npro did not influence dsRNA levels, indicating that the interference was downstream of dsRNA turnover regulation. In conclusion, the capacity of CSFV to replicate in myeloid DC, and prevent IFN-alpha/beta induction and DC maturation, requires both regulated dsRNA levels and the presence of viral Npro.

Animals↗
PubMed2004

The bluetongue virus core: a nano-scale transcription machine.

The replication phase of the bluetongue virus (BTV) infection cycle is initiated when the virus core is delivered into the cytoplasm of a susceptible host cell. The 10 segments of the viral genome remain packaged within the core throughout the replication cycle, helping to prevent the activation of host defence mechanisms that would be caused by direct contact between the dsRNA and the host cell cytoplasm. However, the BTV core is a biochemically active 'nano-scale' machine, which can simultaneously and repeatedly transcribe mRNA from each of the 10 genome segments, which are packaged as a liquid crystal array within a central cavity. These mRNAs, which are also capped and methylated within the core, are extruded into the cytoplasm through pores at the vertices of the icosahedral structure, where they are translated into viral proteins. One copy of each of the viral mRNAs is also assembled with these newly synthesised proteins to form nascent virus particles, which mature by a process that involves -ve RNA strand synthesis on the +ve stand template, thereby reforming dsRNA genome segments within progeny virus cores. The structure of the BTV core particle has been determined to atomic resolution by X-ray crystallography, revealing the organisation and interactions of its major protein components (VP3(T2)-subcore shell and VP7(T13) outer core layer) and important features of the packaged dsRNA. By soaking crystals of BTV cores with metal ions and substrates/products of the transcription reactions prior to analysis by X-ray crystallography, then constructing difference maps, it has been possible to identify binding sites and entry/exit routes for these ions, substrates and products. This has revealed how BTV solves the many logistical problems of multiple and simultaneous transcription from the 10 genome segments within the confined space of the core particle. The crystal structure of the BTV core has also revealed an outer surface festooned with dsRNA. This may represent a further protective strategy adopted by the virus to prevent host cell shut-off, by sequestering any dsRNA that may be released from damaged particles.

Animals↗
PubMed2006

An endornavirus from a hypovirulent strain of the violet root rot fungus, Helicobasidium mompa.

We determined the complete nucleotide (nt) sequence (16,614 nt) of a large double-stranded (ds) RNA (referred to as L1 dsRNA), previously identified as the hypovirulence factor from strain V670 of the violet root rot fungus, Helicobasidium mompa. The positive-strand of L1 dsRNA contained a long open reading frame (ORF) potentially encoding a protein of 5,373 amino acids (molecular mass 603,080 Da) with conserved motifs characteristic of RNA-dependent RNA polymerase (RdRp) and helicase. The ORF is the longest so far reported in the fungal kingdom. The putative RdRp and helicase were shown to be related to putative RdRps and helicases of members of the genus Endornavirus. As is the case with endornaviruses, the coding (sense) strand of L1 dsRNA contained a discontinuity (nick) at nt position 2,552. A region between the RdRp and helicase domains of the polyprotein also had an amino acid sequence, resembling UDP glycosyltransferases (UGTs) in Oryza sativa endornavirus and Phytophthora endornavirus 1. Regions in the L1 dsRNA-encoded protein presumed to contain putative helicase, UGT and RdRp motifs were present at comparable positions to those in other endornaviruses. L1 dsRNA of H. mompa strain V670 was assigned to the genus Endornavirus, and here, we designate it as H. mompa endornavirus 1-670 (HmEV1-670). This represents the first report of a fungal endornavirus whose complete nucleotide sequence has been determined.

Amino Acid Motifs↗
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↗
PubMed2002

Glycine 38 is crucial for the ribonucleolytic activity of human pancreatic ribonuclease on double-stranded RNA.

Human pancreatic ribonuclease (HPR) and bovine seminal ribonuclease (BS-RNase) exhibit significantly higher activity against double stranded RNA (dsRNA), compared to RNase A. The high dsRNA cleavage activity of BS-RNase, in part, has been attributed to glycine residues at positions 38 and 111. HPR possesses a glycine residue at position 38, whereas it has a glutamic acid at position 111. To understand the mechanism of dsRNA degradation by the single strand preferring HPR, we have generated HPR variants containing mutations at positions 38 and 111. Our study shows that Glycine 38 is crucial for the full catalytic activity of the human enzyme on duplex RNA as its substitution with aspartate or alanine results in a drastic reduction in the dsRNA cleavage activity of HPR. The substitution of Glutamate111 with glycine also resulted in the reduction of the dsRNA cleavage activity of HPR, indicating that a glycine residue at 111 is not a requirement for the ribonucleolytic activity on double stranded substrate.

Animals↗
PubMed2003

Double-stranded RNA can mediate the suppression of uracil phosphoribosyltransferase expression in Toxoplasma gondii.

Double-stranded RNA (dsRNA) homologous to the Toxoplasma gondii uracil phosphoribosyltransferase (TgUPRT) gene is able to modulate the UPRT gene expression in T. gondii. The dsRNA, which was produced either from a constructed plasmid or from an in vitro transcription reaction, was capable of down-regulating the expression of TgUPRT. Stably transformed T. gondii expressing the dsRNA, which was capable of growing in the presence of the prodrug 5-fluoro-2(')-deoxyuridine (FDUR), appeared to maintain the engineered plasmid as an extra-chromosomal DNA. When cultured in the absence of the selection pressure, the FDUR resistant parasites slowly reverted to the FDUR sensitive phenotype. The level of the dsRNA necessary to confer FDUR resistance was estimated at 2-8 copies per parasite. More importantly the introduction of the in vitro synthesized dsRNA homologous to the TgUPRT gene into T. gondii can also induce the specific mRNA degradation, resulting in a lowered UPRT activity.

Animals↗
PubMed2002

Molecular dynamics simulation of the RNA complex of a double-stranded RNA-binding domain reveals dynamic features of the intermolecular interface and its hydration.

The interaction between double-stranded RNA (dsRNA) and the third double-stranded domain (dsRBD) from Drosophila Staufen protein represents a paradigm to understand how the dsRBD protein family, one of the most common RNA-binding protein units, binds dsRNA. The nuclear magnetic resonance (NMR) structure of this complex and the x-ray structure of another family member revealed the stereochemical basis for recognition, but also raised new questions. Although the crystallographic studies revealed a highly ordered interface containing numerous water-mediated contacts, NMR suggested extensive residual motion at the interface. To address how interfacial motion contributes to molecular recognition in the dsRBD-dsRNA system, we conducted a 2-ns molecular dynamics simulation of the complex derived from Staufen protein and of the separate protein and RNA components. The results support the observation that a high degree of conformational flexibility is retained upon complex formation and that this involves interfacial residues that are critical for dsRBD-dsRNA binding. The structural origin of this residual flexibility is revealed by the analysis of the trajectory of motion. Individual basic side chains switch continuously from one RNA polar group to another with a residence time seldom exceeding 100 ps, while retaining favorable interaction with RNA throughout much of the simulation. Short-lived water molecules mediate some of these interactions for a large fraction of the trajectory studied here. This result indicates that water molecules are not statically associated with the interface, but continuously exchange with the bulk solvent on a 1-10-ps time scale. This work provides new insight into dsRBD-dsRNA recognition and builds upon a growing body of evidence, suggesting that short-lived dynamic interactions play important roles in protein-nucleic acid interactions.

Binding Sites↗
PubMed1999

Immunoregulatory potential of urothelium: characterization of NF-kappaB signal transduction.

PURPOSE: To characterize the basal and activated form of nuclear factor-kappaB (NF-kappaB) complex in normal urothelial cell cultures after stimulation with tumor necrosis factor-alpha (TNF-alpha), lipopolysaccharide (LPS), and double-stranded ribonucleic acid (dsRNA). MATERIALS AND METHODS: Human urothelial cells cultured from normal bladder specimens underwent immunohistochemical staining and cellular extracts were prepared for Electrophoretic Mobility Shift Assays (EMSA), Western blot analyses, RNA isolation and Northern Blot analyses before and after stimulation with TNF-alpha, LPS, and dsRNA. RESULTS: In normal human urothelial cells, activation of the NF-kappaB complex in response to stimulation with TNF-alpha, LPS, and dsRNA was detected by immunohistochemical methods and EMSA. Depending on the stimulus, a specific NF-kappaB complex was activated as seen by supershift experiments in EMSA. By Western blot, the inhibitor of NF-kappaB complex, IkappaB-alpha, degraded in response to stimulation. Northern blot analysis from total RNA revealed subsequent inducible interleukin-8 (IL-8) mRNA expression of normal urothelial cells when treated with TNF-alpha, LPS, and dsRNA. CONCLUSIONS: Normal human urothelial cells contain basal NF-kappaB complexes in an inactivated state. When these cells are challenged by different agents such as TNF-alpha, LPS, and dsRNA, the cells respond by activation of the NF-kappaB signal transduction pathway, degradation of its inhibitor, IkappaB-alpha, and translocation of this primary factor into the nucleus to induce specific genetic responses such as IL-8 expression.

Cells, Cultured↗
PubMed2005

RNA interference in Caenorhabditis elegans.

RNA interference (RNAi) was first discovered in the nematode Caenorhabditis elegans (Fire et al., 1998; Guo and Kemphues, 1995). The completion of the C. elegans genome in 1998 coupled with the advent of RNAi techniques to knock down gene function ushered in a new age in the field of functional genomics. There are four methods for double-stranded RNA (dsRNA) delivery in C. elegans: (1) injection of dsRNA into any region of the animal (Fire et al., 1998), (2) feeding with bacteria producing dsRNA (Timmons et al., 2001), (3) soaking in dsRNA (Tabara et al., 1998), and (4) in vivo production of dsRNA from transgenic promoters (Tavernarakis et al., 2000). In this chapter, we discuss the molecular genetic mechanisms, techniques, and applications of RNAi in C. elegans.

Animals↗
PubMed2001

RNAi as random degradative PCR: siRNA primers convert mRNA into dsRNAs that are degraded to generate new siRNAs.

In posttranscriptional gene silencing (PTGS), "quelling," and RNA interference (RNAi), 21-25 nucleotide RNA fragments are produced from the initiating dsRNA. These short interfering RNAs (siRNAs) mediate RNAi by an unknown mechanism. Here, we show that GFP and Pp-Luc siRNAs, isolated from a protein complex in Drosophila embryo extract, target mRNA degradation in vitro. Most importantly, these siRNAs, as well as a synthetic 21-nucleotide duplex GFP siRNA, serve as primers to transform the target mRNA into dsRNA. The nascent dsRNA is degraded to eliminate the incorporated target mRNA while generating new siRNAs in a cycle of dsRNA synthesis and degradation. Evidence is presented that mRNA-dependent siRNA incorporation to form dsRNA is carried out by an RNA-dependent RNA polymerase activity (RdRP).

Animals↗
PubMed2000

Cloning, sequencing and expression of the gene that encodes the major neutralisation-specific antigen of African horsesickness virus serotype 9.

A marked improvement in the efficiency of cloning the large double stranded RNA (dsRNA) genome segments of African horsesickness virus (AHSV) was achieved when the dsRNA polyadenylation step was carried out with undenatured rather than strand-separated dsRNA. It is a prerequisite to use dsRNA of very high purity because in the presence of even trace amounts of single stranded RNA, the dsRNA appears to be poorly polyadenylated as judged by its effectiveness as a template for oligo-dT-primed cDNA synthesis. The full-length VP2 gene of AHSV-9, cloned by this approach, was sequenced and it was found to show the highest percentage identity (60%) to VP2 of AHSV-6, providing an explanation of why these two serotypes show some cross protection. The VP2 protein was also expressed in Spodoptera frugiperda (Sf9) cells by means of a baculovirus recombinant. The yield of the expressed VP2 was high, but the protein was found to be largely insoluble. Nine smaller, truncated VP2 peptides were subsequently expressed in insect cells, but no significant improvement in solubility of the peptides, as compared to that of the full-sized protein, was observed. A western immunoblot analysis of the overlapping peptides indicated the presence of a strong linear epitope located within a large hydrophilic domain between amino acids 369 and 403.

African Horse Sickness↗
PubMed2002

RNA interference (RNAi) inhibits growth of Plasmodium falciparum.

RNA interference (RNAi) causes degradation of targeted endogenous RNA in many diverse organisms. Erythrocyte-infecting stages of the malaria parasite Plasmodium falciparum were treated with double-stranded RNA (dsRNA) encoding a segment of the gene encoding dihydroorotate dehydrogenase (DHODH). DHODH is an enzyme in pyrimidine biosynthesis, essential for parasite growth. A decrease in parasite growth (P<0.0005) correlated with a decrease in levels of DHODH mRNA. Control treatments with single-stranded RNA, dsRNA encoding the circumsporozoite protein (a stage-specific protein not expressed in the asexual blood stage) and dsRNA encoding a gene from the related organism Toxoplasma gondii did not inhibit growth. As a test for the RNAi assay, parasites were treated with dsRNA encoding chorismate synthase (CS), an enzyme thought to be involved in folate synthesis, to examine the requirement for this enzyme for parasite growth. Growth decreased (P<0.001) though less markedly than by dsRNA encoding DHODH. These results demonstrate the utility of this assay in assessing requirements for gene products, and their potential as chemotherapeutic targets.

Animals↗
PubMed2001

Double-stranded RNA-induced interferon regulatory factor-1 gene expression in FRTL-5 rat thyroid cells.

Double-stranded RNA (dsRNA) plays a role in the regulation of cell growth and apoptosis as well as in the cellular antiviral responses. However, it remains unknown if dsRNA-activated signaling systems are functional in the thyroid. Here we report the presence of the dsRNA-dependent protein kinase (PKR) in FRTL-5 rat thyroid cells. In poly(I)-poly(C) (pIC)-stimulated cells, activation of nuclear factor-kappa B (NF kappa B) binding was clearly induced. Incubation of FRTL-5 cells with pIC resulted in a marked increase in interferon regulatory factor-1 (IRF-1) mRNA and phosphorylated signal transducer and activator of transcription-1 (STAT1) levels. Addition of pIC to cells led to type I interferon (IFN) gene expression, especially IFN beta, which can induce STAT1 phosphorylation, suggesting that dsRNA indirectly induced STAT1 phosphorylation through expression of type I IFN. Thus, our results suggest that the dsRNA-activated signaling pathway may be involved in the regulation of IFN-inducible genes in the thyroid.

Animals↗
PubMed1978

Double stranded RNA in heterogeneous nuclear RNA from normal and chronic lymphocytic leukemic lymphocytes.

Tritium labelled heterogeneous nuclear RNA (HnRNA) from normal and chronic lymphocytic leukemic (CLL) lymphocytes was investigated before and after fractionation into non-poly(A) containing (-HnRNA) and poly(A) containing (+HnRNA) HnRNA with respect to double stranded RNA (dsRNA). Statistically significant higher amounts of rapidly labelled RNA were recovered from CLL lymphocytes when compared to normal cases. Within the CLL cases a significant linear correlation (r = 0.95) was found between white blood cell counts and the amount of dsRNA in total HnRNA. After fractionation into (-) and (+) HnRNAs the ratios of dsRNAs, expressed as the dsRNA in (-) HnRNA divided by the dsRNA in (+) HnRNA, was lower than the corresponding values in normal cases for all the CLL cases except one. The relationship between (+) HnRNA and the total dsRNA level was different when comparing CLL and normal lymphocytes indicating a RNA processing abnormality.

Humans↗
PubMed2002

Spatial and temporal 'knock down' of gene expression by electroporation of double-stranded RNA and morpholinos into early postimplantation mouse embryos.

Here we report the use of double-stranded RNA (dsRNA) and morpholino technologies to specifically 'knock down' gene expression in early postimplantation mouse embryos. Sequence specific interference mediated by either dsRNA or by morpholino has been a useful tool for studying gene function in several organisms. However, specifically for the dsRNA, doubts have been raised about whether it could successfully be applied on vertebrate embryos. We demonstrate that electroporation of dsRNA directed against Otx2 or Foxa2 into postimplantation mouse embryos results in specific knock down of the expression of the respective endogenous genes in a region- and germ-layer specific manner. We also show that electroporation of morpholino directed against Foxa2 into the node of mouse embryos leads to a specific down regulation of Foxa2 expression in the floor plate. Our results demonstrate for the first time that dsRNA and morpholino technologies can be successfully applied in early postimplantation mouse embryos to specifically knock down gene expression.

Animals↗
PubMed2003

Genome-wide RNAi screening in Caenorhabditis elegans.

In Caenorhabditis elegans, introduction of double-stranded RNA (dsRNA) results in the specific inactivation of an endogenous gene with corresponding sequence; this technique is known as RNA interference (RNAi). It has previously been shown that RNAi can be performed by direct microinjection of dsRNA into adult hermaphrodite worms, by soaking worms in a solution of dsRNA, or by feeding worms Escherichia coli expressing target-gene dsRNA. We have developed a simple optimized protocol exploiting this third mode of dsRNA introduction, RNAi by feeding, which allows rapid and effective analysis of gene function in C. elegans. Furthermore, we have constructed a library of bacterial strains corresponding to roughly 86% of the estimated 19,000 predicted genes in C. elegans, and we have used it to perform genome-wide analyses of gene function. This library is publicly available, reusable resource allowing for rapid large-scale RNAi experiments. We have used this library to perform genome-wide analyses of gene function in C. elegans. Here, we describe the protocols used for bacterial library construction and for high-throughput screening in C. elegans using RNAi by feeding.

Animals↗
PubMed2002

The role of RNA editing by ADARs in RNAi.

Adenosine deaminases that act on RNA (ADARs) are RNA-editing enzymes that deaminate adenosines to create inosines in double-stranded RNA (dsRNA). Here we demonstrate that ADARs are not required for RNA interference (RNAi) and that they do not antagonize the pathway to a detectable level when RNAi is initiated by injecting dsRNA. We find, however, that transgenes expressed in the somatic tissues of wild-type animals are silenced in strains with deletions in the two genes encoding ADARs, adr-1 and adr-2. Transgene-induced gene silencing in adr-1;adr-2 mutants depends on genes required for RNAi, suggesting that a dsRNA intermediate is involved. In wild-type animals we detect edited dsRNA corresponding to transgenes, and we propose that editing of this dsRNA prevents somatic transgenes from initiating RNAi in wild-type animals.

Adenosine Deaminase↗