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PubMed1996

Polycistronic (tri- or bicistronic) phytoreoviral segments translatable in both plant and insect cells.

Genomic segment S12 of rice dwarf virus and segment S9 of wound tumor virus, both members of the genus Phytoreovirus, have small out-of-phase overlapping open reading frames (ORFs). Western blot (immunoblot) analysis revealed that rice dwarf virus S12 mRNA specified translation products from the large ORF and two overlapping small ORFs both in rice plant hosts and in Spodoptera frugiperda insect cells. These results provide the first example of a tricistronic mRNA for a segmented double-stranded RNA virus. Similarly, wound tumor virus S9 mRNA was found to direct the synthesis of protein products from both the large ORF and small out-of-frame ORF in S. frugiperda cells. Results of site-specific and deletion mutagenesis studies were consistent with a leaky scanning translation mechanism for the synthesis of the small ORFs.

Animals↗
PubMed1994

Virus-associated down-regulation of the gene encoding cryparin, an abundant cell-surface protein from the chestnut blight fungus, Cryphonectria parasitica.

We report here the cloning and analysis of the gene (Crp) encoding cryparin (CRP) and the suppression of the accumulation of its mRNA by a double-stranded RNA virus. CRP belongs to a group of fungal hydrophobic cell surface proteins and has sequence similarity to cerato-ulmin, a phytotoxin produced by Ophiostoma ulmi, the Dutch elm disease pathogen. Transcripts of the Crp gene represent almost 25% of the mRNA of the fungal cell during the peak of CRP production.

Amino Acid Sequence↗
PubMed1974

"Methylation-coupled" transcription by virus-associated transcriptase of cytoplasmic polyhedrosis virus containing double-stranded RNA.

S-adenosyl-L-methionine (SAM) activated the virus-associated RNA polymerase of cytoplasmic polyhedrosis virus in vitro. Synthesis of single-stranded viral RNA (mRNA) proceeded depending on the presence of SAM.A methyl residue of SAM was incorporated into an RNA molecule. A ribose moiety of adenylic acid in the 5'-terminal region of the nascent RNA was methylated in the very early stage of the transcription. The dependence of the viral transcription on the presence of SAM and the methylation of terminal nucleotide suggests that the transcription of CPV is a "methylation-coupled" reaction.

DNA-Directed RNA Polymerases↗
PubMed1993

Mutants of Ustilago maydis defective in production of one of two polypeptides of KP6 toxin from the preprotoxin.

Double-stranded RNA viruses of Ustilago maydis encode secreted killer toxins to which other cells of the same species and closely related species are sensitive. KP6 toxin consists of two polypeptides, alpha and beta, produced from a single precursor preprotoxin. In this work, we cloned complementary DNA for the toxin-encoding segment of two of the KP6 nonkiller mutants NK3 and NK13 that secrete the beta and alpha polypeptides, respectively. Both sequence analysis of the cDNA clones and in vitro translation of the toxin-encoding double-stranded RNAs showed that both mutants can produce full-length preprotoxins. Cys51 in alpha is converted to Arg in NK3 and Thr25 and Lys42 in beta are changed to Pro and Arg, respectively, in NK13. Although alpha and beta are encoded in a single prepropolypeptide, only the beta polypeptide is secreted by NK3 and only the alpha polypeptide is secreted by NK13. This differential expression of peptides from one precursor is a unique phenomenon. Neither of the nonsecreted polypeptides accumulated in the cytosol. The possible effects of these mutations on preprotoxin folding and their consequences for toxin secretion are discussed.

Amino Acid Sequence↗
PubMed1999

A novel virus-host cell membrane interaction. Membrane voltage-dependent endocytic-like entry of bacteriophage straight phi6 nucleocapsid.

Studies on the virus-cell interactions have proven valuable in elucidating vital cellular processes. Interestingly, certain virus-host membrane interactions found in eukaryotic systems seem also to operate in prokaryotes (Bamford, D.H., M. Romantschuk, and P. J. Somerharju, 1987. EMBO (Eur. Mol. Biol. Organ.) J. 6:1467-1473; Romantschuk, M., V.M. Olkkonen, and D.H. Bamford. 1988. EMBO (Eur. Mol. Biol. Organ.) J. 7:1821-1829). straight phi6 is an enveloped double-stranded RNA virus infecting a gram-negative bacterium. The viral entry is initiated by fusion between the virus membrane and host outer membrane, followed by delivery of the viral nucleocapsid (RNA polymerase complex covered with a protein shell) into the host cytosol via an endocytic-like route. In this study, we analyze the interaction of the nucleocapsid with the host plasma membrane and demonstrate a novel approach for dissecting the early events of the nucleocapsid entry process. The initial binding of the nucleocapsid to the plasma membrane is independent of membrane voltage (DeltaPsi) and the K(+) and H(+) gradients. However, the following internalization is dependent on plasma membrane voltage (DeltaPsi), but does not require a high ATP level or K(+) and H(+) gradients. Moreover, the nucleocapsid shell protein, P8, is the viral component mediating the membrane-nucleocapsid interaction.

Adenosine Triphosphate↗
PubMed2005

Penetration of enveloped double-stranded RNA bacteriophages phi13 and phi6 into Pseudomonas syringae cells.

Bacteriophages phi6 and phi13 are related enveloped double-stranded RNA viruses that infect gram-negative Pseudomonas syringae cells. phi6 uses a pilus as a receptor, and phi13 attaches to the host lipopolysaccharide. We compared the entry-related events of these two viruses, including receptor binding, envelope fusion, peptidoglycan penetration, and passage through the plasma membrane. The infection-related events are dependent on the multiplicity of infection in the case of phi13 but not with phi6. A temporal increase of host outer membrane permeability to lipophilic ions was observed from 1.5 to 4 min postinfection in both virus infections. This enhanced permeability period coincided with the fast dilution of octadecyl rhodamine B-labeled virus-associated lipid molecules. This result is in agreement with membrane fusion, and the presence of temporal virus-derived membrane patches on the outer membrane. Similar to phi6, phi13 contains a thermosensitive lytic enzyme involved in peptidoglycan penetration. The phage entry also caused a limited depolarization of the plasma membrane. Inhibition of host respiration considerably decreased the efficiency of irreversible virus binding and membrane fusion. An active role of cell energy metabolism in restoring the infection-induced defects in the cell envelope was also observed.

Bacteriophage phi 6↗
PubMed1995

Resistance against multiple plant viruses in plants mediated by a double stranded-RNA specific ribonuclease.

Many plant viruses have single-stranded RNAs as their genomes. During the course of replication, genomic RNAs and their complementary template RNAs are likely to form double-stranded (ds) RNA at least transiently. To attack replication intermediates of many plant RNA viruses specifically, we introduced a yeast-derived ds-RNA specific RNase gene called pac 1 into plants. The transformed plants showed a decrease in lesion numbers when they were challenged with tomato mosaic virus, and a delay in the appearance of symptoms when inoculated with cucumber mosaic virus or potato virus Y.

Mosaic Viruses↗
PubMed1983

Separation of the complementary strands of double-stranded cucumber mosaic virus-associated RNA 5 and peanut stunt virus-associated RNA 5.

The double-stranded forms of CARNA 5 and PARNA 5, viral satellites of the cucumovirus group, after denaturation and polyacrylamide gel electrophoresis under appropriate conditions allow their complementary strands to be separated and fractionated. These fractionated (+) and (-) strands are free of contaminating viral RNA fragments. They serve as templates for the preparation of cDNAs of opposite polarity, which are used to probe the viral RNA-dependent replication of CARNA 5 and PARNA 5.

Arachis↗
PubMed2006

Expression of toll-like receptors and type 1 interferon specific protein MxA in biliary atresia.

Viral infection and type I interferon have been implicated in the pathogenesis of biliary atresia (BA), but the expression of toll-like receptors (TLRs) that recognize viruses, as well as of type 1 interferon specific signaling molecules are still unknown in BA. Fresh liver tissues were obtained from patients in early and late stage of BA and from patients with choledochal cyst (CC), as well as from normal controls receiving liver resection for benign lesion other than cholestasis or fibrosis. Archived liver tissues from patients with neonatal hepatitis (NH) were obtained for immunohistochemical studies. TLR2, 3, 4, 7 and 9 that recognized Gram-positive bacteria, double-stranded RNA virus, lipopolysaccharide, single-stranded RNA virus and DNA virus, respectively, were studied. Real-time quantitative reverse transcription polymerase chain reaction (QRT-PCR) was used to quantitate TLR, type I interferon specific molecule MxA, interleukin-6 (IL-6) and IL-8 mRNA expression and immunohistochemistry for TLR 7 and MxA protein staining. These results show that there were significantly higher TLR7 and lower TLR3 and TLR9 mRNA expression in early stage of BA than in CC. MxA mRNA expression was also significantly higher in early stage of BA and in CC than in late stage of BA. Immunoreactive TLR7 and MxA staining was higher in early stage of BA than in late stage of BA, NH and CC, which was associated with significantly higher IL-8 mRNA expression in BA than in CC. The results implicate involvement of TLRs, particularly TLR7, and type 1 specific interferon signaling in the pathogenesis of BA, especially in early stage, which is associated with upregulation of inflammatory cytokines IL-8.

Adolescent↗
PubMed1991

Molecular cloning and characterization of W double-stranded RNA, a linear molecule present in Saccharomyces cerevisiae. Identification of its single-stranded RNA form as 20 S RNA.

Most strains of the yeast Saccharomyces cerevisiae harbor a double-stranded RNA (dsRNA) molecule, called W. We obtained W cDNA clones by random priming of denatured W dsRNA followed by reverse transcription. Sequence data of W shows that only one strand ((+)-strand) has coding capacity for a protein with 829 amino acids which spans almost the entire length of the molecule (2.5 kilobases). Within this protein we found a sequence pattern characteristic of RNA dependent RNA polymerases of (+)-strand and double-stranded RNA viruses. W has no homology with other dsRNAs found in S. cerevisiae, such as L-A, L-BC or M1. However, a (+)-strand-specific probe for W hybridized with 20-S RNA. Furthermore, W (+)-strands comigrated with 20 S RNA in strand separation gels. These results suggest that 20 S RNA is a (+)-single-stranded RNA form of W dsRNA itself or a closely related molecule.

Amino Acid Sequence↗
PubMed2004

Novel predicted peptidases with a potential role in the ubiquitin signaling pathway.

A multi-pronged strategy including extensive sequence searches, structural modeling, and analysis of contextual information extracted from domain architectures, genetic screens, and large-scale protein-protein interaction analyses was employed to predict previously undetected components of the eukaryotic ubiquitin (Ub) signaling system. Two novel groups of proteins that are likely to function as de-ubiquitinating and de-SUMOylating peptidases (DUBs) were identified. The first group of putative DUBs, designated PPPDE superfamily (after Permuted Papain fold Peptidases of DsRNA viruses and Eukaryotes), consists of predicted thiol peptidases with a circularly permuted papain-like fold. The inference of the likely DUB function of the PPPDE superfamily proteins is based on the fusions of the catalytic domain to Ub-binding PUG (PUB)/UBA domains and a novel alpha-helical Ub-associated domain (the PUL domain, after PLAP, Ufd3p and Lub1p). The presence of the PPPDE superfamily proteins in most eukaryotic lineages, including basal ones, such as Giardia, suggests a role in deubiquitination of highly conserved proteins involved in key cellular functions, such as cell cycle control. In addition to eukaryotic proteins, the PPPDE superfamily includes predicted proteases from several groups of double-stranded RNA viruses and one single-stranded DNA virus. The apparent recruitment of DUBs for viral polyprotein processing seems to represent a common theme in evolution of viruses. The second group of putative DUBs identified in this study is the WLM (Wss1p-like metalloproteases) family of the Zincin-like superfamily of Zn-dependent peptidases, which are linked to the Ub-system by virtue of fusions with the UB-binding PUG (PUB), Ub-like, and Little Finger domains. More specifically, genetic evidence implicates the WLM family in de-SUMOylation. If validated experimentally, the WLM family proteins will represent the first case of a Zincin-like metalloprotease involvement in Ub-signaling.

Amino Acid Sequence↗
PubMed2005

Brome mosaic virus 1a nucleoside triphosphatase/helicase domain plays crucial roles in recruiting RNA replication templates.

Positive-strand RNA virus RNA replication is invariably membrane associated and frequently involves viral proteins with nucleoside triphosphatase (NTPase)/helicase motifs or activities. Brome mosaic virus (BMV) encodes two RNA replication factors: 1a has a C-terminal NTPase/helicase-like domain, and 2a(pol) has a central polymerase domain. 1a accumulates on endoplasmic reticulum membranes, recruits 2a(pol), and induces 50- to 70-nm membrane invaginations (spherules) serving as RNA replication compartments. 1a also recruits BMV replication templates such as genomic RNA3. In the absence of 2a(pol), 1a dramatically stabilizes RNA3 by transferring RNA3 to a membrane-associated, nuclease-resistant state that appears to correspond to the interior of the 1a-induced spherules. Prior results show that the 1a NTPase/helicase-like domain contributes to RNA recruitment. Here, we tested mutations in the conserved helicase motifs of 1a to further define the roles of this domain in RNA template recruitment. All 1a helicase mutations tested showed normal 1a accumulation, localization to perinuclear endoplasmic reticulum membranes, and recruitment of 2a(pol). Most 1a helicase mutants also supported normal spherule formation. Nevertheless, these mutations severely inhibited RNA replication and 1a-induced stabilization of RNA3 in vivo. For such 1a mutants, the membrane-associated RNA3 pool was both reduced and highly susceptible to added nuclease. Thus, 1a recruitment of viral RNA templates to a membrane-associated, nuclease-resistant state requires additional functions beyond forming spherules and recruiting RNA to membranes, and these functions depend on the 1a helicase motifs. The possibility that, similar to some double-stranded RNA viruses, the 1a NTPase/helicase-like domain may be involved in importing viral RNAs into a preformed replication compartment is discussed.

Bromovirus↗
PubMed1994

NTP binding induces conformational changes in the double-stranded RNA bacteriophage ø6 subviral particles.

Bacteriophage ø6 is a double-stranded RNA virus consisting of a nucleocapsid (NC) surrounded by a membrane. Beneath the NC major coat protein, P8, resides the ø6 RNA polymerase complex which is composed of four early proteins P1, P2, P4, and P7. Protein P1 forms the dodecahedral framework with which the other three proteins are associated. We have developed a new method for the isolation of stable polymerase complex particles which retain their structural integrity and polymerase activity for several days. Purine nucleotides, especially GTP, dGTP, ddGTP, and GDP, stabilized the particle efficiently. Furthermore, binding of any NTP was shown to induce conformational changes in the NC structure, as detected by alterations in the binding properties of NC-specific monoclonal antibodies. In the presence of NTPs, most of the epitopes in protein P4 become more exposed than without NTPs, while the epitopes in protein P8 were either masked or unmasked due to NTP binding. Based on the accessibility of the epitopes of protein P1 on the NC, we postulate that at least part of this protein is also accessible on the NC surface.

Binding Sites↗
PubMed1992

T double-stranded RNA (dsRNA) sequence reveals that T and W dsRNAs form a new RNA family in Saccharomyces cerevisiae. Identification of 23 S RNA as the single-stranded form of T dsRNA.

Some strains of the yeast Saccharomyces cerevisiae harbor a double-stranded RNA (dsRNA) molecule, called T. We obtained T cDNA clones by random priming of denatured T dsRNA followed by reverse transcription. Sequence data of T show that only one strand ((+)-strand) has coding capacity for a protein with 940 amino acids which spans almost the entire length of the molecule (2.9 kilobases). Within this protein we found a sequence pattern characteristic of RNA-dependent RNA polymerases of (+)-strand and double-stranded RNA viruses. Although T has no homology with other dsRNAs found in S. cerevisiae, such as L-A, L-BC, M1, or W, the T-encoded protein shows a high degree of conservation with the W-encoded protein. This conservation extends beyond a region that contains the consensus sequences for RNA-dependent RNA polymerases, suggesting that both T and W are evolutionarily related. With a (+)-strand-specific probe for T we identified 23 S RNA, a new single-stranded RNA (ssRNA) species with a sedimentation coefficient of 23 S. T and 23 S RNA have the same mobility under denaturing conditions with glyoxal, suggesting that 23 S RNA is, in fact, the (+)-single-stranded RNA form of T dsRNA. 23 S RNA synthesis is induced under stress conditions such as heat shock and starvation. The relationship between T and 23 S RNA clearly resembles the one between W and its single-stranded derivative form, 20 S RNA. Thus T and W dsRNAs (and their respective single-stranded species) constitute a new RNA family in S. cerevisiae.

Amino Acid Sequence↗
PubMed1992

Human growth factor for murine interleukin (IL)-9 responsive T cell lines: co-induction with IL-6 in fibroblasts and identification as LIF/HILDA.

Two mouse helper T cell clones that proliferate in response to murine interleukin (IL)-9 could also be grown in conditioned medium of stimulated human connective tissue cells. The activity was not due to known T cell growth factors including human IL-9, which is not effective on mouse cells. This growth-stimulatory activity for TS1 cells (GATS) was co-induced with IL-6 on normal fibroblasts and certain sarcoma cell lines stimulated with IL-1, double-stranded RNA, virus or phorbol ester. However, the conditions for optimal induction and the kinetics of production were found to be different for IL-6 and GATS. GATS from phorbol ester-stimulated human hepatosarcoma cells co-purified with IL-6, but could be separated from it by subsequent cation-exchange fast-protein liquid chromatography and reverse-phase high-performance liquid chromatography. Homogeneous tumor cell-derived GATS was a 25-kDa protein on sodium dodecyl sulfate-polyacrylamide gel electrophoresis, whereas IL-6 produced by these cells appeared in its 23-kDa form. Pure GATS was found to be inactive in the B cell hybridoma growth assay for IL-6. Finally, GATS was identified by NH2-terminal sequence analysis of the mature protein as leukemia inhibitory factor or human interleukin for DA cells (LIF/HILDA). The effect of LIF/HILDA on T cells was not mediated by IL-2, IL-4 or IL-9 production. Since this cytokine has not previously been reported to act on T cells, further investigation of its role in T cell activation should be taken into consideration.

Amino Acid Sequence↗
PubMed1989

Identification of four conserved motifs among the RNA-dependent polymerase encoding elements.

Four consensus sequences are conserved with the same linear arrangement in RNA-dependent DNA polymerases encoded by retroid elements and in RNA-dependent RNA polymerases encoded by plus-, minus- and double-strand RNA viruses. One of these motifs corresponds to the YGDD span previously described by Kamer and Argos (1984). These consensus sequences altogether lead to 4 strictly and 18 conservatively maintained amino acids embedded in a large domain of 120 to 210 amino acids. As judged from secondary structure predictions, each of the 4 motifs, which may cooperate to form a well-ordered domain, places one invariant amino acid in or proximal to turn structures that may be crucial for their correct positioning in a catalytic process. We suggest that this domain may constitute a prerequisite 'polymerase module' implicated in template seating and polymerase activity. At the evolutionary level, the sequence similarities, gap distribution and distances between each motif strongly suggest that the ancestral polymerase module was encoded by an individual genetic element which was most closely related to the plus-strand RNA viruses and the non-viral retroposons. This polymerase module gene may have subsequently propagated in the viral kingdom by distinct gene set recombination events leading to the wide viral variety observed today.

Amino Acid Sequence↗
PubMed1994

Leukocyte recruitment by monocyte chemotactic proteins (MCPs) secreted by human phagocytes.

Phagocyte recruitment is an important immunological phenomenon in inflammation and cancer. A large family of selective chemotactic cytokines, designated chemokines, has recently emerged. Interleukin-8 (IL-8) is the prototype of such neutrophil activating factors, whereas MCP-1 is a well studied monocyte chemotactic protein. In vitro chemotactic assays were used to isolate and identify natural chemokines from mononuclear phagocytes and tumor cells. Additional new chemotactic proteins (MCP-2, MCP-3) attracting monocytes were also discovered by these methods. All chemokines are structurally related and show affinity for heparin. MCP-1, -2 and -3 have a comparable specific activity in monocyte chemotaxis assays. Specific and sensitive radioimmunoassays for MCP-1 and IL-8 were developed to study the regulation of their secretion by leukocytes. Monocytes or monocyte tumor cells produce MCP-1 and/or IL-8 in response to cytokines, virus, double stranded RNA, bacterial endotoxin, mitogen or phorbol ester. Granulocytes were found to secrete only minor amounts of MCP-1 and IL-8.

Amino Acid Sequence↗
PubMed2005

Giardia lamblia: stable expression of green fluorescent protein mediated by giardiavirus.

Giardia lamblia, an early diverging eukaryote that infects several species including humans and a major agent of water-borne diarrhea throughout the world, can be infected with a double-stranded RNA virus, giardiavirus (GLV). A chimeric GLV cDNA and green fluorescent protein (GFP) according to the cis-acting signals of the GLV genome required for expression of foreign gene was constructed and its in vitro transcript was electroporated into GLV-infected G. lamblia trophozoites, GFP was expressed transiently. pGDH5/NEO/GLV was constructed by combining the neomycin resistance cassette in which the neomycin phosphotransferase gene was flanked by Giardia glutamate dehydrogenase (GDH) uncoding regions and the transcription cassette in which the chimera of GLV cDNA and GFP was located downstream from GDH gene promoter on a single plasmid. This plasmid was electroporated into G. lamblia and the transfectants persistently expressed GFP under G418 selection. This stable transfection system should provide a valuable tool for genetic study of G. lamblia.

Animals↗