Host Effect on Arbovirus Replication: Appearance of Defective Interfering Particles in Murine Cells

Serial passage of Semliki Forest virus (SFV) in chicken embryo cells had little effect on SFV yield; however, high multiplicity infection of murine cells with one of the late passage pools (passage 9 SFV) resulted in a virus yield 10- to 20-fold lower than that obtained with earlier passage virus and 80-fold lower than the corresponding yield in chicken cells. This effect was accompanied by a striking decrease in the levels of 42S and 26S RNA and by increased proportions of a small single-stranded viral RNA (molecular weight, 9 x 10(5)) and of a low-molecular-weight replicative form. There was also a reduction in the number of specific membranous structures previously associated with the group A arbovirus replication complex. These results suggested that passage 9 SFV contained defective interfering particles which were detected more readily after one passage in a murine indicator host cell. Identical results were obtained with two different murine cell lines: one a leukemia virus-free clone of AKR cells and the other JLS-V9 cells chronically infected with Rauscher leukemia virus. Host production of RNA tumor virus particles apparently did not affect arbovirus replication.     

Defective Interfering Passages of Sindbis Virus: Nature of the Intracellular Defective Viral RNA

BHK cells infected with defective-interfering passages of Sindbis virus accumulate a species of RNA (20S) that is about half the molecular weight of the major viral mRNA (26S). We have performed competitive hybridization experiments with these species of RNA and have established that 20S RNA contains approximately 50% of the nucleotide sequences present in 26S RNA. Our further studies, however, demonstrate that 20S RNA is unable to carry out the messenger function of 26S RNA. We found very little of the defective RNA associated with polysomes in vivo. In addition, it was unable to stimulate protein synthesis in vitro under conditions in which 26S RNA was translated. We have also examined viral RNA synthesis in BHK cells infected with standard or defective-interfering passages of Sindbis virus. This comparison suggests that defective partioles do not synthesize a functional replicase.     

Prediction for Target Sites of Small Interfering RNA Duplexes in SARS Coronavirus

High doses of ionizing irradiation and chemical mutagens induce random mutations and chromosome aberrations in cells of affected organisms and cause acute symptoms, delayed increased risk of cancer and accelerated aging. The mechanism of disease development remains unclear and no treatment exists for consequences of the mutagenic damage. We have proposed recently that extracellular genomic DNA from tissue fluids of a healthy organism, innate receptor-mediated nuclear delivery of this DNA, and its homologous recombination with cellular genomic sequences might function concertedly as a natural proofreading mechanism for somatic cell genomes. Here we hypothesize that cells dying from irradiation or chemical mutagens release heavily damaged DNA fragments that propagate mutations and chromosome aberrations to DNA-recipient cells via this mechanism, inducing cell death and release of their mutated DNA again into the bloodstream. The repeated release of the mutated DNA followed by its incorporation into cellular genomes would spread mutational damage in the affected organism, thus making this DNA the etiologic agent of either radiation sickness or post-mutagen exposure syndrome. The hypothesis opens a possibility to inhibit and treat the disease via administration of non-mutated genomic DNA fragments that would compete with the circulating mutant DNA fragments, entering cells in greater numbers, leading to replacement of mutant segments in cellular genomes. Injection of fragmented mouse DNA, but not human DNA, into lethally irradiated mice dramatically increased their survival. Similarly, the mouse DNA was more potent than human and salmon DNA in accelerating recovery of the normal leukocyte level in mice treated with the chemical mutagen cyclophosphamide. The species specificity of the DNA therapy suggests that the genomic sequences are the agent producing the effects.     

Structure of a Conserved Golgi Complex-targeting Signal in Coronavirus Envelope Proteins

Coronavirus envelope (CoV E) proteins are ∼100-residue polypeptides with at least one channel-forming α-helical transmembrane (TM) domain. The extramembrane C-terminal tail contains a completely conserved proline, at the center of a predicted β-coil-β motif. This hydrophobic motif has been reported to constitute a Golgi-targeting signal or a second TM domain. However, no structural data for this or other extramembrane domains in CoV E proteins is available. Herein, we show that the E protein in the severe acute respiratory syndrome virus has only one TM domain in micelles, whereas the predicted β-coil-β motif forms a short membrane-bound α-helix connected by a disordered loop to the TM domain. However, complementary results suggest that this motif is potentially poised for conformational change or in dynamic exchange with other conformations.     

Global RNA Structure Analysis of Poliovirus Identifies a Conserved RNA Structure Involved in Viral Replication and Infectivity

The genomes of RNA viruses often contain RNA structures that are crucial for translation and RNA replication and may play additional, uncharacterized roles during the viral replication cycle. For the picornavirus family member poliovirus, a number of functional RNA structures have been identified, but much of its genome, especially the open reading frame, has remained uncharacterized. We have now generated a global RNA structure map of the poliovirus genome using a chemical probing approach that interrogates RNA structure with single-nucleotide resolution. In combination with orthogonal evolutionary analyses, we uncover several conserved RNA structures in the open reading frame of the viral genome. To validate the ability of our global analyses to identify functionally important RNA structures, we further characterized one of the newly identified structures, located in the region encoding the RNA-dependent RNA polymerase, 3D^pol, by site-directed mutagenesis. Our results reveal that the structure is required for viral replication and infectivity, since synonymous mutants are defective in these processes. Furthermore, these defects can be partially suppressed by mutations in the viral protein 3C^pro, which suggests the existence of a novel functional interaction between an RNA structure in the 3D^pol-coding region and the viral protein(s) 3C^pro and/or its precursor 3CD^pro.     

An Isolate of Brome Mosaic Virus Specifically Supports the Replication of a Defective Form of its RNA 3

In one German isolate of brome mosaic virus, a defective form of RNA 3 was detected in addition to intact RNA 3. It was propagated only in barley, but was lost in Chenopodium quinoa and depended for its replication on the RNAs of the virus isolate from which it was derived. It did not induce any change of the symptoms produced in barley.     

Polypyrimidine-tract-binding Protein is a Component of the HCV RNA Replication Complex and Necessary for RNA Synthesis

The machinery for hepatitis C virus (HCV) RNA replication is still poorly characterized. The relationship between HCV RNA replication and translation is also not clear. We have previously shown that a cellular protein polypyrimidine-tract-binding protein (PTB) binds to HCV RNA at several different sites and modulates HCV translation in several ways. Here we show that PTB also participates in RNA replication. By bromouridine triphosphate (BrUTP) labeling and confocal microscopy of cells harboring an HCV replicon, we showed that the newly synthesized HCV RNA was localized to distinct structures in the cytoplasm, which also contain PTB. Membrane flotation analysis demonstrated that a fraction of cytoplasmic PTB was associated with a detergent-resistant membrane (DRM) structure consisting of lipid rafts, which also contained HCV nonstructural proteins and the human vesicle-associated membrane protein-associated protein (hVAP-33). PTB in the DRM was resistant to protease digestion, but became sensitive after treatment with the raft-disrupting agents. PTB in the DRM consisted of multiple isoforms and the brain-specific paralog. By using small interfering RNA (siRNA) of PTB, we showed that silencing of the endogenous PTB reduced the replication of HCV RNA replicon. In a cell-free, de novo HCV RNA synthesis system, HCV RNA synthesis was inhibited by anti-PTB antibody. These studies together indicated that PTB is a part of the HCV RNA replication complex and participates in viral RNA synthesis. Thus, PTB has dual functions in HCV life cycle, including translation and RNA replication.     

Rapamycin and Wortmannin Enhance Replication of a Defective Encephalomyocarditis Virus

Inhibitors of the phosphatidylinositol 3-kinase (PI3 kinase)–FKBP-rapamycin-associated protein (FRAP) pathway, such as rapamycin and wortmannin, induce dephosphorylation and activation of the suppressor of cap-dependent translation, 4E-BP1. Encephalomyocarditis virus (EMCV) infection leads to activation of 4E-BP1 at the time of host translation shutoff. Consistent with these data, rapamycin mildly enhances the synthesis of viral proteins and the shutoff of host cell protein synthesis after EMCV infection. In this study, two defective EMCV strains were generated by deleting portions of the 2A coding region of an infectious cDNA clone. These deletions dramatically decreased the efficiency of viral protein synthesis and abolished the virus-induced shutoff of host translation after infection of BHK-21 cells. Both translation and processing of the P1-2A capsid precursor polypeptide are impaired by the deletions in 2A. The translation and yield of mutant viruses were increased significantly by the presence of rapamycin and wortmannin during infection. Thus, inhibition of the PI3 kinase-FRAP signaling pathway partly complements mutations in 2A protein and reverses a slow-virus phenotype.