Viruses with segmented ribonucleic acid genomes: multiplication of influenza versus reovirus

An overview of dinucleotide and codon usage in all viruses

Viruses are, by far, the most abundant biological entities on earth. They are found in all known ecological niches and are the causative agents of many important diseases in plants and animals. From an evolutionary point of view, since viruses do not share any orthologous genes, there is a general consensus that they are polyphyletic; that is, they do not have a common ancestor. This means that they appeared several times during the course of evolution. For their life cycle, they are always obligate parasites of a free cellular life form, which can be bacteria, archaea, or eukaryotes. More complexity is added to these entities by the fact that their genetic material can be DNA or RNA (double- or single-stranded) or retrotranscribed. Given these features, we wondered if some general rules can be inferred when studying two basic genomic signatures-dinucleotides and codon usage-analyzing all available complete and non-redundant viral sequences. In spite of the obviously biased sample of sequences available, some general features appear to emerge.

Structures of influenza A proteins and insights into antiviral drug targets

The world is currently undergoing a pandemic caused by an H1N1 influenza A virus, the so-called 'swine flu'. The H5N1 ('bird flu') influenza A viruses, now circulating in Asia, Africa and Europe, are extremely virulent in humans, although they have not so far acquired the ability to transfer efficiently from human to human. These health concerns have spurred considerable interest in understanding the molecular biology of influenza A viruses. Recent structural studies of influenza A virus proteins (or fragments) help enhance our understanding of the molecular mechanisms of the viral proteins and the effects of drug resistance to improve drug design. The structures of domains of the influenza RNA-dependent RNA polymerase and the nonstructural NS1A protein provide opportunities for targeting these proteins to inhibit viral replication.

Inactivation of influenza and vesicular stomatitis virion RNA polymerase activities by photoreaction with 4'-substituted psoralens

Irradiation of purified influenza virus and vesicular stomatitis virus (VSV) with long-wavelength UV light in the presence of 4'-substituted psoralens inactivated the virion-associated RNA polymerase activity. Inactivation was apparently due to psoralen modification of the viral genome RNAs, since cations that decrease psoralen binding to nucleic acids had a protective effect, and reconstitution of VSV RNA polymerase activity was inhibited by photoreaction of nucleoprotein cores but not by pretreatment of soluble fraction from dissociated virions. Partially inactivated viral particles synthesized reduced amounts of full-length RNA products in vitro without an increase in prematurely terminated transcripts. VSV leader RNA formation was relatively resistant to psoralen photoinactivation, and sequential transcription was maintained by photoreacted VSV. The all-or-none psoralen effect on virion-associated RNA polymerase activities may be due to a differential photosensitivity of promoter sites or to structural changes in modified viral genome RNAs that prevent formation of new mRNA chains.

Cell-free translation of influenza virus mRNA

Cytoplasmic poly (A)-rich RNA extracted from fowl plague virus-infected cells was found to program efficiently the translation of two major peptides in the wheat germ cell-free system. These peptides have the same electrophoretic mobility, on polyacrylamide gels, as the two major virion proteins M and NP. [35S] methionine tryptic peptide analysis by one-dimensionalthin-layer ionophoresis and finger printing by two-dimensional thin-layer ionophoresis and chromatography show a high degree of similarity between the two in vitro products and the authentic viral proteins M and NP. Although virion RNA is devoid of any poly (A) sequence, it is confirmed here that the viral complementary cytoplasmic RNA contains poly (A) stretches of varying lengths. Intact purified virion was found to promote the synthesis of very low amounts of the same NP and M proteins in this cell-free system. Quantitative aspects of data would indicate that this is due to minute amounts of complementary viral RNA associated with the virion or with the virion RNA itself. In conclusion, it is shown diectly by cell-free translation of authentic viral products that the influenza virion is "negative stranded" (Baltimore, 1971), at least for its two major structural proteins.

Poliovirus-induced infectious double-stranded RNA: Effect of RNA-degrading enzymes

The infectivity of replicative form RNA (RF-RNA) isolated from poliovirus-infected HeLa cells is completely resistant to the action of T-1 RNase but decreases after exposure to RNase A in the presence of 0.3 M NaCl. Under these conditions neither enzyme produces single-stranded nicks in RF-RNA. Three endonuclease-free exonuleases (RNase II, polynucleotide phosphorylase and spleen phosphodiesterase) rapidly destroy the infectivity of single-stranded RNA, but do not alter the infectivity of RF-RNA. It is concluded that RF-RNA does not contain single-stranded ends essential for infectivity. Indirect evidence suggests that all or most of the poly A region at the 3' end of the plus strand of infectious RF-RNA is base-paired to a poly U region at the 5 end of the minus strand.

Structure of B77 sarcoma virus RNA: stabilization of RNA after packaging

Extracellular maturation of Bratislava 77(B77) sarcoma virus RNA involves a stabilization of linkage between 35S subunits since the Tm of 60 to 70S RNA in the presence of 0.5 M NaCl increases from 56 to 67.5 C as the age of the virus increases. This stabilization process is strongly temperature dependent; the rate at 45 C is increased fourfold over the rate at 37 C. As a result of the instability of the immature RNA, denaturation to subunits occurs at room temperature during phenol extraction. This dissociation can be prevented by increasing the NaCl concentration during the extraction. The data support a model which proposes that RNA subunits of oncornaviruses exist as assembled 60 to 70S RNA even in immature virions but that the linkages between subunits are stabilized as a function of time. These linkages appear to be maintained by nucleotide base pairing rather than by protein. However, isolated RNA does not undergo stabilization, suggesting that some other component of the virion is necessary for the process to occur.

Proteins of bacteriophage phi6

We investigated the protein composition of the lipid-containing bacteriophage phi 6. We also studied the synthesis of phage-specific proteins in the host bacterium Pseudomonas phaseolicola HB10Y. The virion was found to contain 10 proteins of the following molecular weights: P1, 93,000; P2, 88,000; P3, 84,000; P4, 36,800; P5, 24,000; P6, 21,000; P7, 19,900; P8, 10,500; P9, 8,700; and P10, less than 6,000. Proteins P3, P9, and P10 were completely extracted from the virion with 1% Triton X-100. Protein P6 was partially extracted. Proteins P8 and P9 were purified by column chromatography. The amino acid composition of P9 was determined and was found to lack methionine. Labeling of viral proteins with [35S]methionine in infected cells indicated that proteins P5, P9, P10, and P11 lacked methionine. Treatment of host cells with UV light before infection allowed the synthesis of P1, P2, P4, and P7; however, the extent of viral protein synthesis fell off exponentially with increasing delay time between irradiation and infection. Treatment of host cells with rifampin during infection allowed preferential synthesis of viral proteins, but the extent of synthesis also fell off exponentially with increasing delay time between the addition of rifampin and the addition of radioactive amino acids. All of the virion proteins were seen in gels prepared from rifampin-treated infected cells. In addition, two proteins, P11 and P12, were observed; their molecular weights were 25,200 and 20,100, respectively. Proteins P1, P2, P4, and P7 were synthesized early, whereas the rest began to increase at 45 min post-infection.

Temperature-sensitive mutants of murine leukemia virus. IV. Further physiological characterization and evidence for genetic recombination

Several temperature-sensitive mutants of the Rauscher strain of murine leukemia virus representing three distinct physiological groups have been further characterized. Genetic recombination between different pairs of these mutants has been demonstrated. Several representative genetic recombinants were isolated and shown to replicate equally well at the permissive (31 C) and nonpermissive (38 C) temperatures and to have serological characteristics of the wild-type parental virus. Alternative models for the mechanisms involved in recombination between type C RNA viruses are discussed.

Fungal viruses

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Comparative studies of wild-type and "cold-mutant" (temperature-sensitive) influenza viruses: polypeptide synthesis by an Asian (H2N2) strain and its cold-adapted variant

The structure and replication of a cold-adapted, temperature-sensitive (TS) mutant of an Asian (H2N2) influenza virus was compared with that of its wild-type (WT) parent. Viruses were grown in a chicken kidney cell system, and at the nonpermissive temperature of 40 C, production of infectious TS virus was about 100,000-fold less than at 35 C, in contrast to WT virus. Major structural polypeptides of each virus grown at 35 C were similar, except that the hemagglutinin glycopolypeptide (HA) of the TS virions was slightly more heterogenous than that of WT virions. Synthesis of viral polypeptides was examined by sodium dodecyl sulfate acrylamide gel electrophoresis of pulse-labeled infected cells. This revealed a defect in the synthesis of TS viral hemagglutinin that was most pronounced at the nonpermissive temperature. Other TS viral polypeptides appeared to be synthesized normally at 40 C. A defect in the TS virus hemagglutinin was also indicated by serological studies that demonstrated that TS virus hemagglutinin had lost antigenic sites present on the WT virus. Thus, it is concluded that the virus mutant examined contains lesions in the hemagglutinin gene, although the possibility of additional unrecognized lesions is not excluded.

Ultrastructural characterization of genome of epizootic hemorrhagic disease virus

Purified epizootic hemorrhagic disease (EHD) virus preparations were treated with urea and sodium perchlorate. The viral ribonucleic acid (RNA) released when spread on protein monolayers according to the Kleinschmidt technique was examined by rotary shadow-casting electron microscopy. The viral RNA released by urea treatment had filaments which frequently formed three to five loop-shaped figures of varied length. In 80% of the virus particles the lengths of the viral RNA released were 2.5 to 4.5 mum. The sodium perchlorate-released viral nucleic acid also appeared linear, and about 70% had lengths of 0.1 to 2.0 mum, the longest filament measuring 5.8 mum. Evidence was obtained that EHD virus contains double-stranded RNA as its genetic material and the molecular weight of the EHD viral RNA was calculated to be 12.2 x to 10(6) to 15.1 x 10(6) daltons.

Cell surface antigen induced by influenza virus

By immunofluorescence staining, a specific surface antigen induced by influenza virus was detected on clone 1-5C-4 cells. The antigen was neither related to hemagglutinin nor dependent on the production of infectious virus. Formation of the virus-specific cell surface antigen was dependent on protein synthesis but independent of viral ribonucleic acid replication.