Conservative replication and transcription of Saccharomyces cerevisiae viral double-stranded RNA in vitro

A structural and primary sequence comparison of the viral RNA-dependent RNA polymerases

A systematic bioinformatic approach to identifying the evolutionarily conserved regions of proteins has verified the universality of a newly described conserved motif in RNA-dependent RNA polymerases (motif F). In combination with structural comparisons, this approach has defined two regions that may be involved in unwinding double-stranded RNA (dsRNA) for transcription. One of these is the N-terminal portion of motif F and the second is a large insertion in motif F present in the RNA-dependent RNA polymerases of some dsRNA viruses.

Yeast killer systems

The killer phenomenon in yeasts has been revealed to be a multicentric model for molecular biologists, virologists, phytopathologists, epidemiologists, industrial and medical microbiologists, mycologists, and pharmacologists. The surprisingly widespread occurrence of the killer phenomenon among taxonomically unrelated microorganisms, including prokaryotic and eukaryotic pathogens, has engendered a new interest in its biological significance as well as its theoretical and practical applications. The search for therapeutic opportunities by using yeast killer systems has conceptually opened new avenues for the prevention and control of life-threatening fungal diseases through the idiotypic network that is apparently exploited by the immune system in the course of natural infections. In this review, the biology, ecology, epidemiology, therapeutics, serology, and idiotypy of yeast killer systems are discussed.

New developments in fungal virology

Although viruses are widely distributed in fungi, their biological significance to their hosts is still poorly understood. A large number of fungal viruses are associated with latent infections of their hosts. With the exception of the killer-immune character in the yeasts, smuts, and hypovirulence in the chestnut blight fungus, fungal properties that can specifically be related to virus infection are not well defined. Mycoviruses are not known to have natural vectors; they are transmitted in nature intracellularly by hyphal anastomosis and heterokaryosis, and are disseminated via spores. Because fungi have a potential for plasmogamy and cytoplasmic exchange during extended periods of their life cycles and because they produce many types of propagules (sexual and asexual spores), often in great profusion, mycoviruses have them accessible to highly efficient means for transmission and spread. It is no surprise, therefore, that fungal viruses are not known to have an extracellular phase to their life cycles. Although extracellular transmission of a few fungal viruses have been demonstrated, using fungal protoplasts, the lack of conventional methods for experimental transmission of these viruses have been, and remains, an obstacle to understanding their biology. The recent application of molecular biological approaches to the study of mycoviral dsRNAs and the improvements in DNA-mediated fungal transformation systems, have allowed a clearer understanding of the molecular biology of mycoviruses to emerge. Considerable progress has been made in elucidating the genome organization and expression strategies of the yeast L-A virus and the unencapsidated RNA virus associated with hypovirulence in the chestnut blight fungus. These recent advances in the biochemical and molecular characterization of the genomes of fungal viruses and associated satellite dsRNAs, as they relate to the biological properties of these viruses and to their interactions with their hosts are the focus of this chapter.

Transcribing and replicating particles in a double-stranded RNA virus from Leishmania

During the replicative cycle of many double-stranded RNA viruses, transcription of particles with a double-stranded RNA genome alternates with replication of particles containing a single-stranded genome. In virions infecting some strains of Leishmania guyanensis the putative transcriptase and replicase activities of the RNA-dependent RNA polymerase were previously detected in vitro. Northern hybridization to RNA of known polarity demonstrates that the single-stranded RNA products are of positive polarity and, by definition, are the products of the viral transcriptase. Re-evaluation of previously published data in the light of these findings suggests that transcription in Leishmania viruses is conservative. Sedimentation in sucrose gradients revealed two types of viral particles; single-stranded RNA particles comprised a small fraction of the virus population and sedimented more slowly than the peak of double-stranded RNA particles. In agreement with the replicative model of other dsRNA viruses, these single-stranded particles co-purified with the viral replicase activity that resulted in double-stranded RNA synthesis. In virus-infected promastigote extracts replicase activity decreased with increasing parasite density in culture, suggesting a correlation between cell division and viral replication.

Generation of infectious nucleocapsids by in vitro assembly of the shell protein on to the polymerase complex of the dsRNA bacteriophage phi 6

A method for the in vitro uncoating of the phi 6 nucleocapsid (NC) was developed. The resulting particle, designated as the NC core, containing the genomic double-stranded (ds) RNA segments and the proteins P1, P2, P4 and P7, was not infectious but had a highly enhanced in vitro transcriptase activity compared to that of the intact NC. The NC shell protein P8 was purified by immunoaffinity chromatography, and it was shown to self-assemble to shell-like structures upon addition of calcium ions. The conditions for the self-assembly of the shell were optimized. Shell reassembly on to the NC cores restored the infectivity but resulted in a decrease of transcriptase activity. No reassembly of the shell on to RNA-less cores (procapsids) produced from a cDNA construction in Escherichia coli was observed. Our results suggest that the intracellular uncoating of the NC is the event activating the phi 6 dsRNA transcriptase and that the NC shell is necessary for infectivity, probably for the passage of the NC through the host cytoplasmic membrane. Packaging of the dsRNA segments into the procapsid appears to be a prerequisite for NC shell assembly.

In vivo mapping of a sequence required for interference with the yeast killer virus

The Saccharomyces cerevisiae viruses are noninfectious double-stranded RNA viruses whose segments are separately encapsidated. A large viral double-stranded RNA (L1; 4580 base pairs) encodes all required viral functions. M1, a double-stranded RNA of 1.9 kilobases, encodes an extracellular toxin (killer toxin) and cellular immunity to that toxin. Some strains contain smaller, S, double-stranded RNAs, derived from M1 by internal deletion. Particles containing these defective interfering RNAs can displace M1 particles by faster replication and thus convert the host strain to a nonkiller phenotype. In this work, we report the development of an assay in which the expression of S plus-strand from an inducible plasmid causes the loss of M1 particles. This assay provides a convenient method for identifying in vivo cis-acting sequences important in viral replication and packaging. We have mapped the sequence involved in interference to a region of 132 base pairs that includes two sequences similar to the viral binding site sequence previously identified in L1 by in vitro experiments.

RNA dependent RNA polymerase activity associated with the double-stranded RNA virus of Giardia lamblia

Giardia lamblia, a parasitic protozoan, can contain a double-stranded RNA (dsRNA) virus, GLV (1). We have identified an RNA polymerase activity present specifically in cultures of GLV infected cells. This RNA polymerase activity is present in crude whole cell lysates as well as in lysates from GLV particles purified from the culture medium. The RNA polymerase has many characteristics common to other RNA polymerases (e.g. it requires divalent cations and all four ribonucleoside triphosphates), yet it is not inhibited by RNA polymerase inhibitors such as alpha-amanitin or rifampicin. The RNA polymerase activity synthesizes RNAs corresponding to one strand of the GLV genome, although under the present experimental conditions, the RNA products of the reaction are not full length viral RNAs. The in vitro products of the RNA polymerase reaction co-sediment through sucrose gradients with viral particles; and purified GLV viral particles have RNA polymerase activity. The RNA polymerase activities within and outside of infected cells closely parallel the amount of virus present during the course of viral infection. The similarities between the RNA polymerase of GLV and the polymerase associated with the dsRNA virus system of yeast are discussed.

Similarity between the picornavirus VP3 capsid polypeptide and the Saccharomyces cerevisiae virus capsid polypeptide

We have compared the sequence of the capsid polypeptide of the Saccharomyces cerevisiae double-stranded RNA virus, ScV, with those of the picornaviruses. A central region of 245 amino acids in the ScV capsid polypeptide of 680 amino acids has significant similarity to the picornavirus VP3. This similarity is more extensive than that already noted for the alphavirus capsid polypeptide and the picornavirus VP3 (Fuller, S.D. and Argos, P, EMBO J. 6, 1099, 1987). Together with the similarity between the ScV RNA polymerase and the picornavirus RNA polymerases, this result implies an evolutionary relationship between a simple double-stranded RNA virus of fungi and the small plus strand RNA animal viruses.

Overlapping genes in a yeast double-stranded RNA virus

The Saccharomyces cerevisiae viruses have a large viral double-stranded RNA which encodes the major viral capsid polypeptide. We have previously shown that this RNA (L1) also encodes a putative viral RNA-dependent RNA polymerase (D. F. Pietras, M. E. Diamond, and J. A. Bruenn, Nucleic Acids Res., 16:6226, 1988). The organization and expression of the viral genome is similar to that of the gag-pol region of the retroviruses. The complete sequence of L1 demonstrates two large open reading frames on the plus strand which overlap by 129 bases. The first is the gene for the capsid polypeptide, and the second is the gene for the putative RNA polymerase. One of the products of in vitro translation of the denatured viral double-stranded RNA is a polypeptide of the size expected of a capsid-polymerase fusion protein, resulting from a -1 frameshift within the overlapping region. A polypeptide of the size expected for a capsid-polymerase fusion product was found in virions, and it was recognized in Western blots (immunoblots) by antibodies to a synthetic peptide derived from the predicted polymerase sequence.

From interferon induction to fungal viruses

Viruses of fungi (mycoviruses) were first discovered in diseased mushrooms. However the finding that the antiviral and interferon-inducing activities of extracts of apparently healthy isolates of a number of Penicillium species were due to the presence of double-stranded (ds) RNA arising from mycovirus infections sparked off an explosion of interest in what has now become a distinct area of virology. Two families of dsRNA mycoviruses are now established: the Totiviridae and the Partitiviridae which comprise isometric viruses with genomes of one or two dsRNA segments respectively. Virus isolates in both families often contain additional satellite dsRNAs, which may in some fungi (e.g. Saccharomyces cerevisiae, Ustilago maydis) code for "killer" proteins which are toxic to other sensitive strains of the same or closely related species. In Endothia parasitica, which causes chestnut blight disease, dsRNA is associated with hypovirulence and is enclosed in lipid-rich vesicles. In Ophiostoma (Ceratocystis) ulmi, which causes Dutch elm disease, dsRNA is associated with the mitochondria and, in some diseased isolates of the fungus, specific dsRNA segments are associated with reduction of cytochrome oxidase and respiratory deficiency, resulting in slow growth and abnormal morphology.

Conservative mechanism of the in vitro transcription of killer virus of yeast

A conservative mechanism of transcription has been proposed for the RNA polymerase activity of the killer virus of yeast, both in vivo and in vitro. This model is supported by the conservation of radioactivity in template double-stranded RNA during transcription in vitro.

Conserved regions in defective interfering viral double-stranded RNAs from a yeast virus

We have completely sequenced a defective interfering viral double-stranded RNA (dsRNA) from the Saccharomyces cerevisiae virus. This RNA (S14) is a simple internal deletion of its parental dsRNA, M1, of 1.9 kilobases. The 5' 964 bases of the M1 plus strand encode the type 1 killer toxin of the yeast. S14 is 793 base pairs (bp) long, with 253 bp from the 5' region of its parental plus strand and 540 bp from the 3' region. All three defective interfering RNAs derived from M1 that have been characterized so far preserve a large 3' region, which includes five repeats of a rotationally symmetrical 11-bp consensus sequence. This 11-bp sequence is not present in the 5' 1 kilobase of the parental RNA or in any of the sequenced regions of unrelated yeast viral dsRNAs, but it is present in the 3' region of the plus strand of another yeast viral dsRNA, M2, that encodes the type 2 killer toxin. The 3' region of 550 bases of the M1 plus strand, previously only partially sequenced, reveals no large open reading frames. Hence only about half of M1 appears to have a coding function.