A Second Double-Stranded RNA Virus from Yeast

Park, Chung‐Mo; Lopinski, John D.; Masuda, Jenny; Tzeng, Tzy-Hwa; Bruenn, Jeremy A.

doi:10.1006/viro.1996.0083

Cited by 46 publications

(43 citation statements)

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“…A further 15 strains carried L-A without the killer phenotype (Table 3). The L-BC dsRNA virus and the 20S and 23S RNA replicons encode only RNA-dependent RNA polymerases and a coat protein (30)(31)(32)(33), so it is unlikely that they provide any host advantage. Nonetheless, each of these RNA replicons is found in wild strains, (Table 3).…”

Section: Resultsmentioning

confidence: 99%

Yeast prions [URE3] and [PSI ⁺ ] are diseases

Nakayashiki

Kurtzman

Edskes

et al. 2005

Proc. Natl. Acad. Sci. U.S.A.

234

232

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Section: Resultsmentioning

confidence: 99%

Yeast prions [URE3] and [PSI ⁺ ] are diseases

Nakayashiki

Kurtzman

Edskes

et al. 2005

Proc. Natl. Acad. Sci. U.S.A.

234

232

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“…Unlike numerous viruses from other genera in the family Totiviridae, which express the RdRp as a CP/RdRp fusion protein consequent to Ϫ1 or ϩ1 ribosomal frameshifting (25,29,35,48,49), the HvV190S RdRp is expressed as a separate, nonfused protein (23). When the RdRp ORF is expressed in Escherichia coli from a monocistronic construct employing its predicted start codon (HvV190S nt positions 2605 to 2607), the translation product is indistinguishable in both size and serological reactivity from the HvV190S particle-associated RdRp (23).…”

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confidence: 99%

RNA Sequence Determinants of a Coupled Termination-Reinitiation Strategy for Downstream Open Reading Frame Translation in Helminthosporium victoriae Virus 190S and Other Victoriviruses (Family Totiviridae)

Havens

Nibert

et al. 2011

J Virol

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The genome-length, dicistronic mRNA of the double-stranded RNA fungal virus Helminthosporium victoriae virus 190S (genus Victorivirus, family Totiviridae) contains two long open reading frames (ORFs) that overlap in the tetranucleotide AUGA. Translation of the downstream ORF, which encodes the RNA-dependent RNA polymerase (RdRp), has been proposed to depend on ribosomal reinitiation following termination of the upstream ORF, which encodes the capsid protein. In the current study, we examined the RNA sequence determinants for RdRp translation in this virus and demonstrated that a coupled termination-reinitiation (stop-restart) strategy is indeed used. Signals for termination-reinitiation are found within a 32-nucleotide stretch of RNA immediately upstream of the AUGA motif, including a predicted pseudoknot structure. The close proximity in which this predicted structure is followed by the upstream ORF's stop codon appears to be especially important for promoting translation of the downstream ORF. The normal strong preferences for an AUG start codon and the canonical sequence context to favor translation initiation appear somewhat relaxed for the downstream ORF. Similar sequence motifs and predicted RNA structures in other victoriviruses suggest that they all share a related stop-restart strategy for RdRp translation. Members of the genus Victorivirus thus provide new and unique opportunities for exploring the molecular mechanisms of translational coupling, which remain only partly understood in this and other systems.The vast majority of eukaryotic mRNAs are monocistronic and, hence, contain only one translated open reading frame (ORF). Some, however, contain two or more ORFs and have an associated mechanism, such as ribosomal frameshifting or coupled termination-reinitiation (stop-restart), to promote regulated translation of the downstream ORF(s). Such multicistronic mRNAs are especially common among eukaryotic RNA viruses.In coupled termination-reinitiation, ribosomes translate the upstream ORF of an mRNA, but upon termination, a proportion of the 40S subunits remain bound to the mRNA and go on to reinitiate at the start codon of the downstream ORF (see review in reference 39). This strategy has been shown to promote the translation of downstream ORFs in the mRNAs of several different plus-or minus-stranded RNA mammalian viruses, including those that encode protein VP2 or VP10 of certain caliciviruses (30,33,34), the BM2 protein of influenza B virus (21, 40), and the M2-2 proteins of respiratory syncytial virus (RSV) and other pneumoviruses (1,15,16). One example of a plus-stranded RNA fungal virus that employs such translational coupling has also been described (17). A stop-restart strategy has been previously proposed for downstream ORF translation from the dicistronic mRNA of the double-stranded RNA (dsRNA) fungal virus Helminthosporium victoriae virus 190S (HvV190S) (45), and identifying RNA sequence determinants for that strategy in HvV190S and related viruses is the focus of this report.HvV190S is the pr...

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“…There is no separate gene coding for an immunity function in these dsRNA viruses; the unprocessed precursor of the mature secreted killer toxin confers immunity. A second helper virus, L-BC, with a genomic organization similar to that of L-A, has also been identified in some S. cerevisiae strains (40), but no killer virus satellites of L-BC are known. Many strains of S. cerevisiae contain L-A and/or L-BC without a killer satellite virus being present (1,37).…”

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confidence: 99%

Evolutionary Capture of Viral and Plasmid DNA by Yeast Nuclear Chromosomes

Frank

Wolfe

2009

Eukaryot Cell

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A 10-kb region of the nuclear genome of the yeast Vanderwaltozyma polyspora contains an unusual cluster of five pseudogenes homologous to five different genes from yeast killer viruses, killer plasmids, the 2m plasmid, and a Penicillium virus. By further database searches, we show that this phenomenon is not unique to V. polyspora but that about 40% of the sequenced genomes of Saccharomycotina species contain integrated copies of genes from DNA plasmids or RNA viruses. We propose the name NUPAVs (nuclear sequences of plasmid and viral origin) for these objects, by analogy to NUMTs (nuclear copies of mitochondrial DNA) and NUPTs (nuclear copies of plastid DNA, in plants) of organellar origin. Although most of the NUPAVs are pseudogenes, one intact and active gene that was formed in this way is the KHS1 chromosomal killer locus of Saccharomyces cerevisiae. We show that KHS1 is a NUPAV related to M2 killer virus double-stranded RNA. Many NUPAVs are located beside tRNA genes, and some contain sequences from a mixture of different extrachromosomal sources. We propose that NUPAVs are sequences that were captured by the nuclear genome during the repair of double-strand breaks that occurred during evolution and that some of their properties may be explained by repeated breakage at fragile chromosomal sites.It is well known that the nuclear genomes of most eukaryotes contain integrated fragments of organellar DNA called NUMTs (nuclear copies of mitochondrial DNA) and NUPTs (nuclear copies of plastid DNA, in plants) (26,29,44,45,57). These fragments are usually pseudogenes, although some NUMTs and NUPTs have become incorporated into functional nuclear genes (38). The NUMTs present in the nuclear genomes of Saccharomycotina yeast species were recently analyzed by Sacerdot et al. (48).In addition to their mitochondrial genomes, yeast species contain a variety of other extranuclear DNA and RNA elements, including viruses and plasmids. These extrachromosomal elements are usually considered to be autonomous entities that do not interact with nuclear DNA. When our laboratory sequenced the genome of the yeast Vanderwaltozyma polyspora (synonym: Kluyveromyces polysporus) (49), we were therefore surprised to find the genomic region we describe here, which contains integrated fragments of several plasmid-and virus-like sequences. We propose that this region was formed by the capture of plasmid and viral sequences by the same mechanism that captures mitochondrial DNA to form NUMTs (43, 65). In a literature search, we could find only one previous report of a similar finding: Utatsu et al. (59) reported the sequences of two regions of nuclear DNA from Zygosaccharomyces rouxii that were highly similar to parts of the 2m-like plasmid pSR1 from that species, but rearranged.Before describing the V. polyspora region, and similar regions found in other species, we will first briefly introduce the extrachromosomal RNA and DNA entities that are known to exist in yeasts. Extrachromosomal nucleic acids are relatively uncommon in yeasts: a broad...

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A Second Double-Stranded RNA Virus from Yeast

Cited by 46 publications

References 0 publications

Yeast prions [URE3] and [PSI ⁺ ] are diseases

Yeast prions [URE3] and [PSI ⁺ ] are diseases

RNA Sequence Determinants of a Coupled Termination-Reinitiation Strategy for Downstream Open Reading Frame Translation in Helminthosporium victoriae Virus 190S and Other Victoriviruses (Family Totiviridae)

Evolutionary Capture of Viral and Plasmid DNA by Yeast Nuclear Chromosomes

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A Second Double-Stranded RNA Virus from Yeast

Cited by 46 publications

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Yeast prions [URE3] and [PSI + ] are diseases

Yeast prions [URE3] and [PSI + ] are diseases

RNA Sequence Determinants of a Coupled Termination-Reinitiation Strategy for Downstream Open Reading Frame Translation in Helminthosporium victoriae Virus 190S and Other Victoriviruses (Family Totiviridae)

Evolutionary Capture of Viral and Plasmid DNA by Yeast Nuclear Chromosomes

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Yeast prions [URE3] and [PSI ⁺ ] are diseases

Yeast prions [URE3] and [PSI ⁺ ] are diseases