Long internal inverted repeat in a yeast viral double-stranded RNA.

The Saccharomyces cerevisiae viruses are non-infectious double-stranded (ds) RNA viruses present in most laboratory strains of yeast. Their genome consists of one or more dsRNAs separately encapsidated in particles composed mainly of one polypeptide, which has a Mr of 88 kdaltons in the best-studied viral subtype. A large viral dsRNA (L1, of 4.7 kb) encodes the capsid polypeptide. We have determined the sequences of a number of cDNA clones homologous to portions of L1 and mapped them by a novel heteroduplex technique. Several of these clones originate from a region of L1 2.3-2.5 kb from the 5' end of the plus strand that contains stop codons in all three reading frames in the plus strand. We therefore suspect that the capsid polypeptide gene lies in the 5' 2.3-2.6 kb of the plus strand. One of the cloned cDNAs has an inverted repeat of 170 bp that appears to be present in its parental RNA. The inverted repeat in L1 is the longest known inverted repeat in a viral dsRNA and the only known non-terminal inverted repeat. It might serve the function of creating two mRNAs from one viral dsRNA.     

Structure and expression of the M2 genomic segment of a type 2 killer virus of yeast.

The M2 double-stranded (ds) RNA species encodes toxin and resistance functions in Saccharomyces cerevisiae strains with the K2 killer specificity. RNA sequence analysis reveals the presence of a large open reading frame on the larger heat-cleavage product of M2 dsRNA, which is translated in vitro to yield a 28 kd polypeptide as a major product. The postulated translation initiator AUG triplet is located within a stem and loop structure near the 5' terminus of the positive strand, which also contains plausible 18S and 5.8S ribosomal RNA binding sites. These features may serve to regulate the translation of the K2 toxin precursor. The M1 (from type 1 yeast killers) and M2 dsRNA species lack extensive sequence homology, although specific features are shared, which may represent structural elements required for gene expression and replication.     

The Ustilago maydis virally encoded KP1 killer toxin

Some strains of the plant-pathogenic fungus Ustilago maydis secrete toxins (killer toxins) that are lethal to susceptible strains of the same fungus. There are three well-characterized killer toxins in U. maydis–KP1, KP4, and KP6–which are secreted by the P1, P4, and P6 subtypes, respectively. These killer toxins are small polypeptides encoded by segments of an endogenous, persistent double-stranded RNA (dsRNA) virus in each U. maydis subtype. In P4 and P6, the M2 dsRNA segment encodes the toxin. In this work, the KP1 killer toxin was purified for internal amino acid sequence analysis, and P1M2 was identified as the KP1 toxin-encoding segment by sequence analysis of cDNA clones. The KP1 toxin is a monomer with a predicted molecular weight of 13.4kDa and does not have extensive sequence similarity with other viral anti-fungal toxins. The P1M2 segment is different from the P4 and P6 toxin-encoding dsRNA segments in that the 3’non-coding region of its plus strand has no sequence homology to the 3’ends of the plus strands of P1M1, P4M2, or P6M2.     

Yeast killer mutants with altered double-stranded ribonucleic acid

Killer strains of Saccharomyces cerevisiae contain two species of double-stranded ribonucleic acid (dsRNA) with molecular weights estimated at 2.5 x 10(6) (L) and 1.4 x 10(6) (M). The M component appears to have a high adenine content. All mutants of killer which are defective for both the toxin and immunity functions lack the M dsRNA. One of these mutants has a novel dsRNA with a molecular weight of 5 x 10(5). Another class of killer mutants contains strains which are defective for either the toxin or the immunity function. They include temperature-sensitive killers, superkillers, and immunity-minus strains. The dsRNA profile of temperature-sensitive killers resembles that of the standard killer. The superkiller has 2.5 times more of the M dsRNA (1.4 x 10(6) daltons) than does the standard killer. Immunity-minus killers have, in addition to the two dsRNAs species of standard killer, a novel dsRNA with a molecular weight of 2.5 x 10(5). The data are consistent with the hypothesis that the M RNA controls toxin production. In addition, the two RNAs, L and M, seem to be regulated together. When the M RNA is missing, the amount of L is either greatly elevated or greatly reduced.     

Translational analysis of the killer-associated virus-like particle dsRNA genome of S. cerevisiae: M dsRNA encodes toxin

The M species (medium sized) dsRNA (1.1–1.4 × 10⁶ daltons) isolated from a toxin-producing yeast killer strain (K⁺R⁺) and three related, defective interfering (suppressive) S species dsRNAs of the yeast killer-associated cytoplasmic multicomponent viral-like particle system were analyzed by in vitro translation in a wheat germ cell-free protein synthesis system. Heat-denatured M species dsRNA programmed the synthesis of two major polypeptides, M-P1 (32,000 daltons) and M-P2 (30,000 daltons). M-P1 has been shown by the criteria of proteolytic peptide mapping and cross-antigenicity to contain the 12,000 dalton polypeptide corresponding to the in vivo produced killer toxin, thus establishing that it is the M species dsRNA which carries the toxin gene. An M species dsRNA obtained from a neutral strain (K^?R⁺) also programmed the in vitro synthesis of a polypeptide identical in molecular weight to M-P1, thus indicating that the cytoplasmic determinant of the mutant neutral phenotype is either a simple point mutation in the dsRNA toxin gene or a mutation in a dsRNA gene which is required for functional toxin production. In vitro translation of each of the three different suppressive S dsRNAs resulted in the production of a polypeptide (S-P1) of approximately 8000 daltons instead of the 32,000 dalton M-P1 polypeptide programmed by M dsRNA. This result is consistent with the heteroduplex analysis of these dsRNAs by Fried and Fink (1978), which shows retention of M dsRNA ends, accompanied by large internal deletions in each of the S dsRNAs translated.     

Expression of double-stranded-RNA-specific RNase III of Escherichia coli is lethal to Saccharomyces cerevisiae.

The gene for the double-stranded RNA (dsRNA)-specific RNase III of Escherichia coli was expressed in Saccharomyces cerevisiae to examine the effects of this RNase activity on the yeast. Induction of the RNase III gene was found to cause abnormal cell morphology and cell death. Whereas double-stranded killer RNA is degraded by RNase III in vitro, killer RNA, rRNA, and some mRNAs were found to be stable in vivo after induction of RNase III. Variants selected for resistance to RNase III induction were isolated at a frequency of 4 X 10(-5) to 5 X 10(-5). Ten percent of these resistant strains had concomitantly lost the capacity to produce killer toxin and M dsRNA while retaining L dsRNA. The genetic alteration leading to RNase resistance was localized within the RNase III-coding region but not in the yeast chromosome. These results indicate that S. cerevisiae contains some essential RNA which is susceptible to E. coli RNase III.     

Genomic and copy-back 3'' termini in Sendai virus defective interfering RNA species

Direct sequencing of nine Sendai virus defective interfering RNA species revealed two kinds of 3'-terminal sequences. Six RNA species had 3' termini identical to the virus genome (negative strand), confirming that internal deletions are a frequent cause of Sendai virus defectiveness. The other three RNA species had 3'-terminal sequences identical to that described as the complement of the 5' terminus of the virus genome (R. A. Lazzarini, J. D. Keene, and M. Schubert, Cell 26:145-154, 1981), indicating that they are of the copy-back type. Extensive homology between these two types of 3' sequences evidently accounts for the ability of the copy-back sequence to function as an initiation signal for viral RNA replication. There may not be a selective advantage of one type of terminus over the other, since one defective interfering strain possessed two RNA species, one of which had the genomic 3' terminus and the other copy-back type.     

Relatedness of the double-stranded RNAs present in yeast virus-like particles.

The relatedness of several double-stranded RNAs (dsRNA's) present in the virus-like particles of yeast was examined by T1 fingerprint analysis. The dsRNA's examined were L, the dsRNA encoding the capsid polypeptide of yeast virus-like particles; M, which appears to code for a toxic polypeptide and for resistance to the effects of the toxin; and two S dsRNA's present in particles analogous to the defective interfering particles of animal viruses. S3, a dsRNA of 0.46 X 10(6) daltons, was derived entirely from M, a dsRNA of 1.2 X 10(6) daltons. S1, a dsRNA of 0.92 X 10(6) daltons, was a duplication of S3. This conclusion has also been reached independently by heteroduplex mapping techniques (H. M. Fried and G. R. Fink, personal communication). S1 and S3, at least in one yeast strain, were unstable in sequence, apparently due to the accumulation of sequence variants of the same molecular weight. L was a species of 3 X 10(6) daltons, unrelated in sequence to M, S1, or S3. S1, S3, and M had a 3' T1 dodecanucleotide in common.     

Nucleotide sequences of influenza virus segments 1 and 3 reveal mosaic structure of a small viral RNA segment

Defective interfering RNAs of influenza virus are small segments derived from viral segments 1, 2 and 3. We present here the complete nucleotide sequences of segments 1 and 3 from the human influenza strain A/PR/8/34 and deduce that the sequence of a small RNA segment from A/NT/60/68, apparently a defective interfering RNA, is derived from five separate regions in segment 3 and from one region in segment 1. These regions, which are located near the termini of the two parental segments, are arranged in the small RNA segment in an alternating fashion: thus a region derived from near a 5′ terminus is adjacent to a region derived from near a 3′ terminus. We propose that the small segment is generated during positive strand synthesis as a result of the viral polymerase pausing at uridine-rich sequences in the template and reinitiating synthesis at another site.     

Dependence of minus-strand synthesis on complete genomic packaging in the double-stranded RNA bacteriophage phi 6.

Bacteriophage phi 6 has a segmented genome consisting of three pieces of double-stranded RNA (dsRNA). The viral procapsid is the structure that packages plus strands, synthesizes the complementary negative strands to form dsRNA, and then transcribes dsRNA to form plus-strand message. The minus-strand synthesis of a particular genomic segment is dependent on prior packaging of the other segments. The 5' end of the plus strand is necessary and sufficient for packaging, while the normal 3' end is necessary for synthesis of the negative strand. We have now investigated the ability of truncated RNA segments which lack the normal 3' end of the molecules to stimulate the synthesis of minus strands of the other segments. Fragments missing the normal 3' ends were able to stimulate the minus-strand synthesis of intact heterologous segments. Minus-strand synthesis of one intact segment could be stimulated by the presence of two truncated nonreplicating segments. The 5' fragments of each single-stranded genomic segment can compete with homologous full-length single-stranded genomic segments in minus-strand synthesis reactions, suggesting that there is a specific binding site in the procapsid for each segment.     

Evolution of defective-interfering double-stranded RNAs of the yeast killer virus.

We have characterized by T1 fingerprint analysis several defective interfering (DI) double-stranded RNAs of the simple yeast virus ScV. A common sequence of about 0.5 to 0.6 kilobase pairs, including both 3' termini of the parental RNA, was present in each DI RNA. Several DI RNAs had novel T1 oligonucleotides not present in their parental RNA.     

A Study of the Transmission and Structure of Double Stranded Rnas Associated with the Killer Phenomenon in SACCHAROMYCES CEREVISIAE

Killer strains contain two double stranded RNAs, L and M. The M dsRNA appears to be necessary for production of a toxin and for resistance to that toxin. Mutant strains have been found that are defective in their ability to kill and in their resistance to toxin. These sensitive, non-killer strains have altered dsRNA composition. One class has no M dsRNA. Another class of sensitive, non-killers called suppressives has no M dsRNA but instead has smaller dsRNAs called S. In diploids resulting from a cross of a wild-type killer by a suppressive the transmission of the M dsRNA is suppressed by the S dsRNA. When a suppressive is crossed by a strain with no M dsRNA, the diploids and all four meiotic spores have the S dsRNA characteristic of the parental suppressive strain. Suppressive strains do not suppress each other. Intercrosses between two different suppressives yields diploids with both parental S dsRNAs. These two S dsRNAs are transmitted to all 4 meiotic progeny. Another class of mutants has been found which is defective for one of the traits but retains the other. One type, temperature-sensitive killers, has a normal dsRNA composition but is unable to kill at 30°. The other type, immunity-minus, has a complex dsRNA pattern. The immunity-minus strain is extremely unstable during mitotic growth and segregates several different types of non-killers. Analysis of the dsRNAs from wild type and the mutants by electron microscopy shows that the L, M, and S dsRNAs are linear. All strains regardless of killer phenotype appear to have the same size L dsRNA.