Reverse transcription of yeast double-stranded RNA and ribosomal RNA using synthetic oligonucleotide primers

A Rapid Method for Sequencing Double-Stranded RNAs Purified from Yeasts and the Identification of a Potent K1 Killer Toxin Isolated from Saccharomyces cerevisiae

Mycoviruses infect a large number of diverse fungal species, but considering their prevalence, relatively few high-quality genome sequences have been determined. Many mycoviruses have linear double-stranded RNA genomes, which makes it technically challenging to ascertain their nucleotide sequence using conventional sequencing methods. Different specialist methodologies have been developed for the extraction of double-stranded RNAs from fungi and the subsequent synthesis of cDNAs for cloning and sequencing. However, these methods are often labor-intensive, time-consuming, and can require several days to produce cDNAs from double-stranded RNAs. Here, we describe a comprehensive method for the rapid extraction and sequencing of dsRNAs derived from yeasts, using short-read next generation sequencing. This method optimizes the extraction of high-quality double-stranded RNAs from yeasts and 3′ polyadenylation for the initiation of cDNA synthesis for next-generation sequencing. We have used this method to determine the sequence of two mycoviruses and a double-stranded RNA satellite present within a single strain of the model yeast Saccharomyces cerevisiae. The quality and depth of coverage was sufficient to detect fixed and polymorphic mutations within viral populations extracted from a clonal yeast population. This method was also able to identify two fixed mutations within the alpha-domain of a variant K1 killer toxin encoded on a satellite double-stranded RNA. Relative to the canonical K1 toxin, these newly reported mutations increased the cytotoxicity of the K1 toxin against a specific species of yeast.

Interfaces of the yeast killer phenomenon

A new prophylactic and therapeutic antimicrobial strategy based on a specific physiological target that is effectively used by killer yeasts in their natural ecological competition is theorized. The natural system exploited is the yeast killer phenomenon previously adopted as an epidemiological marker for intraspecific differentiation of opportunistic yeasts, hyphomycetes, and bacteria. Pathogenic microorganisms (Candida albicans) may be susceptible to the activity of yeast killer toxins due to the presence of specific cell wall receptors. On the basis of the idiotypic network, we report that antiidiotypic antibodies, produced against a monoclonal antibody bearing the receptor-like idiotype, are in vivo protecting animals immunized through idiotypic vaccination and in vitro mimicking the antimicrobial activity of yeast killer toxins, thus acting as antibiotics.

Sequence of the M1-2 region of killer virus double-stranded RNA

A full-length complementary DNA (cDNA) copy of the M1-2 region of the double-stranded genome of the yeast killer virus was synthesized by reverse transcription, utilizing the m in vitro transcript as template and synthetic primers for both strands. The sequence lacks any long open reading frames (ORFs). The internal portion of the M1-2 region includes the sequence that is linked to the subterminal 229 bases of the M1-1 homologous region in the S3 defective-interfering mutant of killer virus double-stranded RNA (dsRNA). Thus, the probable site at which the deletion occurred in S3 has been identified.

Analysis and utilization of the preprotoxin gene encoded in the M1 double-stranded RNA of yeast

The yeast type 1 toxin is a secreted protein which, along with immunity to the toxin, is encoded by an encapsidated double-stranded RNA (dsRNA) as a precursor protein, the preprotoxin. This chapter reviews recent work that has led to sequencing of complementary DNA (cDNA) copies of the preprotoxin gene, expression of toxin and toxin-immunity from cDNA, and use of the cDNA to effect secretion from yeast of a bacterial cellulase.

Double-stranded ribonucleic acid killer systems in yeasts

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Saccharomyces cerevisiae killer virus transcripts contain template-coded polyadenylate tracts

The M double-stranded RNA component of type 1 killer strains of the yeast Saccharomyces cerevisiae contains an internal 200-base pair adenine- and uracil-rich region. The plus strands of this viral genomic RNA contain an internal adenine-rich region which allows these strands to bind to polyuridylate-Sepharose as tightly as do polyadenylated RNAs with 3'-terminal polyadenylated tracts of 70 to 100 residues. Internal template coding of an adenine-rich tract in positive polarity in vivo and in vitro transcripts of M double-stranded RNA may serve as an alternate method of transcript polyadenylation. The 3'-terminal residue of the in vitro m transcript is a non-template-encoded purine residue. The 5' terminus of this transcript is involved in a stem-and-loop structure which includes an AUG initiation codon, along with potential 18S and 5.8S rRNA binding sites. Except for the 3'-terminal residue, transcription in in vitro shows complete fidelity.

Saccharomyces cerevisiae killer virus transcripts contain template-coded polyadenylate tracts

The M double-stranded RNA component of type 1 killer strains of the yeast Saccharomyces cerevisiae contains an internal 200-base pair adenine- and uracil-rich region. The plus strands of this viral genomic RNA contain an internal adenine-rich region which allows these strands to bind to polyuridylate-Sepharose as tightly as do polyadenylated RNAs with 3'-terminal polyadenylated tracts of 70 to 100 residues. Internal template coding of an adenine-rich tract in positive polarity in vivo and in vitro transcripts of M double-stranded RNA may serve as an alternate method of transcript polyadenylation. The 3'-terminal residue of the in vitro m transcript is a non-template-encoded purine residue. The 5' terminus of this transcript is involved in a stem-and-loop structure which includes an AUG initiation codon, along with potential 18S and 5.8S rRNA binding sites. Except for the 3'-terminal residue, transcription in in vitro shows complete fidelity.

Synthesis of a double-stranded cDNA transcript of the killer toxin-coding region of the yeast M1 double-stranded RNA

Reverse transcription of methylmercuryhydroxide-treated M1 double-stranded RNA of yeast produces several discrete single-stranded and double-stranded cDNA's from oligo (dT)12-18 primer. S1 nuclease analysis shows that the longest transcript of the 1.8 kb template, a 2.2 kb molecule, is a 1.1 kb duplex terminated at one end by a hairpin-like structure. The 1.1 kb ds cDNA contains a complete copy of the M1-1, toxin-coding, sequence of M1 double-stranded RNA, and its synthesis is primed from oligo (dT)12-18 that anneals to a sequence within the internal, AU-rich, region of the template.