Structure of polyadenylic acid in the ribonucleic acid of Saccharomyces cerevisiae

Hybrid selection with cDNA-silica

A partial length ovalbumin cDNA-silica was produced using primer extension of (dT)18-silica with annealed partial ovalbumin RNA and reverse transcriptase. This cDNA-silica was used to test whether full-length ovalbumin RNA could be selectively purified in the presence of a large excess of other (mouse muscle) RNA. The cDNA-silica synthesized had minimally 60 pmol cDNA per gram silica and had a capacity for full-length ovalbumin RNA of minimally 38 micrograms/g. Even when other RNA was present in greater than 1000-fold excess, ovalbumin RNA was selectively retained by the cDNA-silica and was eluted in yields of 43% with an enrichment which varied over the range of 29-162-fold in various experiments. These results show that even rare RNAs can be selectively purified in high yield using cDNA-silica. The importance of these results to hybrid selection and subtractive library preparation is discussed.

Affinity chromatography with nucleic acid polymers

Column chromatography utilizing polynucleotides immobilized on solid support is reviewed. This form of affinity chromatography is used for the isolation of polynucleotides and polynucleotide binding proteins, and to a lesser extent for analysis. Several specific applications within these categories have been widely used in the biomedical sciences. Poly(A) mRNA is routinely isolated using oligo(dT) or oligo(dU) supports. Many DNA binding proteins, including transcription factors, restriction endonucleases, and proteins involved in DNA repair, replication, recombination, and transposition have been purified using DNA affinity chromatography. Recently, DNA supports suitable for use in high-performance liquid chromatography have been described and utilized. The current usage of DNA affinity chromatography is reviewed and potential future uses for this technology are speculated upon.

Stationary phase in the yeast Saccharomyces cerevisiae

Growth and proliferation of microorganisms such as the yeast Saccharomyces cerevisiae are controlled in part by the availability of nutrients. When proliferating yeast cells exhaust available nutrients, they enter a stationary phase characterized by cell cycle arrest and specific physiological, biochemical, and morphological changes. These changes include thickening of the cell wall, accumulation of reserve carbohydrates, and acquisition of thermotolerance. Recent characterization of mutant cells that are conditionally defective only for the resumption of proliferation from stationary phase provides evidence that stationary phase is a unique developmental state. Strains with mutations affecting entry into and survival during stationary phase have also been isolated, and the mutations have been shown to affect at least seven different cellular processes: (i) signal transduction, (ii) protein synthesis, (iii) protein N-terminal acetylation, (iv) protein turnover, (v) protein secretion, (vi) membrane biosynthesis, and (vii) cell polarity. The exact nature of the relationship between these processes and survival during stationary phase remains to be elucidated. We propose that cell cycle arrest coordinated with the ability to remain viable in the absence of additional nutrients provides a good operational definition of starvation-induced stationary phase.

High-performance affinity chromatography of messenger RNA

A 50-mer of thymidylic acid, (dT)50, was coupled to silica inside prepacked columns using the N-hydroxysuccinimide chemistry. The resulting (dT)50-silica columns were used to resolve oligomers of adenylic acid, (dA)19-24, and to separate poly(A) mRNA (messenger RNA) from Saccharomyces. Oligomers which differed in length by a single nucleotide base were readily resolved. Using either (dT)50- or (dT)18-silica, poly(A) mRNA could be purified in as little as 8 min. The poly(A) mRNA isolated appeared to be full length and could be used directly for T4 RNA ligase and RNAse A and T1 enzymatic reactions. The (dT)50-silica column was used to fractionate total poly(A) mRNA by tail length. While the separation was primarily due to poly(A) tail length, most fractions appeared to contain multiple tail lengths. Whether this represents an intrinsic feature of the RNA or a limitation of the method is discussed. These studies show that polynucleotides in the kilobase size range can be separated rapidly and with good resolution on DNA-silica.

Identification and comparison of stable and unstable mRNAs in Saccharomyces cerevisiae

We developed a procedure to measure mRNA decay rates in the yeast Saccharomyces cerevisiae and applied it to the determination of half-lives for 20 mRNAs encoded by well-characterized genes. The procedure utilizes Northern (RNA) or dot blotting to quantitate the levels of individual mRNAs after thermal inactivation of RNA polymerase II in an rpb1-1 temperature-sensitive mutant. We compared the results of this procedure with results obtained by two other procedures (approach to steady-state labeling and inhibition of transcription with Thiolutin) and also evaluated whether heat shock alter mRNA decay rates. We found that there are no significant differences in the mRNA decay rates measured in heat-shocked and non-heat-shocked cells and that, for most mRNAs, different procedures yield comparable relative decay rates. Of the 20 mRNAs studied, 11, including those encoded by HIS3, STE2, STE3, and MAT alpha 1, were unstable (t1/2 less than 7 min) and 4, including those encoded by ACT1 and PGK1, were stable (t1/2 greater than 25 min). We have begun to assess the basis and significance of such differences in the decay rates of these two classes of mRNA. Our results indicate that (i) stable and unstable mRNAs do not differ significantly in their poly(A) metabolism; (ii) deadenylation does not destabilize stable mRNAs; (iii) there is no correlation between mRNA decay rate and mRNA size; (iv) the degradation of both stable and unstable mRNAs depends on concomitant translational elongation; and (v) the percentage of rare codons present in most unstable mRNAs is significantly higher than in stable mRNAs.

Identification and comparison of stable and unstable mRNAs in Saccharomyces cerevisiae

We developed a procedure to measure mRNA decay rates in the yeast Saccharomyces cerevisiae and applied it to the determination of half-lives for 20 mRNAs encoded by well-characterized genes. The procedure utilizes Northern (RNA) or dot blotting to quantitate the levels of individual mRNAs after thermal inactivation of RNA polymerase II in an rpb1-1 temperature-sensitive mutant. We compared the results of this procedure with results obtained by two other procedures (approach to steady-state labeling and inhibition of transcription with Thiolutin) and also evaluated whether heat shock alter mRNA decay rates. We found that there are no significant differences in the mRNA decay rates measured in heat-shocked and non-heat-shocked cells and that, for most mRNAs, different procedures yield comparable relative decay rates. Of the 20 mRNAs studied, 11, including those encoded by HIS3, STE2, STE3, and MAT alpha 1, were unstable (t1/2 less than 7 min) and 4, including those encoded by ACT1 and PGK1, were stable (t1/2 greater than 25 min). We have begun to assess the basis and significance of such differences in the decay rates of these two classes of mRNA. Our results indicate that (i) stable and unstable mRNAs do not differ significantly in their poly(A) metabolism; (ii) deadenylation does not destabilize stable mRNAs; (iii) there is no correlation between mRNA decay rate and mRNA size; (iv) the degradation of both stable and unstable mRNAs depends on concomitant translational elongation; and (v) the percentage of rare codons present in most unstable mRNAs is significantly higher than in stable mRNAs.

Messenger RNA degradation in Saccharomyces cerevisiae

The analysis of 17 functional mRNAs and two recombinant mRNAs in the yeast Saccharomyces cerevisiae suggests that the length of an mRNA influences its half-life in this organism. The mRNAs are clearly divisible into two populations when their lengths and half-lives are compared. Differences in ribosome loading amongst the mRNAs cannot account for this division into relatively stable and unstable populations. Also, specific mRNAs seem to be destabilized to differing extents when their translation is disrupted by N-terminus-proximal stop codons. The analysis of a mutant mRNA, generated by the fusion of the yeast PYK1 and URA3 genes, suggests that a destabilizing element exists within the URA3 sequence. The presence of such elements within relatively unstable mRNAs might account for the division between the yeast mRNA populations. On the basis of these, and other previously published observations, a model is proposed for a general pathway of mRNA degradation in yeast. This model may be relevant to other eukaryotic systems. Also, only a minor extension to the model is required to explain how the stability of some eukaryotic mRNAs might be regulated.

The internal polyadenylate tract of yeast killer virus M1 double-stranded RNA is variable in length

The 1.8-kbp M1 double-stranded (ds) RNA from type 1 killer strains of Saccharomyces cerevisiae contains an internal 200-bp adenine- and uracil-rich region. We have previously demonstrated that this region consists primarily of adenine residues on the plus strand of M1 dsRNA and on the full-length, in vitro synthesized (+) transcript (denoted m) of M1 dsRNA, neither of which contains 3'-terminal polyadenylate. We now show that there is variability in the length of the polyadenylate tracts of m transcripts synthesized in vitro by virions purified from either of the K1 diploid killer strains A364A X S7 or A364A X 1384. This variability reflects size differences seen in the corresponding M1 dsRNA genomes which, along with other data presented, localizes the variability in the length of M1 dsRNA to the adenine- and uracil-rich region.

A functional prepro-alpha-factor gene in Saccharomyces yeasts can contain three, four, or five repeats of the mature pheromone sequence

The chromosomal region containing a structural gene for the mating pheromone precursor prepro-alpha-factor was examined in a variety of Saccharomyces yeasts by using a cloned putative prepro-alpha-factor gene of Saccharomyces cerevisiae as the probe. Analysis by restriction endonuclease digestion and Southern blot hybridization indicated that the physical arrangement of this region is highly conserved in all the Saccharomyces species analyzed, but displays length polymorphisms of limited size (50 to 60 base pairs). The observed polymorphisms were shown to be due solely to differences in the number of tandemly arranged spacer peptide/pheromone units within the coding sequence of these genes. Analysis of polyadenylated RNA indicated that these genes specified RNA transcripts and that these RNA molecules could be translated in vitro into prepro-alpha-factor polypeptides immunoprecipitable with anti-alpha-factor antibodies. The sizes of both the mRNAs and the proteins synthesized from them reflected exactly the differences observed in the lengths of the genes. These findings demonstrate conclusively that the putative prepro-alpha-factor DNA cloned from S. cerevisiae, as well as the sequences detected in the other Saccharomyces species, are indeed expressed and functional genes, and suggest that proper proteolytic processing of prepro-alpha-factor is unaffected by the number of pheromone repeats encoded within this precursor protein.

A functional prepro-alpha-factor gene in Saccharomyces yeasts can contain three, four, or five repeats of the mature pheromone sequence

The chromosomal region containing a structural gene for the mating pheromone precursor prepro-alpha-factor was examined in a variety of Saccharomyces yeasts by using a cloned putative prepro-alpha-factor gene of Saccharomyces cerevisiae as the probe. Analysis by restriction endonuclease digestion and Southern blot hybridization indicated that the physical arrangement of this region is highly conserved in all the Saccharomyces species analyzed, but displays length polymorphisms of limited size (50 to 60 base pairs). The observed polymorphisms were shown to be due solely to differences in the number of tandemly arranged spacer peptide/pheromone units within the coding sequence of these genes. Analysis of polyadenylated RNA indicated that these genes specified RNA transcripts and that these RNA molecules could be translated in vitro into prepro-alpha-factor polypeptides immunoprecipitable with anti-alpha-factor antibodies. The sizes of both the mRNAs and the proteins synthesized from them reflected exactly the differences observed in the lengths of the genes. These findings demonstrate conclusively that the putative prepro-alpha-factor DNA cloned from S. cerevisiae, as well as the sequences detected in the other Saccharomyces species, are indeed expressed and functional genes, and suggest that proper proteolytic processing of prepro-alpha-factor is unaffected by the number of pheromone repeats encoded within this precursor protein.

Oligoadenylate is present in the mitochondrial RNA of Saccharomyces cerevisiae

We examined Saccharomyces cerevisiae mitochondrial RNA for polyadenylate. Using hybridization to [3H]polyuridylate as the assay for adenylate sequences, we found adenylate-rich oligonucleotides approximately 8 residues long. Longer polyadenylate was not detected. Most of the adenylate-rich sequence is associated with the large mitochondrial rRNA. The remainder is associated with the 10-12S group of transcripts.

Oligoadenylate is present in the mitochondrial RNA of Saccharomyces cerevisiae

We examined Saccharomyces cerevisiae mitochondrial RNA for polyadenylate. Using hybridization to [3H]polyuridylate as the assay for adenylate sequences, we found adenylate-rich oligonucleotides approximately 8 residues long. Longer polyadenylate was not detected. Most of the adenylate-rich sequence is associated with the large mitochondrial rRNA. The remainder is associated with the 10-12S group of transcripts.

Fluctuation in polyadenylate size and content in exponential- and stationary-phase cells of Saccharomyces cerevisiae

Stationary-phase cells of Saccharomyces cerevisiae were found to have a reduced polyadenylate [poly(A)] content as compared with exponential-phase cells. A sizing procedure for poly(A) was devised to distinguish between alternative hypotheses to explain this reduction. Two major size classes of poly(A) were found. The decreased representation of the larger of the two classes accounted for the majority of the poly(A) loss. The remainder of the loss was accounted for by fewer poly(A)-containing sequences. The smaller of the two poly(A) classes was apparently not of mitochondrial origin and may be added transcriptionally.

Properties of polyadenylate-associated ribonucleic acid from Saccharomyces cerevisiae ascospores

Bulk ribonucleic acid (RNA) was isolated from mechanically disrupted ascospores of Saccharomyces cerevisiae. After two passes over an oligo (dT10) cellulose column, the portion which bound, called poly(A)(+), was characterized. It is heterodisperse in size with a mean molecular weight of approximately 4 X 10(5), but contains some species as large as 7 X 10(5). The base composition is similar to vegetative poly(A)(+) RNA. The polyadenylate segment is also heterogenous in size, ranging from 90 to 20 bases in length, with a peak at approximately 60 nucleotides in length. Pulse-labeling of asci with [3H-methyl]methionine yields two "caps," 7-methyl guanosine-5'-triphosphoryl-5'-adenosine (or guanosine) identical to that found in vegetative poly(A)(+) RNA. The poly(A)(+) RNA in spores is found in polyribosomes which are, on the average, smaller than vegetative ones. Long-term labeling studies indicate that the fraction of poly(A)(+) RNA in spores is similar to that in vegetative cells.