Turnover of polyadenylate-containing ribonucleic acid in Saccharomyces cerevisiae

Characterizing RNA stability genome-wide through combined analysis of PRO-seq and RNA-seq data

BACKGROUND

The concentrations of distinct types of RNA in cells result from a dynamic equilibrium between RNA synthesis and decay. Despite the critical importance of RNA decay rates, current approaches for measuring them are generally labor-intensive, limited in sensitivity, and/or disruptive to normal cellular processes. Here, we introduce a simple method for estimating relative RNA half-lives that is based on two standard and widely available high-throughput assays: Precision Run-On sequencing (PRO-seq) and RNA sequencing (RNA-seq).

RESULTS

Our method treats PRO-seq as a measure of transcription rate and RNA-seq as a measure of RNA concentration, and estimates the rate of RNA decay required for a steady-state equilibrium. We show that this approach can be used to assay relative RNA half-lives genome-wide, with good accuracy and sensitivity for both coding and noncoding transcription units. Using a structural equation model (SEM), we test several features of transcription units, nearby DNA sequences, and nearby epigenomic marks for associations with RNA stability after controlling for their effects on transcription. We find that RNA splicing-related features are positively correlated with RNA stability, whereas features related to miRNA binding and DNA methylation are negatively correlated with RNA stability. Furthermore, we find that a measure based on U1 binding and polyadenylation sites distinguishes between unstable noncoding and stable coding transcripts but is not predictive of relative stability within the mRNA or lincRNA classes. We also identify several histone modifications that are associated with RNA stability.

CONCLUSION

We introduce an approach for estimating the relative half-lives of individual RNAs. Together, our estimation method and systematic analysis shed light on the pervasive impacts of RNA stability on cellular RNA concentrations.

Impact of Methods on the Measurement of mRNA Turnover

The turnover of the RNA molecules is determined by the rates of transcription and RNA degradation. Several methods have been developed to study RNA turnover since the beginnings of molecular biology. Here we summarize the main methods to measure RNA half-life: transcription inhibition, gene control, and metabolic labelling. These methods were used to detect the cellular activity of the mRNAs degradation machinery, including the exo-ribonuclease Xrn1 and the exosome. On the other hand, the study of the differential stability of mature RNAs has been hampered by the fact that different methods have often yielded inconsistent results. Recent advances in the systematic comparison of different method variants in yeast have permitted the identification of the least invasive methodologies that reflect half-lives the most faithfully, which is expected to open the way for a consistent quantitative analysis of the determinants of mRNA stability.

Nucleolar accumulation of poly (A)+ RNA in heat-shocked yeast cells: implication of nucleolar involvement in mRNA transport

Transport of mRNA from the nucleus to the cytoplasm plays an important role in gene expression in eukaryotic cells. In wild-type Schizosaccharomyces pombe cells poly(A)+ RNA is uniformly distributed throughout the nucleoplasm and cytoplasm. However, we found that a severe heat shock blocks mRNA transport in S. pombe, resulting in the accumulation of bulk poly(A)+ RNA, as well as a specific intron-less transcript, in the nucleoli. Pretreatment of cells with a mild heat shock, which induces heat shock proteins, before a severe heat shock protects the mRNA transport machinery and allows mRNA transport to proceed unimpeded. In heat-shocked S. pombe cells, the nucleolar region condensed into a few compact structures. Interestingly, poly(A)+ RNA accumulated predominantly in the condensed nucleolar regions of the heat-shocked cells. These data suggest that the yeast nucleolus may play a role in mRNA transport in addition to its roles in rRNA synthesis and preribosome assembly.

Nucleolar accumulation of poly (A)+ RNA in heat-shocked yeast cells: implication of nucleolar involvement in mRNA transport

Transport of mRNA from the nucleus to the cytoplasm plays an important role in gene expression in eukaryotic cells. In wild-type Schizosaccharomyces pombe cells poly(A)+ RNA is uniformly distributed throughout the nucleoplasm and cytoplasm. However, we found that a severe heat shock blocks mRNA transport in S. pombe, resulting in the accumulation of bulk poly(A)+ RNA, as well as a specific intron-less transcript, in the nucleoli. Pretreatment of cells with a mild heat shock, which induces heat shock proteins, before a severe heat shock protects the mRNA transport machinery and allows mRNA transport to proceed unimpeded. In heat-shocked S. pombe cells, the nucleolar region condensed into a few compact structures. Interestingly, poly(A)+ RNA accumulated predominantly in the condensed nucleolar regions of the heat-shocked cells. These data suggest that the yeast nucleolus may play a role in mRNA transport in addition to its roles in rRNA synthesis and preribosome assembly.

General requirement for RNA polymerase II holoenzymes in vivo

Yeast RNA polymerase II holoenzymes have been described that consist of RNA polymerase II, a subset of general transcription factors, and nine SRB regulatory proteins. The feature that distinguishes the RNA polymerase II holoenzymes from other forms of RNA polymerase II in the cell is their tight association with SRB proteins. We investigated the fraction of genes that require SRB proteins in vivo by examining the effect of temperature-sensitive mutations in SRB genes on transcription by RNA polymerase II. Upon transfer to the restrictive temperature, there is a rapid and general shutdown of mRNA synthesis in srb mutant cells. These data, combined with the observation that essentially all of the SRB protein in cells is tightly associated with RNA polymerase II molecules, argue that SRB-containing holoenzymes are the form of RNA polymerase II recruited to most promoters in the cell.

Efficient translation of poly(A)-deficient mRNAs in Saccharomyces cerevisiae

The polyadenylate tail of eukaryotic mRNAs is thought to influence various metabolic phenomena including mRNA stability, translation initiation, and nucleo-cytoplasmic transport. We have analyzed the fate of mRNAs following inactivation of poly(A) polymerase in Saccharomyces cerevisiae containing a temperature-sensitive, lethal mutation (pap1-1) in the gene for poly(A) polymerase (PAP1). Inactivation of poly(A) polymerase (Pap1) by shifting cells to the nonpermissive temperature resulted in the loss of at least 80% of measurable poly(A) within 60 min. Northern blot analysis revealed the disappearance of some mRNAs (CYH2 and HIS4) consistent with a role for poly(A) tails in mRNA stability. However, other mRNAs (TCM1, PAB1, ACT1, and HTB2) accumulate as poly(A)-deficient (A < approximately 25) transcripts as defined by an inability to bind oligo(dT)-cellulose. Sucrose density gradient analysis of polyribosomes revealed a twofold reduction in the amount of each size class of polyribosomes in shifted cells and a commensurate increase in free ribosomes. However, poly(A)-deficient mRNAs in shifted cells remain associated with the same size polyribosomes as poly(A)+ mRNAs in unshifted cells, indicating normal initiation of translation. RNase mapping of transcripts from pap1-1 cells revealed PAB1 mRNA to be poly(A)- whereas TCM1 exists as equal amounts of poly(A)- and poly(A)+ mRNA 60 min after shift. Interestingly, both of these classes of TCM1 mRNA appear in similar amounts in each polyribosome fraction indicating that ribosomes may not distinguish between them. These findings suggest that under conditions of excess translational capacity, poly(A)- and poly(A)+ mRNAs may initiate translation with comparable efficiencies.

The 5' untranslated region of the PPR1 regulatory gene dictates rapid mRNA decay in yeast

In Saccharomyces cerevisiae, the mRNA encoded by the PPR1 gene is very unstable (t1/2 = 1 min), whereas the mRNA encoded by the URA3 gene is relatively stable (t1/2 = 10 min). To identify cis-acting sequences that dictate mRNA decay rates in yeast, we have constructed PPR1/URA3 gene fusions and measured the half-lives of the resulting chimeric transcripts. The mRNA containing the URA3 coding region fused to the untranslated regions (UTR) of PPR1 decayed at a rate similar to the native PPR1 mRNA, suggesting that the instability of the PPR1 mRNA is not linked to its coding sequence. When the 5'-UTR of PPR1 was replaced by the 5'-UTR of URA3, the chimeric transcript was strongly stabilized, indicating that the 5'-UTR of PPR1 is required for the rapid decay of its mRNA. Fusion of this PPR1 5'-UTR to the URA3 coding region was sufficient to destabilize the chimeric mRNA. We conclude that the PPR1 5'-UTR contains sequence(s) that can promote rapid mRNA decay in yeast.

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.

The FUR1 gene of Saccharomyces cerevisiae: cloning, structure and expression of wild-type and mutant alleles

The FUR1 gene of Saccharomyces cerevisiae encodes uracil phosphoribosyltransferase (UPRTase) which catalyses the conversion of uracil into uridine 5'-monophosphate (UMP) in the pyrimidine salvage pathway. The FUR1 gene is included in a 2.1 kb genomic segment of DNA and is transcribed into a 1 kb poly(A)+mRNA. Sequencing has determined a 753 bp open reading frame capable of encoding a protein of 251 amino acids. The FUR1 genes for three recessive fur1 alleles, having different sensibilities to 5-fluorouridine (5-FUR) but identical levels of resistance to 5-fluorouracil (5-FU), were cloned and sequenced. Single bp changes located in different regions of the gene were found in each mutant. Two in vitro-constructed deletions of the FUR1 gene have been integrated at the chromosomal locus, giving strains with 5-FURR and 5-FURR mutant phenotype. Assays of UPRTase, uridine kinase, uridine ribohydrolase and uridine 5'-monophosphate nucleotidase enzymatic activities, in extracts of strains where the FUR1 gene is overexpressed or deleted, indicate that the FUR1 encoded protein possesses only UPRTase activity.

Genetic characterization and isolation of the Saccharomyces cerevisiae gene coding for uridine monophosphokinase

We selected a 5-fluorouracil-resistant, thermosensitive mutant of the uridine monophosphokinase step in Saccharomyces cerevisiae. The mutant displays very weak thermolabile uridine monophosphokinase activity and wild-type uridine diphosphokinase activity. Growth of the mutant at the non-permissive temperature causes immediate reduction of pyrimidine triphosphate pools to 10% of the wild-type level as well as significantly lowering total RNA and protein synthesis. These conditions also provoke derepression of the first gene of the pathway, URA2, at both the levels of enzymatic activity and transcription. The mutation segregates independently of all known genes of the pyrimidine biosynthetic pathway. The corresponding gene has been isolated on a 4.8 kb fragment by complementation of the mutant phenotype. The new gene, named URA6, codes for a 2.2 kb polyadenylated messenger RNA, exists in a single copy per haploid genome, and was mapped to the centromere of chromosome XI.

Messenger RNA for ribosomal proteins in yeast

The concentrations and mean lifetimes of the messenger RNAs for four ribosomal proteins of the yeast, Saccharomyces cerevisiae, have been determined by the method of approach to equilibrium labeling, using cloned genes as hybridization probes. In cells growing in a minimal medium with glucose as a carbon source, there are roughly equimolar amounts of the four mRNAs, whose half-lives are very similar: 14 +/- 2 minutes, approximately 10% of a generation time. These results lead to an analysis of the economy of mRNA for ribosomal proteins that suggests that the mRNAs may be substantially underutilized.

Messenger ribonucleic acid and protein metabolism during sporulation of Saccharomyces cerevisiae

To investigate differences between growing yeasts and those undergoing sporulation, we compared several parameters of messenger ribonucleic acid (RNA) transcription and translation. The general properties of messenger RNA metabolism were not significantly altered by the starvation conditions accompanying sporulation. The average messenger RNA half-life, calculated from the kinetics of incorporation of [3H]adenine into polyadenylic acid-containing RNA, was 20 min on both cell populations. Furthermore, 1.3 to 1.4% of the total RNA was adenylated in both growing and sporulating cells. However, the proportion of RNA that could be translated in a wheat germ system slowly decreased during sporulation. Within 8 h after the induction of sporulation, isolated RNA stimulated half as much protein synthesis as the equivalent amount of vegetative RNA. There were significant differences in protein synthesis. The percentage of ribosomes in polysomes decreased threefold as the cells entered sporulation. This decrease began within 5 min of the initiation of sporulation, and the steady-state pattern was attained within 120 min. However, the ribosomes were not irreversibly inactivated; they could be reincorporated into polysomes by returning the sporulating cells to growth medium. Though unable to sporulate, strains homozygous for mating type, MAT alpha/MAT alpha, showed a similar decrease in the number of polysomes when placed in sporulation medium. Furthermore, the same shift toward monosomes was observed during stationary phase of growth. We conclude that the redistribution of ribosomes represents a general metabolic response to starvation. Our data indicate that the loss of polysomes is most likely caused by a decrease in the initiation of translation rather than a severe limitation in the amount of messenger RNA. Furthermore, the loss of polysomes is not due to the decreased synthesis of a major class of abundant proteins. Of the 400 vegetative proteins resolved by two-dimensional gel electrophoresis, only 19 were not synthesized by sporulating cells. Approximately 10 to 20% of the cells in a sporulating culture failed to complete ascus formation. We have shown that [35S]methionine is incorporated equivalently into cells committed to sporulation and cells that fail to form asci. Furthermore, the proteins synthesized by these two populations were indistinguishable, on one-dimensional gels. We compared proteins labeled by various protocols, including long-term and pulse-labeling during sporulation and prelabeling during vegetative growth before transfer to sporulation medium. The resulting two-dimensional gel patterns differed significantly. Many spots labeled by the long-term techniques may have arisen by protein processing. We suggest that pulse-labeling produces the most accurate reflection of instantaneous synthesis of proteins.

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.

Level and turnover of polyadenylate-containing ribonucleic acid in Neurospora crassa in different steady states of growth

Mycelia of Neurospora crassa in a steady state of growth in different media have a ribosomal content proportional to the rate of growth. Moreover, both the percentage of polysomes and the average ribosomal activity are about the same at all different growth rates. The content of polyadenylated RNA was determined in three different conditions of exponential growth, which allowed growth rates that ranged from 0.26 to 0.51 duplications/h, and was found to constitute about the same fraction of total RNA (4.5--5.2%). Using a kinetic approach, an equation was derived which allowed determination of the average half-lives of polyadenylated RNA: in each medium the cultures were labeled from the moment of the inoculation with [32P]orthophosphate and were then given a 10-min pulse with [5-3H]uridine when they were in the exponential phase. It was found that the determined half-lives of polyadenylated RNA vary, depending on the growth medium, between 30 and 60 min, but with no direct correlation with the growth rate. Moreover, the rate of synthesis of polyadenylated RNA relative to that of stable RNA decreased with the growth rate. On the basis of previous data on the rates of synthesis of stable RNA, it was possible to make an evaluation of the absolute rate of synthesis of polyadenylated RNA. Whereas the rate of synthesis of stable ribosomal RNA increases as a function of the square of the number of duplications per hour, the increase in the rate of synthesis of polyadenylated RNA with the growth rate is much less consistent. It is concluded that in Neurospora the growth rate does not depend on the rate of synthesis of mRNA but rather on the rate of synthesis of rRNA, which sets both the ribosomal level and the steady-state level of mRNA.

Structure of polyadenylic acid in the ribonucleic acid of Saccharomyces cerevisiae

Investigations of the structure of polyadenylic acid [poly(A)] in yeast have shown that there are two classes of poly(A) distinguished by size and kinetics of synthesis. Each class is found directly on the 3' end of messenger RNA. One class contains poly(A) molecules ranging from 60 to less than 20 nucleotides long. The longest molecules in this poly(A) class are the first to become labeled when cells are exposed to [3H]adenine. Label then appears in progressively smaller molecules. The second class of poly(A) is about 20 nucleotides long. The length homogeneity of this class and the presence in nuclear DNA of many copies of a polythymidylate sequence which is the same length suggests that this poly(A) is synthesized by transcription from DNA.

The half-life of mRNA in Saccharomyces cerevisiae

The decay kinetics of mRNA was studied in a yeast temperature-sensitive mutant, ts136, which is defective in cytoplasmic RNA production at 37 degree C. The disappearance of the synthetic capacity of mRNA was determined by withdrawing equal volumes of ts136 cell culture and pulse-labelling with [35S]methionine at various time intervals after the shift to 37 degrees C from 23 degrees C. The synthesized proteins were separated on a two-dimensional gel electrophoretic system and then quantitatively analyzed for theri incorporated radioactivities by scintillation counting. Our results show that yeast mRNAs have divergent functional half-lives ranging from 4.5 to 41 min, with an average value of 22 min. Each mRNA exhibits a simple exponential decay with its own characteristic dacay pattern. Of the approximately 500 major polypeptides made by yeast cells, which are detectable on autoradiograms of the gels, 80 were arbitrarily selected and the mRNAs coding for those polypeptides were examined for their decay kinetics.

Regulation of acid phosphatase synthesis in Saccharomyces cerevisiae

In Saccharomyces cerevisiae-136ts (Hutchison, H.T., Hartwell, L.H. and McLaughlin, C.S. (1969) J. Bacteriol. 99, 807--814) derepressed acid phosphatase was almost exclusively located outside the permeability barrier. Only a minor part of the activity was associated with the protoplasts; about half of it (48%) in the soluble fraction, the rest bound to the internal (45%) and plasma (7%) membranes. The activity found in the membranes of derepressed cells decreased by 30--40% after addition of inorganic phosphate or cycloheximide suggesting that this activity is the precursor of the external enzyme. The alkaline phosphatase activity level could not be modified by changes in the concentration of inorganic phosphate. Acid phosphatase was not synthesized if the cells were transferred to a low phosphate medium at the moment of incubation at 37 degrees C or in the presence of cycloheximide at 23 degrees C. The data suggested that enzyme formation is the result of the transcription and translation of a specific gene(s) and not the activation of a proenzyme. Inorganic phosphate did not inhibit the translation of mRNA though it may act at the level of the transcription.

Isolation and characterization of an actinomycin D-sensitive mutant of Saccharomyces cerevisiae

A single mutation in Saccharomyces cerevisiae conferred sensitivity to low concentrations of actinomycin D. Treatment with actinomycin D preferentially inhibited synthesis of rRNA's. Residual rRNA synthesized was processed normally. Total protein synthesis and inducibility of the enzyme maltase were relatively unaffected at concentrations of actinomycin D which severely inhibited rRNA synthesis.

Kinetics of glucose repression of yeast cytochrome c

The kinetics of glucose repression of cytochrome c synthesis was measured by a radioimmune assay. When 5 or 10% glucose was added to a derepressed culture, the rate of cytochrome c synthesis was reduced to the repressed level with a half-life of 2 min. The addition of 1 or 0.5% glucose repressed the rate of cytochrome c synthesis to the same level as high glucose concentrations but with a longer half-life of 3 min. Glucose repression had no effect on the stability or function of the cytochrome c protein. Cellular levels of active cytochrome c mRNA during glucose repression were measured by translation of total cellular polyadenylic acid-containing RNA and immunoprecipitation cytochrome c from the translation products. The results of these measurements indicate that glucose represses the rate of cytochrome c synthesis through a reduction in the level of translatable cytochrome c mRNA.

8-hydroxyquinoline inhibition of DNA synthesis and intragenic recombination during yeast meiosis

Complete inhibition of sporulation was observed in two strains of Saccharomyces cerevisiae to which 8-hydroxyquinoline was added at a final concentration of 5 microgram/ml during the initial 4 to 6 h of sporulation. The cells were most sensitive to the inhibitor during 4 to 6 interval beginning at approximately 2 h (T2). Its addition during that interval resulted in 70 to 80% lethality in strain 4579 and about 40% in API at T24. When present from T0 onward, 5 microgram/ml of 8-hydroxyquinoline severely inhibited premeiotic DNA replication and reduced the frequency of intragenic recombination at the ade 2 and leu 2 loci by 70 and 100%, respectively, relative to control cultures which did not have the inhibitor present. During the period when the cells were most sensitive, the incorporation of 14C-leucine into protein and 14C-adenine into RNA was not inhibited nor was the polysome content affected. At 150 microgram/ml of inhibitor, incorporation of labeled precursors into RNA and protein were inhibited and the percentage of active ribosomes was reduced by 35% within 45 min, but neither transcription or translation appeared to be completely inhibited at this concentration of the inhibitor.

Factors influencing the observed half-lives of specific synthetic capacities in Saccharomyces cerevisiae

We have identified a variety of factors affecting the stability of allophanate hydrolase-specific and gross cellular protein synthetic capacities. These synthetic capacities have been extrapolated by many laboratories to represent functional messenger RNAs. Synthetic capacity turnover rates that we measured were greater in diploid organisms than in haploid strains and were proportional to the temperature of the culture medium. The stability of allophanate hydrolase-specific synthetic capacity was not influenced by alterations in the nitrogen source provided in the culture medium, but was increased up to 15-fold by the total inhibition of protein synthesis. Cultures in which protein synthesis was inhibited as little as 20% exhibited hydrolase-specific synthetic capacities more than 2-fold greater than those observed in the absence of inhibition.

Transcriptional units for ribosomal proteins in yeast

The effects of ultraviolet irradiation on the rates of synthesis of individual ribosomal proteins in yeast were examined and compared with the ultraviolet sensitivities of the synthesis of other yeast proteins. It was found that the synthesis of yeast ribosomal proteins is much more sensitive to ultraviolet irradiation than that of other yeast cellular proteins. Taking into account the half-life of yeast mRNA, the results obtained indicate that the genes coding for ribosomal proteins form part of long transcriptional units, which are much longer than the DNA stretch needed to code for a ribosomal protein of average molecular weight. Saturation hybridization of total poly(A)-containing mRNA with yeast nuclear DNA revealed that as much as 30% of DNA is complementary to yeast mRNA. Thus, the primary transcript of a protein gene on the average is about 1.7 times the length of the actual messenger. On the basis of the various experimental data we suggest a clustering of the yeast ribosomal protein genes in a number of common transcriptional units.

Molecular events associated with induction of arginase in Saccharomyces cerevisiae

Arginase, the enzyme responsible for arginine degradation in Saccharomyces cerevisiae, is an inducible protein whose inhibition of ornithine carbamoyl-transferase has been studied extensively. Mutant strains defective in the normal regulation of arginase production have also been isolated. However, in spite of these studies, the macromolecular biosynthetic events involved in production of arginase remain obscure. We have, therefore, studied the requirements of arginase induction. We observed that: (i) 4 min elapsed between the addition of inducer (homoarginine) and the appearance of arginase activity at 30 degrees C; (ii) induction required ribonucleic acid synthesis and a functional rna1 gene product; and (iii) production of arginase-specific synthetic capacity occurred in the absence of protein synthesis but could be expressed only when protein synthesis was not inhibited. Termination of induction by inducer removal, addition of the ribonucleic acid synthesis inhibitor lomofungin, or resuspension of a culture of organisms containing temperature-sensitive rna1 gene products in a medium at 35 degrees C resulted in loss of ability for continued arginase synthesis with half-lives of 5.5, 3.8, and 4.5 min, respectively. These and other recently published data suggest that a variety of inducible or repressible proteins responding rapidly to the environment may be derived from labile synthetic capacities, whereas constitutively produced proteins needed continuously throughout the cell cycle may be derived from synthetic capacities that are significantly more stable.

Evidence that specific and "general" control of ornithine carbamoyltransferase production occurs at the level of transcription in Saccharomyces cerevisiae

Ornithine carbamoyltransferase synthesis is subject to two major regulatory systems in Saccharomyces cerevisiae. One system is specific for the arginine biosynthetic enzymes, whereas the other appears to be general, acting on a variety of other amino acid pathways as well. We observed that the synthetic capacity for continued ornithine carbamoyltransferase synthesis had the same short half-life (ca. 5 to 7 min) whether repression of enzyme production was brought about by action of the specific or general control system. We present evidence suggesting that both control systems regulate accumulation or ornithine carbamoyltransferase-specific synthetic capacity, rather than modulating its expression.

Adenosine utilization in cordycepin-sensitive mutants of Saccharomyces cerevisiae

A purine-requiring, wild-type yeast strain was cordycepin resistant and failed to grow in medium containing adenosine; in contrast, a cordycepin-sensitive mutant (also purine requiring) grew well in medium containing adenosine. The cordycepin-sensitive mutant incorporated [8-14C]adenosine at nine times the wild-type rate, and adenosine completely fulfilled the purine requirement of the cells. Exogenous adenosine rapidly entered the mutant cells, apparently as free nucleoside, and was phosphorylated; uptake displayed concentration-dependent saturation kinetics (Km, 6 mM). Within 10 min 14C radioactivity was being incorporated into nucleic acids.

Rate of synthesis of polyadenylate-containing ribonucleic acid during the yeast cell cycle

The rate of synthesis of polyadenylate-containing ribonucleic acid is constant throughout the cell cycle of Saccharomyces cerevisiae.

Coordinate regulation of the synthesis of eukaryotic ribosomal proteins

We have developed a method of r the direct measurement, in eukaryotic cells, of the synthesis of ribosomal proteins, irrespective of the synthesis of ribosomes. In this way the synthesis of ribosomal proteins has been examined in mutant strains of Saccharomyces cerevisiae, which are unable to synthesize ribosomes under nonpermissive conditions. The results suggest that the synthesis of more than 40 ribosomal proteins is under coordinate control. Under nonpermissive conditions,the synthesis of each h protein declines exponentially to a basal level which is 10-20% fo normal. The kinetics of that decline suggest that an early, if not primary, result of the nonpermissive conditions is the cessation of production of new mRNA for eac of the ribosomal proteins. The coordinate regulation appears not to be influenced directly by the rate of transcription of ribosomal precursor RNA.