Constitutive RNA synthesis for the yeast activator ADR1 and identification of the ADR1-5c mutation: implications in posttranslational control of ADR1

PUF3 acceleration of deadenylation in vivo can operate independently of CCR4 activity, possibly involving effects on the PAB1-mRNP structure

The evolutionarily conserved PUF proteins stimulate CCR4 mRNA deadenylation through binding to 3' untranslated region sequences of specific mRNA. We have investigated the mechanisms by which PUF3 in Saccharomyces cerevisiae accelerates deadenylation of the COX17 mRNA. PUF3 was shown to affect PAN2 deadenylation of the COX17 mRNA independent of the presence of CCR4, suggesting that PUF3 acts through a general mechanism to affect deadenylation. Similarly, eIF4E, the cap-binding translation initiation factor known to control CCR4 deadenylation, was shown to affect PAN2 activity in vivo. PUF3 was found to be required for eIF4E effects on COX17 deadenylation. Both eIF4E and PUF3 effects on deadenylation were shown, in turn, to necessitate a functional poly(A)-binding protein (PAB1) in which removal of the RRM1 (RNA recognition motif 1) domain of PAB1 blocked both their effects on deadenylation. While removal of the proline-rich region (P domain) of PAB1 substantially reduces CCR4 deadenylation at non-PUF3-controlled mRNA and correspondingly blocked eIF4E effects on deadenylation, PUF3 essentially bypassed this P domain requirement. These results indicate that the PAB1-mRNP structure is critical for PUF3 action. We also found that multiple components of the CCR4-NOT deadenylase complex, but not PAN2, interacted with PUF3. PUF3 appears, therefore, both to act independently of CCR4 activity, possibly through effects on PAB1-mRNP structure, and to be capable of retaining the CCR4-NOT complex.

Characterization of a p53-related activation domain in Adr1p that is sufficient for ADR1-dependent gene expression

The yeast transcriptional activator Adr1p controls expression of the glucose-repressible alcohol dehydrogenase gene (ADH2), genes involved in glycerol metabolism, and genes required for peroxisome biogenesis and function. Previous data suggested that promoter-specific activation domains might contribute to expression of the different types of ADR1-dependent genes. By using gene fusions encoding the Gal4p DNA binding domain and portions of Adr1p, we identified a single, strong acidic activation domain spanning amino acids 420-462 of Adr1p. Both acidic and hydrophobic amino acids within this activation domain were important for its function. The critical hydrophobic residues are in a motif previously identified in p53 and related acidic activators. A mini-Adr1 protein consisting of the DNA binding domain of Adr1p fused to this 42-residue activation domain carried out all of the known functions of wild-type ADR1. It conferred stringent glucose repression on the ADH2 locus and on UAS1-containing reporter genes. The putative inhibitory region of Adr1p encompassing the protein kinase A phosphorylation site at Ser-230 is thus not essential for glucose repression mediated by ADR1. Mini-ADR1 allowed efficient derepression of gene expression. In addition it complemented an ADR1-null allele for growth on glycerol and oleate media, indicating efficient activation of genes required for glycerol metabolism and peroxisome biogenesis. Thus, a single activation domain can activate all ADR1-dependent promoters.

Factors affecting Saccharomyces cerevisiae ADH2 chromatin remodeling and transcription

The chromatin structure of the Saccharomyces cerevisiae ADH2 gene is modified during the switch from repressing (high glucose) to derepressing (low glucose) conditions of growth. Loss of protection toward micrococcal nuclease cleavage for the nucleosomes covering the TATA box and the RNA initiation sites (-1 and +1, respectively) is the major modification taking place and is strictly dependent on the presence of the transcriptional activator ADR1. To identify separate functions involved in the transition from a repressed to a transcribing promoter, we have analyzed the ADH2 chromatin organization in various genetic backgrounds. Deletion of the CCR4 gene coding for a general transcription factor impaired ADH2 expression without affecting chromatin remodeling. Growing yeast at 37 degrees C also resulted in chromatin remodeling at the ADH2 locus even under glucose repressing conditions. However, although this temperature-induced remodeling was dependent on the ADR1 protein, no ADH2 mRNA was observed. In addition, inactivating RNA polymerase II (and therefore, elongation) was found to have no effect on the ability to reconfigure nucleosomes. Taken together, these data indicate that chromatin remodeling by itself is insufficient to induce transcription at the ADH2 promoter.

Cloning and sequence determination of the gene encoding sorbitol dehydrogenase from Saccharomyces cerevisiae

The identification of a sorbitol-induced sorbitol dehydrogenase (SDH) activity from Saccharomyces cerevisiae is described. The SDH1 structural gene was isolated from a lambda gt11 yeast genomic library using an antibody to a 40-kDa protein induced in yeast cells growing in medium containing sorbitol. The gene encodes a 357-amino-acid (aa) protein deduced from the nucleotide sequence. Comparison of the aa sequence of the yeast SDH1 with that of sheep liver SDH reveals a 63% overall similarity. Yeast transformants containing the cloned gene carried on a multicopy plasmid express high levels of SDH1 only when grown on sorbitol, suggesting that the cloned gene contains both regulatory and coding sequences.

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.

Identification of three genes required for the glucose-dependent transcription of the yeast transcriptional activator ADR1

Glucose repression of the ADH2 gene from Saccharomyces cerevisiae is mediated by the synthesis and activity of the transcriptional activator ADR1. In this study, we isolated mutations in three new genes (SAF1, SAF2 and SAF3) that suppressed the glucose-insensitive expression of ADH2 caused by the ADR1-5c allele. The mechanism by which the SAF genes maintain ADR1-5c function was investigated. Each of the mutated SAF genes was found to suppress ADR1-5c activity by lowering ADR1-5c steady state mRNA levels 5- to 8-fold under glucose growth conditions. ADR1 mRNA levels were similarly affected by the saf mutations. In contrast, mutations in the SAF genes had little or no effect on ADR1-5c or ADR1 mRNA levels under ethanol growth conditions. The stability of ADR1-5c mRNA was unaffected by mutations in each of the SAF genes, implying that the SAF genes are required for the transcription of ADR1 mRNA under glucose growth conditions. The possible function of the three SAF genes in ADR1 expression is discussed.

The CCR1 (SNF1) and SCH9 protein kinases act independently of cAMP-dependent protein kinase and the transcriptional activator ADR1 in controlling yeast ADH2 expression

cAMP-dependent protein kinase (cAPK) is implicated in the inactivation of the yeast transcriptional activator ADR1, which regulates glucose-repressible ADH2 gene expression. The interdependence of cAPK, SCH9 (a protein kinase that when overexpressed can functionally substitute for cAPK), and the CCR1 (SNF1) protein kinase that is required for ADH2 expression was studied. SCH9 was found to be required for ADH2 expression in contrast to the inhibitory role played by cAPK. CCR1 and SCH9 were observed to affect ADH2 expression independently of both ADR1 and cAPK. In contrast, cAPK was shown to exert its effects on ADH2 solely through ADR1. These results indicate that the SCH9 and CCR1 protein kinases are components of regulatory pathways separate from that utilized by cAPK to control ADR1 activity and ADH2 expression.

The CCR4 gene from Saccharomyces cerevisiae is required for both nonfermentative and spt-mediated gene expression

Mutations in the yeast CCR4 gene inhibit expression of the glucose-repressible alcohol dehydrogenase (ADH2), as well as other nonfermentative genes, and suppress increased ADH2 expression caused by the cre1 and cre2 alleles. Both the cre1 and ccr4 alleles were shown to affect ADH II enzyme activity by altering the levels of ADH2 mRNA. Mutations in either CRE1 or CRE2 bypassed the inhibition of ADH2 expression caused by delta insertions at the ADH2 promoter which displace the ADH2 activation sequences 336 bp upstream of the TATA element. These cre1 and cre2 effects were suppressible by the ccr4 allele. The cre1 and ccr4 mutations also affected ADH2 expression when all the ADH2 regulatory sequences upstream of the TATA element were deleted. The relationship of the CRE genes to the SPT genes, which when mutated are capable of bypassing the inhibition of HIS4 expression caused by a delta promoter insertion (his4-912 delta allele), was examined. Both the cre1 and cre2 mutations allowed his4-912 delta expression. ccr4 mutations were able to suppress the ability of the cre alleles to increase his4-912 delta expression. CRE2 was shown to be allelic to the SPT6 gene, and CRE1 was found to be allelic to SPT10. We suggest that the CRE genes comprise a general transcriptional control system in yeast that requires the function of the CCR4 gene.

Overexpression of the yeast transcriptional activator ADR1 induces mutation of the mitochondrial genome

It was previously observed that increased dosages of the ADR1 gene, which encodes a yeast transcriptional activator required for alcohol dehydrogenase II (ADH II) expression, cause a decreased rate of growth in medium containing ethanol as the carbon source. Here we show that observed reduction in growth rate is mediated by the ADR1 protein which, when overexpressed, increases the frequency of cytoplasmic petites. Unlike previously characterized mutations known to potentiate petite formation, the ADR1 effect is dominant, with the petite frequency rising concomitantly with increasing ADR1 dosage. The ability of ADR1 to increase the frequency of mitochondrial mutation is correlated with its ability to activate ADH II transcription but is independent of the level of ADH II being expressed. Based on restoration tests using characterized mit- strains, ADR1 appears to cause non-specific deletions within the mitochondrial genome to produce rho- petites. Pedigree analysis of ADR1-overproducing strains indicates that only daughter cells become petite. This pattern is analogous to that observed for petite induction by growth at elevated temperature and by treatment with the acridine dye euflavine. One strain resistant to ADR1-induced petite formation displayed cross-resistance to petite mutation by growth at elevated temperature and euflavine treatment, yet was susceptible to petite induction by ethidium bromide. These results suggest that ADR1 overexpression disrupts the fidelity of mitochondrial DNA replication or repair.

Cyclic AMP-dependent protein kinase phosphorylates and inactivates the yeast transcriptional activator ADR1

It has been proposed in several eukaryotic systems that the regulation of gene transcription involves phosphorylation of specific transcription factors. We report here that the yeast transcriptional activator ADR1 is phosphorylated in vitro by cyclic AMP-dependent protein kinase and that mutations which enhance the ability of ADR1 to activate ADH2 expression decrease ADR1 phosphorylation. We also show that increased kinase activity in vivo inhibits ADH2 expression in an ADR1 allele-specific manner. Our data suggest that glucose repression of ADH2 is in part mediated through a cAMP-dependent phosphorylation-inactivation of the ADR1 regulatory protein.

Cloning and characterization of the CYC8 gene mediating glucose repression in yeast

Mutations in the CYC8 ( = SSN6) gene of Saccharomyces cerevisiae alleviate glucose repression of many glucose-repressible genes. The gene was isolated by screening for complementation of a cyc8 effect on colony morphology. Subclones containing a 5.3-kb SalI-XbaI fragment provided complete complementation. The gene was further localized to 3.5 kb by mapping of the CYC8 mRNA and insertional mutagenesis. Insertion and deletion mutations are viable and produce the same array of phenotypes as point mutations. CYC8 disruptions also had effects on the mating ability and morphology of MAT alpha cells similar to that of tup1 mutations. The nucleotide sequence of a 4866-bp fragment, including CYC8, was determined. One long open reading frame of 966 amino acid predicts a protein of molecular weight 10,7215. The predicted protein is extremely glutamine-rich, with blocks of 16 and 31 glutamines in tandem at the N and C regions, respectively. The CYC8 gene product lacks consensus sequences for DNA-binding domains, suggesting that its function may be different from classical repressor proteins.

The effects of ADR1 and CCR1 gene dosage on the regulation of the glucose-repressible alcohol dehydrogenase from Saccharomyces cerevisiae

The dosage of the transcriptional activator ADR1 was varied in order to study the regulation of the glucose-repressible alcohol dehydrogenase (ADH II) from Saccharomyces cerevisiae. ADH II activity during glucose growth conditions was shown to increase linearly with increasing ADR1 gene dosage. In contrast, under derepressed growth conditions a 100-fold increase in ADR1 copy number resulted in only a 4-fold increase in ADH II expression. Saturation of ADH II gene expression by ADR1 under derepressed conditions was shown not to result from decreased ADR1 transcription. Increases in ADH2 gene dosage in conjunction with high ADR1 gene dosages resulted in increased ADH II activity, indicating that ADH2 was the limiting factor during derepression. Under glucose-repressed conditions the activator CCR1 was not required for ADR1 activity. During derepression increasing ADR1 dosage could partially compensate for a CCR1 defect. Increasing CCR1 gene dosage, however, had no effect on ADH2 expression regardless of the ADR1 allele present. These results suggest that CCR1 acts through ADR1 in controlling ADH2 expression. It was also observed that high numbers of ADR1, or a few copies of ADR1-5c, substantially increased the cell doubling time under ethanol growth conditions, indicating that increased ADR1 activity is toxic.