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

Evolutionarily conserved optimization of amino acid biosynthesis

The "cognate bias hypothesis" states that early in evolutionary history the biosynthetic enzymes for amino acid x gradually lost residues of x, thereby reducing the threshold for deleterious effects of x scarcity. The resulting reduction in cognate amino acid composition of the enzymes comprising a particular amino acid biosynthetic pathway is predicted to confer a selective growth advantage on cells. Bioinformatic evidence from protein-sequence data of two bacterial species previously demonstrated reduced cognate bias in amino acid biosynthetic pathways. Here we show that cognate bias in amino acid biosynthesis is present in the other domains of life-Archaebacteria and Eukaryota. We also observe evolutionarily conserved underrepresentations (e.g., glycine in methionine biosynthesis) and overrepresentations (e.g., tryptophan in asparagine biosynthesis) of amino acids in noncognate biosynthetic pathways, which can be explained by secondary amino acid metabolism. Additionally, we experimentally validate the cognate bias hypothesis using the yeast Saccharomyces cerevisiae. Specifically, we show that the degree to which growth declines following amino acid deprivation is negatively correlated with the degree to which an amino acid is underrepresented in the enzymes that comprise its cognate biosynthetic pathway. Moreover, we demonstrate that cognate fold representation is more predictive of growth advantage than a host of other potential growth-limiting factors, including an amino acid's metabolic cost or its intracellular concentration and compartmental distribution.

Transcriptional regulation of the Kluyveromyces lactis beta-galactosidase gene

We examined the molecular basis for beta-D-galactosidase (EC 3.2.1.23) induction in the yeast Kluyveromyces lactis. The protein synthesis inhibitor anisomycin effectively blocked both protein synthesis and enzyme induction by lactose. Further, hybridization analysis with the cloned beta-galactosidase gene indicated coordinate increases in the concentration of beta-galactosidase messenger ribonucleic acid and enzyme activity. The half-life of beta-galactosidase messenger ribonucleic acid was the same (4.8 +/- 0.4 min) when measured both before and at succeeding times during enzyme induction. These results strongly support the hypothesis that expression of the yeast beta-galactosidase gene is subject to transcriptional regulation.

Structure of the HOM2 gene of Saccharomyces cerevisiae and regulation of its expression

In Saccharomyces cerevisiae the HOM2 gene encodes aspartic semi-aldehyde dehydrogenase (ASA DH). The synthesis of this enzyme had been shown to be derepressed by growth in the presence of high concentrations of methionine. In the present work we have cloned and sequenced the HOM2 gene and found that the promoter region of this gene bears one copy of the consensus sequence for general control of amino acid synthesis. This prompted us to study the regulation of the expression of the HOM2 gene. We have found that ASA DH is the first reported enzyme of the related threonine and methionine pathway to be regulated by the general control of amino acid synthesis.

Physiological control of repressible acid phosphatase gene transcripts in Saccharomyces cerevisiae

We have examined the regulation of repressible acid phosphatase (APase; orthophosphoric-monoester phosphohydrolase [acid optimum], EC 3.1.3.2) in Saccharomyces cerevisiae at the physiological and molecular levels, through a series of repression and derepression experiments. We demonstrated that APase synthesis is tightly regulated throughout the growth phase and is influenced by exogenous and endogenous Pi pools. During growth in a nonlimiting Pi medium, APase is repressed. When external Pi becomes limiting, there is a biphasic appearance of APase mRNA and enzyme. Our data on APase mRNA half-lives and on the flux of intracellular Pi and polyphosphate during derepression are consistent with a mechanism of transcriptional autoregulation for the biphasic appearance of APase mRNA. Accordingly, preculture concentrations of Pi control the level of corepressor generated from intracellular polyphosphate degradation. When cells are fully derepressed, APase mRNA levels are constant, and the maximal linear accumulation rate of APase is observed. A scheme to integrate phosphorus metabolism and phosphatase regulation in S. cerevisiae is proposed.

Physiological control of repressible acid phosphatase gene transcripts in Saccharomyces cerevisiae

We have examined the regulation of repressible acid phosphatase (APase; orthophosphoric-monoester phosphohydrolase [acid optimum], EC 3.1.3.2) in Saccharomyces cerevisiae at the physiological and molecular levels, through a series of repression and derepression experiments. We demonstrated that APase synthesis is tightly regulated throughout the growth phase and is influenced by exogenous and endogenous Pi pools. During growth in a nonlimiting Pi medium, APase is repressed. When external Pi becomes limiting, there is a biphasic appearance of APase mRNA and enzyme. Our data on APase mRNA half-lives and on the flux of intracellular Pi and polyphosphate during derepression are consistent with a mechanism of transcriptional autoregulation for the biphasic appearance of APase mRNA. Accordingly, preculture concentrations of Pi control the level of corepressor generated from intracellular polyphosphate degradation. When cells are fully derepressed, APase mRNA levels are constant, and the maximal linear accumulation rate of APase is observed. A scheme to integrate phosphorus metabolism and phosphatase regulation in S. cerevisiae is proposed.

Participation of transcriptional and post-transcriptional regulatory mechanisms in the control of arginine metabolism in yeast

In yeast, as in other organisms, amino acid biosynthetic pathways share a common regulatory control. The manifestation of this control is that derepression of the enzymes belonging to several amino acid biosynthetic pathways follows amino acid starvation or tRNA discharging. The arginine anabolic and catabolic pathways are, in addition, regulated specifically by arginine in opposite ways by common regulators. We have measured the mRNA levels for four genes subject to the general amino acid control: HIS4, ARG3, ARG4 and CPAII and compared them to the corresponding enzyme levels. Similarly we have measured the mRNA levels for two genes subject to the arginine specific regulation: ARG3 and CAR1, the former gene belongs to the arginine anabolic pathway and the latter to the arginine catabolic one. HIS4, ARG4 and CPAII enzyme and messenger amounts are perfectly coordinated in all the conditions of general repression or derepression tested. However, arginine does not reduce the level of the ARG3 mRNA enough to explain the reduction of ornithine carbamoyltransferase activity nor does it increase the level of the CAR1 mRNA enough to explain the extent of induction of arginase. Coordination of enzyme and ARG3 mRNA is achieved only when the specific control is eliminated. The half-lives of the ARG3 and CAR1 messengers are enhanced in mutants leading to constitutive expression of ornithine carbamoyltransferase and arginase. These data suggest that the control that coordinates the synthesis of all the amino acids in the yeast cell operates at the level of transcription while the arginine specific regulatory mechanism seems to operate at a post-transcriptional level.

Evidence that alpha-isopropylmalate synthase of Saccharomyces cerevisiae is under the "general" control of amino acid biosynthesis

The specific activity and the immunoreactive amount of alpha-isopropylmalate synthase were more than three times above wild-type values in a Saccharomyces cerevisiae mutant (cdr1) with constitutively derepressed levels of enzymes known to be under the "general" control of amino acid biosynthesis. The specific activity was also higher in lysine- and arginine-leaky strains when these were grown under limiting conditions, and in wild-type cells grown in the presence of 5-methyltryptophan. A low specific activity was found in a mutant (ndr1) unable to derepress enzymes of the general control system. Neither isopropylmalate isomerase nor beta-isopropylmalate dehydrogenase responded to general control signals.

Cloning arg3, the gene for ornithine carbamoyltransferase from Saccharomyces cerevisiae: expression in Escherichia coli requires secondary mutations; production of plasmid beta-lactamase in yeast

The yeast arg3 gene, coding for ornithine carbamoyltransferase (carbamoylphosphate:L-ornithine carbamoyltransferase, EC 2.1.3.3), has been cloned on a hybrid pBR322-2-micrometers plasmid. The cloned gene gives a normal regulatory response in yeast. It is not expressed at 35 degrees C when a mutation preventing mRNA export from the nucleus at this temperature is included in the genetic make-up of the carrier strain. In Escherichia coli, no functional expression can be observed from the native yeast arg3 gene. The study of a mutant plasmid (M1) producing low levels of yeast carbamoyltransferase in E. coli has permitted the localization and orientation of arg3 on the plasmid. The mutation involved is a deletion that alters the regulatory response of arg3 in yeast. The plasmid bla gene produces detectable amounts of beta-lactamase (penicillin amido-beta-lactamhydrolase, EC 3.5.2.6) in yeast: the data provide an estimate of the beta-lactamase activity associated with one exemplar of the plasmid expressing arg3 (0.6 units).

Transcriptional regulation of the Kluyveromyces lactis beta-galactosidase gene

We examined the molecular basis for beta-D-galactosidase (EC 3.2.1.23) induction in the yeast Kluyveromyces lactis. The protein synthesis inhibitor anisomycin effectively blocked both protein synthesis and enzyme induction by lactose. Further, hybridization analysis with the cloned beta-galactosidase gene indicated coordinate increases in the concentration of beta-galactosidase messenger ribonucleic acid and enzyme activity. The half-life of beta-galactosidase messenger ribonucleic acid was the same (4.8 +/- 0.4 min) when measured both before and at succeeding times during enzyme induction. These results strongly support the hypothesis that expression of the yeast beta-galactosidase gene is subject to transcriptional regulation.

Regulation of compartmentation of amino acid pools in Saccharomyces cerevisiae and its effects on metabolic control

Compartmentation of intracellular amino acid pools has been studied under various growth conditions in wild-type strains as well as in mutants. Aspartate, glutamate, leucine and isoleucine pools are present in high concentrations in the cytoplasm, while all the other amino acids are more vacuolar. The nature of the nitrogen source for growth, the effectiveness of nitrogen assimilation, the rate of protein synthesis and the presence of high internal basic amino acid pools are important factors in the repartition of amino acid pools between the cytoplasm and the vacuole.

Dual regulation of the synthesis of the arginine pathway carbamoylphosphate synthase of Saccharomyces cerevisiae by specific and general controls of amino acid biosynthesis

The synthesis of the arginine pathway carbamoylphosphate synthase (CPSase A) of Saccharomyces cerevisiae is subject to two control mechanisms. One mechanism is specific for CPSase A and is exerted by arginine; it probably involves a repressor-operator type of interaction. This "specific" mechanism regulates the expression of gene cpaI coding for the small "glutaminase" subunit of CPSase A but has little influence on the production of the large subunit of the enzyme, a product of gene cpaII. This large component, which alone has no biological significance, accumulates freely under conditions of arginine repression. The second mechanism is general: it controls enzyme synthesis in a number of amino acid biosynthetic pathways in addition to the arginine sequence. Two types of evidence that this "general" mechanism participates in the control of CPSase A synthesis are presented: (1) Derepression upon starvation for any amino acid of which the synthesis is subject to this general control; and (2) repression during growth in amino acid-rich medium. In contrast to the specific mechanism, the "general" mechanism regulates the expression of both the cpaI and cpaII genes.

General and lysin specific control of saccharopine dehydrogenase levels in the yeast Saccharomycopsis lipolytica

Lysine supplementation of the growth medium of a wild type strain of the yeast Saccharomycopsis lipolytica specifically results in saccharopine dehydrogenase repression. Starvation of the strain for histidine triggers a general depression of various histidine, leucine, arginine and lysine biosynthetic enzymes, including saccharopine dehydrogenase. These two types of control, specific and general, act independently on saccharopine dehydrogenase expression, since mutants which fail to respond to the specific control still are sensitive to the general one. These mutants were first selected as unable to catabolize lysine, suggesting that a link may exist between saccharopine dehydrogenase specific regulation and activity of the catabolic pathway.

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.

Concerted repression of the synthesis of the arginine biosynthetic enzymes by aminoacids: a comparison between the regulatory mechanisms controlling aminoacid biosyntheses in bacteria and in yeast

It has been shown that in bacteria, besides specific regulatory mechanisms, the synthesis of aminoacid biosynthetic enzymes is also controlled by the endogenous aminoacid pool. The latter regulates the intracellular level of ppGpp, a positive effector of RNA messenger transcription. A similar regulatory control exists in yeast but does not appear to involve the same general effector. This was established by the observation that derepression of the enzymes belonging to several aminoacid biosynthetic pathways follows aminoacid starvation or tRNA discharging. We now report the repression of the arginine pathway by the total aminoacid pool. New mutations affecting the repressibility of the arginine enzymes as well as enzymes belonging to other aminoacid biosyntheses, when cells are grown in the presence of an excess of aminoacids, were identified.

Organization and expression of a two-gene cluster in the arginine biosynthesis of Saccharomyces cerevisiae

In Saccharomyces cerevisiae, argB and argC define two adjacent and complementing loci, with mutants defective in two consecutive steps of arginine biosynthesis: N-acetylglutamate kinase (AG-kinase) and N-acetylglutamyl-phosphate reductase (AGPreductase). These enzymic activities are readily separated by ammonium sulfate fractionation or Sephadex G-200 chromatography. This suggests that each activity is carried in vivo by a different protein. The synthesis of the two enzymes is coordinately regulated, with an 85-fold difference in specific activities between fully repressed and fully derepressed cells. Missence mutations of the argB locus are defective in AGkinase only. Nonsense mutations in the argB locus are defective in both activities. Missense and nonsense mutations in the argC locus are defective in AGPreductase, with a few alleles also showing a reduced level of AGkinase. These data are best explained by assuming that argB and argC are two genes transcribed as a single messenger from argB to argC. This messenger produces in vivo two distinct proteins corresponding to the argB and argC gene products, either because translation can be initiated at the beginning of both genes, or because a large polypeptide is specifically cut in vivo to yield the gene products of argB and argC.

Control of vacuole permeability and protein degradation by the cell cycle arrest signal in Saccharomyces cerevisiae

Saccharomyces cerevisiae responds to deperivation of nutrients by arresting cell division at the unbudded G1 stage. Cells situated outside of G1 at the time of deperivation complete the cell cycle before arresting. This prompted an investigation of the source of nutrients used by these cells to complete division and the mechanisms controlling their availability. We found a close correlation between accumulation of unbudded cells and loss of previously formed allophanate hydrolase activity after nutrient starvation. These losses were not specific to the allantoin, system since they have been observed for a number of other enzymes and also when cellular protein levels were monitored with [3H]leucine. Loss of hydrolase activity was also observed when protein synthesis was inhibited either by addition of inhibitors or loss of the prtl gene product. We found that onset of nutrient starvation brought about release of large quantities of arginine and allantoin normally sequestered in the cell vacuole. Treatment of a cells with alpha-factor resulted in both the release of allantoin and arginine from the cell vacuole and the onset of intracellular protein degradation. These effects were not observed when either alpha cells or a/alpha diploid strains were treated with alpha-factor. These data suggest that release of vacuolar constitutents and protein turnover may be regulated by the G1 arrest signal.

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.

Stability of messenger RNA for nitrate reductase in Neurospora crassa

A method has been developed to study the synthesis and decay of the messenger RNA for nitrate reductase in Neurospora crassa. Glutamine prevents the synthesis of the mRNA which appears to have a half-life of approximately 8.5 min.

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.

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.