A study of the properties of the free amino acid pool and enzyme synthesis in yeast

Modeling and analysis of the macronutrient signaling network in budding yeast

Adaptive modulation of the global cellular growth state of unicellular organisms is crucial for their survival in fluctuating nutrient environments. Because these organisms must be able to respond reliably to ever varying and unpredictable nutritional conditions, their nutrient signaling networks must have a certain inbuilt robustness. In eukaryotes, such as the budding yeast Saccharomyces cerevisiae, distinct nutrient signals are relayed by specific plasma membrane receptors to signal transduction pathways that are interconnected in complex information-processing networks, which have been well characterized. However, the complexity of the signaling network confounds the interpretation of the overall regulatory "logic" of the control system. Here, we propose a literature-curated molecular mechanism of the integrated nutrient signaling network in budding yeast, focusing on early temporal responses to carbon and nitrogen signaling. We build a computational model of this network to reconcile literature-curated quantitative experimental data with our proposed molecular mechanism. We evaluate the robustness of our estimates of the model's kinetic parameter values. We test the model by comparing predictions made in mutant strains with qualitative experimental observations made in the same strains. Finally, we use the model to predict nutrient-responsive transcription factor activities in a number of mutant strains undergoing complex nutrient shifts.

Aerobic fermentation and the depletion of the amino acid pool in yeast cells

The amino acid pool of yeast cells, Saccharomyces cerevisiae, incubated with galactose remains at a constant level for 100 minutes. This is 30 minutes beyond the time at which the oxidative phase of the induced-enzyme formation begins. Washed yeast cells, the pools of which have been depleted 60 per cent by incubation with glucose, do not replenish their pools as do washed cells incubated without a substrate. These facts indicate that the induced enzymes are formed at least partially from pool-replenishing amino acids. The time of onset of pool depletion is the time at which the aerobic fermentation phase of induced-enzyme formation begins for cells incubated with galactose. With 0.1 per cent galactose the respiratory phase begins at 100 minutes but no aerobic fermentation nor pool depletion occurs. The rates of respiration and aerobic fermentation are constant for four glucose concentrations from 0.1 to 1.0 per cent. The amount of aerobicfermentation is proportional to the initial concentration of glucose. Amino acid pool depletion occurs for all concentrations but depletion ceases and is followed by pool replenishment after aerobic fermentation is complete. Ultraviolet radiations, which delay the appearance of the respiratory phase of induced-enzyme formation, completely eliminate both the appearance of aerobic fermentation and pool depletion. The results indicate an intimate association between aerobic fermentation and amino acid pool depletion.

Mitochondrial translation products during release from glucose repression in Saccharomyces cerevisiae

Mitochondrial protein synthesis was studied during release from glucose repression in Saccharomyces cerevisiae cells bearing different mitochondrial genomes. The increase in the rate of the synthesis of mitochondrial translation products was analyzed during respiratory induction. Different kinetic patterns were found for strains having a different structure of mitochondrial mosaic genes, even when the nuclear background was the same. A very limited response of the synthesis of the var1 ribosomal protein to inducing conditions was observed.

Energy requirements for the uptake of L-leucine by Saccharomyces cerevisiae

(1) Substrates capable of activating mitochondrial electron transfer and oxidative phosphorylation, namely, pyruvate, acetate, propionaldehyde and butanol, stimulated the concentrative uptake (transport and accumulation) of L-[14-C]leucine by Saccharomyces cerevisiae (wild type strain 207, starved cells). Under adequate experimental conditions, the L-[14-C]leucine uptake versus the oxygen uptake ratio was almost the same with either pyruvate, acetate or D-glucose as energy sources. Substrate oxidation also increased L-[14-C]leucine incorporation into the cell protein. (2) With S. cerevisiae D261 and D247-2 and propionaldehyde as an energy source, or with strain 207 and glucose as energy source, 2,4-dinitrophenol (50 muM) inhibited L-[14-C]leucine uptake, the inhibition being accompanied by stimulation of respiration. With S. cerevisiae 207 and propionaldehyde as energy source, 2,4-dinitrophenol inhibited both respiration and L-[14-C]leucine uptake, but with respiration being less affected than uptake. Displacement of accumulated L-[14-C]leucine was also inhibited by 2,4-dinitrophenol. (3) In the presence of glucose, and for relatively brief incubation periods, anaerobically grown cells of S. cerevisiae 207 and of a p-minus "petite" mutant of this strain incorporated L-[14-C]leucine with less efficiency than the original wild type strain 207, grown aerobically. With D-glucose as energy source, 2,4-dinitrophenol and iodoacetate inhibited alike L-[14-C]leucine uptake by the respiration competent cells. (4) It is postulated that in respiration-competent yeasts, the mitochondrion contributes to 6-[14-C]leucine uptake by supplying high-energy compounds required for amino acid transport and accumulation. Conversely, the promitochondrion in the anaerobically grown yeast, or the modified mitochondrion in the respiratory deficient mutant, competes for high energy compounds generated by glycolysis in the cytosol.

Methyl-deficient transfer ribonucleic acid and macromolecular synthesis in methionine-starved Saccharomyces cerevisiae

Haploid methionine auxotrophs of Saccharomyces cerevisiae continue to multiply for several hours after withdrawal of a required amino acid from the medium. Macro-molecular synthesis continues during this period of residual growth, although the net ribonucleic acid (RNA) and protein content is constant during the later part of this period. In this study, growth after withdrawal of methionine was in some cases accompanied by accumulation of transfer RNA (tRNA), which was shown by methylation in vitro to be deficient in methyl groups. This phenomenon was shown by only four of nine methionine auxotrophs tested, but no evidence could be found that these four strains had "relaxed" control of RNA synthesis. The nine methionine-requiring strains represent mutations in five different positions in the methionine biosynthesis pathway, and only mutants blocked at two of these five positions accumulated methyl-deficient tRNA. This accumulation therefore appears to be correlated with the position of the strain's block in the pathway of methionine biosynthesis.

Influence of methionine pool composition on the formation of methyl-deficient transfer ribonucleic acid in Saccharomyces cerevisiae

Methionine auxotrophs of Saccharomyces cerevisiae continue to synthesize ribonucleic acid (RNA) after methionine withdrawal. The newly synthesized transfer RNA (tRNA) is methyl-deficient in some strains, but not in all. Whether such tRNA will accumulate depends on the position of the block in the methionine pathway that is carried by the mutant strain. Free methionine rapidly decreases in the intracellular pool of all strains after its removal from the medium. Certain metabolites derived from methionine are removed from the pool relatively slowly after methionine withdrawal. Notable among these is S-adenosylhomocysteine, which is depleted less rapidly from those strains that accumulate methyl-deficient tRNA than from others. S-adenosylhomocysteine is a potent inhibitor of tRNA-methylating enzymes in vitro.

Studies on microbial ribonucleic acid. VI. Appearance of methyl-deficient transfer ribonucleic acid during logarithmic growth of Saccharomyces cerevisiae

Transfer ribonucleic acid (tRNA) that is deficient in methyl groups may be detected in logarithmically growing Saccharomyces cerevisiae. The amount of methyl-deficient tRNA is not constant throughout the logarithmic phase, but is maximal about one generation before the onset of the late growth phase. During this latter phase, the tRNA is fully methylated. The methyl-deficient tRNA is present during a period of high metabolic activity of the cell, characterized by increased RNA and protein content.

Induction of meiosis in yeast : II. Metabolic factors leading to meiosis

Meiosis is induced in yeast by a sequence of events starting with the disappearance of glucose from the growth medium. Preparation for meiosis during the period of the premeiotic mitoses involves: (1) Development of the ability to metabolize acetate; and (2) establishment and maintenance of sufficiently high concentrations of RNA and protein in the cell to support an extensive biosynthetic activity. A new regulation model is proposed on the basis of the results obtained.

Studies on microbial RNA, 3. Formation of submethylated sRNA in Saccharomyces cerevisiae

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