The metabolic network in the yeast Saccharomyces cerevisiae was reconstructed using currently available genomic, biochemical, and physiological information. The metabolic reactions were compartmentalized between the cytosol and the mitochondria, and transport steps between the compartments and the environment were included. A total of 708 structural open reading frames (ORFs) were accounted for in the reconstructed network, corresponding to 1035 metabolic reactions. Further, 140 reactions were included on the basis of biochemical evidence resulting in a genome-scale reconstructed metabolic network containing 1175 metabolic reactions and 584 metabolites. The number of gene functions included in the reconstructed network corresponds to approximately 16% of all characterized ORFs in S. cerevisiae. Using the reconstructed network, the metabolic capabilities of S. cerevisiae were calculated and compared with Escherichia coli. The reconstructed metabolic network is the first comprehensive network for a eukaryotic organism, and it may be used as the basis for in silico analysis of phenotypic functions.

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Genome-Scale Reconstruction of the Saccharomyces cerevisiae Metabolic Network

Fungi are among the most primitive organisms that synthesize sterols. The fungal sterol, ergosterol, is similar to animal sterol, cholesterol, but with significant structural differences. The genetics and biochemistry for most of the steps in sterol biosynthesis have been studied in the yeast, Saccharomyces cerevisiae. Yet, little is known of the precise physiological roles that sterols play in the cell. Work with strains that are auxotrophic for ergosterol has led to the prediction of at least four growth-dependent functions for sterols. Most of the antifungal compounds in medical and agricultural use affect some aspect of sterol synthesis or function. Extensive studies on the modes of action of those substances and research on the effects of altering sterol metabolism by sterol mutants are providing new insights into sterol functions in the cells. In addition, questioning why fungi require ergosterol rather than the simpler cholesterol provides heuristic impetus for further experimentation.

Physiological implications of sterol biosynthesis in yeast.

(1978). Metabolism of Sterols in Yeast. CRC Critical Reviews in Microbiology: Vol. 6, No. 4, pp. 301-341.

Metabolism of sterols in yeast.

Life in the absence of molecular oxygen requires several adaptations. Traditionally, the switch from respiratory metabolism to fermentation has attracted much attention in Saccharomyces cerevisiae, as this is the basis for the use of this yeast in the production of alcohol and in baking. It has also been clear that under anaerobic conditions the yeast is not able to synthesize sterols and unsaturated fatty acids and that for anaerobic growth these have to be added to the media. More recently it has been found that many more factors play a role. Several other biosynthetic reactions also require molecular oxygen and the yeast must have alternatives for these. In addition, the composition of the cell wall and cell membrane show major differences when aerobic and anaerobic cells are compared. All these changes are reflected by the observation that the transcription of more than 500 genes changes significantly between aerobically and anaerobically growing cultures. In this review we will give an overview of the factors that play a role in the survival in the absence of molecular oxygen.

Factors involved in anaerobic growth of Saccharomyces cerevisiae.

Lipid accumulation and fatty acid composition in Candida 107 have been studied using a two-stage continuous culture system in which the first vessel was run under carbon-limited conditions and then the entire output was passed into a second vessel, where lipid accumulation was stimulated by adding only glucose. Maximum lipid accumulation (28% of yeast [dry weight]) occurred for a volume ratio of vessel 1 to vessel 2 of 3:5, with 30 g of glucose per liter being added to vessel 2 operated at 25°C with an aeration rate of between 0.1 and 1.0 volume of air/volume of medium per min. Although the maximum specific rate of lipid formation (0.05 g of lipid/g of yeast per h) was higher than in a nitrogen-limited, single-stage system, the efficiency of lipid formation was much less and never exceeded 14 g of lipid produced per 100 g of glucose consumed. The fatty acid composition was not significantly altered in either the two-stage or single-stage culture (nitrogen-limited) systems by changes in growth temperature (from 19 to 33°C) or aeration rates (0.05 to 1.0 volume of air/volume of medium per min); or, in the two-stage system, by changes in the residence time of the yeast in the second vessel (from 3.2 to 24.4 h), or, in the single-stage system, by changes in pH (from 3.5 to 7.5). Only when the concentration of glucose entering vessel 2 of the two-stage system was less than 30 g/liter did significant changes in the fatty acids occur. Thus, although a two-stage continuous culture system allows lipid accumulation to be separated from the growth phase, it offers no practical advantages over a single-stage system as a means of producing microbial oils and fats.

Lipid accumulation in an oleaginous yeast (Candida 107) growing on glucose under various conditions in a one- and two-stage continuous culture.

Neutral lipids in the cells and cell envelope fractions of aerobic baker's yeast and anaerobic brewer's yeast.

1.

It has been confirmed that under anaerobic conditions at pH 2 pyruvic acid is vigorously decarboxylated by intact baker's yeast, but hardly at all at pH 5.5. Furthermore, the decarboxylation occurs more slowly with semiaerobically cultured than with aerobically cultured baker's yeast.




2.

The penetration of pyruvic acid ethyl ester into the cell is not dependent upon the pH of the medium. The ester is decarboxylated by intact yeast at about the same rate, at pH 2 and 5.5. It is not decarboxylated by a purified preparation of pyruvate decarboxylase (EC 4.1.1.1).




3.

Hydroxypyruvic acid is decarboxylated only slowly by intact yeast at pH 2 and pyruvate decarboxylase. The attachment of a phenyl group to the pyruvic acid molecule increase the permeability, but causes an inhibition of pyruvate decarboxylase.




4.

α-Ketoglutaric acid is decarboxylated neither by intact yeast nor by an enzyme preparation, but with disintegrated yeast a noticeable formation of CO2 is observable. By intact yeast, the γ-ethyl ester of α-ketoglutaric acid reacts towards the acidity of the medium in the same way as does pyruvic acid. With purified pyruvate decarboxylase, the ester is decarboxylated more slowly than α-ketovaleric acid, but more rapidly than α-ketocaproic acid. Nevertheless, it does not penetrate into the intact yeast cell at a weak concentration to the same extent as do the acids last mentioned. α-Ketoglutaric acid diethyl ester behaves in a similar way to pyruvic acid ethyl ester: it penetrates the plasma membrane, and is decarboxylated by yeast but not by a preparation of pyruvate decarboxylase.

Decarboxylation by intact yeast and pyruvate decarboxylase of some derivatives of pyruvic acid and α-ketoglutaric acid

Die mit Einsporen-Kulturen der Backerhefe durchgefuhrten Versuche weisen darauf hin, das die untersuchten homozygotischen Backerhefestamme durch Anpassung imstande waren, Galaktose zu vergaren, so das diese Erscheinung mit der genotypischen Variation nichts zu tun hat.

Heikki Suomalainen

Papers

Neutral lipids in the cells and cell envelope fractions of aerobic baker's yeast and anaerobic brewer's yeast.

Decarboxylation by intact yeast and pyruvate decarboxylase of some derivatives of pyruvic acid and α-ketoglutaric acid

Über die Anpassung der Bäckerhefe an Galaktose