A general model of yeast energy metabolism in aerobic chemostat culture

Yeast as a Touchstone in Post-genomic Research: Strategies for Integrative Analysis in Functional Genomics

The new complexity arising from the genome sequencing projects requires new comprehensive post-genomic strategies: advanced studies in regulatory mechanisms, application of new high-throughput technologies at a genome-wide scale, at the different levels of cellular complexity (genome, transcriptome, proteome and metabolome), efficient analysis of the results, and application of new bioinformatic methods in an integrative or systems biology perspective. This can be accomplished in studies with model organisms under controlled conditions. In this review a perspective of the favourable characteristics of yeast as a touchstone model in post-genomic research is presented. The state-of-the art, latest advances in the field and bottlenecks, new strategies, new regulatory mechanisms, applications (patents) and high-throughput technologies, most of them being developed and validated in yeast, are presented. The optimal characteristics of yeast as a well-defined system for comprehensive studies under controlled conditions makes it a perfect model to be used in integrative, "systems biology" studies to get new insights into the mechanisms of regulation (regulatory networks) responsible of specific phenotypes under particular environmental conditions, to be applied to more complex organisms (e.g. plants, human).

Minimum specific cost control of technological processes realized in a living objects-containing microenvironment

The purpose of the present work is to work out an approach for the development of software and the choice of hardware structures when designing subsystems for automatic control of technological processes realized in living objects containing limited space (microenvironment). The subsystems for automatic control of the microenvironment (SACME) under development use the Devices for Air Prophylactic Treatment, Aeroionization, and Purification (DAPTAP) as execution units for increasing the level of safety and quality of agricultural raw material and foodstuffs, for reducing the losses of agricultural produce during storage and cultivation, as well as for intensifying the processes of activation of agricultural produce and industrial microorganisms. A set of interconnected SACMEs works within the framework of a general microenvironmental system (MES). In this research, the population of baker's yeast is chosen as a basic object of control under the industrial fed-batch cultivation in a bubbling bioreactor. This project is an example of a minimum cost automation approach. The microenvironment optimal control problem for baker's yeast cultivation is reduced from a profit maximum to the maximization of overall yield by the reason that the material flow-oriented specific cost correlates closely with the reciprocal value of the overall yield. Implementation of the project partially solves a local sustainability problem and supports a balance of microeconomical, microecological and microsocial systems within a technological subsystem realized in a microenvironment maintaining an optimal value of economical criterion (e.g. minimum material, flow-oriented specific cost) and ensuring: (a) economical growth (profit increase, raw material saving); (b) high security, safety and quality of agricultural raw material during storage process and of food produce during a technological process; elimination of the contact of gaseous harmful substances with a subproduct during various technological stages; (c) improvement of labour conditions for industrial personnel from an ecological point of view (positive effect of air aeroionization and purification on human organism promoting strengthened health and an increase in life duration, pulverent and gaseous chemical and biological impurity removal). An alternative aspect of a controlled living microenvironment forming is considered.

The budding yeast, Saccharomyces cerevisiae, as a model for aging research: a critical review

In this review we discuss the yeast as a paradigm for the study of aging. The budding yeast Saccharomyces cerevisiae, which can proliferate in both haploid and diploid states, has been used extensively in aging research. The budding yeast divides asymmetrically to form a 'mother' cell and a bud. Two major approaches, 'budding life span' and 'stationary phase' have been used to determine 'senescence' and 'life span' in yeast. Discrepancies observed in metabolic behavior and longevity between cells studied by these two systems raise questions of how 'life span' in yeast is defined and measured. Added to this variability in experimental approach and results is the variety of yeast strains with different genetic make up used as 'wild type' and experimental organisms. Another problematic genetic point in the published studies on yeast is the use of both diploid and haploid strains. We discuss the inherent, advantageous attributes that make the yeast an attractive choice for modern biological research as well as certain pitfalls in the choice of this model for the study of aging. The significance of the purported roles of the Sir2 gene, histone deacetylases, gene silencing, rDNA circles and stress genes in determination of yeast 'life span' and aging is evaluated. The relationship between cultivation conditions and longevity are assessed. Discrepancies between the yeast and mammalian systems with regard to aging are pointed out. We discuss unresolved problems concerning the suitability of the budding yeast for the study of basic aging phenomena.

Respirofermentative metabolism in Kluyveromyces lactis: Insights and perspectives

Yeasts do not form a homogeneous group as far as energy-yielding metabolism is concerned and the fate of pyruvate, a glycolytic intermediate, determines the type of energy metabolism. Kluyveromyces lactis has become an alternative to the traditional yeast Saccharomyces cerevisiae owing to its industrial applications as well as to studies on mitochondrial respiration. In this review we summarize the current knowdeledge about the K. lactis respirofermentative metabolism, taking into account the respiratory capacity of this yeast and the molecular mechanisms controlling its regulation, giving an up-to-date picture.

Dynamic in vivo (31)P nuclear magnetic resonance study of Saccharomyces cerevisiae in glucose-limited chemostat culture during the aerobic-anaerobic shift

The purpose of this work was to analyse in vivo the influence of sudden oxygen depletion on Saccharomyces cerevisiae, grown in glucose-limited chemostat culture, using a recently developed cyclone reactor coupled with (31)P NMR spectroscopy. Before, during and after the transition, intracellular and extracellular phosphorylated metabolites as well as the pHs in the different cellular compartments were monitored with a time resolution of 2.5 min. The employed integrated NMR bioreactor system allowed the defined glucose-limited continuous cultivation of yeast at a density of 75 g DW/l and a p(O(2)) of 30% air saturation. A purely oxidative metabolism was maintained at all times. In vivo (31)P NMR spectra obtained were of excellent quality and even allowed the detection of phosphoenolpyruvate (PEP). During the switch from aerobic to anaerobic conditions, a rapid, significant decrease of intracellular ATP and PEP levels was observed and the cytoplasmic pH decreased from 7.5 to 6.8. This change, which was accompanied by a transient influx of extracellular inorganic phosphate (P(i)), appeared to correlate linearly with the decrease of the ATP concentration, suggesting that the cause of the partial collapse of the plasma membrane pH gradient was a reduced availability of ATP. The complete phosphorous balance established from our measurement data showed that polyphosphate was not the source of the increased intracellular P(i). The derived intracellular P(i), ATP and ADP concentration data confirmed that the glycolytic flux at the level of glyceraldehyde-3-phosphate dehydrogenase, 3-phosphoglycerate kinase and enolase enzymes is mainly controlled by thermodynamic constraints.

A mathematical model for yeast respiro-fermentative physiology

A mechanistic model is presented that describes the respiro-fermentative physiology of yeast. The model assumes the presence of multiple types of glucose carriers and multiple assimilation pathways. Respiro-fermentative physiology is explained by the mechanistic response of the different types of carriers and assimilation pathways on the substrate concentration. At low substrate concentrations, glucose is taken up mainly via a high affinity carrier with a low maximum uptake rate. At high substrate concentrations, this carrier becomes saturated and the main pathway for glucose uptake is via a low affinity carrier with a high maximum uptake rate. The price to pay for the high uptake rate is a lowered assimilation efficiency, resulting in a low biomass yield. Product formation occurs via the pathway with the high uptake rate. The model explains the link between substrate concentration and product formation generally observed in the literature on yeast and bacteria. Model parameter values are estimated by fitting data from the literature. The model distinguishes itself from other models in that it does not rely on the presence of switches, such as the 'critical dilution rate', or on the assumption that the respiratory capacity reaches its maximum during respiro-fermentative metabolism. The present theory is not designed exclusively for the phenomenon of respiro-fermentative physiology: it describes the degradation of substances by heterotrophic micro-organisms in general.

Growth and energy metabolism in aerobic fed-batch cultures of Saccharomyces cerevisiae: simulation and model verification

A kinetic model of overflow metabolism in Saccharomyces cerevisiae was used for simulation of aerobic fed-batch cultivations. An inhibitory effect of ethanol on the maximum respiration of the yeast was observed in the experiments and included in the model. The model predicts respiration, biomass, and ethanol formation and the subsequent ethanol consumption, and was experimentally validated in fed-batch cultivations. Oscillating sugar feed with resulting oscillating carbon dioxide production did not influence the maximum respiration rate, which indicates that the pyruvate dehydrogenase complex is not involved as a bottleneck causing aerobic ethanol formation.

Proton production and consumption pathways in yeast metabolism. A chemostat culture analysis

In this investigation, a method for the accurate quantitative determination of net proton production or consumption in biological cultures has been devised. Cells are cultured under constant pH conditions. The specific rate of proton production or consumption by the culture (qH+, mmol h-1 per g biomass) is proportional to the mmol of base or acid required to maintain constant pH per unit time, and this equivalence is independent of the buffering capacity of the culture medium. The above method has been applied to chemostat cultures of Candida utilis growing on glucose or glycerol as carbon source, and different nitrogen sources. The results indicate that the nitrogen assimilation pathway alone determines the value of qH+, and a fixed stoichiometric relationship between nitrogen uptake rate qN (meq h-1 per g biomass) and qH+ has been found for each nitrogen source employed. Thus, qH+/qN values of +1, 0 and -1 were found for ammonium ions, urea and nitrate respectively. Under oxidative metabolism, the contribution of carbon catabolism to the value of qH+ was undetectable. Sine qN may be related to growth and production of type 1 compounds in fermentation processes, the parameter qH+ was incorporated into a model of growth and energy metabolism in chemostat culture (Castrillo and Ugalde, Yeast 10, 185 - 197, 1994), resulting in adequate simulations of experimentally observed culture performance. Thus, it is suggested that qH+ may be employed as a simple and effective control parameter for biotechnological processes involving biomass-related products.