Flux distributions in anaerobic, glucose-limited continuous cultures of Saccharomyces cerevisiae

A stoichiometric model describing the anaerobic metabolism of Saccharomyces cerevisiae during growth on a defined medium was derived. The model was used to calculate intracellular fluxes based on measurements of the uptake of substrates from the medium, the secretion of products from the cells, and of the rate of biomass formation. Furthermore, measurements of the biomass composition and of the activity of key enzymes were used in the calculations. The stoichiometric network consists of 37 pathway reactions involving 43 compounds of which 13 were measured (acetate, CO2, ethanol, glucose, glycerol, NH4+, pyruvate, succinate, carbohydrates, DNA, lipids, proteins and RNA). The model was used to calculate the production rates of malate and fumarate and the ethanol measurement was used to validate the model. All rate measurements were performed on glucose-limited continuous cultures in a high-performance bioreactor. Carbon balances closed within 98%. The calculations comprised flux distributions at specific growth rates of 0.10 and 0.30 h-1. The fluxes through reactions located around important branch points of the metabolism were compared, i.e. the split between the pentose phosphate and the Embden-Meyerhoff-Parnas pathways. Also the model was used to show the probable existence of a redox shunt across the inner mitochondrial membrane consisting of the reactions catalysed by the mitochondrial and the cytosolic alcohol dehydrogenase. Finally it was concluded that cytosolic isocitrate dehydrogenase is probably not present during growth on glucose. The importance of basing the flux analysis on accurate measurements was demonstrated through a sensitivity analysis. It was found that the accuracy of the measurements of CO2, ethanol, glucose, glycerol and protein was critical for the correct calculation of the flux distribution.

On the topological features of optimal metabolic pathway regimes

In this work, the stoichiometric metabolic network of Escherichia coli has been formulated as a comprehensive mathematical programming model, with a view to identifying the optimal redirection of metabolic fluxes so that the yield of particular metabolites is maximized. Computation and analysis has shown that the over-production of a given metabolite at various cell growth rates is only possible for a finite ordered set of metabolic structures which, in addition, are metabolite-specific. Each regime has distinct topological features, although the actual flux values differ. Application of the model to the production of 20 amino acids on four carbon sources (glucose, glycerol, lactate, and citrate) has also indicated that, for fixed cell composition, the maximum amino acid yield decreases linearly with increasing cell growth rate. However, when the cell composition varies with cell growth rate, the amino-acid yield varies in a nonlinear manner. Medium optimization studies have also demonstrated that, of the above substrates, glucose and glycerol are the most efficient from the energetic viewpoint. Finally, model predictions are analyzed in the light of experimental data.

A new balance equation of reducing equivalents for data consistency check and bioprocess calculation

The reducing equivalent (RE) balance is a basic equation for data consistency check and calculations of bioprocesses. The macroscopic approach is often used because it does not require detailed knowledge of metabolic pathways. In this work, the conventional Minkevich-Eroshin balance equation is examined with data of anaerobic glycerol conversion by Klebsiella pneumoniae and Clostridium butyricum as examples. It is shown that the Minkevich-Eroshin equation is very insensitive to measurement errors in products of less dominance and/or with relatively low reductance degree. Relatively large deviations from experimental values are encountered when the Minkevich-Eroshin equation is used for the calculations of these products. To overcome some of these shortcomings an improved RE balance equation is proposed that is based on 'reductance equations' of substrate conversion into the individual carbon containing products (including biomass). The proposed new equation significantly improves the performance of the RE balance equation for data consistency check and for the calculations of unknown variables with relatively low reductance degree. The rationale for this is that it considers merely the REs that really participate in the bioreactions. The use of the proposed method requires no detailed knowledge of metabolic pathways and is therefore of macroscopic nature. It can be reduced to the pathway balance equation if the pathways are known.

Regulation of Clostridium acetobutylicum metabolism as revealed by mixed-substrate steady-state continuous cultures: role of NADH/NAD ratio and ATP pool

Glycerol-glucose-fed (molar ratio of 2) chemostat cultures of Clostridium acetobutylicum were glucose limited but glycerol sufficient and had a high intracellular NADH/NAD ratio (I. Vasconcelos, L. Girbal, and P. Soucaille, J. Bacteriol. 176:1443-1450, 1994). We report here that the glyceraldehyde-3-phosphate dehydrogenase, one of the key enzymes of the glycolytic pathway, is inhibited by high NADH/NAD ratios. Partial substitution of glucose by pyruvate while maintaining glycerol concentration at a constant level allowed a higher consumption of glycerol in steady-state continuous cultures. However, glycerol-sufficient cultures had a constant flux through the glyceraldehyde-3-phosphate dehydrogenase and a constant NADH/NAD ratio. A high substitution of glucose by pyruvate [P/(G+P) value of 0.67 g/g] provided a carbon-limited culture with butanol and butyrate as the major end products. In this alcohologenic culture, the induction of the NADH-dependent butyraldehyde and the ferredoxin-NAD(P) reductases and the higher expression of alcohol dehydrogenases were related to a high NADH/NAD ratio and a low intracellular ATP concentration. In three different steady-state cultures, the in vitro phosphotransbutyrylase and butyrate-kinase activities decreased with the intracellular ATP concentration, suggesting a transcriptional regulation of these two genes, which are arranged in an operon (K. A. Walter, R. V. Nair, R. V. Carry, G. N. Bennett, and E. T. Papoutsakis, Gene 134:107-111, 1993).

Intracellular Concentrations of Coenzyme A and Its Derivatives from Clostridium acetobutylicum ATCC 824 and Their Roles in Enzyme Regulation

Intracellular levels of coenzyme A (CoA) and its derivatives involved in the metabolic pathways for Clostridium acetobutylicum ATCC 824 were analyzed by using reverse-phase high-performance liquid chromatography (HPLC). During the shift from the acidogenic to the solventogenic or stationary growth phase, the concentration of butyryl-CoA increased rapidly and the concentrations of free CoA and acetyl-CoA decreased. These changes were accompanied by a rapid increase of the solvent pathway enzyme activity and a decrease of the acid pathway enzyme activity. Assays with several non-solvent-producing mutant strains were also carried out. Upon entry of the mutant strains to the stationary phase, the butyryl-CoA concentrations for these mutant strains were comparable to those for the wild type even though the mutants were deficient in solvent-producing enzymes. Levels of acetoacetyl-CoA, β-hydroxy-butyryl-CoA, and crotonyl-CoA compounds in both wild-type and mutant extracts were below HPLC detection thresholds (<21 μM).

Cellular and metabolic engineering. An overview

Metabolic engineering is defined as the purposeful modification of intermediary metabolism using recombinant DNA techniques. Cellular engineering, a more inclusive term, is defined as the purposeful modification of cell properties using the same techniques. Examples of cellular and metabolic engineering are divided into five categories: 1. Improved production of chemicals already produced by the host organism; 2. Extended substrate range for growth and product formation; 3. Addition of new catabolic activities for degradation of toxic chemicals; 4. Production of chemicals new to the host organism; and 5. Modification of cell properties. Over 100 examples of cellular and metabolic engineering are summarized. Several molecular biological, analytical chemistry, and mathematical and computational tools of relevance to cellular and metabolic engineering are reviewed. The importance of host selection and gene selection is emphasized. Finally, some future directions and emerging areas are presented.

The use of stoichiometric relations for the description and analysis of microbial cultures

A general method is described, which enables the derivation of predictive fermentation equations for any microbiological process. The method combines the well-known achievements of the elemental balance approach with microscopic, metabolic balances and biochemical restrictions, using the key intermediates concept. Special attention is paid to the distinction between independent and dependent flow variables of a system. The method is fully illustrated for the very simple example of heterotrophic growth on a single substrate without product formation. Other examples include growth on mixed substrates and the description of catabolic and anabolic product formation.

Network rigidity and metabolic engineering in metabolite overproduction

In order to enhance the yield and productivity of metabolite production, researchers have focused almost exclusively on enzyme amplification or other modifications of the product pathway. However, overproduction of many metabolites requires significant redirection of flux distributions in the primary metabolism, which may not readily occur following product deregulation because metabolic pathways have evolved to exhibit control architectures that resist flux alterations at branch points. This problem can be addressed through the use of some general concepts of metabolic rigidity, which include a means for identifying and removing rigid branch points within an experimental framework.

Effects of propionate and acetate additions on solvent production in batch cultures of Clostridium acetobutylicum

Addition of acetate or propionate to uncontrolled-pH batch cultures does not affect the initiation of solventogenesis but does enhance final solvent concentrations compared with those of unchallenged cultures. This observation can be explained in terms of the increased buffering capacity of the medium brought about by the added acids, resulting in protection against premature growth inhibition due to low culture pH values at the end of the fermentation. The uptake of propionic acid from the medium does not proceed solely via the coenzyme A-transferase pathway, since less acetone than propanol is formed. Therefore, at least 50% of the propionic acid is taken up through the reversed kinase-phosphotransbutyrylase reaction pathway.

A non-passive mechanism of butyrate excretion operates during acidogenic fermentation of methanol by Eubacterium limosum

The inhibitory effects of organic acids produced as fermentation end-products during methylotrophic growth of the acidogenic anaerobe, Eubacterium limosum have been investigated. Precise quantification of the intracellular concentrations of acetate and butyrate, together with delta pH measurements indicate that butyrate efflux cannot be explained by a process of passive diffusion. Intracellular concentrations of butyrate were significantly lower than those of the culture broth. It is argued that growth inhibition by butyrate is due to energetic limitations resulting from the energy drain associated with this non-passive efflux mechanism.

Transport of substrates and metabolites and their effect on cell metabolism (in butyric-acid and methylotrophic fermentations)

The two components, delta pH and delta psi, of the membrane protonmotive force (delta p) effect and are affected by the transport of many substrates and metabolites. Because the integrity (or restoration) of the delta p requires the expenditure of metabolic energy, such transport processes affect the overall cell bioenergetics. However, the transport or high concentrations of certain substrates and metabolites can have more serious effects on cell metabolism because they partially or completely abolish either or both the delta pH and delta psi. If the cells cannot eventually restore the collapsed component(s) of the delta p, complete growth inhibition and cell death become inevitable. In the butanol/acetone fermentation of Clostridium acetobutylicum, the transport and the presence of key metabolites (acetic and butyric acids, and butanol) have serious and some necessary effects on the delta p. Acetic and butyric acids act as uncouplers of the delta pH, thereby reducing the internal pH. Using other acid uncouplers (such as acetoacetate, which is metabolized by the cells, or FCCP, which is not metabolized by the cells), we found that a lower pHo combined with the metabolic-energy drain of the uncoupling effect and high internal acid concentrations are implicated in the mechanism(s) of solventogenesis. Thus, the production or presence (or both) of the two acids (acetic and butyric) is beneficial to the initiation of solvent production. The transport mechanisms of CH3OH, CH2O, and HCOOH in obligate CH3OH utilizers (methylotrophs) were also discussed in detail. We showed that CH3OH is actively transported by the cells at the expense of metabolic energy and that its transport significantly affects the dynamics of continuous bioreactors. The accumulation of CH2O was found to be driven by the membrane delta p. Finally, formate was accumulated by the delta pH according to the general transport mechanism of short-chain fatty acids. The inhibition of growth by formate was explained by its uncoupling effect on the cells. Growth inhibition by CH3OH appeared to be related to the severe reduction of the membrane delta pH and cell pHi by relatively low CH3OH concentrations.