An integrated metabolic modeling approach to describe the energy efficiency ofEscherichia coli fermentations under oxygen-limited conditions: Cellular energetics, carbon flux, and acetate production

Genome-scale models of metabolism and expression predict the metabolic burden of recombinant protein expression

The production of recombinant proteins in a host using synthetic constructs such as plasmids comes at the cost of detrimental effects such as reduced growth, energetic inefficiencies, and other stress responses, collectively known as metabolic burden. Increasing the number of copies of the foreign gene increases the metabolic load but increases the expression of the foreign protein. Thus, there is a trade-off between biomass and product yield in response to changes in heterologous gene copy number. This work proposes a computational method, rETFL (recombinant Expression and Thermodynamic Flux), for analyzing and predicting the responses of recombinant organisms to the introduction of synthetic constructs. rETFL is an extension to the ETFL formulations designed to reconstruct models of metabolism and expression (ME-models). We have illustrated the capabilities of the method in four studies to (i) capture the growth reduction in plasmid-containing E. coli and recombinant protein production; (ii) explore the trade-off between biomass and product yield as plasmid copy number is varied; (iii) predict the emergence of overflow metabolism in recombinant E. coli in agreement with experimental data; and (iv) investigate the individual pathways and enzymes affected by the presence of the plasmid. We anticipate that rETFL will serve as a comprehensive platform for integrating available omics data for recombinant organisms and making context-specific predictions that can help optimize recombinant expression systems for biopharmaceutical production and gene therapy.

A General Process-Based Model for Describing the Metabolic Shift in Microbial Cell Cultures

The metabolic shift between respiration and fermentation at high glucose concentration is a widespread phenomenon in microbial world, and it is relevant for the biotechnological exploitation of microbial cell factories, affecting the achievement of high-cell-densities in bioreactors. Starting from a model already developed for the yeast Saccharomyces cerevisiae, based on the System Dynamics approach, a general process-based model for two prokaryotic species of biotechnological interest, such as Escherichia coli and Bacillus subtilis, is proposed. The model is based on the main assumption that glycolytic intermediates act as central catabolic hub regulating the shift between respiratory and fermentative pathways. Furthermore, the description of a mixed fermentation with secondary by-products, characteristic of bacterial metabolism, is explicitly considered. The model also represents the inhibitory effect on growth and metabolism of self-produced toxic compounds relevant in assessing the late phases of high-cell density culture. Model simulations reproduced data from experiments reported in the literature with different strains of non-recombinant and recombinant E. coli and B. subtilis cultured in both batch and fed-batch reactors. The proposed model, based on simple biological assumptions, is able to describe the main dynamics of two microbial species of relevant biotechnological interest. It demonstrates that a reductionist System Dynamics approach to formulate simplified macro-kinetic models can provide a robust representation of cell growth and accumulation in the medium of fermentation by-products.

Comprehensive analysis of metabolic sensitivity of 1,4-butanediol producing Escherichia coli toward substrate and oxygen availability

Nowadays, chemical production of 1,4-butanediol is supplemented by biotechnological processes using a genetically modified Escherichia coli strain, which is an industrial showcase of successful application of metabolic engineering. However, large scale bioprocess performance can be affected by presence of physical and chemical gradients in bioreactors which are a consequence of imperfect mixing and limited oxygen transfer. Hence, upscaling comes along with local and time dependent fluctuations of cultivation conditions. This study emphasizes on scale-up related effects of microbial 1,4-butanediol production by comprehensive bioprocess characterization in lab scale. Due to metabolic network constraints 1,4-butanediol formation takes place under oxygen limited microaerobic conditions, which can be hardly realized in large scale bioreactor. The purpose of this study was to assess the extent to which substrate and oxygen availability influence the productivity. It was found, that the substrate specific product yield and the production rate are higher under substrate excess than under substrate limitation. Furthermore, the level of oxygen supply within microaerobic conditions revealed strong effects on product and by-product formation. Under strong oxygen deprivation nearly 30% of the consumed carbon is converted into 1,4-butanediol, whereas an increase in oxygen supply results in 1,4-butanediol reduction of 77%. Strikingly, increasing oxygen availability leads to strong increase of main by-product acetate as well as doubled carbon dioxide formation. The study provides clear evidence that scale-up of microaerobic bioprocesses constitute a substantial challenge. Although oxygen is strictly required for product formation, the data give clear evidence that terms of anaerobic and especially aerobic conditions strongly interfere with 1,4-butanediol production.

Effect of pH and dilution rate on specific production rate of extra cellular metabolites by Lactobacillus salivarius UCO_979C in continuous culture

The effect of pH and dilution rate on the production of extracellular metabolites of Lactobacillus salivarius UCO_979 was studied. The experiments were carried out in continuous mode, with chemically defined culture medium at a temperature of 37 °C, 200 rpm agitation and synthetic air flow of 100 ml/min. Ethanol, acetic acid, formic acid, lactic acid and glucose were quantified through HPLC, while exopolysaccharide (EPS) was extracted with ethanol and quantified through the Dubois method. The results showed no linear trends for the specific production of lactic acid, EPS, acetic acid and ethanol, while the specific glucose consumption and ATP production rates showed linear trends. There was a metabolic change of the strain for dilution rates below 0.3 h(-1). The pH had a significant effect on the metabolism of the strain, which was evidenced by a higher specific glucose consumption and increased production of ATP at pH 6 compared with that obtained at pH 7. This work shows not only the metabolic capabilities of L. salivarius UCO_979C, but also shows that it is possible to quantify some molecules associated with its current use as gastrointestinal probiotic, especially regarding the production of organic acids and EPS.

A metabolic network stoichiometry analysis of microbial growth and product formation

Using available biochemical information, metabolic networks have been constructed to describe the biochemistry of growth of Saccharomyces cerevisiae and Candida utilis on a wide variety of carbon substrates. All networks contained only two fitted parameters, the P/O ratio and a maintenance coefficient. It is shown that with a growth-associated maintenance coefficient, K, of 1.37 mol ATP/ C-mol protein for both yeasts and P/O ratios of 1.20 and 1.53 for S. cerevisiae and C. utilis, respectively, measured biomass yields could be described accurately. A metabolic flux analysis of aerobic growth of S. cerevisiae on glucose/ethanol mixtures predicted five different metabolic flux regimes upon transition from 100% glucose to 100% ethanol. The metabolic network constructed for growth of S. cerevisiae on glucose was applied to perform a theoretical exercise on the overproduction of amino acids. It is shown that theoretical operational product yield values can be substantially lower than calculated maximum product yields. A practical case of lysine production was analyzed with respect to theoretical bottlenecks limiting product formation. Predictions of network-derived irreversibility limits for Y(sp) (mu) functions were compared with literature data. The comparisons show that in real systems such irreversibility constraints may be of relevance. It is concluded that analysis of metabolic network stoichiometry is a useful tool to detect metabolic limits and to guide process intensification studies. (c) 1995 John Wiley & Sons, Inc.

Reductive stress in microbes: implications for understanding Mycobacterium tuberculosis disease and persistence

Mycobacterium tuberculosis (Mtb) is a remarkably successful pathogen that is capable of persisting in host tissues for decades without causing disease. Years after initial infection, the bacilli may resume growth, the outcome of which is active tuberculosis (TB). In order to establish infection, resist host defences and re-emerge, Mtb must coordinate its metabolism with the in vivo environmental conditions and nutrient availability within the primary site of infection, the lung. Maintaining metabolic homeostasis for an intracellular pathogen such as Mtb requires a carefully orchestrated series of oxidation-reduction reactions, which, if unbalanced, generate oxidative or reductive stress. The importance of oxidative stress in microbial pathogenesis has been appreciated and well studied over the past several decades. However, the role of its counterpart, reductive stress, has been largely ignored. Reductive stress is defined as an aberrant increase in reducing equivalents, the magnitude and identity of which is determined by host carbon source utilisation and influenced by the presence of host-generated gases (e.g. NO, CO, O(2) and CO(2)). This increased reductive power must be dissipated for bacterial survival. To recycle reducing equivalents, microbes have evolved unique electron 'sinks' that are distinct for their particular environmental niche. In this review, we describe the specific mechanisms that some microbes have evolved to dispel reductive stress. The intention of this review is to introduce the concept of reductive stress, in tuberculosis research in particular, in the hope of stimulating new avenues of investigation.

Very high-level production and export in Escherichia coli of a cellulose binding domain for use in a generic secretion-affinity fusion system

A novel expression vector pTugA, previously constructed in our laboratory, was modified to provide kanamycin resistance (pTugK) and used to direct the synthesis of polypeptides as fusions with the C- or N-terminus of a cellulose binding domain which serves as the affinity tag in a novel secretion-affinity fusion system. Fed-batch fermentation strategies were applied to production in recombinant E. coli TOPP5 of the cellulose binding domain (CBD) from the Cellulomonas fimi cellulase Cex. The pTugK expression vector, which codes for the Cex leader sequence that directs the recombinant protein to the periplasm of E. coli, was shown to remain stable at very high-cell densities. Recombinant cell densities in excess of 90 g (dry cell weight)/L were achieved using media and feed solutions optimized using a 2(n) factorial design. Optimization of inducer (isophenyl-thio-beta-D-galactopyranoside) concentration and the time of induction led to soluble, fully active CBD(Cex) production levels in excess of 8 g/L.

Minimizing acetate formation in E. coli fermentations

Escherichia coli remains the best-established production organism in industrial biotechnology. However, when aerobic fermentation runs at high growth rates, considerable amounts of acetate are accumulated as by-product. This by-product has negative effects on growth and protein production. Over the last 20 years, substantial research efforts have been expended on reducing acetate accumulation during aerobic growth of E. coli on glucose. From the onset it was clear that this quest would not be a simple or uncomplicated one. Simple deletion of the acetate pathway reduced the acetate accumulation, but other by-products were formed. This mini review gives a clear outline of these research efforts and their outcome, including bioprocess level approaches and genetic approaches. Recently, the latter seems to have some promising results.

Process control for enhanced L-phenylalanine production using different recombinant Escherichia coli strains

A novel fed-batch approach for the production of L-phenylalanine (L-Phe) with recombinant E. coli is presented concerning the on-line control of the key fermentation parameters glucose and tyrosine. Two different production strains possessing either the tyrosine feedback resistant aroF(fbr) (encoding tyrosine feedback resistant DAHP-synthase (3-desoxy-D-arabino-heptusonate-7-phosphate)) or the wild-type aroF(wt) were used as model systems to elucidate the necessity of finding an individual process optimum for each genotype. With the aid of tyrosine control, wild-type aroF(wt) could be used for L-Phe production achieving higher final L-Phe titers (34 g/L) than the aroF(fbr) strain (28 g/L) and providing higher DAHP-synthase activities. With on-line glucose control, an optimum glucose concentration of 5 g/L could be identified that allowed a sufficient carbon supply for L-Phe production while at the same time an overflow metabolism leading to acetate by-product formation was avoided. The process approach is suitable for other production strains not only in lab-scale but also in pilot-scale bioreactors.

Fed-batch cultures of Escherichia coli cells with oxygen-dependent nar promoter systems

The recombinant proteins produced from Escherichia coli as a host cell need to be made at as low a cost as possible because of the end of the monopoly following expiry of the patent on early pharmaceutical proteins, and thus expanding applications to non-pharmaceutical large-scale products. We review in this article how the various promoters used in recombinant E. coli could affect its protein products, especially with emphasis on relatively new oxygen-dependent nar promoters for beta-galactosidase production. Several studies carried out in the authors' laboratory show that the nar promoter does not require any chemicals except 1% nitrate and oxygen for protein production. And according to recent work with the modified strains it is possible to produce the enzyme (beta-galactosidase) even without the nitrate ions at 45% of its total protein content when its cell density reached OD = 176.

Development of bioreaction engineering

In addition to summarizing the early investigations in bioreaction engineering, the present short review covers the development of the field in the last 50 years. A brief overview of the progress of the fundamentals is presented in the first part of this article and the key issues of bioreaction engineering are advanced in its second part.

Characterization of growth and acid formation in a Bacillus subtilis pyruvate kinase mutant

Based on measurements and theoretical analyses, we identified deletion of pyruvate kinase (PYK) activity as a possible route for elimination of acid formation in Bacillus subtilis cultures grown on glucose minimal media. Evidence consistent with the attenuation of PYK flux has come from metabolic flux calculations, metabolic pool and enzymatic activity measurements, and a series of nuclear magnetic resonance experiments, all suggesting a nearly complete inhibition of PYK activity for glucose-citrate fed cultures in which the amount of acid formation was nearly zero. In this paper, we report the construction and characterization of a pyk mutant of B. subtilis. Our results demonstrate an almost complete elimination of acid production in cultures of the pyk mutant in glucose minimal medium. The substantial reduction in acid production is accompanied by increased CO(2) production and a reduced rate of growth. Metabolic analysis indicated a dramatic increase in intracellular pools of phosphoenolpyruvate (PEP) and glucose-6-P in the pyk mutant. The high concentrations of PEP and glucose-6-P could explain the decreased growth rate of the mutant. The substantial accumulation of PEP does not occur in Escherichia coli pyk mutants. The very high concentration of PEP which accumulates in the B. subtilis pyk mutant could be exploited for production of various aromatics.

Acetate metabolism in a pta mutant of Escherichia coli W3110: importance of maintaining acetyl coenzyme A flux for growth and survival

In order to study the physiological role of acetate metabolism in Escherichia coli, the growth characteristics of an E. coli W3100 pta mutant defective in phosphotransacetylase, the first enzyme of the acetate pathway, were investigated. The pta mutant grown on glucose minimal medium excreted unusual by-products such as pyruvate, D-lactate, and L-glutamate instead of acetate. In an analysis of the sequential consumption of amino acids by the pta mutant growing in tryptone broth (TB), a brief lag between the consumption of amino acids normally consumed was observed, but no such lag occurred for the wild-type strain. The pta mutant was found to grow slowly on glucose, TB, or pyruvate, but it grew normally on glycerol or succinate. The defective growth and starvation survival of the pta mutant were restored by the introduction of poly-beta-hydroxybutyrate (PHB) synthesis genes (phbCAB) from Alcaligenes eutrophus, indicating that the growth defect of the pta mutant was due to a perturbation of acetyl coenzyme A (CoA) flux. By the stoichiometric analysis of the metabolic fluxes of the central metabolism, it was found that the amount of pyruvate generated from glucose transport by the phosphoenolpyruvate-dependent phosphotransferase system (PTS) exceeded the required amount of precursor metabolites downstream of pyruvate for biomass synthesis. These results suggest that E. coli excretes acetate due to the pyruvate flux from PTS and that any method which alleviates the oversupply of acetyl CoA would restore normal growth to the pta mutant.

On-line detection of acetate formation in Escherichia coli cultures using dissolved oxygen responses to feed transients

Recombinant protein production in Escherichia coli can be significantly reduced by acetate accumulation. It is demonstrated that acetate production can be detected on-line with a standard dissolved oxygen sensor by superimposing short pulses to the substrate feed rate. Assuming that acetate formation is linked to a respiratory limitation, a model for dissolved oxygen responses to transients in substrate feed rate is derived. The model predicts a clear change in the character of the transient response when acetate formation starts. The predicted effect was verified in fed-batch cultivations of E. coli TOPP1 and E. coli BL21(DE3), both before and after induction of recombinant protein production. It was also observed that the critical specific glucose uptake rate, at which acetate formation starts, was significantly decreased after induction. On-line detection of acetate formation with a standard sensor opens up new possibilities for feedback control of substrate feeding.

Metabolic flux analysis for efficient pyruvate fermentation using vitamin-auxotrophic yeast of Torulopsis glabrata

The metabolism of a vitamin-auxotrophic pyruvate-producing microorganism, Torulopsis glabrata IFO 0005, was investigated by metabolic flux analysis. Particular attention was focused on the effect of culture conditions, such as dissolved oxygen (DO) concentration and thiamine concentration, on specific pathway activities. The results of metabolic flux analysis indicate that the thiamine concentration significantly affected pyruvate dehydrogenase and pyruvate decarboxylase activities, and plays an important role in cell growth and pyruvate production. Metabolic flux analysis was also utilized to clarify the metabolism of this strain during pyruvate fermentation under different oxygen supply conditions, and the reason for the enhanced pyruvate production under conditions of 30-40% DO concentration was clarified from the viewpoint of intracellular flux distributions. Based on the analysis of the effect of thiamine concentration on the metabolic fluxes, we conducted a fed-batch experiment where the initial thiamine concentration was reduced to 30 microg/l and thiamine was added at 10 microg/l during fermentation when the cell growth rate decreased to 0.2 h(-1). With separate addition of thiamine, the overall pyruvate yield could be improved by 15% due to the decrease of ethanol production.

On-line metabolic pathway analysis based on metabolic signal flow diagram

In this work, an integrated modeling approach based on a metabolic signal flow diagram and cellular energetics was used to model the metabolic pathway analysis for the cultivation of yeast on glucose. This approach enables us to make a clear analysis of the flow direction of the carbon fluxes in the metabolic pathways as well as of the degree of activation of a particular pathway for the synthesis of biomaterials for cell growth. The analyses demonstrate that the main metabolic pathways of Saccharomyces cerevisiae change significantly during batch culture. Carbon flow direction is toward glycolysis to satisfy the increase of requirement for precursors and energy. The enzymatic activation of TCA cycle seems to always be at normal level, which may result in the overflow of ethanol due to its limited capacity. The advantage of this approach is that it adopts both virtues of the metabolic signal flow diagram and the simple network analysis method, focusing on the investigation of the flow directions of carbon fluxes and the degree of activation of a particular pathway or reaction loop. All of the variables used in the model equations were determined on-line; the information obtained from the calculated metabolic coefficients may result in a better understanding of cell physiology and help to evaluate the state of the cell culture process.

Effect of oxygen supply on metabolism of immobilized and suspended Escherichia coli

The effect of reduced oxygen supply on the production of a recombinant protein (plasmid-encoded beta-galactosidase) was investigated in Escherichia coli. A novel modified bubble tank reactor was used to provide a direct comparison between immobilized and suspended cells in identical environments except for the immobilization matrix. Decreased oxygen supply led to increased beta-galactosidase synthesis by both immobilized and suspended cells. Immobilized cells produced similar amounts of beta-galactosidase as the suspended cells. Lactose consumption and acetate production, on a per cell basis, were significantly higher in immobilized cells, suggesting that immobilized cells utilized fermentative metabolism. However, a transport analysis of the immobilized cell system showed that immobilized cells were not subject to either external or internal mass transfer gradients.

The effect of cellular energetics on foreign protein production

Escherichia coli strain F-122 was used to determine if there are additional physiological effects, other than decreasing energetic efficiency accompanied by the excretion of the acetate, on foreign protein production. This organism was the host for expressing HIV582-beta-galactosidase fusion protein under the control of the trp promoter, with ampicillin resistance. By comparing parallel batch cultures with and without acetate addition, it was found that the presence of acetate in the media did not influence beta-galactosidase activity. In these experiments, it appears that the low protein productivity often observed during acetate formation is the result of inefficient cell metabolism, rather than acetate acting as a specific inhibitor of protein production.