Growth-coupled anaerobic production of isobutanol from glucose in minimal medium with Escherichia coli

BACKGROUND

The microbial production of isobutanol holds promise to become a sustainable alternative to fossil-based synthesis routes for this important chemical. Escherichia coli has been considered as one production host, however, due to redox imbalance, growth-coupled anaerobic production of isobutanol from glucose in E. coli is only possible if complex media additives or small amounts of oxygen are provided. These strategies have a negative impact on product yield, productivity, reproducibility, and production costs.

RESULTS

In this study, we propose a strategy based on acetate as co-substrate for resolving the redox imbalance. We constructed the E. coli background strain SB001 (ΔldhA ΔfrdA ΔpflB) with blocked pathways from glucose to alternative fermentation products but with an enabled pathway for acetate uptake and subsequent conversion to ethanol via acetyl-CoA. This strain, if equipped with the isobutanol production plasmid pIBA4, showed robust exponential growth (µ = 0.05 h-1) under anaerobic conditions in minimal glucose medium supplemented with small amounts of acetate. In small-scale batch cultivations, the strain reached a glucose uptake rate of 4.8 mmol gDW-1 h-1, a titer of 74 mM and 89% of the theoretical maximal isobutanol/glucose yield, while secreting only small amounts of ethanol synthesized from acetate. Furthermore, we show that the strain keeps a high metabolic activity also in a pulsed fed-batch bioreactor cultivation, even if cell growth is impaired by the accumulation of isobutanol in the medium.

CONCLUSIONS

This study showcases the beneficial utilization of acetate as a co-substrate and redox sink to facilitate growth-coupled production of isobutanol under anaerobic conditions. This approach holds potential for other applications with different production hosts and/or substrate-product combinations.

Characterizing and utilizing oxygen-dependent promoters for efficient dynamic metabolic engineering

Promoters adjust cellular gene expression in response to internal or external signals and are key elements for implementing dynamic metabolic engineering concepts in fermentation processes. One useful signal is the dissolved oxygen content of the culture medium, since production phases often proceed in anaerobic conditions. Although several oxygen-dependent promoters have been described, a comprehensive and comparative study is missing. The goal of this work is to systematically test and characterize 15 promoter candidates that have been previously reported to be induced upon oxygen depletion in Escherichia coli. For this purpose, we developed a microtiter plate-level screening using an algal oxygen-independent flavin-based fluorescent protein and additionally employed flow cytometry analysis for verification. Various expression levels and dynamic ranges could be observed, and six promoters (nar-strong, nar-medium, nar-weak, nirB-m, yfiD-m, and fnrF8) appear particularly suited for dynamic metabolic engineering applications. We demonstrate applicability of these candidates for dynamic induction of enforced ATP wasting, a metabolic engineering approach to increase productivity of microbial strains that requires a narrow level of ATPase expression for optimal function. The selected candidates exhibited sufficient tightness under aerobic conditions while, under complete anaerobiosis, driving expression of the cytosolic F₁-subunit of the ATPase from E. coli to levels that resulted in unprecedented specific glucose uptake rates. We finally utilized the nirB-m promoter to demonstrate the optimization of a two-stage lactate production process by dynamically enforcing ATP wasting, which is automatically turned on in the anaerobic (growth-arrested) production phase to boost the volumetric productivity. Our results are valuable for implementing metabolic control and bioprocess design concepts that use oxygen as signal for regulation and induction.

Deciphering the physiological response of Escherichia coli under high ATP demand

One long-standing question in microbiology is how microbes buffer perturbations in energy metabolism. In this study, we systematically analyzed the impact of different levels of ATP demand in Escherichia coli under various conditions (aerobic and anaerobic, with and without cell growth). One key finding is that, under all conditions tested, the glucose uptake increases with rising ATP demand, but only to a critical level beyond which it drops markedly, even below wild-type levels. Focusing on anaerobic growth and using metabolomics and proteomics data in combination with a kinetic model, we show that this biphasic behavior is induced by the dual dependency of the phosphofructokinase on ATP (substrate) and ADP (allosteric activator). This mechanism buffers increased ATP demands by a higher glycolytic flux but, as shown herein, it collapses under very low ATP concentrations. Model analysis also revealed two major rate-controlling steps in the glycolysis under high ATP demand, which could be confirmed experimentally. Our results provide new insights on fundamental mechanisms of bacterial energy metabolism and guide the rational engineering of highly productive cell factories.

Cell-free multi-enzyme synthesis and purification of uridine diphosphate galactose

High costs and low availability of UDP‐galactose hampers the enzymatic synthesis of valuable oligosaccharides such as human milk oligosaccharides. Here, we report the development of a platform for the scalable, biocatalytic synthesis and purification of UDP‐galactose. UDP‐galactose was produced with a titer of 48 mM (27.2 g/L) in a small‐scale batch process (200 μL) within 24 h using 0.02 g_enzyme/g_product. Through in‐situ ATP regeneration, the amount of ATP (0.6 mM) supplemented was around 240‐fold lower than the stoichiometric equivalent required to achieve the final product yield. Chromatographic purification using porous graphic carbon adsorbent yielded UDP‐galactose with a purity of 92 %. The synthesis was transferred to 1 L preparative scale production in a stirred tank bioreactor. To further reduce the synthesis costs here, the supernatant of cell lysates was used bypassing expensive purification of enzymes. Here, 23.4 g/L UDP‐galactose were produced within 23 h with a synthesis yield of 71 % and a biocatalyst load of 0.05 g_{total_protein}/g_product. The costs for substrates per gram of UDP‐galactose synthesized were around 0.26 €/g.

Increasing ATP turnover boosts productivity of 2,3-butanediol synthesis in Escherichia coli

Background

The alcohol 2,3-butanediol (2,3-BDO) is an important chemical and an Escherichia coli producer strain was recently engineered for bio-based production of 2,3-BDO. However, further improvements are required for realistic applications.

Results

Here we report that enforced ATP wasting, implemented by overexpressing the genes of the ATP-hydrolyzing F₁-part of the ATPase, leads to significant increases of yield and especially of productivity of 2,3-BDO synthesis in an E. coli producer strain under various cultivation conditions. We studied aerobic and microaerobic conditions as well as growth-coupled and growth-decoupled production scenarios. In all these cases, the specific substrate uptake and 2,3-BDO synthesis rate (up to sixfold and tenfold higher, respectively) were markedly improved in the ATPase strain compared to a control strain. However, aerobic conditions generally enable higher productivities only with reduced 2,3-BDO yields while high product yields under microaerobic conditions are accompanied with low productivities. Based on these findings we finally designed and validated a three-stage process for optimal conversion of glucose to 2,3-BDO, which enables a high productivity in combination with relatively high yield. The ATPase strain showed again superior performance and finished the process twice as fast as the control strain and with higher 2,3-BDO yield.

Conclusions

Our results demonstrate the high potential of enforced ATP wasting as a generic metabolic engineering strategy and we expect more applications to come in the future.

Supplementary Information

The online version contains supplementary material available at 10.1186/s12934-021-01554-x.

ATPase-based implementation of enforced ATP wasting in Saccharomyces cerevisiae for improved ethanol production

BACKGROUND

Enforced ATP wasting has been recognized as a promising metabolic engineering strategy to enhance the microbial production of metabolites that are coupled to ATP generation. It also appears to be a suitable approach to improve production of ethanol by Saccharomyces cerevisiae. In the present study, we constructed different S. cerevisiae strains with heterologous expression of genes of the ATP-hydrolyzing F₁-part of the ATPase enzyme to induce enforced ATP wasting and quantify the resulting effect on biomass and ethanol formation.

RESULTS

In contrast to genomic integration, we found that episomal expression of the αβγ subunits of the F₁-ATPase genes of Escherichia coli in S. cerevisiae resulted in significantly increased ATPase activity, while neither genomic integration nor episomal expression of the β subunit from Trichoderma reesei could enhance ATPase activity. When grown in minimal medium under anaerobic growth-coupled conditions, the strains expressing E. coli's F₁-ATPase genes showed significantly improved ethanol yield (increase of 10% compared to the control strain). However, elevated product formation reduces biomass formation and, therefore, volumetric productivity. We demonstrate that this negative effect can be overcome under growth-decoupled (nitrogen-starved) operation with high and constant biomass concentration. Under these conditions, which mimic the second (production) phase of a two-stage fermentation process, the ATPase-expressing strains showed significant improvement in volumetric productivity (up to 111%) compared to the control strain.

CONCLUSIONS

Our study shows that expression of genes of the F₁-portion of E. coli's ATPase induces ATPase activity in S. cerevisiae and can be a promising way to improve ethanol production. This ATP-wasting strategy can be easily applied to other metabolites of interest, whose formation is coupled to ATP generation.

Broadening the Scope of Enforced ATP Wasting as a Tool for Metabolic Engineering in Escherichia coli

The targeted increase of cellular adenosine triphosphate (ATP) turnover (enforced ATP wasting) has recently been recognized as a promising tool for metabolic engineering when product synthesis is coupled with net ATP formation. The goal of the present study is to further examine and to further develop the concept of enforced ATP wasting and to broaden its scope for potential applications. In particular, considering the fermentation products synthesized by Escherichia coli under anaerobic conditions as a proxy for target chemical(s), i) a new genetic module for dynamic and gradual induction of the F₁ -part of the ATPase is developed and it is found that ii) induction of the ATPase leads to higher metabolic activity and increased product formation in E. coli under anaerobic conditions, and that iii) ATP wasting significantly increases substrate uptake and productivity of growth-arrested cells, which is vital for its use in two-stage processes. To the best of the authors' knowledge, the glucose uptake rate of 6.49 mmol gCDW^-1  h^-1 achieved with enforced ATP wasting is the highest value reported for nongrowing E. coli cells. In summary, this study shows that enforced ATP wasting can be used to improve yield and titer (in growth-coupled processes) as well as volumetric productivity (in two-stage processes) depending on which of the performance measures is more crucial for the process and product of interest.

Aspergillus niger is a superior expression host for the production of bioactive fungal cyclodepsipeptides

Background

Fungal cyclodepsipeptides (CDPs) are non-ribosomally synthesized peptides produced by a variety of filamentous fungi and are of interest to the pharmaceutical industry due to their anticancer, antimicrobial and anthelmintic bioactivities. However, both chemical synthesis and isolation of CDPs from their natural producers are limited due to high costs and comparatively low yields. These challenges might be overcome by heterologous expression of the respective CDP-synthesizing genes in a suitable fungal host. The well-established industrial fungus Aspergillus niger was recently genetically reprogrammed to overproduce the cyclodepsipeptide enniatin B in g/L scale, suggesting that it can generally serve as a high production strain for natural products such as CDPs. In this study, we thus aimed to determine whether other CDPs such as beauvericin and bassianolide can be produced with high titres in A. niger, and whether the generated expression strains can be used to synthesize new-to-nature CDP derivatives.

Results

The beauvericin and bassianolide synthetases were expressed under control of the tuneable Tet-on promoter, and titres of about 350–600 mg/L for bassianolide and beauvericin were achieved when using optimized feeding conditions, respectively. These are the highest concentrations ever reported for both compounds, whether isolated from natural or heterologous expression systems. We also show that the newly established Tet-on based expression strains can be used to produce new-to-nature beauvericin derivatives by precursor directed biosynthesis, including the compounds 12-hydroxyvalerate-beauvericin and bromo-beauvericin. By feeding deuterated variants of one of the necessary precursors (d-hydroxyisovalerate), we were able to purify deuterated analogues of beauvericin and bassianolide from the respective A. niger expression strains. These deuterated compounds could potentially be used as internal standards in stable isotope dilution analyses to evaluate and quantify fungal spoilage of food and feed products.

Conclusion

In this study, we show that the product portfolio of A. niger can be expanded from enniatin to other CDPs such as beauvericin and bassianolide, as well as derivatives thereof. This illustrates the capability of A. niger to produce a range of different peptide natural products in titres high enough to become industrially relevant.

Electronic supplementary material

The online version of this article (10.1186/s40694-018-0048-3) contains supplementary material, which is available to authorized users.

[Comparison of side effects of infusion of glucose and glucose substitutes at different doses]

Glucose, fructose, sorbitol or xylitol were infused for four hours at different dose levels to metabolically healthy volunteers. The metabolic effects of the so-called glucose substitutes were compared to that of glucose. Even at very high doses (2.0 g/kg bodyweight per hour) of infusion of glucose or fructose a steady state was attained. This, however, was not the case with xylitol or sorbitol at lower doses (i.e. 0.5 g/kg bodyweight per hour), where no steady state was reached. The blood glucose concentration is not influenced by any of the glucose substitutes. During infusion of very high doses of fructose a small increase in serum insulin level is found, however, without any alteration in blood glucose concentration. Glucose as well as glucose substitutes cause an immediate suppression of free fatty acid concentrations in serum. In case of glucose there is a manifold increase in fatty acid concentration after the infusion is terminated. On the other hand, the free fatty acid concentration remains low even several hours following termination of the high-dosed fructose infusion. Theoretically one would expect an increase in triglyceride concentration, at least at the high dosed carbohydrate infusions. In contrast to this theoretical expectation, in the case of glucose and of xylitol a significant reduction of triglyceride concentration in serum was observed. Fructose and sorbitol did not exhibit this effect. Glucose and fructose are well utilized in metabolically healthy subjects. The maximum turnover rates for both polyols are lower. Unlike glucose, the glucose substitutes obviously do not cause any serious disturbation in hormonal regulations. Only in the case of glucose, counterregulation is seen following the termination of the infusion.

[Use of xylitol as sugar substitute in diabetic children]

In 24 diabetic children treated with insulin xylitol was used as a sugar substitute for four weeks in an amount of 30 gms/day. In one case only the xylitol application was terminated before the end of the dietetic period because of diarrhoea. The other children tolerated xylitol fairly well, three of the children found the polyol too sweet. Because of incomplete data, the values of only 18 children were compiled. A significant increase of serum uric acid concentration measuring 1 mg/100 ml was the main side effect of xylitol usage. This effect was favoured by the fact that diabetic children do not use sucrose. As was shown earlier, a sucrose free period is the precondition for the possibility to find a xylitol induced hyperuricemia. In metabolically healthy children the existence of a sucrose induced hyperuricemia is also to be expected, this xylitol effect is, therefore, obviously without pathophysiological significance. Xylitol is suited for use as a sugar substitute in diabetic diet and in caries prophylaxis if the limited dose is observed.

[Tests with human volunteers on parenteral utilization of maltose]

Intravenous infusions of maltose were performed using human volunteers. Four volunteers received maltose in a dose of 0.25 g/kg bodyweight and hour during eight hours. A follow-up period of three hours was added. Six volunteers received maltose in a dose of 0.125 g/kg bodyweight and hour during twelve hours. Only with the lower dose of maltose (0.125 g/kg b.w.) a steady state is reached after six hour continuous infusion. However even under these conditions maltose concentration in blood reaches the high concentration of 70 mg/100 ml. Using the double infusion rate, no steady state is attained when the infusions lasted for eight hours, despite maltose concentration in blood measured 150 mg/100 ml at this time. By measuring different metabolic parameters (fatty acid concentration, phosphate concentration) it is shown that parenterally applicated maltose is metabolized in the human. On the other hand, adverse reactions were not observed. The concentrations of uric acid and bilirubin remain constant and the activity of SGOT is not altered. Renal excretion of sugar measures 25-35% of the maltose administered parenterally. It is concluded that the glucose in urine stems from direct intra tubular hydrolysis of maltose achieved by the neutral maltase of the kidneys. The lack of attaining constant blood concentration for maltose during the infusions and the high renal loss of sugar shows that maltose is not suited as the single substrate for parenteral nutrition. However, there remains the possibility to use maltose in combination with glucose substitutes. The metabolic behaviour of maltose is similar to glucose, it differs from glucose substitutes.

[Effect of amino acid infusions on fructose-induced chemical blood changes in intensive care patients]

Influence of the infusion of amino acid solutions on metabolic changes caused by parenteral nutrition with fructose. In eleven unconscious polytraumatized patients of the intensive care station, intravenous infusions with fructose (0.5 g/kg bodyweight and hour) were performed. During the last 24 hours of the 72 hours infusion period, amino acid solutions (1.0 g/kg bodyweight and 24 hours) were given in addition to fructose. The investigations were initiated after an eight hour "starvation period" preinfusion. During this time only electrolytes were given. For comparison 48 hours intravenous infusions with fructose (0.5 g/kg B.W. and hour) were performed with six healthy volunteers. In both groups of subjects the intravenous fructose was metabolized very well, renal losses were less than 2% of the whole amount given. Considering the metabolic healthy volunteers, the blood glucose concentration remained unaltered despite the high dosage carbohydrate infusion. The patients of the intensive care station showed a slight increase of blood glucose values which were elevated already before infusion. Additionally, during fructose infusions, the increase in blood lactate concentration was more pronounced in the intensive care patients than in healthy volunteers. However, in contrast to the healthy volunteers, no increase in serum bilirubin concentration and only a slight increase in serum uric acid concentration was observed in the intensive care patients, despite the high-dose fructose infusion for 72 hours. Additionally, the fructose-induced hypertriglyceridemia was of a minor degree in the intensive care patients. In volunteers the increase in triglyceride concentration was 200% in 48 hours, whereas only a 50% increase was observed in intensive care patients during 72 hours. The pronounced nitrogen sparing effect of fructose in healthy volunteers was not seen in the intensive care patients to the same degree. The most prominent side effect of the fructose infusions in intensive care patients was the strong decrease in serum phosphate concentration seen in some patients. The additional infusion of amino acid solutions lead to a further diminution of the slight alterations caused by fructose infusions. In conclusion, it can be stated that total parenteral nutrition with fructose and amino acid solutions is possible in intensive care patients without danger of side effects. However, it should be mnetioned that hyperalimentation can cause fatty liver.

[Are maltose infusions suitable for infusion therapy]

The suitability of maltose for parenteral nutrition was investigated in metabolically healthy volunteers. A solution containing 20% of maltose was infused intravenously for four hours using three different doses (0.125 g/kg; 0.25 g/kg; 0.5 g/kg BW/h). Following cessation of the infusions the laboratory controls were carried on for four more hours. The infusions of maltose were tolerated without any complications. However, only when using the lowest dosage a steady state in blood concentration of maltose was reached, i.e. in the case of 0.125 g/kg BW/h. The results show that in humans the metabolic capacity for maltose is limited. The glucose concentration in blood remained almost unaltered during maltose infusion, while the serum insulin concentration was slightly elevated. A further sign for metabolism of maltose was the decrease in free fatty acid concentration. Because of the low metabolic capacity for maltose the urinary loss (in the form of maltose and glucose) is high with greater infusion rates and amounts to 20-30% of the intravenous load. A greater part of the sugar excreted in the urine consists of glucose, despite an almost normal blood glucose concentration. Considering the results of the experiments with volunteers it is concluded that maltose is not suited for intravenous therapy. Because of the low metabolic capacity of the human organism the renal losses are too great.

[Changes in serum electrolyte concentration and electrolyte excretion induced through infusion of glucose or glucose-exchange substances]

The metabolic effects of intravenous infusion of glucose, fructose, sorbitol or xylitol were investigated using human volunteers. The infusion period was 4 hours or 48 hours. Serum phosphate concentration decreased quickly and independent on the kind of the carbohydrate used. On the other hand, the serum concentration of potassium or sodium did not show any greater deviations from normal. Considering the renal excretion, greater differences between the single substances were seen. Renal potassium excretion was increased especially during xylitol infusions, and not as much during sorbitol infusions, as compared to infusions with glucose or with fructose. These differences were demonstrated especially for the first 12 hours of the infusions periond. During the infusions of glucose or of fructose an oral substitution of the electrolytes was suggicient. However, during xylitol infusions an intravenous substitution of potassium salts was necessary, despite the fact that the changes in serum concentration were only small. It is emphasized to carefully monitor serum electrolyte concentration and renal electrolyte excretion during long lasting intravenous infusions therapy.

[Parenteral feeding. Biochemical and clinical findings during continuous long-term infusion of glucose, fructose, sorbitol and xylitol. 2. Clinical aspects, discussion and results]

Four groups of six volunteers were given continuous infusions of glucose, fructose, sorbitol and xylitol in a dosage of 0.25 g/kg body weight over 48 hours. All solutions were well tolerated provided that potassium was supplemented in sufficient amounts. During the first 12 hour period of xylitol infusion renal potassium loss was greater than during infusion of all other substrates. No substantial differences in the alterations of the other parameters were noted between glucose and glucose substitutes. The only exception was the rise in serum uric acid concentration during infusion of xylitol and of fructose, which was not noted during infusion of glucose or sorbitol. The concentration of serum bilirubin was elevated during infusion of all four substances. The decrease in serum free fatty acid concentration was equally caused by glucose, fructose, xylitol or sorbitol. The increase in serum triglyceride concentration was observed earlier during the infusion of glucose substitutes as compared to glucose. Blood glucose concentration was only elevated during infusion of glucose. In the post infusion period there was quick rise in fatty acid concentration after cessation of glucose infusion. This normalisation occurred more slowly after stopping fructose and particulary xylitol or sorbitol. These results have no indications for adverse effects of the continuous infusions of glucose or glucose substitutes.

[Changes in serum electrolyte concentration and in urinary electrolyte excretion during the infusion of glucose or glucose substitutes]

In groups of volunteers the concentration differences of phosphate potassium and sodium in serum were measured during 48-hour continuous infusion of glucose or glucose substitutes (fructose, sorbitol or xylitol). The dosage was 0.25 g/kg BW/hour. Additionally, the effect of fructose infusion in a dosage of 0.5 g/kg BW/hour was observed. Besides, the urinary excretion of sodium and of potassium was analysed. In contrast to short-term and high-dosed infusions of glucose or glucose substitutes, the phosphate concentration in serum was scarcely influenced. Only during high-dosed fructose infusion and during infusion of xylitol and sorbitol a small decrease in serum phosphate concentration was noticed. The effect of xylitol is pronounced. Additionally, the sodium concentration in serum was especially decreased during xylitol infusion. With regard to the sodium excretion - and less pronounced with regard to the potassium excretion - a gradual adaptation to the infusion of the electrolyte-free solution is observed. The excretion of the cations is more and more decreased. In particular the excretion of sodium and of potassium is very high in the initial period, i.e. in the course of the first twelve hours of the xylitol infusions. On the other hand, the potassium excretion is very low in the final period of the infusion of xylitol (during 36 hours up to 48 hours) in comparison to the other sugars.