Metabolic engineering under uncertainty. I: framework development

Standard bioprocess conditions have been widely applied for the microbial conversion of raw material to essential industrial products. Successful metabolic engineering (ME) strategies require a comprehensive framework to manage the complexity embedded in cellular metabolism, to explore the impacts of bioprocess conditions on the cellular responses, and to deal with the uncertainty of the physiochemical parameters. We have recently developed a computational and statistical framework that is based on Metabolic Control Analysis and uses a Monte Carlo method to simulate the uncertainty in the values of the system parameters [Wang, L., Birol, I., Hatzimanikatis, V., 2004. Metabolic control analysis under uncertainty: framework development and case studies. Biophys. J. 87(6), 3750-3763]. In this work, we generalize this framework to incorporate the central cellular processes, such as cell growth, and different bioprocess conditions, such as different types of bioreactors. The framework provides the mathematical basis for the quantification of the interactions between intracellular metabolism and extracellular conditions, and it is readily applicable to the identification of optimal ME targets for the improvement of industrial processes [Wang, L., Hatzimanikatis, V., 2005. Metabolic engineering under uncertainty. II: analysis of yeast metabolism. Submitted].     

The interplay between sulphur and selenium metabolism influences the intracellular redox balance in Saccharomyces cerevisiae

Selenium (Se) is an essential element for most eukaryotic organisms, including humans. The balance between Se toxicity and its beneficial effects is very delicate. It has been demonstrated that a diet enriched with Se has cancer prevention potential in humans. The most popular commercial Se supplementation is selenized yeast, which is produced in a fermentation process using an inorganic source of Se. Here, we show that the uptake of Se, Se toxic effects and intracellular Se-metabolite profile are largely influenced by the level of sulphur source supplied during the fermentation. A Yap1-dependent oxidative stress response is active when yeast actively metabolizes Se, and this response is linked to the generation of intracellular redox imbalance. The redox imbalance derives from a disproportionate ratio between the reduced and oxidized forms of glutathione and also from the influence of Se metabolism on the central carbon metabolism. The observed increase in glycerol production rate, concomitant with the inhibition of ethanol formation in the presence of Se, can be ascribed to the occurrence of redox imbalance that triggers glycerol biosynthesis to replenish the pool of NAD(+) .     

Understanding and improving NADPH-dependent reactions by nongrowing Escherichia coli cells

We have shown that whole Escherichia coli cells overexpressing NADPH-dependent cyclohexanone monooxygenase carry out a model Baeyer-Villiger oxidation with high volumetric productivity (0.79 g epsilon-caprolactone/L.h ) under nongrowing conditions (Walton, A. Z.; Stewart, J. D. Biotechnol. Prog. 2002, 18, 262-268). This is approximately 20-fold higher than the space-time yield for reactions that used growing cells of the same strain. Here, we show that the intracellular stability of cyclohexanone monooxygenase and the rate of substrate transport across the cell membrane were the key limitations on the overall reaction duration and rate, respectively. Directly measuring the levels of intracellular nicotinamide cofactors under bioprocess conditions suggested that E. coli cells could support even more efficient NADPH-dependent bioconversions if a more suitable enzyme-substrate pair were identified. This was demonstrated by reducing ethyl acetoacetate with whole cells of an E. coli strain that overexpressed an NADPH-dependent, short-chain dehydrogenase from baker's yeast (Saccharomyces cerevisiae). Under glucose-fed, nongrowing conditions, this reduction proceeded with a space-time yield of 2.0 g/L.h and a final product titer of 15.8 g/L using a biocatalyst:substrate ratio (g/g) of only 0.37. These values are significantly higher than those obtained previously. Moreover, the stoichiometry linking ketone reduction and glucose consumption (2.3 +/- 0.1) suggested that the citric acid cycle supplied the bulk of the intracellular NADPH under our process conditions. This information can be used to improve the efficiency of glucose utilization even further by metabolic engineering strategies that increase carbon flux through the pentose phosphate pathway.     

Influence of selenium sources on age-related and mild heat stress-related changes of blood and liver glutathione redox cycle in broiler chickens (Gallus domesticus)

Selenium is an essential trace element that up-regulates a major component of the antioxidant defense mechanism by controlling the body's glutathione (GSH) pool and its major Se-containing antioxidant enzyme, glutathione peroxidase (GPX). Evidence has emerged suggesting that organic selenium, natural seleno-amino acids found in plants, grains and selenized yeast, maintains the antioxidant defense system more efficiently than inorganic selenium. Inorganic selenium is a pro-oxidant, whereas organic selenium possesses antioxidant properties itself. As a pro-oxidant, inorganic selenium is not suitable for animals or humans. Therefore, we examined the GSH–GPX system in broiler chickens and determined that organic selenium was indeed more beneficial than inorganic selenium. Chickens fed the organic selenium as Sel-Plex^®, a selenized yeast, had elevated GPX activity in both blood and liver in a thermoneutral environment and after heat distress. More importantly, the ability to reduce the oxidized glutathione (GSSG to 2 GSH) was enhanced and facilitated by maintenance of glutathione reductase activity. Organic selenium-fed chickens were less affected by mild heat distress than inorganic selenium-fed chickens, and this assessment was based upon less induction of heat shock protein 70 (hsp70) in organic selenium-fed chickens. Our results clearly show that heat distress, a potent inducer of oxidative stress and hsp70, can be partially ameliorated by feeding organic selenium. We attribute this observation to an enhanced GSH–GPX antioxidant system in organic selenium-fed chickens.     

Applications of metabolic modeling to drive bioprocess development for the production of value-added chemicals

Increasing numbers of value added chemicals are being produced using microbial fermentation strategies. Computational modeling and simulation of microbial metabolism is rapidly becoming an enabling technology that is driving a new paradigm to accelerate the bioprocess development cycle. In particular, constraint-based modeling and the development of genome-scale models of industrial microbes are finding increasing utility across many phases of the bioprocess development workflow. Herein, we review and discuss the requirements and trends in the industrial application of this technology as we build toward integrated computational/experimental platforms for bioprocess engineering. Specifically we cover the following topics: (1) genome-scale models as genetically and biochemically consistent representations of metabolic networks; (2) the ability of these models to predict, assess, and interpret metabolic physiology and flux states of metabolism; (3) the model-guided integrative analysis of high throughput ‘omics’ data; (4) the reconciliation and analysis of on- and off-line fermentation data as well as flux tracing data; (5) model-aided strain design strategies and the integration of calculated biotransformation routes; and (6) control and optimization of the fermentation processes. Collectively, constraint-based modeling strategies are impacting the iterative characterization of metabolic flux states throughout the bioprocess development cycle, while also driving metabolic engineering strategies and fermentation optimization.     

Accelerated Determination of Selenomethionine in Selenized Yeast: Validation of Analytical Method

The purpose of this study was to reduce the extraction time, to hours instead of days, for quantification of the selenomethionine (SeMet) content of selenized yeast. An accelerated method using microwave-assisted enzymatic extraction and ultrasonication was optimized and applied to certified reference material (selenized yeast reference material (SELM)-1). Quantitation of SeMet in the extracts was performed by liquid chromatography with inductively coupled plasma mass spectrometry. The limits of detection and quantitation were 5 ppb SeMet and 15 ppb SeMet respectively and the signal response was linear up to 1,500 ppb SeMet. The average recovery of spiked SeMet from the selenized yeast matrix was 97.7 %. Analysis of an SELM-1 using this method resulted in 100.9 % recovery of the certified value (3448?±?146 ppm SeMet). This method is suitable for fast reliable determination of SeMet in selenized yeast.     

A guide to metabolic flux analysis in metabolic engineering: Methods,tools and applications

The field of metabolic engineering is primarily concerned with improving the biological production of value-added chemicals, fuels and pharmaceuticals through the design, construction and optimization of metabolic pathways, redirection of intracellular fluxes, and refinement of cellular properties relevant for industrial bioprocess implementation. Metabolic network models and metabolic fluxes are central concepts in metabolic engineering, as was emphasized in the first paper published in this journal, “Metabolic fluxes and metabolic engineering” (Metabolic Engineering, 1: 1–11, 1999). In the past two decades, a wide range of computational, analytical and experimental approaches have been developed to interrogate the capabilities of biological systems through analysis of metabolic network models using techniques such as flux balance analysis (FBA), and quantify metabolic fluxes using constrained-based modeling approaches such as metabolic flux analysis (MFA) and more advanced experimental techniques based on the use of stable-isotope tracers, i.e. ¹³C-metabolic flux analysis (¹³C-MFA). In this review, we describe the basic principles of metabolic flux analysis, discuss current best practices in flux quantification, highlight potential pitfalls and alternative approaches in the application of these tools, and give a broad overview of pragmatic applications of flux analysis in metabolic engineering practice.     

Biotechnological production of γ-decalactone,a peach like aroma,by <Emphasis Type="Italic">Yarrowia lipolytica</Emphasis>

The request for new flavourings increases every year. Consumer perception that everything natural is better is causing an increase demand for natural aroma additives. Biotechnology has become a way to get natural products. γ-Decalactone is a peach-like aroma widely used in dairy products, beverages and others food industries. In more recent years, more and more studies and industrial processes were endorsed to cost-effect this compound production. One of the best-known methods to produce γ-decalactone is from ricinoleic acid catalyzed by Yarrowia lipolytica, a generally regarded as safe status yeast. As yet, several factors affecting γ-decalactone production remain to be fully understood and optimized. In this review, we focus on the aromatic compound γ-decalactone and its production by Y. lipolytica. The metabolic pathway of lactone production and degradation are addressed. Critical analysis of novel strategies of bioprocess engineering, metabolic and genetic engineering and other strategies for the enhancement of the aroma productivity are presented.     

Concurrent quantitative HPLC–mass spectrometry profiling of small selenium species in human serum and urine after ingestion of selenium supplements

Selenium metabolic patterns in the human body originating from five distinct selenium dietary sources, selenate, selenite, selenomethionine (SeMet), methylselenocysteine (MeSeCys) and selenized yeast, were investigated by performing concurrent HPLC–mass spectrometric analysis of human serum and urine. Total selenium and selenium species time profiles were generated by sampling and analyzing serum and urine from volunteers treated with selenium supplements, up to 5 and 24 h following ingestion, respectively. We found that an increase in total serum selenium levels, accompanied by elevated selenium urinary excretion, was the common pattern for all treatments, except for that of selenite supplementation. Selenosugar 1 was a universal serum metabolite in all treatments, indicating that ingested selenium is favorably metabolized to the sugar. Except for selenite and selenized yeast ingestion, these patterns were reflected in the urine time series of the different treatments. Selenosugar 1 was the major selenium species present in urine in all treatments except for the selenate treatment, accounting for about 80% of the identified excreted species within 24 h of ingestion. Furthermore, the urinary metabolite trimethylselenonium ion (TMSe) was detected for the first time in human background serum by using HPLC coupled to elemental and molecular mass spectrometry. The concurrent monitoring of non-protein selenium species in both body fluids provides the relation between bioavailability and excretion of the individual ingested species and of their metabolic products, while the combined use of elemental and molecular mass spectrometry enables the accurate quantitation of structurally confirmed species. This successfully applied approach is anticipated to be a useful tool for more extensive future studies into human selenium metabolism.     

Metabolic flux analysis for serine alkaline protease fermentation by Bacillus licheniformis in a defined medium: effects of the oxygen transfer rate.

The metabolic fluxes through the central carbon pathways in the bioprocess for serine alkaline protease (SAP) production by Bacillus licheniformis were calculated by the metabolic flux-based stoichiometric model based on the proposed metabolic network that contains 102 metabolites and 133 reaction fluxes using the time profiles of citrate, dry cell, organic acids, amino acids, and SAP as the constraints. The model was solved by minimizing the SAP accumulation rate in the cell. The effects of the oxygen-transfer rate (OTR) on the metabolic fluxes were investigated in a defined medium where citrate was used as the sole carbon source. The central pathways were active for the growth and the SAP synthesis in all the periods of the bioprocess at low (LOT), medium (MOT), and high (HOT) oxygen-transfer conditions. The flux partitioning in the TCA cycle at alpha-ketoglutarate towards glutamate group and at oxalacetate (OA) toward aspartic acid group amino acids were dependent on the OTR. The flux of the anaplerotic reaction that connects the TCA cycle either from malate or OA to the gluconeogenesis pathway via the main branch point pyruvate (Pyr) was also influenced by the OTR. With the decrease in the OTR, the intracellular flux values after glycerate 3-phosphate (PG3) in the gluconeogenesis pathway and the specific growth rate decreased. The total ATP-generation rate increased with the increase in OTR. The pathway towards the aspartic acid family amino acids which is important for sporulation that precedes the SAP synthesis were all active throughout the bioprocess. Metabolic flux analysis results at LOT, MOT, and HOT conditions encourage the design of an oxygen-transfer strategy in the bioreactor; moreover, asparagine synthetase or aspartate kinase could be the potential metabolic engineering sites due to the low value of the flux from the branch point aspartate toward asparagine.     

How reliable are Chinese hamster ovary (CHO) cell genome-scale metabolic models?

Genome-scale metabolic models (GEMs) possess the power to revolutionize bioprocess and cell line engineering workflows thanks to their ability to predict and understand whole-cell metabolism in silico. Despite this potential, it is currently unclear how accurately GEMs can capture both intracellular metabolic states and extracellular phenotypes. Here, we investigate this knowledge gap to determine the reliability of current Chinese hamster ovary (CHO) cell metabolic models. We introduce a new GEM, iCHO2441, and create CHO-S and CHO-K1 specific GEMs. These are compared against iCHO1766, iCHO2048, and iCHO2291. Model predictions are assessed via comparison with experimentally measured growth rates, gene essentialities, amino acid auxotrophies, and ¹³C intracellular reaction rates. Our results highlight that all CHO cell models are able to capture extracellular phenotypes and intracellular fluxes, with the updated GEM outperforming the original CHO cell GEM. Cell line-specific models were able to better capture extracellular phenotypes but failed to improve intracellular reaction rate predictions in this case. Ultimately, this work provides an updated CHO cell GEM to the community and lays a foundation for the development and assessment of next-generation flux analysis techniques, highlighting areas for model improvements.     

Optimizing high-throughput metabolomic biomarker screening: a study of quenching solutions to freeze intracellular metabolism in CHO cells

Metabolomics is a rapidly emerging tool for studying and optimizing both media and bioprocess development for culturing recombinant mammalian cells that are used in protein production processes. Quenching of the cells is crucial to fix their metabolic status at the time of sampling. Three precooled quenching solutions were tested for their ability to fix the metabolic activity of CHO cells: phosphate-buffered saline (PBS) (pH 7.4; 0.5°C), 60% methanol with 70?mM HEPES (pH 7.4; -20°C), and 60% methanol with 0.85% (w/v) ammonium bicarbonate (AMBIC) (pH 7.4; -20°C). The metabolic activity of the sampled CHO cells was assessed by determining the intracellular levels of ATP using a bioluminescence assay and selected metabolites with LC-MS/MS. We found the precooled PBS (pH 7.4; 0.5°C) to be the optimal quenching reagent for fixing intracellular metabolism. Importantly, the structural integrity of the cell membrane was maintained and highest yields were obtained for intracellular levels of ATP as well as for 18 out of 28 intracellular metabolites. In contrast to the previously reported studies, buffered methanol quenching was not applicable for suspension cultured CHO cells as cellular membrane integrity was affected. We recommend that the cells are quenched and washed simultaneously to keep the sampling time to a minimum and to prevent any further metabolic activity in the cells. We observed that additional washing steps are not required. Our analyses suggest that methanol as quenching solution, even in combination with a buffer substance, appears not suitable for quenching sensitive mammalian cells. The protocol we report herein is a simple cell sampling method that enables high-throughput metabolomic analyses and is suitable for a large number of samples.     

Examining the feasibility of bulk commodity production in <Emphasis Type="Italic">Escherichia coli</Emphasis>

Escherichia coli is currently used by many research institutions and companies around the world as a platform organism for the development of bio-based production processes for bulk biochemicals. A given bulk biochemical bioprocess must be economically competitive with current production routes. Ideally the viability of each bioprocess should be evaluated prior to commencing research, both by metabolic network analysis (to determine the maximum theoretical yield of a given biocatalyst) and by techno-economic analysis (TEA; to determine the conditions required to make the bioprocess cost-competitive). However, these steps are rarely performed. Here we examine theoretical yields and review available TEA for bulk biochemical production in E. coli. In addition, we examine fermentation feedstocks and review recent strain engineering approaches to achieve industrially-relevant production, using examples for which TEA has been performed: ethanol, poly-3-hydroxybutyrate, and 1,3-propanediol.     

Know-how and know-why in biochemical engineering

This contribution analyzes the position of biochemical engineering in general and bioprocess engineering particularly in the force fields between fundamental science and applications, and between academia and industry. By using culture technology as an example, it can be shown that bioprocess engineering has moved slowly but steadily from an empirical art concerned with mainly know-how to a science elucidating the know-why of culture behavior. Highly powerful monitoring tools enable biochemical engineers to understand and explain quantitatively the activity of cellular culture on a metabolic basis. Among these monitoring tools are not just semi-online analyses of culture broth by HPLC, GC and FIA, but, increasingly, also noninvasive methods such as midrange IR, Raman and capacitance spectroscopy, as well as online calorimetry. The detailed and quantitative insight into the metabolome and the fluxome that bioprocess engineers are establishing offers an unprecedented opportunity for building bridges between molecular biology and engineering biosciences. Thus, one of the major tasks of biochemical engineering sciences is not developing new know-how for industrial applications, but elucidating the know-why in biochemical engineering by conducting research on the underlying scientific fundamentals.     

On the controllability of continuous fermentation processes

Simulation may be used as a powerful tool for accelerating bioprocess design. This paper demonstrates the use of simulations in exploring the nature and impact of the interactions that exist in a typical bioprocess for the recovery of an intracellular protein. The study shows that an integrated approach to design must be adopted in order to achieve acceptable process designs. Data from a fed-batch fermentation, with verified models for cell harvesting, cell disruption and cell debris removal have been integrated to demonstrate the consequence of process design and operating decisions on the resulting process performance. The trade-offs between product recovery and the extent of cell debris removal for a range of operating conditions have been represented through a series of windows of operation which show how process conditions must be altered in order for given process performance levels to be realised. The capacity to account for process performance including the impact of interactions is seen as a pre-requisite for rigorous bioprocess sequence design and optimisation.     

Effect of inorganic and organic forms of selenium supplementation on development of larval Heliothis virescens

Selenium (Se) is an essential micronutrient for vertebrates though little is known about the effects on insects. Herbivorous insect larvae acquire Se from plant tissues in the inorganic form of sodium selenate and sodium selenite, and in the organic form of selenoamino acids, selenomethionine, and selenocystine. In this study, we document the effects of dietary supplementation with sodium selenite, sodium selenate, selenocystine, selenomethionine, and selenized yeast on the developmental rate of Heliothis virescens (Fabricius) (Lepidoptera: Noctuidae). Larvae tolerated high levels of Se (500 µg g^?1 Se) as sodium selenate and to a lesser extent as selenocystine. Lower levels of sodium selenite (>1 µg g^?1 Se) caused increased mortality, reduced rates of pupation, more pupal/adult intermediates, and reduced adult emergence. Selenomethionine proved toxic to larvae at levels above 25 µg g^?1 Se, significantly delaying pupation and raising mortality. Provision of Se as selenized yeast, which contains primarily selenomethionine, was also extremely detrimental to larval development and survival. The results indicate that the impact of dietary Se supplement for insects may differ from vertebrates.     

Dynamic metabolic engineering for increasing bioprocess productivity

Yield and productivity are critical for the economics and viability of a bioprocess. In metabolic engineering, the main objective is the increase of a target metabolite production through genetic engineering. However, genetic manipulations usually result in lower productivity due to growth impairment. Previously, it has been shown that the dynamic control of metabolic fluxes can increase the amount of product formed in an anaerobic batch fermentation of Escherichia coli. In order to apply this control strategy, the genetic toggle switch is used to manipulate key fluxes of the metabolic network. We have designed and analyzed an integrated computational model for the dynamic control of gene expression. This controller, when coupled to the metabolism of E. coli, resulted in increased bioprocess productivity.     

On-line monitoring of lipid storage in yeasts using impedance spectroscopy

Bioremediation technologies and many environmentally sound biosyntheses rely on the catalytic potential of whole cells. For analyzing and controlling such processes robust real-time indicators for the concentration of intact cells such as impedance are required. The conventional method measures the capacitances of cell suspensions at one or two frequencies and correlates them with biomass concentrations. However, cell inclusions such as lipid droplets or overproduced enzymes may block intracellular ion paths, thereby possibly modifying the dielectric properties of the cells. To test the hypothesis that the total impedance spectrum into the analysis may provide useful information about cell inclusions, the impedance spectrum of a technical culture of the oleaginous yeast Arxula adeninivorans was measured and evaluated every 15 s. This yeast is a good test object since it stores the excess of assimilated carbon in experimentally controllable lipid droplets. Upon correction for possible impedance signal interferences, we derived different empirical methods suitable to indicate incipient lipid formation. The methods were designed to act on-line and are thus principally suited for real-time monitoring of cell inclusions. In search for optimised bioprocess monitoring we tested a heuristic spectrum analysis using integrative statistics (RDA). With this approach we were able to accurately detect the formation of cell inclusions, which is potentially valuable for future bioprocess control strategies.     

应用最大熵原理通过酶控制通量预测突变体的通量分布

在代谢工程和系统生物学领域, 计算机模拟比以往更为有效的应用于生物过程的分析和优化。胞内代谢通量可以用代谢通量分析和基元模式分析来估算。由于测定数据的不足和误差, 以及基元途径的冗余, 经常很难得到准确的代谢通量分布数据。本研究提出一种基于最大熵原理的算法来计算基元模式系数。欠定和不确定条件下, 通过胞外代谢通量数据估算胞内代谢通量分布。为了检验算法的可行性, 对杂交瘤细胞、枯草芽孢杆菌和大肠杆菌的胞内代谢通量分布做了估算。本研究提出的基于最大熵原理的优化算法避免了对细胞状态的生理学假设。与其他目标函数相比, 可以更为可靠和可行的估算胞内代谢通量分布。