Model based optimization of the fed-batch production of a highly active transglutaminase variant in Escherichia coli

A process for the production of a thermostable variant of a microbial transglutaminase was developed. The transglutaminase variant produced, carried a single amino acid exchange (serine replaced by proline at position 2) and showed a nearly doubled specific activity of 46.1 Umg(-1) compared to the wild-type enzyme. Based on a model based optimization strategy, intracellular soluble production in Escherichia coli was optimized. After parameter identification and only two fed-batch cultivations, a space time yield of 1438 U(TG)L(-1)h(-1) was obtained which is 175% higher than the highest values published so far (extracellular production using Corynebacterium ammoniagenes). High carbon source concentrations during expression were found to increase the product formation. Prior to the fed-batch cultivation, the host strain was adapted from complex medium to minimal medium by serial dilution. Upon transfer to the minimal medium, initially the maximal growth rate dropped to 0.13 h(-1). After the six consecutive cultivations the rate increased to 0.47 h(-1) and the portion of the complex medium was reduced to 1 ppm. Using the adapted cells, temperature after induction and IPTG-concentration were investigated by satellite batch cultivation according to a Design of Experiment (DoE) plan. The product yield was strongly influenced by the temperature after induction but not by the inductor concentration. The highest specific activity of 1386 Ug(-1) bio dry mass was obtained at 29°C and 0.7 mM IPTG.     

Substrate and energy costs of the production of exocellular enzymes by Bacillus licheniformis

Substrate and energy costs of the production of exocellular enzymes from glucose and citrate by B. Iicheniformis S1684 as well as molar growth yields corrected for these costs of product formation were calculated using data from chemostat experiments. The calculations showed that 1.46-1.73 mol glucose and 2.31-2.77 mol citrate are needed for formation and excretion of 1 mol protein. Consequently, the values of the maximal product yield from substrate (Y(psm') g/mol) are 80 < Y(psm) < 95 when product is formed from glucose and 50 < Y(psm) < 60 when product is formed from citrate. The higher substrate costs for product formation from citrate are due to a higher level of CO(2) production during protein formation and a higher substrate requirement for the energy supply of product formation and excretion than when product is formed from glucose. The theoretical ATP requirement for protein synthesis could be determined reasonably well, but the energy costs of protein excretion could not be determined exactly. The energy costs of protein formation are higher than those of biomass formation or protein excretion. Molar growth yields corrected for the substrate costs of product formation were high, indicating a high efficiency of growth.Growth and production parameters were determined as well from experimental data of recycling fermentor experiments using a parameter optimization procedure based on a mathematical model describing biomass growth as a linear function of the substrate consumption rate and the rate of product formation as a linear function of biomass growth rate. The fitting procedure yielded two growth and production domains during glucose limitation. In the first domain the values for the maximal growth yield and maintenance coefficient were in agreement with those found in chemostat experiments at corresponding values of Y(spm). Domain 2 could be described best with linear growth and product formation. In domain 2 the rate of product formation decreased and more substrate became available for biomass formation. As a consequence the specific growth rate increased in the shift from domain 1 to 2. Domain 2 behavior most probably is caused by the rel-status of B. Iicheniformis S1684.     

Parameter estimation with a novel gradient-based optimization method for biological lattice-gas cellular automaton models

Lattice-gas cellular automata (LGCAs) can serve as stochastic mathematical models for collective behavior (e.g. pattern formation) emerging in populations of interacting cells. In this paper, a two-phase optimization algorithm for global parameter estimation in LGCA models is presented. In the first phase, local minima are identified through gradient-based optimization. Algorithmic differentiation is adopted to calculate the necessary gradient information. In the second phase, for global optimization of the parameter set, a multi-level single-linkage method is used. As an example, the parameter estimation algorithm is applied to a LGCA model for early in vitro angiogenic pattern formation.     

Acetic acid production by Acetogenium kivui in continuous culture — kinetic studies and computer simulations

Summary This work considers the continuous production of acetic acid by the homoacetogenic and thermophilic bacterium Acetogenium kivui. A mathematical model for the growth kinetics has been developed. The unstructured model for growth and product formation includes product and substrate inhibition as well as maintenance energy effects. The associated model parameters have been identified by non-linear optimization and evidenced experimentally in continuous culture as steady-state data. By using a mineral medium with glucose as the energy and carbon source for the bacteria proper carbon balances are available. The model permits good predictions of steady-state concentrations. Offprint requests to: J. von Eysmondt     

Maturity and product formation in cultures of microorganisms

The concept of a maturation time (t_m) for a product formation by a microbial culture is developed and a simple method is described for determining this parameter and also the product formation rate constant (k_p) from batch culture experiments. The concept has been utilized in a general model for the prediction of steady state product concentrations in single-stage continuous-flow culture systems.     

Optimization of medium compositions favoring butanol and 1,3-propanediol production from glycerol by Clostridium pasteurianum

Medium compositions favoring butanol and 1,3-propanediol (1,3-PDO) production from glycerol by Clostridium pasteurianum DSM525 were investigated using statistical experimental designs. Medium components affecting butanol and 1,3-PDO production were screened using a fractional factorial experimental design. Among the six tested variables (phosphate buffer, MnSO4·H2O, MgSO4·7H2O, FeSO4·7H2O, (NH4)2SO4, and yeast extract), FeSO4·7H2O, (NH4)2SO4, and yeast extract were found to be significant variables for further optimization of medium using a Box-Behnken design. Optimal butanol (0.98 g/L/h) and 1,3-PDO (1.19 g/L/h) productivities were predicted by the corresponding quadratic model for each product and the models were validated experimentally under optimized conditions. The optimal medium composition for butanol production was significantly different from that for 1,3-PDO production (0.06 vs. 0 g/L for FeSO4·7H2O, 7.35 vs. 0 g/L for (NH4)2SO4, and 5.08 vs. 8.0 g/L for yeast extract), suggesting that the product formation from glycerol by C. pasteurianum DSM525 can be controlled by changing medium compositions.     

Kinetics of hydrogen peroxide decomposition by catalase: hydroxylic solvent effects

The effect of water–alcohol (methanol, ethanol, propan-1-ol, propan-2-ol, ethane-1,2-diol and propane-1,2,3-triol) binary mixtures on the kinetics of hydrogen peroxide decomposition in the presence of bovine liver catalase is investigated. In all solvents, the activity of catalase is smaller than in water. The results are discussed on the basis of a simple kinetic model. The kinetic constants for product formation through enzyme–substrate complex decomposition and for inactivation of catalase are estimated. The organic solvents are characterized by several physical properties: dielectric constant (D), hydrophobicity (log P), concentration of hydroxyl groups ([OH]), polarizability (α), Kamlet-Taft parameter (β) and Kosower parameter (Z). The relationships between the initial rate, kinetic constants and medium properties are analyzed by linear and multiple linear regression.     

Filamentous fungi in microtiter plates—an easy way to optimize itaconic acid production with Aspergillus terreus

Itaconic acid is an important industrial building block and is produced by the filamentous fungi Aspergillus terreus. To make the optimization process more efficient, a scale-down from shake flasks to microtiter plates was performed. This resulted in comparable product formations, and 87.7 g/L itaconic acid was formed after 10 days of cultivation in the microtiter plate. The components of the minimal medium were varied independently for a media optimization. This resulted in an increase of the itaconic acid concentration by a variation of the KH₂PO₄ and CuSO₄ concentrations. The cultivation with a higher KH₂PO₄ concentration in a 400-mL bioreactor showed an increase in the maximum productivity of 1.88 g/L/h, which was an increase of 74 % in comparison to the reference. Neither the phosphate concentration nor the nitrogen sources were limited at the start of the product formation. This showed that a limitation of these substances is not necessary for the itaconic acid formation.     

Utilizing high-throughput experimentation to enhance specific productivity of an <Emphasis Type="Italic">E.coli</Emphasis>T7 expression system by phosphate limitation

Background  

The specific productivity of cultivation processes can be optimized, amongst others, by using genetic engineering of strains, choice of suitable host/vector systems or process optimization (e.g. choosing the right induction time). A further possibility is to reduce biomass buildup in favor of an enhanced product formation, e.g. by limiting secondary substrates in the medium, such as phosphate. However, with conventional techniques (e.g. small scale cultivations in shake flasks), it is very tedious to establish optimal conditions for cell growth and protein expression, as the start of protein expression (induction time) and the degree of phosphate limitation have to be determined in numerous concerted, manually conducted experiments.     

In situ detection of spontaneous superoxide anion and singlet oxygen production by mitochondria in rat liver and small intestine

In the present study, the endogenous formation of reactive oxygen species was localized in rat liver and small intestine. The 3,3′-diaminobenzidine (DAB)-Mn²⁺ technique in which cobalt ions were included in the incubation medium was applied to unfixed cryostat sections of intact tissues. Addition of manganese ions to the DAB-Co²⁺- containing medium greatly increased the amounts of final reaction product formed compared with incubations with only DAB and cobalt ions. In liver, a blue final reaction product was deposited, particularly in hepatocytes surrounding portal tracts. In the small intestine, the DAB--cobalt complex was mainly found at the basal side of enterocytes. Goblet cells remained unstained. Electron microscopical images revealed that an electron-dense reaction product was exclusively present at both inner and outer membranes and at the intermembrane space in mitochondria of liver parenchymal cells and duodenal enterocytes. It was shown that the spontaneous formation of final reaction product was enzymatic and dependent on the presence of oxygen in the medium. Sulphide decreased the reaction, which may indicate that cytochrome c oxidase was partially involved. Benzoquinone and histidine, which are scavengers of superoxide anions and singlet oxygen respectively, reduced the amount of final reaction product considerably. Furthermore, the formation of final reaction product was sensitive to specific inhibitors of NADH:coenzyme Q reductase and aldehydeoxidase, indicating that these enzymes were at least partly responsible for the generation of superoxide anions and singlet oxygen and for the formation of the DAB--cobalt complex. This revised version was published online in November 2006 with corrections to the Cover Date.     

Development of suspension culture of Podophyllum hexandrum for production of podophyllotoxin

A suspension culture of Podophyllum hexandrum was established. As the cultures grew, reduction in cell viability, biomass and product yield were associated with browning of culture medium, clumping of cells and drop in medium pH. Supplementation of the medium with both polyvinylpyrrollidone (PVP) and pectinase eliminated these problems. PVP at 10 g l^–1 was optimum for both growth of and product formation in P. hexandrum suspension cultures.     

Physiological relation between respiration activity and heterologous expression of selected benzoylformate decarboxylase variants in <Emphasis Type="Italic">Escherichia coli</Emphasis>

Background  

The benzoylformate decarboxylase (BFD) from Pseudomonas putida is a biotechnologically interesting biocatalyst. It catalyses the formation of chiral 2-hydroxy ketones, which are important building blocks for stereoselective syntheses. To optimise the enzyme function often the amino acid composition is modified to improve the performance of the enzyme. So far it was assumed that a relatively small modification of the amino acid composition of a protein does not significantly influence the level of expression or media requirements. To determine, which effects these modifications might have on cultivation and product formation, six different BFD-variants with one or two altered amino acids and the wild type BFD were expressed in Escherichia coli SG13009 pKK233-2. The oxygen transfer rate (OTR) as parameter for growth and metabolic activity of the different E. coli clones was monitored on-line in LB, TB and modified PanG mineral medium with the Respiratory Activity MOnitoring System (RAMOS).     

A medium optimization strategy for improvement of growth and methane production by Methanobacterium thermoautotrophicum

Methanobacterium thermoautotrophicum, strain Hveragerdi, has been cultivated in a completely defined mineral salts medium, under strictly anaerobic conditions with CO₂ and H₂ as sole carbon and energy source, respectively. During optimization of the medium an iron limitation was identified that could not be overcome by the simple addition of iron—or iron complexed with nitrilotriacetate (NTA)—to the medium, due to the formation of insoluble FeS complexes. In order to define a medium optimization strategy, and to avoid laborious empirical optimization procedures, a theoretical model has been developed in order to describe the solubility of iron and other mineral species in the medium as a function of the concentration of sulfur and NTA. This model may be applied for the optimization of any medium component. With this information sulfide has been replaced by a combination of cysteine and thiosulphate in conjunction with a non-toxic reducing agent (titanium (III) citrate). Using this defined medium precipitation was avoided and an iron limitation was overcome resulting in a 5-fold improvement of the final biomass concentration from 2–3 g l⁻¹ to 11.2 g l⁻¹ together with a 2-fold increase (from 45 to almost 100%) in the conversion of CO₂ and H₂ to CH₄, even at gas flow rates as high as 6 l min⁻¹.     

Framework for online optimization of recombinant protein expression in high-cell-density Escherichia coli cultures using GFP-fusion monitoring

A framework for the online optimization of protein induction using green fluorescent protein (GFP)-monitoring technology was developed for high-cell-density cultivation of Escherichia coli. A simple and unstructured mathematical model was developed that described well the dynamics of cloned chloramphenicol acetyltransferase (CAT) production in E. coli JM105 was developed. A sequential quadratic programming (SQP) optimization algorithm was used to estimate model parameter values and to solve optimal open-loop control problems for piecewise control of inducer feed rates that maximize productivity. The optimal inducer feeding profile for an arabinose induction system was different from that of an isopropyl-beta-D-thiogalactopyranoside (IPTG) induction system. Also, model-based online parameter estimation and online optimization algorithms were developed to determine optimal inducer feeding rates for eventual use of a feedback signal from a GFP fluorescence probe (direct product monitoring with 95-minute time delay). Because the numerical algorithms required minimal processing time, the potential for product-based and model-based online optimal control methodology can be realized.     

Substrate uptake,phosphorus repression,and effect of seed culture on glycopeptide antibiotic production: Process model development and experimental validation

Actinomycetes, the soil borne bacteria which exhibit filamentous growth, are known for their ability to produce a variety of secondary metabolites including antibiotics. Industrial scale production of such antibiotics is typically carried out in a multi‐substrate medium where the product formation may experience catabolite repression by one or more of the substrates. Availability of reliable process models is a key bottleneck in optimization of such processes. Here we present a structured kinetic model to describe the growth, substrate uptake and product formation for the glycopeptide antibiotic producer strain Amycolatopsis balhimycina DSM5908. The model is based on the premise that the organism is an optimal strategist and that the various metabolic pathways are regulated via key rate limiting enzymes. Further, the model accounts for substrate inhibition and catabolite repression. The model is also able to predict key phenomena such as simultaneous uptake of glucose and glycerol but with different specific uptake rates, and inhibition of glycopeptide production by high intracellular phosphate levels. The model is successfully applied to both production and seed medium with varying compositions and hence has good predictive ability over a variety of operating conditions. The model parameters are estimated via a well‐designed experimental plan. Adequacy of the proposed model was established via checking the model sensitivity to its parameters and confidence interval calculations. The model may have applications in optimizing seed transfer, medium composition, and feeding strategy for maximizing production. Biotechnol. Bioeng. 2010;105: 109–120. © 2009 Wiley Periodicals, Inc.     

Trace levels of the CHO host cell protease cathepsin D caused particle formation in a monoclonal antibody product

Chinese hamster ovary (CHO) cells are often used to produce therapeutic monoclonal antibodies (mAbs). CHO cells express many host cell proteins (HCPs) required for their growth. Interactions of HCPs with mAbs can sometimes result in co‐purification of trace levels of ‘hitchhiker’ HCPs during the manufacturing process. Purified mAb‐1 product produced in early stages of process optimization had high HCP levels. In addition, these lots formed delayed‐onset particles containing mAb‐1 and its heavy chain C‐terminal fragments. Studies were performed to determine the cause of the observed particle formation and to optimize the purification for improved HCP clearance. Protease activity and inhibitor stability studies confirmed that an aspartyl protease was responsible for fragmentation of mAb‐1 resulting in particle formation. An affinity resin was used to selectively capture aspartyl proteases from the mAb‐1 product. Mass spectrometry identified the captured aspartyl protease as CHO cathepsin D. A wash step at high pH with salt and caprylate was implemented during the protein A affinity step to disrupt the HCP–mAb interactions and improve HCP clearance. The product at the end of purification using the optimized process had very low HCP levels, did not contain detectable protease activity, and did not form particles. Spiking of CHO cathepsin D back into mAb‐1 product from the optimized process confirmed that it was the cause of the particle formation. This work demonstrated that process optimization focused on removal of HCPs was successful in eliminating particle formation in the final mAb‐1 product. © 2015 American Institute of Chemical Engineers Biotechnol. Prog., 31:1360–1369, 2015     

Intracellular response to process optimization and impact on productivity and product aggregates for a high‐titer CHO cell process

A key goal in process development for antibodies is to increase productivity while maintaining or improving product quality. During process development of an antibody, titers were increased from 4 to 10 g/L while simultaneously decreasing aggregates. Process development involved optimization of media and feed formulations, feed strategy, and process parameters including pH and temperature. To better understand how CHO cells respond to process changes, the changes were implemented in a stepwise manner. The first change was an optimization of the feed formulation, the second was an optimization of the medium, and the third was an optimization of process parameters. Multiple process outputs were evaluated including cell growth, osmolality, lactate production, ammonium concentration, antibody production, and aggregate levels. Additionally, detailed assessment of oxygen uptake, nutrient and amino acid consumption, extracellular and intracellular redox environment, oxidative stress, activation of the unfolded protein response (UPR) pathway, protein disulfide isomerase (PDI) expression, and heavy and light chain mRNA expression provided an in‐depth understanding of the cellular response to process changes. The results demonstrate that mRNA expression and UPR activation were unaffected by process changes, and that increased PDI expression and optimized nutrient supplementation are required for higher productivity processes. Furthermore, our findings demonstrate the role of extra‐ and intracellular redox environment on productivity and antibody aggregation. Processes using the optimized medium, with increased concentrations of redox modifying agents, had the highest overall specific productivity, reduced aggregate levels, and helped cells better withstand the high levels of oxidative stress associated with increased productivity. Specific productivities of different processes positively correlated to average intracellular values of total glutathione. Additionally, processes with the optimized media maintained an oxidizing intracellular environment, important for correct disulfide bond pairing, which likely contributed to reduced aggregate formation. These findings shed important understanding into how cells respond to process changes and can be useful to guide future development efforts to enhance productivity and improve product quality.     

Evaluation of two unstructured mathematical models for the penicillin G fedbatch fermentation

The mathematical model for the penicillin G fed-batch fermentation proposed by Heijnen et al. (1979) is compared with the model of Bajpai & Reuß (1980). Although the general structure of these models is similar, the difference in metabolic assumptions and specific growth and production kinetics results in a completely different behaviour towards product optimization. A detailed analysis of both models reveals some physical and biochemical shortcomings. It is shown that it is impossible to make a reliable estimation of the model parameters, only using experimental data of simple constant glucose feed rate fermentations with low initial substrate amount. However, it is demonstrated that some model parameters might be key factors in concluding whether or not altering the substrate feeding strategy has an important influence on the final amount of product.It is illustrated that feeding strategy optimization studies can be a tool in designing experiments for parameter estimation purposes.     

杂交瘤细胞的大量培养

杂交瘤细胞的大量培养是一项迅速发展的技术。本文评述了杂交瘤细胞培养条件和代谢调控方面的研究进展,包括反应器培养中的过程参数优化、细胞损伤和保护、营养物质利用和有害副产物的形成、细胞生长和单抗分泌的动力学以及长期培养的稳定性等问题。同时,本文也讨论了在生物反应器中培养杂交瘤细胞的操作模式和控制策略的研究工作,特别是近年来备受重视的灌注培养和补料培养。