Enhancement of human granulocyte-colony stimulating factor production in recombinant E. coli using batch cultivation

Development of inexpensive and simple culture media is always favorable for recombinant protein over-expression in E. coli. The effects of medium composition on the production of recombinant human granulocyte-colony stimulating factor (rh-GCSF) were investigated in batch culture of E. coli BL21 (DE3) [pET23a-hgcsf]. First, the optimum medium for production of rh-GCSF was determined; and, then it was shown that mixture of amino acid addition at induction time, which was determined on the basis of amino acids frequency in the recombinant protein, increases recombinant protein expression level significantly. Furthermore, the effect of glucose concentration on productivity of rh-GCSF was investigated; 20 g/l of glucose will result in maximum attainable biomass and rh-GCSF in this process. At optimum conditions, a cell dry weight of 10.5 g/l, an expression level of about 35% of total cellular protein, rh-GCSF concentration of 1.75 ± 0.1 g/l, and overall rh-GCSF yield of 165 ± 5 mg/g were obtained.     

Production of a sterol esterase from Ophiostoma piceae in batch and fed‐batch bioprocesses using different Pichia pastoris phenotypes as cell factory

The potential biotechnological applications for the Ophiostoma piceae sterol esterase (OPE) are conditioned to the availability of high enzyme amounts at low prices. This enzyme is a versatile biocatalyst with different biotechnological applications. In this work a systematic study on its heterologous production in different Pichia pastoris strains and operational strategies is presented. The best results were obtained using an AOX1 defective yeast strain in a fed‐batch bioprocess using methanol as inducer substrate at a set point of 2.5 g L^?1 and sorbitol as cosubstrate by means of a preprogramed exponential feeding rate at a μ = 0.02 h^?1, reaching 30 U mL^?1 of enzyme and a volumetric productivity of 403.5 U L^?1 h^?1. These values are twofold higher than those obtained with a Mut⁺ phenotype using methanol a sole carbon source. OPE was the main protein secreted by the yeast, 55% for Mut^s versus 25% for Mut^+. © 2014 American Institute of Chemical Engineers Biotechnol. Prog., 30:1012–1020, 2014     

Effect of culture conditions on batch growth of Saccharomycopsis lipolytica on olive oil

Summary Batch cultures of Saccharomycopsis lipolytica were grown in minimal medium with olive oil as carbon source. Inocula of glucose-grown cells commenced growth with little lag at rates largely unaffected by variations in the stirring rate or oil concentration. However, growth rates declined when the medium pH was below 7.0. In all cultures, media pH declined with increasing cell concentration. Cell composition during exponential growth was 42% protein and 2% fat. Carbon-limited cells maintained this composition after oil exhaustion but during nitrogen- and oxygen-limited growth, protein content decreased and fat content increased although the protein decrease was only transient with oxygen limitation. Yield coefficients for triglyceride were near unity for all cultures. Free acid concentrations rose rapidly after inoculation. As fermentations progressed, free glycerol appeared and concentrations of di- and monoglycerides passed through maximal values although peak concentrations of di- and monoglycerides persisted for extended times in oxygen- and nitrogen-limited cultures respectively. The fraction of free glycerol consumed was greater in oxygen-limited than in carbon- or nitrogen-limited culture. The basic requirements for growth of yeasts on fatty wastes are discussed with reference to these observations.     

Cometabolic degradation of chloroallyl alcohols in batch and continuous cultures

The biodegradation of chloroallyl alcohols by pure and mixed bacterial cultures was investigated. Only 2-chloroallyl alcohol and cis- and trans-3-chloroallyl alcohol served as growth substrate for pure cultures. The other chloroallyl alcohols could be cometabolically degraded during growth on 2-chloroallyl alcohol. Cometabolic degradation of trichloroallyl alcohol, which was the most recalcitrant congener, by a Pseudomonas strain isolated on 2-chloroallyl alcohol resulted in 60% dechlorination. Efficient degradation of a mixture of chloroallyl alcohols in continuous culture could only be achieved in the presence of a satellite population. The mixed culture degraded 99% of the total chloroallyl alcohols added with 71% chloride release. The culture contained strains with a new catabolic potential. The results indicate the importance of mixed cultures and genetic adaptation for efficient chloroallyl alcohol removal.     

Assimilatory sulfur metabolism in marine microorganisms: Sulfur metabolism,protein synthesis,and growth of Pseudomonas halodurans and Alteromonas luteo-violaceus during unperturbed batch growth

Analysis of the distribution of ³⁵S-sulfate and ¹⁴C-glutamate in major biochemical components of the two marine bacteria, Pseudomonas halodurans and Alteromonas luteo-violaceus, was compared with cell density and total cellular protein during exponential growth in batch culture. For both organisms, the sulfur distribution was restricted principally to the low molecular weight organic and protein fractions, which together accounted for over 90% of the total sulfur. Carbon was more widely distributed, with these two fractions containing only 70% of the total label.Growth rate constants calculated from increases in cell numbers, protein, and ³⁵S and ¹⁴C in the various fractions indicated nearly balanced growth in A. luteo-violaceus, with constants derived from all biosynthetic parameters agreeing within 5% during the exponential phase. In contrast, protein synthesis and ³⁵S incorporation into residue protein constants were 30% higher than constants derived from cell counts and incorporation of ¹⁴C in P. halodurans. Therefore the cellular protein content P. halodurans varied over a two-fold range, with maximum protein per cell in the late exponential phase. A distinct reduction in the rate constants for total protein and ³⁵S incorporation into residue protein foreshadowed entry into the stationary phase more than one generation before other parameters.Incorporation of ³⁵S-sulfate into residue protein paralleled protein synthesis in both bacteria. The weight percent S in protein agreed well with the composition of an average protein derived from the literature. Sulfur incorporation into protein may be a useful measurement of marine bacterial protein synthesis.Abbreviations L.M.W. low molecular weight - TCA trichloroacetic acid - CFU colony forming unit     

Lactic acid production by batch fermentation of whey permeate: A mathematical model

Summary The batch fermentation of whey permeate to lactic acid was improved by supplementing the broth with enzyme-hydrolyzed whey protein. A mathematical model based on laboratory results predicts to a 99% confidence limit the kinetics of this fermentation. Cell growth, acid production and protein and sugar use rates are defined in quantifiable terms related to the state of cell metabolism. The model shows that the constants of the Leudeking-Piret model are not true constants, but must vary with the medium composition, and especially the peptide average molecular weight. The kinetic mechanism on which the model is based also is presented.Nomenclature K _i lactic acid inhibition constant (g/l) - K _pr protein saturation constant during cell growth (g/l) - K _pr protein saturation constant during maintenance (g/l) - K _s lactose saturation constant (g/l) - [LA] lactic acid concentration (g/l) - [PR] protein concentration (g/l) - [S] lactose concentration (g/l) - t time (h) - [X] cell mass concentration (g/l) - , fermentation constants of Leudeking and Piret - specific growth rate (l/h) - Y _{g, LA/S} acid yield during cell growth (g acid/g sugar) - Y _{m, LA/S} acid yield during maintenance (g acid/g sugar) - Y _x/pr yield (g cells/g protein) - specific sugar use rate during cell growth (g sugar/h·g cell) - specific sugar use rate during maintenance (g sugar/h·cell)     

Effect of oxygen on batch yogurt cultures

A yogurt culture (Streptococcus thermophilus 15HA + Lactobacillus delbrueckii subsp. bulgaricus 2-11) was studied in conditions of aerobic batch fermentation (10–40% dissolved oxygen in milk). The growth and acidification of S. thermophilus 15HA were stimulated at 20% oxygen concentration and the lactic acid process in a mixed culture was shortened by 1 h (2.5 h for the aerobic culture and 3.5 h for the anaerobic mixed culture). Streptococcus thermophilus 15HA oxygen tolerance was significantly impaired at oxygen concentrations in the milk above 30%. Though S. thermophilus 15HA was able to overcome to some extent the impact of high oxygen concentration (40%), the lactic acid produced was insufficient to coagulate the milk casein (4.0 g lactic acid l⁻¹ in the mixed culture and 3.8 g lactic acid l⁻¹ in the pure culture). A dramatic decrease in the viable cell count of L. delbrueckii subsp. bulgaricus 2-11 in the pure and mixed cultures was recorded at 30% dissolved oxygen. This revised version was published online in July 2006 with corrections to the Cover Date.     

Studies on exopolysaccharide release by diazotrophic batch cultures of Cyanospira capsulata

Summary Diazotrophic batch cultures of Cyanospira capsulata producing large amounts of a soluble exopolysaccharide (EPS) were studied over a period of about 30 days under continuous illumination. The thickness of the capsule surrounding the trichomes remained almost the same throughout the growth phases and the EPS was continuously released into the medium at a rate which was roughly constant throughout the culture period. A mean EPS productivity of about 6 g m^–2 day^–1 was attained. Purified EPS samples exhibited a saccharidic composition consisting of four neutral sugars (glucose, mannose, fucose and arabinose) and galacturonic acid in a molar ratio of 1:1:1:1:2, respectively. The EPS was also characterized by the presence of pyruvic residues and by a protein content of about 2%. O-Acetyl groups and sulphate residues were not detected. The massive release of this polysaccharidic material into the liquid medium made the cultures progressively more viscous. Offprint requests to: M. Vincenzini     

Parallel steady state studies on a milliliter scale accelerate fed‐batch bioprocess design for recombinant protein production with Escherichia coli

In general, fed‐batch processes are applied for recombinant protein production with Escherichia coli (E. coli). However, state of the art methods for identifying suitable reaction conditions suffer from severe drawbacks, i.e. direct transfer of process information from parallel batch studies is often defective and sequential fed‐batch studies are time‐consuming and cost‐intensive. In this study, continuously operated stirred‐tank reactors on a milliliter scale were applied to identify suitable reaction conditions for fed‐batch processes. Isopropyl β‐d ‐1‐thiogalactopyranoside (IPTG) induction strategies were varied in parallel‐operated stirred‐tank bioreactors to study the effects on the continuous production of the recombinant protein photoactivatable mCherry (PAmCherry) with E. coli. Best‐performing induction strategies were transferred from the continuous processes on a milliliter scale to liter scale fed‐batch processes. Inducing recombinant protein expression by dynamically increasing the IPTG concentration to 100 µM led to an increase in the product concentration of 21% (8.4 g L^?1) compared to an implemented high‐performance production process with the most frequently applied induction strategy by a single addition of 1000 µM IPGT. Thus, identifying feasible reaction conditions for fed‐batch processes in parallel continuous studies on a milliliter scale was shown to be a powerful, novel method to accelerate bioprocess design in a cost‐reducing manner. © 2016 American Institute of Chemical Engineers Biotechnol. Prog., 32:1426–1435, 2016     

Biphasic nitrogenase activity in Azospirillum brasilense in long lasting batch cultures

Long lasting batch cultures of Azospirillum brasilense SP 7 ATCC 29145 grown in liquid malate medium for 8–14 days without any fixed nitrogen source exhibited a biphasic nitrogenase activity, when incubated under gas atmospheres of 99.0% N₂ and 1.0% O₂ or 99.5% N₂ and 0.5% O₂ respectively. Maximum specific nitrogenase activity was 1100 nmol C₂H₄·mg protein^-1·h^-1. Poly-3-hydroxybutanoic acid (PHBA) synthesis and growth of the cells also showed two phases. Maxima and minima of glutamine synthetase activity developed synchronously with nitrogenase activity, whereas those of glutamate dehydrogenase and alanine aminotransferase were reverse. During a 192 h period of growth protein increased 3–4-fold and PHBA 25 fold. At maximum accumulation of the polymer the PHBA-nitrogen ratio was 6:1 or 8:1. Azospirillum brasilense was also able to fix nitrogen on agar surfaces exposed to air, but nitrogen fixation was monophasic under these conditions during a 14 d period. Specific nitrogenase activity was dependent on the type and concentration of the source of fixed nitrogen (leucine, ammonia) in solidified media. With 1 mM leucine maximum specific nitrogenase activity was 110 nmol C₂H₄·mg protein^-1·h^-1.Non-Standard Abbreviations PHBA poly-3-hydroxybutanoic acid - TAPS tris(hydroxymethyl)methylaminopropane sulfonic acid - TES N-tris(hydroxymethyl)methyl-2-aminoethane sulfonic acid - TRICINE N-tris(hydroxymethyl)methylglycine - TRIS tris(hydroxymethyl)aminomethane     

Application of data consistency tests and new parameter estimation methods to microbial growth on corn dust in batch culture

The microorganism Candida utilis was grown on both filtered and unfiltered substrate obtained from enzymatic hydrolysis of starch in corn dust. For growth on filtered substrate, the average integrated biomass energetic yield value based on biomass-substrate data was η = 0.55 and for growth on unfiltered substrate an average yield value of η = 0.59 was obtained. Material and energy balances showed that the presence of unfiltered corn residue in the media had no significant effect on the yields. Statistical methods were developed and used to obtain best estimates of the growth parameters. Values of the biomass energetic yield corrected for maintenance (η_max = 0.619) and the maintenance coefficient (m_e = 0.043) were obtained for growth on filtered substrate. Values of η_max = 0.741 and m_e = 0.142 were obtained for the growth on unfiltered substrate. The consistency of data and parameter estimates was relatively good for filtered substrate; however, parameter estimates for unfiltered substrate were not consistent. Growth experiments without filtration of the products of starch hydrolysis resulted in protein-enriched products with about 39.73% protein.     

A fed‐batch based cultivation mode in Escherichia coli results in improved specific activity of a novel chimeric‐truncated form of tissue plasminogen activator

Aims

A novel chimeric‐truncated form of tissue‐type plasminogen activator (t‐PA) with improved fibrin affinity and resistance to PAI was successfully produced in CHO expression system during our previous studies. Considering advantages of prokaryotic expression systems, the aim in this study was to produce the novel protein in Escherichia coli (BL21) strain and compare the protein potency in batch and fed‐batch processes.

Methods and Results

The expression cassette for the novel t‐PA was prepared in pET‐28a(+). The E. coli expression procedure was compared in traditional batch and newly developed fed batch, EnBase^® Flo system. The protein was purified in soluble format, and potency results were identified using Chromolize t‐PA Assay Kit. The fed‐batch fermentation mode, coupled with a Ni‐NTA affinity purification procedure under native condition, resulted in higher amounts of soluble protein, and about a 30% of improvement in the specific activity of the resulted recombinant protein (46·66 IU mg^?1) compared to traditional batch mode (35·8 IU mg^?1).

Conclusions

Considering the undeniable advantages of expression in the prokaryotic expression systems such as E. coli for recombinant protein production, applying alternative methods of cultivation is a promising approach. In this study, fed‐batch cultivation methods showed the potential to replace miss‐folded formats of protein with proper folded, soluble form with improved potency.

Significance and Impact of the Study

Escherichia coli expression of recombinant proteins still counts for nearly 40% of marketed biopharmaceuticals. The major drawback of this system is the lack of appropriate post‐translational modifications, which may cause potency loss/decline. Therefore, applying alternative methods of cultivation as investigated here is a promising approach to overcome potency decrease problem in this protein production system.     

Expression of mutations and protein release by yeast conditional autolytic mutants in batch and continuous cultures

Thermosensitive mutant strains of Saccharomyces cerevisiae that fail to generate an osmotically stable cell wall when grown at a non-permissive temperature release their cell contents upon expression of the mutation. Therefore, they may represent an alternative for the production of homologous or heterologous protein preparations. In order to analyse the expression of two of these mutations, lyt2 and slt2, we grew the corresponding strains under precisely defined conditions in batch and continuous fermentors. A switch in the temperature of batch cultures from 24° C to 37° C determined lysis of the cells with a significant release of intracellular enzymes. These include alkaline phosphatase and periplasmic proteins such as glucan-degrading enzymes, the pattern of cell lysis and protein release being maintained for about 6 h. One-stage continuous cultures of a lyt2 mutant were maintained for long periods at 37° C; a fraction of the population lysed and released the indicated proteins, but eventually a revertant of the lytic phenotype was selected. To avoid this, a two-stage continuous culture system was developed by connecting two fermentors in series, the effluent from the first one at 24°C being fed to the second one adjusted to 37° C. A steady state of cell lysis and protein liberation was reached in the second-stage fermentor without any evidence of selection of revertants. This system can be very useful for developing conditions for the use of yeast strains to produce protein preparations. Correspondence to: C. Nombela     

The potential of random forest and neural networks for biomass and recombinant protein modeling in Escherichia coli fed‐batch fermentations

Product quality assurance strategies in production of biopharmaceuticals currently undergo a transformation from empirical “quality by testing” to rational, knowledge‐based “quality by design” approaches. The major challenges in this context are the fragmentary understanding of bioprocesses and the severely limited real‐time access to process variables related to product quality and quantity. Data driven modeling of process variables in combination with model predictive process control concepts represent a potential solution to these problems. The selection of statistical techniques best qualified for bioprocess data analysis and modeling is a key criterion. In this work a series of recombinant Escherichia coli fed‐batch production processes with varying cultivation conditions employing a comprehensive on‐ and offline process monitoring platform was conducted. The applicability of two machine learning methods, random forest and neural networks, for the prediction of cell dry mass and recombinant protein based on online available process parameters and two‐dimensional multi‐wavelength fluorescence spectroscopy is investigated. Models solely based on routinely measured process variables give a satisfying prediction accuracy of about ± 4% for the cell dry mass, while additional spectroscopic information allows for an estimation of the protein concentration within ± 12%. The results clearly argue for a combined approach: neural networks as modeling technique and random forest as variable selection tool.     

Yields of alginates produced by fluorescent pseudomonads in batch culture

Summary Saprophytic and plant pathogenic fluorescent pseudomonads are possible sources of bacterial alginates to be used as substitutes for algal alginates for certain commercial applications. In this study, a total of 115 strains of fluorescentPseudomonas species (P. cichorii, P. fiuorescens, P. syringae andP. viridiflava) were tested for yields of alginates when grown in batch culture in a proprietary liquid medium (PLM). The PLM contained either fructose or glucose (both at 5%, w/v) as the primary carbon and energy source. For comparison, selected strains were also grown in a modified Vogel and Bonner medium (MVBM) containing gluconate (5%, w/v) and formulated to support maximal alginate production by the human pathogenP. aeruginosa. After five days of incubation at 24°C with shaking (250–300 r.p.m.), alginates were harvested from the culture fluids by precipitation with three volumes of isopropanol. Maximum yields of alginates, based on assays for uronic acid content of precipitable material, were 5 g L^–1 for PLM with fructose, 3 g L^–1 for PLM with glucose and 9 g L^–1 for MVBM.Reference to a brand or firm name does not constitute an endorsement by the US Department of Agriculture over others of a similar nature not mentioned.     

A mathematical model for RNA bacteriophage production in batch culture

The interaction between male-specific RNA phages and bacterial cells as well as the complete life cycle of RNA phages in the host cells are complicated phenomena. In this study, a mathematical model is proposed to describe the kinetics of RNA phage production in batch culture. The model consists of several important considerations: (1) adsorption and desorption of phages on cell pili, (2) injection and transport of viral RNA, (3) viral protein synthesis, (4) phage maturation, and (5) cell lysis. Experimental data of MS2 RNA phage production in E. coli C 300o bacteria culture were used to evaiuate the model parameters. Reasonably good fit was obtained between the model and one set of data. However, simulation study based on the estimated parameter values revealed a discrepancy between experimental observation and model prediction. It seems that variation both in F-piliation and in the competence of cells to be infected by phages through different phasae of growth must be taken into account in order to make the model useful.     

Hydrolysis of rice bran oil using immobilized lipase in a stirred batch reactor

Candida cylindracea lipase was immobilized by adsorption on acid washed glass beads. It was observed that protein loading of the support depends on the size of the particle, with smaller particle containing higher amount of protein per unit weight. Initial reaction rate linearly varied up to enzyme concentration of 17.25 U/mL. Amount of free fatty acids produced was linearly proportional up to the enzyme loading of 1650 μg/g of bead. Achievement of chemical equilibrium took longer time in the case of less protein loading. Degree of hydrolysis was found to decrease in second and third consecutive batch operations on repeated use of immobilized lipase.     

Enzymatic modification of vegetable protein: Mechanism,kinetics, and production of soluble and partially soluble protein in a batch reactor

Enzymatic hydrolysis of insoluble soybean protein by a protease enzyme produced by Penicillium duponti K 1104, was investigated in a batch reactor. The reaction conditions were 30–55°C and pH 3.4–3.7. The mechanism of solubilization of the insoluble protein by the Penicillium duponti enzyme was deduced from a series of experiments. Kinetic models were developed that involved adsorption followed by peptic digestion of protein, inhibition of low-molecular-weight peptides, and enzyme deactivation. The uncoupled kinetic parameters were estimated using the Marquardt nonlinear parameter estimation algorithm. A bang–bang production of soluble and partially soluble protein is suggested for higher productivity. The essential amino acids pattern of the enzyme-Hydrolyzed soy protein was comparable with the unhydrolyzed protein isolate. Aggregation of the soluble protein for an extended time was observable. The low-molecular-weight soluble protein was incorporated into noncarbonated beverages. The amount of protein that could be incorporated into a can of 355 ml noncarbonated beverage, without observable changes in the optical density and also aggregation of the protein, was 2.5 g soluble protein. Beverages with caramel color showed excessive decrease in optical density and precipitation. The kinetics and diffusion in a multipore immobilized-enzyme recycle reactor will be considered in part II of this series.     

Production of cellulases in batch culture using a mutant strain of Trichoderma reesei growing on soluble carbon source

Trichoderma reesei Rut-C30 is a highly derepressed mutant which synthesised active cellulases in culture media containing glucose and lactose as the only carbon sources. The maximum biomass, filter paper and specific filter paper activities for cell growth on 20 g glucose l^–1 were 20 g dry cell wt l^–1, 1.9 FPU ml^–1 and 4.8 FPU mg^–1 protein respectively, while on 40 g glucose l^–1 were 25 g dry cell wt l^–1, 4.5 FPU ml^–1 and 6.2 FPU mg^–1 protein, respectively. This strain had a higher specific filter paper activity (6.2 FPU mg^–1 protein) than was produced by other T. reesei mutants (3.6 FPU mg^–1 protein).     

Zymobacter palmae pyruvate decarboxylase production process development: Cloning in Escherichia coli,fed‐batch culture and purification

Pyruvate decarboxylase (PDC) is responsible for the decarboxylation of pyruvate, producing acetaldehyde and carbon dioxide and is of high interest for industrial applications. PDC is a very powerful tool in the enzymatic synthesis of chiral amines by combining it with transaminases when alanine is used as amine donor. However, one of the main drawback that hampers its use in biocatalysis is its production and the downstream processing on scale. In this paper, a production process of PDC from Zymobacter palmae has been developed. The enzyme has been cloned and overexpressed in Escherichia coli. It is presented, for the first time, the evaluation of the production of recombinant PDC in a bench‐scale bioreactor, applying a substrate‐limiting fed‐batch strategy which led to a volumetric productivity and a final PDC specific activity of 6942 U L^?1h^?1 and 3677 U gDCW^?1 (dry cell weight). Finally, PDC was purified in fast protein liquid chromatography equipment by ion exchange chromatography. The developed purification process resulted in 100% purification yield and a purification factor of 3.8.