Enzyme controlled glucose auto-delivery for high cell density cultivations in microplates and shake flasks

Background

Here we describe a novel cultivation method, called EnBase?, or enzyme-based-substrate-delivery, for the growth of microorganisms in millilitre and sub-millilitre scale which yields 5 to 20 times higher cell densities compared to standard methods. The novel method can be directly applied in microwell plates and shake flasks without any requirements for additional sensors or liquid supply systems. EnBase is therefore readily applicable for many high throughput applications, such as DNA production for genome sequencing, optimisation of protein expression, production of proteins for structural genomics, bioprocess development, and screening of enzyme and metagenomic libraries.

Results

High cell densities with EnBase are obtained by applying the concept of glucose-limited fed-batch cultivation which is commonly used in industrial processes. The major difference of the novel method is that no external glucose feed is required, but glucose is released into the growth medium by enzymatic degradation of starch. To cope with the high levels of starch necessary for high cell density cultivation, starch is supplied to the growing culture suspension by continuous diffusion from a storage gel. Our results show that the controlled enzyme-based supply of glucose allows a glucose-limited growth to high cell densities of OD₆₀₀ = 20 to 30 (corresponding to 6 to 9 g l^-1 cell dry weight) without the external feed of additional compounds in shake flasks and 96-well plates. The final cell density can be further increased by addition of extra nitrogen during the cultivation. Production of a heterologous triosphosphate isomerase in E. coli BL21(DE3) resulted in 10 times higher volumetric product yield and a higher ratio of soluble to insoluble product when compared to the conventional production method.

Conclusion

The novel EnBase method is robust and simple-to-apply for high cell density cultivation in shake flasks and microwell plates. The potential of the system is that the microbial growth rate and oxygen consumption can be simply controlled by the amount (and principally also by the activity) of the starch-degrading enzyme. This solves the problems of uncontrolled growth, oxygen limitation, and severe pH drop in shaken cultures. In parallel the method provides the basis for enhanced cell densities. The feasibility of the new method has been shown for 96-well plates and shake flasks and we believe that it can easily be adapted to different microwell and deepwell plate formats and shake flasks. Therefore EnBase will be a helpful tool especially in high throughput applications.     

Fed-batch production of recombinant beta-galactosidase using the universal stress promoters uspA and uspB in high cell density cultivations

A high-level production system using the universal stress promoters uspA and uspB in a fed-batch cultivation based on minimal medium was designed. In development it was shown that a standard industrial fed-batch protocol could not be used for this purpose since it failed to induce the levels of product as compared to the basal level. Instead, a batch protocol followed by a low constant feed of glucose was shown to give full induction. The levels of the product protein, beta-galactosidase, corresponded to approximately 25% of the total protein. Higher levels were found using the uspA than uspB vectors where uspA showed considerably higher basal level. The data indicate that the sigma(70) regulated promoter, uspA, although affected by the alarmone guanosine tetraphosphate, ppGpp, worked partly in a similar manner to constitutive promoters. An industrial high cell density fed-batch cultivation on the basis of the suggested fed-batch protocol and the uspA promoter gave a final beta-galatosidase concentration of 7 g/L and a final cell concentration of 65 g/L. The heterogeneity in production of the individual cell was measured by fluorescence microscopy. The data show that there is a process time independent heterogeneity in production, which is suggested to be caused by heterogeneity in the substrate uptake rate of the individual cell.     

Solid state fermentation reactors: from lab scale to pilot plant

Relatively many workers in the world are studying different aspects in SSF processes but few are working on reactor design and scale-up. From about 10 years, we are developing reactors from lab scale to pilot plant, based on the same technology, reactor design and flowsheet to allow fermentation with a deep layer (up to 1 m in the pilot plant). These reactors have all a forced aeration and the possibility or not to agitate. Regulations of temperature and water content of the culture are monitored by a special device.     

Application of dielectric spectroscopy for monitoring high cell density in monoclonal antibody producing CHO cell cultivations

The application of dielectric spectroscopy was frequently investigated as an on-line cell culture monitoring tool; however, it still requires supportive data and experience in order to become a robust technique. In this study, dielectric spectroscopy was used to predict viable cell density (VCD) at industrially relevant high levels in concentrated fed-batch culture of Chinese hamster ovary cells producing a monoclonal antibody for pharmaceutical purposes. For on-line dielectric spectroscopy measurements, capacitance was scanned within a wide range of frequency values (100–19,490 kHz) in six parallel cell cultivation batches. Prior to detailed mathematical analysis of the collected data, principal component analysis (PCA) was applied to compare dielectric behavior of the cultivations. PCA analysis resulted in detecting measurement disturbances. By using the measured spectroscopic data, partial least squares regression (PLS), Cole–Cole, and linear modeling were applied and compared in order to predict VCD. The Cole–Cole and the PLS model provided reliable prediction over the entire cultivation including both the early and decline phases of cell growth, while the linear model failed to estimate VCD in the later, declining cultivation phase. In regards to the measurement error sensitivity, remarkable differences were shown among PLS, Cole–Cole, and linear modeling. VCD prediction accuracy could be improved in the runs with measurement disturbances by first derivative pre-treatment in PLS and by parameter optimization of the Cole–Cole modeling.     

Ethanol production from glucose and xylose by separated and co-culture processes using high cell density systems

Media containing xylose and/or glucose were tested utilizing Zymomonas mobilis or Saccharomyces diastaticus and Pichia stipitis. The best fermentation results were obtained in separated glucose (180 g/litre) and xylose (80 g/litre) fermentations utilizing Zymomonas mobilis and Pichia stipitis strains, respectively. In these conditions, the maximum ethanol concentrations achieved were 86·2 g/litre and 29 g/litre, respectively. The complete conversion of a glucose and xylose mixture (50 g/litre) was obtained using a respiratory deficient mutant of Saccharomyces diastaticus co-cultivated with Pichia stipitis in continuous culture. Using the co-culture process, the maximum ethanol concentration was 21·5 g/litre (Yp/s=0·45 g/g) and the maximum volumetric ethanol productivity was 4·3 g/(litre × h).     

Operation of an aerobic granular pilot scale SBR plant to treat swine slurry

A pilot-scale Sequencing Batch Reactor was operated during 307 days in order to treat swine slurry characterized by its high variable composition: organic and nitrogen applied loading rates and C/N ratio were 1.4–6.3 kg COD_s/(m³ d), 0.5–2.5 kg N/(m³ d) and 1.9–9.4 g COD_s/(g N), respectively. Aerobic granules successfully developed in the reactor and their physical properties remained rather stable despite the feeding composition variability. Organic and ammonia removal efficiency reached 61–73% and 56–77%, respectively, however ammonia was mainly oxidized to nitrite. The reactor had a good biomass retention capacity to select for granular biomass. However, its efficiency to retain the solids present in the feeding was low. Aerobic granulation in SBR systems appears as an interesting alternative to treat slurry in small livestock facilities where the implementation of anaerobic digestion systems is not a feasible option or the removal of nitrogenous compounds is required.     

The use of elements of the E. coli Ntr-system for the design of an optimized recombinant expression system for high cell density cultivations.

The inducible glnA promoter 2 of the E. coli glutamine synthetase gene is suitable as an expression unit for the production of recombinant proteins at low and high cell densities. It is active when the concentration of ammonium as the sole nitrogen source in the culture medium is below 1 mM. This nitrogen regulatory system was optimized by introduction of expression cassettes consisting of additional elements of the ntr-system. These artificial constructions result in enhanced recombinant gene expression in the production phase. Furthermore, the basic recombinant protein level during the growth phase is reduced due to a tighter promoter control. A three- to four-fold higher accumulation of chloramphenicol-acetyltransferase (as reporter protein) and of anti-EGF-receptor miniantibodies was achieved by increasing the amount of the final regulator molecule NtrC approximately P via plasmidal co-expression of the ntrC gene. The introduction of a modified glnA promoter 1 inverse to glnAp2 lowered the basic activity of glnAp2 to about one half. It is assumed that under nitrogen excess conditions sigma 70-RNA polymerase binds at glnAp1 and thereby prevents most of the binding of sigma 54-RNA polymerase at glnAp2. The optimized expression systems were successfully applied in low and high cell density cultivations. In the fed-batch phase of high cell density cultivations recombinant protein formation was induced through external nitrogen limitation under FIA-controlled concentration of glucose as carbon source.     

A shaken disposable bioreactor system for controlled insect cell cultivations at milliliter‐scale

While wave‐mixed and stirred bag bioreactors are common devices for rapid, safe insect cell culture‐based production at liter‐scale, orbitally shaken disposable flasks are mainly used for screening studies at milliliter‐scale. In contrast to the two aforementioned bag bioreactor types, which can be operated with standard or disposable sensors, shaker flasks have not been instrumented until recently. The combination of 250 mL disposable shake flasks with PreSens's Shake Flask Reader enables both pH and dissolved oxygen to be measured, as well as allowing characterization of oxygen mass transfer. Volumetric oxygen transfer coefficients (k_La‐values) for PreSens 250 mL disposable shake flasks, which were determined for the first time in insect cell culture medium at varying culture volumes and shaker frequencies, ranged between 4.4 and 37.9/h. Moreover, it was demonstrated that online monitoring of dissolved oxygen in shake flasks is relevant for limitation‐free growth of insect cells up to high cell densities in batch mode (1.6×10⁷ cells/mL) and for the efficient expression of an intracellular model protein.     

Hydrothermal treatment of wheat straw at pilot plant scale using a three-step reactor system aiming at high hemicellulose recovery, high cellulose digestibility and low lignin hydrolysis

A pilot plant (IBUS) consisting of three reactors was used for hydrothermal treatment of wheat straw (120-150 kg/h) aiming at co-production of bioethanol (from sugars) and electricity (from lignin). The first reactor step was pre-soaking at 80 degrees C, the second extraction of hemicellulose at 170-180 degrees C and the third improvement of the enzymatic cellulose convertibility at 195 degrees C. Water added to the third reactor passed countercurrent to straw. The highest water addition (600 kg/h) gave the highest hemicellulose recovery (83%). With no water addition xylose degradation occurred resulting in low hemicellulose recovery (33%) but also in high glucose yield in the enzymatic hydrolysis (72 g/100g glucose in straw). Under these conditions most of the lignin was retained in the fibre fraction, which resulted in a lignin rich residue with high combustion energy (up to 31 MJ/kg) after enzymatic hydrolysis of cellulose and hemicellulose.     

Biodegradation of VOCs from printing press air by an on-site pilot plant bioscrubber and laboratory scale continuous yeast cultures

The volatile organic compound composition (VOCs) of printing press air wasfound to contain mostly ethanol, but also ethyl acetate, 1-propanol, 2-propanol,1-methoxy-2-propanol and 3-ethoxy-1-propanol. A pilot plant bioscrubber inoculatedwith a mixed microbial population was constructed on-site. The bioscrubber wasable to treat the polluted gas efficiently. It, however, suffered from strong wall growthand blockages in the column. The efficiencies of the pilot plant and a bioreactor iscompared. The yeasts Candida guilliermondii and Saccharomyces cerevisiae known to tolerate ethanol were selected instead of mixed population to avoid the wall growth and blockages in the bioreactor. The removal of the VOCs both individually and as a complex mixture was tested in a microcultivation system and in continuous chemostat cultures with and without cell recycling. The Candida yeast could use all the compounds as a carbon source while growth of S. cerevisiae was markedly slower on the methoxylated and ethoxylated propanols. Best total removal of the VOCs was 99% and achieved by C. guilliermondii. The only compound that was not totally removable in the chemostat experiment with C. guilliermondii was 1-methoxy-2-propanol. In laboratory scale the total and volumetric removal of VOCs by C. guilliermondii was more efficient compared to the pilot plant encouraging to scale up and applying the yeast bioreactor to real field conditions.     

Cell separation from high cell density broths of Alcaligenes eutrophus by using a coagulant

Summary Alcaligenes eutrophus was successfully recovered from high cell density broths by pre-treatment with polyaluminium hydroxide chloride silicate as a coagulant at 36–90 mg Al/l. The optimum pH range for cell coagulation was 10–12. Subsequent centrifugation (45×g) and filtration (pore size 0.5 mm) gave a cell recovery of higher than 90%. The energy demand for cell recovery with the coagulant was only 3–11% of that without it.     

A measurement system to detect small plant movements

A measurement system based on a photodiode array technique is presented, together with some results from recordings of phototropic responses of Avena sativa L. (cv. Seger I) coleoptiles.
A commercial photodiode array (RL-256G) was used, controlled by a likewise commercial control board RC-301. Electronic circuits were built to connect the control board to the interface card IO-801 of an Apple IIe microcomputer. The circuits constitute a fast temporary memory, which mainly contains two shift registers and two timers. Programs, which control the measurements, have been written and are presented.
Detailed recordings of blue light induced phototropic movements are presented: resolution and other features of the equipment are discussed.     

Clarification of recombinant proteins from high cell density mammalian cell culture systems using new improved depth filters

Increasingly high cell density, high product titer cell cultures containing mammalian cells are being used for the production of recombinant proteins. These high productivity cultures are placing a larger burden on traditional downstream clarification and purification operations due to higher product and impurity levels. Controlled flocculation and precipitation of mammalian cell culture suspensions by acidification or using polymeric flocculants have been employed to enhance clarification throughput and downstream filtration operations. While flocculation is quite effective in agglomerating cell debris and process related impurities such as (host cell) proteins and DNA, the resulting suspension is generally not easily separable solely using conventional depth filtration techniques. As a result, centrifugation is often used for clarification of cells and cell debris before filtration, which can limit process configurations and flexibility due to the investment and fixed nature of a centrifuge. To address this challenge, novel depth filter designs were designed which results in improved primary and secondary direct depth filtration of flocculated high cell density mammalian cell cultures systems feeds, thereby providing single‐use clarification solution. A framework is presented here for optimizing the particle size distribution of the mammalian cell culture systems with the pore size distribution of the gradient depth filter using various pre‐treatment conditions resulting in increased depth filter media utilization and improved clarification capacity. Feed conditions were optimized either by acidification or by polymer flocculation which resulted in the increased average feed particle‐size and improvements in throughput with improved depth filters for several mammalian systems. Biotechnol. Bioeng. 2013; 110: 1964–1972. © 2013 Wiley Periodicals, Inc.     

Comparative proteomic analysis of high cell density cultivations with two recombinant Bacillus megaterium strains for the production of a heterologous dextransucrase

High cell density cultivations were performed under identical conditions for two Bacillus megaterium strains (MS941 and WH320), both carrying a heterologous dextransucrase (dsrS) gene under the control of the xylA promoter. At characteristic points of the cultivations (end of batch, initial feeding, before and after induction) the proteome was analyzed based on two dimensional gel electrophoresis and mass spectrometric protein identification using the protein database "bmegMEC.v2" recently made available.     

Growth limitation of Lemna minor due to high plant density

The effect of high population densities on the growth rate of Lemna minor (L.) was studied under laboratory conditions at 23 °C in a medium with sufficient nutrients. At high population densities, we found a non-linear decreasing growth rate with increasing L. minor density. Above a L. minor biomass of ca. 180 g dry weight (DW) m⁻², the net growth rate became negative. At a density of 9 g DW m⁻², a maximum relative growth rate of ca. 0.3 d⁻¹ was found. At very low densities (<9 g m⁻²), we observed an inverse density dependence (or Allee effect). Probably, this lower growth rate was due to lower local temperatures within such partly covered L. minor decks. On the basis of these experimental results and literature data, a simple model was created. To test the model, the density of duckweed in three different Dutch ditches was monitored for 9 weeks in spring. Within this period, full coverage of the ditches by duckweed was reached. The maximum density increased with rising air temperature. The model described the field data well, suggesting that crowding is an important factor in limitation of duckweed growth.     

Imputation of missing genotypes from sparse to high density using long-range phasing

Related individuals share potentially long chromosome segments that trace to a common ancestor. We describe a phasing algorithm (ChromoPhase) that utilizes this characteristic of finite populations to phase large sections of a chromosome. In addition to phasing, our method imputes missing genotypes in individuals genotyped at lower marker density when more densely genotyped relatives are available. ChromoPhase uses a pedigree to collect an individual's (the proband) surrogate parents and offspring and uses genotypic similarity to identify its genomic surrogates. The algorithm then cycles through the relatives and genomic surrogates one at a time to find shared chromosome segments. Once a segment has been identified, any missing information in the proband is filled in with information from the relative. We tested ChromoPhase in a simulated population consisting of 400 individuals at a marker density of 1500/M, which is approximately equivalent to a 50K bovine single nucleotide polymorphism chip. In simulated data, 99.9% loci were correctly phased and, when imputing from 100 to 1500 markers, more than 87% of missing genotypes were correctly imputed. Performance increased when the number of generations available in the pedigree increased, but was reduced when the sparse genotype contained fewer loci. However, in simulated data, ChromoPhase correctly imputed at least 12% more genotypes than fastPHASE, depending on sparse marker density. We also tested the algorithm in a real Holstein cattle data set to impute 50K genotypes in animals with a sparse 3K genotype. In these data 92% of genotypes were correctly imputed in animals with a genotyped sire. We evaluated the accuracy of genomic predictions with the dense, sparse, and imputed simulated data sets and show that the reduction in genomic evaluation accuracy is modest even with imperfectly imputed genotype data. Our results demonstrate that imputation of missing genotypes, and potentially full genome sequence, using long-range phasing is feasible.     

Selective evaluation of high density lipoprotein from mouse small intestine by an in situ perfusion technique

The small intestine (SI) is the second-greatest source of HDL in mice. However, the selective evaluation of SI-derived HDL (SI-HDL) has been difficult because even the origin of HDL obtained in vivo from the intestinal lymph duct of anesthetized rodents is doubtful. To shed light on this question, we have developed a novel in situ perfusion technique using surgically isolated mouse SI, with which the possible filtration of plasma HDL into the SI lymph duct can be prevented. With the developed method, we studied the characteristics of and mechanism for the production and regulation of SI-HDL. Nascent HDL particles were detected in SI lymph perfusates in WT mice, but not in ABCA1 KO mice. SI-HDL had a high protein content and was smaller than plasma HDL. SI-HDL was rich in TG and apo AIV compared with HDL in liver perfusates. SI-HDL was increased by high-fat diets and reduced in apo E KO mice. In conclusion, with our in situ perfusion model that enables the selective evaluation of SI-HDL, we demonstrated that ABCA1 plays an important role in intestinal HDL production, and SI-HDL is small, dense, rich in apo AIV, and regulated by nutritional and genetic factors.     

Feeding strategies enhance high cell density cultivation and protein expression in milliliter scale bioreactors

Miniature bioreactors under parallel fed‐batch operations are not only useful screening tools for bioprocess development but also provide a suitable basis for eventual scale‐up. In this study, three feeding strategies were investigated: besides the established intermittent feeding by a liquid handler, an optimized microfluidic device and a new enzymatic release system were applied for parallel fed‐batch cultivation of Escherichia coli HMS174(DE3) and BL21(DE3) strains in stirred‐tank bioreactors on a 10 mL scale. Lower fluctuation in dissolved oxygen (DO) and higher optical densities were measured in fed‐batch processes applying the microfluidic device or the enzymatic glucose/fructose release system (conversion of intermittently added sucrose by an invertase), but no difference in dry cell weights (DCW) were observed. With all three feeding strategies high cell densities were realized on a milliliter scale with final optical density measured at 600 nm (OD₆₀₀) of 114–133 and final DCW concentrations of 69–70 g L^–1. The effect of feeding strategies on the expression of two heterologous proteins was investigated. Whereas no impact was observed on the expression of the spider silk protein eADF4(C16), the fluorescence of enhanced green fluorescence protein (eGFP) was reproducibly lower, if an intermittent glucose feed was applied. Thus, the impact of feeding strategy on expression is strongly dependent on the E. coli strain and/or expressed protein. As a completely continuous feed supply is difficult to realize in miniature bioreactors, the enzymatic release approach from this study can be easily applied in all microfluidic system to reduce fluctuations of glucose supply and DO concentrations.