On-line monitoring of intracellular ATP concentration in Escherichia coli fermentations

A method was developed to provide a real-time measurement of intracellular adenosine 5'-triphosophate (ATP) concentrations in growing Escherichia coli. The bacteria to be monitored must first be modified by inserting the cDNA for firefly luciferase expressed from a constitutive promoter. Such a construct leads to constant specific activity of firefly luciferase during both the lag phase and exponential growth. When the luciferase substrate, D-luciferin, is added to the medium, ATP within the cells is utilized in the luciferase-catalyzed reaction that produces light. The light is carried from the bioreactor to a computer-based detector by an optical fiber. The detected per cell light emission varies during exponential growth. Analysis of cytoplasm extracts shows that this variance is related to changes in the ATP concentration, which ranges from 1 to 6 times the literature value for K(M). Experimental analyses demonstrated that inner filter effects are not a significant factor affecting the use of this system. The method was tested in a benchtop fermentor at cell densities above 13 g/L dry cell weight. A correction factor based on the accumulated light data is calculated and used in real time to account for consumption of luciferin from the culture broth by the light producing reaction. Dissolved oxygen concentrations must be kept above 15% of air saturation to ensure constant light output, but no detectable increase in oxygen demand is seen. The method does not significantly affect growth or production rates. (c) 1996 John Wiley & Sons, Inc.     

Identification of critical batch operating parameters in fed-batch recombinant E. coli fermentations using decision tree analysis

To develop a useful fermentation process model, it is first necessary to identify which batch operating parameters are critical in determining the process outcome. To identify critical processing inputs in large databases, we have explored the use of Decision Tree Analysis with the decision metrics of Gain (i.e., Shannon Entropy changes), Gain Ratio, and a multiple hypergeometric distribution. The usefulness of this approach lies in its ability to treat "categorical" variables, which are typical of archived fermentation databases, as well as "continuous" variables. In this work, we demonstrate the use of Decision Tree Analysis for the problem of optimizing recombinant green fluorescent protein production in E. coli. A database of 85 fermentations was generated to examine the effect of 15 process input parameters on final biomass yield, maximum recombinant protein concentration, and productivity. The use of Decision Tree Analysis led to a considerable reduction in the fermentation database through the identification of the significant as well as insignificant inputs. However, different decision metrics selected different inputs and different numbers of inputs to classify the data for each output.     

On-line monitoring of mammalian cell and yeast fermentations with a commercial biochemical analyzer

A commercial analyzer was tested for on-line monitoring of fermentations. A new sample block was constructed to effectively degas the fermentation broth. The robust analyzer accurately measured glucose up to 110 mmol/l and lactate up to 21 mmol/l at a frequency of 1 measurement per 2 minutes directly in suspensions of mammalian and yeast cells.     

On-line monitoring of nine different batch cultures of E. coli by mid-infrared spectroscopy, using a single spectra library for calibration

A single spectra library was used to monitor on-line, by mid-infrared spectroscopy, nine different batch cultures of Escherichia coli performed with various medium compositions, including chemically complex formulations. Whereas the classic chemometrics approach would have required the preparation and measurement of hundreds of standards, only six spectra were included in the library. These included the molar absorbance of the four main metabolites (i.e. glucose, glycerol, ammonium and acetate), and the remaining two were drift spectra found by factor analysis. The accuracy of the prediction was not altered by a change of the carbon source, the ammonium concentration or even the addition of chemically undefined compounds, such as yeast extract and peptone. The standard errors of prediction averaged over the nine experiments were 8.0, 12.3, 5.9 and 5.6 mM for glucose, glycerol, ammonium and acetate, respectively. Inclusion of two drift spectra in the library provided an estimation of how noisy an experiment was. This also allowed detection of batch cultures that require further investigation, namely runs which were subject to large signal drift or during which an unexpected compound was produced, without having to carry out time-consuming off-line analyses.     

On-line monitoring of ethanol,acetaldehyde and glycerol during industrial fermentations with Saccharomyces cerevisiae

Industrial fermentations carried out in a 500-1 bioreactor were monitored on-line by a prototype of a split-flow modified thermal biosensor. Acetaldehyde and glycerol in the extracellular broth were monitored over the first 48 h of fed-batch fermentations. The aim was to determine the usefulness of these secondary metabolites for on-line monitoring and control. When fermentation of the 13–16 g/l batch sugar was monitored, using immobilised aldehyde dehydrogenase, the acetaldehyde reached a peak value of 0.3 g/l. With immobilised alcohol oxidase a much larger peak of 3.5 g/l ethanol was seen immediately after the acetaldehyde peak. When glycerokinase was used a delayed peak of 1 g/l glycerol was monitored. Of the three metabolites monitored, the ethanol proved the most valuable indicator of suitable timing for the start of the feeding phase and later for controlling and preventing overfeed using the on-line biosensor system.     

In situ 2D fluorometry and chemometric monitoring of mammalian cell cultures

The main objective of the present study was to investigate the use of in situ 2D fluorometry for monitoring key bioprocess variables in mammalian cell cultures, namely the concentration of viable cells and the concentration of recombinant proteins. All studies were conducted using a recombinant Baby Hamster Kidney (BHK) cell line expressing a fusion glycoprotein IgG1-IL2 cultured in batch and fed-batch modes. It was observed that the intensity of fluorescence signals in the excitation/emission wavelength range of amino acids, vitamins and NAD(P)H changed along culture time, although the dynamics of single fluorophors could not be correlated with the dynamics of the target state variables. Therefore, multivariate chemometric modeling was adopted as a calibration methodology. 2D fluorometry produced large volumes of redundant spectral data, which were first filtered by principal components analysis (PCA). Then, a partial least squares (PLS) regression was applied to correlate the reduced fluorescence maps with the target state variables. Two validation strategies were used to evaluate the predictive capacity of the developed PLS models. Accurate estimations of viable cells density (r(2) = 0.95; 99.2% of variance captured in the training set; r(2) = 0.91; 97.7% of variance captured in the validation set) and of glycoprotein concentration (r(2) = 0.99 and 99.7% of variance captured in the training set; r(2) = 0.99 and 99.3% of variance captured in the validation set) were obtained over a wide range of reactor operation conditions. The results presented herein confirm that 2D fluorometry constitutes a reliable methodology for on-line monitoring of viable cells and recombinant protein concentrations in mammalian cell cultures.     

Characterization of lycopene-overproducing E. coli strains in high cell density fermentations

Previous work identified two recombinant strains of Escherichia coli capable of significant lycopene overproduction. These strains were constructed by superimposing the deletion of three genes, selected through combinatorial and systematic searches of the metabolic landscape, onto a previously engineered strain over-expressing critical genes in the lycopene biosynthesis pathway. In this paper, we characterize the performance of these two strains in comparison to the parental, pre-engineered strain. Specifically, high cell density fermentations were performed after identifying optimized putative operating parameters. High oxygen levels and increased pH values were found to be critical for increasing both specific and volumetric product titers. Carbon balances suggest linkages between glutamate, NADPH, formate, and alanine levels with lycopene overproduction. Furthermore, lycopene production reached nearly 220 mg/l from approximately 27 g dry cell weight/l in these reactors, which is the highest value reported to date for E. coli.     

Assessment of physiological conditions in E. coli fermentations by epifluorescent microscopy and image analysis

The development of monitoring methods for assessing the physiological state of microorganisms during recombinant fermentation processes has been encouraged by the need to evaluate the influence of processing conditions in recombinant protein production. In this work, a technique based on microscopy and image analysis was developed that allows the simultaneous quantification of parameters associated with viability and fluorescent protein production in recombinant Escherichia coli fermentations. Images obtained from light microscopy with phase contrast are used to assess the total number of cells in a given sample and, from epifluorescence microscopy, both protein producing and injured cells are evaluated using two different fluorochromes: propidium iodide and enhanced yellow fluorescent protein. This technique revealed the existence of different cell populations in the recombinant E. coli fermentation broth that were evaluated along four batch fermentations, complementing information obtained with standard techniques to study the effects of the temperature and induction time in recombinant protein production processes. © 2009 American Institute of Chemical Engineers Biotechnol. Prog., 2009     

Tunable recombinant protein expression with E. coli in a mixed-feed environment

Controlling the recombinant protein production rate in Escherichia coli is of utmost importance to ensure product quality and quantity. Up to now, only the genetic construct, introduced into E. coli, and the specific growth rate of the culture were used to influence and stir the productivity. However, bioprocess technological means to control or even tune the productivity of E. coli are scarce. Here, we present a novel method for the process-technological control over the recombinant protein expression rate in E. coli. A mixed-feed fed-batch bioprocess based on the araBAD promoter expression system using both d-glucose and l-arabinose as assimilable C-sources was designed. Using the model product green fluorescent protein, we show that the specific product formation rate can be efficiently tuned even on the cellular level only via the uptake rate of l-arabinose. This novel approach introduces an additional degree of freedom for the design of recombinant bioprocesses with E. coli. We anticipate that the presented method will result in significant quality and robustness improvement as well as cost and process time reduction for recombinant bacterial bioprocesses in the future.     

Modelling of E.coli fermentations: comparison of multicompartment and variable structure models

Two novel approaches for modelling processes that can be described by a sequence of phases (metabolic states) are suggested and applied to Escherichia Coli fermentations. The first approach uses a multi-compartment model framework, coupled with knowledge-based logic. In the second approach the multi-compartment model is reduced into the Variable Structure Model consisting of a battery of alternative submodels, each of which qualitatively represents one of the process steps. Furthermore, simulated intracellular process variables are compared with the output of a multi-wavelength fluorosensor and excitation-emission pairs that predict best these variables are identified.     

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.     

Regulated secretion and purification of recombinant antibodies in E. coli.

A plasmid for optimized protein expression of recombinant Fv antibodies (pOPE) in E. coli was used to express the variable domains of the murine monoclonal antibody HD39 specific for the human B-cell surface antigen CD22. The production of Fv antibodies by pOPE can be regulated over a wide range by varying the IPTG concentration. Antibodies that can discriminate between secreted and nonsecreted Fv antibody fragments were used to show that secretion is the limiting step for the production of functional Fv antibodies. IPTG concentrations above 20 microM increased the total antibody production, but did not yield larger amounts of secreted Fv antibodies. The addition of five histidines to the C terminus facilitates an easy single-step enrichment procedure based on immobilized metal affinity chromatography.     

Expression and characterization of recombinant bovine lactoferrin in E. coli

Lactoferrin is a member of the transferrin family of iron-binding proteins with a number of properties, including antibacterial activity against a broad spectrum of Gram-negative and Gram-positive bacteria. bovine lactoferrin cDNA was isolated, cloned and expressed as a fusion protein. The amino acid sequence of the fusion was analyzed and compared with other species. Crystallographic data were used to compare structural differences between bovine and human lactoferrin in 3-D models. A thioredoxin fusion protein was expressed and shown to have a different molecular weight compared with native bLf. After purification using Ni-NTA, the yield of recombinant bovine lactoferrin was 15.3 mg/l with a purity of 90.3 %. Recombinant bLf and pepsin-digested rbLf peptides demonstrated antibacterial activity of 79.8 and 86.9 %, respectively. The successful expression of functional, active and intact rbLf allows us to study the biochemical interactions of antimicrobial proteins and peptides and will facilitate their study as immunomodulators.     

大肠杆菌异源重组蛋白质的变性与复性

描述了大肠杆菌异源重组蛋白质的形成、制备、变性和复性,综述了国内外变性、复性的有效方法。     

重组人干扰素—β在大肠杆菌中的表达与活性分析

利用定点突变技术将人干扰素-β第17位半胱氨酸编码序列突变为丝氨酸(IFN-βser17),DNA序列分析证明了其核苷酸序列的正确性,并在大肠杆菌TAP106中获得高效表达,IFN-βser17表达量达20%,用Westemblot得到单一条带,细胞病变抑制法测定其比活性达(2～3)×107U/mg.INF-βser17的比活性和稳定性均超过天然人IFN-β.     

Protein expression in E. coli minicells by recombinant plasmids.

The polypeptides synthesized in E. coli minicells from recombinant plasmids containing DNA fragments from cauliflower mosaic virus, Drosophila melanogaster, and mouse mitochondria were examined. Molecularly cloned fragments of cauliflower mosaic virus DNA directed the synthesis of high levels of three polypeptides, which were synthesized entirely from within the cloned virus DNA fragments independent of their insertion into the plasmid vehicles. Several fragments of D. melanogaster DNA were capable of initiating polypeptide synthesis; however, termination of these polypeptides was dependent upon the insertion into the plasmid vehicle. The majority of D. melanogaster DNA fragments examined did not direct the detectable synthesis of any polypeptides. Insertion of DNA into the Eco RI site of ColE1 and pSC101 plasmids resulted in the altered expression of plasmid-encoded polypeptides. In the case of ColE1, this site of insertion lies within the colicin E1 structural gene, and insertion of foreign DNA into the site results in the synthesis of an inactive truncated colicin E1 molecule. It is probable that the Eco RI site in pSC101 lies within the structural gene for a polypeptide involved in tetracycline resistance, and insertion of DNA into this site may also result in the synthesis of a truncated or elongated polypeptide.     

Targeted amino-terminal acetylation of recombinant proteins in E. coli

One major limitation in the expression of eukaryotic proteins in bacteria is an inability to post-translationally modify the expressed protein. Amino-terminal acetylation is one such modification that can be essential for protein function. By co-expressing the fission yeast NatB complex with the target protein in E.coli, we report a simple and widely applicable method for the expression and purification of functional N-terminally acetylated eukaryotic proteins.     

Expression of murine interleukin-2 cDNA in E. coli and biological activities of recombinant murine interleukin-2

Murine interleukin-2 (MIL-2) cDNA was inserted into an expression vector carrying an Escherichia coli tryptophan promoter and was expressed in E. coli. Recombinant MIL-2 produced by E. coli supported the growth of murine CTLL-2 cells, but not that of human T-cell blasts. Recombinant MIL-2 strongly inhibited the binding of recombinant human IL-2 (HIL-2) to murine responder cells, but only very weakly inhibited the binding to human responder cells. Moreover, recombinant MIL-2 induced secondary alloantigen specific cytotoxic T lymphocytes (2 degrees CTL) from memory CTL and activated natural killer (NK) cells in murine systems in the same manner as recombinant HIL-2. The results suggest that the species hierarchy (that MIL-2 derived from native cell culture does not act on human T-cells) is due to the protein moiety, not the sugar moiety, and is to be ascribed to the difference in binding affinity of MIL-2 and HIL-2 to murine and human responder cells respectively, and that recombinant MIL-2 shares identical biological and immunological activities with recombinant HIL-2. Thus, MIL-2 might be a convenient tool for extensive studies of the pharmacological and physiological activities of IL-2 in murine models.     

Optimized conditions for high-level expression and purification of recombinant human interleukin-2 in E. coli

Interleukin-2 (IL-2), a potent cytokine has been used in anti-cancer therapy for over a decade now. IL-2, originally identified as a growth factor for T lymphocytes is a 15 kDa hydrophobic glycoprotein that induces the activation, clonal proliferation and differentiation of T and B-lymphocytes and enhances the cytotoxicity of monocytes and natural killer (NK) cells. Here, we report a simple method for the cloning, high-level expression and purification of IL-2 protein, which can be easily extended to other bioactive therapeutic proteins. The IL-2 gene was amplified from human spleen cDNA and cloned in a prokaryotic (E. coli) expression system. An optimal expression of the IL-2 protein was determined by varying the expression conditions like temperature, inducer concentration and duration of induction. The protein was expressed as inclusion bodies and a panel of reagents including detergents, urea and guanidine hydrochloride were used to solubilize it. After solubilization, the protein was renatured and subjected to a single step gel-filtration chromatography to yield immunobioactive IL-2 protein with > 99% purity.