On-line simultaneous monitoring of glucose and acetate with FIA during high cell density fermentation of recombinant E. coli

Control algorithms and strategies of feeding for fed-batch fermentation of Escherichia coli: a review of 40 years of experience

Fed-batch cultivation is a well-known type of submerged fermentation that is frequently used in manufacture of recombinant proteins and various kinds of enzymes, owing to its ability to produce products with high concentrations and high efficiency. In fed-batch culture, several issues must be considered; most of them are also presented in batch culture. However, feed flow rate calculation only corresponds to fed-batch fermentation and its value has a significant impact on productivity, efficiency, final concentration of product, formation of by-products, and viscosity of the culture. From this background, the present review article is an effort to gather the information on feeding strategies for fed-batch cultivation of Escherichia coli, which is a well-known microorganism in the production of recombinant proteins and industrial enzymes, especially for therapeutic applications. Moreover, this review is an aid to comprehend and compare the fundamental concept of different feeding strategies and their advantages and drawbacks.

High throughput automated microbial bioreactor system used for clone selection and rapid scale-down process optimization

High throughput automated fermentation systems have become a useful tool in early bioprocess development. In this study, we investigated a 24 x 15 mL single use microbioreactor system, ambr 15f, designed for microbial culture. We compared the fed‐batch growth and production capabilities of this system for two Escherichia coli strains, BL21 (DE3) and MC4100, and two industrially relevant molecules, hGH and scFv. In addition, different carbon sources were tested using bolus, linear or exponential feeding strategies, showing the capacity of the ambr 15f system to handle automated feeding. We used power per unit volume (P/V) as a scale criterion to compare the ambr 15f with 1 L stirred bioreactors which were previously scaled‐up to 20 L with a different biological system, thus showing a potential 1,300 fold scale comparability in terms of both growth and product yield. By exposing the cells grown in the ambr 15f system to a level of shear expected in an industrial centrifuge, we determined that the cells are as robust as those from a bench scale bioreactor. These results provide evidence that the ambr 15f system is an efficient high throughput microbial system that can be used for strain and molecule selection as well as rapid scale‐up. © 2017 The Authors Biotechnology Progress published by Wiley Periodicals, Inc. on behalf of American Institute of Chemical Engineers Biotechnol. Prog., 34:58–68, 2018

A Comparative Proteome Analysis of Escherichia coli ΔrelA Mutant Cells

The bacterial RelA-dependent stringent response exerts a strong influence over various processes. In this work, the impact of the relA gene mutation in Escherichia coli cells was evaluated by a quantitative proteomics analysis, employing stable-isotope labeling and high-resolution mass spectrometry. Chemostat cultures of E. coli W3110 and ΔrelA mutant strains were performed at two dilution rates (0.1 and 0.2 h⁻¹) to assess the influence of the relA gene mutation in steady-state protein levels. A total of 121 proteins showed significant alterations in their abundance when comparing the proteome of mutant to wild-type cells. The relA gene mutation induced changes on key cellular processes, including the amino acids and nucleotide biosynthesis, the lipid metabolism, transport activities, transcription and translation processes, and responses to stress. Furthermore, some of those changes were more pronounced under specific growth conditions, as the most significant differences in protein ratios were observed at one of the dilution rates. An effect of the relA gene mutation in the acetate overflow was also observed, which confers interesting characteristics to this mutant strain that could be useful in the production of recombinant proteins. Overall, these results provide a valuable insight into the E. coli stringent response under defined steady-state conditions, suggesting that this stress response might influence multiple metabolic processes like the acetate overflow or the catabolite repression.

Monitoring lipase/esterase activity by stopped flow in a sequential injection analysis system using p-nitrophenyl butyrate

Lipases and esterases are biocatalysts used at the laboratory and industrial level. To obtain the maximum yield in a bioprocess, it is important to measure key variables, such as enzymatic activity. The conventional method for monitoring hydrolytic activity is to take out a sample from the bioreactor to be analyzed off-line at the laboratory. The disadvantage of this approach is the long time required to recover the information from the process, hindering the possibility to develop control systems. New strategies to monitor lipase/esterase activity are necessary. In this context and in the first approach, we proposed a lab-made sequential injection analysis system to analyze off-line samples from shake flasks. Lipase/esterase activity was determined using p-nitrophenyl butyrate as the substrate. The sequential injection analysis allowed us to measure the hydrolytic activity from a sample without dilution in a linear range from 0.05-1.60 U/mL, with the capability to reach sample dilutions up to 1000 times, a sampling frequency of five samples/h, with a kinetic reaction of 5 min and a relative standard deviation of 8.75%. The results are promising to monitor lipase/esterase activity in real time, in which optimization and control strategies can be designed.

Influence of the RelA Activity on E. coli Metabolism by Metabolite Profiling of Glucose-Limited Chemostat Cultures

Metabolite profiling of E. coli W3110 and the isogenic ΔrelA mutant cells was used to characterize the RelA-dependent stringent control of metabolism under different growth conditions. Metabolic profiles were obtained by gas chromatography–mass spectrometry (GC-MS) analysis and revealed significant differences between E. coli strains grown at different conditions. Major differences between the two strains were assessed in the levels of amino acids and fatty acids and their precursor metabolites, especially when growing at the lower dilution rates, demonstrating differences in their metabolic behavior. Despite the fatty acid biosynthesis being the most affected due to the lack of the RelA activity, other metabolic pathways involving succinate, lactate and threonine were also affected. Overall, metabolite profiles indicate that under nutrient-limiting conditions the RelA-dependent stringent response may be elicited and promotes key changes in the E. coli metabolism.

Production, purification and diagnostic application of filarial recombinant protein WbSXP-1 expressed in salt inducible Escherichia coli

Wuchereria bancrofti protein WbSXP-1 was identified and established as a potential candidate for the diagnosis of lymphatic filariasis. For the economic production of rWbSXP-1, osmotically (salt) inducible Escherichia coli GJ1158 was preferred. Cultivation and expression was optimized in 3 L airlift bioreactor (ALB) and was successfully extended to 30 L ALB. Purification of rWbSXP-1 his-tag protein was optimized in technical scale using FPLC and the maximal recovery of rWbSXP-1 with significant level of purity was achieved using the combination of IMAC and gel filtration. Quality criteria for immuno-reactivity of purified rWbSXP-1 were established for diagnostic applications. Enhancement of sensitivity in rapid diagnostic format was optimized to effectively detect weak to strong antibody reactivity in individuals exposed to lymphatic filariasis. Performance of the rapid format during field evaluation was successful. The accelerated stability assessment of the rapid format satisfied the requirements of WHO-cGMP norms. This investigation presents a successful technical scale production and purification of rWbSXP-1 considering the future industrial application and an enhanced rapid flow through antibody assay for the diagnosis of human lymphatic filariasis.

Future aspects of bioprocess monitoring

Nature has the impressive ability to efficiently and precisely control biological processes by applying highly evolved principles and using minimal space and relatively simple building blocks. The challenge is to transfer these principles into technically applicable and precise analytical systems that can be used for many applications. This article summarizes some of the new approaches in sensor technology and control strategies for different bioprocesses such as fermentations, biotransformations, and downstream processes. It focuses on bio- and chemosensors, optical sensors, DNA and protein chip technology, software sensors, and modern aspects of data evaluation for improved process monitoring and control.

An electrochemical method for simultaneous detection and identification of Escherichia coli, Staphylococcus aureus and Salmonella choleraesuis using a glucose oxidase-peroxidase composite biosensor

Quantification of bacterial pollution by amperometric detection at 0.0 V of glucose consumption at a graphite-Teflon-glucose oxidase-peroxidase-ferrocene composite biosensor under flow injection conditions is reported. Using Escherichia coli as the model bacterium, the composition of the growing medium was optimized. A constant glucose concentration of 4.0 x 10(-4) M was added to the culture medium. The relative response to glucose, expressed as the ratio between the amperometric signal and the signal at incubation time t = 0 multiplied by 100, as a function of E. coli concentration, showed a typical behaviour. Limits of detection of 6.5 x 10(2) or 6.5 cfu mL(-1) were achieved after 3 or 7 h of incubation, respectively, with no pre-concentration step. The detection of bacteria did not affect the lifetime of the biosensor. The feasibility of the detection of Staphylococcus aureus and Salmonella choleraesuis throughout the glucose consumption measurement at the composite biosensor is also demonstrated. The capability of bacterial identification by evaluation of bacterial growth in the culture medium containing the antibiotics polymyxin B, vancomycin, erythromycin, bacitracin, chloramphenicol, tetracycline and ciprofloxacin, was investigated. Each micro-organism tested exhibited a different antibiotic susceptibility profile, thus suggesting the possibility of bacteria differentiation. A rapid methodology for screening of bacteria is proposed.

Evaluation of the effects and interactions of mixing and oxygen transfer on the production of Fab’ antibody fragments in Escherichia coli fermentation with gas blending

Fermentations carried out at 450-L and 20-L scale to produce Fab' antibody fragments indicated a serious problem to control levels of dissolved oxygen in the broth due to the large oxygen demand at high cell densities. Dissolved oxygen tension (DOT) dropped to zero during the induction phase and it was hypothesised that this could limit product formation due to inadequate oxygen supply. A gas blending system at 20-L scale was employed to address this problem and a factorial 2(2) experimental design was executed to evaluate independently the effects and interaction of two main engineering factors: agitation rate and DOT level (both related to mixing and oxygen transfer in the broth) on Fab' yields. By comparison to the non-gas blending system, results in the gas blending system at same scale showed an increase in the production of Fab' by 77% independent of the DOT level when using an agitation rate of 500 rpm level and by 50% at an agitation rate of 1,000 rpm with 30% DOT. Product localisation in the cell periplasm of >90% was obtained in all fermentations. Results obtained encourage further studies at 450-L scale initially, to evaluate the potential of gas blending for the industrial production of Fab' antibody fragments.