1
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Kemmer A, Cai L, Born S, Cruz Bournazou MN, Neubauer P. Enzyme-Mediated Exponential Glucose Release: A Model-Based Strategy for Continuous Defined Fed-Batch in Small-Scale Cultivations. Bioengineering (Basel) 2024; 11:107. [PMID: 38391593 PMCID: PMC10886149 DOI: 10.3390/bioengineering11020107] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2023] [Revised: 01/05/2024] [Accepted: 01/18/2024] [Indexed: 02/24/2024] Open
Abstract
Miniaturized cultivation systems offer the potential to enhance experimental throughput in bioprocess development. However, they usually lack the miniaturized pumps necessary for fed-batch mode, which is commonly employed in industrial bioprocesses. An alternative are enzyme-mediated glucose release systems from starch-derived polymers, facilitating continuous glucose supply. Nevertheless, while the glucose release, and thus the feed rate, is controlled by the enzyme concentration, it also strongly depends on the type of starch derivative, and the culture conditions as well as pH and temperature. So far it was not possible to implement controlled feeding strategies (e.g., exponential feeding). In this context, we propose a model-based approach to achieve precise control over enzyme-mediated glucose release in cultivations. To this aim, an existing mathematical model was integrated into a computational framework to calculate setpoints for enzyme additions. We demonstrate the ability of the tool to maintain different pre-defined exponential growth rates during Escherichia coli cultivations in parallel mini-bioreactors integrated into a robotic facility. Although in this case study, the intermittent additions of enzyme and dextrin were performed by a liquid handler, the approach is adaptable to manual applications. Thus, we present a straightforward and robust approach for implementing defined continuous fed-batch processes in small-scale systems, where continuous feeding was only possible with low accuracy or high technical efforts until now.
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Affiliation(s)
- Annina Kemmer
- Institute of Biotechnology, Chair of Bioprocess Engineering, Technische Universität Berlin, 13355 Berlin, Germany
| | - Linda Cai
- Institute of Biotechnology, Chair of Bioprocess Engineering, Technische Universität Berlin, 13355 Berlin, Germany
| | - Stefan Born
- Institute of Biotechnology, Chair of Bioprocess Engineering, Technische Universität Berlin, 13355 Berlin, Germany
| | - M Nicolas Cruz Bournazou
- Institute of Biotechnology, Chair of Bioprocess Engineering, Technische Universität Berlin, 13355 Berlin, Germany
| | - Peter Neubauer
- Institute of Biotechnology, Chair of Bioprocess Engineering, Technische Universität Berlin, 13355 Berlin, Germany
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2
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Fan Q, Waldburger S, Neubauer P, Riedel SL, Gimpel M. Implementation of a high cell density fed-batch for heterologous production of active [NiFe]-hydrogenase in Escherichia coli bioreactor cultivations. Microb Cell Fact 2022; 21:193. [PMID: 36123684 PMCID: PMC9484157 DOI: 10.1186/s12934-022-01919-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2022] [Accepted: 09/07/2022] [Indexed: 11/13/2022] Open
Abstract
Background O2-tolerant [NiFe]-hydrogenases offer tremendous potential for applications in H2-based technology. As these metalloenzymes undergo a complicated maturation process that requires a dedicated set of multiple accessory proteins, their heterologous production is challenging, thus hindering their fundamental understanding and the development of related applications. Taking these challenges into account, we selected the comparably simple regulatory [NiFe]-hydrogenase (RH) from Cupriavidus necator as a model for the development of bioprocesses for heterologous [NiFe]-hydrogenase production. We already reported recently on the high-yield production of catalytically active RH in Escherichia coli by optimizing the culture conditions in shake flasks. Results In this study, we further increase the RH yield and ensure consistent product quality by a rationally designed high cell density fed-batch cultivation process. Overall, the bioreactor cultivations resulted in ˃130 mg L−1 of catalytically active RH which is a more than 100-fold increase compared to other RH laboratory bioreactor scale processes with C. necator. Furthermore, the process shows high reproducibility of the previously selected optimized conditions and high productivity. Conclusions This work provides a good opportunity to readily supply such difficult-to-express complex metalloproteins economically and at high concentrations to meet the demand in basic and applied studies. Supplementary Information The online version contains supplementary material available at 10.1186/s12934-022-01919-w.
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Affiliation(s)
- Qin Fan
- Chair of Bioprocess Engineering, Technische Universität Berlin, Ackerstr. 76, ACK24, D-13355, Berlin, Germany
| | - Saskia Waldburger
- Chair of Bioprocess Engineering, Technische Universität Berlin, Ackerstr. 76, ACK24, D-13355, Berlin, Germany
| | - Peter Neubauer
- Chair of Bioprocess Engineering, Technische Universität Berlin, Ackerstr. 76, ACK24, D-13355, Berlin, Germany
| | - Sebastian L Riedel
- Chair of Bioprocess Engineering, Technische Universität Berlin, Ackerstr. 76, ACK24, D-13355, Berlin, Germany
| | - Matthias Gimpel
- Chair of Bioprocess Engineering, Technische Universität Berlin, Ackerstr. 76, ACK24, D-13355, Berlin, Germany.
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3
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Streamlining cell-free protein synthesis biosensors for use in human fluids: In situ RNase inhibitor production during extract preparation. Biochem Eng J 2022. [DOI: 10.1016/j.bej.2021.108158] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
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4
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Kamel S, Walczak MC, Kaspar F, Westarp S, Neubauer P, Kurreck A. Thermostable adenosine 5'-monophosphate phosphorylase from Thermococcus kodakarensis forms catalytically active inclusion bodies. Sci Rep 2021; 11:16880. [PMID: 34413335 PMCID: PMC8376864 DOI: 10.1038/s41598-021-96073-5] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2020] [Accepted: 08/04/2021] [Indexed: 11/24/2022] Open
Abstract
Catalytically active inclusion bodies (CatIBs) produced in Escherichia coli are an interesting but currently underexplored strategy for enzyme immobilization. They can be purified easily and used directly as stable and reusable heterogenous catalysts. However, very few examples of CatIBs that are naturally formed during heterologous expression have been reported so far. Previous studies have revealed that the adenosine 5′-monophosphate phosphorylase of Thermococcus kodakarensis (TkAMPpase) forms large soluble multimers with high thermal stability. Herein, we show that heat treatment of soluble protein from crude extract induces aggregation of active protein which phosphorolyse all natural 5′-mononucleotides. Additionally, inclusion bodies formed during the expression in E. coli were found to be similarly active with 2–6 folds higher specific activity compared to these heat-induced aggregates. Interestingly, differences in the substrate preference were observed. These results show that the recombinant thermostable TkAMPpase is one of rare examples of naturally formed CatIBs.
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Affiliation(s)
- Sarah Kamel
- Chair of Bioprocess Engineering, Technische Universität Berlin, Straße des 17. Juni 135, 10623, Berlin, Germany
| | - Miriam C Walczak
- Chair of Bioprocess Engineering, Technische Universität Berlin, Straße des 17. Juni 135, 10623, Berlin, Germany.,BioNukleo GmbH, Ackerstraße 76, 13355, Berlin, Germany
| | - Felix Kaspar
- Chair of Bioprocess Engineering, Technische Universität Berlin, Straße des 17. Juni 135, 10623, Berlin, Germany.,BioNukleo GmbH, Ackerstraße 76, 13355, Berlin, Germany
| | - Sarah Westarp
- Chair of Bioprocess Engineering, Technische Universität Berlin, Straße des 17. Juni 135, 10623, Berlin, Germany.,BioNukleo GmbH, Ackerstraße 76, 13355, Berlin, Germany
| | - Peter Neubauer
- Chair of Bioprocess Engineering, Technische Universität Berlin, Straße des 17. Juni 135, 10623, Berlin, Germany
| | - Anke Kurreck
- Chair of Bioprocess Engineering, Technische Universität Berlin, Straße des 17. Juni 135, 10623, Berlin, Germany. .,BioNukleo GmbH, Ackerstraße 76, 13355, Berlin, Germany.
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5
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Soltani M, Hunt JP, Bundy BC. Rapid RNase inhibitor production to enable low-cost, on-demand cell-free protein synthesis biosensor use in human body fluids. Biotechnol Bioeng 2021; 118:3973-3983. [PMID: 34185319 DOI: 10.1002/bit.27874] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2021] [Revised: 05/24/2021] [Accepted: 05/25/2021] [Indexed: 12/22/2022]
Abstract
Human body fluids contain biomarkers which are used extensively for prognostication, diagnosis, monitoring, and evaluation of different treatments for a variety of diseases and disorders. The application of biosensors based on cell-free protein synthesis (CFPS) offers numerous advantages including on-demand and at-home use for fast, accurate detection of a variety of biomarkers in human fluids at an affordable price. However, current CFPS-based biosensors use commercial RNase inhibitors to inhibit different RNases present in human fluids and this reagent is approximately 90% of the expense of these biosensors. Here the flexible nature of Escherichia coli-lysate-based CFPS was used for the first time to produce murine RNase Inhibitor (m-RI) and to optimize its soluble and active production by tuning reaction temperature, reaction time, reduced potential, and addition of GroEL/ES folding chaperons. Furthermore, RNase inhibition activity of m-RI with the highest activity and stability was determined against increasing amounts of three human fluids of serum, saliva, and urine (0%-100% v/v) in lyophilized CFPS reactions. To further demonstrate the utility of the CFPS-produced m-RI, a lyophilized saliva-based glutamine biosensor was demonstrated to effectively work with saliva samples. Overall, the use of CFPS-produced m-RI reduces the total reagent costs of CFPS-based biosensors used in human body fluids approximately 90%.
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Affiliation(s)
- Mehran Soltani
- Department of Chemical Engineering, Brigham Young University, Provo, Utah, USA
| | - J Porter Hunt
- Department of Chemical Engineering, Brigham Young University, Provo, Utah, USA
| | - Bradley C Bundy
- Department of Chemical Engineering, Brigham Young University, Provo, Utah, USA
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6
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Method for high-efficiency fed-batch cultures of recombinant Escherichia coli. Methods Enzymol 2021; 659:189-217. [PMID: 34752285 DOI: 10.1016/bs.mie.2021.05.004] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023]
Abstract
Fed-batch processes are commonly used in industry to obtain sufficient biomass and associated recombinant protein or plasmids. In research laboratories, it is more common to use batch cultures, as the setup of fed-batch processes can be challenging. This method outlines a robust and reliable means to generate Escherichia coli biomass in a minimum amount of fermentation time using a standardized fed-batch process. Final cell densities can reach over 50g dry cell weight per liter (gdcw/L) depending on the strain. This method uses a predefined exponential feeding strategy and conservative induction protocol to achieve these targets without multiple trial and error studies. If desired, productivity can be optimized by balancing the induction time and feed rates. This method utilizes cost-efficient defined media, minimizes process control complexity, and potentially aids downstream purification.
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7
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Ongey EL, Santolin L, Waldburger S, Adrian L, Riedel SL, Neubauer P. Bioprocess Development for Lantibiotic Ruminococcin-A Production in Escherichia coli and Kinetic Insights Into LanM Enzymes Catalysis. Front Microbiol 2019; 10:2133. [PMID: 31572338 PMCID: PMC6753504 DOI: 10.3389/fmicb.2019.02133] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2019] [Accepted: 08/30/2019] [Indexed: 11/13/2022] Open
Abstract
Ruminococcin-A (RumA) is a peptide antibiotic with post-translational modifications including thioether cross-links formed from non-canonical amino acids, called lanthionines, synthesized by a dedicated lanthionine-generating enzyme RumM. RumA is naturally produced by Ruminococcus gnavus, which is part of the normal bacterial flora in the human gut. High activity of RumA against pathogenic Clostridia has been reported, thus allowing potential exploitation of RumA for clinical applications. However, purifying RumA from R. gnavus is challenging due to low production yields (<1 μg L-1) and difficulties to cultivate the obligately anaerobic organism. We recently reported the reconstruction of the RumA biosynthesis machinery in Escherichia coli where the fully modified and active peptide was expressed as a fusion protein together with GFP. In the current study we developed a scale-up strategy for the biotechnologically relevant heterologous production of RumA, aimed at overproducing the peptide under conditions comparable with those in industrial production settings. To this end, glucose-limited fed-batch cultivation was used. Firstly, parallel cultivations were performed in 24-microwell plates using the enzyme-based automated glucose-delivery cultivation system EnPresso® B to determine optimal conditions for IPTG induction. We combined the bioprocess development with ESI-MS and tandem ESI-MS to monitor modification of the precursor peptide (preRumA) during bioreactor cultivation. Dehydration of threonine and serine residues in the core peptide, catalyzed by RumM, occurs within 1 h after IPTG induction while formation of thioether cross-bridges occur around 2.5 h after induction. Our data also supplies important information on modification kinetics especially with respect to the fluctuations observed in the various dehydrated precursor peptide versions or intermediates produced at different time points during bioreactor cultivation. Overall, protein yields obtained from the bioreactor cultivations were >120 mg L-1 for the chimeric construct and >150 mg L-1 for RumM. The correlation observed between microscale and lab-scale bioreactor cultivations suggests that the process is robust and realistically applicable to industrial-scale conditions.
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Affiliation(s)
- Elvis L Ongey
- Bioprocess Engineering, Institute of Biotechnology, Technische Universität Berlin, Berlin, Germany
| | - Lara Santolin
- Bioprocess Engineering, Institute of Biotechnology, Technische Universität Berlin, Berlin, Germany
| | - Saskia Waldburger
- Bioprocess Engineering, Institute of Biotechnology, Technische Universität Berlin, Berlin, Germany
| | - Lorenz Adrian
- Department of Isotope Biogeochemistry, Helmholtz Centre for Environmental Research, Leipzig, Germany.,Chair of Geobiotechnology, Institute of Biotechnology, Technische Universität Berlin, Berlin, Germany
| | - Sebastian L Riedel
- Bioprocess Engineering, Institute of Biotechnology, Technische Universität Berlin, Berlin, Germany
| | - Peter Neubauer
- Bioprocess Engineering, Institute of Biotechnology, Technische Universität Berlin, Berlin, Germany
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8
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Jansen R, Tenhaef N, Moch M, Wiechert W, Noack S, Oldiges M. FeedER: a feedback-regulated enzyme-based slow-release system for fed-batch cultivation in microtiter plates. Bioprocess Biosyst Eng 2019; 42:1843-1852. [PMID: 31399865 PMCID: PMC6800402 DOI: 10.1007/s00449-019-02180-z] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2019] [Accepted: 07/23/2019] [Indexed: 11/09/2022]
Abstract
With the advent of modern genetic engineering methods, microcultivation systems have become increasingly important tools for accelerated strain phenotyping and bioprocess engineering. While these systems offer sophisticated capabilities to screen batch processes, they lack the ability to realize fed-batch processes, which are used more frequently in industrial bioprocessing. In this study, a novel approach to realize a feedback-regulated enzyme-based slow-release system (FeedER), allowing exponential fed-batch for microscale cultivations, was realized by extending our existing Mini Pilot Plant technology with a customized process control system. By continuously comparing the experimental growth rates with predefined set points, the automated dosage of Amyloglucosidase enzyme for the cleavage of dextrin polymers into d-glucose monomers is triggered. As a prerequisite for stable fed-batch operation, a constant pH is maintained by automated addition of ammonium hydroxide. We show the successful application of FeedER to study fed-batch growth of different industrial model organisms including Corynebacterium glutamicum, Pichia pastoris, and Escherichia coli. Moreover, the comparative analysis of a C. glutamicum GFP producer strain, cultivated under microscale batch and fed-batch conditions, revealed two times higher product yields under slow growing fed-batch operation. In summary, FeedER enables to run 48 parallel fed-batch experiments in an automated and miniaturized manner, and thereby accelerates industrial bioprocess development at the screening stage.
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Affiliation(s)
- Roman Jansen
- Forschungszentrum Jülich, Institute of Bio- and Geosciences, Biotechnology (IBG-1), Jülich, Germany
| | - Niklas Tenhaef
- Forschungszentrum Jülich, Institute of Bio- and Geosciences, Biotechnology (IBG-1), Jülich, Germany.,Bioeconomy Science Center (BioSC), Forschungszentrum Jülich GmbH, Jülich, Germany
| | - Matthias Moch
- Forschungszentrum Jülich, Institute of Bio- and Geosciences, Biotechnology (IBG-1), Jülich, Germany
| | - Wolfgang Wiechert
- Forschungszentrum Jülich, Institute of Bio- and Geosciences, Biotechnology (IBG-1), Jülich, Germany.,RWTH Aachen University, Computational Systems Biotechnology (AVT.CSB), Aachen, Germany
| | - Stephan Noack
- Forschungszentrum Jülich, Institute of Bio- and Geosciences, Biotechnology (IBG-1), Jülich, Germany.,Bioeconomy Science Center (BioSC), Forschungszentrum Jülich GmbH, Jülich, Germany
| | - Marco Oldiges
- Forschungszentrum Jülich, Institute of Bio- and Geosciences, Biotechnology (IBG-1), Jülich, Germany. .,Institute of Biotechnology, RWTH Aachen University, Aachen, Germany.
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9
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Keil T, Landenberger M, Dittrich B, Selzer S, Büchs J. Precultures Grown under Fed‐Batch Conditions Increase the Reliability and Reproducibility of High‐Throughput Screening Results. Biotechnol J 2019; 14:e1800727. [DOI: 10.1002/biot.201800727] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2018] [Revised: 06/21/2019] [Indexed: 12/23/2022]
Affiliation(s)
- Timm Keil
- AVT—Biochemical EngineeringRWTH Aachen UniversityForckenbeckstraße 51 52074 Aachen Germany
| | - Markus Landenberger
- AVT—Biochemical EngineeringRWTH Aachen UniversityForckenbeckstraße 51 52074 Aachen Germany
| | - Barbara Dittrich
- DWI—Leibniz Institute for Interactive MaterialsRWTH Aachen University52074 Aachen Germany
| | | | - Jochen Büchs
- AVT—Biochemical EngineeringRWTH Aachen UniversityForckenbeckstraße 51 52074 Aachen Germany
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10
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Haby B, Hans S, Anane E, Sawatzki A, Krausch N, Neubauer P, Cruz Bournazou MN. Integrated Robotic Mini Bioreactor Platform for Automated, Parallel Microbial Cultivation With Online Data Handling and Process Control. SLAS Technol 2019; 24:569-582. [PMID: 31288593 DOI: 10.1177/2472630319860775] [Citation(s) in RCA: 20] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
During process development, the experimental search space is defined by the number of experiments that can be performed in specific time frames but also by its sophistication (e.g., inputs, sensors, sampling frequency, analytics). High-throughput liquid-handling stations can perform a large number of automated experiments in parallel. Nevertheless, the experimental data sets that are obtained are not always relevant for development of industrial bioprocesses, leading to a high rate of failure during scale-up. We present an automated mini bioreactor platform that enables parallel cultivations in the milliliter scale with online monitoring and control, well-controlled conditions, and advanced feeding strategies similar to industrial processes. The combination of two liquid handlers allows both automated mini bioreactor operation and at-line analysis in parallel. A central database enables end-to-end data exchange and fully integrated device and process control. A model-based operation algorithm allows for the accurate performance of complex cultivations for scale-down studies and strain characterization via optimal experimental redesign, significantly increasing the reliability and transferability of data throughout process development. The platform meets the tradeoff between experimental throughput and process control and monitoring comparable to laboratory-scale bioreactors.
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Affiliation(s)
- Benjamin Haby
- Institute of Biotechnology, Technische Universität, Berlin, Germany
| | - Sebastian Hans
- Institute of Biotechnology, Technische Universität, Berlin, Germany
| | - Emmanuel Anane
- Institute of Biotechnology, Technische Universität, Berlin, Germany
| | - Annina Sawatzki
- Institute of Biotechnology, Technische Universität, Berlin, Germany
| | - Niels Krausch
- Institute of Biotechnology, Technische Universität, Berlin, Germany
| | - Peter Neubauer
- Institute of Biotechnology, Technische Universität, Berlin, Germany
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11
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Joachim M, Maguire N, Schäfer J, Gerlach D, Czermak P. Process Intensification for an Insect Antimicrobial Peptide Elastin-Like Polypeptide Fusion Produced in Redox-Engineered Escherichia coli. Front Bioeng Biotechnol 2019; 7:150. [PMID: 31316976 PMCID: PMC6610315 DOI: 10.3389/fbioe.2019.00150] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2019] [Accepted: 06/06/2019] [Indexed: 12/31/2022] Open
Abstract
Peptides and proteins containing disulfide bonds can be produced in Escherichia coli by targeting the oxidizing periplasm, co-expressing isomerases or chaperons, refolding from inclusion bodies, or by using redox-engineered E. coli strains. Thus far, protein expression in glutathione reductase and thioredoxin reductase deficient (Δgor ΔtrxB) E. coli strains has required a complex medium. However, a chemically defined medium suitable for large-scale production would be preferable for industrial applications. Recently, we developed a minimal medium supplemented with iron (M9i) for high-density cultivation using E. coli Rosetta gami B(DE3)pLysS cells. Here we show that M9i is suitable for the production of insect metalloproteinase inhibitor (IMPI), which contains five disulfide bonds, in the same E. coli strain. We demonstrated the scalability of the new fed-batch process by combining the scale-up criteria of constant dissolved oxygen (DO) and matching volumetric power inputs (P/V) at the borders of the stirrer cascade. Process intensification was achieved by investigating production feed rates and different induction times. We improved product titers by ~200-fold compared to the standard process in complex medium while maintaining the activity of the IMPI protein. Our results show for the first time that it is possible to produce active proteins containing multiple disulfide bonds in a Δgor ΔtrxB E. coli strain using M9i medium. The success of scale-up and process intensification shows that the industrial production of complex recombinant proteins in such strains using chemically defined M9i minimal medium is feasible.
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Affiliation(s)
- Mathias Joachim
- Department of Life Science Engineering, Institute of Bioprocess Engineering and Pharmaceutical Technology, University of Applied Sciences Mittelhessen, Giessen, Germany.,Faculty of Biology and Chemistry, Justus Liebig University, Giessen, Germany
| | - Nicolas Maguire
- Department of Bioresources of Fraunhofer, Institute for Molecular Biology and Applied Ecology IME, Giessen, Germany
| | - Johannes Schäfer
- Department of Life Science Engineering, Institute of Bioprocess Engineering and Pharmaceutical Technology, University of Applied Sciences Mittelhessen, Giessen, Germany
| | - Doreen Gerlach
- Department of Bioresources of Fraunhofer, Institute for Molecular Biology and Applied Ecology IME, Giessen, Germany
| | - Peter Czermak
- Department of Life Science Engineering, Institute of Bioprocess Engineering and Pharmaceutical Technology, University of Applied Sciences Mittelhessen, Giessen, Germany.,Faculty of Biology and Chemistry, Justus Liebig University, Giessen, Germany.,Department of Bioresources of Fraunhofer, Institute for Molecular Biology and Applied Ecology IME, Giessen, Germany
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12
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Gawin A, Peebo K, Hans S, Ertesvåg H, Irla M, Neubauer P, Brautaset T. Construction and characterization of broad-host-range reporter plasmid suitable for on-line analysis of bacterial host responses related to recombinant protein production. Microb Cell Fact 2019; 18:80. [PMID: 31064376 PMCID: PMC6505264 DOI: 10.1186/s12934-019-1128-7] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2019] [Accepted: 04/26/2019] [Indexed: 12/22/2022] Open
Abstract
BACKGROUND Bacteria are widely used as hosts for recombinant protein production due to their rapid growth, simple media requirement and ability to produce high yields of correctly folded proteins. Overproduction of recombinant proteins may impose metabolic burden to host cells, triggering various stress responses, and the ability of the cells to cope with such stresses is an important factor affecting both cell growth and product yield. RESULTS Here, we present a versatile plasmid-based reporter system for efficient analysis of metabolic responses associated with availability of cellular resources utilized for recombinant protein production and host capacity to synthesize correctly folded proteins. The reporter plasmid is based on the broad-host range RK2 minimal replicon and harbors the strong and inducible XylS/Pm regulator/promoter system, the ppGpp-regulated ribosomal protein promoter PrpsJ, and the σ32-dependent synthetic tandem promoter Pibpfxs, each controlling expression of one distinguishable fluorescent protein. We characterized the responsiveness of all three reporters in Escherichia coli by quantitative fluorescence measurements in cell cultures cultivated under different growth and stress conditions. We also validated the broad-host range application potential of the reporter plasmid by using Pseudomonas putida and Azotobacter vinelandii as hosts. CONCLUSIONS The plasmid-based reporter system can be used for analysis of the total inducible recombinant protein production, the translational capacity measured as transcription level of ribosomal protein genes and the heat shock-like response revealing aberrant protein folding in all studied Gram-negative bacterial strains.
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Affiliation(s)
- Agnieszka Gawin
- Department of Biotechnology and Food Science, Norwegian University of Science and Technology, Sem Sælandsvei 6-8, 7491 Trondheim, Norway
| | - Karl Peebo
- Center of Food and Fermentation Technologies, Akadeemia tee 15a, 12618 Tallinn, Estonia
| | - Sebastian Hans
- Bioprocess Engineering, Institute of Biotechnology, Technische Universität Berlin, Ackerstrasse 76, 13355 Berlin, Germany
| | - Helga Ertesvåg
- Department of Biotechnology and Food Science, Norwegian University of Science and Technology, Sem Sælandsvei 6-8, 7491 Trondheim, Norway
| | - Marta Irla
- Department of Biotechnology and Food Science, Norwegian University of Science and Technology, Sem Sælandsvei 6-8, 7491 Trondheim, Norway
| | - Peter Neubauer
- Bioprocess Engineering, Institute of Biotechnology, Technische Universität Berlin, Ackerstrasse 76, 13355 Berlin, Germany
| | - Trygve Brautaset
- Department of Biotechnology and Food Science, Norwegian University of Science and Technology, Sem Sælandsvei 6-8, 7491 Trondheim, Norway
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13
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Haby B, Glauche F, Hans S, Nicolas Cruz-Bournazou M, Neubauer P. Stammcharakterisierung mittels on-line-Redesign von Experimenten. ACTA ACUST UNITED AC 2018. [DOI: 10.1007/s12268-018-0889-6] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
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14
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Hemmerich J, Noack S, Wiechert W, Oldiges M. Microbioreactor Systems for Accelerated Bioprocess Development. Biotechnol J 2018; 13:e1700141. [PMID: 29283217 DOI: 10.1002/biot.201700141] [Citation(s) in RCA: 96] [Impact Index Per Article: 16.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2017] [Revised: 12/15/2017] [Indexed: 12/14/2022]
Abstract
In recent years, microbioreactor (MBR) systems have evolved towards versatile bioprocess engineering tools. They provide a unique solution to combine higher experimental throughput with extensive bioprocess monitoring and control, which is indispensable to develop economically and ecologically competitive bioproduction processes. MBR systems are based either on down-scaled stirred tank reactors or on advanced shaken microtiter plate cultivation devices. Importantly, MBR systems make use of optical measurements for non-invasive, online monitoring of important process variables like biomass concentration, dissolved oxygen, pH, and fluorescence. The application range of MBR systems can be further increased by integration into liquid handling robots, enabling automatization and, thus standardization, of various handling and operation procedures. Finally, the tight integration of quantitative strain phenotyping with bioprocess development under industrially relevant conditions greatly increases the probability of finding the right combination of producer strain and bioprocess control strategy. This review will discuss the current state of the art in the field of MBR systems and we can readily conclude that their importance for industrial biotechnology will further increase in the near future.
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Affiliation(s)
- Johannes Hemmerich
- Forschungszentrum Jülich, Institute of Bio- and Geosciences - Biotechnology (IBG-1), Wilhelm-Johnen Straße 1, 52425, Jülich, Germany.,Bioeconomy Science Center (BioSC), c/o Forschungszentrum Jülich, 52425 Jülich, Germany
| | - Stephan Noack
- Forschungszentrum Jülich, Institute of Bio- and Geosciences - Biotechnology (IBG-1), Wilhelm-Johnen Straße 1, 52425, Jülich, Germany.,Bioeconomy Science Center (BioSC), c/o Forschungszentrum Jülich, 52425 Jülich, Germany
| | - Wolfgang Wiechert
- RWTH Aachen University, Computational Systems Biotechnology (AVT.CSB), Forckenbeckstraße 51, 52074 Aachen, Germany.,Bioeconomy Science Center (BioSC), c/o Forschungszentrum Jülich, 52425 Jülich, Germany
| | - Marco Oldiges
- Forschungszentrum Jülich, Institute of Bio- and Geosciences - Biotechnology (IBG-1), Wilhelm-Johnen Straße 1, 52425, Jülich, Germany.,RWTH Aachen University, Institute of Biotechnology, Worringer Weg 3, 52074 Aachen, Germany.,Bioeconomy Science Center (BioSC), c/o Forschungszentrum Jülich, 52425 Jülich, Germany
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15
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Chrast L, Chaloupkova R, Damborsky J. Gram-scale production of recombinant microbial enzymes in shake flasks. FEMS Microbiol Lett 2017; 365:4693837. [DOI: 10.1093/femsle/fnx265] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2017] [Accepted: 12/02/2017] [Indexed: 11/14/2022] Open
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16
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Glauche F, Glazyrina J, Cruz Bournazou MN, Kiesewetter G, Cuda F, Goelling D, Raab A, Lang C, Neubauer P. Detection of growth rate-dependent product formation in miniaturized parallel fed-batch cultivations. Eng Life Sci 2017; 17:1215-1220. [PMID: 32624749 PMCID: PMC6999230 DOI: 10.1002/elsc.201600029] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2016] [Revised: 04/28/2017] [Accepted: 07/24/2017] [Indexed: 12/22/2022] Open
Abstract
Saccharomyces cerevisiae is a popular expression system for recombinant proteins. In most cases, production processes are performed as carbon-limited fed-batch cultures to avoid aerobic ethanol formation. Especially for constitutive expression systems, the specific product formation rate depends on the specific growth rate. The development of optimal feeding strategies strongly depends on laboratory-scale cultivations, which are time and resource consuming, especially when continuous experiments are carried out. It is therefore beneficial for accelerated process development to look at alternatives. In this study, S. cerevisiae AH22 secreting a heterologous endo-polygalacturonase (EPG) was characterized in microwell plates with an enzyme-based fed-batch medium. Through variation of the glucose release rate, different growth profiles were established and the impact on EPG secretion was analyzed. Product formation rates of 200-400 U (gx h)-1 were determined. As a reference, bioreactor experiments using the change-stat cultivation technique were performed. The growth-dependent product formation was analyzed over dilution rates of D = 0.01-0.35 with smooth change of D at a rate of 0.003 h-2. EPG production was found to be comparable with a qp of 400 U (gx h)-1 at D = 0.27 h-1. The presented results indicate that parallel miniaturized fed-batch cultures can be applied to determine product formation profiles of putative production strains. With further automation and parallelization of the concept, strain characterization can be performed in shorter time.
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Affiliation(s)
- Florian Glauche
- Chair of Bioprocess EngineeringTechnische Universität BerlinBerlinGermany
| | - Julia Glazyrina
- Chair of Bioprocess EngineeringTechnische Universität BerlinBerlinGermany
| | | | | | - Fabian Cuda
- Chair of Bioprocess EngineeringTechnische Universität BerlinBerlinGermany
| | | | | | | | - Peter Neubauer
- Chair of Bioprocess EngineeringTechnische Universität BerlinBerlinGermany
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17
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Kohl A, Srinivasamurthy V, Böttcher D, Kabisch J, Bornscheuer UT. Co-expression of an alcohol dehydrogenase and a cyclohexanone monooxygenase for cascade reactions facilitates the regeneration of the NADPH cofactor. Enzyme Microb Technol 2017; 108:53-58. [PMID: 29108627 DOI: 10.1016/j.enzmictec.2017.09.003] [Citation(s) in RCA: 38] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2017] [Revised: 08/22/2017] [Accepted: 09/10/2017] [Indexed: 02/06/2023]
Abstract
The introduction of a three-enzyme cascade (comprising a cyclohexanone monooxygenase (CHMO), an alcohol dehydrogenase (ADH) and a lipase (CAL-A)) for the production of oligo-ε-caprolactone provided self-sufficiency with respect to NADPH-cofactor regeneration and reduced inhibiting effects on the central CHMO enzyme. For further optimization of cofactor regeneration, now a co-expression of CHMO and ADH in E. coli using a Duet™ vector was performed. This led to higher conversion values of the substrate cyclohexanol in whole-cell biocatalysis compared to an expression of both enzymes from two separate plasmids. Furthermore, a more advantageous balance of expression levels between the partial cascade enzymes was achieved via engineering of the ribosome binding site. This contributed to an even faster cofactor regeneration rate.
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Affiliation(s)
- Anna Kohl
- Institute of Biochemistry, Department of Biotechnology & Enzyme Catalysis, Greifswald University, Felix-Hausdorff-Str. 4, 17489 Greifswald, Germany
| | - Vishnu Srinivasamurthy
- Institute of Biochemistry, Department of Biotechnology & Enzyme Catalysis, Greifswald University, Felix-Hausdorff-Str. 4, 17489 Greifswald, Germany
| | - Dominique Böttcher
- Institute of Biochemistry, Department of Biotechnology & Enzyme Catalysis, Greifswald University, Felix-Hausdorff-Str. 4, 17489 Greifswald, Germany
| | - Johannes Kabisch
- Department of Biology, Computer-aided Synthetic Biology, Technische Universität Darmstadt, Schnittspahnstr. 10, 64287 Darmstadt, Germany
| | - Uwe T Bornscheuer
- Institute of Biochemistry, Department of Biotechnology & Enzyme Catalysis, Greifswald University, Felix-Hausdorff-Str. 4, 17489 Greifswald, Germany.
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18
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Rezaie F, Davami F, Mansouri K, Agha Amiri S, Fazel R, Mahdian R, Davoudi N, Enayati S, Azizi M, Khalaj V. Cytosolic expression of functional Fab fragments in Escherichia coli
using a novel combination of dual SUMO expression cassette and EnBase®
cultivation mode. J Appl Microbiol 2017; 123:134-144. [DOI: 10.1111/jam.13483] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2017] [Revised: 04/19/2017] [Accepted: 05/02/2017] [Indexed: 12/22/2022]
Affiliation(s)
- F. Rezaie
- Medical Biotechnology Department; Biotechnology Research Center; Pasteur Institute of Iran; Tehran Iran
| | - F. Davami
- Medical Biotechnology Department; Biotechnology Research Center; Pasteur Institute of Iran; Tehran Iran
| | - K. Mansouri
- Medical Biology Research Center; Kermanshah University of Medical Sciences; Kermanshah Iran
| | - S. Agha Amiri
- Medical Biotechnology Department; Biotechnology Research Center; Pasteur Institute of Iran; Tehran Iran
| | - R. Fazel
- Medical Biotechnology Department; Biotechnology Research Center; Pasteur Institute of Iran; Tehran Iran
| | - R. Mahdian
- Molecular Medicine Department; Biotechnology Research Center; Pasteur Institute of Iran; Tehran Iran
| | - N. Davoudi
- Medical Biotechnology Department; Biotechnology Research Center; Pasteur Institute of Iran; Tehran Iran
| | - S. Enayati
- Medical Biotechnology Department; Biotechnology Research Center; Pasteur Institute of Iran; Tehran Iran
| | - M. Azizi
- Medical Biotechnology Department; Biotechnology Research Center; Pasteur Institute of Iran; Tehran Iran
| | - V. Khalaj
- Medical Biotechnology Department; Biotechnology Research Center; Pasteur Institute of Iran; Tehran Iran
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19
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Wellenbeck W, Mampel J, Naumer C, Knepper A, Neubauer P. Fast-track development of a lactase production process with Kluyveromyces lactis by a progressive parameter-control workflow. Eng Life Sci 2016; 17:1185-1194. [PMID: 32624746 DOI: 10.1002/elsc.201600031] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2016] [Revised: 08/12/2016] [Accepted: 09/07/2016] [Indexed: 11/12/2022] Open
Abstract
The time-to-market challenge is key to success for consumer goods affiliated industries. In recent years, the dairy industry faces a fast and constantly growing demand for enzymatically produced lactose-free milk products, mainly driven by emerging markets in South America and Asia. In order to take advantage of this opportunity, we developed a fermentation process for lactase (β-galactosidase) from Kluyveromyces lactis within short time. Here, we describe the process of stepwise increasing the level of control over relevant process parameters during scale-up that established a highly efficient and stable production system. Process development started with evolutionary engineering to generate catabolite-derepressed variants of the K. lactis wild-type strain. A high-throughput screening mimicking fed-batch cultivation identified a constitutive lactase overproducer with 260-fold improved activity of 4.4 U per milligram dry cell weight when cultivated in glucose minimal medium. During scale-up, process control was progressively increased up to the level of conventional, fully controlled fed-batch cultivations by simulating glucose feed, applying pH- and dissolved oxygen tension (DOT)-sensor technology to small scale, and by the use of a milliliter stirred tank bioreactor. Additionally, process development was assisted by design-of-experiments optimization of the growth medium employing the response surface methodology.
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Affiliation(s)
- Wenzel Wellenbeck
- BRAIN AG (Biotechnology Research and Information Network) Zwingenberg Germany
| | - Jörg Mampel
- BRAIN AG (Biotechnology Research and Information Network) Zwingenberg Germany
| | - Christian Naumer
- BRAIN AG (Biotechnology Research and Information Network) Zwingenberg Germany
| | - Andreas Knepper
- Bioprocess Engineering Department of Biotechnology Technische Universität Berlin Berlin Germany
| | - Peter Neubauer
- Bioprocess Engineering Department of Biotechnology Technische Universität Berlin Berlin Germany
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20
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Glauche F, Pilarek M, Bournazou MNC, Grunzel P, Neubauer P. Design of experiments-based high-throughput strategy for development and optimization of efficient cell disruption protocols. Eng Life Sci 2016; 17:1166-1172. [PMID: 32624744 DOI: 10.1002/elsc.201600030] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2016] [Revised: 05/26/2016] [Accepted: 07/25/2016] [Indexed: 01/13/2023] Open
Abstract
Efficient and reproducible cell lysis is a crucial step during downstream processing of intracellular products. The composition of an optimal lysis buffer should be chosen depending on the organism, its growth status, the applied detection methods, and even the target molecule. Especially for high-throughput applications, where sample volumes are limited, the adaptation of a lysis buffer to the specific campaign is an urgent need. Here, we present a general design of experiments-based strategy suitable for eight constituents and demonstrate the strength of this approach by the development of an efficient lysis buffer for Gram-negative bacteria, which is applicable in a high-throughput format in a short time. The concentrations of four lysis-inducing chemical agents EDTA, lysozyme, Triton X-100, and polymyxin B were optimized for maximal soluble protein concentration and ß-galactosidase activity in a 96-well format on a Microlab Star liquid handling platform under design of experiments methodology. The resulting lysis buffer showed the same performance as a commercially available lysis buffer. The developed protocol resulted in an optimized buffer within only three runs. The established procedure can be easily applied to adapt the lysis buffer to other strains and target molecules.
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Affiliation(s)
- Florian Glauche
- Chair of Bioprocess Engineering, Institute of Biotechnology Technische Universität Berlin Berlin Germany
| | - Maciej Pilarek
- Faculty of Chemical and Process Engineering Warsaw University of Technology Warsaw Poland
| | | | - Petra Grunzel
- Chair of Bioprocess Engineering, Institute of Biotechnology Technische Universität Berlin Berlin Germany
| | - Peter Neubauer
- Chair of Bioprocess Engineering, Institute of Biotechnology Technische Universität Berlin Berlin Germany
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21
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Krause M, Neubauer A, Neubauer P. The fed-batch principle for the molecular biology lab: controlled nutrient diets in ready-made media improve production of recombinant proteins in Escherichia coli. Microb Cell Fact 2016; 15:110. [PMID: 27317421 PMCID: PMC4912726 DOI: 10.1186/s12934-016-0513-8] [Citation(s) in RCA: 43] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2016] [Accepted: 06/09/2016] [Indexed: 11/10/2022] Open
Abstract
While the nutrient limited fed-batch technology is the standard of the cultivation of microorganisms and production of heterologous proteins in industry, despite its advantages in view of metabolic control and high cell density growth, shaken batch cultures are still the standard for protein production and expression screening in molecular biology and biochemistry laboratories. This is due to the difficulty and expenses to apply a controlled continuous glucose feed to shaken cultures. New ready-made growth media, e.g. by biocatalytic release of glucose from a polymer, offer a simple solution for the application of the fed-batch principle in shaken plate and flask cultures. Their wider use has shown that the controlled diet not only provides a solution to obtain significantly higher cell yields, but also in many cases folding of the target protein is improved by the applied lower growth rates; i.e. final volumetric yields for the active protein can be a multiple of what is obtained in complex medium cultures. The combination of the conventional optimization approaches with new and easy applicable growth systems has revolutionized recombinant protein production in Escherichia coli in view of product yield, culture robustness as well as significantly increased cell densities. This technical development establishes the basis for successful miniaturization and parallelization which is now an important tool for synthetic biology and protein engineering approaches. This review provides an overview of the recent developments, results and applications of advanced growth systems which use a controlled glucose release as substrate supply.
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Affiliation(s)
- Mirja Krause
- />Laboratory of Bioprocess Engineering, Department of Biotechnology, Chair of Bioprocess Engineering, Technische Universität Berlin, Ackerstr. 76, ACK 24, 13355 Berlin, Germany
- />Laboratory of Developmental Biology, Faculty of Biochemistry and Molecular Medicine, Biocenter Oulu, University of Oulu, Aapistie 5A, 90220 Oulu, Finland
| | | | - Peter Neubauer
- />Laboratory of Bioprocess Engineering, Department of Biotechnology, Chair of Bioprocess Engineering, Technische Universität Berlin, Ackerstr. 76, ACK 24, 13355 Berlin, Germany
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22
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Ongey EL, Neubauer P. Lanthipeptides: chemical synthesis versus in vivo biosynthesis as tools for pharmaceutical production. Microb Cell Fact 2016; 15:97. [PMID: 27267232 PMCID: PMC4897893 DOI: 10.1186/s12934-016-0502-y] [Citation(s) in RCA: 68] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2016] [Accepted: 06/01/2016] [Indexed: 01/15/2023] Open
Abstract
Lanthipeptides (also called lantibiotics for those with antibacterial activities) are ribosomally synthesized post-translationally modified peptides having thioether cross-linked amino acids, lanthionines, as a structural element. Lanthipeptides have conceivable potentials to be used as therapeutics, however, the lack of stable, high-yield, well-characterized processes for their sustainable production limit their availability for clinical studies and further pharmaceutical commercialization. Though many reviews have discussed the various techniques that are currently employed to produce lanthipeptides, a direct comparison between these methods to assess industrial applicability has not yet been described. In this review we provide a synoptic comparison of research efforts on total synthesis and in vivo biosynthesis aimed at fostering lanthipeptides production. We further examine current applications and propose measures to enhance product yields. Owing to their elaborate chemical structures, chemical synthesis of these biomolecules is economically less feasible for large-scale applications, and hence biological production seems to be the only realistic alternative.
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Affiliation(s)
- Elvis Legala Ongey
- Chair of Bioprocess Engineering, Department of Biotechnology, Technische Universität Berlin, Ackerstraße 76, ACK24, 13355, Berlin, Germany.
| | - Peter Neubauer
- Chair of Bioprocess Engineering, Department of Biotechnology, Technische Universität Berlin, Ackerstraße 76, ACK24, 13355, Berlin, Germany
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23
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Tripathi NK. Production and Purification of Recombinant Proteins fromEscherichia coli. CHEMBIOENG REVIEWS 2016. [DOI: 10.1002/cben.201600002] [Citation(s) in RCA: 44] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
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24
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Sun Z, Guo T, Liu Y, Liu Q, Fang Y. The Roles of Arabidopsis CDF2 in Transcriptional and Posttranscriptional Regulation of Primary MicroRNAs. PLoS Genet 2015; 11:e1005598. [PMID: 26473486 PMCID: PMC4608766 DOI: 10.1371/journal.pgen.1005598] [Citation(s) in RCA: 38] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2015] [Accepted: 09/21/2015] [Indexed: 01/24/2023] Open
Abstract
The precise regulation of microRNA (miRNA) transcription and processing is important for eukaryotic development. Plant miRNAs are first transcribed as stem-loop primary miRNAs (pri-miRNAs) by RNA polymerase II,then cleaved in the nucleus into mature miRNAs by Dicer-like 1 (DCL1). We identified a cycling DOF transcription factor, CDF2, which interacts with DCL1 and regulates the accumulation of a population of miRNAs. CDF2 binds directly to the promoters of some miRNAs and works as a transcription activator or repressor for these miRNA genes. CDF2 binds preferentially to the pri-miRNAs regulated by itself and affects DCL1-mediated processing of these pri-miRNAs. Genetically, CDF2 works in the same pathway as miR156 or miR172 to control flowering. We conclude that CDF2 regulates a group of pri-miRNAs at both the transcriptional and posttranscriptional levels to maintain proper levels of their mature miRNAs to control plant development. CDFs were identified to play roles in the blue light signaling. This study reveals that CDF2 acts as a transcriptional activator or repressor of a group of microRNA (miRNA) genes and binds to the pri-miRNA transcripts. This study demonstrates that CDF2 interacts with the Dicer-like 1 (DCL1) complex and suppresses the processing of primary miRNAs. Genetic analysis shows that CDF2 works in the same pathway as miR156 or miR172 to control flowering. The finding that the miRNA accumulation is regulated by a factor at both the transcriptional and posttranscriptional levels may have a broad impact on the miRNA biogenesis field. The regulation of miRNA abundance by CDF2 sheds light on the roles of miRNAs in the light signaling pathways.
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Affiliation(s)
- Zhenfei Sun
- National Key Laboratory of Plant Molecular Genetics, Shanghai Institute of Plant Physiology and Ecology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai, China
| | - Tongtong Guo
- National Key Laboratory of Plant Molecular Genetics, Shanghai Institute of Plant Physiology and Ecology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai, China
| | - Yin Liu
- National Key Laboratory of Plant Molecular Genetics, Shanghai Institute of Plant Physiology and Ecology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai, China
| | - Qi Liu
- National Key Laboratory of Plant Molecular Genetics, Shanghai Institute of Plant Physiology and Ecology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai, China
| | - Yuda Fang
- National Key Laboratory of Plant Molecular Genetics, Shanghai Institute of Plant Physiology and Ecology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai, China
- * E-mail:
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25
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Glauche F, John GT, Arain S, Knepper A, Neubauer A, Goelling D, Lang C, Violet N, King R, Neubauer P. Toward Microbioreactor Arrays. ACTA ACUST UNITED AC 2015; 20:438-46. [DOI: 10.1177/2211068215573924] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2014] [Indexed: 11/16/2022]
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26
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Li J, Jaitzig J, Lu P, Süssmuth RD, Neubauer P. Scale-up bioprocess development for production of the antibiotic valinomycin in Escherichia coli based on consistent fed-batch cultivations. Microb Cell Fact 2015; 14:83. [PMID: 26063334 PMCID: PMC4464625 DOI: 10.1186/s12934-015-0272-y] [Citation(s) in RCA: 28] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2015] [Accepted: 05/08/2015] [Indexed: 02/05/2023] Open
Abstract
Background Heterologous production of natural products in Escherichia coli has emerged as an attractive strategy to obtain molecules of interest. Although technically feasible most of them are still constrained to laboratory scale production. Therefore, it is necessary to develop reasonable scale-up strategies for bioprocesses aiming at the overproduction of targeted natural products under industrial scale conditions. To this end, we used the production of the antibiotic valinomycin in E. coli as a model system for scalable bioprocess development based on consistent fed-batch cultivations. Results In this work, the glucose limited fed-batch strategy based on pure mineral salt medium was used throughout all scales for valinomycin production. The optimal glucose feed rate was initially detected by the use of a biocatalytically controlled glucose release (EnBase® technology) in parallel cultivations in 24-well plates with continuous monitoring of pH and dissolved oxygen. These results were confirmed in shake flasks, where the accumulation of valinomycin was highest when the specific growth rate decreased below 0.1 h−1. This correlation was also observed for high cell density fed-batch cultivations in a lab-scale bioreactor. The bioreactor fermentation produced valinomycin with titers of more than 2 mg L−1 based on the feeding of a concentrated glucose solution. Valinomycin production was not affected by oscillating conditions (i.e. glucose and oxygen) in a scale-down two-compartment reactor, which could mimic similar situations in industrial bioreactors, suggesting that the process is very robust and a scaling of the process to a larger industrial scale appears a realistic scenario. Conclusions Valinomycin production was scaled up from mL volumes to 10 L with consistent use of the fed-batch technology. This work presents a robust and reliable approach for scalable bioprocess development and represents an example for the consistent development of a process for a heterologously expressed natural product towards the industrial scale.
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Affiliation(s)
- Jian Li
- Chair of Bioprocess Engineering, Department of Biotechnology, Technische Universität Berlin, Ackerstraße 76, ACK24, 13355, Berlin, Germany. .,Department of Chemical and Biological Engineering, Northwestern University, 2145 Sheridan Road, Evanston, IL, 60208, USA.
| | - Jennifer Jaitzig
- Chair of Bioprocess Engineering, Department of Biotechnology, Technische Universität Berlin, Ackerstraße 76, ACK24, 13355, Berlin, Germany.
| | - Ping Lu
- Chair of Bioprocess Engineering, Department of Biotechnology, Technische Universität Berlin, Ackerstraße 76, ACK24, 13355, Berlin, Germany.
| | - Roderich D Süssmuth
- Department of Chemistry, Technische Universität Berlin, Straße des 17. Juni 124, 10623, Berlin, Germany.
| | - Peter Neubauer
- Chair of Bioprocess Engineering, Department of Biotechnology, Technische Universität Berlin, Ackerstraße 76, ACK24, 13355, Berlin, Germany.
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27
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Wewetzer SJ, Kunze M, Ladner T, Luchterhand B, Roth S, Rahmen N, Kloß R, Costa e Silva A, Regestein L, Büchs J. Parallel use of shake flask and microtiter plate online measuring devices (RAMOS and BioLector) reduces the number of experiments in laboratory-scale stirred tank bioreactors. J Biol Eng 2015; 9:9. [PMID: 26265936 PMCID: PMC4531433 DOI: 10.1186/s13036-015-0005-0] [Citation(s) in RCA: 51] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2014] [Accepted: 05/12/2015] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Conventional experiments in small scale are often performed in a 'Black Box' fashion, analyzing only the product concentration in the final sample. Online monitoring of relevant process characteristics and parameters such as substrate limitation, product inhibition and oxygen supply is lacking. Therefore, fully equipped laboratory-scale stirred tank bioreactors are hitherto required for detailed studies of new microbial systems. However, they are too spacious, laborious and expensive to be operated in larger number in parallel. Thus, the aim of this study is to present a new experimental approach to obtain dense quantitative process information by parallel use of two small-scale culture systems with online monitoring capabilities: Respiration Activity MOnitoring System (RAMOS) and the BioLector device. RESULTS The same 'mastermix' (medium plus microorganisms) was distributed to the different small-scale culture systems: 1) RAMOS device; 2) 48-well microtiter plate for BioLector device; and 3) separate shake flasks or microtiter plates for offline sampling. By adjusting the same maximum oxygen transfer capacity (OTRmax), the results from the RAMOS and BioLector online monitoring systems supplemented each other very well for all studied microbial systems (E. coli, G. oxydans, K. lactis) and culture conditions (oxygen limitation, diauxic growth, auto-induction, buffer effects). CONCLUSIONS The parallel use of RAMOS and BioLector devices is a suitable and fast approach to gain comprehensive quantitative data about growth and production behavior of the evaluated microorganisms. These acquired data largely reduce the necessary number of experiments in laboratory-scale stirred tank bioreactors for basic process development. Thus, much more quantitative information is obtained in parallel in shorter time.
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Affiliation(s)
- S. J. Wewetzer
- />RWTH Aachen University, AVT - Biochemical Engineering, Worringer Weg 1, 52074 Aachen, Germany
| | - M. Kunze
- />RWTH Aachen University, AVT - Biochemical Engineering, Worringer Weg 1, 52074 Aachen, Germany
| | - T. Ladner
- />RWTH Aachen University, AVT - Biochemical Engineering, Worringer Weg 1, 52074 Aachen, Germany
| | - B. Luchterhand
- />RWTH Aachen University, AVT - Biochemical Engineering, Worringer Weg 1, 52074 Aachen, Germany
| | - S. Roth
- />RWTH Aachen University, AVT - Biochemical Engineering, Worringer Weg 1, 52074 Aachen, Germany
| | - N. Rahmen
- />RWTH Aachen University, AVT - Biochemical Engineering, Worringer Weg 1, 52074 Aachen, Germany
| | - R. Kloß
- />RWTH Aachen University, AVT - Biochemical Engineering, Worringer Weg 1, 52074 Aachen, Germany
| | - A. Costa e Silva
- />University of Minho, CEB - Centre of Biological Engineering, Campus de Gualtar, 4700-057 Braga, Portugal
| | - L. Regestein
- />RWTH Aachen University, AVT - Biochemical Engineering, Worringer Weg 1, 52074 Aachen, Germany
| | - J. Büchs
- />RWTH Aachen University, AVT - Biochemical Engineering, Worringer Weg 1, 52074 Aachen, Germany
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28
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Jaitzig J, Li J, Süssmuth RD, Neubauer P. Reconstituted biosynthesis of the nonribosomal macrolactone antibiotic valinomycin in Escherichia coli. ACS Synth Biol 2014; 3:432-8. [PMID: 24350980 DOI: 10.1021/sb400082j] [Citation(s) in RCA: 45] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/22/2023]
Abstract
The structural complexity of nonribosomal peptides (NRPs) impeding economic chemical synthesis and poor cultivability of source organisms limits the development of bioprocesses for novel bioactive compounds. Since nonribosomal peptide synthetases (NRPSs) assemble NRPs from simple amino acid building blocks, heterologous expression of NRPSs in a robust and easy to manipulate expression host is an attractive strategy to make pharmaceutically relevant NRPs more accessible and is also a basis for engineering of these enzymes to generate novel synthetic bioactive compounds. Here we show a systematic approach for the heterologous expression of the 654 kDa heterodimeric valinomycin synthetase (VlmSyn) from Streptomyces tsusimaensis in a soluble and active form in Escherichia coli. VlmSyn activity and precursor requirements were determined in vitro and provided evidence for a previously proposed model of valinomycin biosynthesis. In vivo production of recombinant valinomycin, a macrolactone antibiotic with reported antifungal, antibacterial, and antiviral activities, was achieved using an engineered E. coli strain growing in inexpensive media and independent of the supplementation with precursors and further optimization of the cultivation conditions. Tailoring of VlmSyn in E. coli paves the way to the production of novel valinomycin analogues in the future.
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Affiliation(s)
- Jennifer Jaitzig
- Institut für Biotechnologie and ‡Institut für Chemie, Technische Universität Berlin, D-10623 Berlin, Germany
| | - Jian Li
- Institut für Biotechnologie and ‡Institut für Chemie, Technische Universität Berlin, D-10623 Berlin, Germany
| | - Roderich D. Süssmuth
- Institut für Biotechnologie and ‡Institut für Chemie, Technische Universität Berlin, D-10623 Berlin, Germany
| | - Peter Neubauer
- Institut für Biotechnologie and ‡Institut für Chemie, Technische Universität Berlin, D-10623 Berlin, Germany
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Automated microbioreactor systems for pharmaceutical bioprocessing: profiling of seeding and induction conditions in high-throughput fermentations. ACTA ACUST UNITED AC 2014. [DOI: 10.4155/pbp.14.18] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
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Fu Z, Verderame TD, Leighton JM, Sampey BP, Appelbaum ER, Patel PS, Aon JC. Exometabolome analysis reveals hypoxia at the up-scaling of a Saccharomyces cerevisiae high-cell density fed-batch biopharmaceutical process. Microb Cell Fact 2014; 13:32. [PMID: 24593159 PMCID: PMC4016033 DOI: 10.1186/1475-2859-13-32] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2013] [Accepted: 02/19/2014] [Indexed: 12/11/2022] Open
Abstract
BACKGROUND Scale-up to industrial production level of a fermentation process occurs after optimization at small scale, a critical transition for successful technology transfer and commercialization of a product of interest. At the large scale a number of important bioprocess engineering problems arise that should be taken into account to match the values obtained at the small scale and achieve the highest productivity and quality possible. However, the changes of the host strain's physiological and metabolic behavior in response to the scale transition are still not clear. RESULTS Heterogeneity in substrate and oxygen distribution is an inherent factor at industrial scale (10,000 L) which affects the success of process up-scaling. To counteract these detrimental effects, changes in dissolved oxygen and pressure set points and addition of diluents were applied to 10,000 L scale to enable a successful process scale-up. A comprehensive semi-quantitative and time-dependent analysis of the exometabolome was performed to understand the impact of the scale-up on the metabolic/physiological behavior of the host microorganism. Intermediates from central carbon catabolism and mevalonate/ergosterol synthesis pathways were found to accumulate in both the 10 L and 10,000 L scale cultures in a time-dependent manner. Moreover, excreted metabolites analysis revealed that hypoxic conditions prevailed at the 10,000 L scale. The specific product yield increased at the 10,000 L scale, in spite of metabolic stress and catabolic-anabolic uncoupling unveiled by the decrease in biomass yield on consumed oxygen. CONCLUSIONS An optimized S. cerevisiae fermentation process was successfully scaled-up to an industrial scale bioreactor. The oxygen uptake rate (OUR) and overall growth profiles were matched between scales. The major remaining differences between scales were wet cell weight and culture apparent viscosity. The metabolic and physiological behavior of the host microorganism at the 10,000 L scale was investigated with exometabolomics, indicating that reduced oxygen availability affected oxidative phosphorylation cascading into down- and up-stream pathways producing overflow metabolism. Our study revealed striking metabolic and physiological changes in response to hypoxia exerted by industrial bioprocess up-scaling.
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Affiliation(s)
- Zhibiao Fu
- Department of Microbial and Cell Culture Development, Research and Development, GlaxoSmithKline, 709 Swedeland Road, King of Prussia, PA 19406, USA
| | - Thomas D Verderame
- Department of Process Engineering Manufacturing, Global Manufacturing and Supply, GlaxoSmithKline, 893 River Road, Conshohocken, PA 19428, USA
| | - Julie M Leighton
- Department of Microbial and Cell Culture Development, Research and Development, GlaxoSmithKline, 709 Swedeland Road, King of Prussia, PA 19406, USA
| | - Brante P Sampey
- Metabolon, Inc, 617 Davis Drive, Suite 400, Durham, NC 27713, USA
| | - Edward R Appelbaum
- Department of Microbial and Cell Culture Development, Research and Development, GlaxoSmithKline, 709 Swedeland Road, King of Prussia, PA 19406, USA
| | - Pramatesh S Patel
- Department of Microbial and Cell Culture Development, Research and Development, GlaxoSmithKline, 709 Swedeland Road, King of Prussia, PA 19406, USA
| | - Juan C Aon
- Department of Microbial and Cell Culture Development, Research and Development, GlaxoSmithKline, 709 Swedeland Road, King of Prussia, PA 19406, USA
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Peck GR, Bowden TR, Shiell BJ, Michalski WP. INCREASED BACTERIAL CELL DENSITY AND RECOMBINANT PROTEIN YIELD USING A COMMERCIAL MICROBIAL CULTIVATION SYSTEM. Prep Biochem Biotechnol 2013; 44:217-30. [DOI: 10.1080/10826068.2013.797435] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/26/2022]
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Grunzel P, Pilarek M, Steinbrück D, Neubauer A, Brand E, Kumke MU, Neubauer P, Krause M. Mini-scale cultivation method enables expeditious plasmid production inEscherichia coli. Biotechnol J 2013; 9:128-36. [DOI: 10.1002/biot.201300177] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2013] [Revised: 09/11/2013] [Accepted: 09/26/2013] [Indexed: 11/11/2022]
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Li J, Jaitzig J, Hillig F, Süssmuth R, Neubauer P. Enhanced production of the nonribosomal peptide antibiotic valinomycin in Escherichia coli through small-scale high cell density fed-batch cultivation. Appl Microbiol Biotechnol 2013; 98:591-601. [PMID: 24419900 DOI: 10.1007/s00253-013-5309-8] [Citation(s) in RCA: 31] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2013] [Revised: 09/24/2013] [Accepted: 10/01/2013] [Indexed: 11/24/2022]
Abstract
Nonribosomal peptides (NRPs), a large family of natural products, possess numerous pharmaceutically significant bioactivities. However, many native microbial producers of NRPs are not cultivable or have low production yields making mass production infeasible. The recombinant production of natural products in a surrogate host has emerged as a strategy to overcome these limitations. De novo recombinant production of the NRP antibiotic valinomycin in an engineered Escherichia coli host strain was established with the necessary biosynthetic pathway constituents from Streptomyces tsusimaensis. In the present study, the initially modest valinomycin yields could be significantly increased from 0.3 up to 2.4 mg L⁻¹ by switching from a batch to an enzyme-based fed-batch mode in shake flasks. A subsequent design of experiment-driven optimization of parallel fed-batch cultivations in 24-well plates with online monitoring of dissolved oxygen and pH led to valinomycin yields up to 6.4 mg L⁻¹. Finally, repeated glucose polymer feeding to enzyme-based high cell density cultivations in shake flasks resulted in cell densities of OD₆₀₀>50 and a valinomycin titer of appr. 10 mg L⁻¹. This represents a 33-fold improvement compared to the initial batch cultivations and is the highest concentration of a nonribosomal peptide which has been produced in E. coli without feeding of specific precursors so far to our knowledge. Also, such a small-scale optimization under fed-batch conditions may be generally applicable for the development and scale-up of natural product production processes in E. coli.
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Affiliation(s)
- Jian Li
- Chair of Bioprocess Engineering, Department of Biotechnology, Technische Universität Berlin, Ackerstraße 71-76, ACK24, 13355, Berlin, Germany
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Ukkonen K, Veijola J, Vasala A, Neubauer P. Effect of culture medium, host strain and oxygen transfer on recombinant Fab antibody fragment yield and leakage to medium in shaken E. coli cultures. Microb Cell Fact 2013; 12:73. [PMID: 23895637 PMCID: PMC3733871 DOI: 10.1186/1475-2859-12-73] [Citation(s) in RCA: 39] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2013] [Accepted: 07/16/2013] [Indexed: 11/13/2022] Open
Abstract
Background Fab antibody fragments in E. coli are usually directed to the oxidizing periplasmic space for correct folding. From periplasm Fab fragments may further leak into extracellular medium. Information on the cultivation parameters affecting this leakage is scarce, and the unpredictable nature of Fab leakage is problematic regarding consistent product recovery. To elucidate the effects of cultivation conditions, we investigated Fab expression and accumulation into either periplasm or medium in E. coli K-12 and E. coli BL21 when grown in different types of media and under different aeration conditions. Results Small-scale Fab expression demonstrated significant differences in yield and ratio of periplasmic to extracellular Fab between different culture media and host strains. Expression in a medium with fed-batch-like glucose feeding provided highest total and extracellular yields in both strains. Unexpectedly, cultivation in baffled shake flasks at 150 rpm shaking speed resulted in higher yield and accumulation of Fabs into culture medium as compared to cultivation at 250 rpm. In the fed-batch medium, extracellular fraction in E. coli K-12 increased from 2-17% of total Fab at 250 rpm up to 75% at 150 rpm. This was partly due to increased lysis, but also leakage from intact cells increased at the lower shaking speed. Total Fab yield in E. coli BL21 in glycerol-based autoinduction medium was 5 to 9-fold higher at the lower shaking speed, and the extracellular fraction increased from ≤ 10% to 20-90%. The effect of aeration on Fab localization was reproduced in multiwell plate by variation of culture volume. Conclusions Yield and leakage of Fab fragments are dependent on expression strain, culture medium, aeration rate, and the combination of these parameters. Maximum productivity in fed-batch-like conditions and in autoinduction medium is achieved under sufficiently oxygen-limited conditions, and lower aeration also promotes increased Fab accumulation into extracellular medium. These findings have practical implications for screening applications and small-scale Fab production, and highlight the importance of maintaining consistent aeration conditions during scale-up to avoid changes in product yield and localization. On the other hand, the dependency of Fab leakage on cultivation conditions provides a practical way to manipulate Fab localization.
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Affiliation(s)
- Kaisa Ukkonen
- Department of Process and Environmental Engineering, Bioprocess Engineering Laboratory, University of Oulu, Oulu, Finland.
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Neubauer P, Cruz N, Glauche F, Junne S, Knepper A, Raven M. Consistent development of bioprocesses from microliter cultures to the industrial scale. Eng Life Sci 2013. [DOI: 10.1002/elsc.201200021] [Citation(s) in RCA: 82] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022] Open
Affiliation(s)
- Peter Neubauer
- Bioprocess Engineering, Department of Biotechnology; Technische Universität Berlin; Berlin; Germany
| | - Nicolas Cruz
- Bioprocess Engineering, Department of Biotechnology; Technische Universität Berlin; Berlin; Germany
| | - Florian Glauche
- Bioprocess Engineering, Department of Biotechnology; Technische Universität Berlin; Berlin; Germany
| | - Stefan Junne
- Bioprocess Engineering, Department of Biotechnology; Technische Universität Berlin; Berlin; Germany
| | - Andreas Knepper
- Bioprocess Engineering, Department of Biotechnology; Technische Universität Berlin; Berlin; Germany
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Ruiz J, Fernández-Castané A, de Mas C, González G, López-Santín J. From laboratory to pilot plant E. coli fed-batch cultures: optimizing the cellular environment for protein maximization. J Ind Microbiol Biotechnol 2013; 40:335-43. [PMID: 23338174 DOI: 10.1007/s10295-012-1226-6] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2012] [Accepted: 12/22/2012] [Indexed: 12/19/2022]
Abstract
For recombinant protein production in E. coli fed-batch cultures, post-induction conditions have great influence in the quantity and quality of the product. The present paper covers the effect of different factors affecting the cellular environment in recombinant aldolase (rhamnulose-1-phosphate aldolase, RhuA) production. An operational mode employing an exponential addition profile for constant specific growth rate has been analyzed, in order to understand and define possible modifications with influence on post-induction cellular behavior. A constant addition profile has been demonstrated to render higher specific aldolase production than the exponential addition profile, probably due to a more constant environment for the cells. On the other hand, amino acid (leucine) supplementation has proven to increase protein quality in terms of activity units (U) per unit mass of RhuA (U mg(-1) RhuA), alleviating metabolic overload. Based on the above, a production process was set up and scaled up to pilot plant. Resulting production was double that of a standard laboratory operation, 45,000 U L(-1), and almost all the protein retained the 6xHis-tag with the highest quality, 11.3 U mg(-1) RhuA.
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Affiliation(s)
- J Ruiz
- Departament d'Enginyeria Química, Escola d'Enginyeria, Universitat Autònoma de Barcelona, Bellaterra, Catalunya, Spain
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Casteleijn MG, Urtti A, Sarkhel S. Expression without boundaries: Cell-free protein synthesis in pharmaceutical research. Int J Pharm 2013; 440:39-47. [DOI: 10.1016/j.ijpharm.2012.04.005] [Citation(s) in RCA: 39] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2011] [Revised: 04/01/2012] [Accepted: 04/03/2012] [Indexed: 11/15/2022]
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38
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Comparative investigations on thermostable pyrimidine nucleoside phosphorylases from Geobacillus thermoglucosidasius and Thermus thermophilus. ACTA ACUST UNITED AC 2012. [DOI: 10.1016/j.molcatb.2012.02.006] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
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39
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Pilarek M, Brand E, Hillig F, Krause M, Neubauer P. Enhanced plasmid production in miniaturized high-cell-density cultures of Escherichia coli supported with perfluorinated oxygen carrier. Bioprocess Biosyst Eng 2012. [PMID: 23178986 PMCID: PMC3722437 DOI: 10.1007/s00449-012-0861-7] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/30/2022]
Abstract
A simple method for plasmid minipreps in closed 1.5 mL microcentrifuge tubes using a cultivation medium with internal substrate delivery (EnBase(®)) in combination with a two-phase perfluorodecalin (PFD) system supplying additional oxygen to the E. coli culture is described. The procedure can simply be performed on a thermoshaker using only 50 μL cultivation volume. Twenty and twenty-five percent higher cell densities and plasmid concentration, respectively, were obtained with the additional oxygen delivery system when compared to cultures without PFD. Compared to standard 2 mL LB cultures ninefold higher cell densities and eightfold higher plasmid concentrations were achieved for the smaller culture volume. The μL-scale cultures can be directly utilized in further plasmid purification without any centrifugation step or the subsequent removal of the supernatant. This simplifies the routine procedure considerably. Furthermore, the new method is very robust considering the time of cultivation. Highest plasmid concentrations were already obtained after only 6 h of cultivation, but the plasmid concentration remained high (87 % of the maximum) even until 8 h of cultivation. Aside from the advantage of this method for the daily routine, we believe that it could also be applied to automated high-throughput processes.
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Affiliation(s)
- Maciej Pilarek
- Chair of Bioprocess Engineering, Department of Biotechnology, Technische Universität Berlin, Berlin, Germany.
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40
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Rohe P, Venkanna D, Kleine B, Freudl R, Oldiges M. An automated workflow for enhancing microbial bioprocess optimization on a novel microbioreactor platform. Microb Cell Fact 2012; 11:144. [PMID: 23113930 PMCID: PMC3526558 DOI: 10.1186/1475-2859-11-144] [Citation(s) in RCA: 87] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2012] [Accepted: 10/29/2012] [Indexed: 02/04/2023] Open
Abstract
BACKGROUND High-throughput methods are widely-used for strain screening effectively resulting in binary information regarding high or low productivity. Nevertheless achieving quantitative and scalable parameters for fast bioprocess development is much more challenging, especially for heterologous protein production. Here, the nature of the foreign protein makes it impossible to predict the, e.g. best expression construct, secretion signal peptide, inductor concentration, induction time, temperature and substrate feed rate in fed-batch operation to name only a few. Therefore, a high number of systematic experiments are necessary to elucidate the best conditions for heterologous expression of each new protein of interest. RESULTS To increase the throughput in bioprocess development, we used a microtiter plate based cultivation system (Biolector) which was fully integrated into a liquid-handling platform enclosed in laminar airflow housing. This automated cultivation platform was used for optimization of the secretory production of a cutinase from Fusarium solani pisi with Corynebacterium glutamicum. The online monitoring of biomass, dissolved oxygen and pH in each of the microtiter plate wells enables to trigger sampling or dosing events with the pipetting robot used for a reliable selection of best performing cutinase producers. In addition to this, further automated methods like media optimization and induction profiling were developed and validated. All biological and bioprocess parameters were exclusively optimized at microtiter plate scale and showed perfect scalable results to 1 L and 20 L stirred tank bioreactor scale. CONCLUSIONS The optimization of heterologous protein expression in microbial systems currently requires extensive testing of biological and bioprocess engineering parameters. This can be efficiently boosted by using a microtiter plate cultivation setup embedded into a liquid-handling system, providing more throughput by parallelization and automation. Due to improved statistics by replicate cultivations, automated downstream analysis, and scalable process information, this setup has superior performance compared to standard microtiter plate cultivation.
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Affiliation(s)
- Peter Rohe
- Institute of Bio- and Geosciences, IBG-1: Biotechnology, Systems Biotechnology, Forschungszentrum Jülich GmbH, 52425, Jülich, Germany
| | - Deepak Venkanna
- Institute of Bio- and Geosciences, IBG-1: Biotechnology, Systems Biotechnology, Forschungszentrum Jülich GmbH, 52425, Jülich, Germany
| | - Britta Kleine
- Institute of Bio- and Geosciences, IBG-1: Biotechnology, Systemic Microbiology, Forschungszentrum Jülich GmbH, 52425, Jülich, Germany
| | - Roland Freudl
- Institute of Bio- and Geosciences, IBG-1: Biotechnology, Systemic Microbiology, Forschungszentrum Jülich GmbH, 52425, Jülich, Germany
| | - Marco Oldiges
- Institute of Bio- and Geosciences, IBG-1: Biotechnology, Systems Biotechnology, Forschungszentrum Jülich GmbH, 52425, Jülich, Germany
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41
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Kondragunta B, Joshi BH, Han J, Brorson KA, Puri RK, Moreira AR, Rao G. Bioreactor environment-sensitive sentinel genes as novel metrics for cell culture scale-down comparability. Biotechnol Prog 2012; 28:1138-51. [DOI: 10.1002/btpr.1606] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2012] [Revised: 07/11/2012] [Indexed: 12/18/2022]
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42
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Bower DM, Lee KS, Ram RJ, Prather KL. Fed-batch microbioreactor platform for scale down and analysis of a plasmid DNA production process. Biotechnol Bioeng 2012; 109:1976-86. [DOI: 10.1002/bit.24498] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2012] [Revised: 03/07/2012] [Accepted: 03/08/2012] [Indexed: 02/03/2023]
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Enzyme-based glucose delivery as a high content screening tool in yeast-based whole-cell biocatalysis. Appl Microbiol Biotechnol 2012; 94:931-7. [PMID: 22258642 DOI: 10.1007/s00253-011-3850-x] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2011] [Revised: 12/17/2011] [Accepted: 12/19/2011] [Indexed: 02/06/2023]
Abstract
The influence of glucose release on growth and biotransformation of yeasts was examined by using the medium EnBase® Flo in shake flasks. The medium contains a polysaccharide acting as substrate, which is degraded to glucose by the addition of an enzyme. In the present paper, this medium was adapted for the cultivation of yeasts by increasing the complex components (booster) and the enzyme concentrations to guarantee a higher glucose release rate. Important changes were an increase of the complex component booster to 10-15% and an increased glucose release by increasing the enzyme content to 15 U L(-1). The 20 yeasts investigated in the present work showed an improvement of growth and biomass production when cultivated with the EnBase medium in comparison to yeast extract dextrose (YED) medium. Values of optical densities (OD(600)) of approximately 40 AU (corresponding to over 60 g L(-1) wet cell weight) were achieved for all 20 yeast strains tested. During the following screening of the yeasts in whole-cell biotransformation, an improvement of the conversion for 19 out of the 20 yeasts cultivated with the EnBase Flo medium could be observed. The biomass from the EnBase Flo cultivation showed a higher conversion activity in the reduction of 2-butanone to (R/S)-2-butanol. The enantioselectivity (ee) of 15 yeast strains showed an improvement by using the EnBase medium. The number of yeasts with an ee >97% increased from zero with YED to six with EnBase medium. Thus, the use of a glucose release cultivation strategy in the screening process for transformation approaches provides significant benefits compared to standard batch approaches.
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Glucose-limited high cell density cultivations from small to pilot plant scale using an enzyme-controlled glucose delivery system. N Biotechnol 2012; 29:235-42. [DOI: 10.1016/j.nbt.2011.11.004] [Citation(s) in RCA: 33] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2011] [Revised: 10/07/2011] [Accepted: 11/02/2011] [Indexed: 11/22/2022]
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45
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Ukkonen K, Vasala A, Ojamo H, Neubauer P. High-yield production of biologically active recombinant protein in shake flask culture by combination of enzyme-based glucose delivery and increased oxygen transfer. Microb Cell Fact 2011; 10:107. [PMID: 22152005 PMCID: PMC3258199 DOI: 10.1186/1475-2859-10-107] [Citation(s) in RCA: 45] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2011] [Accepted: 12/12/2011] [Indexed: 11/22/2022] Open
Abstract
This report describes the combined use of an enzyme-based glucose release system (EnBase®) and high-aeration shake flask (Ultra Yield Flask™). The benefit of this combination is demonstrated by over 100-fold improvement in the active yield of recombinant alcohol dehydrogenase expressed in E. coli. Compared to Terrific Broth and ZYM-5052 autoinduction medium, the EnBase system improved yield mainly through increased productivity per cell. Four-fold increase in oxygen transfer by the Ultra Yield Flask contributed to higher cell density with EnBase but not with the other tested media, and consequently the product yield per ml of EnBase culture was further improved.
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46
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Uhlig C, Kabisch J, Palm GJ, Valentin K, Schweder T, Krell A. Heterologous expression, refolding and functional characterization of two antifreeze proteins from Fragilariopsis cylindrus (Bacillariophyceae). Cryobiology 2011; 63:220-8. [PMID: 21884691 DOI: 10.1016/j.cryobiol.2011.08.005] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2011] [Revised: 08/12/2011] [Accepted: 08/15/2011] [Indexed: 11/25/2022]
Abstract
Antifreeze proteins (AFPs) provide protection for organisms subjected to the presence of ice crystals. The psychrophilic diatom Fragilariopsis cylindrus which is frequently found in polar sea ice carries a multitude of AFP isoforms. In this study we report the heterologous expression of two antifreeze protein isoforms from F. cylindrus in Escherichia coli. Refolding from inclusion bodies produced proteins functionally active with respect to crystal deformation, recrystallization inhibition and thermal hysteresis. We observed a reduction of activity in the presence of the pelB leader peptide in comparison with the GS-linked SUMO-tag. Activity was positively correlated to protein concentration and buffer salinity. Thermal hysteresis and crystal deformation habit suggest the affiliation of the proteins to the hyperactive group of AFPs. One isoform, carrying a signal peptide for secretion, produced a thermal hysteresis up to 1.53°C±0.53°C and ice crystals of hexagonal bipyramidal shape. The second isoform, which has a long preceding N-terminal sequence of unknown function, produced thermal hysteresis of up to 2.34°C±0.25°C. Ice crystals grew in form of a hexagonal column in presence of this protein. The different sequences preceding the ice binding domain point to distinct localizations of the proteins inside or outside the cell. We thus propose that AFPs have different functions in vivo, also reflected in their specific TH capability.
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Affiliation(s)
- Christiane Uhlig
- Alfred Wegener Institute for Polar and Marine Research, Bremerhaven, Germany.
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47
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Szeker K, Niemitalo O, Casteleijn MG, Juffer AH, Neubauer P. High-temperature cultivation and 5' mRNA optimization are key factors for the efficient overexpression of thermostable Deinococcus geothermalis purine nucleoside phosphorylase in Escherichia coli. J Biotechnol 2011; 156:268-74. [PMID: 21871934 DOI: 10.1016/j.jbiotec.2011.08.009] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2011] [Revised: 08/05/2011] [Accepted: 08/10/2011] [Indexed: 11/16/2022]
Abstract
Overexpression of genes from thermophiles in Escherichia coli is an attractive approach towards the large-scale production of thermostable biocatalysts. However, various factors can challenge efficient heterologous protein expression--one example is the formation of stable 5' mRNA secondary structures that can impede an efficient translation initiation. In this work, we describe the expression optimization of purine nucleoside phosphorylase from the thermophilic microbe Deinococcus geothermalis in E. coli. Poor expression levels caused by stable secondary 5' mRNA structure formation were addressed by two different approaches: (i) increasing the cultivation temperature above the range used typically for recombinant protein expression and (ii) optimizing the 5' mRNA sequence for reduced secondary structures in the translation initiation region. The increase of the cultivation temperature from 30°C to 42°C allowed a more than 10-fold increase of activity per cell and optimizing the 5' mRNA gene sequence further increased the activity per cell 1.7-fold at 42°C. Thus, the combination of high-temperature cultivation and 5' sequence optimization is described as an effective approach to overcome poor expression levels resulting from stable secondary 5' mRNA structure formation. We suggest that this method is especially suitable for improving the expression of proteins derived from thermophiles in E. coli.
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Affiliation(s)
- Kathleen Szeker
- Department of Biotechnology, Technische Universität Berlin, Ackerstrasse 71-76, Berlin, Germany.
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Šiurkus J, Neubauer P. Heterologous production of active ribonuclease inhibitor in Escherichia coli by redox state control and chaperonin coexpression. Microb Cell Fact 2011; 10:65. [PMID: 21824411 PMCID: PMC3161860 DOI: 10.1186/1475-2859-10-65] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2011] [Accepted: 08/08/2011] [Indexed: 01/26/2023] Open
Abstract
Background Eukaryotic Ribonuclease inhibitor (RI), belonging to the RNH1 family, is distinguished by unique features - a high sensitivity to oxidation due to the large number of reduced cysteins and a high hydrophobicity, which made most production approaches so far unsuccessful or resulted in very low yields. In this work efficient in vivo folding of native RI in the Escherichia coli cytoplasm was obtained by external addition of a reducing agent in tandem with oxygen limitation and overproduction of a molecular chaperonin. After optimisation of the production conditions in the shake flask scale the process was scaled up to high cell densities by applying a glucose limited fed-batch procedure. Results RI production in a T7 RNA polymerase based system results in accumulation of aggregated inactive product in inclusion bodies. Combination of addition of the reductant DTT, low production temperature and coexpression of the chaperonin GroELS resulted in high level production of approximately 25 mg g-1 CDW active RI in E. coli ER2566 pET21b, corresponding to approximately 800 kU g-1 cell wet weight. Further conditional screening under fed-batch-like conditions with the EnBase® technology and scale up into the bioreactor scale resulted in an efficient high cell density glucose and oxygen limited fed-batch process with a final cell dry weight of 25 g L-1 and a total RI yield of app. 625 mg L-1 (volumetric activity of 80,000 kU L-1). The E. coli based production constructs showed a very high robustness. The recombinant culture maintained its productivity despite the combination of the toxic growth conditions, the substrate limited production mode in tandem with a high level expression of several recombinant proteins, the set of molecular chaperonins and the target protein (RI). Conclusions High level production of active RI in E. coli in a T7 RNA polymerase expression system depends on the following factors: (i) addition of a reducing agent, (ii) low production temperature, (iii) oxygen limitation, and (iii) co-overexpression of the chaperonin GroELS. The study indicates the strength of applying fed-batch cultivation techniques for the efficient optimisation of production factors already at the screening stage for fast and straight forward bioprocess development even for target proteins which show a complex folding behaviour. In our case none of the approaches alone would have resulted in significant accumulation of active RI.
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Affiliation(s)
- Juozas Šiurkus
- Thermo Fisher Scientific, V.Graiciuno 8, LT-02241 Vilnius, Lithuania
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Cavallaro AS, Mahony D, Commins M, Mahony TJ, Mitter N. Endotoxin-free purification for the isolation of bovine viral diarrhoea virus E2 protein from insoluble inclusion body aggregates. Microb Cell Fact 2011; 10:57. [PMID: 21787435 PMCID: PMC3160874 DOI: 10.1186/1475-2859-10-57] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2011] [Accepted: 07/26/2011] [Indexed: 01/30/2023] Open
Abstract
Background Protein expression in Escherichia coli may result in the recombinant protein being expressed as insoluble inclusion bodies. In addition, proteins purified from E. coli contain endotoxins which need to be removed for in vivo applications. The structural protein, E2, from Bovine Viral Diarrhoea Virus (BVDV) is a major immunogenic determinant, and is an ideal candidate as a subunit vaccine. The E2 protein contains 17 cysteine residues creating difficulties in E. coli expression. In this report we outline a procedure for successfully producing soluble and endotoxin-free BVDV E2 protein from inclusion bodies (IB). Results The expression of a truncated form of BVDV-E2 protein (E2-T1) in E. coli resulted in predominantly aggregated insoluble IB. Solubilisation of E2-T1 with high purity and stability from IB aggregates was achieved using a strong reducing buffer containing 100 mM Dithiothreitol. Refolding by dialysis into 50 mM Tris (pH 7.0) containing 0.2% Igepal CA630 resulted in a soluble but aggregated protein solution. The novel application of a two-phase extraction of inclusion body preparations with Triton X-114 reduced endotoxin in solubilised E2-T1 to levels suitable for in vivo use without affecting protein yields. Dynamic light scattering analyses showed 37.5% of the protein was monomeric, the remaining comprised of soluble aggregates. Mice immunised with E2-T1 developed a high titre antibody response by ELISA. Western hybridisation analysis showed E2-T1 was recognised by sera from immunised mice and also by several BVDV-E2 polyclonal and monoclonal antibodies. Conclusion We have developed a procedure using E. coli to produce soluble E2-T1 protein from IB, and due to their insoluble nature we utilised a novel approach using Triton X-114 to efficiently remove endotoxin. The resultant protein is immunogenic and detectable by BVDV-E2 specific antibodies indicating its usefulness for diagnostic applications and as a subunit vaccine. The optimised E. coli expression system for E2-T1 combined with methodologies for solubilisation, refolding and integrated endotoxin removal presented in this study should prove useful for other vaccine applications.
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Affiliation(s)
- Antonino S Cavallaro
- Queensland Agricultural Biotechnology Facility, Agri-Science Queensland, Queensland, Australia
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Pilarek M, Glazyrina J, Neubauer P. Enhanced growth and recombinant protein production of Escherichia coli by a perfluorinated oxygen carrier in miniaturized fed-batch cultures. Microb Cell Fact 2011; 10:50. [PMID: 21708024 PMCID: PMC3141378 DOI: 10.1186/1475-2859-10-50] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2011] [Accepted: 06/27/2011] [Indexed: 11/28/2022] Open
Abstract
Background Liquid perfluorochemicals (PFCs) are interesting oxygen carriers in medicine and biotechnology with a high solubility for oxygen. They have been repeatedly used for improving oxygen transfer into prokaryotic and eukaryotic cell cultures, however their application is still limited. Here we show the great benefit of air/oxygen saturated perfluorodecalin (PFD) for high cell density cultivation of Escherichia coli in microwell plates and their positive effect on the soluble production of a correctly folded heterologously expressed alcohol dehydrogenase. Results In EnBase® cultivations the best effect was seen with PFD saturated with oxygen enriched air (appr. 10 μM oxygen per ml) when PFD was added at the time of induction. In contrast the effect of PFD was negligible when it was added already at the time of inoculation. Optimisation of addition time and content of loaded oxygen into the PFD resulted in an increased the cell density by 40% compared to control cultures, and correspondingly also the product yield increased, demonstrated at the example of a recombinant alcohol dehydrogenase. Conclusions PFCs are a valuable additive in miniaturized cell culture formats. For production of recombinant proteins in low cell density shaken cultures the addition of oxygen-enriched PFD makes the process more robust, i.e. a high product yield is not any more limited to a very narrow cell density window during which the induction has to be done. The positive effect of PFD was even more obvious when it was added during high cell density cultures. The effect of the PFD phase depends on the amount of oxygen which is loaded into the PFD and which thus is a matter of optimisation.
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Affiliation(s)
- Maciej Pilarek
- Department of Biotechnology and Bioprocess Engineering, Faculty of Chemical and Process Engineering, Warsaw University of Technology, Poland
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