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Rohr K, Gremm L, Geinitz B, Jourdier E, Wiechert W, Ben Chaabane F, Oldiges M. Optimizing microbioreactor cultivation strategies for Trichoderma reesei: from batch to fed-batch operations. Microb Cell Fact 2024; 23:112. [PMID: 38622596 DOI: 10.1186/s12934-024-02371-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2024] [Accepted: 03/18/2024] [Indexed: 04/17/2024] Open
Abstract
BACKGROUND Filamentous fungi have long been recognized for their exceptional enzyme production capabilities. Among these, Trichoderma reesei has emerged as a key producer of various industrially relevant enzymes and is particularly known for the production of cellulases. Despite the availability of advanced gene editing techniques for T. reesei, the cultivation and characterization of resulting strain libraries remain challenging, necessitating well-defined and controlled conditions with higher throughput. Small-scale cultivation devices are popular for screening bacterial strain libraries. However, their current use for filamentous fungi is limited due to their complex morphology. RESULTS This study addresses this research gap through the development of a batch cultivation protocol using a microbioreactor for cellulase-producing T. reesei strains (wild type, RutC30 and RutC30 TR3158) with offline cellulase activity analysis. Additionally, the feasibility of a microscale fed-batch cultivation workflow is explored, crucial for mimicking industrial cellulase production conditions. A batch cultivation protocol was developed and validated using the BioLector microbioreactor, a Round Well Plate, adapted medium and a shaking frequency of 1000 rpm. A strong correlation between scattered light intensity and cell dry weight underscores the reliability of this method in reflecting fungal biomass formation, even in the context of complex fungal morphology. Building on the batch results, a fed-batch strategy was established for T. reesei RutC30. Starting with a glucose concentration of 2.5 g l- 1 in the batch phase, we introduced a dual-purpose lactose feed to induce cellulase production and prevent carbon catabolite repression. Investigating lactose feeding rates from 0.3 to 0.75 g (l h)- 1 , the lowest rate of 0.3 g (l h)- 1 revealed a threefold increase in cellobiohydrolase and a fivefold increase in β -glucosidase activity compared to batch processes using the same type and amount of carbon sources. CONCLUSION We successfully established a robust microbioreactor batch cultivation protocol for T. reesei wild type, RutC30 and RutC30 TR3158, overcoming challenges associated with complex fungal morphologies. The study highlights the effectiveness of microbioreactor workflows in optimizing cellulase production with T. reesei, providing a valuable tool for simultaneous assessment of critical bioprocess parameters and facilitating efficient strain screening. The findings underscore the potential of microscale fed-batch strategies for enhancing enzyme production capabilities, revealing insights for future industrial applications in biotechnology.
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Affiliation(s)
- Katja Rohr
- Institute of Bio- and Geosciences, IBG-1: Biotechnology, Forschungszentrum Jülich GmbH, Wilhelm-Johnen-Straße, 52428, Jülich, Germany
- Institute of Biotechnology, RWTH Aachen University, Worringerweg 3, 52074, Aachen, Germany
| | - Lisa Gremm
- Institute of Bio- and Geosciences, IBG-1: Biotechnology, Forschungszentrum Jülich GmbH, Wilhelm-Johnen-Straße, 52428, Jülich, Germany
- Institute of Biotechnology, RWTH Aachen University, Worringerweg 3, 52074, Aachen, Germany
| | - Bertram Geinitz
- Institute of Bio- and Geosciences, IBG-1: Biotechnology, Forschungszentrum Jülich GmbH, Wilhelm-Johnen-Straße, 52428, Jülich, Germany
| | - Etienne Jourdier
- IFP Énergies nouvelles, 1 et 4 avenue de Bois-Préau, 92852, Rueil-Malmaison, France
| | - Wolfgang Wiechert
- Institute of Bio- and Geosciences, IBG-1: Biotechnology, Forschungszentrum Jülich GmbH, Wilhelm-Johnen-Straße, 52428, Jülich, Germany
- Computational Systems Biotechnology (AVT.CSB), RWTH Aachen University, 52074, Aachen, Germany
| | - Fadhel Ben Chaabane
- IFP Énergies nouvelles, 1 et 4 avenue de Bois-Préau, 92852, Rueil-Malmaison, France
| | - Marco Oldiges
- Institute of Bio- and Geosciences, IBG-1: Biotechnology, Forschungszentrum Jülich GmbH, Wilhelm-Johnen-Straße, 52428, Jülich, Germany.
- Institute of Biotechnology, RWTH Aachen University, Worringerweg 3, 52074, Aachen, Germany.
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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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Sparviero S, Barth L, Keil T, Dinter C, Berg C, Lattermann C, Büchs J. Black glucose-releasing silicon elastomer rings for fed-batch operation allow measurement of the oxygen transfer rate from the top and optical signals from the bottom for each well of a microtiter plate. BMC Biotechnol 2023; 23:5. [PMID: 36864427 PMCID: PMC9983259 DOI: 10.1186/s12896-023-00775-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2022] [Accepted: 02/22/2023] [Indexed: 03/04/2023] Open
Abstract
BACKGROUND In industrial microbial biotechnology, fed-batch processes are frequently used to avoid undesirable biological phenomena, such as substrate inhibition or overflow metabolism. For targeted process development, fed-batch options for small scale and high throughput are needed. One commercially available fed-batch fermentation system is the FeedPlate®, a microtiter plate (MTP) with a polymer-based controlled release system. Despite standardisation and easy incorporation into existing MTP handling systems, FeedPlates® cannot be used with online monitoring systems that measure optically through the transparent bottom of the plate. One such system that is broadly used in biotechnological laboratories, is the commercial BioLector. To allow for BioLector measurements, while applying the polymer-based feeding technology, positioning of polymer rings instead of polymer disks at the bottom of the well has been proposed. This strategy has a drawback: measurement requires an adjustment of the software settings of the BioLector device. This adjustment modifies the measuring position relative to the wells, so that the light path is no longer blocked by the polymer ring, but, traverses through the inner hole of the ring. This study aimed at overcoming that obstacle and allowing for measurement of fed-batch cultivations using a commercial BioLector without adjustment of the relative measurement position within each well. RESULTS Different polymer ring heights, colours and positions in the wells were investigated for their influence on maximum oxygen transfer capacity, mixing time and scattered light measurement. Several configurations of black polymer rings were identified that allow measurement in an unmodified, commercial BioLector, comparable to wells without rings. Fed-batch experiments with black polymer rings with two model organisms, E. coli and H. polymorpha, were conducted. The identified ring configurations allowed for successful cultivations, measuring the oxygen transfer rate and dissolved oxygen tension, pH, scattered light and fluorescence. Using the obtained online data, glucose release rates of 0.36 to 0.44 mg/h could be determined. They are comparable to formerly published data of the polymer matrix. CONCLUSION The final ring configurations allow for measurements of microbial fed-batch cultivations using a commercial BioLector without requiring adjustments of the instrumental measurement setup. Different ring configurations achieve similar glucose release rates. Measurements from above and below the plate are possible and comparable to measurements of wells without polymer rings. This technology enables the generation of a comprehensive process understanding and target-oriented process development for industrial fed-batch processes.
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Affiliation(s)
- Sarah Sparviero
- Aachener Verfahrenstechnik - Biochemical Engineering, RWTH Aachen University, Forckenbeckstr. 51, 52074, Aachen, Germany
| | - Laura Barth
- Aachener Verfahrenstechnik - Biochemical Engineering, RWTH Aachen University, Forckenbeckstr. 51, 52074, Aachen, Germany
| | - Timm Keil
- Aachener Verfahrenstechnik - Biochemical Engineering, RWTH Aachen University, Forckenbeckstr. 51, 52074, Aachen, Germany
| | - Carl Dinter
- Aachener Verfahrenstechnik - Biochemical Engineering, RWTH Aachen University, Forckenbeckstr. 51, 52074, Aachen, Germany
| | - Christoph Berg
- Aachener Verfahrenstechnik - Biochemical Engineering, RWTH Aachen University, Forckenbeckstr. 51, 52074, Aachen, Germany
| | | | - Jochen Büchs
- Aachener Verfahrenstechnik - Biochemical Engineering, RWTH Aachen University, Forckenbeckstr. 51, 52074, Aachen, Germany.
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4
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Wollborn D, Munkler LP, Horstmann R, Germer A, Blank LM, Büchs J. Predicting high recombinant protein producer strains of Pichia pastoris Mut S using the oxygen transfer rate as an indicator of metabolic burden. Sci Rep 2022; 12:11225. [PMID: 35780248 PMCID: PMC9250517 DOI: 10.1038/s41598-022-15086-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2022] [Accepted: 06/17/2022] [Indexed: 11/09/2022] Open
Abstract
The methylotrophic yeast Pichia pastoris (Komagataella phaffii) is a widely used host for recombinant protein production. In this study, a clonal library of P. pastoris MutS strains (S indicates slow methanol utilization) was screened for high green fluorescent protein (GFP) production. The expression cassette was under the control of the methanol inducible AOX promoter. The growth behavior was online-monitored in 48-well and 96-well microtiter plates by measuring the oxygen transfer rate (OTR). By comparing the different GFP producing strains, a correlation was established between the slope of the cumulative oxygen transfer during the methanol metabolization phase and the strain’s production performance. The correlation corresponds to metabolic burden during methanol induction. The findings were validated using a pre-selected strain library (7 strains) of high, medium, and low GFP producers. For those strains, the gene copy number was determined via Whole Genome Sequencing. The results were consistent with the described OTR correlation. Additionally, a larger clone library (45 strains) was tested to validate the applicability of the proposed method. The results from this study suggest that the cumulative oxygen transfer can be used as a screening criterion for protein production performance that allows for a simple primary screening process, facilitating the pre-selection of high producing strains.
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Affiliation(s)
- David Wollborn
- Chair of Biochemical Engineering (AVT.BioVT), RWTH Aachen University, 52074, Aachen, Germany
| | - Lara Pauline Munkler
- Chair of Biochemical Engineering (AVT.BioVT), RWTH Aachen University, 52074, Aachen, Germany
| | - Rebekka Horstmann
- Chair of Biochemical Engineering (AVT.BioVT), RWTH Aachen University, 52074, Aachen, Germany
| | - Andrea Germer
- iAMB - Institute of Applied Microbiology, RWTH Aachen University, 52074, Aachen, Germany
| | - Lars Mathias Blank
- iAMB - Institute of Applied Microbiology, RWTH Aachen University, 52074, Aachen, Germany
| | - Jochen Büchs
- Chair of Biochemical Engineering (AVT.BioVT), RWTH Aachen University, 52074, Aachen, Germany.
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5
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Teworte S, Malcı K, Walls LE, Halim M, Rios-Solis L. Recent advances in fed-batch microscale bioreactor design. Biotechnol Adv 2021; 55:107888. [PMID: 34923075 DOI: 10.1016/j.biotechadv.2021.107888] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2021] [Revised: 11/25/2021] [Accepted: 12/11/2021] [Indexed: 12/17/2022]
Abstract
Advanced fed-batch microbioreactors mitigate scale up risks and more closely mimic industrial cultivation practices. Recently, high throughput microscale feeding strategies have been developed which improve the accessibility of microscale fed-batch cultivation irrespective of experimental budget. This review explores such technologies and their role in accelerating bioprocess development. Diffusion- and enzyme-controlled feeding achieve a continuous supply of substrate while being simple and affordable. More complex feed profiles and greater process control require additional hardware. Automated liquid handling robots may be programmed to predefined feed profiles and have the sensitivity to respond to deviations in process parameters. Microfluidic technologies have been shown to facilitate both continuous and precise feeding. Holistic approaches, which integrate automated high-throughput fed-batch cultivation with strategic design of experiments and model-based optimisation, dramatically enhance process understanding whilst minimising experimental burden. The incorporation of real-time data for online optimisation of feed conditions can further refine screening. Although the technologies discussed in this review hold promise for efficient, low-risk bioprocess development, the expense and complexity of automated cultivation platforms limit their widespread application. Future attention should be directed towards the development of open-source software and reducing the exclusivity of hardware.
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Affiliation(s)
- Sarah Teworte
- Institute for Bioengineering, School of Engineering, University of Edinburgh, The King's Buildings, Edinburgh EH9 3DW, Scotland, United Kingdom
| | - Koray Malcı
- Institute for Bioengineering, School of Engineering, University of Edinburgh, The King's Buildings, Edinburgh EH9 3DW, Scotland, United Kingdom; Centre for Synthetic and Systems Biology, University of Edinburgh, The King's Buildings, Edinburgh EH9 3DW, Scotland, United Kingdom
| | - Laura E Walls
- Institute for Bioengineering, School of Engineering, University of Edinburgh, The King's Buildings, Edinburgh EH9 3DW, Scotland, United Kingdom; Centre for Synthetic and Systems Biology, University of Edinburgh, The King's Buildings, Edinburgh EH9 3DW, Scotland, United Kingdom
| | - Murni Halim
- Department of Bioprocess Technology, Faculty of Biotechnology and Biomolecular Sciences, Universiti Putra Malaysia, 43400 UPM Serdang, Selangor Darul Ehsan, Malaysia
| | - Leonardo Rios-Solis
- Institute for Bioengineering, School of Engineering, University of Edinburgh, The King's Buildings, Edinburgh EH9 3DW, Scotland, United Kingdom; Centre for Synthetic and Systems Biology, University of Edinburgh, The King's Buildings, Edinburgh EH9 3DW, Scotland, United Kingdom.
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6
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Jansen R, Morschett H, Hasenklever D, Moch M, Wiechert W, Oldiges M. Microbioreactor-assisted cultivation workflows for time-efficient phenotyping of protein producing Aspergillus niger in batch and fed-batch mode. Biotechnol Prog 2021; 37:e3144. [PMID: 33745237 DOI: 10.1002/btpr.3144] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2020] [Revised: 02/20/2021] [Accepted: 02/28/2021] [Indexed: 11/10/2022]
Abstract
In recent years, many fungal genomes have become publicly available. In combination with novel gene editing tools, this allows for accelerated strain construction, making filamentous fungi even more interesting for the production of valuable products. However, besides their extraordinary production and secretion capacities, fungi most often exhibit challenging morphologies, which need to be screened for the best operational window. Thereby, combining genetic diversity with various environmental parameters results in a large parameter space, creating a strong demand for time-efficient phenotyping technologies. Microbioreactor systems, which have been well established for bacterial organisms, enable an increased cultivation throughput via parallelization and miniaturization, as well as enhanced process insight via non-invasive online monitoring. Nevertheless, only few reports about microtiter plate cultivation for filamentous fungi in general and even less with online monitoring exist in literature. Moreover, screening under batch conditions in microscale, when a fed-batch process is performed in large-scale might even lead to the wrong identification of optimized parameters. Therefore, in this study a novel workflow for Aspergillus niger was developed, allowing for up to 48 parallel microbioreactor cultivations in batch as well as fed-batch mode. This workflow was validated against lab-scale bioreactor cultivations to proof scalability. With the optimized cultivation protocol, three different micro-scale fed-batch strategies were tested to identify the best protein production conditions for intracellular model product GFP. Subsequently, the best feeding strategy was again validated in a lab-scale bioreactor.
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Affiliation(s)
- Roman Jansen
- Forschungszentrum Jülich GmbH, Institute of Bio- and Geosciences, IBG-1: Biotechnology, Jülich, Germany.,Institute of Biotechnology, RWTH Aachen University, Aachen, Germany
| | - Holger Morschett
- Forschungszentrum Jülich GmbH, Institute of Bio- and Geosciences, IBG-1: Biotechnology, Jülich, Germany
| | - Dennis Hasenklever
- Forschungszentrum Jülich GmbH, Institute of Bio- and Geosciences, IBG-1: Biotechnology, Jülich, Germany
| | - Matthias Moch
- Forschungszentrum Jülich GmbH, Institute of Bio- and Geosciences, IBG-1: Biotechnology, Jülich, Germany
| | - Wolfgang Wiechert
- Forschungszentrum Jülich GmbH, Institute of Bio- and Geosciences, IBG-1: Biotechnology, Jülich, Germany.,Computational Systems Biotechnology, RWTH Aachen University, Jülich, Germany
| | - Marco Oldiges
- Forschungszentrum Jülich GmbH, Institute of Bio- and Geosciences, IBG-1: Biotechnology, Jülich, Germany.,Institute of Biotechnology, RWTH Aachen University, Aachen, Germany
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7
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Liebal UW, Fabry BA, Ravikrishnan A, Schedel CV, Schmitz S, Blank LM, Ebert BE. Genome-scale model reconstruction of the methylotrophic yeast Ogataea polymorpha. BMC Biotechnol 2021; 21:23. [PMID: 33722219 PMCID: PMC7962355 DOI: 10.1186/s12896-021-00675-w] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2020] [Accepted: 12/04/2020] [Indexed: 11/10/2022] Open
Abstract
Background Ogataea polymorpha is a thermotolerant, methylotrophic yeast with significant industrial applications. While previously mainly used for protein synthesis, it also holds promise for producing platform chemicals. O. polymorpha has the distinct advantage of using methanol as a substrate, which could be potentially derived from carbon capture and utilization streams. Full development of the organism into a production strain and estimation of the metabolic capabilities require additional strain design, guided by metabolic modeling with a genome-scale metabolic model. However, to date, no genome-scale metabolic model is available for O. polymorpha. Results To overcome this limitation, we used a published reconstruction of the closely related yeast Komagataella phaffii as a reference and corrected reactions based on KEGG and MGOB annotation. Additionally, we conducted phenotype microarray experiments to test the suitability of 190 substrates as carbon sources. Over three-quarter of the substrate use was correctly reproduced by the model and 27 new substrates were added, that were not present in the K. phaffii reference model. Conclusion The developed genome-scale metabolic model of O. polymorpha will support the engineering of synthetic metabolic capabilities and enable the optimization of production processes, thereby supporting a sustainable future methanol economy. Supplementary Information The online version contains supplementary material available at (10.1186/s12896-021-00675-w).
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Affiliation(s)
- Ulf W Liebal
- Institute of Applied Microbiology-iAMB, Aachen Biology and Biotechnology-ABBt, RWTH Aachen University, Worringer Weg 1, Aachen, 52074, Germany
| | - Brigida A Fabry
- Institute of Applied Microbiology-iAMB, Aachen Biology and Biotechnology-ABBt, RWTH Aachen University, Worringer Weg 1, Aachen, 52074, Germany
| | - Aarthi Ravikrishnan
- Genome Institute of Singapore, 60 Biopolis Street, Genome, 03-01, Singapore, 138672, Singapore
| | - Constantin Vl Schedel
- Institute of Applied Microbiology-iAMB, Aachen Biology and Biotechnology-ABBt, RWTH Aachen University, Worringer Weg 1, Aachen, 52074, Germany
| | - Simone Schmitz
- Institute of Applied Microbiology-iAMB, Aachen Biology and Biotechnology-ABBt, RWTH Aachen University, Worringer Weg 1, Aachen, 52074, Germany
| | - Lars M Blank
- Institute of Applied Microbiology-iAMB, Aachen Biology and Biotechnology-ABBt, RWTH Aachen University, Worringer Weg 1, Aachen, 52074, Germany.
| | - Birgitta E Ebert
- Institute of Applied Microbiology-iAMB, Aachen Biology and Biotechnology-ABBt, RWTH Aachen University, Worringer Weg 1, Aachen, 52074, Germany.,Australian Institute for Bioengineering and Nanotechnology, The University of Queensland, Brisbane, QLD 4072, Australia.,CSIRO Future Science Platform in Synthetic Biology, Commonwealth Scientific and Industrial Research Organisation (CSIRO), Black Mountain, ACT 2601, Australia
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8
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Habicher T, Klein T, Becker J, Daub A, Büchs J. Screening for optimal protease producing Bacillus licheniformis strains with polymer-based controlled-release fed-batch microtiter plates. Microb Cell Fact 2021; 20:51. [PMID: 33622330 PMCID: PMC7903736 DOI: 10.1186/s12934-021-01541-2] [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: 10/03/2020] [Accepted: 02/10/2021] [Indexed: 11/21/2022] Open
Abstract
Background Substrate-limited fed-batch conditions have the favorable effect of preventing overflow metabolism, catabolite repression, oxygen limitation or inhibition caused by elevated substrate or osmotic concentrations. Due to these favorable effects, fed-batch mode is predominantly used in industrial production processes. In contrast, screening processes are usually performed in microtiter plates operated in batch mode. This leads to a different physiological state of the production organism in early screening and can misguide the selection of potential production strains. To close the gap between screening and production conditions, new techniques to enable fed-batch mode in microtiter plates have been described. One of these systems is the ready-to-use and disposable polymer-based controlled-release fed-batch microtiter plate (fed-batch MTP). In this work, the fed-batch MTP was applied to establish a glucose-limited fed-batch screening procedure for industrially relevant protease producing Bacillus licheniformis strains. Results To achieve equal initial growth conditions for different clones with the fed-batch MTP, a two-step batch preculture procedure was developed. Based on this preculture procedure, the standard deviation of the protease activity of glucose-limited fed-batch main culture cultivations in the fed-batch MTP was ± 10%. The determination of the number of replicates revealed that a minimum of 6 parallel cultivations were necessary to identify clones with a statistically significant increased or decreased protease activity. The developed glucose-limited fed-batch screening procedure was applied to 13 industrially-relevant clones from two B. licheniformis strain lineages. It was found that 12 out of 13 clones (92%) were classified similarly as in a lab-scale fed-batch fermenter process operated under glucose-limited conditions. When the microtiter plate screening process was performed in batch mode, only 5 out of 13 clones (38%) were classified similarly as in the lab-scale fed-batch fermenter process. Conclusion The glucose-limited fed-batch screening process outperformed the usual batch screening process in terms of the predictability of the clone performance under glucose-limited fed-batch fermenter conditions. These results highlight that the implementation of glucose-limited fed-batch conditions already in microtiter plate scale is crucial to increase the precision of identifying improved protease producing B. licheniformis strains. Hence, the fed-batch MTP represents an efficient high-throughput screening tool that aims at closing the gap between screening and production conditions.
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Affiliation(s)
- Tobias Habicher
- RWTH Aachen University, AVT - Biochemical Engineering, Forckenbeckstraße 51, 52074, Aachen, Germany
| | - Tobias Klein
- BASF SE, Carl-Bosch-Straße 38, 67056, Ludwigshafen am Rhein, Germany
| | - Jacqueline Becker
- BASF SE, Carl-Bosch-Straße 38, 67056, Ludwigshafen am Rhein, Germany
| | - Andreas Daub
- BASF SE, Carl-Bosch-Straße 38, 67056, Ludwigshafen am Rhein, Germany
| | - Jochen Büchs
- RWTH Aachen University, AVT - Biochemical Engineering, Forckenbeckstraße 51, 52074, Aachen, Germany.
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9
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Keil T, Dittrich B, Lattermann C, Büchs J. Optimized polymer-based glucose release in microtiter plates for small-scale E. coli fed-batch cultivations. J Biol Eng 2020; 14:24. [PMID: 32874201 PMCID: PMC7457294 DOI: 10.1186/s13036-020-00247-0] [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: 05/18/2020] [Accepted: 08/19/2020] [Indexed: 11/10/2022] Open
Abstract
Background Small-scale cultivation vessels, which allow fed-batch operation mode, become more and more important for fast and reliable early process development. Recently, the polymer-based feeding system was introduced to allow fed-batch conditions in microtiter plates. Maximum glucose release rates of 0.35 mg/h per well (48-well-plate) at 37 °C can be achieved with these plates, depending on the media properties. The fed-batch cultivation of fluorescent protein-expressing E. coli at oxygen transfer rate levels of 5 mmol/L/h proved to be superior compared to simple batch cultivations. However, literature suggests that higher glucose release rates than achieved with the currently available fed-batch microtiter plate are beneficial, especially for fast-growing microorganisms. During the fed-batch phase of the cultivation, a resulting oxygen transfer rate level of 28 mmol/L/h should be achieved. Results Customization of the polymer matrix enabled a considerable increase in the glucose release rate of more than 250% to up to 0.90 mg/h per well. Therefore, the molecular weight of the prepolymer and the addition of a hydrophilic PDMS-PEG copolymer allowed for the individual adjustment of a targeted glucose release rate. The newly developed polymer matrix was additionally invariant to medium properties like the osmotic concentration or the pH-value. The glucose release rate of the optimized matrix was constant in various synthetic and complex media. Fed-batch cultivations of E. coli in microtiter plates with the optimized matrix revealed elevated oxygen transfer rates during the fed-batch phase of approximately 28 mmol/L/h. However, these increased glucose release rates resulted in a prolonged initial batch phase and oxygen limitations. The newly developed polymer-based feeding system provides options to manufacture individual feed rates in a range from 0.24–0.90 mg/h per well. Conclusions The optimized polymer-based fed-batch microtiter plate allows higher reproducibility of fed-batch experiments since cultivation media properties have almost no influence on the release rate. The adjustment of individual feeding rates in a wide range supports the early process development for slow, average and fast-growing microorganisms in microtiter plates. The study underlines the importance of a detailed understanding of the metabolic behavior (through online monitoring techniques) to identify optimal feed rates.
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Affiliation(s)
- Timm Keil
- AVT - Biochemical Engineering, RWTH Aachen University, Forckenbeckstraße 51, 52074 Aachen, Germany
| | - Barbara Dittrich
- DWI - Leibniz Institute for Interactive Materials, Forckenbeckstraße 50, 52074 Aachen, Germany
| | | | - Jochen Büchs
- AVT - Biochemical Engineering, RWTH Aachen University, Forckenbeckstraße 51, 52074 Aachen, Germany
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10
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Morschett H, Jansen R, Neuendorf C, Moch M, Wiechert W, Oldiges M. Parallelized microscale fed-batch cultivation in online-monitored microtiter plates: implications of media composition and feed strategies for process design and performance. J Ind Microbiol Biotechnol 2020; 47:35-47. [PMID: 31673873 PMCID: PMC6971147 DOI: 10.1007/s10295-019-02243-w] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2019] [Accepted: 10/15/2019] [Indexed: 01/10/2023]
Abstract
Limited throughput represents a substantial drawback during bioprocess development. In recent years, several commercial microbioreactor systems have emerged featuring parallelized experimentation with optical monitoring. However, many devices remain limited to batch mode and do not represent the fed-batch strategy typically applied on an industrial scale. A workflow for 32-fold parallelized microscale cultivation of protein secreting Corynebacterium glutamicum in microtiter plates incorporating online monitoring, pH control and feeding was developed and validated. Critical interference of the essential media component protocatechuic acid with pH measurement was revealed, but was effectively resolved by 80% concentration reduction without affecting biological performance. Microfluidic pH control and feeding (pulsed, constant and exponential) were successfully implemented: Whereas pH control improved performance only slightly, feeding revealed a much higher optimization potential. Exponential feeding with µ = 0.1 h-1 resulted in the highest product titers. In contrast, other performance indicators such as biomass-specific or volumetric productivity resulted in different optimal feeding regimes.
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Affiliation(s)
- Holger Morschett
- Institute of Bio- and Geosciences, IBG-1: Biotechnology, Forschungszentrum Jülich GmbH, Jülich, Germany
| | - Roman Jansen
- Institute of Bio- and Geosciences, IBG-1: Biotechnology, Forschungszentrum Jülich GmbH, Jülich, Germany
- Institute of Biotechnology, RWTH Aachen University, Aachen, Germany
| | - Christian Neuendorf
- Institute of Bio- and Geosciences, IBG-1: Biotechnology, Forschungszentrum Jülich GmbH, Jülich, Germany
| | - Matthias Moch
- Institute of Bio- and Geosciences, IBG-1: Biotechnology, Forschungszentrum Jülich GmbH, Jülich, Germany
| | - Wolfgang Wiechert
- Institute of Bio- and Geosciences, IBG-1: Biotechnology, Forschungszentrum Jülich GmbH, Jülich, Germany
- Computational Systems Biotechnology, RWTH Aachen University, Aachen, Germany
| | - Marco Oldiges
- Institute of Bio- and Geosciences, IBG-1: Biotechnology, Forschungszentrum Jülich GmbH, Jülich, Germany.
- Institute of Biotechnology, RWTH Aachen University, Aachen, Germany.
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11
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Keil T, Dittrich B, Rührer J, Morschett H, Lattermann C, Möller M, Büchs J. Polymer-based ammonium-limited fed-batch cultivation in shake flasks improves lipid productivity of the microalga Chlorella vulgaris. BIORESOURCE TECHNOLOGY 2019; 291:121821. [PMID: 31352167 DOI: 10.1016/j.biortech.2019.121821] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/24/2019] [Revised: 07/12/2019] [Accepted: 07/15/2019] [Indexed: 06/10/2023]
Abstract
The aim of this work was to study ammonium-limited fed-batch conditions in heterotrophic C. vulgaris shake flask cultivations. Therefore, an innovative polymer-based ammonium release technique (polymer beads) was developed. Using these beads in shake flasks, C. vulgaris cultivations resulted in simultaneous growth and lipid accumulation. Lipid productivity was increased by 43% compared to batch cultivations. Furthermore, by online monitoring of the metabolic activity (RAMOS technique), unlimited growth and depletion of nutrients could be identified. A previously unknown sulfur limitation was detected in the applied Bold's Basal Medium. Combining the ammonium release beads with the RAMOS technique proved to be an efficient method for microalgae process development.
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Affiliation(s)
- T Keil
- AVT - Biochemical Engineering, RWTH Aachen University, Forckenbeckstraße 51, 52074 Aachen, Germany
| | - B Dittrich
- DWI - Leibniz Institute for Interactive Materials, RWTH Aachen University Forckenbeckstraße 50, 52074 Aachen, Germany
| | - J Rührer
- AVT - Biochemical Engineering, RWTH Aachen University, Forckenbeckstraße 51, 52074 Aachen, Germany
| | - H Morschett
- Institute of Bio- and Geosciences: IBG-1: Biotechnology, Forschungszentrum Jülich GmbH, Wilhelm-Johnen-Straße, 52428 Jülich, Germany
| | - C Lattermann
- Kuhner Shaker GmbH, Kaiserstraße 100, 52134 Herzogenrath, Germany
| | - M Möller
- DWI - Leibniz Institute for Interactive Materials, RWTH Aachen University Forckenbeckstraße 50, 52074 Aachen, Germany; Textile and Macromolecular Chemistry, RWTH Aachen University, Worringerweg 1, 52074 Aachen, Germany
| | - J Büchs
- AVT - Biochemical Engineering, RWTH Aachen University, Forckenbeckstraße 51, 52074 Aachen, Germany.
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12
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Narayanan H, Luna MF, Stosch M, Cruz Bournazou MN, Polotti G, Morbidelli M, Butté A, Sokolov M. Bioprocessing in the Digital Age: The Role of Process Models. Biotechnol J 2019; 15:e1900172. [DOI: 10.1002/biot.201900172] [Citation(s) in RCA: 90] [Impact Index Per Article: 18.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2019] [Revised: 07/15/2019] [Indexed: 12/20/2022]
Affiliation(s)
- Harini Narayanan
- Institute for Chemical and Bioengineering ETHZ Zurich Switzerland
| | - Martin F. Luna
- Institute for Chemical and Bioengineering ETHZ Zurich Switzerland
| | | | - Mariano Nicolas Cruz Bournazou
- Institute for Chemical and Bioengineering ETHZ Zurich Switzerland
- DataHow AGc/o ETH ZurichHCI, F137Vladimir‐Prelog‐Weg 1 8093 Zurich Switzerland
| | - Gianmarco Polotti
- DataHow AGc/o ETH ZurichHCI, F137Vladimir‐Prelog‐Weg 1 8093 Zurich Switzerland
| | - Massimo Morbidelli
- Institute for Chemical and Bioengineering ETHZ Zurich Switzerland
- DataHow AGc/o ETH ZurichHCI, F137Vladimir‐Prelog‐Weg 1 8093 Zurich Switzerland
| | - Alessandro Butté
- Institute for Chemical and Bioengineering ETHZ Zurich Switzerland
- DataHow AGc/o ETH ZurichHCI, F137Vladimir‐Prelog‐Weg 1 8093 Zurich Switzerland
| | - Michael Sokolov
- Institute for Chemical and Bioengineering ETHZ Zurich Switzerland
- DataHow AGc/o ETH ZurichHCI, F137Vladimir‐Prelog‐Weg 1 8093 Zurich Switzerland
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13
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Habicher T, Rauls EKA, Egidi F, Keil T, Klein T, Daub A, Büchs J. Establishing a Fed-Batch Process for Protease Expression with Bacillus licheniformis in Polymer-Based Controlled-Release Microtiter Plates. Biotechnol J 2019; 15:e1900088. [PMID: 31471944 DOI: 10.1002/biot.201900088] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2019] [Revised: 08/06/2019] [Indexed: 12/19/2022]
Abstract
Introducing fed-batch mode in early stages of development projects is crucial for establishing comparable conditions to industrial fed-batch fermentation processes. Therefore, cost efficient and easy to use small-scale fed-batch systems that can be integrated into existing laboratory equipment and workflows are required. Recently, a novel polymer-based controlled-release fed-batch microtiter plate is described. In this work, the polymer-based controlled-release fed-batch microtiter plate is used to investigate fed-batch cultivations of a protease producing Bacillus licheniformis culture. Therefore, the oxygen transfer rate (OTR) is online-monitored within each well of the polymer-based controlled-release fed-batch microtiter plate using a µRAMOS device. Cultivations in five individual polymer-based controlled-release fed-batch microtiter plates of two production lots show good reproducibility with a mean coefficient of variation of 9.2%. Decreasing initial biomass concentrations prolongs batch phase while simultaneously postponing the fed-batch phase. The initial liquid filling volume affects the volumetric release rate, which is directly translated in different OTR levels of the fed-batch phase. An increasing initial osmotic pressure within the mineral medium decreases both glucose release and protease yield. With the volumetric glucose release rate as scale-up criterion, microtiter plate- and shake flask-based fed-batch cultivations are highly comparable. On basis of the small-scale fed-batch cultivations, a mechanistic model is established and validated. Model-based simulations coincide well with the experimentally acquired data.
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Affiliation(s)
- Tobias Habicher
- AVT-Biochemical Engineering, RWTH Aachen University, Aachen, 52074, Germany
| | - Edward K A Rauls
- AVT-Biochemical Engineering, RWTH Aachen University, Aachen, 52074, Germany
| | - Franziska Egidi
- AVT-Biochemical Engineering, RWTH Aachen University, Aachen, 52074, Germany
| | - Timm Keil
- AVT-Biochemical Engineering, RWTH Aachen University, Aachen, 52074, Germany
| | - Tobias Klein
- White Biotechnology Research Unit, BASF SE, Ludwigshafen am Rhein, 67063, Germany
| | - Andreas Daub
- Chemical Engineering Industrial Biotechnology, BASF SE, Ludwigshafen am Rhein, 67063, Germany
| | - Jochen Büchs
- AVT-Biochemical Engineering, RWTH Aachen University, Aachen, 52074, Germany
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14
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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: 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: 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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15
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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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16
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Habicher T, Czotscher V, Klein T, Daub A, Keil T, Büchs J. Glucose‐containing polymer rings enable fed‐batch operation in microtiter plates with parallel online measurement of scattered light, fluorescence, dissolved oxygen tension, and pH. Biotechnol Bioeng 2019; 116:2250-2262. [DOI: 10.1002/bit.27077] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2019] [Revised: 05/20/2019] [Accepted: 05/28/2019] [Indexed: 12/21/2022]
Affiliation(s)
- Tobias Habicher
- AVT—Biochemical EngineeringRWTH Aachen UniversityAachen Germany
| | - Vroni Czotscher
- AVT—Biochemical EngineeringRWTH Aachen UniversityAachen Germany
| | - Tobias Klein
- White Biotechnology Research UnitBASF SELudwigshafen am Rhein Germany
| | - Andreas Daub
- Chemical Engineering Industrial BiotechnologyBASF SELudwigshafen am Rhein Germany
| | - Timm Keil
- AVT—Biochemical EngineeringRWTH Aachen UniversityAachen Germany
| | - Jochen Büchs
- AVT—Biochemical EngineeringRWTH Aachen UniversityAachen Germany
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17
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Müller J, Hütterott A, Habicher T, Mußmann N, Büchs J. Validation of the transferability of membrane-based fed-batch shake flask cultivations to stirred-tank reactor using three different protease producing Bacillus strains. J Biosci Bioeng 2019; 128:599-605. [PMID: 31151898 DOI: 10.1016/j.jbiosc.2019.05.003] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/11/2019] [Revised: 05/09/2019] [Accepted: 05/09/2019] [Indexed: 10/26/2022]
Abstract
Most industrial fermentation processes are operated in fed-batch mode to overcome catabolite repression, undesired by-product formation and oxygen limitation. To maintain comparable process conditions during screening of optimal production strains, the implementation of a fed-batch mode at small scale is crucial. In this study, three different protease producing Bacillus species, Bacillus aeolius, B. licheniformis and B. pumilus, were cultivated using the previously described membrane-based fed-batch shake flasks. Under carbon-limited conditions, catabolite repression was avoided, so that proteases were produced in all strains. Protease yields of B. aeolius and B. licheniformis increased 1.5-fold relative to batch cultivations. To validate process scalability between shake flasks and stirred tank reactors, membrane-based fed-batch shake flask cultivations were transferred to laboratory-scale stirred tank reactors with equal feeding rates. Despite inevitable differences between the scales such as pH control, feed supply and feed start, comparable results were achieved. Oxygen transfer rates of B. licheniformis and B. pumilus measured with the respiration activity monitoring system (RAMOS) in shake flasks and in stirred tank reactor with an off-gas analyzer were almost identical in both cultivation systems. The protease activities referring to the total consumed glucose were also mostly comparable. A slight decrease from shake flask to stirred tank reactor could be observed, which is presumably due to differences in pH control. This study successfully demonstrates the transferability of membrane-based fed-batch shake flask cultivations to laboratory-scale stirred tank reactors.
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Affiliation(s)
- Janina Müller
- AVT - Biochemical Engineering, RWTH Aachen University, Forckenbeckstraße 51, Aachen 52074, Germany.
| | - Anne Hütterott
- AVT - Biochemical Engineering, RWTH Aachen University, Forckenbeckstraße 51, Aachen 52074, Germany.
| | - Tobias Habicher
- AVT - Biochemical Engineering, RWTH Aachen University, Forckenbeckstraße 51, Aachen 52074, Germany.
| | - Nina Mußmann
- International R&D Laundry and Homecare, Henkel AG & Co KGaA, Henkelstr. 67, Düsseldorf 40589, Germany.
| | - Jochen Büchs
- AVT - Biochemical Engineering, RWTH Aachen University, Forckenbeckstraße 51, Aachen 52074, Germany.
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18
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Habicher T, John A, Scholl N, Daub A, Klein T, Philip P, Büchs J. Introducing substrate limitations to overcome catabolite repression in a protease producing Bacillus licheniformis strain using membrane-based fed-batch shake flasks. Biotechnol Bioeng 2019; 116:1326-1340. [PMID: 30712275 DOI: 10.1002/bit.26948] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/04/2018] [Revised: 01/22/2019] [Accepted: 01/30/2019] [Indexed: 11/11/2022]
Abstract
To overcome catabolite repression, industrial fermentation processes are usually operated in substrate-limited fed-batch mode. Therefore, the implementation of such an operating mode at small scale is crucial to maintain comparable process conditions. In this study, Bacillus licheniformis, a well-known producer of proteases, was cultivated with carbon (glucose)- and nitrogen (ammonium)-limited fed-batch conditions using the previously introduced membrane-based fed-batch shake flasks. A repression of protease production by glucose and ammonium was thus avoided and yields increased 1.5- and 2.1-fold relative to batch, respectively. An elevated feeding rate of glucose caused depletion of ammonium, which was recognizable within the oxygen transfer rate (OTR) signal measured with the Respiration Activity MOnitoring System (RAMOS). Ammonium limitation was prevented by feeding ammonium simultaneously with glucose. The OTR signal clearly indicated the initiation of the fed-batch phase and gave direct feedback on the nutrient release kinetics. Increased feeding rates of glucose and ammonium led to an elevated protease activity without affecting the protease yield (YP/Glu ). In addition to YP/Glu , protease yields were determined based on the metabolized amount of oxygen ( Y P / O 2 ) . The results showed that the protease production correlated with the amount of consumed glucose as well as with the amount of consumed oxygen. The membrane-based fed-batch shake flask in combination with the RAMOS device is a powerful combination to investigate the effect of substrate-limited fed-batch conditions.
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Affiliation(s)
- Tobias Habicher
- AVT - Biochemical Engineering, RWTH Aachen University, Aachen, Germany
| | - Arian John
- AVT - Biochemical Engineering, RWTH Aachen University, Aachen, Germany
| | - Niklas Scholl
- AVT - Biochemical Engineering, RWTH Aachen University, Aachen, Germany
| | - Andreas Daub
- Chemical Engineering Industrial Biotechnology, BASF SE, Ludwigshafen am Rhein, Germany
| | - Tobias Klein
- White Biotechnology Research Unit, BASF SE, Ludwigshafen am Rhein, Germany
| | - Priya Philip
- AVT - Biochemical Engineering, RWTH Aachen University, Aachen, Germany
| | - Jochen Büchs
- AVT - Biochemical Engineering, RWTH Aachen University, Aachen, Germany
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19
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Keil T, Dittrich B, Lattermann C, Habicher T, Büchs J. Polymer-based controlled-release fed-batch microtiter plate - diminishing the gap between early process development and production conditions. J Biol Eng 2019; 13:18. [PMID: 30833982 PMCID: PMC6387502 DOI: 10.1186/s13036-019-0147-6] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2018] [Accepted: 02/11/2019] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Fed-batch conditions are advantageous for industrial cultivations as they avoid unfavorable phenomena appearing in batch cultivations. Those are for example the formation of overflow metabolites, catabolite repression, oxygen limitation or inhibition due to elevated osmotic concentrations. For both, the early bioprocess development and the optimization of existing bioprocesses, small-scale reaction vessels are applied to ensure high throughput, low costs and prompt results. However, most conventional small-scale procedures work in batch operation mode, which stands in contrast to fed-batch conditions in large-scale bioprocesses. Extensive expenditure for installations and operation accompany almost all cultivation systems in the market allowing fed-batch conditions in small-scale. An alternative, more cost efficient enzymatic glucose release system is strongly influenced by environmental conditions. To overcome these issues, this study investigates a polymer-based fed-batch system for controlled substrate release in microtiter plates. RESULTS Immobilizing a solid silicone matrix with embedded glucose crystals at the bottom of each well of a microtiter plate is a suitable technique for implementing fed-batch conditions in microtiter plates. The results showed that the glucose release rate depends on the osmotic concentration, the pH and the temperature of the medium. Moreover, the applied nitrogen source proved to influence the glucose release rate. A new developed mathematical tool predicts the glucose release for various media conditions. The two model organisms E. coli and H. polymorpha were cultivated in the fed-batch microtiter plate to investigate the general applicability for microbial systems. Online monitoring of the oxygen transfer rate and offline analysis of substrate, product, biomass and pH confirmed that fed-batch conditions are comparable to large-scale cultivations. Furthermore, due to fed-batch conditions in microtiter plates, product formation could be enhanced by the factor 245 compared to batch cultivations. CONCLUSIONS The polymer-based fed-batch microtiter plate represents a sophisticated and cost efficient system to mimic typical industrial fed-batch conditions in small-scale. Thus, a more reliable strain screening and early process development can be performed. A systematical scale-down with low expenditure of work, time and money is possible.
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Affiliation(s)
- T. Keil
- AVT - Biochemical Engineering, RWTH Aachen University, Forckenbeckstraße 51, 52074 Aachen, Germany
| | - B. Dittrich
- DWI – Leibniz Institute for Interactive Materials, RWTH Aachen University, Forckenbeckstraße 50, 52074 Aachen, Germany
| | - C. Lattermann
- Kuhner Shaker GmbH, Kaiserstraße 100, 52134 Herzogenrath, Germany
| | - T. Habicher
- AVT - Biochemical Engineering, RWTH Aachen University, Forckenbeckstraße 51, 52074 Aachen, Germany
| | - J. Büchs
- AVT - Biochemical Engineering, RWTH Aachen University, Forckenbeckstraße 51, 52074 Aachen, Germany
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21
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Improved microscale cultivation of Pichia pastoris for clonal screening. Fungal Biol Biotechnol 2018; 5:8. [PMID: 29750118 PMCID: PMC5932850 DOI: 10.1186/s40694-018-0053-6] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2017] [Accepted: 03/28/2018] [Indexed: 11/10/2022] Open
Abstract
Background Expanding the application of technical enzymes, e.g., in industry and agriculture, commands the acceleration and cost-reduction of bioprocess development. Microplates and shake flasks are massively employed during screenings and early phases of bioprocess development, although major drawbacks such as low oxygen transfer rates are well documented. In recent years, miniaturization and parallelization of stirred and shaken bioreactor concepts have led to the development of novel microbioreactor concepts. They combine high cultivation throughput with reproducibility and scalability, and represent promising tools for bioprocess development. Results Parallelized microplate cultivation of the eukaryotic protein production host Pichia pastoris was applied effectively to support miniaturized phenotyping of clonal libraries in batch as well as fed-batch mode. By tailoring a chemically defined growth medium, we show that growth conditions are scalable from microliter to 0.8 L lab-scale bioreactor batch cultivation with different carbon sources. Thus, the set-up allows for a rapid physiological comparison and preselection of promising clones based on online data and simple offline analytics. This is exemplified by screening a clonal library of P. pastoris constitutively expressing AppA phytase from Escherichia coli. The protocol was further modified to establish carbon-limited conditions by employing enzymatic substrate-release to achieve screening conditions relevant for later protein production processes in fed-batch mode. Conclusion The comparison of clonal rankings under batch and fed-batch-like conditions emphasizes the necessity to perform screenings under process-relevant conditions. Increased biomass and product concentrations achieved after fed-batch microscale cultivation facilitates the selection of top producers. By reducing the demand to conduct laborious and cost-intensive lab-scale bioreactor cultivations during process development, this study will contribute to an accelerated development of protein production processes. Electronic supplementary material The online version of this article (10.1186/s40694-018-0053-6) contains supplementary material, which is available to authorized users.
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Hemmerich J, Freier L, Wiechert W, von Lieres E, Oldiges M. Generic Protocol for Optimization of Heterologous Protein Production Using Automated Microbioreactor Technology. J Vis Exp 2017. [PMID: 29286407 PMCID: PMC5755569 DOI: 10.3791/56234] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022] Open
Abstract
A core business in industrial biotechnology using microbial production cell factories is the iterative process of strain engineering and optimization of bioprocess conditions. One important aspect is the improvement of cultivation medium to provide an optimal environment for microbial formation of the product of interest. It is well accepted that the media composition can dramatically influence overall bioprocess performance. Nutrition medium optimization is known to improve recombinant protein production with microbial systems and thus, this is a rewarding step in bioprocess development. However, very often standard media recipes are taken from literature, since tailor-made design of the cultivation medium is a tedious task that demands microbioreactor technology for sufficient cultivation throughput, fast product analytics, as well as support by lab robotics to enable reliability in liquid handling steps. Furthermore, advanced mathematical methods are required for rationally analyzing measurement data and efficiently designing parallel experiments such as to achieve optimal information content. The generic nature of the presented protocol allows for easy adaption to different lab equipment, other expression hosts, and target proteins of interest, as well as further bioprocess parameters. Moreover, other optimization objectives like protein production rate, specific yield, or product quality can be chosen to fit the scope of other optimization studies. The applied Kriging Toolbox (KriKit) is a general tool for Design of Experiments (DOE) that contributes to improved holistic bioprocess optimization. It also supports multi-objective optimization which can be important in optimizing both upstream and downstream processes.
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Affiliation(s)
- Johannes Hemmerich
- IBG-1: Biotechnology, Forschungszentrum Jülich; Research Center Jülich, Bioeconomy Science Center (BioSC)
| | - Lars Freier
- IBG-1: Biotechnology, Forschungszentrum Jülich; Research Center Jülich, Bioeconomy Science Center (BioSC)
| | - Wolfgang Wiechert
- IBG-1: Biotechnology, Forschungszentrum Jülich; Research Center Jülich, Bioeconomy Science Center (BioSC); Computational Systems Biotechnology (AVT.CSB), RWTH Aachen University
| | - Eric von Lieres
- IBG-1: Biotechnology, Forschungszentrum Jülich; Research Center Jülich, Bioeconomy Science Center (BioSC);
| | - Marco Oldiges
- IBG-1: Biotechnology, Forschungszentrum Jülich; Research Center Jülich, Bioeconomy Science Center (BioSC); Institute for Biotechnology, RWTH Aachen University;
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23
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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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24
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Raddatz L, de Vries I, Austerjost J, Lavrentieva A, Geier D, Becker T, Beutel S, Scheper T. Additive manufactured customizable labware for biotechnological purposes. Eng Life Sci 2017; 17:931-939. [PMID: 32624842 DOI: 10.1002/elsc.201700055] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2017] [Revised: 05/09/2017] [Accepted: 07/13/2017] [Indexed: 12/29/2022] Open
Abstract
Yet already developed in the 1980s, the rise of 3D printing technology did not start until the beginning of this millennium as important patents expired, which opened the technology to a whole new group of potential users. One of the first who used this manufacturing tool in biotechnology was Lücking et al. in 2012, demonstrating potential uses 1, 2. This study shows applications of custom-built 3D-printed parts for biotechnological experiments. It gives an overview about the objects' computer-aided design (CAD) followed by its manufacturing process and basic studies on the used printing material in terms of biocompatibility and manageability. Using the stereolithographic (SLA) 3D-printing technology, a customizable shake flask lid was developed, which was successfully used to perform a bacterial fed-batch shake flask cultivation. The lid provides Luer connectors and tube adapters, allowing both sampling and feeding without interrupting the process. In addition, the digital blueprint the lid is based on, is designed for a modular use and can be modified to fit specific needs. All connectors can be changed and substituted in this CAD software-based file. Hence, the lid can be used for other applications, as well. The used printing material was tested for biocompatibility and showed no toxic effects neither on mammalian, nor on bacteria cells. Furthermore an SDS-PAGE-comb was drawn and printed and its usability evaluated to demonstrate the usefulness of 3D printing for everyday labware. The used manufacturing technique for the comb (multi jet printing, MJP) generates highly smooth surfaces, allowing this application.
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Affiliation(s)
- Lukas Raddatz
- Institute of Technical Chemistry Gottfried-Wilhelm-Leibniz Universität Hannover Germany.,Institute of Brewing and Beverage Technology, Forschungszentrum Weihenstephan Technische Universität München Germany
| | - Ingo de Vries
- Institute of Technical Chemistry Gottfried-Wilhelm-Leibniz Universität Hannover Germany
| | - Jonas Austerjost
- Institute of Technical Chemistry Gottfried-Wilhelm-Leibniz Universität Hannover Germany.,Institute of Brewing and Beverage Technology, Forschungszentrum Weihenstephan Technische Universität München Germany
| | - Antonina Lavrentieva
- Institute of Technical Chemistry Gottfried-Wilhelm-Leibniz Universität Hannover Germany
| | - Dominik Geier
- Institute of Brewing and Beverage Technology, Forschungszentrum Weihenstephan Technische Universität München Germany
| | - Thomas Becker
- Institute of Brewing and Beverage Technology, Forschungszentrum Weihenstephan Technische Universität München Germany
| | - Sascha Beutel
- Institute of Technical Chemistry Gottfried-Wilhelm-Leibniz Universität Hannover Germany
| | - Thomas Scheper
- Institute of Technical Chemistry Gottfried-Wilhelm-Leibniz Universität Hannover Germany
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25
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Philip P, Meier K, Kern D, Goldmanns J, Stockmeier F, Bähr C, Büchs J. Systematic evaluation of characteristics of the membrane-based fed-batch shake flask. Microb Cell Fact 2017; 16:122. [PMID: 28716035 PMCID: PMC5514527 DOI: 10.1186/s12934-017-0741-6] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2017] [Accepted: 07/11/2017] [Indexed: 11/20/2022] Open
Abstract
BACKGROUND The initial part of process development involves extensive screening programs to identify optimal biological systems and cultivation conditions. For a successful scale-up, the operation mode on screening and production scale must be as close as possible. To enable screening under fed-batch conditions, the membrane-based fed-batch shake flask was developed. It is a shake flask mounted with a central feed reservoir with an integrated rotating membrane tip for a controlled substrate release. Building on the previously provided proof of principle for this tool, this work extends its application by constructive modifications and improved methodology to ensure reproducible performance. RESULTS The previously limited operation window was expanded by a systematic analysis of reservoir set-up variations for cultivations with the fast-growing organism Escherichia coli. Modifying the initial glucose concentration in the reservoir as well as interchanging the built-in membrane, resulted in glucose release rates and oxygen transfer rate levels during the fed-batch phase varying up to a factor of five. The range of utilizable membranes was extended from dialysis membranes to porous microfiltration membranes with the design of an appropriate membrane tip. The alteration of the membrane area, molecular weight cut-off and liquid volume in the reservoir offered additional parameters to fine-tune the duration of the initial batch phase, the oxygen transfer rate level of the fed-batch phase and the duration of feeding. It was shown that a homogeneous composition of the reservoir without a concentration gradient is ensured up to an initial glucose concentration of 750 g/L. Finally, the experimental validity of fed-batch shake flask cultivations was verified with comparable results obtained in a parallel fed-batch cultivation in a laboratory-scale stirred tank reactor. CONCLUSIONS The membrane-based fed-batch shake flask is a reliable tool for small-scale screening under fed-batch conditions filling the gap between microtiter plates and scaled-down stirred tank reactors. The implemented reservoir system offers various set-up possibilities, which provide a wide range of process settings for diverse biological systems. As a screening tool, it accurately reflects the cultivation conditions in a fed-batch stirred tank reactor and enables a more efficient bioprocess development.
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Affiliation(s)
- P. Philip
- AVT-Biochemical Engineering, RWTH Aachen University, Forckenbeckstraße 51, 52074 Aachen, Germany
| | - K. Meier
- AVT-Biochemical Engineering, RWTH Aachen University, Forckenbeckstraße 51, 52074 Aachen, Germany
| | - D. Kern
- AVT-Biochemical Engineering, RWTH Aachen University, Forckenbeckstraße 51, 52074 Aachen, Germany
| | - J. Goldmanns
- AVT-Biochemical Engineering, RWTH Aachen University, Forckenbeckstraße 51, 52074 Aachen, Germany
| | - F. Stockmeier
- AVT-Biochemical Engineering, RWTH Aachen University, Forckenbeckstraße 51, 52074 Aachen, Germany
| | - C. Bähr
- AVT-Biochemical Engineering, RWTH Aachen University, Forckenbeckstraße 51, 52074 Aachen, Germany
| | - J. Büchs
- AVT-Biochemical Engineering, RWTH Aachen University, Forckenbeckstraße 51, 52074 Aachen, Germany
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Hohmann HP, van Dijl JM, Krishnappa L, Prágai Z. Host Organisms:Bacillus subtilis. Ind Biotechnol (New Rochelle N Y) 2016. [DOI: 10.1002/9783527807796.ch7] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022] Open
Affiliation(s)
- Hans-Peter Hohmann
- Nutrition Innovation Center R&D Biotechnology; DSM Nutritional Products Ltd; Wurmisweg 576 CH-4303 Kaiseraugst Switzerland
| | - Jan M. van Dijl
- University of Groningen, University Medical Center Groningen; Department of Medical Microbiology; Hanzeplein 1 9700 RB Groningen The Netherlands
| | - Laxmi Krishnappa
- University of Groningen, University Medical Center Groningen; Department of Medical Microbiology; Hanzeplein 1 9700 RB Groningen The Netherlands
| | - Zoltán Prágai
- Nutrition Innovation Center R&D Biotechnology; DSM Nutritional Products Ltd; Wurmisweg 576 CH-4303 Kaiseraugst Switzerland
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27
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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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Luchterhand B, Nolten J, Hafizovic S, Schlepütz T, Wewetzer SJ, Pach E, Meier K, Wandrey G, Büchs J. Newly designed and validated impedance spectroscopy setup in microtiter plates successfully monitors viable biomass online. Biotechnol J 2015; 10:1259-68. [DOI: 10.1002/biot.201400534] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2014] [Revised: 03/13/2015] [Accepted: 05/19/2015] [Indexed: 11/06/2022]
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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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30
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Giese H, Kruithof P, Meier K, Sieben M, Antonov E, Hommes RW, Büchs J. Improvement and scale-down of a Trichoderma reesei shake flask protocol to microtiter plates enables high-throughput screening. J Biosci Bioeng 2014; 118:702-9. [DOI: 10.1016/j.jbiosc.2014.05.016] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2014] [Revised: 05/20/2014] [Accepted: 05/21/2014] [Indexed: 10/25/2022]
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31
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Delvigne F, Zune Q, Lara AR, Al-Soud W, Sørensen SJ. Metabolic variability in bioprocessing: implications of microbial phenotypic heterogeneity. Trends Biotechnol 2014; 32:608-16. [DOI: 10.1016/j.tibtech.2014.10.002] [Citation(s) in RCA: 86] [Impact Index Per Article: 8.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2014] [Revised: 09/24/2014] [Accepted: 10/01/2014] [Indexed: 12/19/2022]
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32
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Faust G, Janzen NH, Bendig C, Römer L, Kaufmann K, Weuster-Botz D. Feeding strategies enhance high cell density cultivation and protein expression in milliliter scale bioreactors. Biotechnol J 2014; 9:1293-303. [DOI: 10.1002/biot.201400346] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/04/2014] [Revised: 07/18/2014] [Accepted: 08/05/2014] [Indexed: 12/23/2022]
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Käß F, Prasad A, Tillack J, Moch M, Giese H, Büchs J, Wiechert W, Oldiges M. Rapid assessment of oxygen transfer impact for Corynebacterium glutamicum. Bioprocess Biosyst Eng 2014; 37:2567-77. [DOI: 10.1007/s00449-014-1234-1] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2014] [Accepted: 06/02/2014] [Indexed: 10/25/2022]
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Hemmerich J, Adelantado N, Barrigón JM, Ponte X, Hörmann A, Ferrer P, Kensy F, Valero F. Comprehensive clone screening and evaluation of fed-batch strategies in a microbioreactor and lab scale stirred tank bioreactor system: application on Pichia pastoris producing Rhizopus oryzae lipase. Microb Cell Fact 2014; 13:36. [PMID: 24606982 PMCID: PMC4007594 DOI: 10.1186/1475-2859-13-36] [Citation(s) in RCA: 39] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2013] [Accepted: 02/27/2014] [Indexed: 11/15/2022] Open
Abstract
Background In Pichia pastoris bioprocess engineering, classic approaches for clone selection and bioprocess optimization at small/micro scale using the promoter of the alcohol oxidase 1 gene (PAOX1), induced by methanol, present low reproducibility leading to high time and resource consumption. Results An automated microfermentation platform (RoboLector) was successfully tested to overcome the chronic problems of clone selection and optimization of fed-batch strategies. Different clones from Mut+P. pastoris phenotype strains expressing heterologous Rhizopus oryzae lipase (ROL), including a subset also overexpressing the transcription factor HAC1, were tested to select the most promising clones. The RoboLector showed high performance for the selection and optimization of cultivation media with minimal cost and time. Syn6 medium was better than conventional YNB medium in terms of production of heterologous protein. The RoboLector microbioreactor was also tested for different fed-batch strategies with three clones producing different lipase levels. Two mixed substrates fed-batch strategies were evaluated. The first strategy was the enzymatic release of glucose from a soluble glucose polymer by a glucosidase, and methanol addition every 24 hours. The second strategy used glycerol as co-substrate jointly with methanol at two different feeding rates. The implementation of these simple fed-batch strategies increased the levels of lipolytic activity 80-fold compared to classical batch strategies used in clone selection. Thus, these strategies minimize the risk of errors in the clone selection and increase the detection level of the desired product. Finally, the performance of two fed-batch strategies was compared for lipase production between the RoboLector microbioreactor and 5 liter stirred tank bioreactor for three selected clones. In both scales, the same clone ranking was achieved. Conclusion The RoboLector showed excellent performance in clone selection of P. pastoris Mut+ phenotype. The use of fed-batch strategies using mixed substrate feeds resulted in increased biomass and lipolytic activity. The automated processing of fed-batch strategies by the RoboLector considerably facilitates the operation of fermentation processes, while reducing error-prone clone selection by increasing product titers. The scale-up from microbioreactor to lab scale stirred tank bioreactor showed an excellent correlation, validating the use of microbioreactor as a powerful tool for evaluating fed-batch operational strategies.
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Affiliation(s)
| | | | | | | | | | | | - Frank Kensy
- m2p-labs GmbH, Arnold-Sommerfeld-Ring 2, Baesweiler 52499, Germany.
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Wilming A, Bähr C, Kamerke C, Büchs J. Fed-batch operation in special microtiter plates: a new method for screening under production conditions. ACTA ACUST UNITED AC 2014; 41:513-25. [DOI: 10.1007/s10295-013-1396-x] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2013] [Accepted: 12/22/2013] [Indexed: 10/25/2022]
Abstract
Abstract
Batch and fed-batch operation result in completely different physiological conditions for cultivated microorganisms or cells. To close the gap between screening, which is hitherto exclusively performed in batch mode, and fed-batch production processes, a special microtiter plate was developed that allows screening in fed-batch mode. The fed-batch microtiter plate (FB-MTP) enables 44 parallel fed-batch experiments at small scale. A small channel filled with a hydrogel connects a reservoir well with a culture well. The nutrient compound diffuses from the reservoir well through the hydrogel into the culture well. Hence, the feed rate can easily be adjusted to the needs of the cultured microorganisms by changing the geometry of the hydrogel channel and the driving concentration gradient. Any desired compound including liquid nutrients like glycerol can be fed to the culture. In combination with an optical measuring device (BioLector), online monitoring of these 44 fed-batch cultures is possible. Two Escherichia coli strains and a Hansenula polymorpha strain were successfully cultivated in the new FB-MTP. As a positive impact of the fed-batch mode on the used strains, a fourfold increase in product formation was observed for E. coli. For H. polymorpha, the use of fed-batch mode resulted in a strong increase in product formation, whereas no measurable product formation was observed in batch mode. In conclusion, the newly developed fed-batch microtiter plate is a versatile, easy-to-use, disposable system to perform fed-batch cultivations at small scale. Screening cultures in high-throughput under online monitoring are possible similar to cultivations under production conditions.
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Affiliation(s)
- Anja Wilming
- grid.1957.a 000000010728696X AVT-Biochemical Engineering RWTH Aachen University Sammelbau Biologie, Worringerweg 1 52074 Aachen Germany
| | - Cornelia Bähr
- grid.1957.a 000000010728696X AVT-Biochemical Engineering RWTH Aachen University Sammelbau Biologie, Worringerweg 1 52074 Aachen Germany
| | - Claudia Kamerke
- grid.1957.a 000000010728696X AVT-Biochemical Engineering RWTH Aachen University Sammelbau Biologie, Worringerweg 1 52074 Aachen Germany
| | - Jochen Büchs
- grid.1957.a 000000010728696X AVT-Biochemical Engineering RWTH Aachen University Sammelbau Biologie, Worringerweg 1 52074 Aachen Germany
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Suppi S, Michelson T, Viigand K, Alamäe T. Repression vs. activation of MOX, FMD, MPP1 and MAL1 promoters by sugars in Hansenula polymorpha: the outcome depends on cell's ability to phosphorylate sugar. FEMS Yeast Res 2012; 13:219-32. [PMID: 23164245 DOI: 10.1111/1567-1364.12023] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2012] [Accepted: 11/08/2012] [Indexed: 12/01/2022] Open
Abstract
A high-throughput approach was used to assess the effect of mono- and disaccharides on MOX, FMD, MPP1 and MAL1 promoters in Hansenula polymorpha. Site-specifically designed strains deficient for (1) hexokinase, (2) hexokinase and glucokinase, (3) maltose permease or (4) maltase were used as hosts for reporter plasmids in which β-glucuronidase (Gus) expression was controlled by these promoters. The reporter strains were grown on agar plates containing varied carbon sources and Gus activity was measured in permeabilized cells on microtitre plates. We report that monosaccharides (glucose, fructose) repress studied promoters only if phosphorylated in the cell. Glucose-6-phosphate was proposed as a sugar repression signalling metabolite for H. polymorpha. Intriguingly, glucose and fructose strongly activated expression from these promoters in strains lacking both hexokinase and glucokinase, indicating that unphosphorylated monosaccharides have promoter-derepressing effect. We also show that maltose and sucrose must be internalized and split into monosaccharides to exert repression on MOX promoter. We demonstrate that at yeast growth on glucose-containing agar medium, glucose-limitation is rapidly created that promotes derepression of methanol-specific promoters and that derepression is specifically enhanced in hexokinase-negative strain. We recommend double kinase-negative and hexokinase-negative mutants as hosts for heterologous protein production from MOX and FMD promoters.
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Affiliation(s)
- Sandra Suppi
- Institute of Molecular and Cell Biology, University of Tartu, Tartu, Estonia
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37
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Bähr C, Leuchtle B, Lehmann C, Becker J, Jeude M, Peinemann F, Arbter R, Büchs J. Dialysis shake flask for effective screening in fed-batch mode. Biochem Eng J 2012. [DOI: 10.1016/j.bej.2012.08.012] [Citation(s) in RCA: 30] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
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38
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Hansen S, Hariskos I, Luchterhand B, Büchs J. Development of a modified Respiration Activity Monitoring System for accurate and highly resolved measurement of respiration activity in shake flask fermentations. J Biol Eng 2012; 6:11. [PMID: 22901278 PMCID: PMC3490767 DOI: 10.1186/1754-1611-6-11] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2012] [Accepted: 07/26/2012] [Indexed: 11/13/2022] Open
Abstract
Background The Respiration Activity Monitoring System (RAMOS) is an established device to measure on-line the oxygen transfer rate (OTR), thereby, yielding relevant information about metabolic activities of microorganisms and cells during shake flask fermentations. For very fast-growing microbes, however, the RAMOS technique provides too few data points for the OTR. Thus, this current study presents a new model based evaluation method for generating much more data points to enhance the information content and the precision of OTR measurements. Results In cultivations with E.coli BL21 pRSET eYFP-IL6, short diauxic and even triauxic metabolic activities were detected with much more detail compared to the conventional evaluation method. The decline of the OTR during the stop phases during oxygen limitations, which occur when the inlet and outlet valves of the RAMOS flask were closed for calibrating the oxygen sensor, were also detected. These declines reflected a reduced oxygen transfer due to the stop phases. In contrast to the conventional calculation method the new method was almost independent from the number of stop phases chosen in the experiments. Conclusions This new model based evaluation method unveils new peaks of metabolic activity which otherwise would not have been resolved by the conventional RAMOS evaluation method. The new method yields substantially more OTR data points, thereby, enhancing the information content and the precision of the OTR measurements. Furthermore, oxygen limitations can be detected by a decrease of the OTR during the stop phases.
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Affiliation(s)
- Sven Hansen
- AVT, Biochemical Engineering, RWTH Aachen University, Worringerweg 1, Aachen, 52074, Germany.
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Jourdier E, Poughon L, Larroche C, Monot F, Ben Chaabane F. A new stoichiometric miniaturization strategy for screening of industrial microbial strains: application to cellulase hyper-producing Trichoderma reesei strains. Microb Cell Fact 2012; 11:70. [PMID: 22646695 PMCID: PMC3434075 DOI: 10.1186/1475-2859-11-70] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2012] [Accepted: 05/30/2012] [Indexed: 11/15/2022] Open
Abstract
Background During bioprocess development, secondary screening is a key step at the boundary between laboratory and industrial conditions. To ensure an effective high-throughput screening, miniaturized laboratory conditions must mimic industrial conditions, especially for oxygen transfer, feeding capacity and pH stabilization. Results A feeding strategy has been applied to develop a simple screening procedure, in which a stoichiometric study is combined with a standard miniaturization procedure. Actually, the knowledge of all nutriments and base or acid requirements leads to a great simplification of pH stabilization issue of miniaturized fed-batch cultures. Applied to cellulase production by Trichoderma reesei, this strategy resulted in a stoichiometric mixed feed of carbon and nitrogen sources. While keeping the pH between shake flask and stirred bioreactor comparable, the developed shake flask protocol reproduced the strain behaviour under stirred bioreactor conditions. Compared to a an already existing miniaturized shake flasks protocol, the cellulase concentration was increased 5-fold, reaching about 10 g L-1. Applied to the secondary screening of several clones, the newly developed protocol succeeded in selecting a clone with a high industrial potential. Conclusions The understanding of a bioprocess stoichiometry contributed to define a simpler and more effective miniaturization. The suggested strategy can potentially be applied to other fed-batch processes, for the screening of either strain collections or experimental conditions.
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Affiliation(s)
- Etienne Jourdier
- IFP Energies nouvelles, 1 et 4 avenue de Bois-Préau, 92852 Rueil-Malmaison, France
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Wenk P, Hemmerich J, Müller C, Kensy F. Hochparallele Bioprozessentwicklung in geschüttelten Mikrobioreaktoren. CHEM-ING-TECH 2012. [DOI: 10.1002/cite.201100206] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
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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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Hegde S, Pant T, Pradhan K, Badiger M, Gadgil M. Controlled release of nutrients to mammalian cells cultured in shake flasks. Biotechnol Prog 2011; 28:188-95. [DOI: 10.1002/btpr.729] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2011] [Revised: 09/08/2011] [Indexed: 11/11/2022]
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Fluorescent proteins in microbial biotechnology—new proteins and new applications. Biotechnol Lett 2011; 34:175-86. [DOI: 10.1007/s10529-011-0767-5] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2011] [Accepted: 09/29/2011] [Indexed: 10/17/2022]
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Scheidle M, Dittrich B, Klinger J, Ikeda H, Klee D, Büchs J. Controlling pH in shake flasks using polymer-based controlled-release discs with pre-determined release kinetics. BMC Biotechnol 2011; 11:25. [PMID: 21429210 PMCID: PMC3076237 DOI: 10.1186/1472-6750-11-25] [Citation(s) in RCA: 46] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2010] [Accepted: 03/23/2011] [Indexed: 11/27/2022] Open
Abstract
Background There are significant differences in the culture conditions between small-scale screenings and large-scale fermentation processes. Production processes are usually conducted in fed-batch cultivation mode with active pH-monitoring and control. In contrast, screening experiments in shake flasks are usually conducted in batch mode without active pH-control, but with high buffer concentrations to prevent excessive pH-drifts. These differences make it difficult to compare results from screening experiments and laboratory and technical scale cultivations and, thus, complicate rational process development. In particular, the pH-value plays an important role in fermentation processes due to the narrow physiological or optimal pH-range of microorganisms. To reduce the differences between the scales and to establish a pH-control in shake flasks, a newly developed easy to use polymer-based controlled-release system is presented in this paper. This system consists of bio-compatible silicone discs embedding the alkaline reagent Na2CO3. Since the sodium carbonate is gradually released from the discs in pre-determined kinetics, it will ultimately compensate the decrease in pH caused by the biological activity of microorganisms. Results The controlled-release discs presented here were successfully used to cultivate E. coli K12 and E. coli BL21 pRSET eYFP-IL6 in mineral media with glucose and glycerol as carbon (C) sources, respectively. With glucose as the C-source it was possible to reduce the required buffer concentration in shake flask cultures by 50%. Moreover, with glycerol as the C-source, no buffer was needed at all. Conclusions These novel polymer-based controlled-release discs allowed buffer concentrations in shake flask media to be substantially reduced or omitted, while the pH remains in the physiological range of the microorganisms during the whole cultivation time. Therefore, the controlled-release discs allow a better control of the pH, than merely using high buffer concentrations. The conditions applied here, i.e. with significantly reduced buffer concentrations, enhance the comparability of the culture conditions used in screening experiments and large-scale fermentation processes.
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Affiliation(s)
- Marco Scheidle
- Aachener Verfahrenstechnik - Biochemical Engineering, RWTH Aachen University, Sammelbau Biologie, Worringer Weg 1, D-52074 Aachen, Germany
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Waegeman H, Beauprez J, Maertens J, De Mey M, Demolder L, Foulquié-Moreno MR, Boon N, Charlier D, Soetaert W. Validation study of 24 deepwell microtiterplates to screen libraries of strains in metabolic engineering. J Biosci Bioeng 2010; 110:646-52. [PMID: 20696615 DOI: 10.1016/j.jbiosc.2010.07.008] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2010] [Revised: 07/08/2010] [Accepted: 07/17/2010] [Indexed: 11/29/2022]
Abstract
In this study we validated the use of 24 square deepwell microtiterplates to screen large libraries of metabolically engineered strains by investigating the optimization of succinate production. Wild type E. coli MG1655 and 11 derived mutants were physiologically evaluated by growth in 24 deepwell MTPs and 2L benchtop bioreactors. Growth parameters, product yields and byproduct formation were determined for all mutants. The results show that similar average values and standard deviations for these parameters were obtained. Especially a high correlation was noticed for the acetate byproduct yield and the succinate production rate. For these parameters there was no significant difference for 8 out of 12 strains between MTPs and 2L bioreactors. However a lower maximum growth rate was observed in 2L reactors as opposed to 24 deepwell plates for 9 out of 12 mutants which could be linked to the higher amount of dead cells in the benchtop bioreactors (12% vs. 2% in MTPs). Finally, a cluster-based approach was used to select good producer strains, i.e. strains with a high succinate yield and succinate production rate. Bad, intermediate and good producer strains were clustered in the same groups for MTPs and benchtop bioreactors for 11 out of the 12 investigated strains.
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Affiliation(s)
- Hendrik Waegeman
- Centre of Expertise-Industrial Biotechnology and Biocatalysis, Department of Biochemical and Microbial Technology, Ghent University, Coupure Links 653, B-9000 Ghent, Belgium.
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Current awareness on yeast. Yeast 2010. [DOI: 10.1002/yea.1718] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022] Open
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Funke M, Buchenauer A, Schnakenberg U, Mokwa W, Diederichs S, Mertens A, Müller C, Kensy F, Büchs J. Microfluidic biolector-microfluidic bioprocess control in microtiter plates. Biotechnol Bioeng 2010; 107:497-505. [DOI: 10.1002/bit.22825] [Citation(s) in RCA: 79] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
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Development of an α-amylase reporter system for efficient screening of clones with highly expressed heterologous protein in Hansenula polymorpha. Biotechnol Lett 2010; 32:1473-9. [DOI: 10.1007/s10529-010-0314-9] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2010] [Accepted: 05/11/2010] [Indexed: 11/27/2022]
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Siurkus J, Panula-Perälä J, Horn U, Kraft M, Rimseliene R, Neubauer P. Novel approach of high cell density recombinant bioprocess development: optimisation and scale-up from microliter to pilot scales while maintaining the fed-batch cultivation mode of E. coli cultures. Microb Cell Fact 2010; 9:35. [PMID: 20487563 PMCID: PMC2890543 DOI: 10.1186/1475-2859-9-35] [Citation(s) in RCA: 61] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2010] [Accepted: 05/20/2010] [Indexed: 01/17/2023] Open
Abstract
Background Bioprocess development of recombinant proteins is time consuming and laborious as many factors influence the accumulation of the product in the soluble and active form. Currently, in most cases the developmental line is characterised by a screening stage which is performed under batch conditions followed by the development of the fed-batch process. Performing the screening already under fed-batch conditions would limit the amount of work and guarantee that the selected favoured conditions also work in the production scale. Results Here, for the first time, high throughput multifactorial screening of a cloning library is combined with the fed-batch technique in 96-well plates, and a strategy is directly derived for scaling to bioreactor scale. At the example of a difficult to express protein, an RNase inhibitor, it is demonstrated that screening of various vector constructs and growth conditions can be performed in a coherent line by (i) applying a vector library with promoters and ribosome binding sites of different strength and various fusion partners together with (ii) an early stage use of the fed-batch technology. It is shown that the EnBase® technology provides an easy solution for controlled cultivation conditions in the microwell scale. Additionally the high cell densities obtained provide material for various analyses from the small culture volumes. Crucial factors for a high yield of the target protein in the actual case were (i) the fusion partner, (ii) the use of of a mineral salt medium together with the fed-batch technique, and (iii) the preinduction growth rate. Finally, it is shown that the favorable conditions selected in the microwell plate and shake flask scales also work in the bioreactor. Conclusions Cultivation media and culture conditions have a major impact on the success of a screening procedure. Therefore the application of controlled cultivation conditions is pivotal. The consequent use of fed-batch conditons from the first screening phase not only shortens the developmental line by guarantying that the selected conditions are relevant for the scale up, but in our case also standard batch cultures failed to select the right clone or conditions at all.
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Affiliation(s)
- Juozas Siurkus
- Laboratory of Bioprocess Engineering, Department of Biotechnology, Technische Universität Berlin, Ackerstr 71-76, D-13355 Berlin, Germany
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