1
|
Li S, Ye Z, Moreb EA, Menacho-Melgar R, Golovsky M, Lynch MD. 2-Stage microfermentations. Metab Eng Commun 2024; 18:e00233. [PMID: 38665924 PMCID: PMC11043886 DOI: 10.1016/j.mec.2024.e00233] [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: 02/05/2024] [Revised: 03/27/2024] [Accepted: 04/03/2024] [Indexed: 04/28/2024] Open
Abstract
Cell based factories can be engineered to produce a wide variety of products. Advances in DNA synthesis and genome editing have greatly simplified the design and construction of these factories. It has never been easier to generate hundreds or even thousands of cell factory strain variants for evaluation. These advances have amplified the need for standardized, higher throughput means of evaluating these designs. Toward this goal, we have previously reported the development of engineered E. coli strains and associated 2-stage production processes to simplify and standardize strain engineering, evaluation and scale up. This approach relies on decoupling growth (stage 1), from production, which occurs in stationary phase (stage 2). Phosphate depletion is used as the trigger to stop growth as well as induce heterologous expression. Here, we describe in detail the development of protocols for the evaluation of engineered E. coli strains in 2-stage microfermentations. These protocols are readily adaptable to the evaluation of strains producing a wide variety of protein as well as small molecule products. Additionally, by detailing the approach to protocol development, these methods are also adaptable to additional cellular hosts, as well as other 2-stage processes with various additional triggers.
Collapse
Affiliation(s)
- Shuai Li
- Department of Chemistry, Duke University, Durham, NC, USA
| | - Zhixia Ye
- Department of Biomedical Engineering, Duke University, Durham, NC, USA
| | - Eirik A. Moreb
- Department of Biomedical Engineering, Duke University, Durham, NC, USA
| | | | | | - Michael D. Lynch
- Department of Biomedical Engineering, Duke University, Durham, NC, USA
| |
Collapse
|
2
|
Sparviero S, Dicke MD, Rosch TM, Castillo T, Salgado-Lugo H, Galindo E, Peña C, Büchs J. Yeast extracts from different manufacturers and supplementation of amino acids and micro elements reveal a remarkable impact on alginate production by A. vinelandii ATCC9046. Microb Cell Fact 2023; 22:99. [PMID: 37170263 PMCID: PMC10176783 DOI: 10.1186/s12934-023-02112-3] [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: 02/23/2023] [Accepted: 05/03/2023] [Indexed: 05/13/2023] Open
Abstract
BACKGROUND In research and production, reproducibility is a key factor, to meet high quality and safety standards and maintain productivity. For microbial fermentations, complex substrates and media components are often used. The complex media components can vary in composition, depending on the lot and manufacturing process. These variations can have an immense impact on the results of biological cultivations. The aim of this work was to investigate and characterize the influence of the complex media component yeast extract on cultivations of Azotobacter vinelandii under microaerobic conditions. Under these conditions, the organism produces the biopolymer alginate. The focus of the investigation was on the respiration activity, cell growth and alginate production. RESULTS Yeast extracts from 6 different manufacturers and 2 different lots from one manufacturer were evaluated. Significant differences on respiratory activity, growth and production were observed. Concentration variations of three different yeast extracts showed that the performance of poorly performing yeast extracts can be improved by simply increasing their concentration. On the other hand, the results with well-performing yeast extracts seem to reach a saturation, when their concentration is increased. Cultivations with poorly performing yeast extract were supplemented with grouped amino acids, single amino acids and micro elements. Beneficial results were obtained with the supplementation of copper sulphate, cysteine or a combination of both. Furthermore, a correlation between the accumulated oxygen transfer and the final viscosity (as a key performance indicator), was established. CONCLUSION The choice of yeast extract is crucial for A. vinelandii cultivations, to maintain reproducibility and comparability between cultivations. The proper use of specific yeast extracts allows the cultivation results to be specifically optimised. In addition, supplements can be applied to modify and improve the properties of the alginate. The results only scratch the surface of the underlying mechanisms, as they are not providing explanations on a molecular level. However, the findings show the potential of optimising media containing yeast extract for alginate production with A. vinelandii, as well as the potential of targeted supplementation of the media.
Collapse
Affiliation(s)
- Sarah Sparviero
- Aachener Verfahrenstechnik - Chair of Biochemical Engineering, RWTH Aachen University, Bldg. NGP², Forckenbeckstr. 51, 52074, Aachen, Germany
| | - Max Daniel Dicke
- Aachener Verfahrenstechnik - Chair of Biochemical Engineering, RWTH Aachen University, Bldg. NGP², Forckenbeckstr. 51, 52074, Aachen, Germany
| | - Tobias M Rosch
- Aachener Verfahrenstechnik - Chair of Biochemical Engineering, RWTH Aachen University, Bldg. NGP², Forckenbeckstr. 51, 52074, Aachen, Germany
| | - Tania Castillo
- Departamento de Ingeniería Celular y Biocatálisis, Instituto de Biotecnología, UNAM, Universidad Nacional Autónoma de México, Ave. Universidad 2001, Col. Chamilpa, 62210, Cuernavaca, Morelos, México
| | - Holjes Salgado-Lugo
- Departamento de Ingeniería Celular y Biocatálisis, Instituto de Biotecnología, UNAM, Universidad Nacional Autónoma de México, Ave. Universidad 2001, Col. Chamilpa, 62210, Cuernavaca, Morelos, México
- Programa Investigadoras e Investigadores por México del CONACyT, Consejo Nacional de Ciencia y Tecnología, 03940, Mexico City, México
| | - Enrique Galindo
- Departamento de Ingeniería Celular y Biocatálisis, Instituto de Biotecnología, UNAM, Universidad Nacional Autónoma de México, Ave. Universidad 2001, Col. Chamilpa, 62210, Cuernavaca, Morelos, México
| | - Carlos Peña
- Departamento de Ingeniería Celular y Biocatálisis, Instituto de Biotecnología, UNAM, Universidad Nacional Autónoma de México, Ave. Universidad 2001, Col. Chamilpa, 62210, Cuernavaca, Morelos, México
| | - Jochen Büchs
- Aachener Verfahrenstechnik - Chair of Biochemical Engineering, RWTH Aachen University, Bldg. NGP², Forckenbeckstr. 51, 52074, Aachen, Germany.
| |
Collapse
|
3
|
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.
Collapse
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.
| |
Collapse
|
4
|
Velazquez D, Sigala JC, Martínez LM, Gaytán P, Gosset G, Lara AR. Glucose transport engineering allows mimicking fed-batch performance in batch mode and selection of superior producer strains. Microb Cell Fact 2022; 21:183. [PMID: 36071458 PMCID: PMC9450411 DOI: 10.1186/s12934-022-01906-1] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2022] [Accepted: 08/09/2022] [Indexed: 11/26/2022] Open
Abstract
Background Fed-batch mode is the standard culture technology for industrial bioprocesses. Nevertheless, most of the early-stage cell and process development is carried out in batch cultures, which can bias the initial selection of expression systems. Cell engineering can provide an alternative to fed-batch cultures for high-throughput screening and host selection. We have previously reported a library of Escherichia coli strains with single and multiple deletions of genes involved in glucose transport. Compared to their wild type (W3110), the mutant strains displayed lower glucose uptake, growth and aerobic acetate production rates. Therefore, when cultured in batch mode, such mutants may perform similar to W3110 cultured in fed-batch mode. To test that hypothesis, we evaluated the constitutive expression of the green fluorescence protein (GFP) in batch cultures in microbioreactors using a semi defined medium supplemented with 10 or 20 g/L glucose + 0.4 g yeast extract/g glucose. Results The mutant strains cultured in batch mode displayed a fast-growth phase (growth rate between 0.40 and 0.60 h−1) followed by a slow-growth phase (growth rate between 0.05 and 0.15 h−1), similar to typical fed-batch cultures. The phase of slow growth is most probably caused by depletion of key amino acids. Three mutants attained the highest GFP fluorescence. Particularly, a mutant named WHIC (ΔptsHIcrr, ΔmglABC), reached a GFP fluorescence up to 14-fold greater than that of W3110. Strain WHIC was cultured in 2 L bioreactors in batch mode with 100 g/L glucose + 50 g/L yeast extract. These cultures were compared with exponentially fed-batch cultures of W3110 maintaining the same slow-growth of WHIC (0.05 h−1) and using the same total amount of glucose and yeast extract than in WHIC cultures. The WHIC strain produced approx. 450 mg/L GFP, while W3110 only 220 mg/L. Conclusion The combination of cell engineering and high throughput screening allowed the selection of a particular mutant that mimics fed-batch behavior in batch cultures. Moreover, the amount of GFP produced by the strain WHIC was substantially higher than that of W3110 under both, batch and fed-batch schemes. Therefore, our results represent a valuable technology for accelerated bioprocess development. Supplementary Information The online version contains supplementary material available at 10.1186/s12934-022-01906-1.
Collapse
Affiliation(s)
- Daniela Velazquez
- Departamento de Procesos y Tecnología, Universidad Autónoma Metropolitana, Vasco de Quiroga 4871, 05348, Mexico City, Mexico
| | - Juan-Carlos Sigala
- Departamento de Procesos y Tecnología, Universidad Autónoma Metropolitana, Vasco de Quiroga 4871, 05348, Mexico City, Mexico
| | - Luz María Martínez
- Departamento de Ingeniería Celular y Biocatálisis, Instituto de Biotecnología, Universidad Nacional Autónoma de México, Avenida Universidad 2001, Col. Chamilpa, 62210, Cuernavaca, MOR, Mexico
| | - Paul Gaytán
- Departamento de Ingeniería Celular y Biocatálisis, Instituto de Biotecnología, Universidad Nacional Autónoma de México, Avenida Universidad 2001, Col. Chamilpa, 62210, Cuernavaca, MOR, Mexico
| | - Guillermo Gosset
- Departamento de Ingeniería Celular y Biocatálisis, Instituto de Biotecnología, Universidad Nacional Autónoma de México, Avenida Universidad 2001, Col. Chamilpa, 62210, Cuernavaca, MOR, Mexico
| | - Alvaro R Lara
- Departamento de Procesos y Tecnología, Universidad Autónoma Metropolitana, Vasco de Quiroga 4871, 05348, Mexico City, Mexico.
| |
Collapse
|
5
|
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.
Collapse
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.
| |
Collapse
|
6
|
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.
Collapse
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
| |
Collapse
|
7
|
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.
Collapse
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.
| |
Collapse
|
8
|
Fink M, Cserjan-Puschmann M, Reinisch D, Striedner G. High-throughput microbioreactor provides a capable tool for early stage bioprocess development. Sci Rep 2021; 11:2056. [PMID: 33479431 PMCID: PMC7819997 DOI: 10.1038/s41598-021-81633-6] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2020] [Accepted: 01/04/2021] [Indexed: 12/22/2022] Open
Abstract
Tremendous advancements in cell and protein engineering methodologies and bioinformatics have led to a vast increase in bacterial production clones and recombinant protein variants to be screened and evaluated. Consequently, an urgent need exists for efficient high-throughput (HTP) screening approaches to improve the efficiency in early process development as a basis to speed-up all subsequent steps in the course of process design and engineering. In this study, we selected the BioLector micro-bioreactor (µ-bioreactor) system as an HTP cultivation platform to screen E. coli expression clones producing representative protein candidates for biopharmaceutical applications. We evaluated the extent to which generated clones and condition screening results were transferable and comparable to results from fully controlled bioreactor systems operated in fed-batch mode at moderate or high cell densities. Direct comparison of 22 different production clones showed great transferability. We observed the same growth and expression characteristics, and identical clone rankings except one host-Fab-leader combination. This outcome demonstrates the explanatory power of HTP µ-bioreactor data and the suitability of this platform as a screening tool in upstream development of microbial systems. Fast, reliable, and transferable screening data significantly reduce experiments in fully controlled bioreactor systems and accelerate process development at lower cost.
Collapse
Affiliation(s)
- Mathias Fink
- Christian Doppler Laboratory for Production of Next-Level Biopharmaceuticals in E. Coli, Department of Biotechnology, University of Natural Resources and Life Sciences, Muthgasse 18, 1190, Vienna, Austria
| | - Monika Cserjan-Puschmann
- Christian Doppler Laboratory for Production of Next-Level Biopharmaceuticals in E. Coli, Department of Biotechnology, University of Natural Resources and Life Sciences, Muthgasse 18, 1190, Vienna, Austria.
| | - Daniela Reinisch
- Boehringer Ingelheim RCV GmbH & Co KG, Dr. Boehringer-Gasse 5-11, 1120, Vienna, Austria
| | - Gerald Striedner
- Christian Doppler Laboratory for Production of Next-Level Biopharmaceuticals in E. Coli, Department of Biotechnology, University of Natural Resources and Life Sciences, Muthgasse 18, 1190, Vienna, Austria
| |
Collapse
|
9
|
High-throughput screening for high-efficiency small-molecule biosynthesis. Metab Eng 2020; 63:102-125. [PMID: 33017684 DOI: 10.1016/j.ymben.2020.09.004] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2020] [Revised: 08/31/2020] [Accepted: 09/01/2020] [Indexed: 01/14/2023]
Abstract
Systems metabolic engineering faces the formidable task of rewiring microbial metabolism to cost-effectively generate high-value molecules from a variety of inexpensive feedstocks for many different applications. Because these cellular systems are still too complex to model accurately, vast collections of engineered organism variants must be systematically created and evaluated through an enormous trial-and-error process in order to identify a manufacturing-ready strain. The high-throughput screening of strains to optimize their scalable manufacturing potential requires execution of many carefully controlled, parallel, miniature fermentations, followed by high-precision analysis of the resulting complex mixtures. This review discusses strategies for the design of high-throughput, small-scale fermentation models to predict improved strain performance at large commercial scale. Established and promising approaches from industrial and academic groups are presented for both cell culture and analysis, with primary focus on microplate- and microfluidics-based screening systems.
Collapse
|
10
|
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.
Collapse
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
| |
Collapse
|
11
|
Leavell MD, Singh AH, Kaufmann-Malaga BB. High-throughput screening for improved microbial cell factories, perspective and promise. Curr Opin Biotechnol 2020; 62:22-28. [DOI: 10.1016/j.copbio.2019.07.002] [Citation(s) in RCA: 25] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2019] [Revised: 07/24/2019] [Accepted: 07/27/2019] [Indexed: 01/11/2023]
|
12
|
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.
Collapse
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.
| |
Collapse
|
13
|
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.
Collapse
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
| |
Collapse
|
14
|
Keil T, Landenberger M, Dittrich B, Selzer S, Büchs J. Precultures Grown under Fed‐Batch Conditions Increase the Reliability and Reproducibility of High‐Throughput Screening Results. Biotechnol J 2019; 14:e1800727. [DOI: 10.1002/biot.201800727] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2018] [Revised: 06/21/2019] [Indexed: 12/23/2022]
Affiliation(s)
- Timm Keil
- AVT—Biochemical EngineeringRWTH Aachen UniversityForckenbeckstraße 51 52074 Aachen Germany
| | - Markus Landenberger
- AVT—Biochemical EngineeringRWTH Aachen UniversityForckenbeckstraße 51 52074 Aachen Germany
| | - Barbara Dittrich
- DWI—Leibniz Institute for Interactive MaterialsRWTH Aachen University52074 Aachen Germany
| | | | - Jochen Büchs
- AVT—Biochemical EngineeringRWTH Aachen UniversityForckenbeckstraße 51 52074 Aachen Germany
| |
Collapse
|
15
|
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
| |
Collapse
|