1
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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.
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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
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2
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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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3
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Abedin S, Ranjbari J, Haeri A, Vahidi H, Moghimi HR. Design and Characterization of an Osmotic Pump System for Optimal Feeding and pH Control in E. coli Culture to Increase Biomass. IRANIAN JOURNAL OF PHARMACEUTICAL RESEARCH : IJPR 2024; 23:e138677. [PMID: 39005735 PMCID: PMC11246646 DOI: 10.5812/ijpr-138677] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 06/28/2023] [Revised: 08/08/2023] [Accepted: 08/19/2023] [Indexed: 07/16/2024]
Abstract
Background Batch cultures used for various purposes, such as expression screening and recombinant protein production in laboratories, usually have some drawbacks due to the bolus addition of carbon sources, such as glucose and buffers, that lead to overflow metabolism, decreased pH, high osmolality, low biomass yield, and low protein production. Objectives This study aimed to overcome the problems of batch culture using the controlled release concept by a controlled porosity osmotic pump (CPOP) system. Methods The CPOP was formulated with glucose as a carbon source feeding and sodium carbonate as a pH modifier in the core of the tablet that was coated with a semipermeable membrane containing cellulose acetate and polyethylene glycol (PEG) 400. The release rate was regulated with Eudragit L100 as a retardant agent in the core and PEG 400 as a pore-former agent in the coating membrane. Fourier-transform infrared spectroscopy (FT-IR) and scanning electron microscopy (SEM) were used to elucidate compatibility between components and release mechanism, respectively. The in-vitro release of glucose and Na2CO3 studies were performed for 24 hours in a mineral culture medium (M9). Then, the effectiveness of CPOP in the growth of Escherichia coli (E. coli BL21) as a microorganism model was evaluated. Glucose consumption, changes in medium's pH, and acetate concentration as a by-product were also monitored during the bacterial growth. Results Fourier-transform infrared spectroscopy confirmed the compatibility between the components in the osmotic pump, and SEM elucidated the release mechanism due to in-situ delivery pores created by dissolving soluble components (PEG 400) on the coated membrane upon contact with the dissolution medium. The in-vitro release studies indicated that the osmotic pump was able to deliver glucose and sodium carbonate in a zero-order manner. The use of CPOP in E. coli (BL21) cultivation resulted in a statistically significant improvement in biomass (over 80%), maintaining the pH of the medium (above 6.8) during the exponential phase, and reducing metabolic by-product formation (acetate), compared to bolus feeding (P < 0.05). Conclusions The use of CPOP, which is capable of controlled release of glucose as a carbon source and sodium carbonate as a pH modifier, can overcome the drawbacks of bolus feeding, such as decreased pH, increased acetate concentration, and low productivity. It has a good potential for commercialization.
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Affiliation(s)
- Saeedeh Abedin
- Department of Pharmaceutics and Pharmaceutical Nanotechnology, School of Pharmacy, Shahid Beheshti University of Medical Sciences, Tehran, Iran
| | - Javad Ranjbari
- Department of Biotechnology, School of Advanced Technologies in Medicine, Shahid Beheshti University of Medical Sciences, Tehran, Iran
| | - Azadeh Haeri
- Department of Pharmaceutics and Pharmaceutical Nanotechnology, School of Pharmacy, Shahid Beheshti University of Medical Sciences, Tehran, Iran
| | - Hossein Vahidi
- Department of Pharmaceutics and Pharmaceutical Nanotechnology, School of Pharmacy, Shahid Beheshti University of Medical Sciences, Tehran, Iran
| | - Hamid Reza Moghimi
- Department of Pharmaceutics and Pharmaceutical Nanotechnology, School of Pharmacy, Shahid Beheshti University of Medical Sciences, Tehran, Iran
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4
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Matamouros S, Gensch T, Cerff M, Sachs CC, Abdollahzadeh I, Hendriks J, Horst L, Tenhaef N, Tenhaef J, Noack S, Graf M, Takors R, Nöh K, Bott M. Growth-rate dependency of ribosome abundance and translation elongation rate in Corynebacterium glutamicum differs from that in Escherichia coli. Nat Commun 2023; 14:5611. [PMID: 37699882 PMCID: PMC10497606 DOI: 10.1038/s41467-023-41176-y] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2021] [Accepted: 08/24/2023] [Indexed: 09/14/2023] Open
Abstract
Bacterial growth rate (µ) depends on the protein synthesis capacity of the cell and thus on the number of active ribosomes and their translation elongation rate. The relationship between these fundamental growth parameters have only been described for few bacterial species, in particular Escherichia coli. Here, we analyse the growth-rate dependency of ribosome abundance and translation elongation rate for Corynebacterium glutamicum, a gram-positive model species differing from E. coli by a lower growth temperature optimum and a lower maximal growth rate. We show that, unlike in E. coli, there is little change in ribosome abundance for µ <0.4 h-1 in C. glutamicum and the fraction of active ribosomes is kept above 70% while the translation elongation rate declines 5-fold. Mathematical modelling indicates that the decrease in the translation elongation rate can be explained by a depletion of translation precursors.
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Affiliation(s)
- Susana Matamouros
- Institute of Bio- and Geosciences, IBG-1: Biotechnology, Forschungszentrum Jülich, Jülich, Germany.
| | - Thomas Gensch
- Institute of Biological Information Processing, IBI-1: Molecular and Cellular Physiology, Forschungszentrum Jülich, Jülich, Germany
| | - Martin Cerff
- Institute of Bio- and Geosciences, IBG-1: Biotechnology, Forschungszentrum Jülich, Jülich, Germany
| | - Christian C Sachs
- Institute of Bio- and Geosciences, IBG-1: Biotechnology, Forschungszentrum Jülich, Jülich, Germany
| | - Iman Abdollahzadeh
- Institute of Biological Information Processing, IBI-1: Molecular and Cellular Physiology, Forschungszentrum Jülich, Jülich, Germany
| | - Johnny Hendriks
- Institute of Biological Information Processing, IBI-1: Molecular and Cellular Physiology, Forschungszentrum Jülich, Jülich, Germany
| | - Lucas Horst
- Institute of Bio- and Geosciences, IBG-1: Biotechnology, Forschungszentrum Jülich, Jülich, Germany
| | - Niklas Tenhaef
- Institute of Bio- and Geosciences, IBG-1: Biotechnology, Forschungszentrum Jülich, Jülich, Germany
| | - Julia Tenhaef
- Institute of Bio- and Geosciences, IBG-1: Biotechnology, Forschungszentrum Jülich, Jülich, Germany
| | - Stephan Noack
- Institute of Bio- and Geosciences, IBG-1: Biotechnology, Forschungszentrum Jülich, Jülich, Germany
| | - Michaela Graf
- Institute of Biochemical Engineering, University of Stuttgart, Stuttgart, Germany
| | - Ralf Takors
- Institute of Biochemical Engineering, University of Stuttgart, Stuttgart, Germany
| | - Katharina Nöh
- Institute of Bio- and Geosciences, IBG-1: Biotechnology, Forschungszentrum Jülich, Jülich, Germany
| | - Michael Bott
- Institute of Bio- and Geosciences, IBG-1: Biotechnology, Forschungszentrum Jülich, Jülich, Germany.
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5
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Müller C, Bakkes PJ, Lenz P, Waffenschmidt V, Helleckes LM, Jaeger KE, Wiechert W, Knapp A, Freudl R, Oldiges M. Accelerated strain construction and characterization of C. glutamicum protein secretion by laboratory automation. Appl Microbiol Biotechnol 2022; 106:4481-4497. [PMID: 35759036 PMCID: PMC9259529 DOI: 10.1007/s00253-022-12017-7] [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: 04/07/2022] [Revised: 06/01/2022] [Accepted: 06/04/2022] [Indexed: 11/02/2022]
Abstract
Secretion of bacterial proteins into the culture medium simplifies downstream processing by avoiding cell disruption for target protein purification. However, a suitable signal peptide for efficient secretion needs to be identified, and currently, there are no tools available to predict optimal combinations of signal peptides and target proteins. The selection of such a combination is influenced by several factors, including protein biosynthesis efficiency and cultivation conditions, which both can have a significant impact on secretion performance. As a result, a large number of combinations must be tested. Therefore, we have developed automated workflows allowing for targeted strain construction and secretion screening using two platforms. Key advantages of this experimental setup include lowered hands-on time and increased throughput. In this study, the automated workflows were established for the heterologous production of Fusarium solani f. sp. pisi cutinase in Corynebacterium glutamicum. The target protein was monitored in culture supernatants via enzymatic activity and split GFP assay. Varying spacer lengths between the Shine-Dalgarno sequence and the start codon of Bacillus subtilis signal peptides were tested. Consistent with previous work on the secretory cutinase production in B. subtilis, a ribosome binding site with extended spacer length to up to 12 nt, which likely slows down translation initiation, does not necessarily lead to poorer cutinase secretion by C. glutamicum. The best performing signal peptides for cutinase secretion with a standard spacer length were identified in a signal peptide screening. Additional insights into the secretion process were gained by monitoring secretion stress using the C. glutamicum K9 biosensor strain. KEY POINTS: • Automated workflows for strain construction and screening of protein secretion • Comparison of spacer, signal peptide, and host combinations for cutinase secretion • Signal peptide screening for secretion by C. glutamicum using the split GFP assay.
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Affiliation(s)
- Carolin Müller
- Institute of Bio- and Geosciences IBG-1, Biotechnology, Forschungszentrum Jülich GmbH, 52425, Jülich, Germany.,Institute of Biotechnology, RWTH Aachen University, 52062, Aachen, Germany
| | - Patrick J Bakkes
- Institute of Bio- and Geosciences IBG-1, Biotechnology, Forschungszentrum Jülich GmbH, 52425, Jülich, Germany
| | - Patrick Lenz
- Institute of Molecular Enzyme Technology, Heinrich Heine University Düsseldorf, Forschungszentrum Jülich, 52425, Jülich, Germany
| | - Vera Waffenschmidt
- Institute of Bio- and Geosciences IBG-1, Biotechnology, Forschungszentrum Jülich GmbH, 52425, Jülich, Germany
| | - Laura M Helleckes
- Institute of Bio- and Geosciences IBG-1, Biotechnology, Forschungszentrum Jülich GmbH, 52425, Jülich, Germany.,Institute of Biotechnology, RWTH Aachen University, 52062, Aachen, Germany
| | - Karl-Erich Jaeger
- Institute of Bio- and Geosciences IBG-1, Biotechnology, Forschungszentrum Jülich GmbH, 52425, Jülich, Germany.,Institute of Molecular Enzyme Technology, Heinrich Heine University Düsseldorf, Forschungszentrum Jülich, 52425, Jülich, Germany
| | - Wolfgang Wiechert
- Institute of Bio- and Geosciences IBG-1, Biotechnology, Forschungszentrum Jülich GmbH, 52425, Jülich, Germany.,Computational Systems Biotechnology (AVT.CSB), RWTH Aachen University, 52062, Aachen, Germany
| | - Andreas Knapp
- Institute of Molecular Enzyme Technology, Heinrich Heine University Düsseldorf, Forschungszentrum Jülich, 52425, Jülich, Germany.,Castrol Germany GmbH, 41179, Mönchengladbach, Germany
| | - Roland Freudl
- Institute of Bio- and Geosciences IBG-1, Biotechnology, Forschungszentrum Jülich GmbH, 52425, Jülich, Germany
| | - Marco Oldiges
- Institute of Bio- and Geosciences IBG-1, Biotechnology, Forschungszentrum Jülich GmbH, 52425, Jülich, Germany. .,Institute of Biotechnology, RWTH Aachen University, 52062, Aachen, Germany.
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6
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Osthege M, Tenhaef N, Zyla R, Müller C, Hemmerich J, Wiechert W, Noack S, Oldiges M. bletl - A Python package for integrating BioLector microcultivation devices in the Design-Build-Test-Learn cycle. Eng Life Sci 2022; 22:242-259. [PMID: 35382539 PMCID: PMC8961055 DOI: 10.1002/elsc.202100108] [Citation(s) in RCA: 15] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2021] [Revised: 01/16/2022] [Accepted: 01/28/2022] [Indexed: 12/13/2022] Open
Abstract
Microbioreactor (MBR) devices have emerged as powerful cultivation tools for tasks of microbial phenotyping and bioprocess characterization and provide a wealth of online process data in a highly parallelized manner. Such datasets are difficult to interpret in short time by manual workflows. In this study, we present the Python package bletl and show how it enables robust data analyses and the application of machine learning techniques without tedious data parsing and preprocessing. bletl reads raw result files from BioLector I, II and Pro devices to make all the contained information available to Python-based data analysis workflows. Together with standard tooling from the Python scientific computing ecosystem, interactive visualizations and spline-based derivative calculations can be performed. Additionally, we present a new method for unbiased quantification of time-variable specific growth rateμ ⃗ t based on unsupervised switchpoint detection with Student-t distributed random walks. With an adequate calibration model, this method enables practitioners to quantify time-variable growth rate with Bayesian uncertainty quantification and automatically detect switch-points that indicate relevant metabolic changes. Finally, we show how time series feature extraction enables the application of machine learning methods to MBR data, resulting in unsupervised phenotype characterization. As an example, Neighbor Embedding (t-SNE) is performed to visualize datasets comprising a variety of growth/DO/pH phenotypes.
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Affiliation(s)
- Michael Osthege
- Forschungszentrum Jülich GmbHJülichGermany
- Institute of BiotechnologyRWTH Aachen UniversityAachenGermany
| | | | | | - Carolin Müller
- Forschungszentrum Jülich GmbHJülichGermany
- Institute of BiotechnologyRWTH Aachen UniversityAachenGermany
| | | | - Wolfgang Wiechert
- Forschungszentrum Jülich GmbHJülichGermany
- Computational Systems Biotechnology (AVT.CSB)RWTH Aachen UniversityAachenGermany
| | | | - Marco Oldiges
- Forschungszentrum Jülich GmbHJülichGermany
- Institute of BiotechnologyRWTH Aachen UniversityAachenGermany
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7
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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: 16] [Impact Index Per Article: 5.3] [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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8
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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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9
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Tenhaef N, Stella R, Frunzke J, Noack S. Automated Rational Strain Construction Based on High-Throughput Conjugation. ACS Synth Biol 2021; 10:589-599. [PMID: 33593066 DOI: 10.1021/acssynbio.0c00599] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/12/2023]
Abstract
Molecular cloning is the core of synthetic biology, as it comprises the assembly of DNA and its expression in target hosts. At present, however, cloning is most often a manual, time-consuming, and repetitive process that highly benefits from automation. The automation of a complete rational cloning procedure, i.e., from DNA creation to expression in the target host, involves the integration of different operations and machines. Examples of such workflows are sparse, especially when the design is rational (i.e., the DNA sequence design is fixed and not based on randomized libraries) and the target host is less genetically tractable (e.g., not sensitive to heat-shock transformation). In this study, an automated workflow for the rational construction of plasmids and their subsequent conjugative transfer into the biotechnological platform organism Corynebacterium glutamicum is presented. The whole workflow is accompanied by a custom-made software tool. As an application example, a rationally designed library of transcription factor-biosensors based on the regulator Lrp was constructed and characterized. A sensor with an improved dynamic range was obtained, and insights from the screening provided evidence for a dual regulator function of C. glutamicum Lrp.
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Affiliation(s)
- Niklas Tenhaef
- Institute of Bio- and Geosciences − IBG-1: Biotechnology, Forschungszentrum Jülich GmbH, Jülich 52425, Germany
| | - Robert Stella
- Institute of Bio- and Geosciences − IBG-1: Biotechnology, Forschungszentrum Jülich GmbH, Jülich 52425, Germany
| | - Julia Frunzke
- Institute of Bio- and Geosciences − IBG-1: Biotechnology, Forschungszentrum Jülich GmbH, Jülich 52425, Germany
| | - Stephan Noack
- Institute of Bio- and Geosciences − IBG-1: Biotechnology, Forschungszentrum Jülich GmbH, Jülich 52425, Germany
- Bioeconomy Science Center (BioSC), Forschungszentrum Jülich, Jülich 52425, Germany
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10
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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: 18] [Impact Index Per Article: 6.0] [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.
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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
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Tripathi NK, Shrivastava A. Recent Developments in Bioprocessing of Recombinant Proteins: Expression Hosts and Process Development. Front Bioeng Biotechnol 2019; 7:420. [PMID: 31921823 PMCID: PMC6932962 DOI: 10.3389/fbioe.2019.00420] [Citation(s) in RCA: 251] [Impact Index Per Article: 50.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2019] [Accepted: 11/29/2019] [Indexed: 12/22/2022] Open
Abstract
Infectious diseases, along with cancers, are among the main causes of death among humans worldwide. The production of therapeutic proteins for treating diseases at large scale for millions of individuals is one of the essential needs of mankind. Recent progress in the area of recombinant DNA technologies has paved the way to producing recombinant proteins that can be used as therapeutics, vaccines, and diagnostic reagents. Recombinant proteins for these applications are mainly produced using prokaryotic and eukaryotic expression host systems such as mammalian cells, bacteria, yeast, insect cells, and transgenic plants at laboratory scale as well as in large-scale settings. The development of efficient bioprocessing strategies is crucial for industrial production of recombinant proteins of therapeutic and prophylactic importance. Recently, advances have been made in the various areas of bioprocessing and are being utilized to develop effective processes for producing recombinant proteins. These include the use of high-throughput devices for effective bioprocess optimization and of disposable systems, continuous upstream processing, continuous chromatography, integrated continuous bioprocessing, Quality by Design, and process analytical technologies to achieve quality product with higher yield. This review summarizes recent developments in the bioprocessing of recombinant proteins, including in various expression systems, bioprocess development, and the upstream and downstream processing of recombinant proteins.
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Affiliation(s)
- Nagesh K. Tripathi
- Bioprocess Scale Up Facility, Defence Research and Development Establishment, Gwalior, India
| | - Ambuj Shrivastava
- Division of Virology, Defence Research and Development Establishment, Gwalior, India
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