1
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Irreversible and reversible impact on cellular behavior upon intra-experimental process parameter shifts in a CHO semi-continuous perfusion process. Biochem Eng J 2023. [DOI: 10.1016/j.bej.2023.108876] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/25/2023]
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2
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Bayer B, Duerkop M, Striedner G, Sissolak B. Model Transferability and Reduced Experimental Burden in Cell Culture Process Development Facilitated by Hybrid Modeling and Intensified Design of Experiments. Front Bioeng Biotechnol 2022; 9:740215. [PMID: 35004635 PMCID: PMC8733703 DOI: 10.3389/fbioe.2021.740215] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2021] [Accepted: 11/22/2021] [Indexed: 12/22/2022] Open
Abstract
Reliable process development is accompanied by intense experimental effort. The utilization of an intensified design of experiments (iDoE) (intra-experimental critical process parameter (CPP) shifts combined) with hybrid modeling potentially reduces process development burden. The iDoE can provide more process response information in less overall process time, whereas hybrid modeling serves as a commodity to describe this behavior the best way. Therefore, a combination of both approaches appears beneficial for faster design screening and is especially of interest at larger scales where the costs per experiment rise significantly. Ideally, profound process knowledge is gathered at a small scale and only complemented with few validation experiments on a larger scale, saving valuable resources. In this work, the transferability of hybrid modeling for Chinese hamster ovary cell bioprocess development along process scales was investigated. A two-dimensional DoE was fully characterized in shake flask duplicates (300 ml), containing three different levels for the cultivation temperature and the glucose concentration in the feed. Based on these data, a hybrid model was developed, and its performance was assessed by estimating the viable cell concentration and product titer in 15 L bioprocesses with the same DoE settings. To challenge the modeling approach, 15 L bioprocesses also comprised iDoE runs with intra-experimental CPP shifts, impacting specific cell rates such as growth, consumption, and formation. Subsequently, the applicability of the iDoE cultivations to estimate static cultivations was also investigated. The shaker-scale hybrid model proved suitable for application to a 15 L scale (1:50), estimating the viable cell concentration and the product titer with an NRMSE of 10.92% and 17.79%, respectively. Additionally, the iDoE hybrid model performed comparably, displaying NRMSE values of 13.75% and 21.13%. The low errors when transferring the models from shaker to reactor and between the DoE and the iDoE approach highlight the suitability of hybrid modeling for mammalian cell culture bioprocess development and the potential of iDoE to accelerate process characterization and to improve process understanding.
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Affiliation(s)
- Benjamin Bayer
- Department of Biotechnology, University of Natural Resources and Life Sciences, Vienna, Austria.,Novasign GmbH, Vienna, Austria
| | - Mark Duerkop
- Department of Biotechnology, University of Natural Resources and Life Sciences, Vienna, Austria.,Novasign GmbH, Vienna, Austria
| | - Gerald Striedner
- Department of Biotechnology, University of Natural Resources and Life Sciences, Vienna, Austria.,Novasign GmbH, Vienna, Austria
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3
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Kager J, Herwig C. Monte Carlo-Based Error Propagation for a More Reliable Regression Analysis across Specific Rates in Bioprocesses. Bioengineering (Basel) 2021; 8:160. [PMID: 34821726 PMCID: PMC8614739 DOI: 10.3390/bioengineering8110160] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2021] [Revised: 10/14/2021] [Accepted: 10/19/2021] [Indexed: 11/29/2022] Open
Abstract
During process development, bioprocess data need to be converted into applicable knowledge. Therefore, it is crucial to evaluate the obtained data under the usage of transparent and reliable data reduction and correlation techniques. Within this contribution, we show a generic Monte Carlo error propagation and regression approach applied to two different, industrially relevant cultivation processes. Based on measurement uncertainties, errors for cell-specific growth, uptake, and production rates were determined across an evaluation chain, with interlinked inputs and outputs. These uncertainties were subsequently included in regression analysis to derive the covariance of the regression coefficients and the confidence bounds for prediction. The usefulness of the approach is shown within two case studies, based on the relations across biomass-specific rate control limits to guarantee high productivities in E. coli, and low lactate formation in a CHO cell fed-batch could be established. Besides the possibility to determine realistic errors on the evaluated process data, the presented approach helps to differentiate between reliable and unreliable correlations and prevents the wrong interpretations of relations based on uncertain data.
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Affiliation(s)
- Julian Kager
- Competence Center CHASE GmbH, 4040 Linz, Austria
- Research Division Biochemical Engineering, Institute of Chemical, Environmental and Bioscience Engineering, Technische Universität Wien, 1060 Vienna, Austria
| | - Christoph Herwig
- Research Division Biochemical Engineering, Institute of Chemical, Environmental and Bioscience Engineering, Technische Universität Wien, 1060 Vienna, Austria
- Christian Doppler Laboratory for Mechanistic and Physiological Methods for Improved Bioprocesses, Technische Universität Wien, Gumpendorfer Straße 1a, 1060 Vienna, Austria
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4
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Tang HW, Abbasiliasi S, Ng ZJ, Lee YY, Tang TK, Tan JS. Insight into the pilot-scale fed-batch fermentation for production of Enterococcus faecium CW3801 using molasses-based medium. Prep Biochem Biotechnol 2021; 52:691-700. [PMID: 34647854 DOI: 10.1080/10826068.2021.1986721] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/20/2022]
Abstract
Enterococcus sp. has been used as starters in food fermentation due to their probiotic and antimicrobial properties in food biopreservation. The antimicrobial properties were mainly contributed by the bacteriocin called enterocin. Hence, the availability of a cost-effective pilot-scale cultivation conditions is a necessity for the production of probiotic bacteria. This study aims to investigate optimization of medium composition using sugarcane molasses as a carbon source using response surface methodology and the potential use of fed-batch cultivation for improvement of the cell viability of Enterococcus faecium CW3801 for the use as a probiotic starter culture. Two feeding strategies (ramp and constant) were applied in fed-batch cultivation for enhancement of the production of E. faecium in a 2-L stirred tank bioreactor using the optimized medium and scaled up to a 15-L bioreactor. Optimized fermentation medium which comprised of 10% (v/v) of molasses and 10 g/L of yeast extract at pH 7 yielded maximum cell viability of 29.4 × 1011 CFU/mL with 3900 AU/mL of bacteriocin-like inhibitory substances (BLIS) activity. In the fed-batch, the cell viability (8.4 × 1013) and dry cell weight (6.34 g/L) reached the highest in optimized medium when the ramp (stepwise) feeding was applied. In scaling up to 15-L bioreactor, the growth of E. faecium was achieved at 2.3 × 1013 CFU/mL with the dry cell weight of 5.28 g/L under the same condition. The BLIS in 15-L bioreactor was 6% higher than the 2-L bioreactor. This study demonstrated that molasses and yeast extract are good feedstock for the growth of E. faecium. The E. faecium, a non-vancomycin resistant enterococcus (VRE) was successfully produced by a fed-batch cultivation approach and scaled up to a 15-L bioreactor using a ramp feeding strategy. Results from this study revealed that the fed-batch cultivation using molasses-based medium has industrial potential for the production of probiotics.
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Affiliation(s)
- Hock Wei Tang
- Bioprocess Technology, School of Industrial Technology, Universiti Sains Malaysia, Pulau Pinang, Malaysia
| | - Sahar Abbasiliasi
- Halal Products Research Institute, Universiti Putra Malaysia, Serdang, Malaysia
| | - Zhang Jin Ng
- Bioprocess Technology, School of Industrial Technology, Universiti Sains Malaysia, Pulau Pinang, Malaysia
| | - Yee-Ying Lee
- School of Science, Monash University Malaysia, Selangor, Malaysia
| | - Teck-Kim Tang
- International Joint Laboratory on Plant Oils Processing and Safety, Institute of Bioscience, University Putra Malaysia, Serdang, Malaysia
| | - Joo Shun Tan
- Bioprocess Technology, School of Industrial Technology, Universiti Sains Malaysia, Pulau Pinang, Malaysia
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5
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Hahm J, Bauer A, Jung S, Zell N, Boßle F, Buchholz R, Lindenberger C. Process Parameter Screening for the Microalga
Chlamydomonas asymmetrica
in Batch and Turbidostat Cultivations. CHEM-ING-TECH 2021. [DOI: 10.1002/cite.202100046] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Affiliation(s)
| | | | - Sun‐Hwa Jung
- FAU Branch Campus Busan Busan South Korea
- Ostbayerische Technische Hochschule Amberg-Weiden Faculty of Department of Mechanical Engineering/Environmental Technology Amberg Germany
| | - Niklas Zell
- Ostbayerische Technische Hochschule Amberg-Weiden Faculty of Department of Mechanical Engineering/Environmental Technology Amberg Germany
| | - Fabian Boßle
- Ostbayerische Technische Hochschule Amberg-Weiden Faculty of Department of Mechanical Engineering/Environmental Technology Amberg Germany
| | | | - Christoph Lindenberger
- FAU Branch Campus Busan Busan South Korea
- Ostbayerische Technische Hochschule Amberg-Weiden Faculty of Department of Mechanical Engineering/Environmental Technology Amberg Germany
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6
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Liu P, Wang S, Li C, Zhuang Y, Xia J, Noorman H. Dynamic response of Aspergillus niger to periodical glucose pulse stimuli in chemostat cultures. Biotechnol Bioeng 2021; 118:2265-2282. [PMID: 33666237 DOI: 10.1002/bit.27739] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2020] [Revised: 01/05/2021] [Accepted: 01/21/2021] [Indexed: 12/15/2022]
Abstract
In industrial large-scale bioreactors, microorganisms encounter heterogeneous substrate concentration conditions, which can impact growth or product formation. Here we carried out an extended (12 h) experiment of repeated glucose pulsing with a 10-min period to simulate fluctuating glucose concentrations with Aspergillus niger producing glucoamylase, and investigated its dynamic response by rapid sampling and quantitative metabolomics. The 10-min period represents worst-case conditions, as in industrial bioreactors the average cycling duration is usually in the order of 1 min. We found that cell growth and the glucoamylase productivity were not significantly affected, despite striking metabolomic dynamics. Periodical dynamic responses were found across all central carbon metabolism pathways, with different time scales, and the frequently reported ATP paradox was confirmed for this A. niger strain under the dynamic conditions. A thermodynamics analysis revealed that several reactions of the central carbon metabolism remained in equilibrium even under periodical dynamic conditions. The dynamic response profiles of the intracellular metabolites did not change during the pulse exposure, showing no significant adaptation of the strain to the more than 60 perturbation cycles applied. The apparent high tolerance of the glucoamylase producing A. niger strain for extreme variations in the glucose availability presents valuable information for the design of robust industrial microbial hosts.
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Affiliation(s)
- Peng Liu
- State Key Laboratory of Bioreactor Engineering, East China University of Science and Technology, Shanghai, China
| | - Shuai Wang
- State Key Laboratory of Bioreactor Engineering, East China University of Science and Technology, Shanghai, China
| | - Chao Li
- State Key Laboratory of Bioreactor Engineering, East China University of Science and Technology, Shanghai, China
| | - Yingping Zhuang
- State Key Laboratory of Bioreactor Engineering, East China University of Science and Technology, Shanghai, China
| | - Jianye Xia
- State Key Laboratory of Bioreactor Engineering, East China University of Science and Technology, Shanghai, China
| | - Henk Noorman
- DSM Biotechnology Center, Delft, The Netherlands
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7
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Potential of Integrating Model-Based Design of Experiments Approaches and Process Analytical Technologies for Bioprocess Scale-Down. ADVANCES IN BIOCHEMICAL ENGINEERING/BIOTECHNOLOGY 2021. [PMID: 33381857 DOI: 10.1007/10_2020_154] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 08/18/2023]
Abstract
Typically, bioprocesses on an industrial scale are dynamic systems with a certain degree of variability, system inhomogeneities, and even population heterogeneities. Therefore, the scaling of such processes from laboratory to industrial scale and vice versa is not a trivial task. Traditional scale-down methodologies consider several technical parameters, so that systems on the laboratory scale tend to qualitatively reflect large-scale effects, but not the dynamic situation in an industrial bioreactor over the entire process, from the perspective of a cell. Supported by the enormous increase in computing power, the latest scientific focus is on the application of dynamic models, in combination with computational fluid dynamics to quantitatively describe cell behavior. These models allow the description of possible cellular lifelines which in turn can be used to derive a regime analysis for scale-down experiments. However, the approaches described so far, which were for a very few process examples, are very labor- and time-intensive and cannot be validated easily. In parallel, alternatives have been developed based on the description of the industrial process with hybrid process models, which describe a process mechanistically as far as possible in order to determine the essential process parameters with their respective variances. On-line analytical methods allow the characterization of population heterogeneity directly in the process. This detailed information from the industrial process can be used in laboratory screening systems to select relevant conditions in which the cell and process related parameters reflect the situation in the industrial scale. In our opinion, these technologies, which are available in research for modeling biological systems, in combination with process analytical techniques are so far developed that they can be implemented in industrial routines for faster development of new processes and optimization of existing ones.
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Nieto-Taype MA, Garcia-Ortega X, Albiol J, Montesinos-Seguí JL, Valero F. Continuous Cultivation as a Tool Toward the Rational Bioprocess Development With Pichia Pastoris Cell Factory. Front Bioeng Biotechnol 2020; 8:632. [PMID: 32671036 PMCID: PMC7330098 DOI: 10.3389/fbioe.2020.00632] [Citation(s) in RCA: 20] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2019] [Accepted: 05/22/2020] [Indexed: 12/15/2022] Open
Abstract
The methylotrophic yeast Pichia pastoris (Komagataella phaffii) is currently considered one of the most promising hosts for recombinant protein production (RPP) and metabolites due to the availability of several tools to efficiently regulate the recombinant expression, its ability to perform eukaryotic post-translational modifications and to secrete the product in the extracellular media. The challenge of improving the bioprocess efficiency can be faced from two main approaches: the strain engineering, which includes enhancements in the recombinant expression regulation as well as overcoming potential cell capacity bottlenecks; and the bioprocess engineering, focused on the development of rational-based efficient operational strategies. Understanding the effect of strain and operational improvements in bioprocess efficiency requires to attain a robust knowledge about the metabolic and physiological changes triggered into the cells. For this purpose, a number of studies have revealed chemostat cultures to provide a robust tool for accurate, reliable, and reproducible bioprocess characterization. It should involve the determination of key specific rates, productivities, and yields for different C and N sources, as well as optimizing media formulation and operating conditions. Furthermore, studies along the different levels of systems biology are usually performed also in chemostat cultures. Transcriptomic, proteomic and metabolic flux analysis, using different techniques like differential target gene expression, protein description and 13C-based metabolic flux analysis, are widely described as valued examples in the literature. In this scenario, the main advantage of a continuous operation relies on the quality of the homogeneous samples obtained under steady-state conditions, where both the metabolic and physiological status of the cells remain unaltered in an all-encompassing picture of the cell environment. This contribution aims to provide the state of the art of the different approaches that allow the design of rational strain and bioprocess engineering improvements in Pichia pastoris toward optimizing bioprocesses based on the results obtained in chemostat cultures. Interestingly, continuous cultivation is also currently emerging as an alternative operational mode in industrial biotechnology for implementing continuous process operations.
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Affiliation(s)
- Miguel Angel Nieto-Taype
- Department of Chemical, Biological and Environmental Engineering, School of Engineering, Universitat Autònoma de Barcelona, Bellaterra, Spain
| | - Xavier Garcia-Ortega
- Department of Chemical, Biological and Environmental Engineering, School of Engineering, Universitat Autònoma de Barcelona, Bellaterra, Spain
| | - Joan Albiol
- Department of Chemical, Biological and Environmental Engineering, School of Engineering, Universitat Autònoma de Barcelona, Bellaterra, Spain
| | - José Luis Montesinos-Seguí
- Department of Chemical, Biological and Environmental Engineering, School of Engineering, Universitat Autònoma de Barcelona, Bellaterra, Spain
| | - Francisco Valero
- Department of Chemical, Biological and Environmental Engineering, School of Engineering, Universitat Autònoma de Barcelona, Bellaterra, Spain
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9
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Gränicher G, Coronel J, Trampler F, Jordan I, Genzel Y, Reichl U. Performance of an acoustic settler versus a hollow fiber-based ATF technology for influenza virus production in perfusion. Appl Microbiol Biotechnol 2020; 104:4877-4888. [PMID: 32291490 PMCID: PMC7228903 DOI: 10.1007/s00253-020-10596-x] [Citation(s) in RCA: 25] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/31/2019] [Revised: 03/10/2020] [Accepted: 03/31/2020] [Indexed: 12/24/2022]
Abstract
Process intensification and integration is crucial regarding an ever increasing pressure on manufacturing costs and capacities in biologics manufacturing. For virus production in perfusion mode, membrane-based alternating tangential flow filtration (ATF) and acoustic settler are the commonly described cell retention technologies. While acoustic settlers allow for continuous influenza virus harvesting, the use of commercially available membranes for ATF systems typically results in the accumulation of virus particles in the bioreactor vessel. Accordingly, with one single harvest at the end of a cultivation, this increases the risk of lowering the product quality. To assess which cell retention device would be most suitable for influenza A virus production, we compared various key performance figures using AGE1.CR.pIX cells at concentrations between 25 and 50 × 106 cells/mL at similar infection conditions using either an ATF system or an acoustic settler. Production yields, process-related impurities, and aggregation of viruses and other large molecules were evaluated. Taking into account the total number of virions from both the bioreactor and the harvest vessel, a 1.5-3.0-fold higher volumetric virus yield was obtained for the acoustic settler. In addition, fewer large-sized aggregates (virus particles and other molecules) were observed in the harvest taken directly from the bioreactor. In contrast, similar levels of process-related impurities (host cell dsDNA, total protein) were obtained in the harvest for both retention systems. Overall, a clear advantage was observed for continuous virus harvesting after the acoustic settler operation mode was optimized. This development may also allow direct integration of subsequent downstream processing steps. KEY POINTS: • High suspension cell density, immortalized avian cell line, influenza vaccine.
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Affiliation(s)
- Gwendal Gränicher
- Bioprocess Engineering, Max Planck Institute for Dynamics of Complex Technical Systems, Sandtorstr. 1, 39106, Magdeburg, Germany.
| | - Juliana Coronel
- Bioprocess Engineering, Max Planck Institute for Dynamics of Complex Technical Systems, Sandtorstr. 1, 39106, Magdeburg, Germany
| | - Felix Trampler
- SonoSep Technologies, Waldgasse 7, 2371, Hinterbrühl, Austria
| | - Ingo Jordan
- ProBioGen AG, Goethestr 54, 13086, Berlin, Germany
| | - Yvonne Genzel
- Bioprocess Engineering, Max Planck Institute for Dynamics of Complex Technical Systems, Sandtorstr. 1, 39106, Magdeburg, Germany.
| | - Udo Reichl
- Bioprocess Engineering, Max Planck Institute for Dynamics of Complex Technical Systems, Sandtorstr. 1, 39106, Magdeburg, Germany
- Bioprocess Engineering, Otto-von-Guericke-University Magdeburg, Universitätsplatz 2, 39106, Magdeburg, Germany
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10
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Vasilakou E, van Loosdrecht MCM, Wahl SA. Escherichia coli metabolism under short-term repetitive substrate dynamics: adaptation and trade-offs. Microb Cell Fact 2020; 19:116. [PMID: 32471427 PMCID: PMC7260802 DOI: 10.1186/s12934-020-01379-0] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2020] [Accepted: 05/25/2020] [Indexed: 12/04/2022] Open
Abstract
Background Microbial metabolism is highly dependent on the environmental conditions. Especially, the substrate concentration, as well as oxygen availability, determine the metabolic rates. In large-scale bioreactors, microorganisms encounter dynamic conditions in substrate and oxygen availability (mixing limitations), which influence their metabolism and subsequently their physiology. Earlier, single substrate pulse experiments were not able to explain the observed physiological changes generated under large-scale industrial fermentation conditions. Results In this study we applied a repetitive feast–famine regime in an aerobic Escherichia coli culture in a time-scale of seconds. The regime was applied for several generations, allowing cells to adapt to the (repetitive) dynamic environment. The observed response was highly reproducible over the cycles, indicating that cells were indeed fully adapted to the regime. We observed an increase of the specific substrate and oxygen consumption (average) rates during the feast–famine regime, compared to a steady-state (chemostat) reference environment. The increased rates at same (average) growth rate led to a reduced biomass yield (30% lower). Interestingly, this drop was not followed by increased by-product formation, pointing to the existence of energy-spilling reactions. During the feast–famine cycle, the cells rapidly increased their uptake rate. Within 10 s after the beginning of the feeding, the substrate uptake rate was higher (4.68 μmol/gCDW/s) than reported during batch growth (3.3 μmol/gCDW/s). The high uptake led to an accumulation of several intracellular metabolites, during the feast phase, accounting for up to 34% of the carbon supplied. Although the metabolite concentrations changed rapidly, the cellular energy charge remained unaffected, suggesting well-controlled balance between ATP producing and ATP consuming reactions. Conclusions The adaptation of the physiology and metabolism of E. coli under substrate dynamics, representative for large-scale fermenters, revealed the existence of several cellular mechanisms coping with stress. Changes in the substrate uptake system, storage potential and energy-spilling processes resulted to be of great importance. These metabolic strategies consist a meaningful step to further tackle reduced microbial performance, observed under large-scale cultivations.
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Affiliation(s)
- Eleni Vasilakou
- Department of Biotechnology, Delft University of Technology, Van der Maasweg, 2629 HZ, Delft, The Netherlands.
| | - Mark C M van Loosdrecht
- Department of Biotechnology, Delft University of Technology, Van der Maasweg, 2629 HZ, Delft, The Netherlands
| | - S Aljoscha Wahl
- Department of Biotechnology, Delft University of Technology, Van der Maasweg, 2629 HZ, Delft, The Netherlands.
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11
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Wang G, Haringa C, Tang W, Noorman H, Chu J, Zhuang Y, Zhang S. Coupled metabolic-hydrodynamic modeling enabling rational scale-up of industrial bioprocesses. Biotechnol Bioeng 2019; 117:844-867. [PMID: 31814101 DOI: 10.1002/bit.27243] [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: 10/11/2019] [Revised: 11/28/2019] [Accepted: 11/30/2019] [Indexed: 12/13/2022]
Abstract
Metabolomics aims to address what and how regulatory mechanisms are coordinated to achieve flux optimality, different metabolic objectives as well as appropriate adaptations to dynamic nutrient availability. Recent decades have witnessed that the integration of metabolomics and fluxomics within the goal of synthetic biology has arrived at generating the desired bioproducts with improved bioconversion efficiency. Absolute metabolite quantification by isotope dilution mass spectrometry represents a functional readout of cellular biochemistry and contributes to the establishment of metabolic (structured) models required in systems metabolic engineering. In industrial practices, population heterogeneity arising from fluctuating nutrient availability frequently leads to performance losses, that is reduced commercial metrics (titer, rate, and yield). Hence, the development of more stable producers and more predictable bioprocesses can benefit from a quantitative understanding of spatial and temporal cell-to-cell heterogeneity within industrial bioprocesses. Quantitative metabolomics analysis and metabolic modeling applied in computational fluid dynamics (CFD)-assisted scale-down simulators that mimic industrial heterogeneity such as fluctuations in nutrients, dissolved gases, and other stresses can procure informative clues for coping with issues during bioprocessing scale-up. In previous studies, only limited insights into the hydrodynamic conditions inside the industrial-scale bioreactor have been obtained, which makes case-by-case scale-up far from straightforward. Tracking the flow paths of cells circulating in large-scale bioreactors is a highly valuable tool for evaluating cellular performance in production tanks. The "lifelines" or "trajectories" of cells in industrial-scale bioreactors can be captured using Euler-Lagrange CFD simulation. This novel methodology can be further coupled with metabolic (structured) models to provide not only a statistical analysis of cell lifelines triggered by the environmental fluctuations but also a global assessment of the metabolic response to heterogeneity inside an industrial bioreactor. For the future, the industrial design should be dependent on the computational framework, and this integration work will allow bioprocess scale-up to the industrial scale with an end in mind.
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Affiliation(s)
- Guan Wang
- State Key Laboratory of Bioreactor Engineering, East China University of Science and Technology, Shanghai, People's Republic of China
| | - Cees Haringa
- Transport Phenomena, Chemical Engineering Department, Delft University of Technology, Delft, The Netherlands.,DSM Biotechnology Center, Delft, The Netherlands
| | - Wenjun Tang
- DSM Biotechnology Center, Delft, The Netherlands
| | - Henk Noorman
- DSM Biotechnology Center, Delft, The Netherlands.,Bioprocess Engineering, Department of Biotechnology, Delft University of Technology, Delft, The Netherlands
| | - Ju Chu
- State Key Laboratory of Bioreactor Engineering, East China University of Science and Technology, Shanghai, People's Republic of China
| | - Yingping Zhuang
- State Key Laboratory of Bioreactor Engineering, East China University of Science and Technology, Shanghai, People's Republic of China
| | - Siliang Zhang
- State Key Laboratory of Bioreactor Engineering, East China University of Science and Technology, Shanghai, People's Republic of China
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12
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García-Ortega X, Cámara E, Ferrer P, Albiol J, Montesinos-Seguí JL, Valero F. Rational development of bioprocess engineering strategies for recombinant protein production in Pichia pastoris (Komagataella phaffii) using the methanol-free GAP promoter. Where do we stand? N Biotechnol 2019; 53:24-34. [DOI: 10.1016/j.nbt.2019.06.002] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2018] [Revised: 06/07/2019] [Accepted: 06/08/2019] [Indexed: 12/25/2022]
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13
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Priyanka, Kumar J, Gomes J, Rathore AS. Implementing Process Analytical Technology for the Production of Recombinant Proteins in Escherichia coli Using an Advanced Controller Scheme. Biotechnol J 2019; 14:e1800556. [PMID: 31329337 DOI: 10.1002/biot.201800556] [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: 11/29/2018] [Revised: 06/17/2019] [Indexed: 01/04/2023]
Abstract
The performance of a bioreactor in meeting process goals is affected by the microorganism used, medium composition, and operating conditions. A typical bioreactor uses a supervisory control and data acquisition (SCADA) system for control, and a combination of software and hardware tools for real-time data analysis. However, when the process is disrupted by utility or instrumentation failure, typical process controllers may be unable to reinstate normal operating conditions before the cells in the reactor shift to unfavorable metabolic regimes. The objective of this study is to examine how the response of a controller affects process recovery when disruptive incidences occur under a process analytical technology (PAT) framework. The process used for this investigation is the production of lethal toxin-neutralizing factor (LTNF) by Escherichia coli (E. coli), which is controlled by a decoupled input-output-linearizing controller (DIOLC). The performance of the DIOLC is compared to a proportional integral derivative (PID) controller subjected to the same conditions. The disruptions are introduced manually and the effect of controller action on process recovery and LTNF synthesis is measured in terms of peak purity and concentration. It is observed that DIOLC performs better after reinstating operating conditions and results in a meaningful improvement in performance.
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Affiliation(s)
- Priyanka
- Department of Chemical Engineering, Indian Institute of Technology Delhi, Hauz Khas, New Delhi, 110016, India
| | - Jashwant Kumar
- Department of Chemical Engineering, Indian Institute of Technology Delhi, Hauz Khas, New Delhi, 110016, India
| | - James Gomes
- Kusuma School of Biological Sciences, Indian Institute of Technology Delhi, Hauz Khas, New Delhi, 110016, India
| | - Anurag S Rathore
- Department of Chemical Engineering, Indian Institute of Technology Delhi, Hauz Khas, New Delhi, 110016, India
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14
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Mauerhofer LM, Pappenreiter P, Paulik C, Seifert AH, Bernacchi S, Rittmann SKMR. Methods for quantification of growth and productivity in anaerobic microbiology and biotechnology. Folia Microbiol (Praha) 2019; 64:321-360. [PMID: 30446943 PMCID: PMC6529396 DOI: 10.1007/s12223-018-0658-4] [Citation(s) in RCA: 30] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2018] [Accepted: 10/12/2018] [Indexed: 12/17/2022]
Abstract
Anaerobic microorganisms (anaerobes) possess a fascinating metabolic versatility. This characteristic makes anaerobes interesting candidates for physiological studies and utilizable as microbial cell factories. To investigate the physiological characteristics of an anaerobic microbial population, yield, productivity, specific growth rate, biomass production, substrate uptake, and product formation are regarded as essential variables. The determination of those variables in distinct cultivation systems may be achieved by using different techniques for sampling, measuring of growth, substrate uptake, and product formation kinetics. In this review, a comprehensive overview of methods is presented, and the applicability is discussed in the frame of anaerobic microbiology and biotechnology.
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Affiliation(s)
- Lisa-Maria Mauerhofer
- Archaea Physiology & Biotechnology Group, Archaea Biology and Ecogenomics Division, Department of Ecogenomics and Systems Biology, Universität Wien, Althanstraße 14, 1090, Wien, Austria
| | - Patricia Pappenreiter
- Institute for Chemical Technology of Organic Materials, Johannes Kepler University Linz, Linz, Austria
| | - Christian Paulik
- Institute for Chemical Technology of Organic Materials, Johannes Kepler University Linz, Linz, Austria
| | | | | | - Simon K-M R Rittmann
- Archaea Physiology & Biotechnology Group, Archaea Biology and Ecogenomics Division, Department of Ecogenomics and Systems Biology, Universität Wien, Althanstraße 14, 1090, Wien, Austria.
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16
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Valero F. Recent Advances in Pichia pastoris as Host for Heterologous Expression System for Lipases: A Review. Methods Mol Biol 2018; 1835:205-216. [PMID: 30109654 DOI: 10.1007/978-1-4939-8672-9_11] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
The production of heterologous lipases is one of the most promising strategies to increase the productivity of the bioprocesses and to reduce costs, with the final objective that more industrial lipase applications could be implemented.In this chapter, an overview of the new success in synthetic biology, with traditional molecular genetic techniques and bioprocess engineering in the last 5 years in the cell factory Pichia pastoris, the most promising host system for heterologous lipase production, is presented.The goals get on heterologous Candida antarctica, Rhizopus oryzae, and Candida rugosa lipases, three of the most common lipases used in biocatalysis, are showed. Finally, new cell factories producing heterologous lipases are presented.
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Affiliation(s)
- Francisco Valero
- Departament d'Enginyeria Química, Biològica i Ambiental. EE, Universitat Autònoma de Barcelona, Barcelona, Spain.
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17
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Optimization of Bioethanol In Silico Production Process in a Fed-Batch Bioreactor Using Non-Linear Model Predictive Control and Evolutionary Computation Techniques. ENERGIES 2017. [DOI: 10.3390/en10111763] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/05/2023]
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18
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Windram OPF, Rodrigues RTL, Lee S, Haines M, Bayer TS. Engineering microbial phenotypes through rewiring of genetic networks. Nucleic Acids Res 2017; 45:4984-4993. [PMID: 28369627 PMCID: PMC5416768 DOI: 10.1093/nar/gkx197] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2017] [Accepted: 03/13/2017] [Indexed: 11/12/2022] Open
Abstract
The ability to program cellular behaviour is a major goal of synthetic biology, with applications in health, agriculture and chemicals production. Despite efforts to build 'orthogonal' systems, interactions between engineered genetic circuits and the endogenous regulatory network of a host cell can have a significant impact on desired functionality. We have developed a strategy to rewire the endogenous cellular regulatory network of yeast to enhance compatibility with synthetic protein and metabolite production. We found that introducing novel connections in the cellular regulatory network enabled us to increase the production of heterologous proteins and metabolites. This strategy is demonstrated in yeast strains that show significantly enhanced heterologous protein expression and higher titers of terpenoid production. Specifically, we found that the addition of transcriptional regulation between free radical induced signalling and nitrogen regulation provided robust improvement of protein production. Assessment of rewired networks revealed the importance of key topological features such as high betweenness centrality. The generation of rewired transcriptional networks, selection for specific phenotypes, and analysis of resulting library members is a powerful tool for engineering cellular behavior and may enable improved integration of heterologous protein and metabolite pathways.
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Affiliation(s)
- Oliver P F Windram
- Centre for Synthetic Biology and Innovation and Department of Life Sciences, Imperial College London, London SW7 2AZ, UK
| | - Rui T L Rodrigues
- Centre for Synthetic Biology and Innovation and Department of Life Sciences, Imperial College London, London SW7 2AZ, UK
| | - Sangjin Lee
- Centre for Synthetic Biology and Innovation and Department of Life Sciences, Imperial College London, London SW7 2AZ, UK
| | - Matthew Haines
- Centre for Synthetic Biology and Innovation and Department of Life Sciences, Imperial College London, London SW7 2AZ, UK
| | - Travis S Bayer
- Centre for Synthetic Biology and Innovation and Department of Life Sciences, Imperial College London, London SW7 2AZ, UK
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Alonso S, Rendueles M, Díaz M. Tunable decoupled overproduction of lactobionic acid in Pseudomonas taetrolens through temperature-control strategies. Process Biochem 2017. [DOI: 10.1016/j.procbio.2017.04.034] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
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Yenkie KM, Wu W, Maravelias CT. Synthesis and analysis of separation networks for the recovery of intracellular chemicals generated from microbial-based conversions. BIOTECHNOLOGY FOR BIOFUELS 2017; 10:119. [PMID: 28503196 PMCID: PMC5422901 DOI: 10.1186/s13068-017-0804-2] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/20/2017] [Accepted: 04/25/2017] [Indexed: 05/19/2023]
Abstract
BACKGROUND Bioseparations can contribute to more than 70% in the total production cost of a bio-based chemical, and if the desired chemical is localized intracellularly, there can be additional challenges associated with its recovery. Based on the properties of the desired chemical and other components in the stream, there can be multiple feasible options for product recovery. These options are composed of several alternative technologies, performing similar tasks. The suitability of a technology for a particular chemical depends on (1) its performance parameters, such as separation efficiency; (2) cost or amount of added separating agent; (3) properties of the bioreactor effluent (e.g., biomass titer, product content); and (4) final product specifications. Our goal is to first synthesize alternative separation options and then analyze how technology selection affects the overall process economics. To achieve this, we propose an optimization-based framework that helps in identifying the critical technologies and parameters. RESULTS We study the separation networks for two representative classes of chemicals based on their properties. The separation network is divided into three stages: cell and product isolation (stage I), product concentration (II), and product purification and refining (III). Each stage exploits differences in specific product properties for achieving the desired product quality. The cost contribution analysis for the two cases (intracellular insoluble and intracellular soluble) reveals that stage I is the key cost contributor (>70% of the overall cost). Further analysis suggests that changes in input conditions and technology performance parameters lead to new designs primarily in stage I. CONCLUSIONS The proposed framework provides significant insights for technology selection and assists in making informed decisions regarding technologies that should be used in combination for a given set of stream/product properties and final output specifications. Additionally, the parametric sensitivity provides an opportunity to make crucial design and selection decisions in a comprehensive and rational manner. This will prove valuable in the selection of chemicals to be produced using bioconversions (bioproducts) as well as in creating better bioseparation flow sheets for detailed economic assessment and process implementation on the commercial scale.
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Affiliation(s)
- Kirti M. Yenkie
- Department of Chemical and Biological Engineering, University of Wisconsin-Madison, 1415 Engineering Drive, Madison, WI 53706-1691 USA
| | - Wenzhao Wu
- Department of Chemical and Biological Engineering, University of Wisconsin-Madison, 1415 Engineering Drive, Madison, WI 53706-1691 USA
| | - Christos T. Maravelias
- Department of Chemical and Biological Engineering, University of Wisconsin-Madison, 1415 Engineering Drive, Madison, WI 53706-1691 USA
- DOE Great Lakes Bioenergy Research Center, University of Wisconsin-Madison, 1552 University Ave, Madison, WI 53726 USA
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Cabello J, Morales M, Revah S. Carbon dioxide consumption of the microalga Scenedesmus obtusiusculus under transient inlet CO 2 concentration variations. THE SCIENCE OF THE TOTAL ENVIRONMENT 2017; 584-585:1310-1316. [PMID: 28187940 DOI: 10.1016/j.scitotenv.2017.02.002] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/15/2016] [Revised: 01/31/2017] [Accepted: 02/01/2017] [Indexed: 06/06/2023]
Abstract
The extensive microalgae diversity offers considerable versatility for a wide range of biotechnological applications in environmental and production processes. Microalgal cultivation is based on CO2 fixation via photosynthesis and, consequently, it is necessary to evaluate, in a short time and reliable way, the effect of the CO2 gas concentration on the consumption rate and establish the tolerance range of different strains and the amount of inorganic carbon that can be incorporated into biomass in order to establish the potential for industrial scale application. Dynamic experiments allow calculating the short-term microalgal photosynthetic activity of strains in photobioreactors. In this paper, the effect of step-changes in CO2 concentration fed to a 20L bubble column photobioreactor on the CO2 consumption rate of Scenedesmus obtusiusculus was evaluated at different operation times. The highest apparent CO2 consumption rate (336μmolm-2s-1 and 5.6% of CO2) was 6530mgCO2gb-1d-1 and it decreased to 222mgCO2gb-1d-1 when biomass concentration increased of 0.5 to 3.1gbL-1 and 5.6% of CO2 was fed. For low CO2 concentrations (<3.8%) the pH remained close to the optimal value (7.5 and 8). The CO2 consumption rates show that S. obtusiusculus was not limited by CO2 availability for concentrations above of 3.8%. The CO2 mass balance showed that 90% of the C-CO2 transferred was used for S. obtusiusculus growth.
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Affiliation(s)
- Juan Cabello
- Departamento de Ingeniería de Procesos e Hidráulica, Universidad Autónoma Metropolitana-Iztapalapa, San Rafael Atlixco 186, C.P. 09340 Cd. de México, Mexico
| | - Marcia Morales
- Departamento de Procesos y Tecnología, Universidad Autónoma Metropolitana-Cuajimalpa, Av. Vasco de Quiroga 4871, Colonia Santa Fe Cuajimalpa, C.P. 05300 Cd. de México, Mexico.
| | - Sergio Revah
- Departamento de Procesos y Tecnología, Universidad Autónoma Metropolitana-Cuajimalpa, Av. Vasco de Quiroga 4871, Colonia Santa Fe Cuajimalpa, C.P. 05300 Cd. de México, Mexico.
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Sommeregger W, Sissolak B, Kandra K, von Stosch M, Mayer M, Striedner G. Quality by control: Towards model predictive control of mammalian cell culture bioprocesses. Biotechnol J 2017; 12. [DOI: 10.1002/biot.201600546] [Citation(s) in RCA: 103] [Impact Index Per Article: 14.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2016] [Revised: 02/17/2017] [Accepted: 03/09/2017] [Indexed: 11/05/2022]
Affiliation(s)
| | - Bernhard Sissolak
- DBT - University of Natural Resources and Life Sciences (BOKU); Vienna Austria
| | - Kulwant Kandra
- DBT - University of Natural Resources and Life Sciences (BOKU); Vienna Austria
| | | | | | - Gerald Striedner
- DBT - University of Natural Resources and Life Sciences (BOKU); Vienna Austria
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Wurm DJ, Hausjell J, Ulonska S, Herwig C, Spadiut O. Mechanistic platform knowledge of concomitant sugar uptake in Escherichia coli BL21(DE3) strains. Sci Rep 2017; 7:45072. [PMID: 28332595 PMCID: PMC5362885 DOI: 10.1038/srep45072] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2016] [Accepted: 02/20/2017] [Indexed: 12/22/2022] Open
Abstract
When producing recombinant proteins, the use of Escherichia coli strain BL21(DE3) in combination with the T7-based pET-expression system is often the method of choice. In a recent study we introduced a mechanistic model describing the correlation of the specific glucose uptake rate (qs,glu) and the corresponding maximum specific lactose uptake rate (qs,lac,max) for a pET-based E. coli BL21(DE3) strain producing a single chain variable fragment (scFv). We showed the effect of qs,lac,max on productivity and product location underlining its importance for recombinant protein production. In the present study we investigated the mechanistic qs,glu/qs,lac,max correlation for four pET-based E. coli BL21(DE3) strains producing different recombinant products and thereby proved the mechanistic model to be platform knowledge for E. coli BL21(DE3). However, we found that the model parameters strongly depended on the recombinant product. Driven by this observation we tested different dynamic bioprocess strategies to allow a faster investigation of this mechanistic correlation. In fact, we succeeded and propose an experimental strategy comprising only one batch cultivation, one fed-batch cultivation as well as one dynamic experiment, to reliably determine the mechanistic model for qs,glu/qs,lac,max and get trustworthy model parameters for pET-based E. coli BL21(DE3) strains which are the basis for bioprocess development.
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Affiliation(s)
- David J Wurm
- Research Division Biochemical Engineering, Institute of Chemical Engineering, Vienna University of Technology, Vienna, Austria
| | - Johanna Hausjell
- Research Division Biochemical Engineering, Institute of Chemical Engineering, Vienna University of Technology, Vienna, Austria
| | - Sophia Ulonska
- Research Division Biochemical Engineering, Institute of Chemical Engineering, Vienna University of Technology, Vienna, Austria
| | - Christoph Herwig
- Research Division Biochemical Engineering, Institute of Chemical Engineering, Vienna University of Technology, Vienna, Austria.,Christian Doppler Laboratory for Mechanistic and Physiological Methods for Improved Bioprocesses, Institute of Chemical Engineering, Vienna University of Technology, Vienna, Austria
| | - Oliver Spadiut
- Research Division Biochemical Engineering, Institute of Chemical Engineering, Vienna University of Technology, Vienna, Austria.,Christian Doppler Laboratory for Mechanistic and Physiological Methods for Improved Bioprocesses, Institute of Chemical Engineering, Vienna University of Technology, Vienna, Austria
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Effects of glycerol supply and specific growth rate on methanol-free production of CALB by P. pastoris: functional characterisation of a novel promoter. Appl Microbiol Biotechnol 2017; 101:3163-3176. [PMID: 28130631 PMCID: PMC5380701 DOI: 10.1007/s00253-017-8123-x] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/03/2016] [Revised: 01/03/2017] [Accepted: 01/10/2017] [Indexed: 12/20/2022]
Abstract
As Pichia pastoris (syn. Komagataella sp.) yeast can secrete pure recombinant proteins at high rates, it is a desirable production system. The function of a novel synthetic variant of the AOX1 promoter was characterised comprehensively using a strain secreting Candida antarctica lipase B (CALB) as a model. A new time-saving approach was introduced to determine, in only one experiment, the hitherto unknown relationship between specific product formation rate (qp) and specific growth rate (μ). Tight control of recombinant protein formation was possible in the absence of methanol, while using glycerol as a sole carbon/energy source. CALB was not synthesised during batch cultivation in excess glycerol (>10 g l−1) and at a growth rate close to μmax (0.15 h−1). Between 0.017 and 0.115 h−1 in glycerol-limited fedbatch cultures, basal levels of qp > 0.4 mg g−1 h−1 CALB were reached, independent of the μ at which the culture grew. At μ > 0.04 h−1, an elevated qp occurred temporarily during the first 20 h after changing to fedbatch mode and decreased thereafter to basal. In order to accelerate the determination of the qp(μ) relationship (kinetics of product formation), the entire μ range was covered in a single fedbatch experiment. By linearly increasing and decreasing glycerol addition rates, μ values were repeatedly shifted from 0.004 to 0.074 h−1 and vice versa. Changes in qp were related to changes in μ. A rough estimation of μ range suitable for production was possible in a single fedbatch, thus significantly reducing the experimental input over previous approaches comprising several experiments.
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López-Meza J, Araíz-Hernández D, Carrillo-Cocom LM, López-Pacheco F, Rocha-Pizaña MDR, Alvarez MM. Using simple models to describe the kinetics of growth, glucose consumption, and monoclonal antibody formation in naive and infliximab producer CHO cells. Cytotechnology 2016; 68:1287-300. [PMID: 26091615 PMCID: PMC4960177 DOI: 10.1007/s10616-015-9889-2] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2014] [Accepted: 05/13/2015] [Indexed: 12/12/2022] Open
Abstract
Despite their practical and commercial relevance, there are few reports on the kinetics of growth and production of Chinese hamster ovary (CHO) cells-the most frequently used host for the industrial production of therapeutic proteins. We characterize the kinetics of cell growth, substrate consumption, and product formation in naive and monoclonal antibody (mAb) producing recombinant CHO cells. Culture experiments were performed in 125 mL shake flasks on commercial culture medium (CD Opti CHO™ Invitrogen, Carlsbad, CA, USA) diluted to different glucose concentrations (1.2-4.8 g/L). The time evolution of cell, glucose, lactic acid concentration and monoclonal antibody concentrations was monitored on a daily basis for mAb-producing cultures and their naive counterparts. The time series were differentiated to calculate the corresponding kinetic rates (rx = d[X]/dt; rs = d[S]/dt; rp = d[mAb]/dt). Results showed that these cell lines could be modeled by Monod-like kinetics if a threshold substrate concentration value of [S]t = 0.58 g/L (for recombinant cells) and [S]t = 0.96 g/L (for naïve cells), below which growth is not observed, was considered. A set of values for μmax, and Ks was determined for naive and recombinant cell cultures cultured at 33 and 37 °C. The yield coefficient (Yx/s) was observed to be a function of substrate concentration, with values in the range of 0.27-1.08 × 10(7) cell/mL and 0.72-2.79 × 10(6) cells/mL for naive and recombinant cultures, respectively. The kinetics of mAb production can be described by a Luedeking-Piret model (d[mAb]/dt = αd[X]/dt + β[X]) with values of α = 7.65 × 10(-7) µg/cell and β = 7.68 × 10(-8) µg/cell/h for cultures conducted in batch-agitated flasks and batch and instrumented bioreactors operated in batch and fed-batch mode.
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Affiliation(s)
- Julián López-Meza
- Centro de Biotecnología-FEMSA, Tecnológico de Monterrey at Monterrey, Ave. Eugenio Garza Sada 2501 Sur, C.P. 64849, Monterrey, Nuevo León, Mexico
| | - Diana Araíz-Hernández
- Centro de Biotecnología-FEMSA, Tecnológico de Monterrey at Monterrey, Ave. Eugenio Garza Sada 2501 Sur, C.P. 64849, Monterrey, Nuevo León, Mexico
| | - Leydi Maribel Carrillo-Cocom
- Facultad de Ingeniería Química, Universidad Autónoma de Yucatán, Periférico Norte kilómetro 33.5, C.P. 97203, Mérida, Yucatán, Mexico
| | - Felipe López-Pacheco
- Centro de Biotecnología-FEMSA, Tecnológico de Monterrey at Monterrey, Ave. Eugenio Garza Sada 2501 Sur, C.P. 64849, Monterrey, Nuevo León, Mexico
| | - María Del Refugio Rocha-Pizaña
- Centro de Biotecnología-FEMSA, Tecnológico de Monterrey at Monterrey, Ave. Eugenio Garza Sada 2501 Sur, C.P. 64849, Monterrey, Nuevo León, Mexico
| | - Mario Moisés Alvarez
- Centro de Biotecnología-FEMSA, Tecnológico de Monterrey at Monterrey, Ave. Eugenio Garza Sada 2501 Sur, C.P. 64849, Monterrey, Nuevo León, Mexico.
- Biomaterials Innovation Research Center, Division of Biomedical Engineering, Department of Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, 02139, USA.
- Harvard-Massachusetts Institute of Technology Division of Health Sciences and Technology, Massachusetts Institute of Technology, Cambridge, MA, 02139, USA.
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Wurm DJ, Veiter L, Ulonska S, Eggenreich B, Herwig C, Spadiut O. The E. coli pET expression system revisited-mechanistic correlation between glucose and lactose uptake. Appl Microbiol Biotechnol 2016; 100:8721-9. [PMID: 27229726 PMCID: PMC5035661 DOI: 10.1007/s00253-016-7620-7] [Citation(s) in RCA: 43] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2016] [Revised: 05/01/2016] [Accepted: 05/07/2016] [Indexed: 12/21/2022]
Abstract
Therapeutic monoclonal antibodies are mainly produced in mammalian cells to date. However, unglycosylated antibody fragments can also be produced in the bacterium Escherichia coli which brings several advantages, like growth on cheap media and high productivity. One of the most popular E. coli strains for recombinant protein production is E. coli BL21(DE3) which is usually used in combination with the pET expression system. However, it is well known that induction by isopropyl β-d-1-thiogalactopyranoside (IPTG) stresses the cells and can lead to the formation of insoluble inclusion bodies. In this study, we revisited the pET expression system for the production of a novel antibody single-chain variable fragment (scFv) with the goal of maximizing the amount of soluble product. Thus, we (1) investigated whether lactose favors the recombinant production of soluble scFv compared to IPTG, (2) investigated whether the formation of soluble product can be influenced by the specific glucose uptake rate (qs,glu) during lactose induction, and (3) determined the mechanistic correlation between the specific lactose uptake rate (qs,lac) and qs,glu. We found that lactose induction gave a much greater amount of soluble scFv compared to IPTG, even when the growth rate was increased. Furthermore, we showed that the production of soluble protein could be tuned by varying qs,glu during lactose induction. Finally, we established a simple model describing the mechanistic correlation between qs,lac and qs,glu allowing tailored feeding and prevention of sugar accumulation. We believe that this mechanistic model might serve as platform knowledge for E. coli.
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Affiliation(s)
- David Johannes Wurm
- Research Division Biochemical Engineering, Institute of Chemical Engineering, Vienna University of Technology, Vienna, Austria
| | - Lukas Veiter
- Research Division Biochemical Engineering, Institute of Chemical Engineering, Vienna University of Technology, Vienna, Austria
| | - Sophia Ulonska
- Research Division Biochemical Engineering, Institute of Chemical Engineering, Vienna University of Technology, Vienna, Austria
| | - Britta Eggenreich
- Research Division Biochemical Engineering, Institute of Chemical Engineering, Vienna University of Technology, Vienna, Austria
- Christian Doppler Laboratory for Mechanistic and Physiological Methods for Improved Bioprocesses, Institute of Chemical Engineering, Vienna University of Technology, Vienna, Austria
| | - Christoph Herwig
- Research Division Biochemical Engineering, Institute of Chemical Engineering, Vienna University of Technology, Vienna, Austria
- Christian Doppler Laboratory for Mechanistic and Physiological Methods for Improved Bioprocesses, Institute of Chemical Engineering, Vienna University of Technology, Vienna, Austria
| | - Oliver Spadiut
- Research Division Biochemical Engineering, Institute of Chemical Engineering, Vienna University of Technology, Vienna, Austria.
- Christian Doppler Laboratory for Mechanistic and Physiological Methods for Improved Bioprocesses, Institute of Chemical Engineering, Vienna University of Technology, Vienna, Austria.
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Konakovsky V, Clemens C, Müller MM, Bechmann J, Berger M, Schlatter S, Herwig C. Metabolic Control in Mammalian Fed-Batch Cell Cultures for Reduced Lactic Acid Accumulation and Improved Process Robustness. Bioengineering (Basel) 2016; 3:bioengineering3010005. [PMID: 28952567 PMCID: PMC5597163 DOI: 10.3390/bioengineering3010005] [Citation(s) in RCA: 29] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2015] [Revised: 09/25/2015] [Accepted: 01/04/2016] [Indexed: 01/17/2023] Open
Abstract
Biomass and cell-specific metabolic rates usually change dynamically over time, making the "feed according to need" strategy difficult to realize in a commercial fed-batch process. We here demonstrate a novel feeding strategy which is designed to hold a particular metabolic state in a fed-batch process by adaptive feeding in real time. The feed rate is calculated with a transferable biomass model based on capacitance, which changes the nutrient flow stoichiometrically in real time. A limited glucose environment was used to confine the cell in a particular metabolic state. In order to cope with uncertainty, two strategies were tested to change the adaptive feed rate and prevent starvation while in limitation: (i) inline pH and online glucose concentration measurement or (ii) inline pH alone, which was shown to be sufficient for the problem statement. In this contribution, we achieved metabolic control within a defined target range. The direct benefit was two-fold: the lactic acid profile was improved and pH could be kept stable. Multivariate Data Analysis (MVDA) has shown that pH influenced lactic acid production or consumption in historical data sets. We demonstrate that a low pH (around 6.8) is not required for our strategy, as glucose availability is already limiting the flux. On the contrary, we boosted glycolytic flux in glucose limitation by setting the pH to 7.4. This new approach led to a yield of lactic acid/glucose (Y L/G) around zero for the whole process time and high titers in our labs. We hypothesize that a higher carbon flux, resulting from a higher pH, may lead to more cells which produce more product. The relevance of this work aims at feeding mammalian cell cultures safely in limitation with a desired metabolic flux range. This resulted in extremely stable, low glucose levels, very robust pH profiles without acid/base interventions and a metabolic state in which lactic acid was consumed instead of being produced from day 1. With this contribution, we wish to extend the basic repertoire of available process control strategies, which will open up new avenues in automation technology and radically improve process robustness in both process development and manufacturing.
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Affiliation(s)
- Viktor Konakovsky
- Institute of Chemical Engineering, Division of Biochemical Engineering, Vienna University of Technology, Gumpendorfer Strasse 1A 166-4, 1060 Vienna, Austria.
| | - Christoph Clemens
- Boehringer Ingelheim Pharma GmbH & Co. KG Dep. Bioprocess Development, Biberach, Germany.
| | - Markus Michael Müller
- Boehringer Ingelheim Pharma GmbH & Co. KG Dep. Bioprocess Development, Biberach, Germany.
| | - Jan Bechmann
- Boehringer Ingelheim Pharma GmbH & Co. KG Dep. Bioprocess Development, Biberach, Germany.
| | - Martina Berger
- Boehringer Ingelheim Pharma GmbH & Co. KG Dep. Bioprocess Development, Biberach, Germany.
| | - Stefan Schlatter
- Boehringer Ingelheim Pharma GmbH & Co. KG Dep. Bioprocess Development, Biberach, Germany.
| | - Christoph Herwig
- Institute of Chemical Engineering, Division of Biochemical Engineering, Vienna University of Technology, Gumpendorfer Strasse 1A 166-4, 1060 Vienna, Austria.
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Looser V, Bruhlmann B, Bumbak F, Stenger C, Costa M, Camattari A, Fotiadis D, Kovar K. Cultivation strategies to enhance productivity of Pichia pastoris: A review. Biotechnol Adv 2015; 33:1177-93. [DOI: 10.1016/j.biotechadv.2015.05.008] [Citation(s) in RCA: 169] [Impact Index Per Article: 18.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2014] [Revised: 05/11/2015] [Accepted: 05/25/2015] [Indexed: 12/14/2022]
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Advances in synthetic dynamic circuits design: using novel synthetic parts to engineer new generations of gene oscillations. Curr Opin Biotechnol 2015; 36:161-7. [PMID: 26342588 DOI: 10.1016/j.copbio.2015.08.020] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2015] [Revised: 08/11/2015] [Accepted: 08/18/2015] [Indexed: 01/27/2023]
Abstract
As bioengineering applications expand, the need to design and implement circuits that exhibit dynamic properties increases. In particular, schemes that control precise patterns of gene expression as a function of time are essential for balancing multiple metabolic objectives in natural and synthetic systems. Given that modularity has been an important component of dynamic circuits, recent efforts to improve dynamic circuits have focused on replacing old parts for new components that increase the robustness, stability, and tunability. In this review, we show that incorporation of novel components such as regulatory noncoding RNAs (ncRNAs), promoter-transcription factor pairs, and metabolite sensors have allowed traditional dynamic circuits to obtain more robust functionality and improved dynamic properties.
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Rittmann SKMR. A Critical Assessment of Microbiological Biogas to Biomethane Upgrading Systems. ADVANCES IN BIOCHEMICAL ENGINEERING/BIOTECHNOLOGY 2015; 151:117-35. [PMID: 26337846 DOI: 10.1007/978-3-319-21993-6_5] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/02/2022]
Abstract
Microbiological biogas upgrading could become a promising technology for production of methane (CH(4)). This is, storage of irregular generated electricity results in a need to store electricity generated at peak times for use at non-peak times, which could be achieved in an intermediate step by electrolysis of water to molecular hydrogen (H(2)). Microbiological biogas upgrading can be performed by contacting carbon dioxide (CO(2)), H(2) and hydrogenotrophic methanogenic Archaea either in situ in an anaerobic digester, or ex situ in a separate bioreactor. In situ microbiological biogas upgrading is indicated to require thorough bioprocess development, because only low volumetric CH(4) production rates and low CH(4) fermentation offgas content have been achieved. Higher volumetric production rates are shown for the ex situ microbiological biogas upgrading compared to in situ microbiological biogas upgrading. However, the ex situ microbiological biogas upgrading currently suffers from H(2) gas liquid mass transfer limitation, which results in low volumetric CH(4) productivity compared to pure H(2)/CO(2) conversion to CH(4). If waste gas utilization from biological and industrial sources can be shown without reduction in volumetric CH(4) productivity, as well as if the aim of a single stage conversion to a CH(4) fermentation offgas content exceeding 95 vol% can be demonstrated, ex situ microbiological biogas upgrading with pure or enrichment cultures of methanogens could become a promising future technology for almost CO(2)-neutral biomethane production.
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Affiliation(s)
- Simon K-M R Rittmann
- Archaea Biology and Ecogenomics Division, Department of Ecogenomics and Systems Biology, University of Vienna, Althanstraße 14, 1090, Vienna, Austria,
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Wang G, Tang W, Xia J, Chu J, Noorman H, van Gulik WM. Integration of microbial kinetics and fluid dynamics toward model-driven scale-up of industrial bioprocesses. Eng Life Sci 2014. [DOI: 10.1002/elsc.201400172] [Citation(s) in RCA: 61] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022] Open
Affiliation(s)
- Guan Wang
- State Key Laboratory of Bioreactor Engineering; East China University of Science and Technology; Shanghai P. R. China
| | - Wenjun Tang
- State Key Laboratory of Bioreactor Engineering; East China University of Science and Technology; Shanghai P. R. China
| | - Jianye Xia
- State Key Laboratory of Bioreactor Engineering; East China University of Science and Technology; Shanghai P. R. China
| | - Ju Chu
- State Key Laboratory of Bioreactor Engineering; East China University of Science and Technology; Shanghai P. R. China
| | | | - Walter M. van Gulik
- Department of Biotechnology, Kluyver Centre for Genomics of Industrial Fermentation; Delft University of Technology; Delft The Netherlands
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Richard L, Guillouet SE, Uribelarrea JL. Quantification of the transient and long-term response of Saccharomyces cerevisiae to carbon dioxide stresses of various intensities. Process Biochem 2014. [DOI: 10.1016/j.procbio.2014.07.020] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 10/24/2022]
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Wang G, Chu J, Noorman H, Xia J, Tang W, Zhuang Y, Zhang S. Prelude to rational scale-up of penicillin production: a scale-down study. Appl Microbiol Biotechnol 2014; 98:2359-69. [DOI: 10.1007/s00253-013-5497-2] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2013] [Revised: 12/19/2013] [Accepted: 12/22/2013] [Indexed: 12/16/2022]
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Bernacchi S, Rittmann S, H. Seifert A, Krajete A, Herwig C. Experimental methods for screening parameters influencing the growth to product yield (Y (x/CH4)) of a biological methane production (BMP) process performed with Methanothermobacter marburgensis. AIMS BIOENGINEERING 2014. [DOI: 10.3934/bioeng.2014.2.72] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
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Spadiut O, Zalai D, Dietzsch C, Herwig C. Quantitative comparison of dynamic physiological feeding profiles for recombinant protein production with Pichia pastoris. Bioprocess Biosyst Eng 2013; 37:1163-72. [PMID: 24213806 PMCID: PMC4015061 DOI: 10.1007/s00449-013-1087-z] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2013] [Accepted: 10/29/2013] [Indexed: 11/06/2022]
Abstract
Pichia pastoris is widely used for the production of recombinant proteins in industrial biotechnology. In general, industrial production processes describe fed-batch processes based on the specific growth rate. Recently, we introduced the specific substrate uptake rate (qs) as a novel parameter to design fed-batch strategies for P. pastoris. We showed that a dynamic feeding strategy where the feed was adjusted in steps to the maximum specific substrate uptake rate was superior to more traditional strategies in terms of specific productivity. In the present study, we compare three different dynamic feeding strategies based on qs for a recombinant P. pastoris strain with respect to cell physiology, methanol accumulation, productivity and product quality. By comparing (A) a feeding profile at constant high qs, (B) a periodically adjusted feeding profile for a stepwise qs ramp, and (C) a feeding profile at linear increasing qs, we evaluated potential effects of the mode of feeding. Although a dynamic feeding strategy with stepwise increases of qs to qs max resulted in the highest specific productivity, a feeding profile where the feeding rate was stepwise increased to a constant high qs value was superior in terms of the amount of active enzyme produced and in the amount of accumulated methanol. Furthermore, this feeding strategy could be run automatically by integrating an online calculator tool, thus rendering manual interventions by the operator unnecessary.
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Affiliation(s)
- Oliver Spadiut
- Institute of Chemical Engineering, Research Area Biochemical Engineering, Vienna University of Technology, Gumpendorfer Strasse 1a, 1060, Vienna, Austria
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Dynamic Experiments for Bioprocess Parameter Optimization with Extreme Halophilic Archaea. Bioengineering (Basel) 2013. [DOI: 10.3390/bioengineering1010001] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022] Open
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A dynamic method for the investigation of induced state metabolic capacities as a function of temperature. Microb Cell Fact 2013; 12:94. [PMID: 24127686 PMCID: PMC4015482 DOI: 10.1186/1475-2859-12-94] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2013] [Accepted: 09/27/2013] [Indexed: 11/19/2022] Open
Abstract
Background Science-based recombinant bioprocess designs as well as the design of statistical experimental plans for process optimization (Design of Experiments, DoE) demand information on physiological bioprocess boundaries, such as the onset of acetate production, adaptation times, mixed feed metabolic capabilities or induced state maximum metabolic rates as at the desired cultivation temperature. Dynamic methods provide experimental alternatives to determine this information in a fast and efficient way. Information on maximum metabolic capabilities as a function of temperature is needed in case a reduced cultivation temperature is desirable (e.g. to avoid inclusion body formation) and an appropriate feeding profile is to be designed. Results Here, we present a novel dynamic method for the determination of the specific growth rate as a function of temperature for induced recombinant bacterial bioprocesses. The method is based on the control of the residual substrate concentration at non-limiting conditions with dynamic changes in cultivation temperature. The presented method was automated in respect to information extraction and closed loop control by means of in-line Fourier Transformation Infrared Spectroscopy (FTIR) residual substrate measurements and on-line first principle rate-based soft-sensors. Maximum induced state metabolic capabilities as a function of temperature were successfully extracted for a recombinant E. coli C41 fed-batch bioprocess without the need for sampling in a time frame of 20 hours. Conclusions The presented method was concluded to allow the fast and automated extraction of maximum metabolic capabilities (specific growth rate) as a function of temperature. This complements the dynamic toolset necessary for science-based recombinant bacterial bioprocess design and DoE design.
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Bley T. A new generation of bioproduction systems. Eng Life Sci 2013. [DOI: 10.1002/elsc.201370012] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022] Open
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