1
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Jaswal AS, Elangovan R, Mishra S. Optimization of dilution rate and mixed carbon feed for continuous production of recombinant plant sucrose:sucrose 1-fructosyltransferase in Komagataella phaffii. Bioprocess Biosyst Eng 2024:10.1007/s00449-024-03045-w. [PMID: 38904715 DOI: 10.1007/s00449-024-03045-w] [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: 03/28/2024] [Accepted: 06/09/2024] [Indexed: 06/22/2024]
Abstract
The trisaccharide 1-kestose, a major constituent of commercial fructooligosaccharide (FOS) formulations, shows a superior prebiotic effect compared to higher-chain FOS. The plant sucrose:sucrose 1-fructosyltransferases (1-SST) are extensively used for selective synthesis of lower chain FOS. In this study, enhanced recombinant (r) 1-SST production was achieved in Komagataella phaffii (formerly Pichia pastoris) containing three copies of a codon-optimized Festuca arundinacea 1-SST gene. R1-SST production reached 47 U/mL at the shake-flask level after a 96-h methanol induction phase. A chemostat-based strain characterization methodology was adopted to assess the influence of specific growth rate (µ) on cell-specific r1-SST productivity (Qp) and cell-specific oxygen uptake rate (Qo) under two different feeding strategies across dilution rates from 0.02 to 0.05 h-1. The methanol-sorbitol co-feeding strategy significantly reduced Qo by 46 ± 2.4% compared to methanol-only feeding without compromising r1-SST productivity. Based on the data, a dilution rate of 0.025 h-1 was applied for continuous cultivation of recombinant cells to achieve a sustained r1-SST productivity of 5000 ± 64.4 U/L/h for 15 days.
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Affiliation(s)
- Avijeet S Jaswal
- Department of Biochemical Engineering and Biotechnology, Indian Institute of Technology Delhi, Hauz-Khas, New-Delhi, 110016, India
| | - Ravikrishnan Elangovan
- Department of Biochemical Engineering and Biotechnology, Indian Institute of Technology Delhi, Hauz-Khas, New-Delhi, 110016, India
| | - Saroj Mishra
- Department of Biochemical Engineering and Biotechnology, Indian Institute of Technology Delhi, Hauz-Khas, New-Delhi, 110016, India.
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2
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Rebnegger C, Coltman BL, Kowarz V, Peña DA, Mentler A, Troyer C, Hann S, Schöny H, Koellensperger G, Mattanovich D, Gasser B. Protein production dynamics and physiological adaptation of recombinant Komagataella phaffii at near-zero growth rates. Microb Cell Fact 2024; 23:43. [PMID: 38331812 PMCID: PMC10851509 DOI: 10.1186/s12934-024-02314-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2023] [Accepted: 01/23/2024] [Indexed: 02/10/2024] Open
Abstract
BACKGROUND Specific productivity (qP) in yeast correlates with growth, typically peaking at intermediate or maximum specific growth rates (μ). Understanding the factors limiting productivity at extremely low μ might reveal decoupling strategies, but knowledge of production dynamics and physiology in such conditions is scarce. Retentostats, a type of continuous cultivation, enable the well-controlled transition to near-zero µ through the combined retention of biomass and limited substrate supply. Recombinant Komagataella phaffii (syn Pichia pastoris) secreting a bivalent single domain antibody (VHH) was cultivated in aerobic, glucose-limited retentostats to investigate recombinant protein production dynamics and broaden our understanding of relevant physiological adaptations at near-zero growth conditions. RESULTS By the end of the retentostat cultivation, doubling times of approx. two months were reached, corresponding to µ = 0.00047 h-1. Despite these extremely slow growth rates, the proportion of viable cells remained high, and de novo synthesis and secretion of the VHH were observed. The average qP at the end of the retentostat was estimated at 0.019 mg g-1 h-1. Transcriptomics indicated that genes involved in protein biosynthesis were only moderately downregulated towards zero growth, while secretory pathway genes were mostly regulated in a manner seemingly detrimental to protein secretion. Adaptation to near-zero growth conditions of recombinant K. phaffii resulted in significant changes in the total protein, RNA, DNA and lipid content, and lipidomics revealed a complex adaptation pattern regarding the lipid class composition. The higher abundance of storage lipids as well as storage carbohydrates indicates that the cells are preparing for long-term survival. CONCLUSIONS In conclusion, retentostat cultivation proved to be a valuable tool to identify potential engineering targets to decouple growth and protein production and gain important insights into the physiological adaptation of K. phaffii to near-zero growth conditions.
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Affiliation(s)
- Corinna Rebnegger
- CD-Laboratory for Growth-Decoupled Protein Production in Yeast at Department of Biotechnology, University of Natural Resources and Life Sciences (BOKU), Vienna, Austria
- Department of Biotechnology, Institute of Microbiology and Microbial Biotechnology (IMMB), University of Natural Resources and Life Sciences, Vienna, Muthgasse 18, 1190, Vienna, Austria
- Austrian Centre of Industrial Biotechnology (ACIB GmbH), Muthgasse 11, 1190, Vienna, Austria
| | - Benjamin L Coltman
- CD-Laboratory for Growth-Decoupled Protein Production in Yeast at Department of Biotechnology, University of Natural Resources and Life Sciences (BOKU), Vienna, Austria
- Department of Biotechnology, Institute of Microbiology and Microbial Biotechnology (IMMB), University of Natural Resources and Life Sciences, Vienna, Muthgasse 18, 1190, Vienna, Austria
| | - Viktoria Kowarz
- CD-Laboratory for Growth-Decoupled Protein Production in Yeast at Department of Biotechnology, University of Natural Resources and Life Sciences (BOKU), Vienna, Austria
- Department of Biotechnology, Institute of Microbiology and Microbial Biotechnology (IMMB), University of Natural Resources and Life Sciences, Vienna, Muthgasse 18, 1190, Vienna, Austria
| | - David A Peña
- Department of Biotechnology, Institute of Microbiology and Microbial Biotechnology (IMMB), University of Natural Resources and Life Sciences, Vienna, Muthgasse 18, 1190, Vienna, Austria
| | - Axel Mentler
- Department of Forest- and Soil Sciences, Institute of Soil Research, University of Natural Resources and Life Sciences, Vienna, Peter-Jordan-Straße 82, 1190, Vienna, Austria
| | - Christina Troyer
- Department of Chemistry, Institute of Analytical Chemistry, University of Natural Resources and Life Sciences, Vienna, Muthgasse 18, 1190, Vienna, Austria
| | - Stephan Hann
- Department of Chemistry, Institute of Analytical Chemistry, University of Natural Resources and Life Sciences, Vienna, Muthgasse 18, 1190, Vienna, Austria
| | - Harald Schöny
- Department of Analytical Chemistry, Faculty of Chemistry, University of Vienna, Waehringer Straße 38, 1090, Vienna, Austria
| | - Gunda Koellensperger
- Department of Analytical Chemistry, Faculty of Chemistry, University of Vienna, Waehringer Straße 38, 1090, Vienna, Austria
- Vienna Metabolomics Center (VIME), University of Vienna, Althanstraße 14, 1090, Vienna, Austria
| | - Diethard Mattanovich
- CD-Laboratory for Growth-Decoupled Protein Production in Yeast at Department of Biotechnology, University of Natural Resources and Life Sciences (BOKU), Vienna, Austria
- Department of Biotechnology, Institute of Microbiology and Microbial Biotechnology (IMMB), University of Natural Resources and Life Sciences, Vienna, Muthgasse 18, 1190, Vienna, Austria
- Austrian Centre of Industrial Biotechnology (ACIB GmbH), Muthgasse 11, 1190, Vienna, Austria
| | - Brigitte Gasser
- CD-Laboratory for Growth-Decoupled Protein Production in Yeast at Department of Biotechnology, University of Natural Resources and Life Sciences (BOKU), Vienna, Austria.
- Department of Biotechnology, Institute of Microbiology and Microbial Biotechnology (IMMB), University of Natural Resources and Life Sciences, Vienna, Muthgasse 18, 1190, Vienna, Austria.
- Austrian Centre of Industrial Biotechnology (ACIB GmbH), Muthgasse 11, 1190, Vienna, Austria.
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3
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Schiewe T, Gutschmann B, Santolin L, Waldburger S, Neubauer P, Hass R, Riedel SL. Real-time monitoring of biomass during Escherichia coli high-cell-density cultivations by in-line photon density wave spectroscopy. Biotechnol Bioeng 2023; 120:2880-2889. [PMID: 37272419 DOI: 10.1002/bit.28460] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2023] [Revised: 05/19/2023] [Accepted: 05/22/2023] [Indexed: 06/06/2023]
Abstract
An efficient monitoring and control strategy is the basis for a reliable production process. Conventional optical density (OD) measurements involve superpositions of light absorption and scattering, and the results are only given in arbitrary units. In contrast, photon density wave (PDW) spectroscopy is a dilution-free method that allows independent quantification of both effects with defined units. For the first time, PDW spectroscopy was evaluated as a novel optical process analytical technology tool for real-time monitoring of biomass formation in Escherichia coli high-cell-density fed-batch cultivations. Inline PDW measurements were compared to a commercially available inline turbidity probe and with offline measurements of OD and cell dry weight (CDW). An accurate correlation of the reduced PDW scattering coefficient µs ' with CDW was observed in the range of 5-69 g L-1 (R2 = 0.98). The growth rates calculated based on µs ' were comparable to the rates determined with all reference methods. Furthermore, quantification of the reduced PDW scattering coefficient µs ' as a function of the absorption coefficient µa allowed direct detection of unintended process trends caused by overfeeding and subsequent acetate accumulation. Inline PDW spectroscopy can contribute to more robust bioprocess monitoring and consequently improved process performance.
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Affiliation(s)
- Thomas Schiewe
- Institute of Chemistry, innoFSPEC, University of Potsdam, Potsdam, Germany
- PDW Analytics GmbH, Potsdam, Germany
- Institute of Biotechnology, Chair of Bioprocess Engineering, Technische Universität Berlin, Berlin, Germany
| | - Björn Gutschmann
- Institute of Biotechnology, Chair of Bioprocess Engineering, Technische Universität Berlin, Berlin, Germany
| | - Lara Santolin
- Institute of Biotechnology, Chair of Bioprocess Engineering, Technische Universität Berlin, Berlin, Germany
| | - Saskia Waldburger
- Institute of Biotechnology, Chair of Bioprocess Engineering, Technische Universität Berlin, Berlin, Germany
| | - Peter Neubauer
- Institute of Biotechnology, Chair of Bioprocess Engineering, Technische Universität Berlin, Berlin, Germany
| | - Roland Hass
- Institute of Chemistry, innoFSPEC, University of Potsdam, Potsdam, Germany
- PDW Analytics GmbH, Potsdam, Germany
| | - Sebastian L Riedel
- Institute of Biotechnology, Chair of Bioprocess Engineering, Technische Universität Berlin, Berlin, Germany
- Department VIII-Mechanical Engineering, Event Technology and Process Engineering, Environmental and Bioprocess Engineering Laboratory, Berliner Hochschule für Technik, Berlin, Germany
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4
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De Brabander P, Uitterhaegen E, Delmulle T, De Winter K, Soetaert W. Challenges and progress towards industrial recombinant protein production in yeasts: A review. Biotechnol Adv 2023; 64:108121. [PMID: 36775001 DOI: 10.1016/j.biotechadv.2023.108121] [Citation(s) in RCA: 9] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2022] [Revised: 02/07/2023] [Accepted: 02/07/2023] [Indexed: 02/12/2023]
Abstract
Recombinant proteins (RP) are widely used as biopharmaceuticals, industrial enzymes, or sustainable food source. Yeasts, with their ability to produce complex proteins through a broad variety of cheap carbon sources, have emerged as promising eukaryotic production hosts. As such, the prevalence of yeasts as favourable production organisms in commercial RP production is expected to increase. Yet, with the selection of a robust production host on the one hand, successful scale-up is dependent on a thorough understanding of the challenging environment and limitations of large-scale bioreactors on the other hand. In the present work, several prominent yeast species, including Saccharomyces cerevisiae, Pichia pastoris, Yarrowia lipolytica, Kluyveromyces lactis and Kluyveromyces marxianus are reviewed for their current state and performance in commercial RP production. Thereafter, the impact of principal process control parameters, including dissolved oxygen, pH, substrate concentration, and temperature, on large-scale RP production are discussed. Finally, technical challenges of process scale-up are identified. To that end, process intensification strategies to enhance industrial feasibility are summarized, specifically highlighting fermentation strategies to ensure sufficient cooling capacity, overcome oxygen limitation, and increase protein quality and productivity. As such, this review aims to contribute to the pursuit of sustainable yeast-based RP production.
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Affiliation(s)
- Pieter De Brabander
- Centre for Industrial Biotechnology and Biocatalysis (InBio.be), Department of Biotechnology, Faculty of Bioscience Engineering, Ghent University, Coupure Links 653, 9000 Ghent, Belgium; Bio Base Europe Pilot Plant (BBEPP), Rodenhuizekaai 1, 9042 Ghent (Desteldonk), Belgium
| | - Evelien Uitterhaegen
- Bio Base Europe Pilot Plant (BBEPP), Rodenhuizekaai 1, 9042 Ghent (Desteldonk), Belgium
| | - Tom Delmulle
- Centre for Industrial Biotechnology and Biocatalysis (InBio.be), Department of Biotechnology, Faculty of Bioscience Engineering, Ghent University, Coupure Links 653, 9000 Ghent, Belgium
| | - Karel De Winter
- Bio Base Europe Pilot Plant (BBEPP), Rodenhuizekaai 1, 9042 Ghent (Desteldonk), Belgium.
| | - Wim Soetaert
- Centre for Industrial Biotechnology and Biocatalysis (InBio.be), Department of Biotechnology, Faculty of Bioscience Engineering, Ghent University, Coupure Links 653, 9000 Ghent, Belgium; Bio Base Europe Pilot Plant (BBEPP), Rodenhuizekaai 1, 9042 Ghent (Desteldonk), Belgium
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Minden S, Aniolek M, Noorman H, Takors R. Mimicked Mixing-Induced Heterogeneities of Industrial Bioreactors Stimulate Long-Lasting Adaption Programs in Ethanol-Producing Yeasts. Genes (Basel) 2023; 14:genes14050997. [PMID: 37239357 DOI: 10.3390/genes14050997] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2023] [Revised: 04/24/2023] [Accepted: 04/26/2023] [Indexed: 05/28/2023] Open
Abstract
Commercial-scale bioreactors create an unnatural environment for microbes from an evolutionary point of view. Mixing insufficiencies expose individual cells to fluctuating nutrient concentrations on a second-to-minute scale while transcriptional and translational capacities limit the microbial adaptation time from minutes to hours. This mismatch carries the risk of inadequate adaptation effects, especially considering that nutrients are available at optimal concentrations on average. Consequently, industrial bioprocesses that strive to maintain microbes in a phenotypic sweet spot, during lab-scale development, might suffer performance losses when said adaptive misconfigurations arise during scale-up. Here, we investigated the influence of fluctuating glucose availability on the gene-expression profile in the industrial yeast Ethanol Red™. The stimulus-response experiment introduced 2 min glucose depletion phases to cells growing under glucose limitation in a chemostat. Even though Ethanol Red™ displayed robust growth and productivity, a single 2 min depletion of glucose transiently triggered the environmental stress response. Furthermore, a new growth phenotype with an increased ribosome portfolio emerged after complete adaptation to recurring glucose shortages. The results of this study serve a twofold purpose. First, it highlights the necessity to consider the large-scale environment already at the experimental development stage, even when process-related stressors are moderate. Second, it allowed the deduction of strain engineering guidelines to optimize the genetic background of large-scale production hosts.
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Affiliation(s)
- Steven Minden
- Institute of Biochemical Engineering, University of Stuttgart, 70569 Stuttgart, Germany
| | - Maria Aniolek
- Institute of Biochemical Engineering, University of Stuttgart, 70569 Stuttgart, Germany
| | - Henk Noorman
- Royal DSM, 2613 AX Delft, The Netherlands
- Department of Biotechnology, Delft University of Technology, 2628 CD Delft, The Netherlands
| | - Ralf Takors
- Institute of Biochemical Engineering, University of Stuttgart, 70569 Stuttgart, Germany
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6
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Inclusion Body Production in Fed-Batch and Continuous Cultivation. Methods Mol Biol 2023; 2617:87-102. [PMID: 36656518 DOI: 10.1007/978-1-0716-2930-7_6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/20/2023]
Abstract
Various fermentation strategies in industrial biotechnology are applied to produce recombinant target proteins using Escherichia coli. These proteins are often expressed as inclusion bodies (IBs), resulting in a high purity, high stability, and high product titers. In state-of-the-art fed-batch processes, product formation takes place in a short period of time. Sterilization, cleaning, and biomass growth are time consuming steps and reduce the space-time yield. Thus, the interest in establishing continuous cultivations, facilitating higher space-time yields, has been increased in recent years. In this protocol, we provide information and a guide to set-up the production of recombinant proteins in fed-batch, as well as in chemostat continuous cultivations using E. coli.
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7
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Xie D. Continuous biomanufacturing with microbes - upstream progresses and challenges. Curr Opin Biotechnol 2022; 78:102793. [PMID: 36088736 DOI: 10.1016/j.copbio.2022.102793] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2022] [Revised: 07/15/2022] [Accepted: 08/07/2022] [Indexed: 12/14/2022]
Abstract
Current biomanufacturing facilities are mainly built for batch or fed-batch operations, which are subject to low productivities and do not achieve the great bioconversion potential of the rewired cells generated via modern biotechnology. Continuous biomanufacturing should be the future directions for high-yield and low-cost manufacturing of various fermentation products. This review discusses the major challenges and the strategies for continuous biomanufacturing with microbes, which include minimizing contamination risk, enhancing genetic stability over a long-term continuous operation, achieving high product titer, rate, and yield simultaneously by decoupling cell growth from product formation, and using modeling approach to accelerate research and development of continuous biomanufacturing. New strain designs and process engineering strategies, including integration with artificial intelligence, are also discussed for intelligent and the next generation of continuous biomanufacturing.
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Affiliation(s)
- Dongming Xie
- Department of Chemical Engineering, University of Massachusetts Lowell, Lowell, MA 01854, United States.
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8
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Rajpurohit H, Eiteman MA. Nutrient-Limited Operational Strategies for the Microbial Production of Biochemicals. Microorganisms 2022; 10:2226. [PMID: 36363817 PMCID: PMC9695796 DOI: 10.3390/microorganisms10112226] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2022] [Revised: 10/31/2022] [Accepted: 11/07/2022] [Indexed: 08/24/2023] Open
Abstract
Limiting an essential nutrient has a profound impact on microbial growth. The notion of growth under limited conditions was first described using simple Monod kinetics proposed in the 1940s. Different operational modes (chemostat, fed-batch processes) were soon developed to address questions related to microbial physiology and cell maintenance and to enhance product formation. With more recent developments of metabolic engineering and systems biology, as well as high-throughput approaches, the focus of current engineers and applied microbiologists has shifted from these fundamental biochemical processes. This review draws attention again to nutrient-limited processes. Indeed, the sophisticated gene editing tools not available to pioneers offer the prospect of metabolic engineering strategies which leverage nutrient limited processes. Thus, nutrient- limited processes continue to be very relevant to generate microbially derived biochemicals.
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Affiliation(s)
| | - Mark A. Eiteman
- School of Chemical, Materials and Biomedical Engineering, University of Georgia, Athens, GA 30602, USA
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9
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Velazquez D, Sigala JC, Martínez LM, Gaytán P, Gosset G, Lara AR. Glucose transport engineering allows mimicking fed-batch performance in batch mode and selection of superior producer strains. Microb Cell Fact 2022; 21:183. [PMID: 36071458 PMCID: PMC9450411 DOI: 10.1186/s12934-022-01906-1] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2022] [Accepted: 08/09/2022] [Indexed: 11/26/2022] Open
Abstract
Background Fed-batch mode is the standard culture technology for industrial bioprocesses. Nevertheless, most of the early-stage cell and process development is carried out in batch cultures, which can bias the initial selection of expression systems. Cell engineering can provide an alternative to fed-batch cultures for high-throughput screening and host selection. We have previously reported a library of Escherichia coli strains with single and multiple deletions of genes involved in glucose transport. Compared to their wild type (W3110), the mutant strains displayed lower glucose uptake, growth and aerobic acetate production rates. Therefore, when cultured in batch mode, such mutants may perform similar to W3110 cultured in fed-batch mode. To test that hypothesis, we evaluated the constitutive expression of the green fluorescence protein (GFP) in batch cultures in microbioreactors using a semi defined medium supplemented with 10 or 20 g/L glucose + 0.4 g yeast extract/g glucose. Results The mutant strains cultured in batch mode displayed a fast-growth phase (growth rate between 0.40 and 0.60 h−1) followed by a slow-growth phase (growth rate between 0.05 and 0.15 h−1), similar to typical fed-batch cultures. The phase of slow growth is most probably caused by depletion of key amino acids. Three mutants attained the highest GFP fluorescence. Particularly, a mutant named WHIC (ΔptsHIcrr, ΔmglABC), reached a GFP fluorescence up to 14-fold greater than that of W3110. Strain WHIC was cultured in 2 L bioreactors in batch mode with 100 g/L glucose + 50 g/L yeast extract. These cultures were compared with exponentially fed-batch cultures of W3110 maintaining the same slow-growth of WHIC (0.05 h−1) and using the same total amount of glucose and yeast extract than in WHIC cultures. The WHIC strain produced approx. 450 mg/L GFP, while W3110 only 220 mg/L. Conclusion The combination of cell engineering and high throughput screening allowed the selection of a particular mutant that mimics fed-batch behavior in batch cultures. Moreover, the amount of GFP produced by the strain WHIC was substantially higher than that of W3110 under both, batch and fed-batch schemes. Therefore, our results represent a valuable technology for accelerated bioprocess development. Supplementary Information The online version contains supplementary material available at 10.1186/s12934-022-01906-1.
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Affiliation(s)
- Daniela Velazquez
- Departamento de Procesos y Tecnología, Universidad Autónoma Metropolitana, Vasco de Quiroga 4871, 05348, Mexico City, Mexico
| | - Juan-Carlos Sigala
- Departamento de Procesos y Tecnología, Universidad Autónoma Metropolitana, Vasco de Quiroga 4871, 05348, Mexico City, Mexico
| | - Luz María Martínez
- Departamento de Ingeniería Celular y Biocatálisis, Instituto de Biotecnología, Universidad Nacional Autónoma de México, Avenida Universidad 2001, Col. Chamilpa, 62210, Cuernavaca, MOR, Mexico
| | - Paul Gaytán
- Departamento de Ingeniería Celular y Biocatálisis, Instituto de Biotecnología, Universidad Nacional Autónoma de México, Avenida Universidad 2001, Col. Chamilpa, 62210, Cuernavaca, MOR, Mexico
| | - Guillermo Gosset
- Departamento de Ingeniería Celular y Biocatálisis, Instituto de Biotecnología, Universidad Nacional Autónoma de México, Avenida Universidad 2001, Col. Chamilpa, 62210, Cuernavaca, MOR, Mexico
| | - Alvaro R Lara
- Departamento de Procesos y Tecnología, Universidad Autónoma Metropolitana, Vasco de Quiroga 4871, 05348, Mexico City, Mexico.
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Das PK, Sahoo A, Dasu VV. Current status, and the developments of hosts and expression systems for the production of recombinant human cytokines. Biotechnol Adv 2022; 59:107969. [PMID: 35525478 DOI: 10.1016/j.biotechadv.2022.107969] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2021] [Revised: 04/28/2022] [Accepted: 04/29/2022] [Indexed: 02/07/2023]
Abstract
Cytokines consist of peptides, proteins and glycoproteins, which are biological signaling molecules, and boost cell-cell communication in immune reactions to stimulate cellular movements in the place of trauma, inflammation and infection. Recombinant cytokines are designed in such a way that they have generalized immunostimulation action or stimulate specific immune cells when the body encounters immunosuppressive signals from exogenous pathogens or other tumor microenvironments. Recombinant cytokines have improved the treatment processes for numerous diseases. They are also beneficial against novel toxicities that arise due to pharmacologic immunostimulators that lead to an imbalance in the regulation of cytokine. So, the production and use of recombinant human cytokines as therapeutic proteins are significant for medical treatment purposes. For the improved production of recombinant human cytokines, the development of host cells such as bacteria, yeast, fungi, insect, mammal and transgenic plants, and the specific expression systems for individual hosts is necessary. The recent advancements in the field of genetic engineering are beneficial for easy and efficient genetic manipulations for hosts as well as expression cassettes. The use of metabolic engineering and systems biology approaches have tremendous applications in recombinant protein production by generating mathematical models, and analyzing complex biological networks and metabolic pathways via simulations to understand the interconnections between metabolites and genetic behaviors. Further, the bioprocess developments and the optimization of cell culture conditions would enhance recombinant cytokines productivity on large scales.
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Affiliation(s)
- Prabir Kumar Das
- Biochemical Engineering Laboratory, Department of Biosciences and Bioengineering, Indian Institute of Technology Guwahati, Guwahati 781039, Assam, India
| | - Ansuman Sahoo
- Biochemical Engineering Laboratory, Department of Biosciences and Bioengineering, Indian Institute of Technology Guwahati, Guwahati 781039, Assam, India
| | - Veeranki Venkata Dasu
- Biochemical Engineering Laboratory, Department of Biosciences and Bioengineering, Indian Institute of Technology Guwahati, Guwahati 781039, Assam, India.
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Emergence of Phenotypically Distinct Subpopulations Is a Factor in Adaptation of Recombinant Saccharomyces cerevisiae under Glucose-Limited Conditions. Appl Environ Microbiol 2022; 88:e0230721. [PMID: 35297727 DOI: 10.1128/aem.02307-21] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Cells cultured in a nutrient-limited environment can undergo adaptation, which confers improved fitness under long-term energy limitation. We have shown previously how a recombinant Saccharomyces cerevisiae strain, producing a heterologous insulin product, under glucose-limited conditions adapts over time at the average population level. Here, we investigated this adaptation at the single-cell level by application of fluorescence-activated cell sorting (FACS) and showed that the following three apparent phenotypes underlie the adaptive response observed at the bulk level: (i) cells that drastically reduced insulin production (23%), (ii) cells with reduced enzymatic capacity in central carbon metabolism (46%), and (iii) cells that exhibited pseudohyphal growth (31%). We speculate that the phenotypic heterogeneity is a result of different mechanisms to increase fitness. Cells with reduced insulin productivity have increased fitness by reducing the burden of the heterologous insulin production, and the populations with reduced enzymatic capacity of the central carbon metabolism and pseudohyphal growth have increased fitness toward the glucose-limited conditions. The results highlight the importance of considering population heterogeneity when studying adaptation and evolution. IMPORTANCE The yeast Saccharomyces cerevisiae is an attractive microbial host for industrial production and is used widely for manufacturing, e.g., pharmaceuticals. Chemostat cultivation mode is an efficient cultivation strategy for industrial production processes as it ensures a constant, well-controlled cultivation environment. Nevertheless, both the production of a heterologous product and the constant cultivation environment in the chemostat impose a selective pressure on the production organism, which may result in adaptation and loss of productivity. The exact mechanisms behind the observed adaptation and loss of performance are often unidentified. We used a recombinant S. cerevisiae strain producing heterologous insulin and investigated the adaptation occurring during chemostat growth at the single-cell level. We showed that three apparent phenotypes underlie the adaptive response observed at the bulk level in the chemostat. These findings highlight the importance of considering population heterogeneity when studying adaptation in industrial bioprocesses.
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Kumar J, Bhat SU, Rathore AS. Slow post-induction specific growth rate enhances recombinant protein expression in Escherichia coli: Pramlintide multimer and ranibizumab production as case studies. Process Biochem 2022. [DOI: 10.1016/j.procbio.2022.01.009] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 10/19/2022]
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13
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Tellechea-Luzardo J, Hobbs L, Velázquez E, Pelechova L, Woods S, de Lorenzo V, Krasnogor N. Versioning biological cells for trustworthy cell engineering. Nat Commun 2022; 13:765. [PMID: 35140226 PMCID: PMC8828774 DOI: 10.1038/s41467-022-28350-4] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2021] [Accepted: 01/21/2022] [Indexed: 11/18/2022] Open
Abstract
“Full-stack” biotechnology platforms for cell line (re)programming are on the horizon, thanks mostly to (a) advances in gene synthesis and editing techniques as well as (b) the growing integration of life science research with informatics, the internet of things and automation. These emerging platforms will accelerate the production and consumption of biological products. Hence, traceability, transparency, and—ultimately—trustworthiness is required from cradle to grave for engineered cell lines and their engineering processes. Here we report a cloud-based version control system for biotechnology that (a) keeps track and organizes the digital data produced during cell engineering and (b) molecularly links that data to the associated living samples. Barcoding protocols, based on standard genetic engineering methods, to molecularly link to the cloud-based version control system six species, including gram-negative and gram-positive bacteria as well as eukaryote cells, are shown. We argue that version control for cell engineering marks a significant step toward more open, reproducible, easier to trace and share, and more trustworthy engineering biology. Full traceability and transparency are important to establish trust in engineered cell lines. Here the authors argue that version control for cell engineering marks a significant step toward more open, reproducible, traceable and ultimately more trustworthy engineering biology.
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Affiliation(s)
- Jonathan Tellechea-Luzardo
- Interdisciplinary Computing and Complex Biosystems (ICOS) Research Group, Newcastle University, Newcastle Upon Tyne, NE4 5TG, UK
| | - Leanne Hobbs
- Interdisciplinary Computing and Complex Biosystems (ICOS) Research Group, Newcastle University, Newcastle Upon Tyne, NE4 5TG, UK
| | - Elena Velázquez
- Systems and Synthetic Biology Department, Centro Nacional de Biotecnología (CNB-CSIC), 28049, Madrid, Spain
| | - Lenka Pelechova
- Interdisciplinary Computing and Complex Biosystems (ICOS) Research Group, Newcastle University, Newcastle Upon Tyne, NE4 5TG, UK
| | - Simon Woods
- Policy Ethics and Life Sciences (PEALS), Newcastle University, Newcastle Upon Tyne, NE1 7RU, UK
| | - Víctor de Lorenzo
- Systems and Synthetic Biology Department, Centro Nacional de Biotecnología (CNB-CSIC), 28049, Madrid, Spain
| | - Natalio Krasnogor
- Interdisciplinary Computing and Complex Biosystems (ICOS) Research Group, Newcastle University, Newcastle Upon Tyne, NE4 5TG, UK.
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14
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Wang D, Li W, Zhang X, Liang S, Lin Y. Green Process: Improved Semi-Continuous Fermentation of Pichia pastoris Based on the Principle of Vitality Cell Separation. Front Bioeng Biotechnol 2021; 9:777774. [PMID: 34917600 PMCID: PMC8669635 DOI: 10.3389/fbioe.2021.777774] [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: 09/15/2021] [Accepted: 10/28/2021] [Indexed: 11/13/2022] Open
Abstract
The large-scale fermentation of Pichia pastoris for recombinant protein production would be time consuming and produce a large amount of waste yeast. Here we introduce a novel semi-continuous fermentation process for P. pastoris GS115 that can separate vitality cells from broth and recycle the cells to produce high-secretory recombinant pectate lyase. It is based on differences in cell sedimentation coefficients with the formation of salt bridges between metal ions and various cell states. Compared to batch-fed cultivation and general semi-continuous culture, the novel process has significant advantages, such as consuming fewer resources, taking less time, and producing less waste yeast. Sedimentation with the addition of Fe3+ metal ions consumed 14.8 ± 0.0% glycerol, 97.8 ± 1.3% methanol, 55.0 ± 0.9 inorganic salts, 81.5 ± 0.0% time cost, and 77.0 ± 0.1% waste yeast versus batch-fed cultivation to produce an equal amount of protein; in addition, the cost of solid-liquid separation was lower for cells in the collected fermentation broth. The process is economically and environmentally efficient for producing recombinant proteins.
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Affiliation(s)
- Denggang Wang
- South China University of Technology, Guangzhou, China
| | - Wenjie Li
- South China University of Technology, Guangzhou, China
| | - Xinying Zhang
- South China University of Technology, Guangzhou, China
| | - Shuli Liang
- South China University of Technology, Guangzhou, China
| | - Ying Lin
- South China University of Technology, Guangzhou, China
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15
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Zalai D, Kopp J, Kozma B, Küchler M, Herwig C, Kager J. Microbial technologies for biotherapeutics production: Key tools for advanced biopharmaceutical process development and control. DRUG DISCOVERY TODAY. TECHNOLOGIES 2021; 38:9-24. [PMID: 34895644 DOI: 10.1016/j.ddtec.2021.04.001] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/01/2020] [Revised: 03/14/2021] [Accepted: 04/06/2021] [Indexed: 12/26/2022]
Abstract
Current trends in the biopharmaceutical market such as the diversification of therapies as well as the increasing time-to-market pressure will trigger the rethinking of bioprocess development and production approaches. Thereby, the importance of development time and manufacturing costs will increase, especially for microbial production. In the present review, we investigate three technological approaches which, to our opinion, will play a key role in the future of biopharmaceutical production. The first cornerstone of process development is the generation and effective utilization of platform knowledge. Building processes on well understood microbial and technological platforms allows to accelerate early-stage bioprocess development and to better condense this knowledge into multi-purpose technologies and applicable mathematical models. Second, the application of verified scale down systems and in silico models for process design and characterization will reduce the required number of large scale batches before dossier submission. Third, the broader availability of mathematical process models and the improvement of process analytical technologies will increase the applicability and acceptance of advanced control and process automation in the manufacturing scale. This will reduce process failure rates and subsequently cost of goods. Along these three aspects we give an overview of recently developed key tools and their potential integration into bioprocess development strategies.
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Affiliation(s)
- Denes Zalai
- Richter-Helm BioLogics GmbH & Co. KG, Suhrenkamp 59, 22335 Hamburg, Germany.
| | - Julian Kopp
- Research Division Biochemical Engineering, Institute of Chemical Environmental and Bioscience Engineering, Vienna University of Technology, Vienna, Austria
| | - Bence Kozma
- Research Division Biochemical Engineering, Institute of Chemical Environmental and Bioscience Engineering, Vienna University of Technology, Vienna, Austria
| | - Michael Küchler
- Richter-Helm BioLogics GmbH & Co. KG, Suhrenkamp 59, 22335 Hamburg, Germany
| | - Christoph Herwig
- Research Division Biochemical Engineering, Institute of Chemical Environmental and Bioscience Engineering, Vienna University of Technology, Vienna, Austria; Competence Center CHASE GmbH, Altenbergerstraße 69, 4040 Linz, Austria
| | - Julian Kager
- Research Division Biochemical Engineering, Institute of Chemical Environmental and Bioscience Engineering, Vienna University of Technology, Vienna, Austria
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16
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Aravind MK, Varalakshmi P, John SA, Ashokkumar B. Catechol 1,2-Dioxygenase From Paracoccus sp. MKU1-A Greener and Cleaner Bio-Machinery for cis, cis-Muconic Acid Production by Recombinant E. coli. Front Bioeng Biotechnol 2021; 9:703399. [PMID: 34790650 PMCID: PMC8591083 DOI: 10.3389/fbioe.2021.703399] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2021] [Accepted: 10/19/2021] [Indexed: 11/23/2022] Open
Abstract
Cis, cis-muconic acid (ccMA) is known for its industrial importance as a precursor for the synthesis of several biopolymers. Catechol 1,2-dioxygenase (C12O) is involved in aromatic compounds catabolism and ccMA synthesis in a greener and cleaner way. This is the first study on C12O gene from a metabolically versatile Paracoccus sp. MKU1, which was cloned and expressed in E. coli to produce ccMA from catechol. From the E. coli transformant, recombinant C12O enzyme was purified and found to be a homotrimer with a subunit size of 38.6 kDa. The apparent K m and V max for C12O was 12.89 µM and 310.1 U.mg-1, respectively, evidencing high affinity to catechol than previously reported C12Os. The predicted 3D-structure of C12O from MKU1 consisted of five α-helices in N-terminus, one α-helix in C-terminus, and nine β-sheets in C-terminus. Moreover, a unique α-helix signature 'EESIHAN' was identified in C-terminus between 271 and 277 amino acids, however the molecular insight of conservative α-helix remains obscure. Further, fed-batch culture was employed using recombinant E. coli expressing C12O gene from Paracoccus sp. MKU1 to produce ccMA by whole-cells catalyzed bioconversion of catechol. With the successive supply of 120 mM catechol, the transformant produced 91.4 mM (12.99 g/L) of ccMA in 6 h with the purity of 95.7%. This single step conversion of catechol to ccMA using whole-cells reactions of recombinants did not generate any by-products in the reaction mixtures. Thus, the recombinant E. coli expressing high activity C12O from Paracoccus sp. MKU1 holds promise as a potential candidate for yielding high concentrations of ccMA at faster rates in low cost settings.
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Affiliation(s)
- Manikka Kubendran Aravind
- Department of Genetic Engineering, School of Biotechnology, Madurai Kamaraj University, Madurai, India
| | - Perumal Varalakshmi
- Department of Molecular Microbiology, School of Biotechnology, Madurai Kamaraj University, Madurai, India
| | - Swamidoss Abraham John
- Centre for Nanoscience and Nanotechnology, Department of Chemistry, Gandhigram Rural Institute, Gandhigram, India
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17
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A Guideline to Set Up Cascaded Continuous Cultivation with E. coli Bl21 (DE3). METHODS IN MOLECULAR BIOLOGY (CLIFTON, N.J.) 2021; 2436:223-240. [PMID: 34519978 DOI: 10.1007/7651_2021_424] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Indexed: 10/19/2022]
Abstract
Continuous processing allows to maximize space-time yields and is implemented in many industrial branches. However, in manufacturing of value added compounds produced with microbial hosts, continuous processing is not state-of-the-art yet. This is because fluctuating productivity causes unwanted process deviations. Cascaded continuous bioprocessing, unlike conventional continuous process modes, was found to result in stable productivity. This manuscript serves as a guideline how to set up a cascaded continuous cultivation with Escherichia coli BL21 DE(3).
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18
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Sardelli L, Perottoni S, Tunesi M, Boeri L, Fusco F, Petrini P, Albani D, Giordano C. Technological tools and strategies for culturing human gut microbiota in engineered in vitro models. Biotechnol Bioeng 2021; 118:2886-2905. [PMID: 33990954 PMCID: PMC8361989 DOI: 10.1002/bit.27816] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2020] [Revised: 03/29/2021] [Accepted: 05/04/2021] [Indexed: 12/13/2022]
Abstract
The gut microbiota directly impacts the pathophysiology of different human body districts. Consequently, microbiota investigation is an hot topic of research and its in vitro culture has gained extreme interest in different fields. However, the high sensitivity of microbiota to external stimuli, such as sampling procedure, and the physicochemical complexity of the gut environment make its in vitro culture a challenging task. New engineered microfluidic gut-on-a-chip devices have the potential to model some important features of the intestinal structure, but they are usually unable to sustain culture of microbiota over an extended period of time. The integration of gut-on-a-chip devices with bioreactors for continuous bacterial culture would lead to fast advances in the study of microbiota-host crosstalk. In this review, we summarize the main technologies for the continuous culture of microbiota as upstream systems to be coupled with microfluidic devices to study bacteria-host cells communication. The engineering of integrated microfluidic platforms, capable of sustaining both anaerobic and aerobic cultures, would be the starting point to unveil complex biological phenomena proper of the microbiota-host crosstalks, paving to way to multiple research and technological applications.
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Affiliation(s)
- Lorenzo Sardelli
- Department of ChemistryMaterials and Chemical Engineering “Giulio Natta,” Politecnico di MilanoMilanItaly
| | - Simone Perottoni
- Department of ChemistryMaterials and Chemical Engineering “Giulio Natta,” Politecnico di MilanoMilanItaly
| | - Marta Tunesi
- Department of ChemistryMaterials and Chemical Engineering “Giulio Natta,” Politecnico di MilanoMilanItaly
| | - Lucia Boeri
- Department of ChemistryMaterials and Chemical Engineering “Giulio Natta,” Politecnico di MilanoMilanItaly
| | - Federica Fusco
- Department of ChemistryMaterials and Chemical Engineering “Giulio Natta,” Politecnico di MilanoMilanItaly
| | - Paola Petrini
- Department of ChemistryMaterials and Chemical Engineering “Giulio Natta,” Politecnico di MilanoMilanItaly
| | - Diego Albani
- Department of NeuroscienceIstituto di Ricerche Farmacologiche Mario Negri IRCCSMilanItaly
| | - Carmen Giordano
- Department of ChemistryMaterials and Chemical Engineering “Giulio Natta,” Politecnico di MilanoMilanItaly
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19
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Abstract
Recently, there has been a resurgence of interest in continuous bioprocessing as a cost-optimised production strategy, driven by a rising global requirement for recombinant proteins used as biological drugs. This strategy could provide several benefits over traditional batch processing, including smaller bioreactors, smaller facilities, and overall reduced plant footprints and investment costs. Continuous processes may also offer improved product quality and minimise heterogeneity, both in the culture and in the product. In this paper, a model protein, green fluorescent protein (GFP) mut3*, was used to test the recombinant protein expression in an Escherichia coli strain with industrial relevance grown in chemostat. An important factor in enabling stable productivity in continuous cultures is the carbon source. We have studied the viability and heterogeneity of the chemostat cultures using a chemically defined medium based on glucose or glycerol as the single carbon source. As a by-product of biodiesel production, glycerol is expected to become a sustainable alternative substrate to glucose. We have found that although glycerol gives a higher cell density, it also generates higher heterogeneity in the culture and a less stable recombinant protein production. We suggest that manipulating the balance between different subpopulations to increase the proportion of productive cells may be a possible solution for making glycerol a successful alternative to glucose.
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20
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Cascaded processing enables continuous upstream processing with E. coli BL21(DE3). Sci Rep 2021; 11:11477. [PMID: 34075099 PMCID: PMC8169658 DOI: 10.1038/s41598-021-90899-9] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2020] [Accepted: 05/04/2021] [Indexed: 02/05/2023] Open
Abstract
In many industrial sectors continuous processing is already the golden standard to maximize productivity. However, when working with living cells, subpopulation formation causes instabilities in long-term cultivations. In cascaded continuous cultivation, biomass formation and recombinant protein expression can be spatially separated. This cultivation mode was found to facilitate stable protein expression using microbial hosts, however mechanistic knowledge of this cultivation strategy is scarce. In this contribution we present a method workflow to reduce workload and accelerate the establishment of stable continuous processes with E. coli BL21(DE3) exclusively based on bioengineering methods.
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21
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Ong JY, Pence JT, Molik DC, Shepherd HAM, Goodson HV. Yeast grown in continuous culture systems can detect mutagens with improved sensitivity relative to the Ames test. PLoS One 2021; 16:e0235303. [PMID: 33730086 PMCID: PMC7968628 DOI: 10.1371/journal.pone.0235303] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2020] [Accepted: 02/18/2021] [Indexed: 11/20/2022] Open
Abstract
Continuous culture systems allow for the controlled growth of microorganisms over a long period of time. Here, we develop a novel test for mutagenicity that involves growing yeast in continuous culture systems exposed to low levels of mutagen for a period of approximately 20 days. In contrast, most microorganism-based tests for mutagenicity expose the potential mutagen to the biological reporter at a high concentration of mutagen for a short period of time. Our test improves upon the sensitivity of the well-established Ames test by at least 20-fold for each of two mutagens that act by different mechanisms (the intercalator ethidium bromide and alkylating agent methyl methanesulfonate). To conduct the tests, cultures were grown in small, inexpensive continuous culture systems in media containing (potential) mutagen, and the resulting mutagenicity of the added compound was assessed via two methods: a canavanine-based plate assay and whole genome sequencing. In the canavanine-based plate assay, we were able to detect a clear relationship between the amount of mutagen and the number of canavanine-resistant mutant colonies over a period of one to three weeks of exposure. Whole genome sequencing of yeast grown in continuous culture systems exposed to methyl methanesulfonate demonstrated that quantification of mutations is possible by identifying the number of unique variants across each strain. However, this method had lower sensitivity than the plate-based assay and failed to distinguish the different concentrations of mutagen. In conclusion, we propose that yeast grown in continuous culture systems can provide an improved and more sensitive test for mutagenicity.
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Affiliation(s)
- Joseph Y. Ong
- Department of Chemistry and Biochemistry, University of Notre Dame, Notre Dame, Indiana, United States of America
| | - Julia T. Pence
- Department of Chemistry and Biochemistry, University of Notre Dame, Notre Dame, Indiana, United States of America
| | - David C. Molik
- Department of Biological Sciences, University of Notre Dame, Notre Dame, Indiana, United States of America
| | - Heather A. M. Shepherd
- Department of Chemistry and Biochemistry, University of Notre Dame, Notre Dame, Indiana, United States of America
| | - Holly V. Goodson
- Department of Chemistry and Biochemistry, University of Notre Dame, Notre Dame, Indiana, United States of America
- Department of Biological Sciences, University of Notre Dame, Notre Dame, Indiana, United States of America
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22
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Battaglino B, Arduino A, Pagliano C, Sforza E, Bertucco A. Optimization of Light and Nutrients Supply to Stabilize Long-Term Industrial Cultivation of Metabolically Engineered Cyanobacteria: A Model-Based Analysis. Ind Eng Chem Res 2021. [DOI: 10.1021/acs.iecr.0c04887] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Beatrice Battaglino
- BioSolar Lab, Applied Science and Technology Department, Politecnico di Torino, Environment Park, Via Livorno 60, 10144 Torino, Italy
| | - Alessandro Arduino
- Istituto Nazionale di Ricerca Metrologica (INRIM), Strada delle Cacce 91, 10135 Torino, Italy
| | - Cristina Pagliano
- BioSolar Lab, Applied Science and Technology Department, Politecnico di Torino, Environment Park, Via Livorno 60, 10144 Torino, Italy
| | - Eleonora Sforza
- Department of Industrial Engineering, Università di Padova, Via Marzolo 9, 35131 Padova, Italy
| | - Alberto Bertucco
- Department of Industrial Engineering, Università di Padova, Via Marzolo 9, 35131 Padova, Italy
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23
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Zhang Y, Xiong H, Chen Z, Fu Y, Xu Q, Chen N. Effect of fed-batch and chemostat cultivation processes of C. glutamicum CP for L-leucine production. Bioengineered 2021; 12:426-439. [PMID: 33470174 PMCID: PMC8806242 DOI: 10.1080/21655979.2021.1874693] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022] Open
Abstract
Most of the current industrial processes for L-leucine production are based on fermentation, usually in fed-batch operation mode. Although the culture technology has advanced in recent decades, the process still has significant drawbacks. To solve these problems, we investigated the effects of chemostat culture conditions on the production of L-leucine by Corynebacterium glutamicum CP. The dilution rate, the nitrogen source, and the carbon–nitrogen ratio of the medium were optimized. With the addition of ammonium acetate to the chemostat medium, the initial C/N ratio was adjusted to 57.6, and the L-leucine titer reached the highest level at the optimal dilution rate of 0.04 h−1. Compared with fed-batch culture, the L-leucine titer was reduced (from 53.0 to 24.8 g L−1), but the yield from glucose was increased by 10.0% (from 0.30 to 0.33 mol mol−1) and productivity was increased by 58.3% (from 1.2 to 1.9 g L−1 h−1). Moreover, the titer of the by-product L-alanine was significantly reduced (from 8.9 to 0.8 g L−1). In addition, gene expression levels and activity of key enzymes in the synthesis of L-leucine and L-alanine were analyzed to explain the difference of production performance between chemostat culture and fed-batch culture. The results indicate that chemostat culture has great potential to increase the industrial production of L-leucine compared to current fed-batch approaches.
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Affiliation(s)
- Yufu Zhang
- College of Biotechnology, Tianjin University of Science & Technology , Tianjin, P. R. China.,Key Laboratory of Industrial Fermentation Microbiology, Tianjin University of Science & Technology, Ministry of Education , Tianjin, P. R. China.,Tianjin Key Laboratory of Industrial Microbiology, Tianjin University of Science & Technology , Tianjin, P. R. China
| | - Haibo Xiong
- College of Biotechnology, Tianjin University of Science & Technology , Tianjin, P. R. China.,Key Laboratory of Industrial Fermentation Microbiology, Tianjin University of Science & Technology, Ministry of Education , Tianjin, P. R. China.,Tianjin Key Laboratory of Industrial Microbiology, Tianjin University of Science & Technology , Tianjin, P. R. China
| | - Zhichao Chen
- College of Biotechnology, Tianjin University of Science & Technology , Tianjin, P. R. China.,Key Laboratory of Industrial Fermentation Microbiology, Tianjin University of Science & Technology, Ministry of Education , Tianjin, P. R. China.,Tianjin Key Laboratory of Industrial Microbiology, Tianjin University of Science & Technology , Tianjin, P. R. China
| | - Yunpeng Fu
- College of Biotechnology, Tianjin University of Science & Technology , Tianjin, P. R. China.,Key Laboratory of Industrial Fermentation Microbiology, Tianjin University of Science & Technology, Ministry of Education , Tianjin, P. R. China.,Tianjin Key Laboratory of Industrial Microbiology, Tianjin University of Science & Technology , Tianjin, P. R. China
| | - Qingyang Xu
- College of Biotechnology, Tianjin University of Science & Technology , Tianjin, P. R. China.,Key Laboratory of Industrial Fermentation Microbiology, Tianjin University of Science & Technology, Ministry of Education , Tianjin, P. R. China.,Tianjin Key Laboratory of Industrial Microbiology, Tianjin University of Science & Technology , Tianjin, P. R. China
| | - Ning Chen
- College of Biotechnology, Tianjin University of Science & Technology , Tianjin, P. R. China.,Key Laboratory of Industrial Fermentation Microbiology, Tianjin University of Science & Technology, Ministry of Education , Tianjin, P. R. China.,Tianjin Key Laboratory of Industrial Microbiology, Tianjin University of Science & Technology , Tianjin, P. R. China
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24
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Wright NR, Rønnest NP, Sonnenschein N. Single-Cell Technologies to Understand the Mechanisms of Cellular Adaptation in Chemostats. Front Bioeng Biotechnol 2020; 8:579841. [PMID: 33392163 PMCID: PMC7775484 DOI: 10.3389/fbioe.2020.579841] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2020] [Accepted: 11/30/2020] [Indexed: 11/13/2022] Open
Abstract
There is a growing interest in continuous manufacturing within the bioprocessing community. In this context, the chemostat process is an important unit operation. The current application of chemostat processes in industry is limited although many high yielding processes are reported in literature. In order to reach the full potential of the chemostat in continuous manufacture, the output should be constant. However, adaptation is often observed resulting in changed productivities over time. The observed adaptation can be coupled to the selective pressure of the nutrient-limited environment in the chemostat. We argue that population heterogeneity should be taken into account when studying adaptation in the chemostat. We propose to investigate adaptation at the single-cell level and discuss the potential of different single-cell technologies, which could be used to increase the understanding of the phenomena. Currently, none of the discussed single-cell technologies fulfill all our criteria but in combination they may reveal important information, which can be used to understand and potentially control the adaptation.
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Affiliation(s)
- Naia Risager Wright
- Novo Nordisk A/S, Bagsvaerd, Denmark
- Department of Biotechnology and Biomedicine, Technical University of Denmark, Kongens Lyngby, Denmark
| | | | - Nikolaus Sonnenschein
- Department of Biotechnology and Biomedicine, Technical University of Denmark, Kongens Lyngby, Denmark
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25
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Kopp J, Kittler S, Slouka C, Herwig C, Spadiut O, Wurm DJ. Repetitive Fed-Batch: A Promising Process Mode for Biomanufacturing With E. coli. Front Bioeng Biotechnol 2020; 8:573607. [PMID: 33240864 PMCID: PMC7683717 DOI: 10.3389/fbioe.2020.573607] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2020] [Accepted: 10/21/2020] [Indexed: 12/13/2022] Open
Abstract
Recombinant protein production with Escherichia coli is usually carried out in fed-batch mode in industry. As set-up and cleaning of equipment are time- and cost-intensive, it would be economically and environmentally favorable to reduce the number of these procedures. Switching from fed-batch to continuous biomanufacturing with microbials is not yet applied as these cultivations still suffer from time-dependent variations in productivity. Repetitive fed-batch process technology facilitates critical equipment usage, reduces the environmental fingerprint and potentially increases the overall space-time yield. Surprisingly, studies on repetitive fed-batch processes for recombinant protein production can be found for yeasts only. Knowledge on repetitive fed-batch cultivation technology for recombinant protein production in E. coli is not available until now. In this study, a mixed feed approach, enabling repetitive fed-batch technology for recombinant protein production in E. coli, was developed. Effects of the cultivation mode on the space-time yield for a single-cycle fed-batch, a two-cycle repetitive fed-batch, a three-cycle repetitive fed batch and a chemostat cultivation were investigated. For that purpose, we used two different E. coli strains, expressing a model protein in the cytoplasm or in the periplasm, respectively. Our results demonstrate that a repetitive fed-batch for E. coli leads to a higher space-time yield compared to a single-cycle fed-batch and can potentially outperform continuous biomanufacturing. For the first time, we were able to show that repetitive fed-batch technology is highly suitable for recombinant protein production in E. coli using our mixed feeding approach, as it potentially (i) improves product throughput by using critical equipment to its full capacity and (ii) allows implementation of a more economic process by reducing cleaning and set-up times.
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Affiliation(s)
- Julian Kopp
- Research Area Biochemical Engineering, Institute of Chemical Engineering, TU Wien, Vienna, Austria
| | - Stefan Kittler
- Research Area Biochemical Engineering, Institute of Chemical Engineering, TU Wien, Vienna, Austria
| | - Christoph Slouka
- Research Area Biochemical Engineering, Institute of Chemical Engineering, TU Wien, Vienna, Austria
| | - Christoph Herwig
- Research Area Biochemical Engineering, Institute of Chemical Engineering, TU Wien, Vienna, Austria
| | - Oliver Spadiut
- Research Area Biochemical Engineering, Institute of Chemical Engineering, TU Wien, Vienna, Austria
| | - David J Wurm
- Research Area Biochemical Engineering, Institute of Chemical Engineering, TU Wien, Vienna, Austria
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26
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Schuller A, Cserjan-Puschmann M, Köppl C, Grabherr R, Wagenknecht M, Schiavinato M, Dohm JC, Himmelbauer H, Striedner G. Adaptive Evolution in Producing Microtiter Cultivations Generates Genetically Stable Escherichia coli Production Hosts for Continuous Bioprocessing. Biotechnol J 2020; 16:e2000376. [PMID: 33084246 DOI: 10.1002/biot.202000376] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2020] [Revised: 10/06/2020] [Indexed: 01/01/2023]
Abstract
The production of recombinant proteins usually reduces cell fitness and the growth rate of producing cells. The growth disadvantage favors faster-growing non-producer mutants. Therefore, continuous bioprocessing is hardly feasible in Escherichia coli due to the high escape rate. The stability of E. coli expression systems under long-term production conditions and how metabolic load triggered by recombinant gene expression influences the characteristics of mutations are investigated. Iterated fed-batch-like microbioreactor cultivations are conducted under production conditions. The easy-to-produce green fluorescent protein (GFP) and a challenging antigen-binding fragment (Fab) are used as model proteins, and BL21(DE3) and BL21Q strains as expression hosts. In comparative whole-genome sequencing analyses, mutations that allowed cells to grow unhindered despite recombinant protein production are identified. A T7 RNA polymerase expression system is only conditionally suitable for long-term cultivation under production conditions. Mutations leading to non-producers occur in either the T7 RNA polymerase gene or the T7 promoter. The host RNA polymerase-based BL21Q expression system remains stable in the production of GFP in long-term cultivations. For the production of Fab, mutations in lacI of the BL21Q derivatives have positive effects on long-term stability. The results indicate that adaptive evolution carried out with genome-integrated E. coli expression systems in microtiter cultivations under industrial-relevant production conditions is an efficient strain development tool for production hosts.
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Affiliation(s)
- Artur Schuller
- Christian Doppler Laboratory for Production of Next-Level Biopharmaceuticals in E. coli, Department of Biotechnology, University of Natural Resources and Life Sciences, Muthgasse 18, Vienna, A-1190, 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, Vienna, A-1190, Austria
| | - Christoph Köppl
- Christian Doppler Laboratory for Production of Next-Level Biopharmaceuticals in E. coli, Department of Biotechnology, University of Natural Resources and Life Sciences, Muthgasse 18, Vienna, A-1190, Austria
| | - Reingard Grabherr
- Christian Doppler Laboratory for Production of Next-Level Biopharmaceuticals in E. coli, Department of Biotechnology, University of Natural Resources and Life Sciences, Muthgasse 18, Vienna, A-1190, Austria
| | - Martin Wagenknecht
- Boehringer Ingelheim RCV GmbH & Co KG, Dr.-Boehringer-Gasse 5-11, Vienna, A-1120, Austria
| | - Matteo Schiavinato
- Department of Biotechnology, Institute of Computational Biology, University of Natural Resources and Life Sciences, Muthgasse 18, Vienna, A-1190, Austria
| | - Juliane C Dohm
- Department of Biotechnology, Institute of Computational Biology, University of Natural Resources and Life Sciences, Muthgasse 18, Vienna, A-1190, Austria
| | - Heinz Himmelbauer
- Department of Biotechnology, Institute of Computational Biology, University of Natural Resources and Life Sciences, Muthgasse 18, Vienna, A-1190, 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, Vienna, A-1190, Austria
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Gelain L, Kingma E, Geraldo da Cruz Pradella J, Carvalho da Costa A, van der Wielen L, van Gulik WM. Continuous production of enzymes under carbon-limited conditions by Trichoderma harzianum P49P11. Fungal Biol 2020; 125:177-183. [PMID: 33622533 DOI: 10.1016/j.funbio.2020.10.008] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2020] [Revised: 10/19/2020] [Accepted: 10/21/2020] [Indexed: 11/30/2022]
Abstract
Carbon-limited chemostat cultures were performed using different carbon sources (glucose, 10 and 20 g/L; sucrose, 10 g/L; fructose/glucose, 5.26/5.26 g/L; carboxymethyl cellulose, 10 g/L; and carboxymethyl cellulose/glucose, 5/5 g/L) to verify the capability of the wild type strain Trichoderma harzianum to produce extracellular enzymes. All chemostat cultures were carried out at a fixed dilution rate of 0.05 h-1. Experiments using glucose, fructose/glucose and sucrose were performed in duplicate. Glucose condition was found to induce the production of enzymes that can catalyse the hydrolysis of p-nitrophenyl-β-d-glucopyranoside (PNPGase). A concentration of 20 g/L of glucose in the feed provided the highest productivity (1048 ± 16 U/mol h). Extracellular polysaccharides were considered the source of inducers. Based on the obtained results, a new PNPGase production process was developed using mainly glucose. This process raises interesting possibilities of synthesizing the inducer substrate and the induced enzymes in a single step using an easily assimilated carbon source under carbon-limited conditions.
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Affiliation(s)
- Lucas Gelain
- Delft University of Technology, Department of Biotechnology, Van der Maasweg 9, 2629HZ, Delft, the Netherlands; University of Campinas, School of Chemical Engineering, Av. Albert Einstein, 500, Campinas, Brazil.
| | - Esther Kingma
- Delft University of Technology, Department of Biotechnology, Van der Maasweg 9, 2629HZ, Delft, the Netherlands
| | - José Geraldo da Cruz Pradella
- Federal University of São Paulo, Institute of Science and Technology, Av. Cesare Mansueto Giulio Lattes, 1201, S. J. Campos, Brazil
| | - Aline Carvalho da Costa
- University of Campinas, School of Chemical Engineering, Av. Albert Einstein, 500, Campinas, Brazil
| | - Luuk van der Wielen
- Delft University of Technology, Department of Biotechnology, Van der Maasweg 9, 2629HZ, Delft, the Netherlands; University of Limerick, Bernal Institute, V94 T9PX, Limerick, Ireland
| | - Walter M van Gulik
- Delft University of Technology, Department of Biotechnology, Van der Maasweg 9, 2629HZ, Delft, the Netherlands
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Korpys-Woźniak P, Kubiak P, Białas W, Celińska E. Impact of overproduced heterologous protein characteristics on physiological response in Yarrowia lipolytica steady-state-maintained continuous cultures. Appl Microbiol Biotechnol 2020; 104:9785-9800. [PMID: 33025130 PMCID: PMC7595971 DOI: 10.1007/s00253-020-10937-w] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2020] [Revised: 09/23/2020] [Accepted: 09/27/2020] [Indexed: 12/21/2022]
Abstract
Overproduction of recombinant secretory proteins triggers numerous physiological perturbations. Depending on a given heterologous protein characteristics, the producer cell is faced with different challenges which lead to varying responses in terms of its physiology and the target protein production rate. In the present study, we used steady-state-maintained Yarrowia lipolytica cells to investigate the impact of different heterologous proteins on the physiological behavior of the host cells. Such an approach allowed to uncouple the impact of the overproduction of a particular protein from the phenomena that result from growth phase or are caused by the heterogeneity of the analyzed populations. Altogether, eight variants of recombinant strains, individually overproducing heterologous proteins of varying molecular weight (27-65 kDa) and reporting activity (enzymatic and fluorescent) were subjected to chemostat cultivations. The steady-state-maintained cells were analyzed in terms of the substrate utilization, biomass and metabolites production, as well as the reporter protein synthesis. Simplified distribution of carbon and nitrogen between the respective products, as well as expression analysis of the heterologous genes were conducted. The here-obtained data suggest that using a more transcriptionally active promoter results in channeling more C flux towards the target protein, giving significantly higher specific amounts and production rates of the target polypeptide, at the cost of biomass accumulation, and with no significant impact on the polyols production. The extent of the reporter protein's post-translational modifications, i.e., the number of disulfide bonds and glycosylation pattern, strongly impacts the synthesis process. Specific responses in terms of the protein formation kinetics, the gene expression levels, and transcript-to-protein linearity were observed.Key Points• Eight expression systems, producing different reporter proteins were analyzed.• The cells were maintained in steady-state by continuous chemostat culturing.• Protein- and promoter-specific effects were observed.
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Affiliation(s)
- Paulina Korpys-Woźniak
- Department of Biotechnology and Food Microbiology, Poznan University of Life Sciences, ul. Wojska Polskiego 48, 60-627, Poznań, Poland
| | - Piotr Kubiak
- Department of Biotechnology and Food Microbiology, Poznan University of Life Sciences, ul. Wojska Polskiego 48, 60-627, Poznań, Poland
| | - Wojciech Białas
- Department of Biotechnology and Food Microbiology, Poznan University of Life Sciences, ul. Wojska Polskiego 48, 60-627, Poznań, Poland
| | - Ewelina Celińska
- Department of Biotechnology and Food Microbiology, Poznan University of Life Sciences, ul. Wojska Polskiego 48, 60-627, Poznań, Poland.
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Kittler S, Kopp J, Veelenturf PG, Spadiut O, Delvigne F, Herwig C, Slouka C. The Lazarus Escherichia coli Effect: Recovery of Productivity on Glycerol/Lactose Mixed Feed in Continuous Biomanufacturing. Front Bioeng Biotechnol 2020; 8:993. [PMID: 32903513 PMCID: PMC7438448 DOI: 10.3389/fbioe.2020.00993] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2020] [Accepted: 07/29/2020] [Indexed: 12/11/2022] Open
Abstract
Continuous cultivation with Escherichia coli has several benefits compared to classical fed-batch cultivation. The economic benefits would be a stable process, which leads to time independent quality of the product, and hence ease the downstream process. However, continuous biomanufacturing with E. coli is known to exhibit a drop of productivity after about 4–5 days of cultivation depending on dilution rate. These cultivations are generally performed on glucose, being the favorite carbon source for E. coli and used in combination with isopropyl β-D-1 thiogalactopyranoside (IPTG) for induction. In recent works, harsh induction with IPTG was changed to softer induction using lactose for T7-based plasmids, with the result of reducing the metabolic stress and tunability of productivity. These mixed feed systems based on glucose and lactose result in high amounts of correctly folded protein. In this study we used different mixed feed systems with glucose/lactose and glycerol/lactose to investigate productivity of E. coli based chemostats. We tested different strains producing three model proteins, with the final aim of a stable long-time protein expression. While glucose fed chemostats showed the well-known drop in productivity after a certain process time, glycerol fed cultivations recovered productivity after about 150 h of induction, which corresponds to around 30 generation times. We want to further highlight that the cellular response upon galactose utilization in E. coli BL21(DE3), might be causing fluctuating productivity, as galactose is referred to be a weak inducer. This “Lazarus” phenomenon has not been described in literature before and may enable a stabilization of continuous cultivation with E. coli using different carbon sources.
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Affiliation(s)
- Stefan Kittler
- Research Division Biochemical Engineering, Research Group Integrated Bioprocess Development, Institute of Chemical, Environmental and Bioscience Engineering, Vienna University of Technology, Vienna, Austria
| | - Julian Kopp
- Christian Doppler Laboratory for Mechanistic and Physiological Methods for Improved Bioprocesses, Institute of Chemical, Environmental and Bioscience Engineering, TU Vienna, Vienna, Austria
| | - Patrick Gwen Veelenturf
- Christian Doppler Laboratory for Mechanistic and Physiological Methods for Improved Bioprocesses, Institute of Chemical, Environmental and Bioscience Engineering, TU Vienna, Vienna, Austria
| | - Oliver Spadiut
- Research Division Biochemical Engineering, Research Group Integrated Bioprocess Development, Institute of Chemical, Environmental and Bioscience Engineering, Vienna University of Technology, Vienna, Austria
| | - Frank Delvigne
- TERRA Teaching and Research Centre, Microbial Processes and Interactions (MiPI), Gembloux Agro-Bio Tech - Université de Liège, Gembloux, Belgium
| | - Christoph Herwig
- Research Division Biochemical Engineering, Research Group Integrated Bioprocess Development, Institute of Chemical, Environmental and Bioscience Engineering, Vienna University of Technology, Vienna, Austria.,Christian Doppler Laboratory for Mechanistic and Physiological Methods for Improved Bioprocesses, Institute of Chemical, Environmental and Bioscience Engineering, TU Vienna, Vienna, Austria
| | - Christoph Slouka
- Research Division Biochemical Engineering, Research Group Integrated Bioprocess Development, Institute of Chemical, Environmental and Bioscience Engineering, Vienna University of Technology, Vienna, Austria
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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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Wright NR, Wulff T, Palmqvist EA, Jørgensen TR, Workman CT, Sonnenschein N, Rønnest NP, Herrgård MJ. Fluctuations in glucose availability prevent global proteome changes and physiological transition during prolonged chemostat cultivations of
Saccharomyces cerevisiae. Biotechnol Bioeng 2020; 117:2074-2088. [DOI: 10.1002/bit.27353] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2020] [Accepted: 04/09/2020] [Indexed: 11/06/2022]
Affiliation(s)
- Naia R. Wright
- Novo Nordisk A/S Bagsværd Denmark
- The Novo Nordisk Foundation Center for BiosustainabilityTechnical University of Denmark Lyngby Denmark
- Department of Biotechnology and BiomedicineTechnical University of Denmark Lyngby Denmark
| | - Tune Wulff
- The Novo Nordisk Foundation Center for BiosustainabilityTechnical University of Denmark Lyngby Denmark
| | | | - Thomas R. Jørgensen
- The Novo Nordisk Foundation Center for BiosustainabilityTechnical University of Denmark Lyngby Denmark
| | - Christopher T. Workman
- Department of Biotechnology and BiomedicineTechnical University of Denmark Lyngby Denmark
| | - Nikolaus Sonnenschein
- The Novo Nordisk Foundation Center for BiosustainabilityTechnical University of Denmark Lyngby Denmark
- Department of Biotechnology and BiomedicineTechnical University of Denmark Lyngby Denmark
| | | | - Markus J. Herrgård
- The Novo Nordisk Foundation Center for BiosustainabilityTechnical University of Denmark Lyngby Denmark
- BioInnovation Institute København N Denmark
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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: 240] [Impact Index Per Article: 48.0] [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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Kurokawa M, Ying BW. Experimental Challenges for Reduced Genomes: The Cell Model Escherichia coli. Microorganisms 2019; 8:E3. [PMID: 31861355 PMCID: PMC7022904 DOI: 10.3390/microorganisms8010003] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2019] [Revised: 12/11/2019] [Accepted: 12/17/2019] [Indexed: 12/13/2022] Open
Abstract
Genome reduction, as a top-down approach to obtain the minimal genetic information essential for a living organism, has been conducted with bacterial cells for decades. The most popular and well-studied cell models for genome reduction are Escherichia coli strains. As the previous literature intensively introduced the genetic construction and application of the genome-reduced Escherichia coli strains, the present review focuses the design principles and compares the reduced genome collections from the specific viewpoint of growth, which represents a fundamental property of living cells and is an important feature for their biotechnological application. For the extended simplification of the genomic sequences, the approach of experimental evolution and concern for medium optimization are newly proposed. The combination of the current techniques of genomic construction and the newly proposed methodologies could allow us to acquire growing Escherichia coli cells carrying the extensively reduced genome and to address the question of what the minimal genome essential for life is.
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Affiliation(s)
| | - Bei-Wen Ying
- Graduate School of Life and Environmental Sciences, University of Tsukuba, 305-8572 Ibaraki, Japan;
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Kopp J, Slouka C, Spadiut O, Herwig C. The Rocky Road From Fed-Batch to Continuous Processing With E. coli. Front Bioeng Biotechnol 2019; 7:328. [PMID: 31824931 PMCID: PMC6880763 DOI: 10.3389/fbioe.2019.00328] [Citation(s) in RCA: 20] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2019] [Accepted: 10/28/2019] [Indexed: 12/21/2022] Open
Abstract
Escherichia coli still serves as a beloved workhorse for the production of many biopharmaceuticals as it fulfills essential criteria, such as having fast doubling times, exhibiting a low risk of contamination, and being easy to upscale. Most industrial processes in E. coli are carried out in fed-batch mode. However, recent trends show that the biotech industry is moving toward time-independent processing, trying to improve the space-time yield, and especially targeting constant quality attributes. In the 1950s, the term "chemostat" was introduced for the first time by Novick and Szilard, who followed up on the previous work performed by Monod. Chemostat processing resulted in a major hype 10 years after its official introduction. However, enthusiasm decreased as experiments suffered from genetic instabilities and physiology issues. Major improvements in strain engineering and the usage of tunable promotor systems facilitated chemostat processes. In addition, critical process parameters have been identified, and the effects they have on diverse quality attributes are understood in much more depth, thereby easing process control. By pooling the knowledge gained throughout the recent years, new applications, such as parallelization, cascade processing, and population controls, are applied nowadays. However, to control the highly heterogeneous cultivation broth to achieve stable productivity throughout long-term cultivations is still tricky. Within this review, we discuss the current state of E. coli fed-batch process understanding and its tech transfer potential within continuous processing. Furthermore, the achievements in the continuous upstream applications of E. coli and the continuous downstream processing of intracellular proteins will be discussed.
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Affiliation(s)
- Julian Kopp
- Christian Doppler Laboratory for Mechanistic and Physiological Methods for Improved Bioprocesses, Vienna, Austria
| | - Christoph Slouka
- Research Area Biochemical Engineering, Institute of Chemical Engineering, Vienna, Austria
| | - Oliver Spadiut
- Research Area Biochemical Engineering, Institute of Chemical Engineering, Vienna, Austria
| | - Christoph Herwig
- Christian Doppler Laboratory for Mechanistic and Physiological Methods for Improved Bioprocesses, Vienna, Austria
- Research Area Biochemical Engineering, Institute of Chemical Engineering, Vienna, Austria
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Lecca P, Re A. Identifying necessary and sufficient conditions for the observability of models of biochemical processes. Biophys Chem 2019; 254:106257. [DOI: 10.1016/j.bpc.2019.106257] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2019] [Revised: 08/17/2019] [Accepted: 08/25/2019] [Indexed: 12/11/2022]
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Kopp J, Kolkmann AM, Veleenturf PG, Spadiut O, Herwig C, Slouka C. Boosting Recombinant Inclusion Body Production-From Classical Fed-Batch Approach to Continuous Cultivation. Front Bioeng Biotechnol 2019; 7:297. [PMID: 31737617 PMCID: PMC6834550 DOI: 10.3389/fbioe.2019.00297] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2019] [Accepted: 10/15/2019] [Indexed: 11/16/2022] Open
Abstract
State of the art microbial recombinant protein production is regularly performed in fed-batch based cultivations. However, these cultivations suffer from highly time-dependent changes in productivity and product quality, leading to high variations in the downstream process. Continuous biomanufacturing offers the possibility of a time independent process, boosting the time-space-yield of the recombinantly produced protein and further reducing costs for production, also as downstream gets more predictive. In the current work, the continuous production of a pharmaceutically relevant protein in form of an inclusion body in E. coli BL21(DE3) was investigated in single vessel cultivations by varying dilution rates using glycerol as carbon source, inducer (lactose or IPTG) and respective inducer concentrations. Attempts to increase low specific productivities observed in single vessel continuous cultivations, led to the establishment of a continuously operated cascade of two stirred tank reactors to spatially separate biomass formation from recombinant protein production. Process performance was substantially improved compared to a single vessel chemostat culture, as specific productivity and space-time yield were boosted using an optimized cascaded process by about a factor of 100. This study shows the potential of a two-stage continuous process as promising alternative to benchmark fed-batch processes achieving constant inclusion body production at a time-independent level.
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Affiliation(s)
- Julian Kopp
- Christian Doppler Laboratory for Mechanistic and Physiological Methods for Improved Bioprocesses, Institute of Chemical, Environmental and Bioscience Engineering, Vienna University of Technology, Vienna, Austria
| | - Anna-Maria Kolkmann
- Christian Doppler Laboratory for Mechanistic and Physiological Methods for Improved Bioprocesses, Institute of Chemical, Environmental and Bioscience Engineering, Vienna University of Technology, Vienna, Austria
| | - Patrick Gwen Veleenturf
- Christian Doppler Laboratory for Mechanistic and Physiological Methods for Improved Bioprocesses, Institute of Chemical, Environmental and Bioscience Engineering, Vienna University of Technology, Vienna, Austria
| | - Oliver Spadiut
- Research Division Biochemical Engineering, Institute of Chemical, Environmental and Bioscience Engineering, Vienna University of Technology, Vienna, Austria
| | - Christoph Herwig
- Christian Doppler Laboratory for Mechanistic and Physiological Methods for Improved Bioprocesses, Institute of Chemical, Environmental and Bioscience Engineering, Vienna University of Technology, Vienna, Austria.,Research Division Biochemical Engineering, Institute of Chemical, Environmental and Bioscience Engineering, Vienna University of Technology, Vienna, Austria
| | - Christoph Slouka
- Christian Doppler Laboratory for Mechanistic and Physiological Methods for Improved Bioprocesses, Institute of Chemical, Environmental and Bioscience Engineering, Vienna University of Technology, Vienna, Austria
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Special Issue: Recombinant Protein Expression in Microorganisms. Microorganisms 2019; 7:microorganisms7090355. [PMID: 31527389 PMCID: PMC6781282 DOI: 10.3390/microorganisms7090355] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2019] [Accepted: 09/10/2019] [Indexed: 11/17/2022] Open
Abstract
Microorganisms are widely used in industrial biotechnology as cell factories for the sustainable production of a wide range of compounds and chemicals [...].
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Yu L, Wu F, Chen G. Next‐Generation Industrial Biotechnology‐Transforming the Current Industrial Biotechnology into Competitive Processes. Biotechnol J 2019; 14:e1800437. [DOI: 10.1002/biot.201800437] [Citation(s) in RCA: 33] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2018] [Revised: 02/01/2019] [Indexed: 01/16/2023]
Affiliation(s)
- Lin‐Ping Yu
- Ministry of Education Key Laboratory for Bioinformatics, School of Life SciencesTsinghua University New Biology Building 100084 Beijing China
- Center for Synthetic and Systems BiologyTsinghua University New Biology Building 100084 Beijing China
- Tsinghua‐Peking Center for Life SciencesTsinghua University New Biology Building 100084 Beijing China
| | - Fu‐Qing Wu
- Ministry of Education Key Laboratory for Bioinformatics, School of Life SciencesTsinghua University New Biology Building 100084 Beijing China
- Center for Synthetic and Systems BiologyTsinghua University New Biology Building 100084 Beijing China
- Tsinghua‐Peking Center for Life SciencesTsinghua University New Biology Building 100084 Beijing China
| | - Guo‐Qiang Chen
- Ministry of Education Key Laboratory for Bioinformatics, School of Life SciencesTsinghua University New Biology Building 100084 Beijing China
- Center for Synthetic and Systems BiologyTsinghua University New Biology Building 100084 Beijing China
- Tsinghua‐Peking Center for Life SciencesTsinghua University New Biology Building 100084 Beijing China
- Manchester Institute of Biotechnology, Centre for Synthetic BiologyThe University of Manchester 131 Princess Street Manchester M1 7DN UK
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Fragoso-Jiménez JC, Baert J, Nguyen TM, Liu W, Sassi H, Goormaghtigh F, Van Melderen L, Gaytán P, Hernández-Chávez G, Martinez A, Delvigne F, Gosset G. Growth-dependent recombinant product formation kinetics can be reproduced through engineering of glucose transport and is prone to phenotypic heterogeneity. Microb Cell Fact 2019; 18:26. [PMID: 30710996 PMCID: PMC6359759 DOI: 10.1186/s12934-019-1073-5] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2018] [Accepted: 01/23/2019] [Indexed: 12/31/2022] Open
Abstract
Background Escherichia coli W3110 and a group of six isogenic derivatives, each displaying distinct specific rates of glucose consumption were characterized to determine levels of GFP production and population heterogeneity. These strains have single or combinatory deletions in genes encoding phosphoenolpyruvate:sugar phosphotransferase system (PTS) permeases as PtsG and ManX, as well as common components EI, Hpr protein and EIIA, also the non-PTS Mgl galactose/glucose ABC transporter. They have been transformed for expressing GFP based on a lac-based expression vector, which is subject to bistability. Results These strains displayed specific glucose consumption and growth rates ranging from 1.75 to 0.45 g/g h and 0.54 to 0.16 h−1, respectively. The rate of acetate production was strongly reduced in all mutant strains when compared with W3110/pV21. In bioreactor cultures, wild type W3110/pV21 produced 50.51 mg/L GFP, whereas strains WG/pV21 with inactive PTS IICBGlc and WGM/pV21 with the additional inactivation of PTS IIABMan showed the highest titers of GFP, corresponding to 342 and 438 mg/L, respectively. Moreover, we showed experimentally that bistable expression systems, as lac-based ones, induce strong phenotypic segregation among microbial populations. Conclusions We have demonstrated that reduction on glucose consumption rate in E. coli leads to an improvement of GFP production. Furthermore, from the perspective of phenotypic heterogeneity, we observed in this case that heterogeneous systems are also the ones leading to the highest performance. This observation suggests reconsidering the generally accepted proposition stating that phenotypic heterogeneity is generally unwanted in bioprocess applications.![]() Electronic supplementary material The online version of this article (10.1186/s12934-019-1073-5) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Juan Carlos Fragoso-Jiménez
- Departamento de Ingeniería Celular y Biocatálisis, Instituto de Biotecnología, Universidad Nacional Autónoma de México, Cuernavaca, Morelos, Mexico
| | - Jonathan Baert
- Terra Research and Teaching Centre, Microbial Processes and Interactions (MiPI), Gembloux Agro-Bio Tech, University of Liège, Gembloux, Belgium
| | - Thai Minh Nguyen
- Terra Research and Teaching Centre, Microbial Processes and Interactions (MiPI), Gembloux Agro-Bio Tech, University of Liège, Gembloux, Belgium
| | - Wenzheng Liu
- Terra Research and Teaching Centre, Microbial Processes and Interactions (MiPI), Gembloux Agro-Bio Tech, University of Liège, Gembloux, Belgium
| | - Hosni Sassi
- Terra Research and Teaching Centre, Microbial Processes and Interactions (MiPI), Gembloux Agro-Bio Tech, University of Liège, Gembloux, Belgium
| | - Frédéric Goormaghtigh
- Cellular and Molecular Microbiology (CM2), Faculté des Sciences, Université Libre de Bruxelles (ULB), Gosselies, Belgium
| | - Laurence Van Melderen
- Cellular and Molecular Microbiology (CM2), Faculté des Sciences, Université Libre de Bruxelles (ULB), Gosselies, Belgium
| | - Paul Gaytán
- Departamento de Ingeniería Celular y Biocatálisis, Instituto de Biotecnología, Universidad Nacional Autónoma de México, Cuernavaca, Morelos, Mexico
| | - Georgina Hernández-Chávez
- Departamento de Ingeniería Celular y Biocatálisis, Instituto de Biotecnología, Universidad Nacional Autónoma de México, Cuernavaca, Morelos, Mexico
| | - Alfredo Martinez
- Departamento de Ingeniería Celular y Biocatálisis, Instituto de Biotecnología, Universidad Nacional Autónoma de México, Cuernavaca, Morelos, Mexico
| | - Frank Delvigne
- Terra Research and Teaching Centre, Microbial Processes and Interactions (MiPI), Gembloux Agro-Bio Tech, University of Liège, Gembloux, Belgium.
| | - Guillermo Gosset
- Departamento de Ingeniería Celular y Biocatálisis, Instituto de Biotecnología, Universidad Nacional Autónoma de México, Cuernavaca, Morelos, Mexico.
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