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Lara AR, Kunert F, Vandenbroucke V, Taymaz-Nikerel H, Martínez LM, Sigala JC, Delvigne F, Gosset G, Büchs J. Transport-controlled growth decoupling for self-induced protein expression with a glycerol-repressible genetic circuit. Biotechnol Bioeng 2024; 121:1789-1802. [PMID: 38470342 DOI: 10.1002/bit.28697] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2023] [Revised: 01/17/2024] [Accepted: 03/01/2024] [Indexed: 03/13/2024]
Abstract
Decoupling cell formation from recombinant protein synthesis is a potent strategy to intensify bioprocesses. Escherichia coli strains with mutations in the glucose uptake components lack catabolite repression, display low growth rate, no overflow metabolism, and high recombinant protein yields. Fast growth rates were promoted by the simultaneous consumption of glucose and glycerol, and this was followed by a phase of slow growth, when only glucose remained in the medium. A glycerol-repressible genetic circuit was designed to autonomously induce recombinant protein expression. The engineered strain bearing the genetic circuit was cultured in 3.9 g L-1 glycerol + 18 g L-1 glucose in microbioreactors with online oxygen transfer rate monitoring. The growth was fast during the simultaneous consumption of both carbon sources (C-sources), while expression of the recombinant protein was low. When glycerol was depleted, the growth rate decreased, and the specific fluorescence reached values 17% higher than those obtained with a strong constitutive promoter. Despite the relatively high amount of C-source used, no oxygen limitation was observed. The proposed approach eliminates the need for the substrate feeding or inducers addition and is set as a simple batch culture while mimicking fed-batch performance.
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Affiliation(s)
- Alvaro R Lara
- Department of Biological and Chemical Engineering, Aarhus University, Aarhus, Denmark
| | - Flavio Kunert
- Biochemical Engineering (AVT.BioVT), RWTH Aachen University, Aachen, Germany
| | - Vincent Vandenbroucke
- Terra Research and Teaching Centre, Microbial Processes and Interactions (MiPI), Gembloux Agro-Bio Tech, University of Liège, Gembloux, Belgium
| | - Hilal Taymaz-Nikerel
- Department of Genetics and Bioengineering, Istanbul Bilgi University, Istanbul, Turkey
| | - Luz María Martínez
- Instituto de Biotecnología, Universidad Nacional Autónoma de México, Cuernavaca, México
| | - Juan-Carlos Sigala
- Departamento de Procesos y Tecnología, Universidad Autónoma Metropolitana, Ciudad de México, México
| | - Frank Delvigne
- Terra Research and Teaching Centre, Microbial Processes and Interactions (MiPI), Gembloux Agro-Bio Tech, University of Liège, Gembloux, Belgium
| | - Guillermo Gosset
- Instituto de Biotecnología, Universidad Nacional Autónoma de México, Cuernavaca, México
| | - Jochen Büchs
- Biochemical Engineering (AVT.BioVT), RWTH Aachen University, Aachen, Germany
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de la Cruz M, Kunert F, Taymaz-Nikerel H, Sigala JC, Gosset G, Büchs J, Lara AR. Increasing the Pentose Phosphate Pathway Flux to Improve Plasmid DNA Production in Engineered E. coli. Microorganisms 2024; 12:150. [PMID: 38257977 PMCID: PMC10820320 DOI: 10.3390/microorganisms12010150] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2023] [Revised: 01/03/2024] [Accepted: 01/09/2024] [Indexed: 01/24/2024] Open
Abstract
The demand of plasmid DNA (pDNA) as a key element for gene therapy products, as well as mRNA and DNA vaccines, is increasing together with the need for more efficient production processes. An engineered E. coli strain lacking the phosphotransferase system and the pyruvate kinase A gene has been shown to produce more pDNA than its parental strain. With the aim of improving pDNA production in the engineered strain, several strategies to increase the flux to the pentose phosphate pathway (PPP) were evaluated. The simultaneous consumption of glucose and glycerol was a simple way to increase the growth rate, pDNA production rate, and supercoiled fraction (SCF). The overexpression of key genes from the PPP also improved pDNA production in glucose, but not in mixtures of glucose and glycerol. Particularly, the gene coding for the glucose 6-phosphate dehydrogenase (G6PDH) strongly improved the SCF, growth rate, and pDNA production rate. A linear relationship between the G6PDH activity and pDNA yield was found. A higher flux through the PPP was confirmed by flux balance analysis, which also estimates relevant differences in fluxes of the tricarboxylic acid cycle. These results are useful for developing further cell engineering strategies to increase pDNA production and quality.
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Affiliation(s)
- Mitzi de la Cruz
- Departamento de Procesos y Tecnología, Universidad Autónoma Metropolitana, Mexico City 05348, Mexico
| | - Flavio Kunert
- Chair of Biochemical Engineering (AVT.BioVT), RWTH Aachen University, 52074 Aachen, Germany
| | - Hilal Taymaz-Nikerel
- Department of Genetics and Bioengineering, Istanbul Bilgi University, 34060 Istanbul, Turkey
| | - Juan-Carlos Sigala
- Departamento de Procesos y Tecnología, Universidad Autónoma Metropolitana, Mexico City 05348, Mexico
| | - Guillermo Gosset
- Instituto de Biotecnología, Universidad Nacional Autónoma de México, Cuernavaca 62210, Mexico
| | - Jochen Büchs
- Chair of Biochemical Engineering (AVT.BioVT), RWTH Aachen University, 52074 Aachen, Germany
| | - Alvaro R. Lara
- Department of Biological and Chemical Engineering, Aarhus University, 8000 Aarhus, Denmark
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Cordell WT, Avolio G, Takors R, Pfleger BF. Milligrams to kilograms: making microbes work at scale. Trends Biotechnol 2023; 41:1442-1457. [PMID: 37271589 DOI: 10.1016/j.tibtech.2023.05.002] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2023] [Revised: 05/08/2023] [Accepted: 05/09/2023] [Indexed: 06/06/2023]
Abstract
If biomanufacturing can become a sustainable route for producing chemicals, it will provide a critical step in reducing greenhouse gas emissions to fight climate change. However, efforts to industrialize microbial synthesis of chemicals have met with varied success, due, in part, to challenges in translating laboratory successes to industrial scale. With a particular focus on Escherichia coli, this review examines the lessons learned when studying microbial physiology and metabolism under conditions that simulate large-scale bioreactors and methods to minimize cellular waste through reduction of maintenance energy, optimizing the stress response and minimizing culture heterogeneity. With general strategies to overcome these challenges, biomanufacturing process scale-up could be de-risked and the time and cost of bringing promising syntheses to market could be reduced.
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Affiliation(s)
- William T Cordell
- Department of Chemical and Biological Engineering, University of Wisconsin-Madison, Madison, WI 53706, USA
| | - Gennaro Avolio
- Institute of Biochemical Engineering, University of Stuttgart, Stuttgart 70569, Germany
| | - Ralf Takors
- Institute of Biochemical Engineering, University of Stuttgart, Stuttgart 70569, Germany
| | - Brian F Pfleger
- Department of Chemical and Biological Engineering, University of Wisconsin-Madison, Madison, WI 53706, USA; DOE Center Advanced Bioenergy and Bioproducts Innovation, University of Wisconsin-Madison, Madison, WI 53706, USA; DOE Great Lakes Bioenergy Research Center, University of Wisconsin-Madison, Madison, WI 53706, USA.
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Krausch N, Kaspersetz L, Gaytán-Castro RD, Schermeyer MT, Lara AR, Gosset G, Cruz Bournazou MN, Neubauer P. Model-Based Characterization of E. coli Strains with Impaired Glucose Uptake. Bioengineering (Basel) 2023; 10:808. [PMID: 37508835 PMCID: PMC10376147 DOI: 10.3390/bioengineering10070808] [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: 06/09/2023] [Revised: 06/27/2023] [Accepted: 06/28/2023] [Indexed: 07/30/2023] Open
Abstract
The bacterium Escherichia coli is a widely used organism in biotechnology. For high space-time yields, glucose-limited fed-batch technology is the industry standard; this is because an overflow metabolism of acetate occurs at high glucose concentrations. As an interesting alternative, various strains with limited glucose uptake have been developed. However, these have not yet been characterized under process conditions. To demonstrate the efficiency of our previously developed high-throughput robotic platform, in the present work, we characterized three different exemplary E. coli knockout (KO) strains with limited glucose uptake capacities at three different scales (microtiter plates, 10 mL bioreactor system and 100 mL bioreactor system) under excess glucose conditions with different initial glucose concentrations. The extensive measurements of growth behavior, substrate consumption, respiration, and overflow metabolism were then used to determine the appropriate growth parameters using a mechanistic mathematical model, which allowed for a comprehensive comparative analysis of the strains. The analysis was performed coherently with these different reactor configurations and the results could be successfully transferred from one platform to another. Single and double KO mutants showed reduced specific rates for substrate uptake qSmax and acetate production qApmax; meanwhile, higher glucose concentrations had adverse effects on the biomass yield coefficient YXSem. Additional parameters compared to previous studies for the oxygen uptake rate and carbon dioxide production rate indicated differences in the specific oxygen uptake rate qOmax. This study is an example of how automated robotic equipment, together with mathematical model-based approaches, can be successfully used to characterize strains and obtain comprehensive information more quickly, with a trade-off between throughput and analytical capacity.
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Affiliation(s)
- Niels Krausch
- Chair of Bioprocess Engineering, Institute of Biotechnology, Technische Universität Berlin, Ackerstr. 76, 13355 Berlin, Germany
| | - Lucas Kaspersetz
- Chair of Bioprocess Engineering, Institute of Biotechnology, Technische Universität Berlin, Ackerstr. 76, 13355 Berlin, Germany
| | - Rogelio Diego Gaytán-Castro
- Departamento de Ingeniería Celular y Biocatálisis, Instituto de Biotecnología, Universidad Nacional Autónoma de México, Cuernavaca 62209, Mexico
| | - Marie-Therese Schermeyer
- Chair of Bioprocess Engineering, Institute of Biotechnology, Technische Universität Berlin, Ackerstr. 76, 13355 Berlin, Germany
| | - Alvaro R Lara
- Departamento de Procesos y Tecnología, Universidad Autónoma Metropolitana, Mexico City 05348, Mexico
| | - Guillermo Gosset
- Departamento de Ingeniería Celular y Biocatálisis, Instituto de Biotecnología, Universidad Nacional Autónoma de México, Cuernavaca 62209, Mexico
| | - Mariano Nicolas Cruz Bournazou
- Chair of Bioprocess Engineering, Institute of Biotechnology, Technische Universität Berlin, Ackerstr. 76, 13355 Berlin, Germany
- DataHow AG, 8050 Zurich, Switzerland
| | - Peter Neubauer
- Chair of Bioprocess Engineering, Institute of Biotechnology, Technische Universität Berlin, Ackerstr. 76, 13355 Berlin, Germany
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