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Li B, Wu C, Bai S, Zhang D, Xu C, Yuan X, Tian J, Bai J, Li L, Fu J. Enhancement of ε-poly-L-lysine production by Streptomyces albulus FQF-24 with feeding strategies using cassava starch as carbon source. Bioprocess Biosyst Eng 2024:10.1007/s00449-024-03078-1. [PMID: 39150530 DOI: 10.1007/s00449-024-03078-1] [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: 06/11/2024] [Accepted: 08/08/2024] [Indexed: 08/17/2024]
Abstract
ε-Poly-L-lysine (ε-PL) is a natural and wide-spectrum antimicrobial additive. In this study, the production of ε-PL by Streptomyces albulus FQF-24 using cassava starch (CS) as carbon source and the effects of different feeding methods were investigated in a fermenter. The initial shake flask experiments demonstrated the efficient production of ε-PL with CS, achieving the ε-PL production of 1.18 g/L. Subsequent investigations in the fermenter identified that the ideal pH was 3.8 during the ε-PL synthesis phase. Under this condition, the production of ε-PL reached 1.35 g/L. When the pH was maintained at 3.8, the investigation of improvement of feeding composition was carried out in a 5 L fermenter. The intermittent feeding containing CS, inorganic and organic nitrogen sources resulted in the maximum ε-PL production and dry cell weight (DCW) reaching 17.17 g/L and 42.73 g/L. Additionally, continuous feeding with the composition of CS, organic and inorganic nitrogen sources, and inorganic salts further increased ε-PL production and DCW to 27.56 g/L and 38.5 g/L. Summarily, the above results indicate that the fermentation using low-cost CS and continuous feeding strategy with whole medium composition can provide a beneficial reference for the efficient production of ε-PL.
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Affiliation(s)
- Boyan Li
- School of Chemistry and Life Sciences, Suzhou University of Science and Technology, Suzhou, 215009, China
| | - Chenqi Wu
- Suzhou Polytechnic Institute of Agriculture, Suzhou, 215009, China
| | - Senmeng Bai
- School of Chemistry and Life Sciences, Suzhou University of Science and Technology, Suzhou, 215009, China
| | - Di Zhang
- School of Chemistry and Life Sciences, Suzhou University of Science and Technology, Suzhou, 215009, China
| | - Chang Xu
- School of Chemistry and Life Sciences, Suzhou University of Science and Technology, Suzhou, 215009, China
| | - Xiaofeng Yuan
- School of Chemistry and Life Sciences, Suzhou University of Science and Technology, Suzhou, 215009, China
| | - Jiayi Tian
- School of Chemistry and Life Sciences, Suzhou University of Science and Technology, Suzhou, 215009, China
| | - Jing Bai
- School of Chemistry and Life Sciences, Suzhou University of Science and Technology, Suzhou, 215009, China
| | - Liangzhi Li
- School of Chemistry and Life Sciences, Suzhou University of Science and Technology, Suzhou, 215009, China
| | - Jiaolong Fu
- School of Chemistry and Life Sciences, Suzhou University of Science and Technology, Suzhou, 215009, China.
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2
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Kemmer A, Cai L, Born S, Cruz Bournazou MN, Neubauer P. Enzyme-Mediated Exponential Glucose Release: A Model-Based Strategy for Continuous Defined Fed-Batch in Small-Scale Cultivations. Bioengineering (Basel) 2024; 11:107. [PMID: 38391593 PMCID: PMC10886149 DOI: 10.3390/bioengineering11020107] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2023] [Revised: 01/05/2024] [Accepted: 01/18/2024] [Indexed: 02/24/2024] Open
Abstract
Miniaturized cultivation systems offer the potential to enhance experimental throughput in bioprocess development. However, they usually lack the miniaturized pumps necessary for fed-batch mode, which is commonly employed in industrial bioprocesses. An alternative are enzyme-mediated glucose release systems from starch-derived polymers, facilitating continuous glucose supply. Nevertheless, while the glucose release, and thus the feed rate, is controlled by the enzyme concentration, it also strongly depends on the type of starch derivative, and the culture conditions as well as pH and temperature. So far it was not possible to implement controlled feeding strategies (e.g., exponential feeding). In this context, we propose a model-based approach to achieve precise control over enzyme-mediated glucose release in cultivations. To this aim, an existing mathematical model was integrated into a computational framework to calculate setpoints for enzyme additions. We demonstrate the ability of the tool to maintain different pre-defined exponential growth rates during Escherichia coli cultivations in parallel mini-bioreactors integrated into a robotic facility. Although in this case study, the intermittent additions of enzyme and dextrin were performed by a liquid handler, the approach is adaptable to manual applications. Thus, we present a straightforward and robust approach for implementing defined continuous fed-batch processes in small-scale systems, where continuous feeding was only possible with low accuracy or high technical efforts until now.
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Affiliation(s)
- Annina Kemmer
- Institute of Biotechnology, Chair of Bioprocess Engineering, Technische Universität Berlin, 13355 Berlin, Germany
| | - Linda Cai
- Institute of Biotechnology, Chair of Bioprocess Engineering, Technische Universität Berlin, 13355 Berlin, Germany
| | - Stefan Born
- Institute of Biotechnology, Chair of Bioprocess Engineering, Technische Universität Berlin, 13355 Berlin, Germany
| | - M Nicolas Cruz Bournazou
- Institute of Biotechnology, Chair of Bioprocess Engineering, Technische Universität Berlin, 13355 Berlin, Germany
| | - Peter Neubauer
- Institute of Biotechnology, Chair of Bioprocess Engineering, Technische Universität Berlin, 13355 Berlin, Germany
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3
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Malcı K, Santibáñez R, Jonguitud-Borrego N, Santoyo-Garcia JH, Kerkhoven EJ, Rios-Solis L. Improved production of Taxol ® precursors in S. cerevisiae using combinatorial in silico design and metabolic engineering. Microb Cell Fact 2023; 22:243. [PMID: 38031061 PMCID: PMC10687855 DOI: 10.1186/s12934-023-02251-7] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2023] [Accepted: 11/14/2023] [Indexed: 12/01/2023] Open
Abstract
BACKGROUND Integrated metabolic engineering approaches that combine system and synthetic biology tools enable the efficient design of microbial cell factories for synthesizing high-value products. In this study, we utilized in silico design algorithms on the yeast genome-scale model to predict genomic modifications that could enhance the production of early-step Taxol® in engineered Saccharomyces cerevisiae cells. RESULTS Using constraint-based reconstruction and analysis (COBRA) methods, we narrowed down the solution set of genomic modification candidates. We screened 17 genomic modifications, including nine gene deletions and eight gene overexpressions, through wet-lab studies to determine their impact on taxadiene production, the first metabolite in the Taxol® biosynthetic pathway. Under different cultivation conditions, most single genomic modifications resulted in increased taxadiene production. The strain named KM32, which contained four overexpressed genes (ILV2, TRR1, ADE13, and ECM31) involved in branched-chain amino acid biosynthesis, the thioredoxin system, de novo purine synthesis, and the pantothenate pathway, respectively, exhibited the best performance. KM32 achieved a 50% increase in taxadiene production, reaching 215 mg/L. Furthermore, KM32 produced the highest reported yields of taxa-4(20),11-dien-5α-ol (T5α-ol) at 43.65 mg/L and taxa-4(20),11-dien-5-α-yl acetate (T5αAc) at 26.2 mg/L among early-step Taxol® metabolites in S. cerevisiae. CONCLUSIONS This study highlights the effectiveness of computational and integrated approaches in identifying promising genomic modifications that can enhance the performance of yeast cell factories. By employing in silico design algorithms and wet-lab screening, we successfully improved taxadiene production in engineered S. cerevisiae strains. The best-performing strain, KM32, achieved substantial increases in taxadiene as well as production of T5α-ol and T5αAc. These findings emphasize the importance of using systematic and integrated strategies to develop efficient yeast cell factories, providing potential implications for the industrial production of high-value isoprenoids like Taxol®.
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Affiliation(s)
- Koray Malcı
- Institute for Bioengineering, School of Engineering, University of Edinburgh, King's Buildings, Edinburgh, EH9 3BF, UK.
- Centre for Engineering Biology, University of Edinburgh, King's Buildings, Edinburgh, EH9 3BF, UK.
- Department of Bioengineering, Imperial College London, London, SW7 2AZ, UK.
| | - Rodrigo Santibáñez
- Department of Pediatrics, University of California, San Diego, 9500 Gilman Drive, La Jolla, CA, 92093-0760, USA
| | - Nestor Jonguitud-Borrego
- Institute for Bioengineering, School of Engineering, University of Edinburgh, King's Buildings, Edinburgh, EH9 3BF, UK
- Centre for Engineering Biology, University of Edinburgh, King's Buildings, Edinburgh, EH9 3BF, UK
| | - Jorge H Santoyo-Garcia
- Institute for Bioengineering, School of Engineering, University of Edinburgh, King's Buildings, Edinburgh, EH9 3BF, UK
- Centre for Engineering Biology, University of Edinburgh, King's Buildings, Edinburgh, EH9 3BF, UK
| | - Eduard J Kerkhoven
- Department of Life Sciences, Chalmers University of Technology, Kemivägen 10, SE-412 96, Gothenburg, Sweden
- SciLifeLab, Chalmers University of Technology, SE-412 96, Gothenburg, Sweden
- Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, 2800, Kgs, Lyngby, Denmark
| | - Leonardo Rios-Solis
- Institute for Bioengineering, School of Engineering, University of Edinburgh, King's Buildings, Edinburgh, EH9 3BF, UK.
- Centre for Engineering Biology, University of Edinburgh, King's Buildings, Edinburgh, EH9 3BF, UK.
- School of Natural and Environmental Sciences, Molecular Biology and Biotechnology Division, Newcastle University, Newcastle Upon Tyne, NE1 7RU, UK.
- Department of Biochemical Engineering, The Advanced Centre for Biochemical Engineering, University College London, Gower Street, London, WC1E 6BT, UK.
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4
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Benhadda F, Zykwinska A, Colliec-Jouault S, Sinquin C, Thollas B, Courtois A, Fuzzati N, Toribio A, Delbarre-Ladrat C. Marine versus Non-Marine Bacterial Exopolysaccharides and Their Skincare Applications. Mar Drugs 2023; 21:582. [PMID: 37999406 PMCID: PMC10672628 DOI: 10.3390/md21110582] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/02/2023] [Revised: 11/02/2023] [Accepted: 11/05/2023] [Indexed: 11/25/2023] Open
Abstract
Bacteria are well-known to synthesize high molecular weight polysaccharides excreted in extracellular domain, which constitute their protective microenvironment. Several bacterial exopolysaccharides (EPS) are commercially available for skincare applications in cosmetic products due to their unique structural features, conferring valuable biological and/or textural properties. This review aims to give an overview of bacterial EPS, an important group of macromolecules used in cosmetics as actives and functional ingredients. For this purpose, the main chemical characteristics of EPS are firstly described, followed by the basics of the development of cosmetic ingredients. Then, a focus on EPS production, including upstream and downstream processes, is provided. The diversity of EPS used in the cosmetic industry, and more specifically of marine-derived EPS is highlighted. Marine bacteria isolated from extreme environments are known to produce EPS. However, their production processes are highly challenging due to high or low temperatures; yield must be improved to reach economically viable ingredients. The biological properties of marine-derived EPS are then reviewed, resulting in the highlight of the challenges in this field.
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Affiliation(s)
- Fanny Benhadda
- Ifremer, MASAE Microbiologie Aliment Santé Environnement, F-44000 Nantes, France; (F.B.); (S.C.-J.); (C.S.); (C.D.-L.)
- CHANEL Fragrance and Beauty, F-93500 Pantin, France; (N.F.); (A.T.)
| | - Agata Zykwinska
- Ifremer, MASAE Microbiologie Aliment Santé Environnement, F-44000 Nantes, France; (F.B.); (S.C.-J.); (C.S.); (C.D.-L.)
| | - Sylvia Colliec-Jouault
- Ifremer, MASAE Microbiologie Aliment Santé Environnement, F-44000 Nantes, France; (F.B.); (S.C.-J.); (C.S.); (C.D.-L.)
| | - Corinne Sinquin
- Ifremer, MASAE Microbiologie Aliment Santé Environnement, F-44000 Nantes, France; (F.B.); (S.C.-J.); (C.S.); (C.D.-L.)
| | | | | | - Nicola Fuzzati
- CHANEL Fragrance and Beauty, F-93500 Pantin, France; (N.F.); (A.T.)
| | - Alix Toribio
- CHANEL Fragrance and Beauty, F-93500 Pantin, France; (N.F.); (A.T.)
| | - Christine Delbarre-Ladrat
- Ifremer, MASAE Microbiologie Aliment Santé Environnement, F-44000 Nantes, France; (F.B.); (S.C.-J.); (C.S.); (C.D.-L.)
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5
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Kemmer A, Fischer N, Wilms T, Cai L, Groß S, King R, Neubauer P, Cruz Bournazou MN. Nonlinear state estimation as tool for online monitoring and adaptive feed in high throughput cultivations. Biotechnol Bioeng 2023; 120:3261-3275. [PMID: 37497592 DOI: 10.1002/bit.28509] [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: 12/23/2022] [Revised: 05/08/2023] [Accepted: 07/11/2023] [Indexed: 07/28/2023]
Abstract
Robotic facilities that can perform advanced cultivations (e.g., fed-batch or continuous) in high throughput have drastically increased the speed and reliability of the bioprocess development pipeline. Still, developing reliable analytical technologies, that can cope with the throughput of the cultivation system, has proven to be very challenging. On the one hand, the analytical accuracy suffers from the low sampling volumes, and on the other hand, the number of samples that must be treated rapidly is very large. These issues have been a major limitation for the implementation of feedback control methods in miniaturized bioreactor systems, where observations of the process states are typically obtained after the experiment has finished. In this work, we implement a Sigma-Point Kalman Filter in a high throughput platform with 24 parallel experiments at the mL-scale to demonstrate its viability and added value in high throughput experiments. The filter exploits the information generated by the ammonia-based pH control to enable the continuous estimation of the biomass concentration, a critical state to monitor the specific rates of production and consumption in the process. The objective in the selected case study is to ensure that the selected specific substrate consumption rate is tightly controlled throughout the complete Escherichia coli cultivations for recombinant production of an antibody fragment.
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Affiliation(s)
- Annina Kemmer
- Chair of Bioprocess Engineering, Technische Universität Berlin, Berlin, Germany
| | - Nico Fischer
- Chair of Measurement and Control, Technische Universität Berlin, Berlin, Germany
| | - Terrance Wilms
- Chair of Measurement and Control, Technische Universität Berlin, Berlin, Germany
| | - Linda Cai
- Chair of Bioprocess Engineering, Technische Universität Berlin, Berlin, Germany
| | - Sebastian Groß
- Chair of Bioprocess Engineering, Technische Universität Berlin, Berlin, Germany
- wega Informatik (Deutschland) GmbH, Weil am Rhein, Germany
| | - Rudibert King
- Chair of Measurement and Control, Technische Universität Berlin, Berlin, Germany
| | - Peter Neubauer
- Chair of Bioprocess Engineering, Technische Universität Berlin, Berlin, Germany
| | - M Nicolas Cruz Bournazou
- Chair of Bioprocess Engineering, Technische Universität Berlin, Berlin, Germany
- DataHow AG, Dübendorf, Switzerland
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6
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Sedighikamal H, Sattarzadeh A, Karimi Mostofi R, Dinarvand B, Nazarpour M. High-Titer Recombinant Adenovirus 26 Vector GMP Manufacturing in HEK 293 Cells with a Stirred Single-Use Bioreactor for COVID-19 Vaccination Purposes. ACS OMEGA 2023; 8:36720-36728. [PMID: 37841195 PMCID: PMC10568722 DOI: 10.1021/acsomega.3c03007] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/02/2023] [Accepted: 09/14/2023] [Indexed: 10/17/2023]
Abstract
The severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2 virus) pandemic has shown the importance of pursuing various vaccine manufacturing strategies. In the present study, the HEK 293 cells were infected with recombinant adenovirus serotype 26 (rAd26), and the effects of critical process parameters (CPPs) including viable cell density (VCD) at infection time (0.5 × 106, 0.8 × 106, 1.4 × 106, 1.8 × 106, and 2.5 × 106 cells/mL), the multiplicity of infection (MOI) = 3, 6, 9, 12, and 15, and two aeration strategies (high-speed agitation with a sparging system and low-speed agitation with an overlay system) were investigated experimentally. The results of small-scale experiments in 2 L shake flasks (SF 2L) demonstrated that the initial VCD and MOI could affect the cell proliferation and viability. The results at these experiments showed that VCD = 1.4 × 106 cells/mL and MOI = 9 yielded TCID50 /mL = 108.9, at 72 h post-infection (hpi), while the virus titer at VCD = 0.5 × 106 and 0.8 × 106 cells/mL was lower compared to that of VCD = 1.4 × 106 cells/mL. Moreover, our findings showed that VCDs > 1.8 × 106 cells/m with MOI = 9 did not have a positive effect on TCID50 /mL and MOI = 3 and 6 were less efficient, whereas MOI > 12 decreased the viability drastically. In the next step, the optimized CPPs in a small scale were exploited in a 200 L single-use bioreactor (SUB), with good manufacturing practice (GMP) conditions, at RPM = 25 with an overlay system, yielding high-titer rAd26 manufacturing, i.e., TCID50/mL = 108.9, at 72 hpi.
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Affiliation(s)
- Hossein Sedighikamal
- API
Production Plant, Actoverco Biotech Company, Alborz 331325489, Iran
- Division
of Industrial Biotechnology, Department of Chemical Engineering, Sharif University of Technology, Tehran 11365-11155, Iran
| | | | - Reza Karimi Mostofi
- API
Production Plant, Actoverco Biotech Company, Alborz 331325489, Iran
- Department
of Pharmaceutics, Faculty of Pharmacy, Tehran
University of Medical Sciences, Tehran 8741253641, Iran
| | | | - Madineh Nazarpour
- API
Production Plant, Actoverco Biotech Company, Alborz 331325489, Iran
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7
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Santoyo-Garcia JH, Valdivia-Cabrera M, Ochoa-Villarreal M, Casasola-Zamora S, Ripoll M, Escrich A, Moyano E, Betancor L, Halliday KJ, Loake GJ, Rios-Solis L. Increased paclitaxel recovery from Taxus baccata vascular stem cells using novel in situ product recovery approaches. BIORESOUR BIOPROCESS 2023; 10:68. [PMID: 38647629 PMCID: PMC10991628 DOI: 10.1186/s40643-023-00687-8] [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: 04/29/2023] [Accepted: 09/16/2023] [Indexed: 04/25/2024] Open
Abstract
In this study, several approaches were tested to optimise the production and recovery of the widely used anticancer drug Taxol® (paclitaxel) from culturable vascular stem cells (VSCs) of Taxus baccata, which is currently used as a successful cell line for paclitaxel production. An in situ product recovery (ISPR) technique was employed, which involved combining three commercial macro-porous resin beads (HP-20, XAD7HP and HP-2MG) with batch and semi-continuous cultivations of the T. baccata VSCs after adding methyl jasmonate (Me-JA) as an elicitor. The optimal resin combination resulted in 234 ± 23 mg of paclitaxel per kg of fresh-weight cells, indicating a 13-fold improved yield compared to the control (with no resins) in batch cultivation. This resin treatment was further studied to evaluate the resins' removal capacity of reactive oxygen species (ROS), which can cause poor cell growth or reduce product synthesis. It was observed that the ISPR cultivations had fourfold less intracellular ROS concentration than that of the control; thus, a reduced ROS concentration established by the resin contributed to increased paclitaxel yield, contrary to previous studies. These paclitaxel yields are the highest reported to date using VSCs, and this scalable production method could be applied for a diverse range of similar compounds utilising plant cell culture.
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Affiliation(s)
- Jorge H Santoyo-Garcia
- Institute for Bioengineering, School of Engineering, University of Edinburgh, King's Buildings, Edinburgh, EH9 3FB, UK.
- Centre for Engineering Biology, University of Edinburgh, King's Buildings, Edinburgh, EH9 3BF, UK.
| | - Marissa Valdivia-Cabrera
- Institute of Molecular Plant Sciences, School of Biological Sciences, University of Edinburgh, King's Buildings, Edinburgh, EH9 3BF, UK
| | - Marisol Ochoa-Villarreal
- Institute of Molecular Plant Sciences, School of Biological Sciences, University of Edinburgh, King's Buildings, Edinburgh, EH9 3BF, UK
| | | | - Magdalena Ripoll
- Laboratorio de Biotecnología, Universidad ORT Uruguay, Mercedes 1237, 11100, Montevideo, Uruguay
- Graduate Program in Chemistry, Facultad de Química, Universidad de la República, Montevideo, Uruguay
| | - Ainoa Escrich
- Department of Medicine and Life Sciences, Universitat Pompeu Fabra, 08003, Barcelona, Spain
| | - Elisabeth Moyano
- Department of Medicine and Life Sciences, Universitat Pompeu Fabra, 08003, Barcelona, Spain
| | - Lorena Betancor
- Laboratorio de Biotecnología, Universidad ORT Uruguay, Mercedes 1237, 11100, Montevideo, Uruguay
| | - Karen J Halliday
- Institute of Molecular Plant Sciences, School of Biological Sciences, University of Edinburgh, King's Buildings, Edinburgh, EH9 3BF, UK
| | - Gary J Loake
- Institute of Molecular Plant Sciences, School of Biological Sciences, University of Edinburgh, King's Buildings, Edinburgh, EH9 3BF, UK
- Green Bioactives, Douglas House, Pentland Science Park, Midlothian, EH16 0PL, UK
| | - Leonardo Rios-Solis
- Institute for Bioengineering, School of Engineering, University of Edinburgh, King's Buildings, Edinburgh, EH9 3FB, UK.
- Centre for Engineering Biology, University of Edinburgh, King's Buildings, Edinburgh, EH9 3BF, UK.
- School of Natural and Environmental Sciences, Molecular Biology and Biotechnology Division, Newcastle University, Newcastle upon Tyne, NE1 7RU, UK.
- Department of Biochemical Engineering, The Advanced Centre for Biochemical Engineering, University College London, Gower Street, London, WC1E 6BT, UK.
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8
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Santoyo‐Garcia JH, Walls LE, Valdivia‐Cabrera M, Malcı K, Jonguitud‐Borrego N, Halliday KJ, Rios‐Solis L. The synergetic effect from the combination of different adsorption resins in batch and semi-continuous cultivations of S. Cerevisiae cell factories to produce acetylated Taxanes precursors of the anticancer drug Taxol. Biotechnol Bioeng 2023; 120:2160-2174. [PMID: 37428616 PMCID: PMC10952759 DOI: 10.1002/bit.28487] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2022] [Revised: 06/17/2023] [Accepted: 06/22/2023] [Indexed: 07/12/2023]
Abstract
In situ product recovery is an efficient way to intensify bioprocesses as it can perform adsorption of the desired natural products in the cultivation. However, it is common to use only one adsorbent (liquid or solid) to perform the product recovery. For this study, the use of an in situ product recovery method with three combined commercial resins (HP-20, XAD7HP, and HP-2MG) with different chemical properties was performed. A new yeast strain of Saccharomyces cerevisiae was engineered using CRISPR Cas9 (strain EJ2) to deliver heterologous expression of oxygenated acetylated taxanes that are precursors of the anticancer drug Taxol ® (paclitaxel). Microscale cultivations using a definitive screening design (DSD) were set to get the best resin combinations and concentrations to retrieve high taxane titers. Once the best resin treatment was selected by the DSD, semi-continuous cultivation in high throughput microscale was performed to increase the total taxanes yield up to 783 ± 33 mg/L. The best T5α-yl Acetate yield obtained was up to 95 ± 4 mg/L, the highest titer of this compound ever reported by a heterologous expression. It was also observed that by using a combination of the resins in the cultivation, 8 additional uncharacterized taxanes were found in the gas chromatograms compared to the dodecane overlay method. Lastly, the cell-waste reactive oxygen species concentrations from the yeast were 1.5-fold lower in the resin's treatment compared to the control with no adsorbent aid. The possible future implications of this method could be critical for bioprocess intensification, allowing the transition to a semi-continuous flow bioprocess. Further, this new methodology broadens the use of different organisms for natural product synthesis/discovery benefiting from clear bioprocess intensification advantages.
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Affiliation(s)
- Jorge H. Santoyo‐Garcia
- Institute for BioengineeringUniversity of EdinburghEdinburghUK
- Centre for Engineering BiologyUniversity of EdinburghEdinburghUK
| | - Laura E. Walls
- Institute for BioengineeringUniversity of EdinburghEdinburghUK
- Centre for Engineering BiologyUniversity of EdinburghEdinburghUK
| | - Marissa Valdivia‐Cabrera
- Institute of Molecular Plant SciencesSchool of Biological Sciences, University of EdinburghEdinburgh
| | - Koray Malcı
- Institute for BioengineeringUniversity of EdinburghEdinburghUK
- Centre for Engineering BiologyUniversity of EdinburghEdinburghUK
- Present address:
Koray MalcıDepartment of Bioengineering, Imperial College LondonLondonUK
| | - Nestor Jonguitud‐Borrego
- Institute for BioengineeringUniversity of EdinburghEdinburghUK
- Centre for Engineering BiologyUniversity of EdinburghEdinburghUK
| | - Karen J. Halliday
- Institute of Molecular Plant SciencesSchool of Biological Sciences, University of EdinburghEdinburgh
| | - Leonardo Rios‐Solis
- Institute for BioengineeringUniversity of EdinburghEdinburghUK
- Centre for Engineering BiologyUniversity of EdinburghEdinburghUK
- Division of Molecular Biology and BiotechnologySchool of Natural and Environmental Sciences, Newcastle UniversityNewcastle upon TyneUK
- Department of Biochemical Engineering, The Advanced Centre for Biochemical EngineeringUniversity College LondonLondonUnited Kingdom
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9
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Fina A, Millard P, Albiol J, Ferrer P, Heux S. High throughput 13C-metabolic flux analysis of 3-hydroxypropionic acid producing Pichia pastoris reveals limited availability of acetyl-CoA and ATP due to tight control of the glycolytic flux. Microb Cell Fact 2023; 22:117. [PMID: 37380999 DOI: 10.1186/s12934-023-02123-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2023] [Accepted: 05/27/2023] [Indexed: 06/30/2023] Open
Abstract
BACKGROUND Production of 3-hydroxypropionic acid (3-HP) through the malonyl-CoA pathway has yielded promising results in Pichia pastoris (Komagataella phaffii), demonstrating the potential of this cell factory to produce this platform chemical and other acetyl-CoA-derived products using glycerol as a carbon source. However, further metabolic engineering of the original P. pastoris 3-HP-producing strains resulted in unexpected outcomes, e.g., significantly lower product yield and/or growth rate. To gain an understanding on the metabolic constraints underlying these observations, the fluxome (metabolic flux phenotype) of ten 3-HP-producing P. pastoris strains has been characterized using a high throughput 13C-metabolic flux analysis platform. Such platform enabled the operation of an optimised workflow to obtain comprehensive maps of the carbon flux distribution in the central carbon metabolism in a parallel-automated manner, thereby accelerating the time-consuming strain characterization step in the design-build-test-learn cycle for metabolic engineering of P. pastoris. RESULTS We generated detailed maps of the carbon fluxes in the central carbon metabolism of the 3-HP producing strain series, revealing the metabolic consequences of different metabolic engineering strategies aimed at improving NADPH regeneration, enhancing conversion of pyruvate into cytosolic acetyl-CoA, or eliminating by-product (arabitol) formation. Results indicate that the expression of the POS5 NADH kinase leads to a reduction in the fluxes of the pentose phosphate pathway reactions, whereas an increase in the pentose phosphate pathway fluxes was observed when the cytosolic acetyl-CoA synthesis pathway was overexpressed. Results also show that the tight control of the glycolytic flux hampers cell growth due to limited acetyl-CoA biosynthesis. When the cytosolic acetyl-CoA synthesis pathway was overexpressed, the cell growth increased, but the product yield decreased due to higher growth-associated ATP costs. Finally, the six most relevant strains were also cultured at pH 3.5 to assess the effect of a lower pH on their fluxome. Notably, similar metabolic fluxes were observed at pH 3.5 compared to the reference condition at pH 5. CONCLUSIONS This study shows that existing fluoxomics workflows for high-throughput analyses of metabolic phenotypes can be adapted to investigate P. pastoris, providing valuable information on the impact of genetic manipulations on the metabolic phenotype of this yeast. Specifically, our results highlight the metabolic robustness of P. pastoris's central carbon metabolism when genetic modifications are made to increase the availability of NADPH and cytosolic acetyl-CoA. Such knowledge can guide further metabolic engineering of these strains. Moreover, insights into the metabolic adaptation of P. pastoris to an acidic pH have also been obtained, showing the capability of the fluoxomics workflow to assess the metabolic impact of environmental changes.
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Affiliation(s)
- Albert Fina
- Department of Chemical, Biological and Environmental Engineering, Universitat Autònoma de Barcelona, Bellaterra, Catalonia, 08193, Spain
| | - Pierre Millard
- TBI, Université de Toulouse, CNRS, INRAE, INSA, Toulouse, 31077, France
| | - Joan Albiol
- Department of Chemical, Biological and Environmental Engineering, Universitat Autònoma de Barcelona, Bellaterra, Catalonia, 08193, Spain
| | - Pau Ferrer
- Department of Chemical, Biological and Environmental Engineering, Universitat Autònoma de Barcelona, Bellaterra, Catalonia, 08193, Spain.
| | - Stephanie Heux
- TBI, Université de Toulouse, CNRS, INRAE, INSA, Toulouse, 31077, France
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10
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High-Throughput Expression of Inclusion Bodies on an Automated Platform. Methods Mol Biol 2023; 2617:31-47. [PMID: 36656515 DOI: 10.1007/978-1-0716-2930-7_3] [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
In bioprocesses, which target the production of recombinant proteins as inclusion bodies, the upstream process has a decisive influence on the downstream operations, especially regarding cell disruption, inclusion body purity and composition, and refolding yield. Therefore, optimization of the processes in fed-batch mode is a major issue, and screening for strains and process conditions are performed in highly labor, time and cost intensive shake flasks or multiwell plates. Thus, high-throughput experiments performed similar to the industrial operating conditions offer a possibility to develop efficient and robust upstream processes. We present here an automated platform for Escherichia coli fed-batch cultivations in parallelized minibioreactors. The platform allows execution of experiments under multiple conditions while allowing for real-time monitoring of critical process parameters and a controlled fermentation environment. By this, the main factors that affect yields and quality of inclusion bodies can be investigated, speeding up the development process significantly.
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11
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Walls LE, Otoupal P, Ledesma-Amaro R, Velasquez-Orta SB, Gladden JM, Rios-Solis L. Bioconversion of cellulose into bisabolene using Ruminococcus flavefaciens and Rhodosporidium toruloides. BIORESOURCE TECHNOLOGY 2023; 368:128216. [PMID: 36347482 DOI: 10.1016/j.biortech.2022.128216] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/07/2022] [Revised: 10/24/2022] [Accepted: 10/25/2022] [Indexed: 06/16/2023]
Abstract
In this study, organic acids were demonstrated as a promising carbon source for bisabolene production by the non-conventional yeast, Rhodosporidium toruloides, at microscale with a maximum titre of 1055 ± 7 mg/L. A 125-fold scale-up of the optimal process, enhanced bisabolene titres 2.5-fold to 2606 mg/L. Implementation of a pH controlled organic acid feeding strategy at this scale lead to a further threefold improvement in bisabolene titre to 7758 mg/L, the highest reported microbial titre. Finally, a proof-of-concept sequential bioreactor approach was investigated. Firstly, the cellulolytic bacterium Ruminococcus flavefaciens was employed to ferment cellulose, yielding 4.2 g/L of organic acids. R. toruloides was subsequently cultivated in the resulting supernatant, producing 318 ± 22 mg/L of bisabolene. This highlights the feasibility of a sequential bioprocess for the bioconversion of cellulose, into biojet fuel candidates. Future work will focus on enhancing organic acid yields and the use of real lignocellulosic feedstocks to further enhance bisabolene production.
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Affiliation(s)
- Laura E Walls
- Institute for Bioengineering, School of Engineering, University of Edinburgh, Edinburgh EH9 3BF, UK; Centre for Synthetic and Systems Biology (SynthSys), University of Edinburgh, Edinburgh EH9 3BF, UK
| | - Peter Otoupal
- Joint BioEnergy Institute, Lawrence Berkeley National Laboratory, Emeryville, CA 94608, USA; Agile BioFoundry, Department of Energy, Emeryville, CA 94608, USA; Biomaterials and Biomanufacturing Department, Sandia National Laboratories, Livermore, CA 94551, USA
| | - Rodrigo Ledesma-Amaro
- Department of Bioengineering and Imperial College Centre for Synthetic Biology, Imperial College London, London SW7 2AZ, UK
| | | | - John M Gladden
- Joint BioEnergy Institute, Lawrence Berkeley National Laboratory, Emeryville, CA 94608, USA; Agile BioFoundry, Department of Energy, Emeryville, CA 94608, USA; Biomaterials and Biomanufacturing Department, Sandia National Laboratories, Livermore, CA 94551, USA
| | - Leonardo Rios-Solis
- Institute for Bioengineering, School of Engineering, University of Edinburgh, Edinburgh EH9 3BF, UK; Centre for Synthetic and Systems Biology (SynthSys), University of Edinburgh, Edinburgh EH9 3BF, UK; School of Natural and Environmental Sciences, Molecular Biology and Biotechnology Division, Newcastle University, Newcastle Upon Tyne NE1 7RU, UK.
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12
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Kaneko H. Direct prediction of the batch time and process variable profiles using batch process data based on different batch times. Comput Chem Eng 2022. [DOI: 10.1016/j.compchemeng.2022.108072] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
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13
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Bromig L, von den Eichen N, Weuster-Botz D. Control of parallelized bioreactors I: dynamic scheduling software for efficient bioprocess management in high-throughput systems. Bioprocess Biosyst Eng 2022; 45:1927-1937. [PMID: 36255464 DOI: 10.1007/s00449-022-02798-6] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2022] [Accepted: 10/03/2022] [Indexed: 12/28/2022]
Abstract
The shift towards high-throughput technologies and automation in research and development in industrial biotechnology is highlighting the need for increased automation competence and specialized software solutions. Within bioprocess development, the trends towards miniaturization and parallelization of bioreactor systems rely on full automation and digital process control. Thus, mL-scale, parallel bioreactor systems require integration into liquid handling stations to perform a range of tasks stretching from substrate addition to automated sampling and sample analysis. To orchestrate these tasks, the authors propose a scheduling software to fully leverage the advantages of a state-of-the-art liquid handling station (LHS) and to enable improved process control and resource allocation. Fixed sequential order execution, the norm in LHS software, results in imperfect timing of essential operations like feeding or Ph control and execution intervals thereof, that are unknown a priori. However, the duration and control of, e.g., the feeding task and their frequency are of great importance for bioprocess control and the design of experiments. Hence, a software solution is presented that allows the orchestration of the respective operations through dynamic scheduling by external LHS control. With the proposed scheduling software, it is possible to define a dynamic process control strategy based on data-driven real-time prioritization and transparent, user-defined constraints. Drivers for a commercial 48 parallel bioreactor system and the related sensor equipment were developed using the SiLA 2 standard greatly simplifying the integration effort. Furthermore, this paper describes the experimental hardware and software setup required for the application use case presented in the second part.
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Affiliation(s)
- Lukas Bromig
- Chair of Biochemical Engineering, Technical University of Munich, Boltzmannstraße 15, 85748, Garching, Germany
| | - Nikolas von den Eichen
- Chair of Biochemical Engineering, Technical University of Munich, Boltzmannstraße 15, 85748, Garching, Germany
| | - Dirk Weuster-Botz
- Chair of Biochemical Engineering, Technical University of Munich, Boltzmannstraße 15, 85748, Garching, Germany.
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14
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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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15
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Fang Z, Lyu J, Li J, Li C, Zhang Y, Guo Y, Wang Y, Zhang Y, Chen K. Application of bioreactor technology for cell culture-based viral vaccine production: Present status and future prospects. Front Bioeng Biotechnol 2022; 10:921755. [PMID: 36017347 PMCID: PMC9395942 DOI: 10.3389/fbioe.2022.921755] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2022] [Accepted: 07/06/2022] [Indexed: 11/24/2022] Open
Abstract
Bioreactors are widely used in cell culture-based viral vaccine production, especially during the coronavirus disease 2019 (COVID-19) pandemic. In this context, the development and application of bioreactors can provide more efficient and cost-effective vaccine production to meet the global vaccine demand. The production of viral vaccines is inseparable from the development of upstream biological processes. In particular, exploration at the laboratory-scale is urgently required for further development. Therefore, it is necessary to evaluate the existing upstream biological processes, to enable the selection of pilot-scale conditions for academic and industrial scientists to maximize the yield and quality of vaccine development and production. Reviewing methods for optimizing the upstream process of virus vaccine production, this review discusses the bioreactor concepts, significant parameters and operational strategies related to large-scale amplification of virus. On this basis, a comprehensive analysis and evaluation of the various process optimization methods for the production of various viruses (SARS-CoV-2, Influenza virus, Tropical virus, Enterovirus, Rabies virus) in bioreactors is presented. Meanwhile, the types of viral vaccines are briefly introduced, and the established animal cell lines for vaccine production are described. In addition, it is emphasized that the co-development of bioreactor and computational biology is urgently needed to meet the challenges posed by the differences in upstream production scales between the laboratory and industry.
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Affiliation(s)
- Zhongbiao Fang
- Shulan International Medical College, Zhejiang Shuren University, Hangzhou, China
| | - Jingting Lyu
- Shulan International Medical College, Zhejiang Shuren University, Hangzhou, China
| | - Jianhua Li
- Zhejiang Provincial Center for Disease Control and Prevention, Hangzhou, China
| | - Chaonan Li
- Shulan International Medical College, Zhejiang Shuren University, Hangzhou, China
| | - Yuxuan Zhang
- Shulan International Medical College, Zhejiang Shuren University, Hangzhou, China
| | - Yikai Guo
- Shulan International Medical College, Zhejiang Shuren University, Hangzhou, China
| | - Ying Wang
- Shulan International Medical College, Zhejiang Shuren University, Hangzhou, China
- *Correspondence: Ying Wang, ; Yanjun Zhang, ; Keda Chen,
| | - Yanjun Zhang
- Zhejiang Provincial Center for Disease Control and Prevention, Hangzhou, China
- *Correspondence: Ying Wang, ; Yanjun Zhang, ; Keda Chen,
| | - Keda Chen
- Shulan International Medical College, Zhejiang Shuren University, Hangzhou, China
- *Correspondence: Ying Wang, ; Yanjun Zhang, ; Keda Chen,
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16
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Hansen S, Gumprecht A, Micheel L, Hennemann HG, Enzmann F, Blümke W. Implementation of Perforated Concentric Ring Walls Considerably Improves Gas-Liquid Mass Transfer of Shaken Bioreactors. Front Bioeng Biotechnol 2022; 10:894295. [PMID: 35646878 PMCID: PMC9135409 DOI: 10.3389/fbioe.2022.894295] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2022] [Accepted: 04/14/2022] [Indexed: 11/25/2022] Open
Abstract
Since their first use in the 1930s, shake flasks have been a widely used bioreactor type for screening and process development due to a number of advantages. However, the limited gas-liquid mass transfer capacities—resulting from practical operation limits regarding shaking frequency and filling volumes—are a major drawback. The common way to increase the gas-liquid mass transfer in shake flasks with the implementation of baffles is generally not recommended as it comes along with several severe disadvantages. Thus, a new design principle for shaken bioreactors that aims for improving the gas-liquid mass transfer without losing the positive characteristics of unbaffled shake flasks is introduced. The flasks consist of cylindrical glass vessels with implemented perforated concentric ring walls. The ring walls improve the gas-liquid mass transfer via the formation of additional liquid films on both of its sides, whereas the perforations allow for mixing between the compartments. Sulfite oxidation experiments revealed over 200% higher maximum oxygen transfer capacities (OTRmax) compared to conventional shake flasks. In batch cultivations of Escherichia coli BL21 in mineral media, unlimited growth until glucose depletion and oxygen transfer rates (OTR) of up to 138 mmol/L/h instead of an oxygen limitation at 57 mmol/L/h as in normal shake flasks under comparable conditions could be achieved. Even overflow metabolism could be prevented due to sufficient oxygen supply without the use of unconventional shaking conditions or oxygen enrichment. Therefore, we believe that the new perforated ring flask principle has a high potential to considerably improve biotechnological screening and process development steps.
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Affiliation(s)
- Sven Hansen
- Evonik Operations GmbH, Marl, Germany
- *Correspondence: Sven Hansen,
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