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Wang X, Yang Q, Haringa C, Wang Z, Chu J, Zhuang Y, Wang G. An industrial perspective on metabolic responses of Penicillium chrysogenum to periodic dissolved oxygen feast-famine cycles in a scale-down system. Biotechnol Bioeng 2024; 121:3076-3098. [PMID: 39382054 DOI: 10.1002/bit.28782] [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: 02/04/2024] [Revised: 04/16/2024] [Accepted: 06/12/2024] [Indexed: 10/10/2024]
Abstract
While traveling through different zones in large-scale bioreactors, microbes are most likely subjected to fluctuating dissolved oxygen (DO) conditions at the timescales of global circulation time. In this study, to mimic industrial-scale spatial DO gradients, we present a scale-down setup based on dynamic feast/famine regime (150 s) that leads to repetitive cycles with rapid changes in DO availability in glucose-limited chemostat cultures of Penicillium chrysogenum. Such DO feast/famine regime induced a stable and repetitive pattern with a reproducible metabolic response in time, and the dynamic response of intracellular metabolites featured specific differences in terms of both coverage and magnitude in comparison to other dynamic conditions, for example, substrate feast/famine cycles. Remarkably, intracellular sugar polyols were considerably increased as the hallmark metabolites along with a dynamic and higher redox state (NADH/NAD+) of the cytosol. Despite the increased availability of NADPH for penicillin production under the oscillatory DO conditions, this positive effect may be counteracted by the decreased ATP supply. Moreover, it is interesting to note that not only the penicillin productivity was reduced under such oscillating DO conditions, but also that of the unrecyclable byproduct ortho-hydroxyphenyl acetic acid and degeneration of penicillin productivity. Furthermore, dynamic flux profiles showed the most pronounced variations in central carbon metabolism, amino acid (AA) metabolism, energy metabolism and fatty acid metabolism upon the DO oscillation. Taken together, the metabolic responses of P. chrysogenum to DO gradients reported here are important for elucidating metabolic regulation mechanisms, improving bioreactor design and scale-up procedures as well as for constructing robust cell strains to cope with heterogenous industrial culture conditions.
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Affiliation(s)
- Xueting Wang
- State Key Laboratory of Bioreactor Engineering, East China University of Science and Technology (ECUST), Shanghai, People's Republic of China
| | - Qi Yang
- State Key Laboratory of Bioreactor Engineering, East China University of Science and Technology (ECUST), Shanghai, People's Republic of China
| | - Cees Haringa
- Department of Biotechnology, Delft University of Technology, Delft, The Netherlands
| | - Zejian Wang
- State Key Laboratory of Bioreactor Engineering, East China University of Science and Technology (ECUST), Shanghai, People's Republic of China
| | - Ju Chu
- State Key Laboratory of Bioreactor Engineering, East China University of Science and Technology (ECUST), Shanghai, People's Republic of China
- Qingdao Innovation Institute of East China University of Science and Technology, Qingdao, People's Republic of China
| | - Yingping Zhuang
- State Key Laboratory of Bioreactor Engineering, East China University of Science and Technology (ECUST), Shanghai, People's Republic of China
- Qingdao Innovation Institute of East China University of Science and Technology, Qingdao, People's Republic of China
| | - Guan Wang
- State Key Laboratory of Bioreactor Engineering, East China University of Science and Technology (ECUST), Shanghai, People's Republic of China
- Qingdao Innovation Institute of East China University of Science and Technology, Qingdao, People's Republic of China
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2
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Schulz-Mirbach H, Krüsemann JL, Andreadaki T, Nerlich JN, Mavrothalassiti E, Boecker S, Schneider P, Weresow M, Abdelwahab O, Paczia N, Dronsella B, Erb TJ, Bar-Even A, Klamt S, Lindner SN. Engineering new-to-nature biochemical conversions by combining fermentative metabolism with respiratory modules. Nat Commun 2024; 15:6725. [PMID: 39112480 PMCID: PMC11306353 DOI: 10.1038/s41467-024-51029-x] [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: 11/09/2023] [Accepted: 07/28/2024] [Indexed: 08/10/2024] Open
Abstract
Anaerobic microbial fermentations provide high product yields and are a cornerstone of industrial bio-based processes. However, the need for redox balancing limits the array of fermentable substrate-product combinations. To overcome this limitation, here we design an aerobic fermentative metabolism that allows the introduction of selected respiratory modules. These can use oxygen to re-balance otherwise unbalanced fermentations, hence achieving controlled respiro-fermentative growth. Following this design, we engineer and characterize an obligate fermentative Escherichia coli strain that aerobically ferments glucose to stoichiometric amounts of lactate. We then re-integrate the quinone-dependent glycerol 3-phosphate dehydrogenase and demonstrate glycerol fermentation to lactate while selectively transferring the surplus of electrons to the respiratory chain. To showcase the potential of this fermentation mode, we direct fermentative flux from glycerol towards isobutanol production. In summary, our design permits using oxygen to selectively re-balance fermentations. This concept is an advance freeing highly efficient microbial fermentation from the limitations imposed by traditional redox balancing.
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Affiliation(s)
- Helena Schulz-Mirbach
- Max Planck Institute for Terrestrial Microbiology, Karl-von-Frisch-Str. 10, 35043, Marburg, Germany
- Max Planck Institute of Molecular Plant Physiology, Am Mühlenberg 1, 14476, Potsdam-Golm, Germany
| | - Jan Lukas Krüsemann
- Max Planck Institute for Terrestrial Microbiology, Karl-von-Frisch-Str. 10, 35043, Marburg, Germany
- Max Planck Institute of Molecular Plant Physiology, Am Mühlenberg 1, 14476, Potsdam-Golm, Germany
- Department of Biochemistry, Charité Universitätsmedizin Berlin, corporate member of Freie Universität Berlin and Humboldt-Universität, Charitéplatz 1, 10117, Berlin, Germany
| | - Theofania Andreadaki
- Max Planck Institute of Molecular Plant Physiology, Am Mühlenberg 1, 14476, Potsdam-Golm, Germany
| | - Jana Natalie Nerlich
- Department of Biochemistry, Charité Universitätsmedizin Berlin, corporate member of Freie Universität Berlin and Humboldt-Universität, Charitéplatz 1, 10117, Berlin, Germany
| | - Eleni Mavrothalassiti
- Max Planck Institute of Molecular Plant Physiology, Am Mühlenberg 1, 14476, Potsdam-Golm, Germany
| | - Simon Boecker
- Max Planck Institute for Dynamics of Complex Technical Systems, Sandtorstraße 1, 39106, Magdeburg, Germany
- Berliner Hochschule für Technik (BHT), Seestr. 64, 13347, Berlin, Germany
| | - Philipp Schneider
- Max Planck Institute for Dynamics of Complex Technical Systems, Sandtorstraße 1, 39106, Magdeburg, Germany
| | - Moritz Weresow
- Max Planck Institute of Molecular Plant Physiology, Am Mühlenberg 1, 14476, Potsdam-Golm, Germany
| | - Omar Abdelwahab
- Department of Biochemistry, Charité Universitätsmedizin Berlin, corporate member of Freie Universität Berlin and Humboldt-Universität, Charitéplatz 1, 10117, Berlin, Germany
| | - Nicole Paczia
- Max Planck Institute for Terrestrial Microbiology, Karl-von-Frisch-Str. 10, 35043, Marburg, Germany
| | - Beau Dronsella
- Max Planck Institute for Terrestrial Microbiology, Karl-von-Frisch-Str. 10, 35043, Marburg, Germany
- Max Planck Institute of Molecular Plant Physiology, Am Mühlenberg 1, 14476, Potsdam-Golm, Germany
| | - Tobias J Erb
- Max Planck Institute for Terrestrial Microbiology, Karl-von-Frisch-Str. 10, 35043, Marburg, Germany
- Center for Synthetic Microbiology (SYNMIKRO), Karl-von-Frisch-Straße 14, 35043, Marburg, Germany
| | - Arren Bar-Even
- Max Planck Institute of Molecular Plant Physiology, Am Mühlenberg 1, 14476, Potsdam-Golm, Germany
| | - Steffen Klamt
- Max Planck Institute for Dynamics of Complex Technical Systems, Sandtorstraße 1, 39106, Magdeburg, Germany
| | - Steffen N Lindner
- Max Planck Institute of Molecular Plant Physiology, Am Mühlenberg 1, 14476, Potsdam-Golm, Germany.
- Department of Biochemistry, Charité Universitätsmedizin Berlin, corporate member of Freie Universität Berlin and Humboldt-Universität, Charitéplatz 1, 10117, Berlin, Germany.
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3
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Zhao SH, Ji XY, Yuan GZ, Cheng T, Liang HY, Liu SQ, Yang FY, Tang Y, Shi S. A Bibliometric Analysis of the Spatial Transcriptomics Literature from 2006 to 2023. Cell Mol Neurobiol 2024; 44:50. [PMID: 38856921 PMCID: PMC11164738 DOI: 10.1007/s10571-024-01484-3] [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: 11/08/2023] [Accepted: 05/28/2024] [Indexed: 06/11/2024]
Abstract
In recent years, spatial transcriptomics (ST) research has become a popular field of study and has shown great potential in medicine. However, there are few bibliometric analyses in this field. Thus, in this study, we aimed to find and analyze the frontiers and trends of this medical research field based on the available literature. A computerized search was applied to the WoSCC (Web of Science Core Collection) Database for literature published from 2006 to 2023. Complete records of all literature and cited references were extracted and screened. The bibliometric analysis and visualization were performed using CiteSpace, VOSviewer, Bibliometrix R Package software, and Scimago Graphica. A total of 1467 papers and reviews were included. The analysis revealed that the ST publication and citation results have shown a rapid upward trend over the last 3 years. Nature Communications and Nature were the most productive and most co-cited journals, respectively. In the comprehensive global collaborative network, the United States is the country with the most organizations and publications, followed closely by China and the United Kingdom. The author Joakim Lundeberg published the most cited paper, while Patrik L. Ståhl ranked first among co-cited authors. The hot topics in ST are tissue recognition, cancer, heterogeneity, immunotherapy, differentiation, and models. ST technologies have greatly contributed to in-depth research in medical fields such as oncology and neuroscience, opening up new possibilities for the diagnosis and treatment of diseases. Moreover, artificial intelligence and big data drive additional development in ST fields.
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Affiliation(s)
- Shu-Han Zhao
- Guang'an Men Hospital, China Academy of Chinese Medical Sciences, No. 5 Beixiange Street, Xicheng District, Beijing, 100053, People's Republic of China
- Beijing University of Chinese Medicine, No. 11, Beisanhuan East Road, Chaoyang District, Beijing, 100029, People's Republic of China
| | - Xin-Yu Ji
- Institute of Basic Research in Clinical Medicine, China Academy of Chinese Medical Sciences, No. 16 Nanxiaojie, Dongzhimennei Ave, Beijing, 100700, People's Republic of China
| | - Guo-Zhen Yuan
- Guang'an Men Hospital, China Academy of Chinese Medical Sciences, No. 5 Beixiange Street, Xicheng District, Beijing, 100053, People's Republic of China
| | - Tao Cheng
- Guang'an Men Hospital, China Academy of Chinese Medical Sciences, No. 5 Beixiange Street, Xicheng District, Beijing, 100053, People's Republic of China
| | - Hai-Yi Liang
- Beijing University of Chinese Medicine, No. 11, Beisanhuan East Road, Chaoyang District, Beijing, 100029, People's Republic of China
| | - Si-Qi Liu
- Beijing University of Chinese Medicine, No. 11, Beisanhuan East Road, Chaoyang District, Beijing, 100029, People's Republic of China
| | - Fu-Yi Yang
- Beijing University of Chinese Medicine, No. 11, Beisanhuan East Road, Chaoyang District, Beijing, 100029, People's Republic of China
| | - Yang Tang
- School of Chinese Medicine, Beijing University of Chinese Medicine, No. 11, Beisanhuan East Road, Chaoyang District, Beijing, 100029, People's Republic of China.
| | - Shuai Shi
- Guang'an Men Hospital, China Academy of Chinese Medical Sciences, No. 5 Beixiange Street, Xicheng District, Beijing, 100053, People's Republic of China.
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Reynoso-Cereceda GI, Valdez-Cruz NA, Pérez NO, Trujillo-Roldán MA. A comprehensive study of glucose and oxygen gradients in a scaled-down model of recombinant HuGM-CSF production in thermoinduced Escherichia coli fed-batch cultures. Prep Biochem Biotechnol 2024:1-12. [PMID: 38701182 DOI: 10.1080/10826068.2024.2347403] [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: 05/05/2024]
Abstract
The effect of gradients of elevated glucose and low dissolved oxygen in the addition zone of fed-batch E. coli thermoinduced recombinant high cell density cultures can be evaluated through two-compartment scale-down models. Here, glucose was fed in the inlet of a plug flow bioreactor (PFB) connected to a stirred tank bioreactor (STB). E. coli cells diminished growth from 48.2 ± 2.2 g/L in the stage of RP production if compared to control (STB) with STB-PFB experiments, when residence time inside the PFB was 25 s (34.1 ± 3.5 g/L) and 40 s (25.6 ± 5.1 g/L), respectively. The recombinant granulocyte-macrophage colony-stimulating factor (rHuGM-CSF) production decreased from 34 ± 7% of RP in inclusion bodies (IB) in control cultures to 21 ± 8%, and 7 ± 4% during the thermoinduction production phase when increasing residence time inside the PFB to 25 s and 40 s, respectively. This, along with the accumulation of acetic and formic acid (up to 4 g/L), indicates metabolic redirection of central carbon routes through metabolic flow and mixed acid fermentation. Special care must be taken when producing a recombinant protein in heat-induced E. coli, because the yield and productivity of the protein decreases as the size of the bioreactors increases, especially if they are carried at high cell density.
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Affiliation(s)
- Greta I Reynoso-Cereceda
- Departamento de Biología Molecular y Biotecnología, Instituto de Investigaciones Biomédicas, Universidad Nacional Autónoma de México, Cd. Universitaria, Coyoacán, Ciudad de México, México
- Posgrado en Ciencias Biomédicas, Universidad Nacional Autónoma de México, México. Unidad de Posgrado, CDMX, México
| | - Norma A Valdez-Cruz
- Departamento de Biología Molecular y Biotecnología, Instituto de Investigaciones Biomédicas, Universidad Nacional Autónoma de México, Cd. Universitaria, Coyoacán, Ciudad de México, México
- Centro de Nanociencias y Nanotecnología, Universidad Nacional Autónoma de México, Baja California, Mexico
| | - Nestor O Pérez
- Probiomed S.A. de C.V. Planta Tenancingo, Cruce de Carreteras Acatzingo- Zumpahuacan SN, Tenancingo, México
| | - Mauricio A Trujillo-Roldán
- Departamento de Biología Molecular y Biotecnología, Instituto de Investigaciones Biomédicas, Universidad Nacional Autónoma de México, Cd. Universitaria, Coyoacán, Ciudad de México, México
- Centro de Nanociencias y Nanotecnología, Universidad Nacional Autónoma de México, Baja California, Mexico
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Cortada-Garcia J, Haggarty J, Moses T, Daly R, Alison Arnold S, Burgess K. On-line untargeted metabolomics monitoring of an E. coli succinate fermentation process. Biotechnol Bioeng 2022; 119:2757-2769. [PMID: 35798686 PMCID: PMC9541951 DOI: 10.1002/bit.28173] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2022] [Accepted: 06/19/2022] [Indexed: 11/08/2022]
Abstract
The real‐time monitoring of metabolites (RTMet) is instrumental for the industrial production of biobased fermentation products. This study shows the first application of untargeted on‐line metabolomics for the monitoring of undiluted fermentation broth samples taken automatically from a 5 L bioreactor every 5 min via flow injection mass spectrometry. The travel time from the bioreactor to the mass spectrometer was 30 s. Using mass spectrometry allows, on the one hand, the direct monitoring of targeted key process compounds of interest and, on the other hand, provides information on hundreds of additional untargeted compounds without requiring previous calibration data. In this study, this technology was applied in an Escherichia coli succinate fermentation process and 886 different m/z signals were monitored, including key process compounds (glucose, succinate, and pyruvate), potential biomarkers of biomass formation such as (R)‐2,3‐dihydroxy‐isovalerate and (R)‐2,3‐dihydroxy‐3‐methylpentanoate and compounds from the pentose phosphate pathway and nucleotide metabolism, among others. The main advantage of the RTMet technology is that it allows the monitoring of hundreds of signals without the requirement of developing partial least squares regression models, making it a perfect tool for bioprocess monitoring and for testing many different strains and process conditions for bioprocess development.
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Affiliation(s)
- Joan Cortada-Garcia
- Institute of Quantitative Biology, Biochemistry and Biotechnology, School of Biological Sciences, University of Edinburgh, Edinburgh, EH8 9AB, United Kingdom
| | - Jennifer Haggarty
- Institute of Infection, Immunity and Inflammation, Glasgow Polyomics, University of Glasgow, Glasgow, G61 1QH, United Kingdom
| | - Tessa Moses
- EdinOmics, SynthSys - Centre for Synthetic and Systems Biology, School of Biological Sciences, The University of Edinburgh, Edinburgh, EH9 3BF, UK
| | - Rónán Daly
- Institute of Infection, Immunity and Inflammation, Glasgow Polyomics, University of Glasgow, Glasgow, G61 1QH, United Kingdom
| | - S Alison Arnold
- Ingenza Ltd., Roslin Innovation Centre, Roslin, EH25 9RG, United Kingdom
| | - Karl Burgess
- Institute of Quantitative Biology, Biochemistry and Biotechnology, School of Biological Sciences, University of Edinburgh, Edinburgh, EH8 9AB, United Kingdom
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6
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Impact of Elevated Levels of Dissolved CO2 on Performance and Proteome Response of an Industrial 2′-Fucosyllactose Producing Escherichia coli Strain. Microorganisms 2022; 10:microorganisms10061145. [PMID: 35744663 PMCID: PMC9228177 DOI: 10.3390/microorganisms10061145] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2022] [Revised: 05/17/2022] [Accepted: 05/24/2022] [Indexed: 11/23/2022] Open
Abstract
Large-scale microbial industrial fermentations have significantly higher absolute pressure and dissolved CO2 concentrations than otherwise comparable laboratory-scale processes. Yet the effect of increased dissolved CO2 (dCO2) levels is rarely addressed in the literature. In the current work, we have investigated the impact of industrial levels of dCO2 (measured as the partial pressure of CO2, pCO2) in an Escherichia coli-based fed-batch process producing the human milk oligosaccharide 2′-fucosyllactose (2′-FL). The study evaluated the effect of high pCO2 levels in both carbon-limited (C-limited) and carbon/nitrogen-limited (C/N-limited) fed-batch processes. High-cell density cultures were sparged with 10%, 15%, 20%, or 30% CO2 in the inlet air to cover and exceed the levels observed in the industrial scale process. While the 10% enrichment was estimated to achieve similar or higher pCO2 levels as the large-scale fermentation it did not impact the performance of the process. The product and biomass yields started being affected above 15% CO2 enrichment, while 30% impaired the cultures completely. Quantitative proteomics analysis of the C-limited process showed that 15% CO2 enrichment affected the culture on the protein level, but to a much smaller degree than expected. A more significant impact was seen in the dual C/N limited process, which likely stemmed from the effect pCO2 had on nitrogen availability. The results demonstrated that microbial cultures can be seriously affected by elevated CO2 levels, albeit at higher levels than expected.
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Yang Q, Lin W, Xu J, Guo N, Zhao J, Wang G, Wang Y, Chu J, Wang G. Changes in Oxygen Availability during Glucose-Limited Chemostat Cultivations of Penicillium chrysogenum Lead to Rapid Metabolite, Flux and Productivity Responses. Metabolites 2022; 12:metabo12010045. [PMID: 35050169 PMCID: PMC8780904 DOI: 10.3390/metabo12010045] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2021] [Revised: 01/02/2022] [Accepted: 01/03/2022] [Indexed: 02/01/2023] Open
Abstract
Bioreactor scale-up from the laboratory scale to the industrial scale has always been a pivotal step in bioprocess development. However, the transition of a bioeconomy from innovation to commercialization is often hampered by performance loss in titer, rate and yield. These are often ascribed to temporal variations of substrate and dissolved oxygen (for instance) in the environment, experienced by microorganisms at the industrial scale. Oscillations in dissolved oxygen (DO) concentration are not uncommon. Furthermore, these fluctuations can be exacerbated with poor mixing and mass transfer limitations, especially in fermentations with filamentous fungus as the microbial cell factory. In this work, the response of glucose-limited chemostat cultures of an industrial Penicillium chrysogenum strain to different dissolved oxygen levels was assessed under both DO shift-down (60% → 20%, 10% and 5%) and DO ramp-down (60% → 0% in 24 h) conditions. Collectively, the results revealed that the penicillin productivity decreased as the DO level dropped down below 20%, while the byproducts, e.g., 6-oxopiperidine-2-carboxylic acid (OPC) and 6-aminopenicillanic acid (6APA), accumulated. Following DO ramp-down, penicillin productivity under DO shift-up experiments returned to its maximum value in 60 h when the DO was reset to 60%. The result showed that a higher cytosolic redox status, indicated by NADH/NAD+, was observed in the presence of insufficient oxygen supply. Consistent with this, flux balance analysis indicated that the flux through the glyoxylate shunt was increased by a factor of 50 at a DO value of 5% compared to the reference control, favoring the maintenance of redox status. Interestingly, it was observed that, in comparison with the reference control, the penicillin productivity was reduced by 25% at a DO value of 5% under steady state conditions. Only a 14% reduction in penicillin productivity was observed as the DO level was ramped down to 0. Furthermore, intracellular levels of amino acids were less sensitive to DO levels at DO shift-down relative to DO ramp-down conditions; this difference could be caused by different timescales between turnover rates of amino acid pools (tens of seconds to minutes) and DO switches (hours to days at steady state and minutes to hours at ramp-down). In summary, this study showed that changes in oxygen availability can lead to rapid metabolite, flux and productivity responses, and dynamic DO perturbations could provide insight into understanding of metabolic responses in large-scale bioreactors.
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Abstract
Phenol acts as a pollutant even at very low concentrations in water. It is classified as one of the main priority pollutants that need to be treated before being discharged into the environment. If phenolic-based compounds are discharged into the environment without any treatments, they pose serious health risks to humans, animals, and aquatic systems. This review emphasizes the development of advanced technologies for phenol removal. Several technologies have been developed to remove phenol to prevent environmental pollution, such as biological treatment, conventional technologies, and advanced technologies. Among these technologies, heterogeneous catalytic ozonation has received great attention as an effective, environmentally friendly, and sustainable process for the degradation of phenolic-based compounds, which can overcome some of the disadvantages of other technologies. Recently, zeolites have been widely used as one of the most promising catalysts in the heterogeneous catalytic ozonation process to degrade phenol and its derivatives because they provide a large specific surface area, high active site density, and excellent shape-selective properties as a catalyst. Rational design of zeolite-based catalysts with various synthesis methods and pre-defined physiochemical properties including framework, ratio of silica to alumina (SiO2/Al2O3), specific surface area, size, and porosity, must be considered to understand the reaction mechanism of phenol removal. Ultimately, recommendations for future research related to the application of catalytic ozonation technology using a zeolite-based catalyst for phenol removal are also described.
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Ziegler M, Zieringer J, Döring CL, Paul L, Schaal C, Takors R. Engineering of a robust Escherichia coli chassis and exploitation for large-scale production processes. Metab Eng 2021; 67:75-87. [PMID: 34098100 DOI: 10.1016/j.ymben.2021.05.011] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2020] [Revised: 05/30/2021] [Accepted: 05/31/2021] [Indexed: 11/28/2022]
Abstract
In large-scale bioprocesses microbes are exposed to heterogeneous substrate availability reducing the overall process performance. A series of deletion strains was constructed from E. coli MG1655 aiming for a robust phenotype in heterogeneous fermentations with transient starvation. Deletion targets were hand-picked based on a list of genes derived from previous large-scale simulation runs. Each gene deletion was conducted on the premise of strict neutrality towards growth parameters in glucose minimal medium. The final strain of the series, named E. coli RM214, was cultivated continuously in an STR-PFR (stirred tank reactor - plug flow reactor) scale-down reactor. The scale-down reactor system simulated repeated passages through a glucose starvation zone. When exposed to nutrient gradients, E. coli RM214 had a significantly lower maintenance coefficient than E. coli MG1655 (Δms = 0.038 gGlucose/gCDW/h, p < 0.05). In an exemplary protein production scenario E. coli RM214 remained significantly more productive than E. coli MG1655 reaching 44% higher eGFP yield after 28 h of STR-PFR cultivation. This study developed E. coli RM214 as a robust chassis strain and demonstrated the feasibility of engineering microbial hosts for large-scale applications.
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Affiliation(s)
- Martin Ziegler
- University of Stuttgart - Institute of Biochemical Engineering, Allmandring 31, 70569, Stuttgart, Germany.
| | - Julia Zieringer
- University of Stuttgart - Institute of Biochemical Engineering, Allmandring 31, 70569, Stuttgart, Germany.
| | - Clarissa-Laura Döring
- University of Stuttgart - Institute of Biochemical Engineering, Allmandring 31, 70569, Stuttgart, Germany.
| | - Liv Paul
- University of Stuttgart - Institute of Biochemical Engineering, Allmandring 31, 70569, Stuttgart, Germany.
| | - Christoph Schaal
- University of Stuttgart - Institute of Biochemical Engineering, Allmandring 31, 70569, Stuttgart, Germany.
| | - Ralf Takors
- University of Stuttgart - Institute of Biochemical Engineering, Allmandring 31, 70569, Stuttgart, Germany.
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10
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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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11
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Seidel S, Maschke RW, Werner S, Jossen V, Eibl D. Oxygen Mass Transfer in Biopharmaceutical Processes: Numerical and Experimental Approaches. CHEM-ING-TECH 2020. [DOI: 10.1002/cite.202000179] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Affiliation(s)
- Stefan Seidel
- Zurich University of Applied Sciences School of Life Sciences and Facility Management Institute of Chemistry and Biotechnology Grüentalstrasse 14 8820 Wädenswil Switzerland
| | - Rüdiger W. Maschke
- Zurich University of Applied Sciences School of Life Sciences and Facility Management Institute of Chemistry and Biotechnology Grüentalstrasse 14 8820 Wädenswil Switzerland
| | - Sören Werner
- Zurich University of Applied Sciences School of Life Sciences and Facility Management Institute of Chemistry and Biotechnology Grüentalstrasse 14 8820 Wädenswil Switzerland
| | - Valentin Jossen
- Zurich University of Applied Sciences School of Life Sciences and Facility Management Institute of Chemistry and Biotechnology Grüentalstrasse 14 8820 Wädenswil Switzerland
| | - Dieter Eibl
- Zurich University of Applied Sciences School of Life Sciences and Facility Management Institute of Chemistry and Biotechnology Grüentalstrasse 14 8820 Wädenswil Switzerland
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12
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Understanding gradients in industrial bioreactors. Biotechnol Adv 2020; 46:107660. [PMID: 33221379 DOI: 10.1016/j.biotechadv.2020.107660] [Citation(s) in RCA: 31] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2020] [Revised: 10/22/2020] [Accepted: 11/14/2020] [Indexed: 01/07/2023]
Abstract
Gradients in industrial bioreactors have attracted substantial research attention since exposure to fluctuating environmental conditions has been shown to lead to changes in the metabolome, transcriptome as well as population heterogeneity in industrially relevant microorganisms. Such changes have also been found to impact key process parameters like the yield on substrate and the productivity. Hence, understanding gradients is important from both the academic and industrial perspectives. In this review the causes of gradients are outlined, along with their impact on microbial physiology. Quantifying the impact of gradients requires a detailed understanding of both fluid flow inside industrial equipment and microbial physiology. This review critically examines approaches used to investigate gradients including large-scale experimental work, computational methods and scale-down approaches. Avenues for future work have been highlighted, particularly the need for further coordinated development of both in silico and experimental tools which can be used to further the current understanding of gradients in industrial equipment.
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13
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Efficient biosynthesis of polysaccharide welan gum in heat shock protein-overproducing Sphingomonas sp. via temperature-dependent strategy. Bioprocess Biosyst Eng 2020; 44:247-257. [PMID: 32944865 DOI: 10.1007/s00449-020-02438-x] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2020] [Accepted: 08/26/2020] [Indexed: 10/23/2022]
Abstract
Cell growth and product formation are two critical processes in polysaccharide welan biosynthesis, but the conflict between them is often encountered. In this study, a temperature-dependent strategy was designed for two-stage welan production through overexpressing heat shock proteins in Sphingomonas sp. The first stage was cell growth phase with higher TCA cycle activity at 42 °C; the second stage was welan formation phase with higher precursor synthesis pathway activity at 37 °C. The highest welan concentration 37.5 g/L was achieved after two-stage process. Ultimately, this strategy accumulated welan yield of 79.2 g/100 g glucose and productivity of 0.62 g/L/h at 60 h, which were the best reported results so far. The duration of fermentation was shortened. Besides, rheological behavior of welan gum solutions remained stable at wide range of temperature, pH, and NaCl. These results indicated that this approach efficiently improved welan synthesis.
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14
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Wehrs M, Thompson MG, Banerjee D, Prahl JP, Morella NM, Barcelos CA, Moon J, Costello Z, Keasling JD, Shih PM, Tanjore D, Mukhopadhyay A. Investigation of Bar-seq as a method to study population dynamics of Saccharomyces cerevisiae deletion library during bioreactor cultivation. Microb Cell Fact 2020; 19:167. [PMID: 32811554 PMCID: PMC7437010 DOI: 10.1186/s12934-020-01423-z] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2020] [Accepted: 08/11/2020] [Indexed: 12/15/2022] Open
Abstract
Background Despite the latest advancements in metabolic engineering for genome editing and characterization of host performance, the successful development of robust cell factories used for industrial bioprocesses and accurate prediction of the behavior of microbial systems, especially when shifting from laboratory-scale to industrial conditions, remains challenging. To increase the probability of success of a scale-up process, data obtained from thoroughly performed studies mirroring cellular responses to typical large-scale stimuli may be used to derive crucial information to better understand potential implications of large-scale cultivation on strain performance. This study assesses the feasibility to employ a barcoded yeast deletion library to assess genome-wide strain fitness across a simulated industrial fermentation regime and aims to understand the genetic basis of changes in strain physiology during industrial fermentation, and the corresponding roles these genes play in strain performance. Results We find that mutant population diversity is maintained through multiple seed trains, enabling large scale fermentation selective pressures to act upon the community. We identify specific deletion mutants that were enriched in all processes tested in this study, independent of the cultivation conditions, which include MCK1, RIM11, MRK1, and YGK3 that all encode homologues of mammalian glycogen synthase kinase 3 (GSK-3). Ecological analysis of beta diversity between all samples revealed significant population divergence over time and showed feed specific consequences of population structure. Further, we show that significant changes in the population diversity during fed-batch cultivations reflect the presence of significant stresses. Our observations indicate that, for this yeast deletion collection, the selection of the feeding scheme which affects the accumulation of the fermentative by-product ethanol impacts the diversity of the mutant pool to a higher degree as compared to the pH of the culture broth. The mutants that were lost during the time of most extreme population selection suggest that specific biological processes may be required to cope with these specific stresses. Conclusions Our results demonstrate the feasibility of Bar-seq to assess fermentation associated stresses in yeast populations under industrial conditions and to understand critical stages of a scale-up process where variability emerges, and selection pressure gets imposed. Overall our work highlights a promising avenue to identify genetic loci and biological stress responses required for fitness under industrial conditions.
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Affiliation(s)
- Maren Wehrs
- Biological Systems and Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, CA, 94720, USA.,Joint BioEnergy Institute, Lawrence Berkeley National Laboratory, Emeryville, CA, 94608, USA
| | - Mitchell G Thompson
- Biological Systems and Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, CA, 94720, USA.,Joint BioEnergy Institute, Lawrence Berkeley National Laboratory, Emeryville, CA, 94608, USA.,Department of Plant and Microbial Biology, University of California, Berkeley, CA, 94720, USA
| | - Deepanwita Banerjee
- Biological Systems and Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, CA, 94720, USA.,Joint BioEnergy Institute, Lawrence Berkeley National Laboratory, Emeryville, CA, 94608, USA
| | - Jan-Philip Prahl
- Biological Systems and Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, CA, 94720, USA.,Advanced Biofuels and Bioproducts Process Development Unit, Lawrence Berkeley National Laboratory, Emeryville, CA, 94608, USA
| | - Norma M Morella
- Fred Hutchinson Cancer Research Center, Seattle, WA, 98109, USA
| | - Carolina A Barcelos
- Biological Systems and Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, CA, 94720, USA.,Advanced Biofuels and Bioproducts Process Development Unit, Lawrence Berkeley National Laboratory, Emeryville, CA, 94608, USA
| | - Jadie Moon
- Biological Systems and Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, CA, 94720, USA.,Joint BioEnergy Institute, Lawrence Berkeley National Laboratory, Emeryville, CA, 94608, USA
| | - Zak Costello
- Biological Systems and Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, CA, 94720, USA.,Joint BioEnergy Institute, Lawrence Berkeley National Laboratory, Emeryville, CA, 94608, USA.,Department of Energy Agile BioFoundry, Emeryville, CA, 94608, USA
| | - Jay D Keasling
- Biological Systems and Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, CA, 94720, USA.,Joint BioEnergy Institute, Lawrence Berkeley National Laboratory, Emeryville, CA, 94608, USA.,Department of Bioengineering, University of California, Berkeley, CA, 94720, USA.,Department of Chemical and Biomolecular Engineering, University of California, Berkeley, CA, 94720, USA.,Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, DK 2970, Horsholm, Denmark.,Synthetic Biochemistry Center, Institute for Synthetic Biology, Shenzhen Institutes for Advanced Technologies, Shenzhen, China
| | - Patrick M Shih
- Joint BioEnergy Institute, Lawrence Berkeley National Laboratory, Emeryville, CA, 94608, USA.,Environmental Genomics and Systems Biology Division, Lawrence Berkeley National Laboratory, Berkeley, CA, 94720, USA.,Department of Plant Biology, University of California-Davis, Davis, CA, 95616, USA
| | - Deepti Tanjore
- Biological Systems and Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, CA, 94720, USA. .,Advanced Biofuels and Bioproducts Process Development Unit, Lawrence Berkeley National Laboratory, Emeryville, CA, 94608, USA.
| | - Aindrila Mukhopadhyay
- Biological Systems and Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, CA, 94720, USA. .,Joint BioEnergy Institute, Lawrence Berkeley National Laboratory, Emeryville, CA, 94608, USA. .,Environmental Genomics and Systems Biology Division, Lawrence Berkeley National Laboratory, Berkeley, CA, 94720, USA.
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15
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Understanding high ε-poly-l-lysine production by Streptomyces albulus using pH shock strategy in the level of transcriptomics. ACTA ACUST UNITED AC 2019; 46:1781-1792. [DOI: 10.1007/s10295-019-02240-z] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2019] [Accepted: 09/26/2019] [Indexed: 10/25/2022]
Abstract
Abstract
ε-Poly-l-lysine (ε-PL) is a natural food preservative, which exhibits antimicrobial activity against a wide spectra of microorganisms. The production of ε-PL was significantly enhanced by pH shock in our previous study, but the underlying mechanism is poorly understood. According to transcriptional and physiological analyses in this study, the mprA/B and pepD signal transduction system was first proved to be presented and activated in Streptomyces albulus M-Z18 by pH shock, which positively regulated the transcription of ε-PL synthetase (Pls) gene and enhanced the Pls activity during fermentation. Furthermore, pH shock changed the ratio of unsaturation to saturation fatty acid in the membrane through up-regulating the transcription of fatty acid desaturase genes (SAZ_RS14940, SAZ_RS14945). In addition, pH shock also enhanced the transcription of cytochrome c oxidase (SAZ_RS15070, SAZ_RS15075), ferredoxin reductase (SAZ_RS34975) and iron sulfur protein (SAZ_RS31410) genes, and finally resulted in the improvement of cell respiratory activity. As a result, pH shock was considered to influence a wide range of proteins including regulators, fatty acid desaturase, respiratory chain component, and ATP-binding cassette transporter during fermentation. These combined influences might contribute to enhanced ε-PL productivity with pH shock.
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16
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Pan L, Chen X, Wang K, Mao Z. A temporal transcriptomic dynamics study reveals the reason of enhanced ε-poly-L-lysine production in Streptomyces albulus M-Z18 by pH shock. Process Biochem 2019. [DOI: 10.1016/j.procbio.2019.07.012] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 01/22/2023]
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17
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Jaén KE, Velázquez D, Sigala JC, Lara AR. Design of a microaerobically inducible replicon for high-yield plasmid DNA production. Biotechnol Bioeng 2019; 116:2514-2525. [PMID: 31232477 DOI: 10.1002/bit.27091] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2019] [Revised: 06/07/2019] [Accepted: 06/10/2019] [Indexed: 01/11/2023]
Abstract
A pUC-derived replicon inducible by oxygen limitation was designed and tested in fed-batch cultures of Escherichia coli. It included the addition of a second inducible copy of rnaII, the positive replication control element. The rnaII gene was expressed from Ptrc and cloned into pUC18 to test the hypothesis that the ratio of the positive control molecule RNAII to the negative control element, RNAI, was the determinant of plasmid copy number per chromosome (PCN). The construct was evaluated in several E. coli strains. Evaluations of the RNAII/RNAI ratio, PCN and plasmid yield normalized to biomass (YpDNA/X ) were performed and the initial hypothesis was probed. Furthermore, in high cell-density cultures in shake flasks, an outstanding amount of 126 mg/L of plasmid was produced. The microaerobically inducible plasmid was obtained by cloning the rnaII gene under the control of the oxygen-responsive Vitreoscilla stercoraria hemoglobin promoter. For this plasmid, but not for pUC18, the RNAII/RNAI ratio, PCN and YpDNA/X efficiently increased after the shift to the microaerobic regime in fed-batch cultures in a 1 L bioreactor. The YpDNA/X of the inducible plasmid reached 12 mg/g at the end of the fed-batch but the original pUC18 only reached ca. 6 mg/g. The proposed plasmid is a valuable alternative for the operation and scale-up of plasmid DNA production processes in which mass transfer limitations will not represent an issue.
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Affiliation(s)
- Karim E Jaén
- Departamento de Procesos y Tecnología, Universidad Autónoma Metropolitana-Cuajimalpa, Mexico City, Mexico
| | - Daniela Velázquez
- Departamento de Procesos y Tecnología, Universidad Autónoma Metropolitana-Cuajimalpa, Mexico City, Mexico
| | - Juan-Carlos Sigala
- Departamento de Procesos y Tecnología, Universidad Autónoma Metropolitana-Cuajimalpa, Mexico City, Mexico
| | - Alvaro R Lara
- Departamento de Procesos y Tecnología, Universidad Autónoma Metropolitana-Cuajimalpa, Mexico City, Mexico
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18
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Efficacy of medium chain-length polyhydroxyalkanoate biosynthesis from different biochemical pathways under oxygen-limited conditions using Pseudomonas putida LS46. Process Biochem 2019. [DOI: 10.1016/j.procbio.2019.04.013] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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19
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Restrepo-Pineda S, Bando-Campos CG, Valdez-Cruz NA, Trujillo-Roldán MA. Recombinant production of ESAT-6 antigen in thermoinducible Escherichia coli: the role of culture scale and temperature on metabolic response, expression of chaperones, and architecture of inclusion bodies. Cell Stress Chaperones 2019; 24:777-792. [PMID: 31165436 PMCID: PMC6629757 DOI: 10.1007/s12192-019-01006-x] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2018] [Revised: 05/01/2019] [Accepted: 05/06/2019] [Indexed: 12/31/2022] Open
Abstract
The heat-inducible expression system has been widely used to produce recombinant proteins in Escherichia coli. However, the rise in temperature affects cell growth, activates the bacterial Heat-Shock Response (HSR), and promotes the formation of insoluble protein aggregates known as inclusion bodies (IBs). In this work, we evaluate the effect of the culture scale (shake flasks and bioreactors) and induction temperature (39 and 42 °C) on the kinetic behavior of thermoinducible recombinant E. coli ATCC 53606 producing rESAT-6 (6-kDa early-secretory antigenic target from Mycobacterium tuberculosis), compared with cultures grown at 30 °C (without induction). Also, the expression of the major E. coli chaperones (DnaK and GroEL) was analyzed. We found that almost twice maximum biomass and rESAT-6 production were obtained in bioreactors (~ 3.29 g/L of biomass and ~ 0.27 g/L of rESAT-6) than in shake flasks (~ 1.41 g/L of biomass and ~ 0.14 g/L of rESAT-6) when induction was carried out at 42 °C, but similar amounts of rESAT-6 were obtained from cultures induced at 39 °C (~ 0.14 g/L). In all thermo-induced conditions, rESAT-6 was trapped in IBs. Furthermore, DnaK was preferably expressed in the soluble fraction, while GroEL was present in IBs. Importantly, IBs formed at 39 °C, in both shake flasks and bioreactors, were more susceptible to degradation by proteinase-K, indicating a lower amyloid content compared to IBs formed at 42 °C. Our work presents evidence that the culture scale and the induction temperature modify the E. coli metabolic response, expression of chaperones, and structure of the IBs during rESAT-6 protein production in a thermoinducible system.
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Affiliation(s)
- Sara Restrepo-Pineda
- Programa de Investigación de Producción de Biomoléculas, Unidad de Bioprocesos, Departamento de Biología Molecular y Biotecnología, Instituto de Investigaciones Biomédicas, Universidad Nacional Autónoma de México, AP. 70228, CP. 04510 Ciudad de México, Mexico
| | - Carlos G. Bando-Campos
- Programa de Investigación de Producción de Biomoléculas, Departamento de Biología Molecular y Biotecnología, Instituto de Investigaciones Biomédicas, Universidad Nacional Autónoma de México, AP. 70228, 04510 Ciudad de México, CP Mexico
| | - Norma A. Valdez-Cruz
- Programa de Investigación de Producción de Biomoléculas, Departamento de Biología Molecular y Biotecnología, Instituto de Investigaciones Biomédicas, Universidad Nacional Autónoma de México, AP. 70228, 04510 Ciudad de México, CP Mexico
| | - Mauricio A. Trujillo-Roldán
- Programa de Investigación de Producción de Biomoléculas, Unidad de Bioprocesos, Departamento de Biología Molecular y Biotecnología, Instituto de Investigaciones Biomédicas, Universidad Nacional Autónoma de México, AP. 70228, CP. 04510 Ciudad de México, Mexico
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20
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Heins AL, Lundin L, Nunes I, Gernaey KV, Sørensen SJ, Lantz AE. The effect of acetate on population heterogeneity in different cellular characteristics of Escherichia coli in aerobic batch cultures. Biotechnol Prog 2019; 35:e2796. [PMID: 30816011 DOI: 10.1002/btpr.2796] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2018] [Revised: 01/07/2019] [Accepted: 02/22/2019] [Indexed: 01/14/2023]
Abstract
Acetate as the major by-product in industrial-scale bioprocesses with Escherichia coli is found to decrease process efficiency as well as to be toxic to cells, which has several effects like a significant induction of cellular stress responses. However, the underlying phenomena are poorly explored. Therefore, we studied time-resolved population heterogeneity of the E. coli growth reporter strain MG1655/pGS20PrrnBGFPAAV expressing destabilized green fluorescent protein during batch growth on acetate and glucose as sole carbon sources. Additionally, we applied five fluorescent stains targeting different cellular properties (viability as well as metabolic and respiratory activity). Quantitative analysis of flow cytometry data verified that bacterial populations in the bioreactor are more heterogeneous in growth as well as stronger metabolically challenged during growth on acetate as sole carbon source, compared to growth on glucose or acetate after diauxic shift. Interestingly, with acetate as sole carbon source, significant subpopulations were found with some cells that seem to be more robust than the rest of the population. In conclusion, following batch cultures population heterogeneity was evident in all measured parameters. Our approach enabled a deeper study of heterogeneity during growth on the favored substrate glucose as well as on the toxic by-product acetate. Using a combination of activity fluorescent dyes proved to be an accurate and fast alternative as well as a supplement to the use of a reporter strain. However, the choice of combination of stains should be well considered depending on which population traits to aim for.
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Affiliation(s)
- Anna-Lena Heins
- Department of Chemical and Biochemical Engineering, Technical University of Denmark, Kongens Lyngby, Denmark.,Institute of Biochemical Engineering, Technical University of Munich, Garching, Germany
| | - Luisa Lundin
- Department of Biology, Section of Microbiology, University of Copenhagen, Copenhagen, Denmark.,Division of Scientific Support, Becton-Dickison biosciences, Erembodegem, Belgium
| | - Inês Nunes
- Department of Biology, Section of Microbiology, University of Copenhagen, Copenhagen, Denmark
| | - Krist V Gernaey
- Department of Chemical and Biochemical Engineering, Technical University of Denmark, Kongens Lyngby, Denmark
| | - Søren J Sørensen
- Department of Biology, Section of Microbiology, University of Copenhagen, Copenhagen, Denmark
| | - Anna Eliasson Lantz
- Department of Chemical and Biochemical Engineering, Technical University of Denmark, Kongens Lyngby, Denmark
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21
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Kaboré AK, Delaunay S, Blanchard F, Guedon E, Fick M, Olmos E. Study and modeling of fluctuating dissolved oxygen concentration impact on Corynebacterium glutamicum growth in a scale-down bioreactor. Process Biochem 2019. [DOI: 10.1016/j.procbio.2018.10.016] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
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22
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Yu JL, Qian ZG, Zhong JJ. Advances in bio-based production of dicarboxylic acids longer than C4. Eng Life Sci 2018; 18:668-681. [PMID: 32624947 DOI: 10.1002/elsc.201800023] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2018] [Revised: 05/18/2018] [Accepted: 06/13/2018] [Indexed: 12/15/2022] Open
Abstract
Growing concerns of environmental pollution and fossil resource shortage are major driving forces for bio-based production of chemicals traditionally from petrochemical industry. Dicarboxylic acids (DCAs) are important platform chemicals with large market and wide applications, and here the recent advances in bio-based production of straight-chain DCAs longer than C4 from biological approaches, especially by synthetic biology, are reviewed. A couple of pathways were recently designed and demonstrated for producing DCAs, even those ranging from C5 to C15, by employing respective starting units, extending units, and appropriate enzymes. Furthermore, in order to achieve higher production of DCAs, enormous efforts were made in engineering microbial hosts that harbored the biosynthetic pathways and in improving properties of biocatalytic elements to enhance metabolic fluxes toward target DCAs. Here we summarize and discuss the current advantages and limitations of related pathways, and also provide perspectives on synthetic pathway design and optimization for hyper-production of DCAs.
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Affiliation(s)
- Jia-Le Yu
- State Key Laboratory of Microbial Metabolism Joint International Research Laboratory of Metabolic and Developmental Sciences, School of Life Sciences and Biotechnology Shanghai Jiao Tong University Shanghai P. R. China.,State Key Laboratory of Bioreactor Engineering, School of Biotechnology East China University of Science and Technology Shanghai P. R. China
| | - Zhi-Gang Qian
- State Key Laboratory of Microbial Metabolism Joint International Research Laboratory of Metabolic and Developmental Sciences, School of Life Sciences and Biotechnology Shanghai Jiao Tong University Shanghai P. R. China.,Shanghai Collaborative Innovation Center for Biomanufacturing Technology (SCICBT) East China University of Science and Technology Shanghai P. R. China
| | - Jian-Jiang Zhong
- State Key Laboratory of Microbial Metabolism Joint International Research Laboratory of Metabolic and Developmental Sciences, School of Life Sciences and Biotechnology Shanghai Jiao Tong University Shanghai P. R. China.,State Key Laboratory of Bioreactor Engineering, School of Biotechnology East China University of Science and Technology Shanghai P. R. China.,Shanghai Collaborative Innovation Center for Biomanufacturing Technology (SCICBT) East China University of Science and Technology Shanghai P. R. China
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23
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Lange J, Münch E, Müller J, Busche T, Kalinowski J, Takors R, Blombach B. Deciphering the Adaptation of Corynebacterium glutamicum in Transition from Aerobiosis via Microaerobiosis to Anaerobiosis. Genes (Basel) 2018; 9:E297. [PMID: 29899275 PMCID: PMC6027265 DOI: 10.3390/genes9060297] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2018] [Revised: 05/31/2018] [Accepted: 06/07/2018] [Indexed: 01/02/2023] Open
Abstract
Zero-growth processes are a promising strategy for the production of reduced molecules and depict a steady transition from aerobic to anaerobic conditions. To investigate the adaptation of Corynebacterium glutamicum to altering oxygen availabilities, we conceived a triple-phase fermentation process that describes a gradual reduction of dissolved oxygen with a shift from aerobiosis via microaerobiosis to anaerobiosis. The distinct process phases were clearly bordered by the bacteria’s physiologic response such as reduced growth rate, biomass substrate yield and altered yield of fermentation products. During the process, sequential samples were drawn at six points and analyzed via RNA-sequencing, for metabolite concentrations and for enzyme activities. We found transcriptional alterations of almost 50% (1421 genes) of the entire protein coding genes and observed an upregulation of fermentative pathways, a rearrangement of respiration, and mitigation of the basic cellular mechanisms such as transcription, translation and replication as a transient response related to the installed oxygen dependent process phases. To investigate the regulatory regime, 18 transcriptionally altered (putative) transcriptional regulators were deleted, but none of the deletion strains showed noticeable growth kinetics under an oxygen restricted environment. However, the described transcriptional adaptation of C. glutamicum resolved to varying oxygen availabilities provides a useful basis for future process and strain engineering.
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Affiliation(s)
- Julian Lange
- Institute of Biochemical Engineering, University of Stuttgart, Allmandring 31, 70569 Stuttgart, Germany.
| | - Eugenia Münch
- Institute of Biochemical Engineering, University of Stuttgart, Allmandring 31, 70569 Stuttgart, Germany.
| | - Jan Müller
- Institute of Biochemical Engineering, University of Stuttgart, Allmandring 31, 70569 Stuttgart, Germany.
| | - Tobias Busche
- Center for Biotechnology, Bielefeld University, Universitätsstraße 27, 33615 Bielefeld, Germany.
- Institute for Biology-Microbiology, Freie Universität Berlin, Königin-Luise-Str. 12-16, 14195 Berlin, Germany.
| | - Jörn Kalinowski
- Center for Biotechnology, Bielefeld University, Universitätsstraße 27, 33615 Bielefeld, Germany.
| | - Ralf Takors
- Institute of Biochemical Engineering, University of Stuttgart, Allmandring 31, 70569 Stuttgart, Germany.
| | - Bastian Blombach
- Institute of Biochemical Engineering, University of Stuttgart, Allmandring 31, 70569 Stuttgart, Germany.
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24
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Heins AL, Weuster-Botz D. Population heterogeneity in microbial bioprocesses: origin, analysis, mechanisms, and future perspectives. Bioprocess Biosyst Eng 2018. [PMID: 29541890 DOI: 10.1007/s00449-018-1922-3] [Citation(s) in RCA: 45] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
Abstract
Population heterogeneity is omnipresent in all bioprocesses even in homogenous environments. Its origin, however, is only so well understood that potential strategies like bet-hedging, noise in gene expression and division of labour that lead to population heterogeneity can be derived from experimental studies simulating the dynamics in industrial scale bioprocesses. This review aims at summarizing the current state of the different parts of single cell studies in bioprocesses. This includes setups to visualize different phenotypes of single cells, computational approaches connecting single cell physiology with environmental influence and special cultivation setups like scale-down reactors that have been proven to be useful to simulate large-scale conditions. A step in between investigation of populations and single cells is studying subpopulations with distinct properties that differ from the rest of the population with sub-omics methods which are also presented here. Moreover, the current knowledge about population heterogeneity in bioprocesses is summarized for relevant industrial production hosts and mixed cultures, as they provide the unique opportunity to distribute metabolic burden and optimize production processes in a way that is impossible in traditional monocultures. In the end, approaches to explain the underlying mechanism of population heterogeneity and the evidences found to support each hypothesis are presented. For instance, population heterogeneity serving as a bet-hedging strategy that is used as coordinated action against bioprocess-related stresses while at the same time spreading the risk between individual cells as it ensures the survival of least a part of the population in any environment the cells encounter.
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Affiliation(s)
- Anna-Lena Heins
- Institute of Biochemical Engineering, Technical University of Munich, Boltzmannstr. 15, 85748, Garching, Germany.
| | - Dirk Weuster-Botz
- Institute of Biochemical Engineering, Technical University of Munich, Boltzmannstr. 15, 85748, Garching, Germany
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25
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Weber S, Schaepe S, Freyer S, Kopf MH, Dietzsch C. Jet aeration as alternative to overcome mass transfer limitation of stirred bioreactors. Eng Life Sci 2018; 18:244-253. [PMID: 32624903 DOI: 10.1002/elsc.201700169] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2017] [Revised: 12/17/2017] [Accepted: 01/02/2018] [Indexed: 11/05/2022] Open
Abstract
In industrial biotechnology increasing reactor volumes have the potential to reduce production costs. Whenever the achievable space time yield is determined by the mass transfer performance of the reactor, energy efficiency plays an important role to meet the requirements regarding low investment and operating costs. Based on theoretical calculations, compared to bubble column, airlift reactor, and aerated stirred tank, the jet loop reactor shows the potential for an enhanced energetic efficiency at high mass transfer rates. Interestingly, its technical application in standard biotechnological production processes has not yet been realized. Compared to a stirred tank reactor powered by Rushton turbines, maximum oxygen transfer rates about 200% higher were achieved in a jet loop reactor at identical power input in a fed batch fermentation process. Moreover, a model-based analysis of yield coefficients and growth kinetics showed that E. coli can be cultivated in jet loop reactors without significant differences in biomass growth. Based on an aerobic fermentation process, the assessment of energetic oxygen transfer efficiency [kgO2 kW-1 h-1] for a jet loop reactor yielded an improvement of almost 100%. The jet loop reactor could be operated at mass transfer rates 67% higher compared to a stirred tank. Thus, an increase of 40% in maximum space time yield [kg m-3 h-1] could be observed.
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Affiliation(s)
- Sebastian Weber
- Industrial Biotechnology-Chemical and Process Engineering BASF SE Ludwigshafen am Rhein Germany.,Department of Biochemistry/Biotechnology Martin-Luther-University Halle-Wittenberg Halle/Saale Germany
| | - Sebastian Schaepe
- Industrial Biotechnology-Chemical and Process Engineering BASF SE Ludwigshafen am Rhein Germany
| | - Stephan Freyer
- Industrial Biotechnology-Chemical and Process Engineering BASF SE Ludwigshafen am Rhein Germany
| | - Michael-Helmut Kopf
- Industrial Biotechnology-Chemical and Process Engineering BASF SE Ludwigshafen am Rhein Germany
| | - Christian Dietzsch
- Industrial Biotechnology-Chemical and Process Engineering BASF SE Ludwigshafen am Rhein Germany
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Limberg MH, Joachim M, Klein B, Wiechert W, Oldiges M. pH fluctuations imperil the robustness of C. glutamicum to short term oxygen limitation. J Biotechnol 2017; 259:248-260. [DOI: 10.1016/j.jbiotec.2017.08.018] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2017] [Revised: 08/15/2017] [Accepted: 08/16/2017] [Indexed: 11/16/2022]
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Delvigne F, Takors R, Mudde R, van Gulik W, Noorman H. Bioprocess scale-up/down as integrative enabling technology: from fluid mechanics to systems biology and beyond. Microb Biotechnol 2017; 10:1267-1274. [PMID: 28805306 PMCID: PMC5609235 DOI: 10.1111/1751-7915.12803] [Citation(s) in RCA: 38] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2017] [Accepted: 07/12/2017] [Indexed: 11/28/2022] Open
Abstract
Efficient optimization of microbial processes is a critical issue for achieving a number of sustainable development goals, considering the impact of microbial biotechnology in agrofood, environment, biopharmaceutical and chemical industries. Many of these applications require scale-up after proof of concept. However, the behaviour of microbial systems remains unpredictable (at least partially) when shifting from laboratory-scale to industrial conditions. The need for robust microbial systems is thus highly needed in this context, as well as a better understanding of the interactions between fluid mechanics and cell physiology. For that purpose, a full scale-up/down computational framework is already available. This framework links computational fluid dynamics (CFD), metabolic flux analysis and agent-based modelling (ABM) for a better understanding of the cell lifelines in a heterogeneous environment. Ultimately, this framework can be used for the design of scale-down simulators and/or metabolically engineered cells able to cope with environmental fluctuations typically found in large-scale bioreactors. However, this framework still needs some refinements, such as a better integration of gas-liquid flows in CFD, and taking into account intrinsic biological noise in ABM.
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Affiliation(s)
- Frank Delvigne
- TERRA Research CenterMicrobial Processes and Interactions (MiPI)University of LiègeLiègeBelgium
| | - Ralf Takors
- Institute of Biochemical EngineeringUniversity of StuttgartStuttgartGermany
| | - Rob Mudde
- Transport Phenomena SectionDepartment of Chemical EngineeringDelft University of TechnologyDelftThe Netherlands
| | - Walter van Gulik
- Department of BiotechnologyDelft University of TechnologyDelftThe Netherlands
| | - Henk Noorman
- Department of BiotechnologyDelft University of TechnologyDelftThe Netherlands
- DSM Biotechnology CenterDelftThe Netherlands
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Blunt W, Dartiailh C, Sparling R, Gapes D, Levin DB, Cicek N. Microaerophilic environments improve the productivity of medium chain length polyhydroxyalkanoate biosynthesis from fatty acids in Pseudomonas putida LS46. Process Biochem 2017. [DOI: 10.1016/j.procbio.2017.04.028] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 10/19/2022]
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Valdez-Cruz NA, Reynoso-Cereceda GI, Pérez-Rodriguez S, Restrepo-Pineda S, González-Santana J, Olvera A, Zavala G, Alagón A, Trujillo-Roldán MA. Production of a recombinant phospholipase A2 in Escherichia coli using resonant acoustic mixing that improves oxygen transfer in shake flasks. Microb Cell Fact 2017; 16:129. [PMID: 28743267 PMCID: PMC5526256 DOI: 10.1186/s12934-017-0746-1] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2017] [Accepted: 07/20/2017] [Indexed: 01/02/2023] Open
Abstract
Background Shake flasks are widely used during the development of bioprocesses for recombinant proteins. Cultures of recombinant Escherichia coli with orbital mixing (OM) have an oxygen limitation negatively affecting biomass growth and recombinant-protein production. With the aim to improve mixing and aeration in shake flask cultures, we analyzed cultures subjected to OM and the novel resonant acoustic mixing (RAM) by applying acoustic energy to E. coli BL21-Gold (DE3): a producer of recombinant phospholipase A2 (rPLA2) from Micrurus laticollaris snake venom. Results Comparing OM with RAM (200 rpm vs. 7.5g) at the same initial volumetric oxygen transfer coefficient (kLa ≈ 80 h−1) ~69% less biomass was obtained with OM compared with RAM. We analyzed two more conditions increasing agitation until maximal speed (12.5 and 20g), and ~1.6- and ~1.4-fold greater biomass was obtained as compared with cultures at 7.5g. Moreover, the specific growth rate was statistically similar in all cultures carried out in RAM, but ~1.5-fold higher than that in cultures carried out under OM. Almost half of the glucose was consumed in OM, whereas between 80 and 100% of the glucose was consumed in RAM cultures, doubling biomass per glucose yields. Differential organic acid production was observed, but acetate production was prevented at the maximal RAM (20g). The amount of rPLA2 in both, OM and RAM cultures, represented 38 ± 5% of the insoluble protein. A smaller proportion of α-helices and β-sheet of purified inclusion bodies (IBs) were appreciated by ATR-FTIR from cultures carried out under OM, than those from RAM. At maximal agitation by RAM, internal E. coli localization patterns of protein aggregation changed, as well as, IBs proteolytic degradation, in conjunction with the formation of small external vesicles, although these changes did not significantly affect the cell survival response. Conclusions In moderate-cell-density recombinant E. coli BL21-Gold (DE3) cultures, the agitation increases in RAM (up to the maximum) was not enough to avoid the classical oxygen limitation that happens in OM shake flasks. However, RAM presents a decrease of oxygen limitation, resulting in a favorable effect on biomass growth and volumetric rPLA2 production. While under OM a higher recombinant protein yield was obtained. Electronic supplementary material The online version of this article (doi:10.1186/s12934-017-0746-1) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Norma A Valdez-Cruz
- Programa de Investigación de Producción de Biomoléculas, Unidad de Bioprocesos, Departamento de Biología Molecular y Biotecnología, Instituto de Investigaciones Biomédicas, Universidad Nacional Autónoma de México, AP. 70228, CP 04510, Mexico City, Mexico.
| | - Greta I Reynoso-Cereceda
- Programa de Investigación de Producción de Biomoléculas, Unidad de Bioprocesos, Departamento de Biología Molecular y Biotecnología, Instituto de Investigaciones Biomédicas, Universidad Nacional Autónoma de México, AP. 70228, CP 04510, Mexico City, Mexico
| | - Saumel Pérez-Rodriguez
- Programa de Investigación de Producción de Biomoléculas, Unidad de Bioprocesos, Departamento de Biología Molecular y Biotecnología, Instituto de Investigaciones Biomédicas, Universidad Nacional Autónoma de México, AP. 70228, CP 04510, Mexico City, Mexico
| | - Sara Restrepo-Pineda
- Programa de Investigación de Producción de Biomoléculas, Unidad de Bioprocesos, Departamento de Biología Molecular y Biotecnología, Instituto de Investigaciones Biomédicas, Universidad Nacional Autónoma de México, AP. 70228, CP 04510, Mexico City, Mexico
| | - Jesus González-Santana
- Programa de Investigación de Producción de Biomoléculas, Unidad de Bioprocesos, Departamento de Biología Molecular y Biotecnología, Instituto de Investigaciones Biomédicas, Universidad Nacional Autónoma de México, AP. 70228, CP 04510, Mexico City, Mexico
| | - Alejandro Olvera
- Departamento de Medicina Molecular y Bioprocesos, Instituto de Biotecnología, Universidad Nacional Autónoma de México, Cuernavaca, Mor, Mexico
| | - Guadalupe Zavala
- Unidad de Microscopía, Instituto de Biotecnología, Universidad Nacional Autónoma de México, Cuernavaca, Mor, Mexico
| | - Alejandro Alagón
- Departamento de Medicina Molecular y Bioprocesos, Instituto de Biotecnología, Universidad Nacional Autónoma de México, Cuernavaca, Mor, Mexico
| | - Mauricio A Trujillo-Roldán
- Programa de Investigación de Producción de Biomoléculas, Unidad de Bioprocesos, Departamento de Biología Molecular y Biotecnología, Instituto de Investigaciones Biomédicas, Universidad Nacional Autónoma de México, AP. 70228, CP 04510, Mexico City, Mexico
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Delvigne F, Baert J, Sassi H, Fickers P, Grünberger A, Dusny C. Taking control over microbial populations: Current approaches for exploiting biological noise in bioprocesses. Biotechnol J 2017; 12. [PMID: 28544731 DOI: 10.1002/biot.201600549] [Citation(s) in RCA: 30] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2017] [Revised: 04/10/2017] [Accepted: 04/12/2017] [Indexed: 01/19/2023]
Abstract
Phenotypic plasticity of microbial cells has attracted much attention and several research efforts have been dedicated to the description of methods aiming at characterizing phenotypic heterogeneity and its impact on microbial populations. However, different approaches have also been suggested in order to take benefit from noise in a bioprocess perspective, e.g. by increasing the robustness or productivity of a microbial population. This review is dedicated to outline these controlling methods. A common issue, that has still to be addressed, is the experimental identification and the mathematical expression of noise. Indeed, the effective interfacing of microbial physiology with external parameters that can be used for controlling physiology depends on the acquisition of reliable signals. Latest technologies, like single cell microfluidics and advanced flow cytometric approaches, enable linking physiology, noise, heterogeneity in productive microbes with environmental cues and hence allow correctly mapping and predicting biological behavior via mathematical representations. However, like in the field of electronics, signals are perpetually subjected to noise. If appropriately interpreted, this noise can give an additional insight into the behavior of the individual cells within a microbial population of interest. This review focuses on recent progress made at describing, treating and exploiting biological noise in the context of microbial populations used in various bioprocess applications.
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Affiliation(s)
- Frank Delvigne
- University of Liège, TERRA research center, Gembloux Agro-Bio Tech, Microbial Processes and Interactions (MiPI lab), Gembloux, Belgium
| | - Jonathan Baert
- University of Liège, TERRA research center, Gembloux Agro-Bio Tech, Microbial Processes and Interactions (MiPI lab), Gembloux, Belgium
| | - Hosni Sassi
- University of Liège, TERRA research center, Gembloux Agro-Bio Tech, Microbial Processes and Interactions (MiPI lab), Gembloux, Belgium
| | - Patrick Fickers
- University of Liège, TERRA research center, Gembloux Agro-Bio Tech, Microbial Processes and Interactions (MiPI lab), Gembloux, Belgium
| | - Alexander Grünberger
- Forschungszentrum Jülich GmbH, IBG-1: Biotechnology, Jülich, Germany.,Multiscale Bioengineering, Bielefeld University, Bielefeld, Germany
| | - Christian Dusny
- Department Solar Materials, Helmholtz Centre for Environmental Research (UFZ), Leipzig, Germany
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Simen JD, Löffler M, Jäger G, Schäferhoff K, Freund A, Matthes J, Müller J, Takors R. Transcriptional response of Escherichia coli to ammonia and glucose fluctuations. Microb Biotechnol 2017; 10:858-872. [PMID: 28447391 PMCID: PMC5481515 DOI: 10.1111/1751-7915.12713] [Citation(s) in RCA: 35] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/24/2016] [Revised: 03/11/2017] [Accepted: 03/15/2017] [Indexed: 01/22/2023] Open
Abstract
In large‐scale production processes, metabolic control is typically achieved by limited supply of essential nutrients such as glucose or ammonia. With increasing bioreactor dimensions, microbial producers such as Escherichia coli are exposed to changing substrate availabilities due to limited mixing. In turn, cells sense and respond to these dynamic conditions leading to frequent activation of their regulatory programmes. Previously, we characterized short‐ and long‐term strategies of cells to adapt to glucose fluctuations. Here, we focused on fluctuating ammonia supply while studying a continuously running two‐compartment bioreactor system comprising a stirred tank reactor (STR) and a plug‐flow reactor (PFR). The alarmone ppGpp rapidly accumulated in PFR, initiating considerable transcriptional responses after 70 s. About 400 genes were repeatedly switched on/off when E. coli returned to the STR. E. coli revealed highly diverging long‐term transcriptional responses in ammonia compared to glucose fluctuations. In contrast, the induction of stringent regulation was a common feature of both short‐term responses. Cellular ATP demands for coping with fluctuating ammonia supply were found to increase maintenance by 15%. The identification of genes contributing to the increased ATP demand together with the elucidation of regulatory mechanisms may help to create robust cells and processes for large‐scale application.
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Affiliation(s)
- Joana Danica Simen
- Institute of Biochemical Engineering, University of Stuttgart, Allmandring 31, 70569, Stuttgart, Germany
| | - Michael Löffler
- Institute of Biochemical Engineering, University of Stuttgart, Allmandring 31, 70569, Stuttgart, Germany
| | - Günter Jäger
- Institute of Medical Genetics and Applied Genomics, University of Tübingen, Calwerstr. 7, 72076, Tübingen, Germany
| | - Karin Schäferhoff
- Institute of Medical Genetics and Applied Genomics, University of Tübingen, Calwerstr. 7, 72076, Tübingen, Germany
| | - Andreas Freund
- Institute of Biochemical Engineering, University of Stuttgart, Allmandring 31, 70569, Stuttgart, Germany
| | - Jakob Matthes
- Institute of Medical Genetics and Applied Genomics, University of Tübingen, Calwerstr. 7, 72076, Tübingen, Germany
| | - Jan Müller
- Institute of Biochemical Engineering, University of Stuttgart, Allmandring 31, 70569, Stuttgart, Germany
| | - Ralf Takors
- Institute of Biochemical Engineering, University of Stuttgart, Allmandring 31, 70569, Stuttgart, Germany
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Su L, Shen Y, Gao T, Luo J, Wang M. Improvement of AD Biosynthesis Response to Enhanced Oxygen Transfer by Oxygen Vectors in Mycobacterium neoaurum TCCC 11979. Appl Biochem Biotechnol 2017; 182:1564-1574. [DOI: 10.1007/s12010-017-2418-3] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2016] [Accepted: 01/17/2017] [Indexed: 12/01/2022]
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Lange J, Takors R, Blombach B. Zero-growth bioprocesses: A challenge for microbial production strains and bioprocess engineering. Eng Life Sci 2016; 17:27-35. [PMID: 32624726 DOI: 10.1002/elsc.201600108] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2016] [Revised: 08/18/2016] [Accepted: 09/19/2016] [Indexed: 12/20/2022] Open
Abstract
Microbial fermentation of renewable feedstocks is an established technology in industrial biotechnology. Besides strict aerobic or anaerobic modes of operation, novel innovative and industrially applicable fermentation processes were developed connecting the advantages of aerobic and anaerobic conditions in a combined production approach. As a consequence, rapid aerobic biomass formation to high cell densities and subsequent anaerobic high-yield and zero-growth production is realized. Following this strategy, bioprocesses operating with substantial overall yield and productivity can be obtained. Here, we summarize the current knowledge and achievements in such microbial zero-growth production processes and pinpoint to challenges due to the complex adaptation of the cellular metabolism during the cell's passage from aerobiosis to anaerobiosis.
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Affiliation(s)
- Julian Lange
- Institute of Biochemical Engineering University of Stuttgart Stuttgart Germany
| | - Ralf Takors
- Institute of Biochemical Engineering University of Stuttgart Stuttgart Germany
| | - Bastian Blombach
- Institute of Biochemical Engineering University of Stuttgart Stuttgart Germany
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35
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Löffler M, Simen JD, Jäger G, Schäferhoff K, Freund A, Takors R. Engineering E. coli for large-scale production - Strategies considering ATP expenses and transcriptional responses. Metab Eng 2016; 38:73-85. [PMID: 27378496 DOI: 10.1016/j.ymben.2016.06.008] [Citation(s) in RCA: 60] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2016] [Revised: 06/20/2016] [Accepted: 06/30/2016] [Indexed: 01/18/2023]
Abstract
Microbial producers such as Escherichia coli are evolutionarily trained to adapt to changing substrate availabilities. Being exposed to large-scale production conditions, their complex, multilayered regulatory programs are frequently activated because they face changing substrate supply due to limited mixing. Here, we show that E. coli can adopt both short- and long-term strategies to withstand these stress conditions. Experiments in which glucose availability was changed over a short time scale were performed in a two-compartment bioreactor system. Quick metabolic responses were observed during the first 30s of glucose shortage, and after 70s, fundamental transcriptional programs were initiated. Since cells are fluctuating under simulated large-scale conditions, this scenario represents a continuous on/off switching of about 600 genes. Furthermore, the resulting ATP maintenance demands were increased by about 40-50%, allowing us to conclude that hyper-producing strains could become ATP-limited under large-scale production conditions. Based on the observed transcriptional patterns, we identified a number of candidate gene deletions that may reduce unwanted ATP losses. In summary, we present a theoretical framework that provides biological targets that could be used to engineer novel E. coli strains such that large-scale performance equals laboratory-scale expectations.
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Affiliation(s)
- Michael Löffler
- University of Stuttgart, Institute of Biochemical Engineering, Allmandring 31, 70569 Stuttgart, Germany
| | - Joana Danica Simen
- University of Stuttgart, Institute of Biochemical Engineering, Allmandring 31, 70569 Stuttgart, Germany
| | - Günter Jäger
- University of Tübingen, Institute of Medical Genetics and Applied Genomics, Calwerstr. 7, 72076 Tübingen, Germany
| | - Karin Schäferhoff
- University of Tübingen, Institute of Medical Genetics and Applied Genomics, Calwerstr. 7, 72076 Tübingen, Germany
| | - Andreas Freund
- University of Stuttgart, Institute of Biochemical Engineering, Allmandring 31, 70569 Stuttgart, Germany
| | - Ralf Takors
- University of Stuttgart, Institute of Biochemical Engineering, Allmandring 31, 70569 Stuttgart, Germany.
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Chubukov V, Mukhopadhyay A, Petzold CJ, Keasling JD, Martín HG. Synthetic and systems biology for microbial production of commodity chemicals. NPJ Syst Biol Appl 2016; 2:16009. [PMID: 28725470 PMCID: PMC5516863 DOI: 10.1038/npjsba.2016.9] [Citation(s) in RCA: 133] [Impact Index Per Article: 16.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2015] [Revised: 02/01/2016] [Accepted: 02/05/2016] [Indexed: 01/08/2023] Open
Abstract
The combination of synthetic and systems biology is a powerful framework to study fundamental questions in biology and produce chemicals of immediate practical application such as biofuels, polymers, or therapeutics. However, we cannot yet engineer biological systems as easily and precisely as we engineer physical systems. In this review, we describe the path from the choice of target molecule to scaling production up to commercial volumes. We present and explain some of the current challenges and gaps in our knowledge that must be overcome in order to bring our bioengineering capabilities to the level of other engineering disciplines. Challenges start at molecule selection, where a difficult balance between economic potential and biological feasibility must be struck. Pathway design and construction have recently been revolutionized by next-generation sequencing and exponentially improving DNA synthesis capabilities. Although pathway optimization can be significantly aided by enzyme expression characterization through proteomics, choosing optimal relative protein expression levels for maximum production is still the subject of heuristic, non-systematic approaches. Toxic metabolic intermediates and proteins can significantly affect production, and dynamic pathway regulation emerges as a powerful but yet immature tool to prevent it. Host engineering arises as a much needed complement to pathway engineering for high bioproduct yields; and systems biology approaches such as stoichiometric modeling or growth coupling strategies are required. A final, and often underestimated, challenge is the successful scale up of processes to commercial volumes. Sustained efforts in improving reproducibility and predictability are needed for further development of bioengineering.
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Affiliation(s)
- Victor Chubukov
- Joint BioEnergy Institute, Emeryville, CA, USA
- Biological Systems and Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
| | - Aindrila Mukhopadhyay
- Joint BioEnergy Institute, Emeryville, CA, USA
- Biological Systems and Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
| | - Christopher J Petzold
- Joint BioEnergy Institute, Emeryville, CA, USA
- Biological Systems and Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
| | - Jay D Keasling
- Joint BioEnergy Institute, Emeryville, CA, USA
- Biological Systems and Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
- Department of Chemical & Biomolecular Engineering, University of California, Berkeley, CA, USA
- Department of Bioengineering, University of California, Berkeley, CA, USA
| | - Héctor García Martín
- Joint BioEnergy Institute, Emeryville, CA, USA
- Biological Systems and Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
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Efficient L-Alanine Production by a Thermo-Regulated Switch in Escherichia coli. Appl Biochem Biotechnol 2015; 178:324-37. [PMID: 26453031 DOI: 10.1007/s12010-015-1874-x] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2015] [Accepted: 09/24/2015] [Indexed: 10/23/2022]
Abstract
L-Alanine has important applications in food, pharmaceutical and veterinary and is used as a substrate for production of engineered thermoplastics. Microbial fermentation could reduce the production cost and promote the application of L-alanine. However, the presence of L-alanine significantly inhibit cell growth rate and cause a decrease in the ultimate L-alanine productivity. For efficient L-alanine production, a thermo-regulated genetic switch was designed to dynamically control the expression of L-alanine dehydrogenase (alaD) from Geobacillus stearothermophilus on the Escherichia coli B0016-060BC chromosome. The optimal cultivation conditions for the genetically switched alanine production using B0016-060BC were the following: an aerobic growth phase at 33 °C with a 1-h thermo-induction at 42 °C followed by an oxygen-limited phase at 42 °C. In a bioreactor experiment using the scaled-up conditions optimized in a shake flask, B0016-060BC accumulated 50.3 g biomass/100 g glucose during the aerobic growth phase and 96 g alanine/100 g glucose during the oxygen-limited phase, respectively. The L-alanine titer reached 120.8 g/l with higher overall and oxygen-limited volumetric productivities of 3.09 and 4.18 g/l h, respectively, using glucose as the sole carbon source. Efficient cell growth and L-alanine production were reached separately, by switching cultivation temperature. The results revealed the application of a thermo-regulated strategy for heterologous metabolic production and pointed to strategies for improving L-alanine production.
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Effects of oxygen-vectors on the synthesis of epsilon-poly-lysine and the metabolic characterization of Streptomyces albulus PD-1. Biochem Eng J 2015. [DOI: 10.1016/j.bej.2014.11.009] [Citation(s) in RCA: 39] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
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Xia J, Wang G, Lin J, Wang Y, Chu J, Zhuang Y, Zhang S. Advances and Practices of Bioprocess Scale-up. ADVANCES IN BIOCHEMICAL ENGINEERING/BIOTECHNOLOGY 2015; 152:137-51. [PMID: 25636486 DOI: 10.1007/10_2014_293] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/17/2023]
Abstract
: This chapter addresses the update progress in bioprocess engineering. In addition to an overview of the theory of multi-scale analysis for fermentation process, examples of scale-up practice combining microbial physiological parameters with bioreactor fluid dynamics are also described. Furthermore, the methodology for process optimization and bioreactor scale-up by integrating fluid dynamics with biokinetics is highlighted. In addition to a short review of the heterogeneous environment in large-scale bioreactor and its effect, a scale-down strategy for investigating this issue is addressed. Mathematical models and simulation methodology for integrating flow field in the reactor and microbial kinetics response are described. Finally, a comprehensive discussion on the advantages and challenges of the model-driven scale-up method is given at the end of this chapter.
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Affiliation(s)
- Jianye Xia
- State Key Laboratory of Bioreactor Engineering, East China University of Science and Technology, 130 Meilong Road, Shanghai, 200237, China
| | - Guan Wang
- State Key Laboratory of Bioreactor Engineering, East China University of Science and Technology, 130 Meilong Road, Shanghai, 200237, China
| | - Jihan Lin
- State Key Laboratory of Bioreactor Engineering, East China University of Science and Technology, 130 Meilong Road, Shanghai, 200237, China
| | - Yonghong Wang
- State Key Laboratory of Bioreactor Engineering, East China University of Science and Technology, 130 Meilong Road, Shanghai, 200237, China
| | - Ju Chu
- State Key Laboratory of Bioreactor Engineering, East China University of Science and Technology, 130 Meilong Road, Shanghai, 200237, China
| | - Yingping Zhuang
- State Key Laboratory of Bioreactor Engineering, East China University of Science and Technology, 130 Meilong Road, Shanghai, 200237, China
| | - Siliang Zhang
- State Key Laboratory of Bioreactor Engineering, East China University of Science and Technology, 130 Meilong Road, Shanghai, 200237, China.
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Sohm B, Immel F, Bauda P, Pagnout C. Insight into the primary mode of action of TiO2 nanoparticles on Escherichia coli in the dark. Proteomics 2014; 15:98-113. [PMID: 25346333 DOI: 10.1002/pmic.201400101] [Citation(s) in RCA: 74] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2014] [Revised: 09/22/2014] [Accepted: 10/20/2014] [Indexed: 11/09/2022]
Abstract
Large-scale production and incorporation of titanium dioxide nanoparticles (NP-TiO2 ) in consumer products leads to their potential release into the environment and raises the question of their toxicity. The bactericidal mechanism of NP-TiO2 under UV light is known to involve oxidative stress due to the generation of reactive oxygen species. In the dark, several studies revealed that NP-TiO2 can exert toxicological effects. However, the mode of action of these nanoparticles is still controversial. In the present study, we used a combination of fluorescent probes to show that NP-TiO2 causes Escherichia coli membrane depolarization and loss of integrity, leading to higher cell permeability. Using both transcriptomic and proteomic global approaches we showed that this phenomenon translates into a cellular response to osmotic stress, metabolism of cell envelope components and uptake/metabolism of endogenous and exogenous compounds. This primary mechanism of bacterial NP-TiO2 toxicity is supported by the observed massive cell leakage of K(+) /Mg(2+) concomitant with the entrance of extracellular Na(+), and by the depletion of intracellular ATP level.
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Affiliation(s)
- Bénédicte Sohm
- Laboratoire Interdisciplinaire des Environnements Continentaux (LIEC), UMR 7360, Université de Lorraine, Metz, France; CNRS, LIEC, UMR 7360, Metz, France
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Henkel SG, Beek AT, Steinsiek S, Stagge S, Bettenbrock K, de Mattos MJT, Sauter T, Sawodny O, Ederer M. Basic regulatory principles of Escherichia coli's electron transport chain for varying oxygen conditions. PLoS One 2014; 9:e107640. [PMID: 25268772 PMCID: PMC4182436 DOI: 10.1371/journal.pone.0107640] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2014] [Accepted: 08/11/2014] [Indexed: 01/05/2023] Open
Abstract
For adaptation between anaerobic, micro-aerobic and aerobic conditions Escherichia coli's metabolism and in particular its electron transport chain (ETC) is highly regulated. Although it is known that the global transcriptional regulators FNR and ArcA are involved in oxygen response it is unclear how they interplay in the regulation of ETC enzymes under micro-aerobic chemostat conditions. Also, there are diverse results which and how quinones (oxidised/reduced, ubiquinone/other quinones) are controlling the ArcBA two-component system. In the following a mathematical model of the E. coli ETC linked to basic modules for substrate uptake, fermentation product excretion and biomass formation is introduced. The kinetic modelling focusses on regulatory principles of the ETC for varying oxygen conditions in glucose-limited continuous cultures. The model is based on the balance of electron donation (glucose) and acceptance (oxygen or other acceptors). Also, it is able to account for different chemostat conditions due to changed substrate concentrations and dilution rates. The parameter identification process is divided into an estimation and a validation step based on previously published and new experimental data. The model shows that experimentally observed, qualitatively different behaviour of the ubiquinone redox state and the ArcA activity profile in the micro-aerobic range for different experimental conditions can emerge from a single network structure. The network structure features a strong feed-forward effect from the FNR regulatory system to the ArcBA regulatory system via a common control of the dehydrogenases of the ETC. The model supports the hypothesis that ubiquinone but not ubiquinol plays a key role in determining the activity of ArcBA in a glucose-limited chemostat at micro-aerobic conditions.
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Affiliation(s)
| | - Alexander Ter Beek
- Molecular Microbial Physiology, Swammerdam Institute for Life Sciences, University of Amsterdam, Amsterdam, The Netherlands
| | - Sonja Steinsiek
- Experimental Systems Biology, Max-Planck-Institute for Dynamics of Complex Technical Systems, Magdeburg, Germany
| | - Stefan Stagge
- Experimental Systems Biology, Max-Planck-Institute for Dynamics of Complex Technical Systems, Magdeburg, Germany
| | - Katja Bettenbrock
- Experimental Systems Biology, Max-Planck-Institute for Dynamics of Complex Technical Systems, Magdeburg, Germany
| | - M. Joost Teixeira de Mattos
- Molecular Microbial Physiology, Swammerdam Institute for Life Sciences, University of Amsterdam, Amsterdam, The Netherlands
| | - Thomas Sauter
- Life Science Research Unit, Université du Luxembourg, Luxembourg, Luxembourg
| | - Oliver Sawodny
- Institute for System Dynamics, University of Stuttgart, Stuttgart, Germany
| | - Michael Ederer
- Institute for System Dynamics, University of Stuttgart, Stuttgart, Germany
- * E-mail:
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Zhu P, Dong S, Li S, Xu X, Xu H. Improvement of welan gum biosynthesis and transcriptional analysis of the genes responding to enhanced oxygen transfer by oxygen vectors in Sphingomonas sp. Biochem Eng J 2014. [DOI: 10.1016/j.bej.2014.06.011] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/25/2022]
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43
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CO2/HCO3 − perturbations of simulated large scale gradients in a scale-down device cause fast transcriptional responses in Corynebacterium glutamicum. Appl Microbiol Biotechnol 2014; 98:8563-72. [DOI: 10.1007/s00253-014-6014-y] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2014] [Revised: 08/03/2014] [Accepted: 08/05/2014] [Indexed: 10/24/2022]
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44
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Stochastic exposure to sub-lethal high temperature enhances exopolysaccharides (EPS) excretion and improves Bifidobacterium bifidum cell survival to freeze–drying. Biochem Eng J 2014. [DOI: 10.1016/j.bej.2014.04.005] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/05/2023]
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45
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Brognaux A, Francis F, Twizere JC, Thonart P, Delvigne F. Scale-down effect on the extracellular proteome of Escherichia coli: correlation with membrane permeability and modulation according to substrate heterogeneities. Bioprocess Biosyst Eng 2014; 37:1469-85. [DOI: 10.1007/s00449-013-1119-8] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2013] [Accepted: 12/18/2013] [Indexed: 11/27/2022]
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46
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Quantifying the Effects of Frequency and Amplitude of Periodic Oxygen-Related Stress on Recombinant Protein Production in Pichia pastoris. Bioengineering (Basel) 2013. [DOI: 10.3390/bioengineering1010047] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022] Open
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47
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Lorantfy B, Jazini M, Herwig C. Investigation of the physiological response to oxygen limited process conditions of Pichia pastoris Mut+ strain using a two-compartment scale-down system. J Biosci Bioeng 2013; 116:371-9. [DOI: 10.1016/j.jbiosc.2013.03.021] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2013] [Revised: 03/25/2013] [Accepted: 03/27/2013] [Indexed: 11/26/2022]
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48
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Sunya S, Bideaux C, Molina-Jouve C, Gorret N. Short-term dynamic behavior of Escherichia coli in response to successive glucose pulses on glucose-limited chemostat cultures. J Biotechnol 2013; 164:531-42. [DOI: 10.1016/j.jbiotec.2013.01.014] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2012] [Revised: 12/22/2012] [Accepted: 01/14/2013] [Indexed: 01/20/2023]
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49
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Spadiut O, Rittmann S, Dietzsch C, Herwig C. Dynamic process conditions in bioprocess development. Eng Life Sci 2013. [DOI: 10.1002/elsc.201200026] [Citation(s) in RCA: 44] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022] Open
Affiliation(s)
- Oliver Spadiut
- Vienna University of Technology; Institute of Chemical Engineering; Research Area Biochemical Engineering; Vienna; Austria
| | - Simon Rittmann
- Vienna University of Technology; Institute of Chemical Engineering; Research Area Biochemical Engineering; Vienna; Austria
| | - Christian Dietzsch
- Vienna University of Technology; Institute of Chemical Engineering; Research Area Biochemical Engineering; Vienna; Austria
| | - Christoph Herwig
- Vienna University of Technology; Institute of Chemical Engineering; Research Area Biochemical Engineering; Vienna; Austria
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50
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Metabolic responses to recombinant bioprocesses in Escherichia coli. J Biotechnol 2012; 164:396-408. [PMID: 23022453 DOI: 10.1016/j.jbiotec.2012.08.026] [Citation(s) in RCA: 59] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2012] [Revised: 07/09/2012] [Accepted: 08/08/2012] [Indexed: 01/13/2023]
Abstract
Escherichia coli has been widely used for the production of recombinant proteins. However, the unbalances between host metabolism and recombinant biosynthesis continue to hamper the efficiency of these recombinant bioprocesses. The additional drainage of biosynthetic precursors toward recombinant processes burdens severely the metabolism of cells that, ultimately, elicits a series of stress responses, reducing biomass growth and recombinant protein production. Several strategies to overcome these metabolic limitations have been implemented; however, in most cases, improvements in recombinant protein expression were achieved at the expense of biomass growth arrest, which significantly hampers the efficiency of recombinant bioprocesses. With the advent of high throughput techniques and modelling approaches that provide a system-level understanding of the cellular systems, it is now expected that new advances in recombinant bioprocesses are achieved. By providing means to deal with these systems, our understanding on the metabolic behaviour of recombinant cells will advance and can be further explored to the design of suitable hosts and more efficient and cost-effective bioprocesses. Here, we review the major metabolic responses associated with recombinant processes and the engineering strategies relevant to overcome these stresses. Moreover, the advantages of applying systems levels engineering strategies to enhance recombinant protein production in E. coli cells are discussed and future perspectives on the advances of mathematical modelling approaches to study these systems are exposed.
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