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Jouned MA, Kager J, Rajamanickam V, Herwig C, Barz T. A Unique Response Behavior in the Dissolved Oxygen Tension in E. coli Minibioreactor Cultivations with Intermittent Feeding. Bioengineering (Basel) 2023; 10:681. [PMID: 37370611 DOI: 10.3390/bioengineering10060681] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2023] [Revised: 05/21/2023] [Accepted: 05/26/2023] [Indexed: 06/29/2023] Open
Abstract
Intermittent bolus feeding for E. coli cultivations in minibioreactor systems (MBRs) profoundly affects the cell metabolism. Bolus feeding leads to temporal substrate surplus and transient oxygen limitation, which triggers the formation of inhibitory byproducts. Due to the high oxygen demand right after the injection of the substrate, the dissolved oxygen tension (DOT) signal exhibits a negative pulse. This contribution describes and analyzes this DOT response in E. coli minibioreactor cultivations. In addition to gaining information on culture conditions, a unique response behavior in the DOT signal was observed in the analysis. This response appeared only at a dilution ratio per biomass unit higher than a certain threshold. The analysis highlights a plausible relationship between a metabolic adaptation behavior and the newly observed DOT signal segment not reported in the literature. A hypothesis that links particular DOT segments to specific metabolic states is proposed. The quantitative analysis and mechanistic model simulations support this hypothesis and show the possibility of obtaining cell physiological and growth parameters from the DOT signal.
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Affiliation(s)
- M Adnan Jouned
- ICEBE, TU Wien, Gumpendorfer Straße 1a 166/4, 1060 Vienna, Austria
| | - Julian Kager
- Department of Chemical and Biochemical Engineering, Technical University of Denmark, Building 228A, 2800 Kgs. Lyngby, Denmark
| | - Vignesh Rajamanickam
- Boehringer Ingelheim RCV GmbH & Co KG, Biopharmaceuticals Austria, Dr. Boehringer Gasse 5-11, 1120 Vienna, Austria
| | | | - Tilman Barz
- Center for Energy, AIT Austrian Institute of Technology GmbH, Giefinggasse 2, 1210 Vienna, Austria
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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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Yang X, Yang Y, Huang J, Man D, Guo M. Comparisons of urea or ammonium on growth and fermentative metabolism of Saccharomyces cerevisiae in ethanol fermentation. World J Microbiol Biotechnol 2021; 37:98. [PMID: 33969436 DOI: 10.1007/s11274-021-03056-9] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2020] [Accepted: 04/13/2021] [Indexed: 10/21/2022]
Abstract
This work was mainly about the understanding of how urea and ammonium affect growth, glucose consumption and ethanol production of S. cerevisiae, in particular regarding the basic physiology of cell. The basic physiology of cell included intracellular pH, ATP, NADH and enzyme activity. Results showed that fermentation time was reduced by 19% when using urea compared with ammonium. The maximal ethanol production rate using urea was 1.14 g/L/h, increasing 30% comparing with the medium prepared with ammonium. Moreover, urea could decrease the synthesis of glycerol from glucose by 26% comparing with ammonium. The by-product of acetic acid yields decreased from 40 mmol/mol of glucose (with urea) to 24 mmol/mol of glucose (with ammonium). At the end of ethanol fermentation, cell number and pH were greater with urea than ammonium. Comparing with urea, ammonium decreased the intracellular pH by 14% (from 7.1 to 6.1). Urease converting urea into ammonia resulted in a more than 50% lower of ATP when comparing with ammonium. The values of NADH/DCW were 0.21 mg/g and 0.14 mg/g respectively with urea and ammonium, suggesting a 33% lower NADH. The enzyme activity of glyceraldehyde-3-phosphate dehydrogenase (GAPDH) was 0.0225 and 0.0275 U/mg protein respectively with urea and ammonium, which was consistent with the yields of glycerol.
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Affiliation(s)
- Xinchao Yang
- School of Biological Science and Technology, University of Jinan, Jinan, 250022, China.
| | - Yuling Yang
- Linghua Group Limited, Jining, 272073, China
| | - Jiadong Huang
- School of Biological Science and Technology, University of Jinan, Jinan, 250022, China
| | - Deen Man
- Linghua Group Limited, Jining, 272073, China
| | - Maihai Guo
- Linghua Group Limited, Jining, 272073, China
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Mauri M, Vecchione S, Fritz G. Deconvolution of Luminescence Cross-Talk in High-Throughput Gene Expression Profiling. ACS Synth Biol 2019; 8:1361-1370. [PMID: 31095908 DOI: 10.1021/acssynbio.9b00032] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/02/2023]
Abstract
Luciferase reporters have become standard genetic tools to monitor gene expression in real time and in high-throughput using microplate readers. Compared to reporter gene assays based on fluorescence proteins, luciferase reporters have a superior signal-to-noise ratio, since they do not suffer from the high autofluorescence background of the bacterial cell. However, at the same time luciferase reporters have the drawback of constant light emission, which leads to undesired cross-talk between neighboring wells on a microplate. To overcome this limitation, we developed a computational method to correct for luminescence bleed-through and to estimate the "true" luminescence activity for each well of a microplate. As the sole input our algorithm uses the signals measured from a calibration plate, in which the light emitted from a single luminescent well serves as an estimate for the "light-spread function". We show that this light-spread function can be used to deconvolve any other measurement obtained under the same technical conditions. Our analysis demonstrates that the correction preserves low-level signals close to the background and shows that it is universally applicable to different kinds of microplate readers and plate types.
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Affiliation(s)
- Marco Mauri
- LOEWE Center for Synthetic Microbiology and Department of Physics, Philipps-Universität Marburg, 35032 Marburg, Germany
| | - Stefano Vecchione
- LOEWE Center for Synthetic Microbiology and Department of Physics, Philipps-Universität Marburg, 35032 Marburg, Germany
| | - Georg Fritz
- LOEWE Center for Synthetic Microbiology and Department of Physics, Philipps-Universität Marburg, 35032 Marburg, Germany
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Xu B, Ju Y, Soukup RJ, Ramsey DM, Fishel R, Wysocki VH, Wozniak DJ. The Pseudomonas aeruginosa AmrZ C-terminal domain mediates tetramerization and is required for its activator and repressor functions. ENVIRONMENTAL MICROBIOLOGY REPORTS 2016; 8:85-90. [PMID: 26549743 PMCID: PMC4769699 DOI: 10.1111/1758-2229.12354] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/14/2015] [Accepted: 11/01/2015] [Indexed: 05/14/2023]
Abstract
Pseudomonas aeruginosa is an important bacterial opportunistic pathogen, presenting a significant threat towards individuals with underlying diseases such as cystic fibrosis. The transcription factor AmrZ regulates expression of multiple P. aeruginosa virulence factors. AmrZ belongs to the ribbon-helix-helix protein superfamily, in which many members function as dimers, yet others form higher order oligomers. In this study, four independent approaches were undertaken and demonstrated that the primary AmrZ form in solution is tetrameric. Deletion of the AmrZ C-terminal domain leads to loss of tetramerization and reduced DNA binding to both activated and repressed target promoters. Additionally, the C-terminal domain is essential for efficient AmrZ-mediated activation and repression of its targets.
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Affiliation(s)
- Binjie Xu
- Department of Microbiology, The Ohio State University, Columbus, Ohio, 43210
- Department of Center for Microbial Interface Biology, The Ohio State University, Columbus, Ohio, 43210
| | - Yue Ju
- Department of Chemistry and Biochemistry, The Ohio State University, Columbus, Ohio, 43210
| | - Randal J. Soukup
- Department of Molecular, Cellular and Developmental Biology Graduate Program, The Ohio State University, Columbus, Ohio, 43210
| | - Deborah M. Ramsey
- Department of Microbiology and Immunology, Wake Forest School of Medicine, Winston-Salem, NC
| | - Richard Fishel
- Department of Molecular Virology, Immunology, and Medical Genetics, The Ohio State University Wexner Medical Center and Comprehensive Cancer Center, The Ohio State University, Columbus, Ohio, 43210
| | - Vicki H. Wysocki
- Department of Chemistry and Biochemistry, The Ohio State University, Columbus, Ohio, 43210
| | - Daniel J. Wozniak
- Department of Microbiology, The Ohio State University, Columbus, Ohio, 43210
- Department of Microbial Infection and Immunity, The Ohio State University, Columbus, Ohio, 43210
- Department of Center for Microbial Interface Biology, The Ohio State University, Columbus, Ohio, 43210
- All correspondence should be addressed to Daniel J. Wozniak, . Address: BRT 704, 460 W. 12 Ave, Columbus, OH, 43210. Phone: 614-247-7629; Fax: 614-2929-616
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Experimental and statistical analysis of nutritional requirements for the growth of the extremophile Deinococcus geothermalis DSM 11300. Extremophiles 2014; 18:1009-21. [PMID: 25209745 DOI: 10.1007/s00792-014-0671-8] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2013] [Accepted: 07/06/2014] [Indexed: 10/24/2022]
Abstract
Few studies concerning the nutritional requirements of Deinococcus geothermalis DSM 11300 have been conducted to date. Three defined media compositions have been published for the growth of this strain but they were found to be inadequate to achieve growth without limitation. Furthermore, growth curves, biomass concentration and growth rates were generally not available. Analysis in Principal Components was used in this work to compare and consequently to highlight the main compounds which differ between published chemically defined media. When available, biomass concentration, and/or growth rate were superimposed to the PCA analysis. The formulations of the media were collected from existing literature; media compositions designed for the growth of several strains of Deinococcaceae or Micrococcaceae were included. The results showed that a defined medium adapted from Holland et al. (Appl Microbiol Biotechnol 72:1074-1082, 2006) was the best basal medium and was chosen for further studies. A growth rate of 0.03 h(-1) and a final OD600nm of 0.55 were obtained, but the growth was linear. Then, the effects of several medium components on oxygen uptake and biomass production by Deinococcus geothermalis DSM 11300 were studied using a respirometry-based method, to search for the nutritional limitation. The results revealed that the whole yeast extract in the medium with glucose is necessary to obtain a non-limiting growth of Deinococcus geothermalis DSM 11300 at a maximum growth rate of 0.64 h(-1) at 45 °C.
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Grunwald S, Mottet A, Grousseau E, Plassmeier JK, Popović MK, Uribelarrea JL, Gorret N, Guillouet SE, Sinskey A. Kinetic and stoichiometric characterization of organoautotrophic growth of Ralstonia eutropha on formic acid in fed-batch and continuous cultures. Microb Biotechnol 2014; 8:155-63. [PMID: 25123319 PMCID: PMC4321381 DOI: 10.1111/1751-7915.12149] [Citation(s) in RCA: 47] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2014] [Revised: 04/28/2014] [Accepted: 07/06/2014] [Indexed: 11/29/2022] Open
Abstract
Formic acid, acting as both carbon and energy source, is a safe alternative to a carbon dioxide, hydrogen and dioxygen mix for studying the conversion of carbon through the Calvin–Benson–Bassham (CBB) cycle into value-added chemical compounds by non-photosynthetic microorganisms. In this work, organoautotrophic growth of Ralstonia eutropha on formic acid was studied using an approach combining stoichiometric modeling and controlled cultures in bioreactors. A strain deleted of its polyhydroxyalkanoate production pathway was used in order to carry out a physiological characterization. The maximal growth yield was determined at 0.16 Cmole Cmole−1 in a formate-limited continuous culture. The measured yield corresponded to 76% to 85% of the theoretical yield (later confirmed in pH-controlled fed-batch cultures). The stoichiometric study highlighted the imbalance between carbon and energy provided by formic acid and explained the low growth yields measured. Fed-batch cultures were also used to determine the maximum specific growth rate (μmax = 0.18 h−1) and to study the impact of increasing formic acid concentrations on growth yields. High formic acid sensitivity was found in R eutropha since a linear decrease in the biomass yield with increasing residual formic acid concentrations was observed between 0 and 1.5 g l−1.
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Affiliation(s)
- Stephan Grunwald
- Department of Biology, Massachusetts Institute of Technology, Bldg. 68-370, 77 Massachusetts Avenue, Cambridge, MA, 02139, USA; Department of Biotechnology, Beuth Hochschule für Technik Berlin, 13353, Berlin, Germany
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Zeng X, Chen XS, Ren XD, Liu QR, Wang L, Sun QX, Tang L, Mao ZG. Insights into the Role of Glucose and Glycerol as a Mixed Carbon Source in the Improvement of ε-Poly-l-Lysine Productivity. Appl Biochem Biotechnol 2014; 173:2211-24. [DOI: 10.1007/s12010-014-1026-8] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2013] [Accepted: 06/19/2014] [Indexed: 10/25/2022]
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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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Brognaux A, Thonart P, Delvigne F, Neubauer P, Twizere JC, Francis F, Gorret N. Direct and indirect use of GFP whole cell biosensors for the assessment of bioprocess performances: Design of milliliter scale-down bioreactors. Biotechnol Prog 2012; 29:48-59. [DOI: 10.1002/btpr.1660] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2012] [Revised: 10/24/2012] [Indexed: 01/27/2023]
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Sunya S, Delvigne F, Uribelarrea JL, Molina-Jouve C, Gorret N. Comparison of the transient responses of Escherichia coli to a glucose pulse of various intensities. Appl Microbiol Biotechnol 2012; 95:1021-34. [PMID: 22370947 DOI: 10.1007/s00253-012-3938-y] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2011] [Revised: 02/01/2012] [Accepted: 02/01/2012] [Indexed: 11/24/2022]
Abstract
Dynamic stimulus-responses of Escherichia coli DPD2085, yciG::LuxCDABE reporter strain, to glucose pulses of different intensities (0.08, 0.4 and 1 g L(-1)) were compared using glucose-limited chemostat cultures at dilution rate close to 0.15 h(-1). After at least five residence times, the steady-state cultures were disturbed by a pulse of glucose, engendering conditions of glucose excess with concomitant oxygen limitation. In all conditions, glucose consumption, acetate and formate accumulations followed a linear relationship with time. The resulting specific uptake and production rates as well as respiratory rates were rapidly increased within the first seconds, which revealed a high ability of E. coli strain to modulate its metabolism to a new environment. For transition from glucose-excess to glucose-limited conditions, the cells rapidly re-established its pseudo-steady state. The dynamics of transient responses at the macroscopic viewpoint were shown to be independent on the glucose pulse intensity in the tested range. On the contrary, the E. coli biosensor yciG::luxCDABE revealed a transcriptional induction of yciG gene promoter depending on the quantities of the glucose added, through in situ and online monitoring of the bioluminescence emitted by the cells. Despite many studies describing the dynamics of the transient response of E. coli to glucose perturbations, it is the first time that a direct comparison is reported, using the same experimental design (strain, medium and experimental set up), to study the impact of the glucose pulse intensity on the dynamics of microbial behaviour regarding growth, respiration and metabolite productions.
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Affiliation(s)
- Sirichai Sunya
- Université de Toulouse, 135 Avenue de Rangueil, Toulouse, France
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