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Tan Y, Stein LY, Sauvageau D. Methanol bioconversion in Methylotuvimicrobium buryatense 5GB1C through self-cycling fermentation. Bioprocess Biosyst Eng 2023:10.1007/s00449-023-02876-3. [PMID: 37160768 DOI: 10.1007/s00449-023-02876-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2022] [Accepted: 04/18/2023] [Indexed: 05/11/2023]
Abstract
Methanol is an abundant and low-cost next-generation carbon source. While many species of methanotrophic bacteria can convert methanol into valuable bioproducts in bioreactors, Methylotuvimicrobium buryatense 5GB1C stands out as one of the most promising strains for industrialization. It has a short doubling time compared to most methanotrophs, remarkable resilience against contamination, and a suite of tools enabling genetic engineering. When approaching industrial applications, growing M. buryatense 5GB1C on methanol using common batch reactor operation has important limitations; for example methanol toxicity leads to mediocre biomass productivity. Advanced bioreactor operation strategies, such as fed-batch and self-cycling fermentation, have the potential to greatly improve the industrial prospects of methanotrophs growing on methanol. Herein, implementation of fed-batch operation led to a 26-fold increase in biomass density, while two different self-cycling fermentation (SCF) strategies led to 3-fold and 10-fold increases in volumetric biomass productivity. Interestingly, while synchronization is a typical trait of microbial populations undergoing SCF, M. buryatense 5GB1C cultures growing under this mode of operation led to stable, reproducible cycles but no significant synchronization.
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Affiliation(s)
- Yusheng Tan
- Department of Chemical and Materials Engineering, University of Alberta, 9211-116 St. NW, Edmonton, AB, T6G 1H9, Canada
| | - Lisa Y Stein
- Department of Biological Sciences, University of Alberta, Edmonton, AB, Canada
| | - Dominic Sauvageau
- Department of Chemical and Materials Engineering, University of Alberta, 9211-116 St. NW, Edmonton, AB, T6G 1H9, Canada.
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Tan Y, Stein LY, Sauvageau D. The influence of self-cycling fermentation long- and short-cycle schemes on Saccharomyces cerevisiae and Escherichia coli. Sci Rep 2022; 12:13154. [PMID: 35915208 PMCID: PMC9343364 DOI: 10.1038/s41598-022-16831-x] [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: 02/15/2022] [Accepted: 07/18/2022] [Indexed: 11/09/2022] Open
Abstract
Self-cycling fermentation (SCF), a cyclic process in which cells, on average, divide once per cycle, has been shown to lead to whole-culture synchronization and improvements in productivity during bioconversion. Previous studies have shown that the completion of synchronized cell replication sometimes occurs simultaneously with depletion of the limiting nutrient. However, cases in which the end of cell doubling occurred before limiting nutrient exhaustion were also observed. In order to better understand the impact of these patterns on bioprocessing, we investigated the growth of Saccharomyces cerevisiae and Escherichia coli in long- and short-cycle SCF strategies. Three characteristic events were identified during SCF cycles: (1) an optimum in control parameters, (2) the time of completion of synchronized cell division, and (3) the depletion or plateau of the limiting nutrient. Results from this study and literature led to the identification of three potential trends in SCF cycles: (A) co-occurrence of the three key events, (B) cell replication ending prior to the co-occurrence of the other two events, and (C) depletion or plateau of the limiting nutrient occurring later than the co-occurrence of the other two events. Based on these observations, microbial physiological differences were analyzed and a novel definition for SCF is proposed.
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Affiliation(s)
- Yusheng Tan
- Department of Chemical and Materials Engineering, University of Alberta, Edmonton, AB, Canada
| | - Lisa Y Stein
- Department of Biological Sciences, University of Alberta, Edmonton, AB, Canada
| | - Dominic Sauvageau
- Department of Chemical and Materials Engineering, University of Alberta, Edmonton, AB, Canada.
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Tan Y, Agustin RVC, Stein LY, Sauvageau D. Transcriptomic analysis of synchrony and productivity in self-cycling fermentation of engineered yeast producing shikimic acid. BIOTECHNOLOGY REPORTS (AMSTERDAM, NETHERLANDS) 2021; 32:e00691. [PMID: 34934640 PMCID: PMC8660916 DOI: 10.1016/j.btre.2021.e00691] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/06/2021] [Revised: 11/09/2021] [Accepted: 11/23/2021] [Indexed: 05/25/2023]
Abstract
Industrial fermentation provides a wide variety of bioproducts, such as food, biofuels and pharmaceuticals. Self-cycling fermentation (SCF), an advanced automated semi-continuous fermentation approach, has shown significant advantages over batch reactors (BR); including cell synchrony and improved production. Here, Saccharomyces cerevisiae engineered to overproduce shikimic acid was grown under SCF operation. This led to four-fold increases in product yield and volumetric productivity compared to BR. Transcriptomic analyses were performed to understand the cellular mechanisms leading to these increases. Results indicate an up-regulation of a large number of genes related to the cell cycle and DNA replication in the early stages of SCF cycles, inferring substantial synchronization. Moreover, numerous genes related to gluconeogenesis, the citrate cycle and oxidative phosphorylation were significantly up-regulated in the late stages of SCF cycles, consistent with significant increases in shikimic acid yield and productivity.
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Key Words
- BR, Batch reactor
- CER, Carbon dioxide evolution rate
- DDT, Dithiothreitol
- DNA, Deoxyribonucleic acid
- EDTA, Ethylenediaminetetraacetic acid
- FC, Fold change
- OD600, Optical density at 600 nm
- RNA, Ribonucleic acid
- SCF, Self-cycling fermentation
- STP, Standard temperature and pressure
- Saccharomyces cerevisiae
- Self-cycling fermentation (SCF)
- Shikimic acid
- Synchrony
- Transcriptomics
- cDNA, Complementary deoxyribonucleic acid
- mRNA, Messenger ribonucleic acid
- qPCR, Quantitative polymerase chain reaction
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Affiliation(s)
- Yusheng Tan
- Department of Chemical and Materials Engineering, University of Alberta, Edmonton, Alberta, Canada
| | - Roman Vincent C. Agustin
- Department of Chemical and Materials Engineering, University of Alberta, Edmonton, Alberta, Canada
| | - Lisa Y. Stein
- Department of Biological Sciences, University of Alberta, Edmonton, Alberta, Canada
| | - Dominic Sauvageau
- Department of Chemical and Materials Engineering, University of Alberta, Edmonton, Alberta, Canada
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Ciesielski A, Grzywacz R. Dynamic bifurcations in continuous process of bioethanol production under aerobic conditions using Saccharomyces cerevisiae. Biochem Eng J 2020. [DOI: 10.1016/j.bej.2020.107609] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023]
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Layfield JB, Vann LR, Sheppard JD. A Novel Method of Inducing and Retaining Cell Cycle Synchronization in Cultures of Saccharomyces Cerevisiae. JOURNAL OF THE AMERICAN SOCIETY OF BREWING CHEMISTS 2018. [DOI: 10.1094/asbcj-2014-0324-02] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/03/2022]
Affiliation(s)
- J. Blake Layfield
- Department of Food, Bioprocessing and Nutrition Sciences, North Carolina State University, Raleigh, NC
| | - Lucas R. Vann
- Department of Food, Bioprocessing and Nutrition Sciences, North Carolina State University, Raleigh, NC
| | - John D. Sheppard
- Department of Food, Bioprocessing and Nutrition Sciences, North Carolina State University, Raleigh, NC
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Feng S, Srinivasan S, Lin YH. Redox potential-driven repeated batch ethanol fermentation under very-high-gravity conditions. Process Biochem 2012. [DOI: 10.1016/j.procbio.2011.12.018] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
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Li Y, Qian H, Yi Y. Oscillations and multiscale dynamics in a closed chemical reaction system: Second law of thermodynamics and temporal complexity. J Chem Phys 2008; 129:154505. [DOI: 10.1063/1.2995855] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
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Modeling synchronous growth of bacterial populations in phased cultivation. Bioprocess Biosyst Eng 2007; 31:435-43. [PMID: 18084780 DOI: 10.1007/s00449-007-0180-6] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2007] [Accepted: 11/23/2007] [Indexed: 10/22/2022]
Abstract
The phasing technique is a method for synchronizing cell populations in a bioreactor. Periodic changes of substrate supply and depletion can provoke a cell cycle phasing of originally stochastic scattered proliferation patterns. Synchronized cell populations characterized by changes in DNA content distribution can be monitored by flow cytometry. Thus, studies of the dynamics of single cells in specific cell cycle phases are facilitated. Here we present an age structured model framework investigating synchronized populations using delay differential equations. Applying the framework not only cell populations synchronously increasing under balanced growth conditions, but also synchronized cultures growing in continuous phasing experiments can be described. A process model developed for describing phased cultures was fitted to growth data obtained from a synchronous cultivation of Cupriavidus necator. Its potential utility is demonstrated by a quantitative process description and by its ability to identify ways in which the grade of synchrony could be improved.
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Roussel MR, Lloyd D. Observation of a chaotic multioscillatory metabolic attractor by real-time monitoring of a yeast continuous culture. FEBS J 2007; 274:1011-8. [PMID: 17250739 DOI: 10.1111/j.1742-4658.2007.05651.x] [Citation(s) in RCA: 28] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
We monitored a continuous culture of the yeast Saccharomyces cerevisiae by membrane-inlet mass spectrometry. This technique allows very rapid simultaneous measurements (one point every 12 s) of several dissolved gases. During our experiment, the culture exhibited a multioscillatory mode in which the dissolved oxygen and carbon dioxide records displayed periodicities of 13 h, 36 min and 4 min. The 36- and 4-min modes were not visible at all times, but returned at regular intervals during the 13-h cycle. The 4-min mode, which has not previously been described in continuous culture, can also be seen when the culture displays simpler oscillatory behavior. The data can be used to visualize a metabolic attractor of this system, i.e. the set of dissolved gas concentrations which are consistent with the multioscillatory state. Computation of the leading Lyapunov exponent reveals the dynamics on this attractor to be chaotic.
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Affiliation(s)
- Marc R Roussel
- Microbiology Group, Cardiff School of Biosciences, Cardiff University, UK.
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Fritsch M, Starruss J, Loesche A, Mueller S, Bley T. Cell cycle synchronization of Cupriavidus necator by continuous phasing measured via flow cytometry. Biotechnol Bioeng 2006; 92:635-42. [PMID: 16180241 DOI: 10.1002/bit.20647] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
Abstract
The continuous phasing technique was successfully used to obtain a high degree of cell cycle synchrony in cultures of the model organism Ralstonia eutropha JMP 134 (today reclassified into Cupriavidus necator). The responses of the organism were evaluated with flow cytometric determinations of DNA contents and cell size (by fluorescence and forward scatter measurements, respectively, after staining with the DNA-binding dye 4',6-diamidino-2'-phenylindole, DAPI), and cell concentration, after staining with the nucleic acid binding dye LDS-751. The strain was cultivated on a mineral medium with pyruvic acid sodium salt as the limiting carbon and energy source. Famine conditions, and thus cell dormancy, were achieved in every cycle. The best synchronization, according to the determination of DNA contents, was induced with phasing cycle durations of at least 4 h. The method allows the induction of synchrony for an indefinite period if the medium is exchanged rapidly and precisely. The results show that the time required for a complete cell cycle of Cupriavidus necator JMP 134 is independent of the chosen phasing cycle duration, provided that each process cycle lasts at least 3 h which is much longer than the time needed for a single DNA replication cycle. With shorter cycling periods DNA-synthesis is carried out in an uncoupled manner and only weak cell cycle synchrony can be attained. The results also show that DNA-synthesis can only be undertaken by cells when they have exceeded a critical size.
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Affiliation(s)
- M Fritsch
- Dresden University of Technology, Institute of Food Technology and Bioprocess Engineering, Bergstrasse 120, D-01062 Dresden, Germany
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