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Ehrmann AK, Wronska AK, Perli T, de Hulster EAF, Luttik MAH, van den Broek M, Carqueija Cardoso C, Pronk JT, Daran JM. Engineering Saccharomyces cerevisiae for fast vitamin-independent aerobic growth. Metab Eng 2024; 82:201-215. [PMID: 38364997 DOI: 10.1016/j.ymben.2024.01.010] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2023] [Revised: 01/08/2024] [Accepted: 01/26/2024] [Indexed: 02/18/2024]
Abstract
Chemically defined media for cultivation of Saccharomyces cerevisiae strains are commonly supplemented with a mixture of multiple Class-B vitamins, whose omission leads to strongly reduced growth rates. Fast growth without vitamin supplementation is interesting for industrial applications, as it reduces costs and complexity of medium preparation and may decrease susceptibility to contamination by auxotrophic microbes. In this study, suboptimal growth rates of S. cerevisiae CEN.PK113-7D in the absence of pantothenic acid, para-aminobenzoic acid (pABA), pyridoxine, inositol and/or biotin were corrected by single or combined overexpression of ScFMS1, ScABZ1/ScABZ2, ScSNZ1/ScSNO1, ScINO1 and Cyberlindnera fabianii BIO1, respectively. Several strategies were explored to improve growth of S. cerevisiae CEN.PK113-7D in thiamine-free medium. Overexpression of ScTHI4 and/or ScTHI5 enabled thiamine-independent growth at 83% of the maximum specific growth rate of the reference strain in vitamin-supplemented medium. Combined overexpression of seven native S. cerevisiae genes and CfBIO1 enabled a maximum specific growth rate of 0.33 ± 0.01 h-1 in vitamin-free synthetic medium. This growth rate was only 17 % lower than that of a congenic reference strain in vitamin-supplemented medium. Physiological parameters of the engineered vitamin-independent strain in aerobic glucose-limited chemostat cultures (dilution rate 0.10 h-1) grown on vitamin-free synthetic medium were similar to those of similar cultures of the parental strain grown on vitamin-supplemented medium. Transcriptome analysis revealed only few differences in gene expression between these cultures, which primarily involved genes with roles in Class-B vitamin metabolism. These results pave the way for development of fast-growing vitamin-independent industrial strains of S. cerevisiae.
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Affiliation(s)
- Anja K Ehrmann
- Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Kemitorvet, Building 220, 2800 Kgs, Lyngby, Denmark
| | - Anna K Wronska
- Department of Biotechnology, Delft University of Technology, Van der Maasweg 9, 2629 HZ, Delft, the Netherlands
| | - Thomas Perli
- Department of Biotechnology, Delft University of Technology, Van der Maasweg 9, 2629 HZ, Delft, the Netherlands
| | - Erik A F de Hulster
- Department of Biotechnology, Delft University of Technology, Van der Maasweg 9, 2629 HZ, Delft, the Netherlands
| | - Marijke A H Luttik
- Department of Biotechnology, Delft University of Technology, Van der Maasweg 9, 2629 HZ, Delft, the Netherlands
| | - Marcel van den Broek
- Department of Biotechnology, Delft University of Technology, Van der Maasweg 9, 2629 HZ, Delft, the Netherlands
| | - Clara Carqueija Cardoso
- Department of Biotechnology, Delft University of Technology, Van der Maasweg 9, 2629 HZ, Delft, the Netherlands
| | - Jack T Pronk
- Department of Biotechnology, Delft University of Technology, Van der Maasweg 9, 2629 HZ, Delft, the Netherlands
| | - Jean-Marc Daran
- Department of Biotechnology, Delft University of Technology, Van der Maasweg 9, 2629 HZ, Delft, the Netherlands.
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Benisch M, Aoki SK, Khammash M. Unlocking the potential of optogenetics in microbial applications. Curr Opin Microbiol 2024; 77:102404. [PMID: 38039932 DOI: 10.1016/j.mib.2023.102404] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2023] [Revised: 09/07/2023] [Accepted: 11/06/2023] [Indexed: 12/03/2023]
Abstract
Optogenetics is a powerful approach that enables researchers to use light to dynamically manipulate cellular behavior. Since the first published use of optogenetics in synthetic biology, the field has expanded rapidly, yielding a vast array of tools and applications. Despite its immense potential for achieving high spatiotemporal precision, optogenetics has predominantly been employed as a substitute for conventional chemical inducers. In this short review, we discuss key features of microbial optogenetics and highlight applications for understanding biology, cocultures, bioproduction, biomaterials, and therapeutics, in which optogenetics is more fully utilized to realize goals not previously possible by other methods.
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Affiliation(s)
- Moritz Benisch
- Department of Biosystems Science and Engineering (D-BSSE), ETH Zürich, Schanzenstrasse 44, 4056 Basel, Switzerland.
| | - Stephanie K Aoki
- Department of Biosystems Science and Engineering (D-BSSE), ETH Zürich, Schanzenstrasse 44, 4056 Basel, Switzerland.
| | - Mustafa Khammash
- Department of Biosystems Science and Engineering (D-BSSE), ETH Zürich, Schanzenstrasse 44, 4056 Basel, Switzerland.
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Shen D, He X, Weng P, Liu Y, Wu Z. A review of yeast: High cell-density culture, molecular mechanisms of stress response and tolerance during fermentation. FEMS Yeast Res 2022; 22:6775076. [PMID: 36288242 DOI: 10.1093/femsyr/foac050] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2022] [Revised: 09/21/2022] [Accepted: 10/22/2022] [Indexed: 01/07/2023] Open
Abstract
Yeast is widely used in the fermentation industry, and the major challenges in fermentation production system are high capital cost and low reaction rate. High cell-density culture is an effective method to increase the volumetric productivity of the fermentation process, thus making the fermentation process faster and more robust. During fermentation, yeast is subjected to various environmental stresses, including osmotic, ethanol, oxidation, and heat stress. To cope with these stresses, yeast cells need appropriate adaptive responses to acquire stress tolerances to prevent stress-induced cell damage. Since a single stressor can trigger multiple effects, both specific and nonspecific effects, general and specific stress responses are required to achieve comprehensive protection of cells. Since all these stresses disrupt protein structure, the upregulation of heat shock proteins and trehalose genes is induced when yeast cells are exposed to stress. A better understanding of the research status of yeast HCDC and its underlying response mechanism to various stresses during fermentation is essential for designing effective culture control strategies and improving the fermentation efficiency and stress resistance of yeast.
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Affiliation(s)
- Dongxu Shen
- Department of Food Science and Engineering, Ningbo University, Ningbo 315211, P.R. China
| | - Xiaoli He
- Department of Food Science and Engineering, Ningbo University, Ningbo 315211, P.R. China
| | - Peifang Weng
- Department of Food Science and Engineering, Ningbo University, Ningbo 315211, P.R. China
| | - Yanan Liu
- Department of Food Science and Engineering, Ningbo University, Ningbo 315211, P.R. China
| | - Zufang Wu
- Department of Food Science and Engineering, Ningbo University, Ningbo 315211, P.R. China
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Xing H, Zhu L, Wang P, Zhao G, Zhou Z, Yang Y, Zou H, Yan X. Display of receptor-binding domain of SARS-CoV-2 Spike protein variants on the Saccharomyces cerevisiae cell surface. Front Immunol 2022; 13:935573. [PMID: 36032096 PMCID: PMC9412237 DOI: 10.3389/fimmu.2022.935573] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2022] [Accepted: 07/13/2022] [Indexed: 12/18/2022] Open
Abstract
Severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2), the causative agent of coronavirus disease 2019 (COVID-19), represents a significant global human health threat. The most effective way to end the pandemic is through timely vaccination. In this study, the receptor-binding domains (RBDs) of Spike protein of the initial strain of SARS-CoV-2 and its variants, B.1.1.7 (Alpha), B.1.351 (Beta), and B.1.617.1 (Kappa), were successfully displayed on the surface of a Saccharomyces cerevisiae strain for development as a vaccine candidate. To rapidly express the recombinant protein and avoid the need for expensive galactose as an inducer, the gal80 gene of S. cerevisiae was knocked out, and the conventional 72-h culture period was thus successfully shortened to 24 h. Mice vaccinated against variant B.1.617.1 showed robust humoral and cellular immune responses. Moreover, the antiserum in the B.1.671.1 group had neutralizing activity against wild-type RBD and high binding titers against RBD mutants of variants B.1.351 and B.1.1.7. Double deglycosylation at N331Q and N343Q resulted in marked reduction of the affinity of RBD binding to angiotensin converting enzyme 2 (ACE2) and escaped antibody neutralization. This study demonstrates that yeast surface display technology can provide an alternative approach to rapid large-scale preparation of promising SARS-CoV-2 vaccine candidates at low cost.
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Affiliation(s)
- Hongguan Xing
- Shanghai Key Laboratory of Chemical Biology, School of Pharmacy, East China University of Science and Technology, Shanghai, China
- Chinese Academy of Science-Key Laboratory of Synthetic Biology, Chinese Academy of Science Center for Excellence in Molecular Plant Sciences, Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, Shanghai, China
| | - Liyan Zhu
- Key Laboratory of Medical Molecular Virology of Ministry of Education/National Health Commission, School of Basic Medical Sciences, Shanghai Medical College, Fudan University, Shanghai, China
- Department of Process Technology, Zhejiang Hongguan Bio-pharma Co., Ltd., Jiaxing, China
| | - Pingping Wang
- Chinese Academy of Science-Key Laboratory of Synthetic Biology, Chinese Academy of Science Center for Excellence in Molecular Plant Sciences, Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, Shanghai, China
| | - Guoping Zhao
- Chinese Academy of Science-Key Laboratory of Synthetic Biology, Chinese Academy of Science Center for Excellence in Molecular Plant Sciences, Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, Shanghai, China
- Key Laboratory of Medical Molecular Virology of Ministry of Education/National Health Commission, School of Basic Medical Sciences, Shanghai Medical College, Fudan University, Shanghai, China
| | - Zhihua Zhou
- Chinese Academy of Science-Key Laboratory of Synthetic Biology, Chinese Academy of Science Center for Excellence in Molecular Plant Sciences, Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, Shanghai, China
| | - Yi Yang
- Shanghai Key Laboratory of Chemical Biology, School of Pharmacy, East China University of Science and Technology, Shanghai, China
| | - Hong Zou
- Chinese Academy of Sciences Engineering Laboratory for Nutrition, Shanghai Institute of Nutrition and Health, Chinese Academy of Sciences, Shanghai, China
- *Correspondence: Hong Zou, ; Xing Yan,
| | - Xing Yan
- Shanghai Key Laboratory of Chemical Biology, School of Pharmacy, East China University of Science and Technology, Shanghai, China
- Chinese Academy of Science-Key Laboratory of Synthetic Biology, Chinese Academy of Science Center for Excellence in Molecular Plant Sciences, Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, Shanghai, China
- *Correspondence: Hong Zou, ; Xing Yan,
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Corrigendum. Yeast 2022; 39:422. [PMID: 35651285 DOI: 10.1002/yea.3794] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022] Open
Abstract
In [1], the following errors appeared in the published version This article is protected by copyright. All rights reserved.
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Efficient Conversion of Glycerol to Ethanol by an Engineered Saccharomyces cerevisiae Strain. Appl Environ Microbiol 2021; 87:e0026821. [PMID: 34524902 DOI: 10.1128/aem.00268-21] [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: 11/20/2022] Open
Abstract
Glycerol is an eco-friendly solvent that enhances plant biomass decomposition via glycerolysis in many pretreatment methods. Nonetheless, inefficient conversion of glycerol to ethanol by natural Saccharomyces cerevisiae limits its use in these processes. In this study, we have developed an efficient glycerol-converting yeast strain by genetically modifying the oxidation of cytosolic NAD (NADH) by an O2-dependent dynamic shuttle and abolishing both glycerol phosphorylation and biosynthesis in S. cerevisiae strain D452-2, as well as by vigorous expression of whole genes in the dihydroxyacetone (DHA) pathway (Candida utilis glycerol facilitator, Ogataea polymorpha glycerol dehydrogenase, endogenous dihydroxyacetone kinase, and triosephosphate isomerase). The engineered strain showed conversion efficiencies (CE) up to 0.49 g ethanol/g glycerol (98% of theoretical CE), with a production rate of >1 g liter-1 h-1 when glycerol was supplemented in a single fed-batch fermentation in a rich medium. Furthermore, the engineered strain converted a mixture of glycerol and glucose into bioethanol (>86 g/liter) with 92.8% CE. To the best of our knowledge, this is the highest reported titer of bioethanol produced from glycerol and glucose. Notably, we developed a glycerol-utilizing transformant from a parent strain which cannot utilize glycerol as a sole carbon source. The developed strain converted glycerol to ethanol with a productivity of 0.44 g liter-1 h-1 on minimal medium under semiaerobic conditions. Our findings will promote the utilization of glycerol in eco-friendly biorefineries and integrate bioethanol and plant oil industries. IMPORTANCE With the development of efficient lignocellulosic biorefineries, glycerol has attracted attention as an eco-friendly biomass-derived solvent that can enhance the dissociation of lignin and cell wall polysaccharides during the pretreatment process. Coconversion of glycerol with the sugars released from biomass after glycerolysis increases the resources for ethanol production and lowers the burden of component separation. However, low conversion efficiency from glycerol and sugars limits the industrial application of this process. Therefore, the generation of an efficient glycerol-fermenting yeast will promote the applicability of integrated biorefineries. Hence, metabolic flux control in yeast grown on glycerol will lead to the generation of cell factories that produce chemicals, which will boost biodiesel and bioethanol industries. Additionally, the use of glycerol-fermenting yeast will reduce global warming and generation of agricultural waste, leading to the establishment of a sustainable society.
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Walls LE, Martinez JL, Del Rio Chanona EA, Rios-Solis L. Definitive screening accelerates Taxol biosynthetic pathway optimization and scale up in Saccharomyces cerevisiae cell factories. Biotechnol J 2021; 17:e2100414. [PMID: 34649302 DOI: 10.1002/biot.202100414] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2021] [Revised: 10/08/2021] [Accepted: 10/11/2021] [Indexed: 12/22/2022]
Abstract
BACKGROUND Recent technological advancements in synthetic and systems biology have enabled the construction of microbial cell factories expressing diverse heterologous pathways in unprecedentedly short time scales. However, the translation of such laboratory scale breakthroughs to industrial bioprocesses remains a major bottleneck. METHODS AND MAJOR RESULTS In this study, an accelerated bioprocess development approach was employed to optimize the biosynthetic pathway of the blockbuster chemotherapy drug, Taxol. Statistical design of experiments approaches were coupled with an industrially relevant high-throughput microbioreactor system to optimize production of key Taxol intermediates, Taxadien-5α-ol and Taxadien-5α-yl-acetate, in engineered yeast cell factories. The optimal factor combination was determined via data driven statistical modelling and validated in 1 L bioreactors leading to a 2.1-fold improvement in taxane production compared to a typical defined media. Elucidation and mitigation of nutrient limitation enhanced product titers a further two-fold and titers of the critical Taxol precursors, Taxadien-5α-ol and Taxadien-5α-yl-acetate were improved to 34 and 11 mg L-1 , representing a three-fold improvement compared to the highest literature titers in S. cerevisiae. Comparable titers were obtained when the process was scaled up a further five-fold using 5 L bioreactors. CONCLUSIONS The results of this study highlight the benefits of a holistic design of experiments guided approach to expedite early stage bioprocess development.
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Affiliation(s)
- Laura E Walls
- Institute for Bioengineering, School of Engineering, University of Edinburgh, Edinburgh, UK.,Centre for Synthetic and Systems Biology (SynthSys), University of Edinburgh, Edinburgh, UK.,Department of Biotechnology and Biomedicine, Section for Synthetic Biology, Technical University of Denmark, Kongens Lyngby, Denmark
| | - José L Martinez
- Department of Biotechnology and Biomedicine, Section for Synthetic Biology, Technical University of Denmark, Kongens Lyngby, Denmark
| | - E Antonio Del Rio Chanona
- Sargent Centre for Process Systems Engineering, Department of Chemical Engineering, Imperial College London, UK
| | - Leonardo Rios-Solis
- Institute for Bioengineering, School of Engineering, University of Edinburgh, Edinburgh, UK.,Centre for Synthetic and Systems Biology (SynthSys), University of Edinburgh, Edinburgh, UK
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D-Galacturonic acid reduction by S. cerevisiae for L-galactonate production from extracted sugar beet press pulp hydrolysate. Appl Microbiol Biotechnol 2021; 105:5795-5807. [PMID: 34268581 PMCID: PMC8390429 DOI: 10.1007/s00253-021-11433-5] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2021] [Revised: 06/03/2021] [Accepted: 06/25/2021] [Indexed: 11/06/2022]
Abstract
Abstract Pectin-rich residues are considered as promising feedstocks for sustainable production of platform chemicals. Enzymatic hydrolysis of extracted sugar beet press pulp (SBPP) releases the main constituent of pectin, d-galacturonic acid (d-GalA). Using engineered Saccharomyces cerevisiae, d-GalA is then reduced to l-galactonate (l-GalOA) with sorbitol as co-substrate. The current work addresses the combination of enzymatic hydrolysis of pectin in SBPP with a consecutive optimized biotransformation of the released d-GalA to l-GalOA in simple batch processes in stirred-tank bioreactors. Process conditions were first identified with synthetic media, where a product concentration of 9.9 g L-1 L-GalOA was obtained with a product selectivity of 99% (L-GalOA D-GalA-1) at pH 5 with 4% (w/v) sorbitol within 48 h. A very similar batch process performance with a product selectivity of 97% was achieved with potassium citrate buffered SBPP hydrolysate, demonstrating for the first time direct production of L-GalOA from hydrolyzed biomass using engineered S. cerevisiae. Combining the hydrolysis process of extracted SBPP and the biotransformation process with engineered S. cerevisiae paves the way towards repurposing pectin-rich residues as substrates for value-added chemicals. Key points • Efficient bioreduction of D-GalA with S. cerevisiae in stirred-tank reactors • Batch production of L-GalOA by engineered S. cerevisiae with high selectivity • Direct L-GalOA production from hydrolyzed sugar beet press pulp Graphical abstract Bioreduction of D-galacturonic acid to L-galactonate with recombinant Saccharomyces cerevisiae enables for the first time the valorization of hydrolysates from extracted sugar beet press pulp for the sustainable production of value-added chemicals. ![]()
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Optimization of Synthetic Media Composition for Kluyveromyces marxianus Fed-Batch Cultivation. FERMENTATION 2021. [DOI: 10.3390/fermentation7020062] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022] Open
Abstract
The Kluyveromyces marxianus yeast recently has gained considerable attention due to its applicability in high-value-added product manufacturing. In order to intensify the biosynthesis rate of a target product, reaching high biomass concentrations in the reaction medium is mandatory. Fed-batch processes are an attractive and efficient way how to achieve high cell densities. However, depending on the physiology of the particular microbial strain, an optimal media composition should be used to avoid by-product synthesis and, subsequently, a decrease in overall process effi-ciency. Thus, the aim of the present study was to optimise the synthetic growth medium and feeding solution compositions (in terms of carbon, nitrogen, phosphorous, magnesium, and calcium concentrations) for high cell density K. marxianus fed‑batch cultivations. Additionally, the biomass yields from the vitamin mixture and other macro/microelements were identified. A model predictive control algorithm was successfully applied for a fed-batch cultivation control. Biomass growth and substrate consumption kinetics were compared with the mathematical model predictions. Finally, 2‑phenylethanol biosynthesis was induced and its productivity was estimated. The determined optimal macronutrient ratio for K. marxianus biomass growth was identified as C:N:P = 1:0.07:0.011. The maximal attained yeast biomass concentration was close to 70 g·L-1 and the 2-PE biosynthesis rate was 0.372 g·L−1·h−1, with a yield of 74% from 2-phenylalanine.
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