1
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Motamedian E, Berzins K, Muiznieks R, Stalidzans E. OptEnvelope: A target point guided method for growth-coupled production using knockouts. PLoS One 2023; 18:e0294313. [PMID: 37972019 PMCID: PMC10653430 DOI: 10.1371/journal.pone.0294313] [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: 08/04/2023] [Accepted: 10/29/2023] [Indexed: 11/19/2023] Open
Abstract
Finding the best knockout strategy for coupling biomass growth and production of a target metabolite using a mathematic model of metabolism is a challenge in biotechnology. In this research, a three-step method named OptEnvelope is presented based on finding minimal set of active reactions for a target point in the feasible solution space (envelope) using a mixed-integer linear programming formula. The method initially finds the reduced desirable solution space envelope in the product versus biomass plot by removing all inactive reactions. Then, with reinsertion of the deleted reactions, OptEnvelope attempts to reduce the number of knockouts so that the desirable production envelope is preserved. Additionally, OptEnvelope searches for envelopes with higher minimum production rates or fewer knockouts by evaluating different target points within the desired solution space. It is possible to limit the maximal number of knockouts. The method was implemented on metabolic models of E. coli and S. cerevisiae to test the method benchmarking the capability of these industrial microbes for overproduction of acetate and glycerol under aerobic conditions and succinate and ethanol under anaerobic conditions. The results illustrate that OptEnvelope is capable to find multiple strong coupled envelopes located in the desired solution space because of its novel target point oriented strategy of envelope search. The results indicate that E. coli is more appropriate to produce acetate and succinate while S. cerevisiae is a better host for glycerol production. Gene deletions for some of the proposed reaction knockouts have been previously reported to increase the production of these metabolites in experiments. Both organisms are suitable for ethanol production, however, more knockouts for the adaptation of E. coli are required. OptEnvelope is available at https://github.com/lv-csbg/optEnvelope.
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Affiliation(s)
- Ehsan Motamedian
- Institute of Microbiology and Biotechnology, Computational Systems Biology Group, University of Latvia, Riga, Latvia
| | - Kristaps Berzins
- Institute of Microbiology and Biotechnology, Computational Systems Biology Group, University of Latvia, Riga, Latvia
| | - Reinis Muiznieks
- Institute of Microbiology and Biotechnology, Computational Systems Biology Group, University of Latvia, Riga, Latvia
| | - Egils Stalidzans
- Institute of Microbiology and Biotechnology, Computational Systems Biology Group, University of Latvia, Riga, Latvia
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2
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Sun Y, Zhang T, Lu B, Li X, Jiang L. Application of cofactors in the regulation of microbial metabolism: A state of the art review. Front Microbiol 2023; 14:1145784. [PMID: 37113222 PMCID: PMC10126289 DOI: 10.3389/fmicb.2023.1145784] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2023] [Accepted: 03/15/2023] [Indexed: 04/29/2023] Open
Abstract
Cofactors are crucial chemicals that maintain cellular redox balance and drive the cell to do synthetic and catabolic reactions. They are involved in practically all enzymatic activities that occur in live cells. It has been a hot research topic in recent years to manage their concentrations and forms in microbial cells by using appropriate techniques to obtain more high-quality target products. In this review, we first summarize the physiological functions of common cofactors, and give a brief overview of common cofactors acetyl coenzyme A, NAD(P)H/NAD(P)+, and ATP/ADP; then we provide a detailed introduction of intracellular cofactor regeneration pathways, review the regulation of cofactor forms and concentrations by molecular biological means, and review the existing regulatory strategies of microbial cellular cofactors and their application progress, to maximize and rapidly direct the metabolic flux to target metabolites. Finally, we speculate on the future of cofactor engineering applications in cell factories. Graphical Abstract.
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Affiliation(s)
- Yang Sun
- State Key Laboratory of Materials-Oriented Chemical Engineering, College of Food Science and Light Industry, Nanjing Tech University, Nanjing, China
| | - Ting Zhang
- State Key Laboratory of Materials-Oriented Chemical Engineering, College of Food Science and Light Industry, Nanjing Tech University, Nanjing, China
| | - Bingqian Lu
- State Key Laboratory of Materials-Oriented Chemical Engineering, College of Food Science and Light Industry, Nanjing Tech University, Nanjing, China
| | - Xiangfei Li
- Engineering Laboratory for Industrial Microbiology Molecular Beeding of Anhui Province, College of Biologic and Food Engineering, Anhui Polytechnic University, Wuhu, China
- *Correspondence: Xiangfei Li,
| | - Ling Jiang
- State Key Laboratory of Materials-Oriented Chemical Engineering, College of Food Science and Light Industry, Nanjing Tech University, Nanjing, China
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3
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Roldán-López D, Muñiz-Calvo S, Daroqui N, Knez M, Guillamón JM, Pérez-Torrado R. The potential role of yeasts in the mitigation of health issues related to beer consumption. Crit Rev Food Sci Nutr 2022; 64:3059-3074. [PMID: 36222026 DOI: 10.1080/10408398.2022.2129584] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/03/2022]
Abstract
Food consumption of healthier products has become an essential trend in the food sector. This is also the case in beer, a biochemical process of transformation performed by yeast cells. More and more studies proclaim the need to reduce ethanol content in alcoholic drinks, certainly the most important health issue of beer consumption. In this review we gather key health issues related to beer consumption and the last advances regarding the use of yeast to attenuate those health problems. Furthermore, we have included the latest findings about the general positive impact of yeast in health as a consequence of its ability to biotransform polyphenolic compounds present in the wort, producing healthy compounds as hydroxytyrosol or melatonin, and its ability to perform as a probiotic driver. Besides, a group of population with chronic diseases as diabetes or celiac disease could take advantage of low carbohydrate or gluten-free beers, respectively. The role of yeast in beer production has been traditionally associated to its fermentative power. But here we have found a change in this dogma in the last years toward yeasts being a main driver to enhance healthy aspects of beer. The key findings are discussed and possible future directions are proposed.
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Affiliation(s)
- David Roldán-López
- Department of Food Biotechnology, Instituto de Agroquímica y Tecnología de los Alimentos, IATA-CSIC, Paterna, Spain
| | - Sara Muñiz-Calvo
- Department of Food Biotechnology, Instituto de Agroquímica y Tecnología de los Alimentos, IATA-CSIC, Paterna, Spain
| | - Noemi Daroqui
- Department of Food Biotechnology, Instituto de Agroquímica y Tecnología de los Alimentos, IATA-CSIC, Paterna, Spain
| | - Masa Knez
- Department of Food Biotechnology, Instituto de Agroquímica y Tecnología de los Alimentos, IATA-CSIC, Paterna, Spain
| | - Jose Manuel Guillamón
- Department of Food Biotechnology, Instituto de Agroquímica y Tecnología de los Alimentos, IATA-CSIC, Paterna, Spain
| | - Roberto Pérez-Torrado
- Department of Food Biotechnology, Instituto de Agroquímica y Tecnología de los Alimentos, IATA-CSIC, Paterna, Spain
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4
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Biotechnological Approaches to Lowering the Ethanol Yield during Wine Fermentation. Biomolecules 2021; 11:biom11111569. [PMID: 34827567 PMCID: PMC8615690 DOI: 10.3390/biom11111569] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2021] [Revised: 10/16/2021] [Accepted: 10/20/2021] [Indexed: 11/17/2022] Open
Abstract
One of the most prominent consequences of global climate warming for the wine industry is a clear increase of the sugar content in grapes, and thus the alcohol level in wines. Among the several approaches to address this important issue, this review focuses on biotechnological solutions, mostly relying on the selection and improvement of wine yeast strains for reduced ethanol yields. Other possibilities are also presented. Researchers are resorting to both S. cerevisiae and alternative wine yeast species for the lowering of alcohol yields. In addition to the use of selected strains under more or less standard fermentation conditions, aerobic fermentation is increasingly being explored for this purpose. Genetic improvement is also playing a role in the development of biotechnological tools to counter the increase in the wine alcohol levels. The use of recombinant wine yeasts is restricted to research, but its contribution to the advancement of the field is still relevant. Furthermore, genetic improvement by non-GMO approaches is providing some interesting results, and will probably result in the development of commercial yeast strains with a lower alcohol yield in the near future. The optimization of fermentation processes using natural isolates is, anyway, the most probable source of advancement in the short term for the production of wines with lower alcohol contents.
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5
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Baptista SL, Costa CE, Cunha JT, Soares PO, Domingues L. Metabolic engineering of Saccharomyces cerevisiae for the production of top value chemicals from biorefinery carbohydrates. Biotechnol Adv 2021; 47:107697. [PMID: 33508428 DOI: 10.1016/j.biotechadv.2021.107697] [Citation(s) in RCA: 37] [Impact Index Per Article: 12.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2020] [Revised: 01/11/2021] [Accepted: 01/13/2021] [Indexed: 12/16/2022]
Abstract
The implementation of biorefineries for a cost-effective and sustainable production of energy and chemicals from renewable carbon sources plays a fundamental role in the transition to a circular economy. The US Department of Energy identified a group of key target compounds that can be produced from biorefinery carbohydrates. In 2010, this list was revised and included organic acids (lactic, succinic, levulinic and 3-hydroxypropionic acids), sugar alcohols (xylitol and sorbitol), furans and derivatives (hydroxymethylfurfural, furfural and furandicarboxylic acid), biohydrocarbons (isoprene), and glycerol and its derivatives. The use of substrates like lignocellulosic biomass that impose harsh culture conditions drives the quest for the selection of suitable robust microorganisms. The yeast Saccharomyces cerevisiae, widely utilized in industrial processes, has been extensively engineered to produce high-value chemicals. For its robustness, ease of handling, genetic toolbox and fitness in an industrial context, S. cerevisiae is an ideal platform for the founding of sustainable bioprocesses. Taking these into account, this review focuses on metabolic engineering strategies that have been applied to S. cerevisiae for converting renewable resources into the previously identified chemical targets. The heterogeneity of each chemical and its manufacturing process leads to inevitable differences between the development stages of each process. Currently, 8 of 11 of these top value chemicals have been already reported to be produced by recombinant S. cerevisiae. While some of them are still in an early proof-of-concept stage, others, like xylitol or lactic acid, are already being produced from lignocellulosic biomass. Furthermore, the constant advances in genome-editing tools, e.g. CRISPR/Cas9, coupled with the application of innovative process concepts such as consolidated bioprocessing, will contribute for the establishment of S. cerevisiae-based biorefineries.
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Affiliation(s)
- Sara L Baptista
- CEB - Centre of Biological Engineering, University of Minho, Campus Gualtar, Braga, Portugal
| | - Carlos E Costa
- CEB - Centre of Biological Engineering, University of Minho, Campus Gualtar, Braga, Portugal
| | - Joana T Cunha
- CEB - Centre of Biological Engineering, University of Minho, Campus Gualtar, Braga, Portugal
| | - Pedro O Soares
- CEB - Centre of Biological Engineering, University of Minho, Campus Gualtar, Braga, Portugal
| | - Lucília Domingues
- CEB - Centre of Biological Engineering, University of Minho, Campus Gualtar, Braga, Portugal.
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6
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Zhang B, Ren L, Wang Y, Xu D, Zhang S, Wang H, Wang H, Zeng X, Xin B, Li F. Glycerol production through TPI1 defective Kluyveromyces marxianus at high temperature with glucose, fructose, and xylose as feedstock. Biochem Eng J 2020. [DOI: 10.1016/j.bej.2020.107689] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
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7
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Fan J, Zhang Z, Long C, He B, Hu Z, Jiang C, Zeng B. Identification and functional characterization of glycerol dehydrogenase reveal the role in kojic acid synthesis in Aspergillus oryzae. World J Microbiol Biotechnol 2020; 36:136. [PMID: 32783085 DOI: 10.1007/s11274-020-02912-4] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2020] [Accepted: 08/06/2020] [Indexed: 02/02/2023]
Abstract
Glycerol dehydrogenase has been identified and characterized functionally in many species. However, little is known about glycerol dehydrogenase genes and their functions in Aspergillus oryzae. Here, a total of 45 glycerol dehydrogenase genes in Aspergillus oryzae were identified and renamed from AoGld1 to AoGld45 according to their chromosome distribution. They were classified into three groups based on phylogenetic analysis. Synteny analysis revealed that thirteen AoGld genes are conserved among Aspergillus species. Promoter analysis displayed that AoGld3 and AoGld13 harbored multiple binding elements of GATA-type transcription factors and zinc-finger protein msnA that were involved in nitrogen and kojic acid metabolism, respectively. Moreover, the AoGld3 deletion strain Δgld3 was generated by the CRISPR/Cas9 system, which had no visible growth defects compared with the control wild-type strain under the control and osmotic stress treatments. However, disruption of AoGld3 led to the inhibition of kojic acid production, and the expression of kojA, kojR was down-regulated in the Δgld3 strain. Furthermore, when kojA or kojR was overexpressed in the Δgld3 strain, the yield of kojic acid was restored, suggesting that AoGld3 is involved in kojic acid production through affecting the expression of kojR and kojA. Taken together, these findings provide new insights into our understanding of glycerol dehydrogenase and establish foundation for further study of their roles in Aspergillus oryzae.
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Affiliation(s)
- Junxia Fan
- Jiangxi Key Laboratory of Bioprocess Engineering and Co-Innovation Center for In-Vitro Diagnostic Reagents and Devices of Jiangxi Province, College of Life Sciences, Jiangxi Science and Technology Normal University, Nanchang, 330013, China
| | - Zhe Zhang
- Jiangxi Key Laboratory of Bioprocess Engineering and Co-Innovation Center for In-Vitro Diagnostic Reagents and Devices of Jiangxi Province, College of Life Sciences, Jiangxi Science and Technology Normal University, Nanchang, 330013, China.
| | - Chuannan Long
- Jiangxi Key Laboratory of Bioprocess Engineering and Co-Innovation Center for In-Vitro Diagnostic Reagents and Devices of Jiangxi Province, College of Life Sciences, Jiangxi Science and Technology Normal University, Nanchang, 330013, China
| | - Bin He
- Jiangxi Key Laboratory of Bioprocess Engineering and Co-Innovation Center for In-Vitro Diagnostic Reagents and Devices of Jiangxi Province, College of Life Sciences, Jiangxi Science and Technology Normal University, Nanchang, 330013, China
| | - Zhihong Hu
- Jiangxi Key Laboratory of Bioprocess Engineering and Co-Innovation Center for In-Vitro Diagnostic Reagents and Devices of Jiangxi Province, College of Life Sciences, Jiangxi Science and Technology Normal University, Nanchang, 330013, China
| | - Chunmiao Jiang
- Jiangxi Key Laboratory of Bioprocess Engineering and Co-Innovation Center for In-Vitro Diagnostic Reagents and Devices of Jiangxi Province, College of Life Sciences, Jiangxi Science and Technology Normal University, Nanchang, 330013, China
| | - Bin Zeng
- Jiangxi Key Laboratory of Bioprocess Engineering and Co-Innovation Center for In-Vitro Diagnostic Reagents and Devices of Jiangxi Province, College of Life Sciences, Jiangxi Science and Technology Normal University, Nanchang, 330013, China.
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8
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Celik Z, Cabaroglu T, Krieger-Weber S. Impact of malolactic fermentation on the volatile composition of Turkish Kalecik karası red wines. JOURNAL OF THE INSTITUTE OF BREWING 2018. [DOI: 10.1002/jib.540] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
Affiliation(s)
- Z.D. Celik
- Department of Biotechnology; Çukurova University; Adana Turkey
- Agriculture Faculty, Food Engineering Department; Çukurova University; Adana Turkey
| | - T. Cabaroglu
- Agriculture Faculty, Food Engineering Department; Çukurova University; Adana Turkey
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9
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Gao YT, Zhang YS, Wen X, Song XW, Meng D, Li BJ, Wang MY, Tao YQ, Zhao H, Guan WQ, Du G. The glycerol and ethanol production kinetics in low-temperature wine fermentation usingSaccharomyces cerevisiaeyeast strains. Int J Food Sci Technol 2018. [DOI: 10.1111/ijfs.13910] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Yu-Ting Gao
- Tianjin Key Laboratory of Food Biotechnology; College of Biotechnology and Food Science; Tianjin University of Commerce; Tianjin 300134 China
| | - Yu-Shu Zhang
- Tianjin Key Laboratory of Food Biotechnology; College of Biotechnology and Food Science; Tianjin University of Commerce; Tianjin 300134 China
| | - Xiang Wen
- Tianjin Key Laboratory of Food Biotechnology; College of Biotechnology and Food Science; Tianjin University of Commerce; Tianjin 300134 China
| | - Xiao-Wan Song
- Tianjin Key Laboratory of Food Biotechnology; College of Biotechnology and Food Science; Tianjin University of Commerce; Tianjin 300134 China
| | - Dan Meng
- Tianjin Key Laboratory of Food Biotechnology; College of Biotechnology and Food Science; Tianjin University of Commerce; Tianjin 300134 China
| | - Bing-Juan Li
- Tianjin Key Laboratory of Food Biotechnology; College of Biotechnology and Food Science; Tianjin University of Commerce; Tianjin 300134 China
| | - Mei-Yan Wang
- Tianjin Key Laboratory of Food Biotechnology; College of Biotechnology and Food Science; Tianjin University of Commerce; Tianjin 300134 China
| | - Yong-Qing Tao
- Tianjin Key Laboratory of Food Biotechnology; College of Biotechnology and Food Science; Tianjin University of Commerce; Tianjin 300134 China
| | - Hui Zhao
- Tianjin Key Laboratory of Food Biotechnology; College of Biotechnology and Food Science; Tianjin University of Commerce; Tianjin 300134 China
| | - Wen-Qiang Guan
- Tianjin Key Laboratory of Food Biotechnology; College of Biotechnology and Food Science; Tianjin University of Commerce; Tianjin 300134 China
| | - Gang Du
- Tianjin Key Laboratory of Food Biotechnology; College of Biotechnology and Food Science; Tianjin University of Commerce; Tianjin 300134 China
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10
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Karabín M, Jelínek L, Kotrba P, Cejnar R, Dostálek P. Enhancing the performance of brewing yeasts. Biotechnol Adv 2017; 36:691-706. [PMID: 29277309 DOI: 10.1016/j.biotechadv.2017.12.014] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2017] [Revised: 11/23/2017] [Accepted: 12/20/2017] [Indexed: 12/26/2022]
Abstract
Beer production is one of the oldest known traditional biotechnological processes, but is nowadays facing increasing demands not only for enhanced product quality, but also for improved production economics. Targeted genetic modification of a yeast strain is one way to increase beer quality and to improve the economics of beer production. In this review we will present current knowledge on traditional approaches for improving brewing strains and for rational metabolic engineering. These research efforts will, in the near future, lead to the development of a wider range of industrial strains that should increase the diversity of commercial beers.
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Affiliation(s)
- Marcel Karabín
- Department of Biotechnology, University of Chemistry and Technology, Prague, Technická 5, 16628 Prague 6, Czech Republic
| | - Lukáš Jelínek
- Department of Biotechnology, University of Chemistry and Technology, Prague, Technická 5, 16628 Prague 6, Czech Republic
| | - Pavel Kotrba
- Department of Biochemistry and Microbiology, University of Chemistry and Technology, Prague, Technická 5, 16628 Prague 6, Czech Republic
| | - Rudolf Cejnar
- Department of Biotechnology, University of Chemistry and Technology, Prague, Technická 5, 16628 Prague 6, Czech Republic
| | - Pavel Dostálek
- Department of Biotechnology, University of Chemistry and Technology, Prague, Technická 5, 16628 Prague 6, Czech Republic.
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11
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Dzialo MC, Park R, Steensels J, Lievens B, Verstrepen KJ. Physiology, ecology and industrial applications of aroma formation in yeast. FEMS Microbiol Rev 2017; 41:S95-S128. [PMID: 28830094 PMCID: PMC5916228 DOI: 10.1093/femsre/fux031] [Citation(s) in RCA: 194] [Impact Index Per Article: 27.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2017] [Accepted: 06/06/2017] [Indexed: 01/05/2023] Open
Abstract
Yeast cells are often employed in industrial fermentation processes for their ability to efficiently convert relatively high concentrations of sugars into ethanol and carbon dioxide. Additionally, fermenting yeast cells produce a wide range of other compounds, including various higher alcohols, carbonyl compounds, phenolic compounds, fatty acid derivatives and sulfur compounds. Interestingly, many of these secondary metabolites are volatile and have pungent aromas that are often vital for product quality. In this review, we summarize the different biochemical pathways underlying aroma production in yeast as well as the relevance of these compounds for industrial applications and the factors that influence their production during fermentation. Additionally, we discuss the different physiological and ecological roles of aroma-active metabolites, including recent findings that point at their role as signaling molecules and attractants for insect vectors.
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Affiliation(s)
- Maria C Dzialo
- Laboratory for Genetics and Genomics, Centre of Microbial and Plant Genetics (CMPG), KU Leuven, Gaston Geenslaan 1, B-3001 Leuven, Belgium
- Laboratory for Systems Biology, VIB Center for Microbiology, Bio-Incubator, Gaston Geenslaan 1, 3001 Leuven, Belgium
| | - Rahel Park
- Laboratory for Genetics and Genomics, Centre of Microbial and Plant Genetics (CMPG), KU Leuven, Gaston Geenslaan 1, B-3001 Leuven, Belgium
- Laboratory for Systems Biology, VIB Center for Microbiology, Bio-Incubator, Gaston Geenslaan 1, 3001 Leuven, Belgium
| | - Jan Steensels
- Laboratory for Genetics and Genomics, Centre of Microbial and Plant Genetics (CMPG), KU Leuven, Gaston Geenslaan 1, B-3001 Leuven, Belgium
- Laboratory for Systems Biology, VIB Center for Microbiology, Bio-Incubator, Gaston Geenslaan 1, 3001 Leuven, Belgium
| | - Bart Lievens
- Laboratory for Process Microbial Ecology and Bioinspirational Management (PME&BIM), Department of Microbial and Molecular Systems, KU Leuven, Campus De Nayer, Fortsesteenweg 30A B-2860 Sint-Katelijne Waver, Belgium
| | - Kevin J Verstrepen
- Laboratory for Genetics and Genomics, Centre of Microbial and Plant Genetics (CMPG), KU Leuven, Gaston Geenslaan 1, B-3001 Leuven, Belgium
- Laboratory for Systems Biology, VIB Center for Microbiology, Bio-Incubator, Gaston Geenslaan 1, 3001 Leuven, Belgium
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12
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Çelik ZD, Erten H, Darici M, Cabaroğlu T. Molecular characterization and technological properties of wine yeasts isolated during spontaneous fermentation of Vitis vinifera L.cv. Narince grape must grown in ancient wine making area Tokat, Anatolia. BIO WEB OF CONFERENCES 2017. [DOI: 10.1051/bioconf/20170902017] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
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13
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Metabolic engineering for high glycerol production by the anaerobic cultures of Saccharomyces cerevisiae. Appl Microbiol Biotechnol 2017; 101:4403-4416. [DOI: 10.1007/s00253-017-8202-z] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2016] [Revised: 02/02/2017] [Accepted: 02/14/2017] [Indexed: 10/20/2022]
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14
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Lin T, Bai X, Hu Y, Li B, Yuan Y, Song H, Yang Y, Wang J. Synthetic
Saccharomyces cerevisiae
‐
Shewanella oneidensis
consortium enables glucose‐fed high‐performance microbial fuel cell. AIChE J 2016. [DOI: 10.1002/aic.15611] [Citation(s) in RCA: 33] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
Affiliation(s)
- Tong Lin
- School of Chemical Engineering and Technology, Key Laboratory of Systems Bioengineering (Ministry of Education), SynBio Research Platform, Collaborative Innovation Centre of Chemical Science and Engineering (Tianjin)Tianjin UniversityTianjin300072 China
| | - Xue Bai
- School of Chemical Engineering and Technology, Key Laboratory of Systems Bioengineering (Ministry of Education), SynBio Research Platform, Collaborative Innovation Centre of Chemical Science and Engineering (Tianjin)Tianjin UniversityTianjin300072 China
| | - Yidan Hu
- School of Chemical Engineering and Technology, Key Laboratory of Systems Bioengineering (Ministry of Education), SynBio Research Platform, Collaborative Innovation Centre of Chemical Science and Engineering (Tianjin)Tianjin UniversityTianjin300072 China
| | - Bingzhi Li
- School of Chemical Engineering and Technology, Key Laboratory of Systems Bioengineering (Ministry of Education), SynBio Research Platform, Collaborative Innovation Centre of Chemical Science and Engineering (Tianjin)Tianjin UniversityTianjin300072 China
| | - Ying‐Jin Yuan
- School of Chemical Engineering and Technology, Key Laboratory of Systems Bioengineering (Ministry of Education), SynBio Research Platform, Collaborative Innovation Centre of Chemical Science and Engineering (Tianjin)Tianjin UniversityTianjin300072 China
| | - Hao Song
- School of Chemical Engineering and Technology, Key Laboratory of Systems Bioengineering (Ministry of Education), SynBio Research Platform, Collaborative Innovation Centre of Chemical Science and Engineering (Tianjin)Tianjin UniversityTianjin300072 China
| | - Yun Yang
- School of Chemistry and EnvironmentBeihang UniversityBeijing100191 China
| | - Jingyu Wang
- Dept. of Chemical Engineering and Materials ScienceUniversity of MinnesotaMinneapolis MN55455
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15
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Zhang J, Sonnenschein N, Pihl TPB, Pedersen KR, Jensen MK, Keasling JD. Engineering an NADPH/NADP + Redox Biosensor in Yeast. ACS Synth Biol 2016; 5:1546-1556. [PMID: 27419466 DOI: 10.1021/acssynbio.6b00135] [Citation(s) in RCA: 56] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
Abstract
Genetically encoded biosensors have emerged as powerful tools for timely and precise in vivo evaluation of cellular metabolism. In particular, biosensors that can couple intercellular cues with downstream signaling responses are currently attracting major attention within health science and biotechnology. Still, there is a need for bioprospecting and engineering of more biosensors to enable real-time monitoring of specific cellular states and controlling downstream actuation. In this study, we report the engineering and application of a transcription factor-based NADPH/NADP+ redox biosensor in the budding yeast Saccharomyces cerevisiae. Using the biosensor, we are able to monitor the cause of oxidative stress by chemical induction, and changes in NADPH/NADP+ ratios caused by genetic manipulations. Because of the regulatory potential of the biosensor, we also show that the biosensor can actuate upon NADPH deficiency by activation of NADPH regeneration. Finally, we couple the biosensor with an expression of dosage-sensitive genes (DSGs) and thereby create a novel tunable sensor-selector useful for synthetic selection of cells with higher NADPH/NADP+ ratios from mixed cell populations. We show that the combination of exploitation and rational engineering of native signaling components is applicable for diagnosis, regulation, and selection of cellular redox states.
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Affiliation(s)
- Jie Zhang
- The
Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Kongens Lyngby, 2800, Denmark
| | - Nikolaus Sonnenschein
- The
Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Kongens Lyngby, 2800, Denmark
| | - Thomas P. B. Pihl
- The
Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Kongens Lyngby, 2800, Denmark
| | - Kasper R. Pedersen
- The
Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Kongens Lyngby, 2800, Denmark
| | - Michael K. Jensen
- The
Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Kongens Lyngby, 2800, Denmark
| | - Jay D. Keasling
- The
Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Kongens Lyngby, 2800, Denmark
- Joint BioEnergy Institute, Emeryville, California 94608, United States
- Biological Systems & Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, California 94720, United States
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Flavor impacts of glycerol in the processing of yeast fermented beverages: a review. Journal of Food Science and Technology 2015; 52:7588-98. [PMID: 26604336 DOI: 10.1007/s13197-015-1977-y] [Citation(s) in RCA: 35] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Revised: 07/05/2015] [Accepted: 07/21/2015] [Indexed: 10/23/2022]
Abstract
Glycerol contributes to the beverage body and fullness. Moreover, it also influences the flavor intensity. As a major byproduct, glycerol not only serves critical roles in yeast osmoregulation and redox balancing, but also acts as the carbon competitor against ethanol in alcoholic fermentation. Therefore, increasing glycerol yield benefits both the flavor and ethanol reduction for the fermented beverages. Glycerol yield has been elevated either by fermentation optimization or by yeast genetic modification. The fermentation optimizations reached maximum 14 g/L glycerol through screening yeast strains and optimizing fermentation parameters. Meanwhile the yeast overexpressing GPD1 (encoding glycerol-3-phosphate dehydrogenase) produced up to 6 folds more glycerol for beer and wine. Except for glycerol improvement, the genetically modified yeasts accumulated dramatically undesirable compounds such as acetaldehyde, acetate and acetoin which are detrimental for beverage flavor. In comparison, the natural high glycerol producers showed strain-specific manner on the yeast-derived aroma compounds like volatile acids, fusel alcohols, esters, and aldehydes. Temperature, sugar concentration, nitrogen composition, oxygen and pH-value, which influence glycerol biosynthesis, also obtained various effects on the production of aromatic compounds. In the current review, we firstly deliberate the organoleptic contributions of glycerol for fermented beverages. Furthermore, glycerol optimization strategies are discussed regarding to the yield improvement, the genes expressions, the overall flavor impacts and the feasibilities in beverage applications. Lastly, for improving beverage flavor by glycerol optimization, a high-throughput platform is proposed to increase the screening capacity of yeast strains and parameters in the processing of fermented beverages.
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Carrau F, Gaggero C, Aguilar PS. Yeast diversity and native vigor for flavor phenotypes. Trends Biotechnol 2015; 33:148-54. [DOI: 10.1016/j.tibtech.2014.12.009] [Citation(s) in RCA: 54] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2014] [Revised: 10/29/2014] [Accepted: 12/31/2014] [Indexed: 01/03/2023]
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Steensels J, Snoek T, Meersman E, Nicolino MP, Voordeckers K, Verstrepen KJ. Improving industrial yeast strains: exploiting natural and artificial diversity. FEMS Microbiol Rev 2014; 38:947-95. [PMID: 24724938 PMCID: PMC4293462 DOI: 10.1111/1574-6976.12073] [Citation(s) in RCA: 257] [Impact Index Per Article: 25.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2013] [Revised: 01/31/2014] [Accepted: 04/02/2014] [Indexed: 12/23/2022] Open
Abstract
Yeasts have been used for thousands of years to make fermented foods and beverages, such as beer, wine, sake, and bread. However, the choice for a particular yeast strain or species for a specific industrial application is often based on historical, rather than scientific grounds. Moreover, new biotechnological yeast applications, such as the production of second-generation biofuels, confront yeast with environments and challenges that differ from those encountered in traditional food fermentations. Together, this implies that there are interesting opportunities to isolate or generate yeast variants that perform better than the currently used strains. Here, we discuss the different strategies of strain selection and improvement available for both conventional and nonconventional yeasts. Exploiting the existing natural diversity and using techniques such as mutagenesis, protoplast fusion, breeding, genome shuffling and directed evolution to generate artificial diversity, or the use of genetic modification strategies to alter traits in a more targeted way, have led to the selection of superior industrial yeasts. Furthermore, recent technological advances allowed the development of high-throughput techniques, such as 'global transcription machinery engineering' (gTME), to induce genetic variation, providing a new source of yeast genetic diversity.
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Affiliation(s)
- Jan Steensels
- Laboratory for Genetics and Genomics, Centre of Microbial and Plant Genetics (CMPG), KU LeuvenLeuven, Belgium
- Laboratory for Systems Biology, VIBLeuven, Belgium
| | - Tim Snoek
- Laboratory for Genetics and Genomics, Centre of Microbial and Plant Genetics (CMPG), KU LeuvenLeuven, Belgium
- Laboratory for Systems Biology, VIBLeuven, Belgium
| | - Esther Meersman
- Laboratory for Genetics and Genomics, Centre of Microbial and Plant Genetics (CMPG), KU LeuvenLeuven, Belgium
- Laboratory for Systems Biology, VIBLeuven, Belgium
| | - Martina Picca Nicolino
- Laboratory for Genetics and Genomics, Centre of Microbial and Plant Genetics (CMPG), KU LeuvenLeuven, Belgium
- Laboratory for Systems Biology, VIBLeuven, Belgium
| | - Karin Voordeckers
- Laboratory for Genetics and Genomics, Centre of Microbial and Plant Genetics (CMPG), KU LeuvenLeuven, Belgium
- Laboratory for Systems Biology, VIBLeuven, Belgium
| | - Kevin J Verstrepen
- Laboratory for Genetics and Genomics, Centre of Microbial and Plant Genetics (CMPG), KU LeuvenLeuven, Belgium
- Laboratory for Systems Biology, VIBLeuven, Belgium
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Borrero-de Acuña JM, Bielecka A, Häussler S, Schobert M, Jahn M, Wittmann C, Jahn D, Poblete-Castro I. Production of medium chain length polyhydroxyalkanoate in metabolic flux optimized Pseudomonas putida. Microb Cell Fact 2014; 13:88. [PMID: 24948031 PMCID: PMC4077159 DOI: 10.1186/1475-2859-13-88] [Citation(s) in RCA: 83] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2014] [Accepted: 06/06/2014] [Indexed: 11/29/2022] Open
Abstract
BACKGROUND Pseudomnas putida is a natural producer of medium chain length polyhydroxyalkanoates (mcl-PHA), a polymeric precursor of bioplastics. A two-fold increase of mcl-PHA production via inactivation of the glucose dehydrogenase gene gcd, limiting the metabolic flux towards side products like gluconate was achieved before. Here, we investigated the overproduction of enzymes catalyzing limiting steps of mcl-PHA precursor formation. RESULTS A genome-based in silico model for P. putida KT2440 metabolism was employed to identify potential genetic targets to be engineered for the improvement of mcl-PHA production using glucose as sole carbon source. Here, overproduction of pyruvate dehydrogenase subunit AcoA in the P. putida KT2440 wild type and the Δgcd mutant strains led to an increase of PHA production. In controlled bioreactor batch fermentations PHA production was increased by 33% in the acoA overexpressing wild type and 121% in the acoA overexpressing Δgcd strain in comparison to P. putida KT2440. Overexpression of pgl-encoding 6-phosphoglucolactonase did not influence PHA production. Transcriptome analyses of engineered PHA producing P. putida in comparison to its parental strains revealed the induction of genes encoding glucose 6-phosphate dehydrogenase and pyruvate dehydrogenase. In addition, NADPH seems to be quantitatively consumed for efficient PHA synthesis, since a direct relationship between low levels of NADPH and high concentrations of the biopolymer were observed. In contrast, intracellular levels of NADH were found increased in PHA producing organisms. CONCLUSION Production of mcl-PHAs was enhanced in P. putida when grown on glucose via overproduction of a pyruvate dehydrogenase subunit (AcoA) in combination with a deletion of the glucose dehydrogenase (gcd) gene as predicted by in silico elementary flux mode analysis.
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Affiliation(s)
| | - Agata Bielecka
- Department of Molecular Bacteriology, Helmholtz Centre for Infection Research, D-38124 Braunschweig, Germany
| | - Susanne Häussler
- Department of Molecular Bacteriology, Helmholtz Centre for Infection Research, D-38124 Braunschweig, Germany
| | - Max Schobert
- Institute of Microbiology, Technische Universität Braunschweig D-38106, Braunschweig, Germany
| | - Martina Jahn
- Institute of Microbiology, Technische Universität Braunschweig D-38106, Braunschweig, Germany
| | - Christoph Wittmann
- Institute of Systems Biotechnology, Saarland University, D-66123 Saarbrücken, Germany
| | - Dieter Jahn
- Institute of Microbiology, Technische Universität Braunschweig D-38106, Braunschweig, Germany
| | - Ignacio Poblete-Castro
- Universidad Andrés Bello, Facultad de Ciencias Biológicas, Biosystems Engineering group, 8340176 Santiago, Chile
- Microbial Drugs group, Helmholtz Centre for Infection Research, D-38124 Braunschweig, Germany
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20
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Tamminen A, Kramer A, Labes A, Wiebe MG. Production of scopularide A in submerged culture with Scopulariopsis brevicaulis. Microb Cell Fact 2014; 13:89. [PMID: 24943257 PMCID: PMC4075624 DOI: 10.1186/1475-2859-13-89] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2014] [Accepted: 06/10/2014] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Marine organisms produce many novel compounds with useful biological activity, but are currently underexploited. Considerable research has been invested in the study of compounds from marine bacteria, and several groups have now recognised that marine fungi also produce an interesting range of compounds. During product discovery, these compounds are often produced only in non-agitated culture conditions, which are unfortunately not well suited for scaling up. A marine isolate of Scopulariopsis brevicaulis, strain LF580, produces the cyclodepsipeptide scopularide A, which has previously only been produced in non-agitated cultivation. RESULTS Scopulariopsis brevicaulis LF580 produced scopularide A when grown in batch and fed-batch submerged cultures. Scopularide A was extracted primarily from the biomass, with approximately 7% being extractable from the culture supernatant. By increasing the biomass density of the cultivations, we were able to increase the volumetric production of the cultures, but it was important to avoid nitrogen limitation. Specific production also increased with increasing biomass density, leading to improvements in volumetric production up to 29-fold, compared with previous, non-agitated cultivations. Cell densities up to 36 g L-1 were achieved in 1 to 10 L bioreactors. Production of scopularide A was optimised in complex medium, but was also possible in a completely defined medium. CONCLUSIONS Scopularide A production has been transferred from a non-agitated to a stirred tank bioreactor environment with an approximately 6-fold increase in specific and 29-fold increase in volumetric production. Production of scopularide A in stirred tank bioreactors demonstrates that marine fungal compounds can be suitable for scalable production, even with the native production organism.
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Affiliation(s)
| | | | | | - Marilyn G Wiebe
- VTT Technical Research Centre of Finland, P,O, Box 1000, FI-02044 VTT, Finland.
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21
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Ito Y, Hirasawa T, Shimizu H. Metabolic engineering of Saccharomyces cerevisiae to improve succinic acid production based on metabolic profiling. Biosci Biotechnol Biochem 2014; 78:151-9. [DOI: 10.1080/09168451.2014.877816] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/25/2022]
Abstract
Abstract
We performed metabolic engineering on the budding yeast Saccharomyces cerevisiae for enhanced production of succinic acid. Aerobic succinic acid production in S. cerevisiae was achieved by disrupting the SDH1 and SDH2 genes, which encode the catalytic subunits of succinic acid dehydrogenase. Increased succinic acid production was achieved by eliminating the ethanol biosynthesis pathways. Metabolic profiling analysis revealed that succinic acid accumulated intracellularly following disruption of the SDH1 and SDH2 genes, which suggests that enhancing the export of intracellular succinic acid outside of cells increases succinic acid production in S. cerevisiae. The mae1 gene encoding the Schizosaccharomyces pombe malic acid transporter was introduced into S. cerevisiae, and as a result, succinic acid production was successfully improved. Metabolic profiling analysis is useful in producing chemicals for metabolic engineering of microorganisms.
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Affiliation(s)
- Yuma Ito
- Department of Bioinformatic Engineering, Graduate School of Information Science and Technology, Osaka University, Osaka, Japan
| | - Takashi Hirasawa
- Department of Bioinformatic Engineering, Graduate School of Information Science and Technology, Osaka University, Osaka, Japan
| | - Hiroshi Shimizu
- Department of Bioinformatic Engineering, Graduate School of Information Science and Technology, Osaka University, Osaka, Japan
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22
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Wu D, Li X, Shen C, Lu J, Chen J, Xie G. Isolation of a haploid from an industrial Chinese rice wine yeast for metabolic engineering manipulation. JOURNAL OF THE INSTITUTE OF BREWING 2013. [DOI: 10.1002/jib.97] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Affiliation(s)
- Dianhui Wu
- The Key Laboratory of Industrial Biotechnology, Ministry of Education; Jiangnan University; 1800 Lihu Road Wuxi 214122 People's Republic of China
- National Engineering Laboratory for Cereal Fermentation Technology; Jiangnan University; 1800 Lihu Road Wuxi 214122 People's Republic of China
- School of Biotechnology; Jiangnan University; 1800 Lihu Road Wuxi 214122 People's Republic of China
| | - Xiaomin Li
- The Key Laboratory of Industrial Biotechnology, Ministry of Education; Jiangnan University; 1800 Lihu Road Wuxi 214122 People's Republic of China
- National Engineering Laboratory for Cereal Fermentation Technology; Jiangnan University; 1800 Lihu Road Wuxi 214122 People's Republic of China
- School of Biotechnology; Jiangnan University; 1800 Lihu Road Wuxi 214122 People's Republic of China
| | - Chao Shen
- The Key Laboratory of Industrial Biotechnology, Ministry of Education; Jiangnan University; 1800 Lihu Road Wuxi 214122 People's Republic of China
- National Engineering Laboratory for Cereal Fermentation Technology; Jiangnan University; 1800 Lihu Road Wuxi 214122 People's Republic of China
- School of Biotechnology; Jiangnan University; 1800 Lihu Road Wuxi 214122 People's Republic of China
| | - Jian Lu
- The Key Laboratory of Industrial Biotechnology, Ministry of Education; Jiangnan University; 1800 Lihu Road Wuxi 214122 People's Republic of China
- National Engineering Laboratory for Cereal Fermentation Technology; Jiangnan University; 1800 Lihu Road Wuxi 214122 People's Republic of China
- School of Biotechnology; Jiangnan University; 1800 Lihu Road Wuxi 214122 People's Republic of China
- Industrial Technology Research Institute of Jiangnan University in Suqian; 888 Renmin Road Suqian 223800 People's Republic of China
| | - Jian Chen
- The Key Laboratory of Industrial Biotechnology, Ministry of Education; Jiangnan University; 1800 Lihu Road Wuxi 214122 People's Republic of China
- National Engineering Laboratory for Cereal Fermentation Technology; Jiangnan University; 1800 Lihu Road Wuxi 214122 People's Republic of China
- School of Biotechnology; Jiangnan University; 1800 Lihu Road Wuxi 214122 People's Republic of China
| | - Guangfa Xie
- School of Biotechnology; Jiangnan University; 1800 Lihu Road Wuxi 214122 People's Republic of China
- National Engineering Research Centre for Chinese Rice Wine; China Shaoxing Rice Wine Group Co. Ltd; Shaoxing 312000 People's Republic of China
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23
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Hirasawa T, Ida Y, Furuasawa C, Shimizu H. Potential of a Saccharomyces cerevisiae recombinant strain lacking ethanol and glycerol biosynthesis pathways in efficient anaerobic bioproduction. Bioengineered 2013; 5:123-8. [PMID: 24247205 DOI: 10.4161/bioe.26569] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022] Open
Abstract
Saccharomyces cerevisiae shows high growth activity under low pH conditions and can be used for producing acidic chemicals such as organic acids as well as fuel ethanol. However, ethanol can also be a problematic by-product in the production of chemicals except for ethanol. We have reported that a stable low-ethanol production phenotype was achieved by disrupting 6 NADH-dependent alcohol dehydrogenase genes of S. cerevisiae. Moreover, the genes encoding the NADH-dependent glycerol biosynthesis enzymes were further disrupted because the ADH-disrupted recombinant strain showed high glycerol production to maintain intracellular redox balance. The recombinant strain incapable producing ethanol and glycerol could have the potential to be a host for producing metabolite(s) whose biosynthesis is coupled with NADH oxidation. Indeed, we successfully achieved almost 100% yield for L-lactate production using this recombinant strain as a host. In addition, the potential of our constructed recombinant strain for efficient bioproduction, particularly under anaerobic conditions, is also discussed.
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Affiliation(s)
- Takashi Hirasawa
- Department of Bioengineering; Tokyo Institute of Technology; Kanagawa, Japan
| | - Yoshihiro Ida
- Department of Bioinformatic Engineering; Graduate School of Information Science and Technology; Osaka University; Osaka, Japan
| | | | - Hiroshi Shimizu
- Department of Bioinformatic Engineering; Graduate School of Information Science and Technology; Osaka University; Osaka, Japan
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24
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Li S, Chen X, Liu L, Chen J. Pyruvate production inCandida glabrata: manipulation and optimization of physiological function. Crit Rev Biotechnol 2013; 36:1-10. [DOI: 10.3109/07388551.2013.811636] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
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25
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Adjustment of trehalose metabolism in wine Saccharomyces cerevisiae strains to modify ethanol yields. Appl Environ Microbiol 2013; 79:5197-207. [PMID: 23793638 DOI: 10.1128/aem.00964-13] [Citation(s) in RCA: 35] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
The ability of Saccharomyces cerevisiae to efficiently produce high levels of ethanol through glycolysis has been the focus of much scientific and industrial activity. Despite the accumulated knowledge regarding glycolysis, the modification of flux through this pathway to modify ethanol yields has proved difficult. Here, we report on the systematic screening of 66 strains with deletion mutations of genes encoding enzymes involved in central carbohydrate metabolism for altered ethanol yields. Five of these strains showing the most prominent changes in carbon flux were selected for further investigation. The genes were representative of trehalose biosynthesis (TPS1, encoding trehalose-6-phosphate synthase), central glycolysis (TDH3, encoding glyceraldehyde-3-phosphate dehydrogenase), the oxidative pentose phosphate pathway (ZWF1, encoding glucose-6-phosphate dehydrogenase), and the tricarboxylic acid (TCA) cycle (ACO1 and ACO2, encoding aconitase isoforms 1 and 2). Two strains exhibited lower ethanol yields than the wild type (tps1Δ and tdh3Δ), while the remaining three showed higher ethanol yields. To validate these findings in an industrial yeast strain, the TPS1 gene was selected as a good candidate for genetic modification to alter flux to ethanol during alcoholic fermentation in wine. Using low-strength promoters active at different stages of fermentation, the expression of the TPS1 gene was slightly upregulated, resulting in a decrease in ethanol production and an increase in trehalose biosynthesis during fermentation. Thus, the mutant screening approach was successful in terms of identifying target genes for genetic modification in commercial yeast strains with the aim of producing lower-ethanol wines.
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26
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Utilization of Saccharomyces cerevisiae recombinant strain incapable of both ethanol and glycerol biosynthesis for anaerobic bioproduction. Appl Microbiol Biotechnol 2013; 97:4811-9. [PMID: 23435983 DOI: 10.1007/s00253-013-4760-x] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2012] [Revised: 01/08/2013] [Accepted: 02/07/2013] [Indexed: 10/27/2022]
Abstract
The yeast Saccharomyces cerevisiae produces ethanol and glycerol as major unwanted byproducts, unless ethanol and glycerol are the target compounds. Minimizing the levels of these byproducts is important for bioproduction processes using yeast cells. In this study, we constructed a yeast strain in which both ethanol and glycerol production pathways were disrupted and examined its culture characteristics. In wild-type yeast strain, metabolic pathways that produce ethanol and glycerol play an important role in reoxidizing nicotinamide adenine dinucleotide (NADH) generated during glycolysis, particularly under anaerobic conditions. Strains in which both pathways were disrupted therefore failed to grow and consume glucose under anaerobic conditions. Introduction of desired metabolic reaction(s) coupled with NADH oxidation enabled the engineered strain to consume substrate and produce target compound(s). Here we introduced NADH-oxidization-coupled L-lactate production mechanisms into a yeast strain incapable of ethanol and glycerol biosynthesis, based on in silico simulation using a genome-scale metabolic model of S. cerevisiae. From the results of in silico simulation based on flux balance analysis, a feasible anaerobic non-growing metabolic state, in which L-lactate yield approached the theoretical maximum, was identified and this phenomenon was verified experimentally. The yeast strain incapable of both ethanol and glycerol biosynthesis is a potentially valuable host for bioproduction coupled with NADH oxidation under anaerobic conditions.
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27
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Evaluation of gene modification strategies for the development of low-alcohol-wine yeasts. Appl Environ Microbiol 2012; 78:6068-77. [PMID: 22729542 DOI: 10.1128/aem.01279-12] [Citation(s) in RCA: 73] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023] Open
Abstract
Saccharomyces cerevisiae has evolved a highly efficient strategy for energy generation which maximizes ATP energy production from sugar. This adaptation enables efficient energy generation under anaerobic conditions and limits competition from other microorganisms by producing toxic metabolites, such as ethanol and CO(2). Yeast fermentative and flavor capacity forms the biotechnological basis of a wide range of alcohol-containing beverages. Largely as a result of consumer demand for improved flavor, the alcohol content of some beverages like wine has increased. However, a global trend has recently emerged toward lowering the ethanol content of alcoholic beverages. One option for decreasing ethanol concentration is to use yeast strains able to divert some carbon away from ethanol production. In the case of wine, we have generated and evaluated a large number of gene modifications that were predicted, or known, to impact ethanol formation. Using the same yeast genetic background, 41 modifications were assessed. Enhancing glycerol production by increasing expression of the glyceraldehyde-3-phosphate dehydrogenase gene, GPD1, was the most efficient strategy to lower ethanol concentration. However, additional modifications were needed to avoid negatively affecting wine quality. Two strains carrying several stable, chromosomally integrated modifications showed significantly lower ethanol production in fermenting grape juice. Strain AWRI2531 was able to decrease ethanol concentrations from 15.6% (vol/vol) to 13.2% (vol/vol), whereas AWRI2532 lowered ethanol content from 15.6% (vol/vol) to 12% (vol/vol) in both Chardonnay and Cabernet Sauvignon juices. Both strains, however, produced high concentrations of acetaldehyde and acetoin, which negatively affect wine flavor. Further modifications of these strains allowed reduction of these metabolites.
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28
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Jayakody LN, Horie K, Hayashi N, Kitagaki H. Improvement of tolerance of Saccharomyces cerevisiae to hot-compressed water-treated cellulose by expression of ADH1. Appl Microbiol Biotechnol 2012; 94:273-83. [DOI: 10.1007/s00253-012-3918-2] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2011] [Revised: 01/02/2012] [Accepted: 01/20/2012] [Indexed: 12/20/2022]
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29
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Huberts DHEW, Niebel B, Heinemann M. A flux-sensing mechanism could regulate the switch between respiration and fermentation. FEMS Yeast Res 2011; 12:118-28. [DOI: 10.1111/j.1567-1364.2011.00767.x] [Citation(s) in RCA: 73] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2011] [Revised: 10/28/2011] [Accepted: 11/16/2011] [Indexed: 12/20/2022] Open
Affiliation(s)
- Daphne H. E. W. Huberts
- Molecular Systems Biology; Groningen Biomolecular Sciences and Biotechnology Institute; University of Groningen; Groningen; The Netherlands
| | - Bastian Niebel
- Molecular Systems Biology; Groningen Biomolecular Sciences and Biotechnology Institute; University of Groningen; Groningen; The Netherlands
| | - Matthias Heinemann
- Molecular Systems Biology; Groningen Biomolecular Sciences and Biotechnology Institute; University of Groningen; Groningen; The Netherlands
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30
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Smidt O, du Preez JC, Albertyn J. Molecular and physiological aspects of alcohol dehydrogenases in the ethanol metabolism of Saccharomyces cerevisiae. FEMS Yeast Res 2011; 12:33-47. [DOI: 10.1111/j.1567-1364.2011.00760.x] [Citation(s) in RCA: 54] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2011] [Revised: 10/31/2011] [Accepted: 11/03/2011] [Indexed: 11/29/2022] Open
Affiliation(s)
| | - James C. du Preez
- Department of Microbial, Biochemical & Food Biotechnology; University of the Free State; Bloemfontein; South Africa
| | - Jacobus Albertyn
- Department of Microbial, Biochemical & Food Biotechnology; University of the Free State; Bloemfontein; South Africa
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31
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Abstract
The production and sale of alcohol-reduced wines, and the lowering of ethanol concentration in wines with alcohol levels greater than acceptable for a specific wine style, poses a number of technical and marketing challenges. Several engineering solutions and wine production strategies that focus upon pre- or postfermentation technologies have been described and patented for production of wines with lower ethanol concentrations than would naturally arise through normal fermentation and wine production techniques. However, consumer perception and acceptance of the sensory quality of wines manufactured by techniques that utilize thermal distillation for alcohol removal is generally unfavorable. This negative perception from consumers has focused attention on nonthermal production processes and the development or selection of specific yeast strains with downregulated or modified gene expression for alcohol production. The information presented in this review will allow winemakers to assess the relative technical merits of each of the technologies described and make decisions regarding implementation of novel winemaking techniques for reducing ethanol concentration in wine.
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Affiliation(s)
- Leigh M Schmidtke
- National Wine and Grape Industry Centre, School of Agricultural and Wine Sciences, Charles Sturt University, Wagga Wagga, NSW 2678, Australia.
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32
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Varman AM, Xiao Y, Leonard E, Tang YJ. Statistics-based model for prediction of chemical biosynthesis yield from Saccharomyces cerevisiae. Microb Cell Fact 2011; 10:45. [PMID: 21689458 PMCID: PMC3145561 DOI: 10.1186/1475-2859-10-45] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2011] [Accepted: 06/21/2011] [Indexed: 11/16/2022] Open
Abstract
Background The robustness of Saccharomyces cerevisiae in facilitating industrial-scale production of ethanol extends its utilization as a platform to synthesize other metabolites. Metabolic engineering strategies, typically via pathway overexpression and deletion, continue to play a key role for optimizing the conversion efficiency of substrates into the desired products. However, chemical production titer or yield remains difficult to predict based on reaction stoichiometry and mass balance. We sampled a large space of data of chemical production from S. cerevisiae, and developed a statistics-based model to calculate production yield using input variables that represent the number of enzymatic steps in the key biosynthetic pathway of interest, metabolic modifications, cultivation modes, nutrition and oxygen availability. Results Based on the production data of about 40 chemicals produced from S. cerevisiae, metabolic engineering methods, nutrient supplementation, and fermentation conditions described therein, we generated mathematical models with numerical and categorical variables to predict production yield. Statistically, the models showed that: 1. Chemical production from central metabolic precursors decreased exponentially with increasing number of enzymatic steps for biosynthesis (>30% loss of yield per enzymatic step, P-value = 0); 2. Categorical variables of gene overexpression and knockout improved product yield by 2~4 folds (P-value < 0.1); 3. Addition of notable amount of intermediate precursors or nutrients improved product yield by over five folds (P-value < 0.05); 4. Performing the cultivation in a well-controlled bioreactor enhanced the yield of product by three folds (P-value < 0.05); 5. Contribution of oxygen to product yield was not statistically significant. Yield calculations for various chemicals using the linear model were in fairly good agreement with the experimental values. The model generally underestimated the ethanol production as compared to other chemicals, which supported the notion that the metabolism of Saccharomyces cerevisiae has historically evolved for robust alcohol fermentation. Conclusions We generated simple mathematical models for first-order approximation of chemical production yield from S. cerevisiae. These linear models provide empirical insights to the effects of strain engineering and cultivation conditions toward biosynthetic efficiency. These models may not only provide guidelines for metabolic engineers to synthesize desired products, but also be useful to compare the biosynthesis performance among different research papers.
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Affiliation(s)
- Arul M Varman
- Department of Energy, Environmental and Chemical Engineering, Washington University, St. Louis, MO 63130, USA
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Mendes FS, González-Pajuelo M, Cordier H, François JM, Vasconcelos I. 1,3-Propanediol production in a two-step process fermentation from renewable feedstock. Appl Microbiol Biotechnol 2011; 92:519-27. [DOI: 10.1007/s00253-011-3369-1] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2011] [Revised: 04/25/2011] [Accepted: 05/04/2011] [Indexed: 12/01/2022]
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34
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Guo ZP, Zhang L, Ding ZY, Shi GY. Minimization of glycerol synthesis in industrial ethanol yeast without influencing its fermentation performance. Metab Eng 2011; 13:49-59. [DOI: 10.1016/j.ymben.2010.11.003] [Citation(s) in RCA: 41] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2010] [Revised: 11/08/2010] [Accepted: 11/16/2010] [Indexed: 10/18/2022]
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Goldman S. Genetic chemistry: production of non-native compounds in yeast. Curr Opin Chem Biol 2010; 14:390-5. [PMID: 20456999 DOI: 10.1016/j.cbpa.2010.03.036] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2010] [Accepted: 03/31/2010] [Indexed: 12/17/2022]
Abstract
The tools and perspectives that chemists bring to the study of biological systems have yielded very important discoveries and opened many new research possibilities over the years (Hopkins AL: Network pharmacology: the next paradigm in drug discovery. Nat Chem Biol 2008, 11:682-690; Lehar J, Stockwell BR, Giaever G, Nislow C: Combination chemical genetics. Nat Chem Biol 2008, 11:674-681. This work describes use of genome level data to discover and understand higher order pleiotropic effects of combinations of drugs). Chemical biology has an ever-growing toolbox that has been expanding its reach into many different aspects of the study and utilization of biological systems (Strombergsson H, Kleywegt G: A chemogenomic view on protein-ligand spaces. BMC Bioinformatics 2009, 10(Suppl 6):S13; Bumpus BB, Evens BS, Thomas PM, Ntai I, Kelleher NI: A proteomics approach to discovering natural products and their biosynthetic pathways. Nat Biotechnol 2009, 27:951-956. This reviews techniques that allow for the identification of biochemical pathways that produce molecules of interest under very specific situations; Altamn KH, Buchner J, Kessler H, Diederich F, Krautler B, Lippard S, Liskamp R, Muller K, Nolan EM, Samori B, et al.: The state of the art of chemical biology. Chembiochem 2009, 10:16-29) including the study and utilization of biological systems in yeast. This review will describe recent successes in the use of yeast for both discovery and production of non-native secondary metabolites focused on pharmaceutically relevant compounds.
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Affiliation(s)
- Stanley Goldman
- Genetic Chemistry Inc. (Evolva Holding Company), 2440 Embarcadero Way, Palo Alto, CA 94303, USA.
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Kennedy CJ, Boyle PM, Waks Z, Silver PA. Systems-level engineering of nonfermentative metabolism in yeast. Genetics 2009; 183:385-97. [PMID: 19564482 PMCID: PMC2746161 DOI: 10.1534/genetics.109.105254] [Citation(s) in RCA: 29] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2009] [Accepted: 06/19/2009] [Indexed: 01/30/2023] Open
Abstract
We designed and experimentally validated an in silico gene deletion strategy for engineering endogenous one-carbon (C1) metabolism in yeast. We used constraint-based metabolic modeling and computer-aided gene knockout simulations to identify five genes (ALT2, FDH1, FDH2, FUM1, and ZWF1), which, when deleted in combination, predicted formic acid secretion in Saccharomyces cerevisiae under aerobic growth conditions. Once constructed, the quintuple mutant strain showed the predicted increase in formic acid secretion relative to a formate dehydrogenase mutant (fdh1 fdh2), while formic acid secretion in wild-type yeast was undetectable. Gene expression and physiological data generated post hoc identified a retrograde response to mitochondrial deficiency, which was confirmed by showing Rtg1-dependent NADH accumulation in the engineered yeast strain. Formal pathway analysis combined with gene expression data suggested specific modes of regulation that govern C1 metabolic flux in yeast. Specifically, we identified coordinated transcriptional regulation of C1 pathway enzymes and a positive flux control coefficient for the branch point enzyme 3-phosphoglycerate dehydrogenase (PGDH). Together, these results demonstrate that constraint-based models can identify seemingly unrelated mutations, which interact at a systems level across subcellular compartments to modulate flux through nonfermentative metabolic pathways.
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Affiliation(s)
- Caleb J Kennedy
- Department of Systems Biology, Harvard Medical School, Boston, Massachusetts 02115, USA
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Sequential injection kinetic flow assay for monitoring glycerol in a sugar fermentation process by Saccharomyces cerevisiae. Appl Biochem Biotechnol 2009; 160:1664-73. [PMID: 19479208 DOI: 10.1007/s12010-009-8675-z] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2009] [Accepted: 05/18/2009] [Indexed: 11/27/2022]
Abstract
A sequential injection system to monitor glycerol in a Saccharomyces cerevisiae fermentation process was developed. The method relies on the rate of formation of nicotinamide adenine dinucleotide in its reduced form (NADH, measured spectrophotometrically at 340 nm) from the reaction of glycerol with NAD(+) cofactor, catalysed by the enzyme glycerol dehydrogenase present in solution. This procedure enables the determination of glycerol between 0.046 and 0.46 g/l, (corresponding to yeast fermentation samples with concentrations up to 50 g/l) with good repeatability (relative standard deviation for n = 10 lower than 2.2% for three different samples) at a sampling frequency of 25/h. The detection and quantification limits using a miniaturised spectrophotometer were 0.13 and 0.44 mM, respectively. Reagent consumption was of 0.45 mumol NAD(+) and 1.8 microg enzyme per assay, and the waste production was 2.8 ml per determination. Results obtained for samples were in agreement with those obtained with a high-performance liquid chromatography method.
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Abstract
The traditional use of the yeast Saccharomyces cerevisiae in alcoholic fermentation has, over time, resulted in substantial accumulated knowledge concerning genetics, physiology, and biochemistry as well as genetic engineering and fermentation technologies. S. cerevisiae has become a platform organism for developing metabolic engineering strategies, methods, and tools. The current review discusses the relevance of several engineering strategies, such as rational and inverse metabolic engineering, evolutionary engineering, and global transcription machinery engineering, in yeast strain improvement. It also summarizes existing tools for fine-tuning and regulating enzyme activities and thus metabolic pathways. Recent examples of yeast metabolic engineering for food, beverage, and industrial biotechnology (bioethanol and bulk and fine chemicals) follow. S. cerevisiae currently enjoys increasing popularity as a production organism in industrial ("white") biotechnology due to its inherent tolerance of low pH values and high ethanol and inhibitor concentrations and its ability to grow anaerobically. Attention is paid to utilizing lignocellulosic biomass as a potential substrate.
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Pham TH, Mauvais G, Vergoignan C, De Coninck J, Dumont F, Lherminier J, Cachon R, Feron G. Gaseous environments modify physiology in the brewing yeastSaccharomyces cerevisiaeduring batch alcoholic fermentation. J Appl Microbiol 2008; 105:858-74. [DOI: 10.1111/j.1365-2672.2008.03821.x] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
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Popp A, Nguyen HTT, Boulahya K, Bideaux C, Alfenore S, Guillouet SE, Nevoigt E. Fermentative production of L-glycerol 3-phosphate utilizing a Saccharomyces cerevisiae strain with an engineered glycerol biosynthetic pathway. Biotechnol Bioeng 2008; 100:497-505. [PMID: 18438874 DOI: 10.1002/bit.21777] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
Interest in L-glycerol 3-phosphate (L-G3P) production via microbial fermentation is due to the compound's potential to replace the unstable substrate dihydroxyacetone phosphate (DHAP) in one-pot enzymatic carbohydrate syntheses. A Saccharomyces cerevisiae strain with deletions in both genes encoding specific L-G3Pases (GPP1 and GPP2) and multicopy overexpression of L-glycerol 3-phosphate dehydrogenase (GPD1) was studied via small-scale (100 mL) batch fermentations under quasi-anaerobic conditions. Intracellular accumulation of L-G3P reached extremely high levels (roughly 200 mM) but thereafter declined. Extracellular L-G3P was also detected and its concentration continuously increased throughout the fermentation, such that most of the total L-G3P was found outside the cells as fermentation concluded. Moreover, in spite of the complete elimination of specific L-G3Pase activity, the strain showed considerable glycerol formation suggesting unspecific dephosphorylation as a mechanism to relieve cells of intracellular L-G3P accumulation. Up-scaling the process employed fed-batch fermentation with repeated glucose feeding, plus an aerobic growth phase followed by an anaerobic product accumulation phase. This produced a final product titer of about 325 mg total L-G3P per liter of fermentation broth.
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Affiliation(s)
- A Popp
- Department of Microbiology and Genetics, Berlin University of Technology, Seestr. 13, D-13353 Berlin, Germany
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Donalies UEB, Nguyen HTT, Stahl U, Nevoigt E. Improvement of Saccharomyces yeast strains used in brewing, wine making and baking. ADVANCES IN BIOCHEMICAL ENGINEERING/BIOTECHNOLOGY 2008; 111:67-98. [PMID: 18463806 DOI: 10.1007/10_2008_099] [Citation(s) in RCA: 33] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/08/2022]
Abstract
Yeast was the first microorganism domesticated by mankind. Indeed, the production of bread and alcoholic beverages such as beer and wine dates from antiquity, even though the fact that the origin of alcoholic fermentation is a microorganism was not known until the nineteenth century. The use of starter cultures in yeast industries became a common practice after methods for the isolation of pure yeast strains were developed. Moreover, effort has been undertaken to improve these strains, first by classical genetic methods and later by genetic engineering. In general, yeast strain development has aimed at improving the velocity and efficiency of the respective production process and the quality of the final products. This review highlights the achievements in genetic engineering of Saccharomyces yeast strains applied in food and beverage industry.
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Affiliation(s)
- Ute E B Donalies
- Department of Microbiology and Genetics, Berlin University of Technology, Seestr. 13, 13353, Berlin, Germany
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Current awareness on yeast. Yeast 2008. [DOI: 10.1002/yea.1458] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022] Open
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