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Topaloğlu A, Esen Ö, Turanlı-Yıldız B, Arslan M, Çakar ZP. From Saccharomyces cerevisiae to Ethanol: Unlocking the Power of Evolutionary Engineering in Metabolic Engineering Applications. J Fungi (Basel) 2023; 9:984. [PMID: 37888240 PMCID: PMC10607480 DOI: 10.3390/jof9100984] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2023] [Revised: 09/25/2023] [Accepted: 09/28/2023] [Indexed: 10/28/2023] Open
Abstract
Increased human population and the rapid decline of fossil fuels resulted in a global tendency to look for alternative fuel sources. Environmental concerns about fossil fuel combustion led to a sharp move towards renewable and environmentally friendly biofuels. Ethanol has been the primary fossil fuel alternative due to its low carbon emission rates, high octane content and comparatively facile microbial production processes. In parallel to the increased use of bioethanol in various fields such as transportation, heating and power generation, improvements in ethanol production processes turned out to be a global hot topic. Ethanol is by far the leading yeast output amongst a broad spectrum of bio-based industries. Thus, as a well-known platform microorganism and native ethanol producer, baker's yeast Saccharomyces cerevisiae has been the primary subject of interest for both academic and industrial perspectives in terms of enhanced ethanol production processes. Metabolic engineering strategies have been primarily adopted for direct manipulation of genes of interest responsible in mainstreams of ethanol metabolism. To overcome limitations of rational metabolic engineering, an alternative bottom-up strategy called inverse metabolic engineering has been widely used. In this context, evolutionary engineering, also known as adaptive laboratory evolution (ALE), which is based on random mutagenesis and systematic selection, is a powerful strategy to improve bioethanol production of S. cerevisiae. In this review, we focus on key examples of metabolic and evolutionary engineering for improved first- and second-generation S. cerevisiae bioethanol production processes. We delve into the current state of the field and show that metabolic and evolutionary engineering strategies are intertwined and many metabolically engineered strains for bioethanol production can be further improved by powerful evolutionary engineering strategies. We also discuss potential future directions that involve recent advancements in directed genome evolution, including CRISPR-Cas9 technology.
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Affiliation(s)
- Alican Topaloğlu
- Department of Molecular Biology and Genetics, Faculty of Science and Letters, Istanbul Technical University, Istanbul 34469, Türkiye; (A.T.); (Ö.E.)
- Dr. Orhan Öcalgiray Molecular Biology, Biotechnology and Genetics Research Center (ITU-MOBGAM), Istanbul Technical University, Istanbul 34469, Türkiye;
| | - Ömer Esen
- Department of Molecular Biology and Genetics, Faculty of Science and Letters, Istanbul Technical University, Istanbul 34469, Türkiye; (A.T.); (Ö.E.)
- Dr. Orhan Öcalgiray Molecular Biology, Biotechnology and Genetics Research Center (ITU-MOBGAM), Istanbul Technical University, Istanbul 34469, Türkiye;
| | - Burcu Turanlı-Yıldız
- Dr. Orhan Öcalgiray Molecular Biology, Biotechnology and Genetics Research Center (ITU-MOBGAM), Istanbul Technical University, Istanbul 34469, Türkiye;
| | - Mevlüt Arslan
- Department of Genetics, Faculty of Veterinary Medicine, Van Yüzüncü Yıl University, Van 65000, Türkiye;
| | - Zeynep Petek Çakar
- Department of Molecular Biology and Genetics, Faculty of Science and Letters, Istanbul Technical University, Istanbul 34469, Türkiye; (A.T.); (Ö.E.)
- Dr. Orhan Öcalgiray Molecular Biology, Biotechnology and Genetics Research Center (ITU-MOBGAM), Istanbul Technical University, Istanbul 34469, Türkiye;
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Liu S, Sun Y, Wei T, Gong D, Wang Q, Zhan Z, Song J. Engineering 3-Hydroxypropionic Acid Production from Glucose in Yarrowia lipolytica through Malonyl-CoA Pathway. J Fungi (Basel) 2023; 9:jof9050573. [PMID: 37233284 DOI: 10.3390/jof9050573] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2023] [Revised: 05/11/2023] [Accepted: 05/12/2023] [Indexed: 05/27/2023] Open
Abstract
3-Hydroxypropionic acid (3-HP) is an important intermediate compound in the chemical industry. Green and environmentally friendly microbial synthesis methods are becoming increasingly popular in a range of industries. Compared to other chassis cells, Yarrowia lipolytica possesses advantages, such as high tolerance to organic acid and a sufficient precursor required to synthesize 3-HP. In this study, gene manipulations, including the overexpression of genes MCR-NCa, MCR-CCa, GAPNSm, ACC1 and ACSSeL641P and knocking out bypass genes MLS1 and CIT2, leading to the glyoxylate cycle, were performed to construct a recombinant strain. Based on this, the degradation pathway of 3-HP in Y. lipolytica was discovered, and relevant genes MMSDH and HPDH were knocked out. To our knowledge, this study is the first to produce 3-HP in Y. lipolytica. The yield of 3-HP in recombinant strain Po1f-NC-14 in shake flask fermentation reached 1.128 g·L-1, and the yield in fed-batch fermentation reached 16.23 g·L-1. These results are highly competitive compared to other yeast chassis cells. This study creates the foundation for the production of 3-HP in Y. lipolytica and also provides a reference for further research in the future.
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Affiliation(s)
- Shiyu Liu
- School of Life Science and Technology, Harbin Institute of Technology, Harbin 150006, China
| | - Yao Sun
- School of Life Science and Technology, Harbin Institute of Technology, Harbin 150006, China
| | - Tianhui Wei
- School of Life Science and Technology, Harbin Institute of Technology, Harbin 150006, China
| | - Dianliang Gong
- School of Life Science and Technology, Harbin Institute of Technology, Harbin 150006, China
| | - Qi Wang
- School of Life Science and Technology, Harbin Institute of Technology, Harbin 150006, China
| | - Zhe Zhan
- School of Life Science and Technology, Harbin Institute of Technology, Harbin 150006, China
| | - Jinzhu Song
- School of Life Science and Technology, Harbin Institute of Technology, Harbin 150006, China
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Da-Silva JR, Correia-Lima L, Fernandes G, Ribeiro-Filho N, Madruga MS, Lima MDS, Muniz MB. Mandacaru fruit pulp (Cereus jamacaru D.C.) as an adjunct and its influence on Beer properties. Food Chem 2023; 406:135066. [PMID: 36462364 DOI: 10.1016/j.foodchem.2022.135066] [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: 08/18/2022] [Revised: 11/16/2022] [Accepted: 11/23/2022] [Indexed: 11/30/2022]
Abstract
Beer is a complex product due to its raw materials (malt, hops, yeast, and water). Beer production can also use other matters as adjuncts. This study investigated the influence of Mandacaru fruit pulp (MFP) as an adjunct on volatile and phenolic compounds, and antioxidant properties of Beer. Worts were produced using four treatments including a control. Fermentations were conducted for 10 days at 18 °C using yeast Lachancea spp, maturated at 3 °C for 15 days, and bottled at 20 °C for 15 days. All compounds were evaluated by HPLC, and GC-MS. Worts' supplementation influenced the volatile and phenolic profile and increased the antioxidant activity of wort and Beer. Beers A (100 g of MFP/L), B (200 g of MFP/L), and C (300 g of MFP/L) presented higher ethanol and glycerol content. Beer C contained the highest antioxidant activity and total phenolic content. Worts' supplemented with MFP increased aroma formation.
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Affiliation(s)
- José Renato Da-Silva
- PPGCTA/Technology Center, Campus I, Federal University of Paraiba, João Pessoa, Paraiba, Brazil
| | - Lys Correia-Lima
- PPGCTA/Technology Center, Campus I, Federal University of Paraiba, João Pessoa, Paraiba, Brazil
| | - Givanildo Fernandes
- PPGCTA/Technology Center, Campus I, Federal University of Paraiba, João Pessoa, Paraiba, Brazil
| | - Normando Ribeiro-Filho
- DSER and PPGA/Centre for Agrarian Science, Campus II, Federal University of Paraiba, Areia, Paraiba, Brazil.
| | - Marta Suely Madruga
- PPGCTA/Technology Center, Campus I, Federal University of Paraiba, João Pessoa, Paraiba, Brazil
| | - Marcos Dos Santos Lima
- Department of Food Technology, Federal Institute of Sertão Pernambucano, Petrolina, Pernambuco, Brazil
| | - Marcelo Barbosa Muniz
- PPGCTA/Technology Center, Campus I, Federal University of Paraiba, João Pessoa, Paraiba, Brazil
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van Aalst AC, de Valk SC, van Gulik WM, Jansen ML, Pronk JT, Mans R. Pathway engineering strategies for improved product yield in yeast-based industrial ethanol production. Synth Syst Biotechnol 2022; 7:554-566. [PMID: 35128088 PMCID: PMC8792080 DOI: 10.1016/j.synbio.2021.12.010] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2021] [Revised: 12/22/2021] [Accepted: 12/23/2021] [Indexed: 12/16/2022] Open
Abstract
Product yield on carbohydrate feedstocks is a key performance indicator for industrial ethanol production with the yeast Saccharomyces cerevisiae. This paper reviews pathway engineering strategies for improving ethanol yield on glucose and/or sucrose in anaerobic cultures of this yeast by altering the ratio of ethanol production, yeast growth and glycerol formation. Particular attention is paid to strategies aimed at altering energy coupling of alcoholic fermentation and to strategies for altering redox-cofactor coupling in carbon and nitrogen metabolism that aim to reduce or eliminate the role of glycerol formation in anaerobic redox metabolism. In addition to providing an overview of scientific advances we discuss context dependency, theoretical impact and potential for industrial application of different proposed and developed strategies.
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Affiliation(s)
- Aafke C.A. van Aalst
- Department of Biotechnology, Delft University of Technology, Van der Maasweg 9, 2629, HZ Delft, the Netherlands
| | - Sophie C. de Valk
- Department of Biotechnology, Delft University of Technology, Van der Maasweg 9, 2629, HZ Delft, the Netherlands
| | - Walter M. van Gulik
- Department of Biotechnology, Delft University of Technology, Van der Maasweg 9, 2629, HZ Delft, the Netherlands
| | - Mickel L.A. Jansen
- DSM Biotechnology Centre, Alexander Fleminglaan 1, 2613, AX Delft, the Netherlands
| | - Jack T. Pronk
- Department of Biotechnology, Delft University of Technology, Van der Maasweg 9, 2629, HZ Delft, the Netherlands
| | - Robert Mans
- Department of Biotechnology, Delft University of Technology, Van der Maasweg 9, 2629, HZ Delft, the Netherlands
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Effect of Yeast Assimilable Nitrogen Content on Fermentation Kinetics, Wine Chemical Composition and Sensory Character in the Production of Assyrtiko Wines. APPLIED SCIENCES-BASEL 2022. [DOI: 10.3390/app12031405] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
Two wild-type Saccharomyces cerevisiae yeast strains (Sa and Sb) were tested for white wine production using Assyrtiko grape of Santorini. A third commercial Saccharomyces strain was also studied for comparison reasons. Two concentrations of yeast extract and diammonium phosphate (DAP) were added to the must (150 and 250 mg/L) in order to evaluate the effect of nitrogen content on the final wine quality. Analytical methods (HPLC, GC-MS) and sensory analysis were employed to assess the quality of the wines. Fermentation kinetics were monitored throughout the experiment. By the second day of fermentation, all strains showed an approximate consumption of 70% of amino acids. Differences among strains were observed regarding inorganic nitrogen requirements. Sb strain resulted in higher concentrations of higher alcohols (1.9-fold) and ketones (5.6-fold) and lower concentrations of esters (1.2-fold) compared to the control, while Sa strain resulted in higher content of fatty acids (2.1-fold). Both indigenous strains scored better results in aroma quality, body and acidity compared to control. The overall evaluation of the data highlights the great potential of the indigenous S. cerevisiae strains as fermentation starters providing promising results in the sector of terroir wines.
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Huang XF, Reardon KF. Quorum-sensing molecules increase ethanol yield from Saccharomyces cerevisiae. FEMS Yeast Res 2021; 21:6424905. [PMID: 34755845 DOI: 10.1093/femsyr/foab056] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2021] [Accepted: 11/05/2021] [Indexed: 11/14/2022] Open
Abstract
One strategy to increase the yield of desired fermentation products is to redirect substrate carbon from biomass synthesis. Non-genetic approaches to alter metabolism may have advantages of general applicability and simple control. The goal of this study was to identify and evaluate chemicals for their ability to inhibit the growth of Saccharomyces cerevisiae while allowing ethanol production with higher yields. Eight potential growth-inhibitory chemicals were screened for their ability to reduce cell growth in 24-well plates. Effective chemicals were then evaluated in cultivations to identify those that simultaneously reduced biomass yield and increased ethanol yield. The yeast quorum-sensing molecules 2-phenylethanol, tryptophol, and tyrosol, were found to increase the ethanol yield of S. cerevisiae JAY 270. These molecules were tested with seven other yeast strains and ethanol yields of up to 15% higher were observed. The effects of 2-phenylethanol and tryptophol were also studied in bioreactor fermentations. These findings demonstrate for the first time that the ethanol yield can be improved by adding yeast quorum-sensing molecules to reduce the cell growth of S. cerevisiae, suggesting a strategy to improve the yield of ethanol and other yeast fermentation products by manipulating native biological control systems.
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Affiliation(s)
- Xing-Feng Huang
- Department of Chemical and Biological Engineering, Colorado State University, Fort Collins, CO
| | - Kenneth F Reardon
- Department of Chemical and Biological Engineering, Colorado State University, Fort Collins, CO
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Pereira R, Ishchuk OP, Li X, Liu Q, Liu Y, Otto M, Chen Y, Siewers V, Nielsen J. Metabolic Engineering of Yeast. Metab Eng 2021. [DOI: 10.1002/9783527823468.ch18] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
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Ribeiro-Filho N, Linforth R, Powell CD, Fisk ID. Influence of essential inorganic elements on flavour formation during yeast fermentation. Food Chem 2021; 361:130025. [PMID: 34029908 DOI: 10.1016/j.foodchem.2021.130025] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2020] [Revised: 04/13/2021] [Accepted: 05/07/2021] [Indexed: 11/25/2022]
Abstract
The relative concentration of available inorganic elements is critical for yeast growth and metabolism and has potential to be a tool leading to directed yeast flavour formation during fermentation. This study investigates the influence of essential inorganic elements during alcoholic fermentation of brewers wort, fermented using three independent yeast strains, Saccharomyces pastorianus W34/70, and Saccharomyces cerevisiae strains M2 and NCYC2592 under a range of conditions replicated for each yeast strain. 10 treatments were applied: 1 control and 9 inorganic supplementations: standard brewers wort, ammonia-nitrogen, inorganic phosphate, potassium, magnesium, copper, zinc, iron, manganese and a composite mixture, Twenty-five chemical markers were evaluated by HPLC (ethanol, glycerol), and GC-MS (aroma). There was a significant change in volatile aroma compounds during fermentation, which was more prominent when supplemented with ammonia nitrogen, inorganic phosphate, potassium or magnesium (P < 0.05). Heavy metal ions mostly had a negative effect on the flavour formation.
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Affiliation(s)
- Normando Ribeiro-Filho
- DSER/Centre of Agrarian Science Campus II, Federal University of Paraiba, Areia, Paraiba, Brazil; Division of Food, Nutrition and Dietetics, School of Biosciences, University of Nottingham, Loughborough, Leicestershire, UK
| | - Robert Linforth
- Division of Food, Nutrition and Dietetics, School of Biosciences, University of Nottingham, Loughborough, Leicestershire, UK
| | - Chris D Powell
- Division of Food, Nutrition and Dietetics, School of Biosciences, University of Nottingham, Loughborough, Leicestershire, UK
| | - Ian D Fisk
- Division of Food, Nutrition and Dietetics, School of Biosciences, University of Nottingham, Loughborough, Leicestershire, UK; The University of Adelaide, North Terrace, Adelaide, South Australia, Australia
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Cellulosic Bioethanol from Industrial Eucalyptus globulus Bark Residues Using Kraft Pulping as a Pretreatment. ENERGIES 2021. [DOI: 10.3390/en14082185] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/22/2023]
Abstract
The pulp and paper industry faces an emerging challenge for valorising wastes and side-streams generated according to the biorefinery concept. Eucalyptus globulus bark, an abundant industrial residue in the Portuguese pulp and paper sector, has a high potential to be converted into biobased products instead of being burned. This work aimed to evaluate the ethanol production from E. globulus bark previously submitted to kraft pulping through separate hydrolysis and fermentation (SHF) configuration. Fed-batch enzymatic hydrolysis provided a concentrated hydrolysate with 161.6 g·L−1 of cellulosic sugars. S. cerevisiae and Ethanol Red® strains demonstrated a very good fermentation performance, despite a negligible xylose consumption. S. passalidarum, a yeast known for its capability to consume pentoses, was studied in a simultaneous co-culture with Ethanol Red®. However, bioethanol production was not improved. The best fermentation performance was achieved by Ethanol Red®, which provided a maximum ethanol concentration near 50 g·L−1 and fermentation efficiency of 80%. Concluding, kraft pulp from E. globulus bark showed a high potential to be converted into cellulosic bioethanol, being susceptible to implementing an integrated biorefinery on the pulp and paper industrial plants.
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Zhang Y, Su M, Qin N, Nielsen J, Liu Z. Expressing a cytosolic pyruvate dehydrogenase complex to increase free fatty acid production in Saccharomyces cerevisiae. Microb Cell Fact 2020; 19:226. [PMID: 33302960 PMCID: PMC7730738 DOI: 10.1186/s12934-020-01493-z] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2020] [Accepted: 12/03/2020] [Indexed: 12/11/2022] Open
Abstract
BACKGROUND Saccharomyces cerevisiae is being exploited as a cell factory to produce fatty acids and their derivatives as biofuels. Previous studies found that both precursor supply and fatty acid metabolism deregulation are essential for enhanced fatty acid synthesis. A bacterial pyruvate dehydrogenase (PDH) complex expressed in the yeast cytosol was reported to enable production of cytosolic acetyl-CoA with lower energy cost and no toxic intermediate. RESULTS Overexpression of the PDH complex significantly increased cell growth, ethanol consumption and reduced glycerol accumulation. Furthermore, to optimize the redox imbalance in production of fatty acids from glucose, two endogenous NAD+-dependent glycerol-3-phosphate dehydrogenases were deleted, and a heterologous NADP+-dependent glyceraldehyde-3-phosphate dehydrogenase was introduced. The best fatty acid producing strain PDH7 with engineering of precursor and co-factor metabolism could produce 840.5 mg/L free fatty acids (FFAs) in shake flask, which was 83.2% higher than the control strain YJZ08. Profile analysis of free fatty acid suggested the cytosolic PDH complex mainly resulted in the increases of unsaturated fatty acids (C16:1 and C18:1). CONCLUSIONS We demonstrated that cytosolic PDH pathway enabled more efficient acetyl-CoA provision with the lower ATP cost, and improved FFA production. Together with engineering of the redox factor rebalance, the cytosolic PDH pathway could achieve high level of FFA production at similar levels of other best acetyl-CoA producing pathways.
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Affiliation(s)
- Yiming Zhang
- Beijing Advanced Innovation Center for Soft Matter Science and Engineering, College of Life Science and Technology, Beijing University of Chemical Technology, No.15 North Third Ring Road East, Chaoyang District, Beijing, 100029, People's Republic of China
| | - Mo Su
- Beijing Advanced Innovation Center for Soft Matter Science and Engineering, College of Life Science and Technology, Beijing University of Chemical Technology, No.15 North Third Ring Road East, Chaoyang District, Beijing, 100029, People's Republic of China
| | - Ning Qin
- Beijing Advanced Innovation Center for Soft Matter Science and Engineering, College of Life Science and Technology, Beijing University of Chemical Technology, No.15 North Third Ring Road East, Chaoyang District, Beijing, 100029, People's Republic of China
| | - Jens Nielsen
- Beijing Advanced Innovation Center for Soft Matter Science and Engineering, College of Life Science and Technology, Beijing University of Chemical Technology, No.15 North Third Ring Road East, Chaoyang District, Beijing, 100029, People's Republic of China.,Department of Biology and Biological Engineering, Chalmers University of Technology, Gothenburg, Sweden.,BioInnovation Institute, Ole Maaløes Vej 3, 2200, Copenhagen N, Denmark
| | - Zihe Liu
- Beijing Advanced Innovation Center for Soft Matter Science and Engineering, College of Life Science and Technology, Beijing University of Chemical Technology, No.15 North Third Ring Road East, Chaoyang District, Beijing, 100029, People's Republic of China.
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Ceccato-Antonini SR, Covre EA. From baker's yeast to genetically modified budding yeasts: the scientific evolution of bioethanol industry from sugarcane. FEMS Yeast Res 2020; 20:6021367. [PMID: 33406233 DOI: 10.1093/femsyr/foaa065] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2020] [Accepted: 12/02/2020] [Indexed: 12/22/2022] Open
Abstract
The peculiarities of Brazilian fuel ethanol fermentation allow the entry of native yeasts that may dominate over the starter strains of Saccharomyces cerevisiae and persist throughout the sugarcane harvest. The switch from the use of baker's yeast as starter to selected budding yeasts obtained by a selective pressure strategy was followed by a wealth of genomic information that enabled the understanding of the superiority of selected yeast strains. This review describes how the process of yeast selection evolved in the sugarcane-based bioethanol industry, the selection criteria and recent advances in genomics that could advance the fermentation process. The prospective use of genetically modified yeast strains, specially designed for increased robustness and product yield, with special emphasis on those obtained by the CRISPR (clustered regularly interspaced palindromic repeats)-Cas9 (CRISPR-associated protein 9) genome-editing approach, is discussed as a possible solution to confer higher performance and stability to the fermentation process for fuel ethanol production.
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Affiliation(s)
- Sandra Regina Ceccato-Antonini
- Laboratory of Agricultural and Molecular Microbiology, Dept Tecnologia Agroindustrial e Socioeconomia Rural, Centro de Ciências Agrárias, Universidade Federal de São Carlos, Via Anhanguera, km 174, 13600-970 Araras, São Paulo State, Brazil
| | - Elizabete Aparecida Covre
- Laboratory of Agricultural and Molecular Microbiology, Dept Tecnologia Agroindustrial e Socioeconomia Rural, Centro de Ciências Agrárias, Universidade Federal de São Carlos, Via Anhanguera, km 174, 13600-970 Araras, São Paulo State, Brazil
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Zazulya A, Semkiv M, Dmytruk K, Sibirny A. Adaptive Evolution for the Improvement of Ethanol Production During Alcoholic Fermentation with the Industrial Strains of Yeast Saccharomyces Cerevisiae. CYTOL GENET+ 2020. [DOI: 10.3103/s0095452720050059] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
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In Vivo Thermodynamic Analysis of Glycolysis in Clostridium thermocellum and Thermoanaerobacterium saccharolyticum Using 13C and 2H Tracers. mSystems 2020; 5:5/2/e00736-19. [PMID: 32184362 PMCID: PMC7380578 DOI: 10.1128/msystems.00736-19] [Citation(s) in RCA: 22] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022] Open
Abstract
Thermodynamics constitutes a key determinant of flux and enzyme efficiency in metabolic networks. Here, we provide new insights into the divergent thermodynamics of the glycolytic pathways of C. thermocellum and T. saccharolyticum, two industrially relevant thermophilic bacteria whose metabolism still is not well understood. We report that while the glycolytic pathway in T. saccharolyticum is as thermodynamically favorable as that found in model organisms, such as E. coli or Saccharomyces cerevisiae, the glycolytic pathway of C. thermocellum operates near equilibrium. The use of a near-equilibrium glycolytic pathway, with potentially increased ATP yield, by this cellulolytic microbe may represent an evolutionary adaptation to growth on cellulose, but it has the drawback of being highly susceptible to product feedback inhibition. The results of this study will facilitate future engineering of high-performance strains capable of transforming cellulosic biomass to biofuels at high yields and titers. Clostridium thermocellum and Thermoanaerobacterium saccharolyticum are thermophilic anaerobic bacteria with complementary metabolic capabilities that utilize distinct glycolytic pathways for the conversion of cellulosic sugars to biofuels. We integrated quantitative metabolomics with 2H and 13C metabolic flux analysis to investigate the in vivo reversibility and thermodynamics of the central metabolic networks of these two microbes. We found that the glycolytic pathway in C. thermocellum operates remarkably close to thermodynamic equilibrium, with an overall drop in Gibbs free energy 5-fold lower than that of T. saccharolyticum or anaerobically grown Escherichia coli. The limited thermodynamic driving force of glycolysis in C. thermocellum could be attributed in large part to the small free energy of the phosphofructokinase reaction producing fructose bisphosphate. The ethanol fermentation pathway was also substantially more reversible in C. thermocellum than in T. saccharolyticum. These observations help explain the comparatively low ethanol titers of C. thermocellum and suggest engineering interventions that can be used to increase its ethanol productivity and glycolytic rate. In addition to thermodynamic analysis, we used our isotope tracer data to reconstruct the T. saccharolyticum central metabolic network, revealing exclusive use of the Embden-Meyerhof-Parnas (EMP) pathway for glycolysis, a bifurcated tricarboxylic acid (TCA) cycle, and a sedoheptulose bisphosphate bypass active within the pentose phosphate pathway. IMPORTANCE Thermodynamics constitutes a key determinant of flux and enzyme efficiency in metabolic networks. Here, we provide new insights into the divergent thermodynamics of the glycolytic pathways of C. thermocellum and T. saccharolyticum, two industrially relevant thermophilic bacteria whose metabolism still is not well understood. We report that while the glycolytic pathway in T. saccharolyticum is as thermodynamically favorable as that found in model organisms, such as E. coli or Saccharomyces cerevisiae, the glycolytic pathway of C. thermocellum operates near equilibrium. The use of a near-equilibrium glycolytic pathway, with potentially increased ATP yield, by this cellulolytic microbe may represent an evolutionary adaptation to growth on cellulose, but it has the drawback of being highly susceptible to product feedback inhibition. The results of this study will facilitate future engineering of high-performance strains capable of transforming cellulosic biomass to biofuels at high yields and titers.
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Fungi (Mold)-Based Lipid Production. Methods Mol Biol 2020. [PMID: 31148121 DOI: 10.1007/978-1-4939-9484-7_3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register]
Abstract
There is an increasing need for the development of alternative energy sources with a focus on reducing greenhouse gas emissions and striving toward a sustainable economy. Bioethanol and biodiesel are currently the primary choices of alternative transportation fuels. At present, biodiesel is not competitive with conventional fuel due to its high price, and the only way to compete with conventional fuel is to improve the quality, reduce the costs, and coproduce value-added products. With the high demand for lipids in the energy sector and other industrial applications, microbial lipids accumulated from microorganisms, especially oleaginous fungi and yeasts have been the important topic of many recent research studies. This chapter summarizes the current status of knowledge and technology about lipid production by oleaginous fungi and yeasts for biofuel applications and other value-added products. The chapter focuses on several aspects such as the most promising oleaginous strains, strain development, improvement of lipid production, methods and protocols to cultivate oleaginous fungi, substrate utilization, fermentation process design, and downstream processing. The feasibility and challenges during the large-scale commercial production of microbial lipids as fuel sources are also discussed. It provides an overview of microbial lipid production biorefinery and also future development directions.
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Ruchala J, Kurylenko OO, Dmytruk KV, Sibirny AA. Construction of advanced producers of first- and second-generation ethanol in Saccharomyces cerevisiae and selected species of non-conventional yeasts (Scheffersomyces stipitis, Ogataea polymorpha). J Ind Microbiol Biotechnol 2019; 47:109-132. [PMID: 31637550 PMCID: PMC6970964 DOI: 10.1007/s10295-019-02242-x] [Citation(s) in RCA: 32] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2019] [Accepted: 10/01/2019] [Indexed: 12/20/2022]
Abstract
This review summarizes progress in the construction of efficient yeast ethanol producers from glucose/sucrose and lignocellulose. Saccharomyces cerevisiae is the major industrial producer of first-generation ethanol. The different approaches to increase ethanol yield and productivity from glucose in S. cerevisiae are described. Construction of the producers of second-generation ethanol is described for S. cerevisiae, one of the best natural xylose fermenters, Scheffersomyces stipitis and the most thermotolerant yeast known Ogataea polymorpha. Each of these organisms has some advantages and drawbacks. S. cerevisiae is the primary industrial ethanol producer and is the most ethanol tolerant natural yeast known and, however, cannot metabolize xylose. S. stipitis can effectively ferment both glucose and xylose and, however, has low ethanol tolerance and requires oxygen for growth. O. polymorpha grows and ferments at high temperatures and, however, produces very low amounts of ethanol from xylose. Review describes how the mentioned drawbacks could be overcome.
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Affiliation(s)
- Justyna Ruchala
- Department of Microbiology and Biotechnology, University of Rzeszow, Zelwerowicza 4, 35-601, Rzeszow, Poland
| | - Olena O Kurylenko
- Department of Molecular Genetics and Biotechnology, Institute of Cell Biology, NAS of Ukraine, Drahomanov Street, 14/16, Lviv, 79005, Ukraine
| | - Kostyantyn V Dmytruk
- Department of Molecular Genetics and Biotechnology, Institute of Cell Biology, NAS of Ukraine, Drahomanov Street, 14/16, Lviv, 79005, Ukraine
| | - Andriy A Sibirny
- Department of Microbiology and Biotechnology, University of Rzeszow, Zelwerowicza 4, 35-601, Rzeszow, Poland.
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Favaro L, Jansen T, van Zyl WH. Exploring industrial and naturalSaccharomyces cerevisiaestrains for the bio-based economy from biomass: the case of bioethanol. Crit Rev Biotechnol 2019; 39:800-816. [DOI: 10.1080/07388551.2019.1619157] [Citation(s) in RCA: 46] [Impact Index Per Article: 9.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Affiliation(s)
- Lorenzo Favaro
- Department of Agronomy Food Natural resources Animals and Environment (DAFNAE), University of Padova, Legnaro, Italy
| | - Trudy Jansen
- Department of Microbiology, Stellenbosch University, Stellenbosch, South Africa
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Kämäräinen J, Nylund M, Aro EM, Kallio P. Comparison of ethanol tolerance between potential cyanobacterial production hosts. J Biotechnol 2018; 283:140-145. [DOI: 10.1016/j.jbiotec.2018.07.034] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2018] [Revised: 07/26/2018] [Accepted: 07/26/2018] [Indexed: 11/25/2022]
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Turner TL, Kim H, Kong II, Liu JJ, Zhang GC, Jin YS. Engineering and Evolution of Saccharomyces cerevisiae to Produce Biofuels and Chemicals. ADVANCES IN BIOCHEMICAL ENGINEERING/BIOTECHNOLOGY 2018; 162:175-215. [PMID: 27913828 DOI: 10.1007/10_2016_22] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
Abstract
To mitigate global climate change caused partly by the use of fossil fuels, the production of fuels and chemicals from renewable biomass has been attempted. The conversion of various sugars from renewable biomass into biofuels by engineered baker's yeast (Saccharomyces cerevisiae) is one major direction which has grown dramatically in recent years. As well as shifting away from fossil fuels, the production of commodity chemicals by engineered S. cerevisiae has also increased significantly. The traditional approaches of biochemical and metabolic engineering to develop economic bioconversion processes in laboratory and industrial settings have been accelerated by rapid advancements in the areas of yeast genomics, synthetic biology, and systems biology. Together, these innovations have resulted in rapid and efficient manipulation of S. cerevisiae to expand fermentable substrates and diversify value-added products. Here, we discuss recent and major advances in rational (relying on prior experimentally-derived knowledge) and combinatorial (relying on high-throughput screening and genomics) approaches to engineer S. cerevisiae for producing ethanol, butanol, 2,3-butanediol, fatty acid ethyl esters, isoprenoids, organic acids, rare sugars, antioxidants, and sugar alcohols from glucose, xylose, cellobiose, galactose, acetate, alginate, mannitol, arabinose, and lactose.
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Affiliation(s)
- Timothy L Turner
- Department of Food Science and Human Nutrition, University of Illinois at Urbana-Champaign, Urbana, IL, 61801, USA
| | - Heejin Kim
- Department of Food Science and Human Nutrition, University of Illinois at Urbana-Champaign, Urbana, IL, 61801, USA.,Carl R. Woese Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, IL, 61801, USA
| | - In Iok Kong
- Department of Food Science and Human Nutrition, University of Illinois at Urbana-Champaign, Urbana, IL, 61801, USA.,Carl R. Woese Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, IL, 61801, USA
| | - Jing-Jing Liu
- Department of Food Science and Human Nutrition, University of Illinois at Urbana-Champaign, Urbana, IL, 61801, USA.,Carl R. Woese Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, IL, 61801, USA
| | - Guo-Chang Zhang
- Department of Food Science and Human Nutrition, University of Illinois at Urbana-Champaign, Urbana, IL, 61801, USA
| | - Yong-Su Jin
- Department of Food Science and Human Nutrition, University of Illinois at Urbana-Champaign, Urbana, IL, 61801, USA. .,Carl R. Woese Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, IL, 61801, USA.
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El-Rotail AAMM, Zhang L, Li Y, Liu SP, Shi GY. A novel constructed SPT15 mutagenesis library of Saccharomyces cerevisiae by using gTME technique for enhanced ethanol production. AMB Express 2017; 7:111. [PMID: 28582970 PMCID: PMC5457369 DOI: 10.1186/s13568-017-0400-7] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2017] [Accepted: 05/04/2017] [Indexed: 01/15/2023] Open
Abstract
During the last few years, the global transcription machinery engineering (gTME) technique has gained more attention as an effective approach for the construction of novel mutants. Genetic strategies (molecular biology methods) were utilized to get mutational for both genes (SPT15 and TAF23) basically existed in the Saccharomyces cerevisiae genome via screening the gTME approach in order to obtain a new mutant S. cerevisiae diploid strain. The vector pYX212 was utilized to transform these genes into the control diploid strain S. cerevisiae through the process of mating between haploids control strains S. cerevisiae (MAT-a [CICC 1374]) and (MAT-α [CICC 31144]), by using the oligonucleotide primers SPT15-EcoRI-FW/SPT15-SalI-RV and TAF23-SalI-FW/TAF23-NheI-RV, respectively. The resultant mutants were examined for a series of stability tests. This study showed how strong the effect of using strategic gTME with the importance of the modification we conducted in Error Prone PCR protocol by increasing MnCl2 concentration instead of MgCl2. More than ninety mutants we obtained in this study were distinguished by a high level production of bio-ethanol as compared to the diploid control strain.
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Affiliation(s)
- Ashraf A. M. M. El-Rotail
- The Key Laboratory of Industrial Biotechnology, Ministry of Education, National Engineering Laboratory for Cereal Fermentation Technology, School of Biotechnology, Jiangnan University, 1800 Lihu Road, Wuxi, 214122 Jiangsu China
- Faculty of Environmental Agricultural Science, El Arish University, El Arish, North Sinai 45526 Egypt
| | - Liang Zhang
- The Key Laboratory of Industrial Biotechnology, Ministry of Education, National Engineering Laboratory for Cereal Fermentation Technology, School of Biotechnology, Jiangnan University, 1800 Lihu Road, Wuxi, 214122 Jiangsu China
| | - Youran Li
- The Key Laboratory of Industrial Biotechnology, Ministry of Education, National Engineering Laboratory for Cereal Fermentation Technology, School of Biotechnology, Jiangnan University, 1800 Lihu Road, Wuxi, 214122 Jiangsu China
| | - Shuang Ping Liu
- The Key Laboratory of Industrial Biotechnology, Ministry of Education, National Engineering Laboratory for Cereal Fermentation Technology, School of Biotechnology, Jiangnan University, 1800 Lihu Road, Wuxi, 214122 Jiangsu China
| | - Gui Yang Shi
- The Key Laboratory of Industrial Biotechnology, Ministry of Education, National Engineering Laboratory for Cereal Fermentation Technology, School of Biotechnology, Jiangnan University, 1800 Lihu Road, Wuxi, 214122 Jiangsu China
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d'Espaux L, Ghosh A, Runguphan W, Wehrs M, Xu F, Konzock O, Dev I, Nhan M, Gin J, Reider Apel A, Petzold CJ, Singh S, Simmons BA, Mukhopadhyay A, García Martín H, Keasling JD. Engineering high-level production of fatty alcohols by Saccharomyces cerevisiae from lignocellulosic feedstocks. Metab Eng 2017; 42:115-125. [PMID: 28606738 DOI: 10.1016/j.ymben.2017.06.004] [Citation(s) in RCA: 65] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2017] [Revised: 05/26/2017] [Accepted: 06/05/2017] [Indexed: 11/17/2022]
Abstract
Fatty alcohols in the C12-C18 range are used in personal care products, lubricants, and potentially biofuels. These compounds can be produced from the fatty acid pathway by a fatty acid reductase (FAR), yet yields from the preferred industrial host Saccharomyces cerevisiae remain under 2% of the theoretical maximum from glucose. Here we improved titer and yield of fatty alcohols using an approach involving quantitative analysis of protein levels and metabolic flux, engineering enzyme level and localization, pull-push-block engineering of carbon flux, and cofactor balancing. We compared four heterologous FARs, finding highest activity and endoplasmic reticulum localization from a Mus musculus FAR. After screening an additional twenty-one single-gene edits, we identified increasing FAR expression; deleting competing reactions encoded by DGA1, HFD1, and ADH6; overexpressing a mutant acetyl-CoA carboxylase; limiting NADPH and carbon usage by the glutamate dehydrogenase encoded by GDH1; and overexpressing the Δ9-desaturase encoded by OLE1 as successful strategies to improve titer. Our final strain produced 1.2g/L fatty alcohols in shake flasks, and 6.0g/L in fed-batch fermentation, corresponding to ~ 20% of the maximum theoretical yield from glucose, the highest titers and yields reported to date in S. cerevisiae. We further demonstrate high-level production from lignocellulosic feedstocks derived from ionic-liquid treated switchgrass and sorghum, reaching 0.7g/L in shake flasks. Altogether, our work represents progress towards efficient and renewable microbial production of fatty acid-derived products.
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Affiliation(s)
- Leo d'Espaux
- DOE Joint BioEnergy Institute, Emeryville, CA 94608, United States; Biological Systems and Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, United States
| | - Amit Ghosh
- DOE Joint BioEnergy Institute, Emeryville, CA 94608, United States; Biological Systems and Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, United States
| | - Weerawat Runguphan
- DOE Joint BioEnergy Institute, Emeryville, CA 94608, United States; Biological Systems and Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, United States
| | - Maren Wehrs
- DOE Joint BioEnergy Institute, Emeryville, CA 94608, United States; Biological Systems and Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, United States
| | - Feng Xu
- DOE Joint BioEnergy Institute, Emeryville, CA 94608, United States; Biological Systems and Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, United States; Biomass Science and Conversion Technology Department, Sandia National Laboratories, Livermore, CA 94551, United States; Biological and Materials Science Center, Sandia National Laboratories, Livermore, CA 94551, United States
| | - Oliver Konzock
- DOE Joint BioEnergy Institute, Emeryville, CA 94608, United States; Biological Systems and Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, United States
| | - Ishaan Dev
- DOE Joint BioEnergy Institute, Emeryville, CA 94608, United States; Biological Systems and Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, United States; Department of Chemical & Biomolecular Engineering, University of California, Berkeley, CA 94720, United States
| | - Melissa Nhan
- DOE Joint BioEnergy Institute, Emeryville, CA 94608, United States; Biological Systems and Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, United States
| | - Jennifer Gin
- DOE Joint BioEnergy Institute, Emeryville, CA 94608, United States; Biological Systems and Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, United States
| | - Amanda Reider Apel
- DOE Joint BioEnergy Institute, Emeryville, CA 94608, United States; Biological Systems and Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, United States
| | - Christopher J Petzold
- DOE Joint BioEnergy Institute, Emeryville, CA 94608, United States; Biological Systems and Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, United States
| | - Seema Singh
- DOE Joint BioEnergy Institute, Emeryville, CA 94608, United States; Biological Systems and Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, United States; Biomass Science and Conversion Technology Department, Sandia National Laboratories, Livermore, CA 94551, United States; Biological and Materials Science Center, Sandia National Laboratories, Livermore, CA 94551, United States
| | - Blake A Simmons
- DOE Joint BioEnergy Institute, Emeryville, CA 94608, United States; Biological Systems and Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, United States; Biomass Science and Conversion Technology Department, Sandia National Laboratories, Livermore, CA 94551, United States; Biological and Materials Science Center, Sandia National Laboratories, Livermore, CA 94551, United States
| | - Aindrila Mukhopadhyay
- DOE Joint BioEnergy Institute, Emeryville, CA 94608, United States; Biological Systems and Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, United States
| | - Héctor García Martín
- DOE Joint BioEnergy Institute, Emeryville, CA 94608, United States; Biological Systems and Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, United States
| | - Jay D Keasling
- DOE Joint BioEnergy Institute, Emeryville, CA 94608, United States; Biological Systems and Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, United States; Department of Chemical & Biomolecular Engineering, University of California, Berkeley, CA 94720, United States; Department of Bioengineering, University of California, Berkeley, CA 94720, United States; The Novo Nordisk Foundation Center for Sustainability, Technical University of Denmark, Denmark.
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Hou J, Qiu C, Shen Y, Li H, Bao X. Engineering of Saccharomyces cerevisiae for the efficient co-utilization of glucose and xylose. FEMS Yeast Res 2017; 17:3861258. [DOI: 10.1093/femsyr/fox034] [Citation(s) in RCA: 57] [Impact Index Per Article: 8.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2017] [Accepted: 06/02/2017] [Indexed: 11/14/2022] Open
Affiliation(s)
- Jin Hou
- State Key Laboratory of Microbial Technology, The School of Life Science, Shandong University, Jinan, 250100, China
| | - Chenxi Qiu
- State Key Laboratory of Microbial Technology, The School of Life Science, Shandong University, Jinan, 250100, China
| | - Yu Shen
- State Key Laboratory of Microbial Technology, The School of Life Science, Shandong University, Jinan, 250100, China
| | - Hongxing Li
- State Key Laboratory of Microbial Technology, The School of Life Science, Shandong University, Jinan, 250100, China
- Shandong Provincial Key Laboratory of Microbial Engineering, Qi Lu University of Technology, Jinan, 250353, China
| | - Xiaoming Bao
- State Key Laboratory of Microbial Technology, The School of Life Science, Shandong University, Jinan, 250100, China
- Shandong Provincial Key Laboratory of Microbial Engineering, Qi Lu University of Technology, Jinan, 250353, China
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Papapetridis I, van Dijk M, van Maris AJA, Pronk JT. Metabolic engineering strategies for optimizing acetate reduction, ethanol yield and osmotolerance in S accharomyces cerevisiae. BIOTECHNOLOGY FOR BIOFUELS 2017; 10:107. [PMID: 28450888 PMCID: PMC5406903 DOI: 10.1186/s13068-017-0791-3] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/21/2017] [Accepted: 04/14/2017] [Indexed: 06/01/2023]
Abstract
BACKGROUND Glycerol, whose formation contributes to cellular redox balancing and osmoregulation in Saccharomyces cerevisiae, is an important by-product of yeast-based bioethanol production. Replacing the glycerol pathway by an engineered pathway for NAD+-dependent acetate reduction has been shown to improve ethanol yields and contribute to detoxification of acetate-containing media. However, the osmosensitivity of glycerol non-producing strains limits their applicability in high-osmolarity industrial processes. This study explores engineering strategies for minimizing glycerol production by acetate-reducing strains, while retaining osmotolerance. RESULTS GPD2 encodes one of two S. cerevisiae isoenzymes of NAD+-dependent glycerol-3-phosphate dehydrogenase (G3PDH). Its deletion in an acetate-reducing strain yielded a fourfold lower glycerol production in anaerobic, low-osmolarity cultures but hardly affected glycerol production at high osmolarity. Replacement of both native G3PDHs by an archaeal NADP+-preferring enzyme, combined with deletion of ALD6, yielded an acetate-reducing strain the phenotype of which resembled that of a glycerol-negative gpd1Δ gpd2Δ strain in low-osmolarity cultures. This strain grew anaerobically at high osmolarity (1 mol L-1 glucose), while consuming acetate and producing virtually no extracellular glycerol. Its ethanol yield in high-osmolarity cultures was 13% higher than that of an acetate-reducing strain expressing the native glycerol pathway. CONCLUSIONS Deletion of GPD2 provides an attractive strategy for improving product yields of acetate-reducing S. cerevisiae strains in low, but not in high-osmolarity media. Replacement of the native yeast G3PDHs by a heterologous NADP+-preferring enzyme, combined with deletion of ALD6, virtually eliminated glycerol production in high-osmolarity cultures while enabling efficient reduction of acetate to ethanol. After further optimization of growth kinetics, this strategy for uncoupling the roles of glycerol formation in redox homeostasis and osmotolerance can be applicable for improving performance of industrial strains in high-gravity acetate-containing processes.
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Affiliation(s)
- Ioannis Papapetridis
- Industrial Microbiology Section, Department of Biotechnology, Delft University of Technology, Van der Maasweg 9, 2629 HZ Delft, The Netherlands
| | - Marlous van Dijk
- Industrial Microbiology Section, Department of Biotechnology, Delft University of Technology, Van der Maasweg 9, 2629 HZ Delft, The Netherlands
- Division of Industrial Biotechnology, Department of Biology and Biological Engineering, Chalmers University of Technology, Kemivägen 10, 41296 Gothenburg, Sweden
| | - Antonius J. A. van Maris
- Industrial Microbiology Section, Department of Biotechnology, Delft University of Technology, Van der Maasweg 9, 2629 HZ Delft, The Netherlands
- Division of Industrial Biotechnology, School of Biotechnology, KTH Royal Institute of Technology, AlbaNova University Centre, 10691 Stockholm, Sweden
| | - Jack T. Pronk
- Industrial Microbiology Section, Department of Biotechnology, Delft University of Technology, Van der Maasweg 9, 2629 HZ Delft, The Netherlands
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Dmytruk KV, Kshanovska BV, Abbas CA, Sibirny A. New methods for positive selection of yeast ethanol overproducing mutants. ACTA ACUST UNITED AC 2016. [DOI: 10.1515/bioeth-2015-0003] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Abstract
AbstractFuel ethanol is an environmentally friendly alternative liquid fuel to the widely used petroleum derived transportation liquid fuels. Since 2007, worldwide fuel ethanol production has increased. Currently ethanol is primarily produced from carbohydrates such as sucrose and starch by fermentation using the yeast Saccharomyces cerevisiae. In this work, new approaches for the selection of S. cerevisiae strains with increased ethanol production from hydrolyzed corn meal are described. An industrial production strain of Saccharomyces cerevisiae AS400 was subjected to positive selection of mutants resistant to toxic concentrations of oxythiamine, trehalose, 3-bromopyruvate, glyoxylic acid, and glucosamine. The selected mutants are characterized by 5-8% increase in ethanol yield (g g-1 of consumed glucose) as compared to the parental industrial ethanol-producing strain. A three-step selection approach that consisted of the use of glyoxylic acid, glucosamine and bromopyruvate resulted in a 12% increase in ethanol yield during fermentation on industrial media. These results indicate that the selected strains are promising candidates for industrial ethanol production.
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Navarrete C, Nielsen J, Siewers V. Enhanced ethanol production and reduced glycerol formation in fps1∆ mutants of Saccharomyces cerevisiae engineered for improved redox balancing. AMB Express 2014; 4:86. [PMID: 26267115 PMCID: PMC4883998 DOI: 10.1186/s13568-014-0086-z] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2014] [Accepted: 11/27/2014] [Indexed: 11/30/2022] Open
Abstract
Ethanol is by volume the largest fermentation product. During ethanol production by Saccharomyces cerevisiae about 4-5% of the carbon source is lost to glycerol production. Different approaches have been proposed for improving the ethanol yield while reducing glycerol production. Here we studied the effect of reducing glycerol export/formation through deletion of the aquaglyceroporin gene FPS1 together with expressing gapN encoding NADP+-dependent non-phosphorylating glyceraldehyde-3-phosphate dehydrogenase from Streptococcus mutans and overexpressing the ATP-NADH kinase gene UTR1 from S. cerevisiae. This strategy will allow reducing the redox balance problem observed when the glycerol pathway is blocked, and hereby improve ethanol production. We found that our strategy enabled increasing the ethanol yield by 4.6% in the case of the best producing strain, compared to the reference strain, without any major effect on the specific growth rate.
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Hou J, Suo F, Wang C, Li X, Shen Y, Bao X. Fine-tuning of NADH oxidase decreases byproduct accumulation in respiration deficient xylose metabolic Saccharomyces cerevisiae. BMC Biotechnol 2014; 14:13. [PMID: 24529074 PMCID: PMC3928090 DOI: 10.1186/1472-6750-14-13] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2013] [Accepted: 02/08/2014] [Indexed: 01/01/2023] Open
Abstract
Background Efficiently utilizing all available carbon from lignocellulosic feedstock presents a major barrier to the production of economically feasible biofuel. Previously, to enable xylose utilization, we introduced a cofactor-dependent xylose reductase (XR) and xylitol dehydrogenase (XDH) pathway, or a cofactor-independent xylose isomerase (XI) pathway, into Saccharomyces cerevisiae. The resulting strains metabolized xylose with high efficiency. However, in both pathway recombinant strains, the cofactor imbalance caused accumulation of the byproducts glycerol and/or xylitol and reduced the ethanol production efficiency. Results In this study, we introduced NADH oxidase from Lactococcus lactis into both XI and XR-XDH pathway recombinant strains. To reduce byproduct accumulation while maintaining xylose metabolism, we optimized the expression level of NADH oxidase by comparing its expression under the control of different promoters and plasmids. In recombinant XI strains, NADH oxidase was expressed at different levels, regulated by the GPD2 promoter or TEF1 promoter in the 2 μ plasmid. The expression under the control of GPD2 promoter decreased glycerol production by 84% and increased the ethanol yield and specific growth rate by 8% and 12%, respectively. In contrast, in the recombinant XR-XDH strains, such expression level was not efficient enough to decrease the byproduct accumulation. Therefore, higher NADH oxidase expression levels were tested. In the strain expressing NADH oxidase under the control of the TEF1 promoter in the centromeric plasmids, xylitol and glycerol production were reduced by 60% and 83%, respectively, without significantly affecting xylose consumption. Conclusions By fine-tuning NADH oxidase expression, we decreased the glycerol or/and xylitol production in both recombinant XI and XR-XDH xylose-metabolizing yeast strains. The optimal NADH oxidase expression levels depend on metabolic pathways. Similar cofactor engineering strategies could maximize the production of other redox dependent metabolites.
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Affiliation(s)
| | | | | | | | | | - Xiaoming Bao
- State Key Laboratory of Microbial Technology, Shandong University, Shanda Nan Road 27, Jinan 250100, China.
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Improvement of NADPH bioavailability in Escherichia coli by replacing NAD(+)-dependent glyceraldehyde-3-phosphate dehydrogenase GapA with NADP (+)-dependent GapB from Bacillus subtilis and addition of NAD kinase. J Ind Microbiol Biotechnol 2013; 40:1449-60. [PMID: 24048943 DOI: 10.1007/s10295-013-1335-x] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2013] [Accepted: 08/28/2013] [Indexed: 02/03/2023]
Abstract
Enzymatic synthesis of some industrially important compounds depends heavily on cofactor NADPH as the reducing agent. This is especially true in the synthesis of chiral compounds that are often used as pharmaceutical intermediates to generate the correct stereochemistry in bioactive products. The high cost and technical difficulty of cofactor regeneration often pose a challenge for such biocatalytic reactions. In this study, to increase NADPH bioavailability, the native NAD(+)-dependent glyceraldehyde-3-phosphate dehydrogenase (GAPDH) gapA gene in Escherichia coli was replaced with a NADP(+)-dependent gapB from Bacillus subtilis. To overcome the limitation of NADP(+) availability, E. coli NAD kinase, nadK was also coexpressed with gapB. The recombinant strains were then tested in three reporting systems: biosynthesis of lycopene, oxidation of cyclohexanone with cyclohexanone monooxygenase (CHMO), and an anaerobic system utilizing 2-haloacrylate reductase (CAA43). In all the reporting systems, replacing NAD(+)-dependent GapA activity with NADP(+)-dependent GapB activity increased the synthesis of NADPH-dependent compounds. The increase was more pronounced when NAD kinase was also overexpressed in the case of the one-step reaction catalyzed by CAA43 which approximately doubled the product yield. These results validate this novel approach to improve NADPH bioavailability in E. coli and suggest that the strategy can be applied in E. coli or other bacterium-based production of NADPH-dependent compounds.
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Engineering of the glycerol decomposition pathway and cofactor regulation in an industrial yeast improves ethanol production. J Ind Microbiol Biotechnol 2013; 40:1153-60. [PMID: 23896974 PMCID: PMC3769588 DOI: 10.1007/s10295-013-1311-5] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2013] [Accepted: 07/08/2013] [Indexed: 11/24/2022]
Abstract
Glycerol is a major by-product of industrial ethanol production and its formation consumes up to 4 % of the sugar substrate. This study modified the glycerol decomposition pathway of an industrial strain of Saccharomyces cerevisiae to optimize the consumption of substrate and yield of ethanol. This study is the first to couple glycerol degradation with ethanol formation, to the best of our knowledge. The recombinant strain overexpressing GCY1 and DAK1, encoding glycerol dehydrogenase and dihydroxyacetone kinase, respectively, in glycerol degradation pathway, exhibited a moderate increase in ethanol yield (2.9 %) and decrease in glycerol yield (24.9 %) compared to the wild type with the initial glucose concentration of 15 % under anaerobic conditions. However, when the mhpF gene, encoding acetylating NAD+-dependent acetaldehyde dehydrogenase from Escherichia coli, was co-expressed in the aforementioned recombinant strain, a further increase in ethanol yield by 5.5 % and decrease in glycerol yield by 48 % were observed for the resultant recombinant strain GDMS1 when acetic acid was added into the medium prior to inoculation compared to the wild type. The process outlined in this study which enhances glycerol consumption and cofactor regulation in an industrial yeast is a promising metabolic engineering strategy to increase ethanol production by reducing the formation of glycerol.
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Nielsen J, Larsson C, van Maris A, Pronk J. Metabolic engineering of yeast for production of fuels and chemicals. Curr Opin Biotechnol 2013; 24:398-404. [DOI: 10.1016/j.copbio.2013.03.023] [Citation(s) in RCA: 235] [Impact Index Per Article: 21.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2012] [Revised: 03/18/2013] [Accepted: 03/27/2013] [Indexed: 01/01/2023]
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