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Yang D, Xu Y, Mo L, Shi M, Wu N, Lu L, Xue F, Xu Q, Zhang C. Enhancing l-Malic Acid Production in Aspergillus niger via Natural Activation of sthA Gene Expression. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2024; 72:4869-4879. [PMID: 38407053 DOI: 10.1021/acs.jafc.3c09321] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/27/2024]
Abstract
The efficient production of l-malic acid using Aspergillus niger requires overcoming challenges in synthesis efficiency and excessive byproduct buildup. This study addresses these hurdles, improving the activity of NADH-dependent malate dehydrogenase (Mdh) in the early stages of the fermentation process. By employing a constitutive promoter to express the Escherichia coli sthA responsible for the transfer of reducing equivalents between NAD(H) and NADP(H) in A. niger, the l-malic acid production was significantly elevated. However, this resulted in conidiation defects of A. niger, limiting industrial viability. To mitigate this, we discovered and utilized the PmfsA promoter, enabling the specific expression of sthA during the fermentation stage. This conditional expression strain showed similar phenotypes to its parent strain while exhibiting exceptional performance in a 5 L fermenter. Notably, it achieved a 65.5% increase in productivity, reduced fermentation cycle by 1.5 days, and lowered succinic acid by 76.2%. This work marks a promising advancement in industrial l-malic acid synthesis via biological fermentation, showcasing the potential of synthetic biology in A. niger for broader applications.
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Affiliation(s)
- Dongdong Yang
- School of Food Science and Pharmaceutical Engineering, Nanjing Normal University, Nanjing 210023, China
| | - Yingyan Xu
- School of Food Science and Pharmaceutical Engineering, Nanjing Normal University, Nanjing 210023, China
| | - Li Mo
- School of Food Science and Pharmaceutical Engineering, Nanjing Normal University, Nanjing 210023, China
| | - Man Shi
- School of Food Science and Pharmaceutical Engineering, Nanjing Normal University, Nanjing 210023, China
| | - Na Wu
- School of Food Science and Pharmaceutical Engineering, Nanjing Normal University, Nanjing 210023, China
| | - Ling Lu
- College of Life Sciences, Nanjing Normal University, Nanjing 210023, China
| | - Feng Xue
- School of Food Science and Pharmaceutical Engineering, Nanjing Normal University, Nanjing 210023, China
| | - Qing Xu
- School of Food Science and Pharmaceutical Engineering, Nanjing Normal University, Nanjing 210023, China
| | - Chi Zhang
- School of Food Science and Pharmaceutical Engineering, Nanjing Normal University, Nanjing 210023, China
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Li X, Gadar-Lopez AE, Chen L, Jayachandran S, Cruz-Morales P, Keasling JD. Mining natural products for advanced biofuels and sustainable bioproducts. Curr Opin Biotechnol 2023; 84:103003. [PMID: 37769513 DOI: 10.1016/j.copbio.2023.103003] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2023] [Revised: 09/03/2023] [Accepted: 09/03/2023] [Indexed: 10/03/2023]
Abstract
Recently, there has been growing interest in the sustainable production of biofuels and bioproducts derived from renewable sources. Natural products, the largest and more structurally diverse group of metabolites, hold significant promise as sources for such bio-based products. However, there are two primary challenges in harnessing natural products' potential: precise mining of biosynthetic gene clusters (BGCs) that can be used as scaffolds or bioparts and their functional expression for biofuel and bioproduct manufacture. In this review, we explore recent advances in the development of bioinformatic tools for BGC mining and the manipulation of various hosts for natural product-based biofuels and bioproducts manufacture. Moreover, we discuss potential strategies for expanding the chemical diversity of biofuels and bioproducts and enhancing their overall yield.
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Affiliation(s)
- Xiaowei Li
- Novo Nordisk Foundation Center for Biosustainability, Danmarks Tekniske Universitet, Kongens Lyngby, Denmark
| | - Adrian E Gadar-Lopez
- Novo Nordisk Foundation Center for Biosustainability, Danmarks Tekniske Universitet, Kongens Lyngby, Denmark
| | - Ling Chen
- Novo Nordisk Foundation Center for Biosustainability, Danmarks Tekniske Universitet, Kongens Lyngby, Denmark
| | - Sidharth Jayachandran
- Novo Nordisk Foundation Center for Biosustainability, Danmarks Tekniske Universitet, Kongens Lyngby, Denmark
| | - Pablo Cruz-Morales
- Novo Nordisk Foundation Center for Biosustainability, Danmarks Tekniske Universitet, Kongens Lyngby, Denmark.
| | - Jay D Keasling
- Novo Nordisk Foundation Center for Biosustainability, Danmarks Tekniske Universitet, Kongens Lyngby, Denmark; Lawrence Berkeley National Laboratory, Biological Systems and Engineering Division, Berkeley, CA, USA; Joint BioEnergy Institute, Emeryville, CA, USA; Departments of Chemical & Biomolecular Engineering and of Bioengineering, University of California, Berkeley, CA 94720, USA; Center for Synthetic Biochemistry, Shenzhen Institutes for Advanced Technologies, Shenzhen, China.
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Zhang FL, Zhang L, Zeng DW, Liao S, Fan Y, Champreda V, Runguphan W, Zhao XQ. Engineering yeast cell factories to produce biodegradable plastics and their monomers: Current status and prospects. Biotechnol Adv 2023; 68:108222. [PMID: 37516259 DOI: 10.1016/j.biotechadv.2023.108222] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2023] [Revised: 07/24/2023] [Accepted: 07/24/2023] [Indexed: 07/31/2023]
Abstract
Traditional plastic products have caused serious environmental pollution due to difficulty to be degraded in the natural environment. In the recent years, biodegradable plastics are receiving increasing attention due to advantages in natural degradability and environmental friendliness. Biodegradable plastics have potential to be used in food, agriculture, industry, medicine and other fields. However, the high production cost of such plastics is the bottleneck that limits their commercialization and application. Yeasts, including budding yeast and non-conventional yeasts, are widely studied to produce biodegradable plastics and their organic acid monomers. Compared to bacteria, yeast strains are more tolerable to multiple stress conditions including low pH and high temperature, and also have other advantages such as generally regarded as safe, and no phage infection. In addition, synthetic biology and metabolic engineering of yeast have enabled its rapid and efficient engineering for bioproduction using various renewable feedstocks, especially lignocellulosic biomass. This review focuses on the recent progress in biosynthesis technology and strategies of monomeric organic acids for biodegradable polymers, including polylactic acid (PLA), polyhydroxyalkanoate (PHA), polybutylene succinate (PBS), and polybutylene adipate terephthalate (PBAT) using yeast cell factories. Improving the performance of yeast as a cell factory and strategies to improve yeast acid stress tolerance are also discussed. In addition, the critical challenges and future prospects for the production of biodegradable plastic monomer using yeast are also discussed.
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Affiliation(s)
- Feng-Li Zhang
- Key Laboratory of Microbial Metabolism, Joint International Research Laboratory of Metabolic & Developmental Sciences, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai 200240, China
| | - Lin Zhang
- SINOPEC Dalian Research Institute of Petroleum and Petrochemicals Co., Ltd., Dalian 116045, China
| | - Du-Wen Zeng
- Key Laboratory of Microbial Metabolism, Joint International Research Laboratory of Metabolic & Developmental Sciences, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai 200240, China
| | - Sha Liao
- SINOPEC Dalian Research Institute of Petroleum and Petrochemicals Co., Ltd., Dalian 116045, China
| | - Yachao Fan
- SINOPEC Dalian Research Institute of Petroleum and Petrochemicals Co., Ltd., Dalian 116045, China
| | - Verawat Champreda
- National Center for Genetic Engineering and Biotechnology (BIOTEC), 113 Thailand Science Park, Phaholyothin Road, Khlong Luang, Pathumthani 12120, Thailand
| | - Weerawat Runguphan
- National Center for Genetic Engineering and Biotechnology (BIOTEC), 113 Thailand Science Park, Phaholyothin Road, Khlong Luang, Pathumthani 12120, Thailand
| | - Xin-Qing Zhao
- Key Laboratory of Microbial Metabolism, Joint International Research Laboratory of Metabolic & Developmental Sciences, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai 200240, China.
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Loss of a Functional Mitochondrial Pyruvate Carrier in Komagataella phaffii Does Not Improve Lactic Acid Production from Glycerol in Aerobic Cultivation. Microorganisms 2023; 11:microorganisms11020483. [PMID: 36838448 PMCID: PMC9967928 DOI: 10.3390/microorganisms11020483] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2023] [Revised: 02/10/2023] [Accepted: 02/13/2023] [Indexed: 02/17/2023] Open
Abstract
Cytosolic pyruvate is an essential metabolite in lactic acid production during microbial fermentation. However, under aerobiosis, pyruvate is transported to the mitochondrial matrix by the mitochondrial pyruvate carrier (MPC) and oxidized in cell respiration. Previous reports using Saccharomyces cerevisiae or Aspergillus oryzae have shown that the production of pyruvate-derived chemicals is improved by deleting the MPC1 gene. A previous lactate-producing K. phaffii strain engineered by our group was used as a host for the deletion of the MPC1 gene. In addition, the expression of a bacterial hemoglobin gene under the alcohol dehydrogenase 2 promoter from Scheffersomyces stipitis, known to work as a hypoxia sensor, was used to evaluate whether aeration would supply enough oxygen to meet the metabolic needs during lactic acid production. However, unlike S. cerevisiae and A. oryzae, the deletion of Mpc1 had no significant impact on lactic acid production but negatively affected cell growth in K. phaffii strains. Furthermore, the relative quantification of the VHb gene revealed that the expression of hemoglobin was detected even in aerobic cultivation, which indicates that the demand for oxygen in the bioreactor could result in functional hypoxia. Overall, the results add to our previously published ones and show that blocking cell respiration using hypoxia is more suitable than deleting Mpc for producing lactic acid in K. phaffii.
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Xi Y, Xu H, Zhan T, Qin Y, Fan F, Zhang X. Metabolic engineering of the acid-tolerant yeast Pichia kudriavzevii for efficient L-malic acid production at low pH. Metab Eng 2023; 75:170-180. [PMID: 36566973 DOI: 10.1016/j.ymben.2022.12.007] [Citation(s) in RCA: 9] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2022] [Revised: 11/27/2022] [Accepted: 12/19/2022] [Indexed: 12/24/2022]
Abstract
Currently, the biological production of L-malic acid (L-MA) is mainly based on the fermentation of filamentous fungi at near-neutral pH, but this process requires large amounts of neutralizing agents, resulting in the generation of waste salts when free acid is obtained in the downstream process, and the environmental hazards associated with the waste salts limit the practical application of this process. To produce L-MA in a more environmentally friendly way, we metabolically engineered the acid-tolerant yeast Pichia kudriavzevii and achieved efficient production of L-MA through low pH fermentation. First, an initial L-MA-producing strain that relies on the reductive tricarboxylic acid (rTCA) pathway was constructed. Subsequently, the L-MA titer and yield were further increased by fine-tuning the flux between the pyruvate and oxaloacetate nodes. In addition, we found that the insufficient supply of NADH for cytoplasmic malate dehydrogenase (MDH) hindered the L-MA production at low pH, which was resolved by overexpressing the soluble pyridine nucleotide transhydrogenase SthA from E. coli. Transcriptomic and metabolomic data showed that overexpression of EcSthA contributed to the activation of the pentose phosphate pathway and provided additional reducing power for MDH by converting NADPH to NADH. Furthermore, overexpression of EcSthA was found to help reduce the accumulation of the by-product pyruvate but had no effect on the accumulation of succinate. In microaerobic batch fermentation in a 5-L fermenter, the best strain, MA009-10-URA3 produced 199.4 g/L L-MA with a yield of 0.94 g/g glucose (1.27 mol/mol), with a productivity of 1.86 g/L/h. The final pH of the fermentation broth was approximately 3.10, meaning that the amount of neutralizer used was reduced by more than 50% compared to the common fermentation processes using filamentous fungi. To our knowledge, this is the first report of the efficient bioproduction of L-MA at low pH and represents the highest yield of L-MA in yeasts reported to date.
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Affiliation(s)
- Yongyan Xi
- Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, 32 West 7th Avenue, Tianjin Airport Economic Area, Tianjin, 300308, PR China; Key Laboratory of Systems Microbial Biotechnology, Chinese Academy of Sciences, Tianjin, 300308, PR China; National Innovation Center for Synthetic Biotechnology, Tianjin, 300308, PR China
| | - Hongtao Xu
- Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, 32 West 7th Avenue, Tianjin Airport Economic Area, Tianjin, 300308, PR China; Key Laboratory of Systems Microbial Biotechnology, Chinese Academy of Sciences, Tianjin, 300308, PR China; National Innovation Center for Synthetic Biotechnology, Tianjin, 300308, PR China
| | - Tao Zhan
- Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, 32 West 7th Avenue, Tianjin Airport Economic Area, Tianjin, 300308, PR China; Key Laboratory of Systems Microbial Biotechnology, Chinese Academy of Sciences, Tianjin, 300308, PR China; National Innovation Center for Synthetic Biotechnology, Tianjin, 300308, PR China
| | - Ying Qin
- Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, 32 West 7th Avenue, Tianjin Airport Economic Area, Tianjin, 300308, PR China; Key Laboratory of Systems Microbial Biotechnology, Chinese Academy of Sciences, Tianjin, 300308, PR China; National Innovation Center for Synthetic Biotechnology, Tianjin, 300308, PR China
| | - Feiyu Fan
- Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, 32 West 7th Avenue, Tianjin Airport Economic Area, Tianjin, 300308, PR China; Key Laboratory of Systems Microbial Biotechnology, Chinese Academy of Sciences, Tianjin, 300308, PR China; National Innovation Center for Synthetic Biotechnology, Tianjin, 300308, PR China.
| | - Xueli Zhang
- Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, 32 West 7th Avenue, Tianjin Airport Economic Area, Tianjin, 300308, PR China; Key Laboratory of Systems Microbial Biotechnology, Chinese Academy of Sciences, Tianjin, 300308, PR China; National Innovation Center for Synthetic Biotechnology, Tianjin, 300308, PR China.
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Zhu P, Luo R, Li Y, Chen X. Metabolic Engineering and Adaptive Evolution for Efficient Production of l-Lactic Acid in Saccharomyces cerevisiae. Microbiol Spectr 2022; 10:e0227722. [PMID: 36354322 PMCID: PMC9769770 DOI: 10.1128/spectrum.02277-22] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2022] [Accepted: 10/15/2022] [Indexed: 11/12/2022] Open
Abstract
l-Lactic acid (LA) is a three-carbon hydroxycarboxylic acid with extensive applications in food, cosmetic, agricultural, pharmaceutical, and bioplastic industries. However, microbial LA production is limited by its intrinsic inefficiency of cellular metabolism. Here, pathway engineering was used to rewire the biosynthetic pathway for LA production in Saccharomyces cerevisiae by screening heterologous l-lactate dehydrogenase, reducing ethanol accumulation, and introducing a bacterial acetyl coenzyme A (acetyl-CoA) synthesis pathway. To improve its intrinsic efficiency of LA export, transporter engineering was conducted by screening the monocarboxylate transporters and then strengthening the capacity of LA export, leading to LA production up to 51.4 g/L. To further enhance its intrinsic efficiency of acid tolerance, adaptive evolution was adopted by cultivating yeast cells with a gradual increase in LA levels during 12 serial subcultures, resulting in a 17.5% increase in LA production to 60.4 g/L. Finally, the engineered strain S.c-NO.2-100 was able to produce 121.5 g/L LA, with a yield of up to 0.81 g/g in a 5-L batch bioreactor. The strategy described here provides a guide for developing efficient cell factories for the production of the other industrially useful organic acids. IMPORTANCE Saccharomyces cerevisiae is one of the most widely engineered cell factories for the production of organic acids. However, microbial production of l-lactic acid is limited by its intrinsic inefficiency of cellular metabolism in S. cerevisiae. Here, the transmission efficiency of the biosynthetic pathway was improved by pathway optimization to increase l-lactic acid production. Then, the synthetic ability for l-lactic acid was further enhanced by adaptive evolution to improve acid tolerance of S. cerevisiae. Based on these strategies, the final engineered S. cerevisiae strain achieved high efficiency of l-lactic acid production. These findings provide new insight into improving the intrinsic efficiency of cellular metabolism and will help to construct superior industrial yeast strains for high-level production of other organic acids.
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Affiliation(s)
- Pan Zhu
- State Key Laboratory of Food Science and Technology, Jiangnan University, Wuxi, China
- State Key Laboratory of Membrane Biology, School of Life Sciences, Tsinghua University, Beijing, China
| | - Rui Luo
- State Key Laboratory of Food Science and Technology, Jiangnan University, Wuxi, China
- Key Laboratory of Industrial Biotechnology, Ministry of Education, Jiangnan University, Wuxi, China
| | - Yize Li
- State Key Laboratory of Food Science and Technology, Jiangnan University, Wuxi, China
- Key Laboratory of Industrial Biotechnology, Ministry of Education, Jiangnan University, Wuxi, China
| | - Xiulai Chen
- State Key Laboratory of Food Science and Technology, Jiangnan University, Wuxi, China
- Key Laboratory of Industrial Biotechnology, Ministry of Education, Jiangnan University, Wuxi, China
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Liu H, Wu X, Ma H, Li J, Liu Z, Guo X, Dong J, Zou S, Luo Y. High-Level Production of Hydroxytyrosol in Engineered Saccharomyces cerevisiae. ACS Synth Biol 2022; 11:3706-3713. [PMID: 36345886 DOI: 10.1021/acssynbio.2c00316] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
Abstract
Hydroxytyrosol (HT) is a valuable aromatic compound with numerous applications. Herein, we enabled the efficient and scalable de novo HT production in engineered Saccharomyces cerevisiae (S. cerevisiae) from glucose. Starting from a tyrosol-overproducing strain, six HpaB/HpaC combinations were investigated, and the best catalytic performance was acquired with HpaB from Pseudomonas aeruginosa (PaHpaB) and HpaC from Escherichia coli (EcHpaC), resulting in 425.7 mg/L HT in shake flasks. Next, weakening the tryptophan biosynthetic pathway through downregulating the expression of TRP2 (encoding anthranilate synthase) further improved the HT titer by 27.2% compared to the base strain. Moreover, the cytosolic NADH supply was improved through introducing the feedback-resistant mutant of the TyrA (the NAD+-dependent chorismate mutase/prephenate dehydrogenase, TyrA*) from E. coli, which further increased the HT titer by 36.9% compared to the base strain. The best performing strain was obtained by optimizing the biosynthesis of HT in S. cerevisiae through a screening for an effective HpaB/HpaC combination, biosynthetic flux rewiring, and cofactor engineering, which enabled the titer of HT reaching 1120.0 mg/L in the shake flask. Finally, the engineered strain produced 6.97 g/L of HT by fed-batch fermentation, which represents the highest titer for de novo HT biosynthesis in microorganisms reported to date.
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Affiliation(s)
- Huayi Liu
- Frontiers Science Center of Synthetic Biology and Key Laboratory of Systems Bioengineering (Ministry of Education), School of Chemical Engineering and Technology, Tianjin University, Tianjin 300072, China
| | - Xinxin Wu
- Frontiers Science Center of Synthetic Biology and Key Laboratory of Systems Bioengineering (Ministry of Education), School of Chemical Engineering and Technology, Tianjin University, Tianjin 300072, China
| | - He Ma
- Frontiers Science Center of Synthetic Biology and Key Laboratory of Systems Bioengineering (Ministry of Education), School of Chemical Engineering and Technology, Tianjin University, Tianjin 300072, China
| | - Jian Li
- Frontiers Science Center of Synthetic Biology and Key Laboratory of Systems Bioengineering (Ministry of Education), School of Chemical Engineering and Technology, Tianjin University, Tianjin 300072, China
| | - Zhenyu Liu
- Frontiers Science Center of Synthetic Biology and Key Laboratory of Systems Bioengineering (Ministry of Education), School of Chemical Engineering and Technology, Tianjin University, Tianjin 300072, China
| | - Xufan Guo
- Frontiers Science Center of Synthetic Biology and Key Laboratory of Systems Bioengineering (Ministry of Education), School of Chemical Engineering and Technology, Tianjin University, Tianjin 300072, China
| | - Jia Dong
- Frontiers Science Center of Synthetic Biology and Key Laboratory of Systems Bioengineering (Ministry of Education), School of Chemical Engineering and Technology, Tianjin University, Tianjin 300072, China
| | - Shaolan Zou
- Frontiers Science Center of Synthetic Biology and Key Laboratory of Systems Bioengineering (Ministry of Education), School of Chemical Engineering and Technology, Tianjin University, Tianjin 300072, China
| | - Yunzi Luo
- Frontiers Science Center of Synthetic Biology and Key Laboratory of Systems Bioengineering (Ministry of Education), School of Chemical Engineering and Technology, Tianjin University, Tianjin 300072, China
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D-Lactic Acid Production from Sugarcane Bagasse by Genetically Engineered Saccharomyces cerevisiae. J Fungi (Basel) 2022; 8:jof8080816. [PMID: 36012804 PMCID: PMC9410322 DOI: 10.3390/jof8080816] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2022] [Revised: 07/26/2022] [Accepted: 07/29/2022] [Indexed: 11/25/2022] Open
Abstract
Lactic acid (LA) is a promising bio-based chemical that has broad applications in food, nutraceutical, and bioplastic industries. However, production of the D-form of LA (D-LA) from fermentative organisms is lacking. In this study, Saccharomyces cerevisiae harboring the D-lactate dehydrogenase (DLDH) gene from Leuconostoc mesenteroides was constructed (CEN.PK2_DLDH). To increase D-LA production, the CRISPR/Cas12a system was used for the deletion of gpd1, gpd2, and adh1 to minimize glycerol and ethanol production. Although an improved D-LA titer was observed for both CEN.PK2_DLDHΔgpd and CEN.PK2_DLDHΔgpdΔadh1, growth impairment was observed. To enhance the D-LA productivity, CEN.PK2_DLDHΔgpd was crossed with the weak acid-tolerant S. cerevisiae BCC39850. The isolated hybrid2 showed a maximum D-LA concentration of 23.41 ± 1.65 g/L, equivalent to the improvement in productivity and yield by 2.2 and 1.5 folds, respectively. The simultaneous saccharification and fermentation using alkaline pretreated sugarcane bagasse by the hybrid2 led to an improved D-LA conversion yield on both the washed solid and whole slurry (0.33 and 0.24 g/g glucan). Our findings show the exploitation of natural yeast diversity and the potential strategy of gene editing combined with conventional breeding on improving the performance of S. cerevisiae for the production of industrially potent products.
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Jang BK, Ju Y, Jeong D, Jung SK, Kim CK, Chung YS, Kim SR. l-Lactic Acid Production Using Engineered Saccharomyces cerevisiae with Improved Organic Acid Tolerance. J Fungi (Basel) 2021; 7:jof7110928. [PMID: 34829217 PMCID: PMC8624227 DOI: 10.3390/jof7110928] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2021] [Revised: 10/29/2021] [Accepted: 10/30/2021] [Indexed: 11/16/2022] Open
Abstract
Lactic acid is mainly used to produce bio-based, bio-degradable polylactic acid. For industrial production of lactic acid, engineered Saccharomyces cerevisiae can be used. To avoid cellular toxicity caused by lactic acid accumulation, pH-neutralizing agents are used, leading to increased production costs. In this study, lactic acid-producing S. cerevisiae BK01 was developed with improved lactic acid tolerance through adaptive laboratory evolution (ALE) on 8% lactic acid. The genetic basis of BK01 could not be determined, suggesting complex mechanisms associated with lactic acid tolerance. However, BK01 had distinctive metabolomic traits clearly separated from the parental strain, and lactic acid production was improved by 17% (from 102 g/L to 119 g/L). To the best of our knowledge, this is the highest lactic acid titer produced by engineered S. cerevisiae without the use of pH neutralizers. Moreover, cellulosic lactic acid production by BK01 was demonstrated using acetate-rich buckwheat husk hydrolysates. Particularly, BK01 revealed improved tolerance against acetic acid of the hydrolysates, a major fermentation inhibitor of lignocellulosic biomass. In short, ALE with a high concentration of lactic acid improved lactic acid production as well as acetic acid tolerance of BK01, suggesting a potential for economically viable cellulosic lactic acid production.
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Affiliation(s)
- Byeong-Kwan Jang
- Major in Food Application Technology, School of Food Science and Biotechnology, Kyungpook National University, Daegu 41566, Korea; (B.-K.J.); (Y.J.); (D.J.); (S.-K.J.)
| | - Yebin Ju
- Major in Food Application Technology, School of Food Science and Biotechnology, Kyungpook National University, Daegu 41566, Korea; (B.-K.J.); (Y.J.); (D.J.); (S.-K.J.)
| | - Deokyeol Jeong
- Major in Food Application Technology, School of Food Science and Biotechnology, Kyungpook National University, Daegu 41566, Korea; (B.-K.J.); (Y.J.); (D.J.); (S.-K.J.)
| | - Sung-Keun Jung
- Major in Food Application Technology, School of Food Science and Biotechnology, Kyungpook National University, Daegu 41566, Korea; (B.-K.J.); (Y.J.); (D.J.); (S.-K.J.)
| | - Chang-Kil Kim
- Department of Horticulture, Kyungpook National University, Daegu 41566, Korea;
| | - Yong-Suk Chung
- Department of Plant Resources and Environment, Jeju National University, Jeju 63243, Korea
- Correspondence: (Y.-S.C.); (S.-R.K.)
| | - Soo-Rin Kim
- Major in Food Application Technology, School of Food Science and Biotechnology, Kyungpook National University, Daegu 41566, Korea; (B.-K.J.); (Y.J.); (D.J.); (S.-K.J.)
- Correspondence: (Y.-S.C.); (S.-R.K.)
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10
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Kim JE, Son SH, Oh SS, Kim SC, Lee JY. Pairing of orthogonal chaperones with a cytochrome P450 enhances terpene synthesis in Saccharomyces cerevisiae. Biotechnol J 2021; 17:e2000452. [PMID: 34269523 DOI: 10.1002/biot.202000452] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2020] [Revised: 06/24/2021] [Accepted: 07/12/2021] [Indexed: 12/16/2022]
Abstract
The supply of terpenes is often limited by their low extraction yield from natural resources, such as plants. Thus, microbial biosynthesis has emerged as an attractive platform for the production of terpenes. Many strategies have been applied to engineer microbes to improve terpene production capabilities; however, functional expression of heterologous proteins such as cytochrome P450 enzymes (P450s) in microbes is a major obstacle. This study reports the successful pairing of cognate chaperones and P450s for functional heterologous expression in Saccharomyces cerevisiae. This chaperone pairing was exploited to facilitate the functional assembly of the protopanaxadiol (PPD) biosynthesis pathway, which consists of a P450 oxygenase and a P450 reductase redox partner originating from Panax ginseng and Arabidopsis thaliana, respectively. We identified several chaperones required for protein folding in P. ginseng and A. thaliana and evaluated the impact of the coexpression of the corresponding chaperones on the synthesis and activity of PPD biosynthesis enzymes. Expression of a chaperone from P. ginseng (PgCPR5), a cognate of PPD biosynthesis enzymes, significantly increased PPD production by more than 2.5-fold compared with that in the corresponding control strain. Thus, pairing of chaperones with heterologous enzymes provides an effective strategy for the construction of challenging biosynthesis pathways in yeast.
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Affiliation(s)
- Jae-Eung Kim
- Research Center for Bio-based Chemistry, Korea Research Institute of Chemical Technology (KRICT), Ulsan, Republic of Korea
| | - So-Hee Son
- Research Center for Bio-based Chemistry, Korea Research Institute of Chemical Technology (KRICT), Ulsan, Republic of Korea.,School of Interdisciplinary Bioscience and Bioengineering, Pohang University of Science and Technology (POSTECH), Pohang, Gyeongbuk, Republic of Korea
| | - Seung Soo Oh
- School of Interdisciplinary Bioscience and Bioengineering, Pohang University of Science and Technology (POSTECH), Pohang, Gyeongbuk, Republic of Korea.,Department of Materials Science and Engineering, Pohang University of Science and Technology (POSTECH), Pohang, Gyeongbuk, Republic of Korea
| | - Sun Chang Kim
- Department of Biological Sciences, Korea Advanced Institute of Science and Technology (KAIST), Daejeon, Republic of Korea
| | - Ju Young Lee
- Research Center for Bio-based Chemistry, Korea Research Institute of Chemical Technology (KRICT), Ulsan, Republic of Korea
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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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12
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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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Yamada R, Kumata Y, Mitsui R, Matsumoto T, Ogino H. Improvement of lactic acid tolerance by cocktail δ-integration strategy and identification of the transcription factor PDR3 responsible for lactic acid tolerance in yeast Saccharomyces cerevisiae. World J Microbiol Biotechnol 2021; 37:19. [PMID: 33428004 DOI: 10.1007/s11274-020-02977-1] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2020] [Accepted: 12/03/2020] [Indexed: 10/22/2022]
Abstract
Although, yeast Saccharomyces cerevisiae is expected to be used as a host for lactic acid production, improvement of yeast lactic acid tolerance is required for efficient non-neutralizing fermentation. In this study, we optimized the expression levels of various transcription factors to improve the lactic acid tolerance of yeast by a previously developed cocktail δ-integration strategy. By optimizing the expression levels of various transcription factors, the maximum D-lactic acid production and yield under non-neutralizing conditions were improved by 1.2. and 1.6 times, respectively. Furthermore, overexpression of PDR3, which is known as a transcription factor involved in multi-drug resistance, effectively improved lactic acid tolerance in yeast. In addition, we clarified for the first time that high expression of PDR3 contributes to the improvement of lactic acid tolerance. PDR3 is considered to be an excellent target gene for studies on yeast stress tolerance and further researches are desired in the future.
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Affiliation(s)
- Ryosuke Yamada
- Department of Chemical Engineering, Osaka Prefecture University, 1-1 Gakuen-cho, Naka-ku, Sakai, Osaka, 599-8531, Japan.
| | - Yuki Kumata
- Department of Chemical Engineering, Osaka Prefecture University, 1-1 Gakuen-cho, Naka-ku, Sakai, Osaka, 599-8531, Japan
| | - Ryosuke Mitsui
- Department of Chemical Engineering, Osaka Prefecture University, 1-1 Gakuen-cho, Naka-ku, Sakai, Osaka, 599-8531, Japan
| | - Takuya Matsumoto
- Department of Chemical Engineering, Osaka Prefecture University, 1-1 Gakuen-cho, Naka-ku, Sakai, Osaka, 599-8531, Japan
| | - Hiroyasu Ogino
- Department of Chemical Engineering, Osaka Prefecture University, 1-1 Gakuen-cho, Naka-ku, Sakai, Osaka, 599-8531, Japan
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14
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Abedi E, Hashemi SMB. Lactic acid production - producing microorganisms and substrates sources-state of art. Heliyon 2020; 6:e04974. [PMID: 33088933 PMCID: PMC7566098 DOI: 10.1016/j.heliyon.2020.e04974] [Citation(s) in RCA: 111] [Impact Index Per Article: 27.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2020] [Revised: 06/08/2020] [Accepted: 09/16/2020] [Indexed: 01/18/2023] Open
Abstract
Lactic acid is an organic compound produced via fermentation by different microorganisms that are able to use different carbohydrate sources. Lactic acid bacteria are the main bacteria used to produce lactic acid and among these, Lactobacillus spp. have been showing interesting fermentation capacities. The use of Bacillus spp. revealed good possibilities to reduce the fermentative costs. Interestingly, lactic acid high productivity was achieved by Corynebacterium glutamicum and E. coli, mainly after engineering genetic modification. Fungi, like Rhizopus spp. can metabolize different renewable carbon resources, with advantageously amylolytic properties to produce lactic acid. Additionally, yeasts can tolerate environmental restrictions (for example acidic conditions), being the wild-type low lactic acid producers that have been improved by genetic manipulation. Microalgae and cyanobacteria, as photosynthetic microorganisms can be an alternative lactic acid producer without carbohydrate feed costs. For lactic acid production, it is necessary to have substrates in the fermentation medium. Different carbohydrate sources can be used, from plant waste as molasses, starchy, lignocellulosic materials as agricultural and forestry residues. Dairy waste also can be used by the addition of supplementary components with a nitrogen source.
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Affiliation(s)
- Elahe Abedi
- Department of Food Science and Technology, College of Agriculture, Fasa University, Fasa, Iran
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15
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Guo H, Wang H, Huo YX. Engineering Critical Enzymes and Pathways for Improved Triterpenoid Biosynthesis in Yeast. ACS Synth Biol 2020; 9:2214-2227. [PMID: 32786348 DOI: 10.1021/acssynbio.0c00124] [Citation(s) in RCA: 22] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
Triterpenoids represent a diverse group of phytochemicals that are widely distributed in the plant kingdom and have many biological activities. The heterologous production of triterpenoids in Saccharomyces cerevisiae has been successfully implemented by introducing various triterpenoid biosynthetic pathways. By engineering related enzymes as well as through yeast metabolism, the yield of various triterpenoids is significantly improved from the milligram per liter scale to the gram per liter scale. This achievement demonstrates that engineering critical enzymes is considered a potential strategy to overcome the main hurdles of the industrial application of these potent natural products. Here, we review strategies for designing enzymes to improve the yield of triterpenoids in S. cerevisiae in terms of three main aspects: 1, elevating the supply of the precursor 2,3-oxidosqualene; 2, optimizing triterpenoid-involved reactions; and 3, lowering the competition of the native sterol pathway. Then, we provide challenges and prospects for further enhancing triterpenoid production in S. cerevisiae.
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Affiliation(s)
- Hao Guo
- Key Laboratory of Molecular Medicine and Biotherapy, School of Life Science, Beijing Institute of Technology, Beijing, 100081, P. R. China
| | - Huiyan Wang
- Key Laboratory of Molecular Medicine and Biotherapy, School of Life Science, Beijing Institute of Technology, Beijing, 100081, P. R. China
| | - Yi-Xin Huo
- Key Laboratory of Molecular Medicine and Biotherapy, School of Life Science, Beijing Institute of Technology, Beijing, 100081, P. R. China
- SIP-UCLA Institute for Technology Advancement, Suzhou, 215123, P. R. China
- Tobacco Research Institute, Chinese Academy of Agricultural Sciences, Qingdao, 266101, P. R. China
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Evaluation of Product Distribution in Chemostat and Batch Fermentation in Lactic Acid-Producing Komagataella phaffii Strains Utilizing Glycerol as Substrate. Microorganisms 2020; 8:microorganisms8050781. [PMID: 32455925 PMCID: PMC7285341 DOI: 10.3390/microorganisms8050781] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2020] [Revised: 05/18/2020] [Accepted: 05/19/2020] [Indexed: 01/03/2023] Open
Abstract
Lactic acid is the monomeric unit of polylactide (PLA), a bioplastic widely used in the packaging, automotive, food, and pharmaceutical industries. Previously, the yeast Komagataella phaffii was genetically modified for the production of lactate from glycerol. For this, the bovine L-lactate dehydrogenase- (LDH)-encoding gene was inserted and the gene encoding the pyruvate decarboxylase (PDC) was disrupted, resulting in the GLp strain. This showed a yield of 67% L-lactic acid and 20% arabitol as a by-product in batches with oxygen limitation. Following up on these results, the present work endeavored to perform a detailed study of the metabolism of this yeast, as well as perturbing arabitol synthesis in an attempt to increase lactic acid titers. The GLp strain was cultivated in a glycerol-limited chemostat at different dilution rates, confirming that the production of both lactic acid and arabitol is dependent on the specific growth rate (and consequently on the concentration of the limiting carbon source) as well as on the oxygen level. Moreover, disruption of the gene encoding arabitol dehydrogenase (ArDH) was carried out, resulting in an increase of 20% in lactic acid and a 50% reduction in arabitol. This study clarifies the underlying metabolic reasons for arabitol formation in K. phaffii and points to ways for improving production of lactic acid using K. phaffii as a biocatalyst.
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Sohn YJ, Kim HT, Baritugo K, Jo SY, Song HM, Park SY, Park SK, Pyo J, Cha HG, Kim H, Na J, Park C, Choi J, Joo JC, Park SJ. Recent Advances in Sustainable Plastic Upcycling and Biopolymers. Biotechnol J 2020; 15:e1900489. [DOI: 10.1002/biot.201900489] [Citation(s) in RCA: 59] [Impact Index Per Article: 14.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2019] [Revised: 02/05/2020] [Indexed: 12/27/2022]
Affiliation(s)
- Yu Jung Sohn
- Division of Chemical Engineering and Materials ScienceEwha Womans University 52 Ewhayeodae‐gil Seodaemun‐gu Seoul 03760 Republic of Korea
| | - Hee Taek Kim
- Biobased Chemistry Research Center, Advanced Convergent Chemistry DivisionKorea Research Institute of Chemical Technology P.O.Box 107, 141 Gajeong‐ro, Yuseong‐gu Daejeon 34114 Republic of Korea
| | - Kei‐Anne Baritugo
- Division of Chemical Engineering and Materials ScienceEwha Womans University 52 Ewhayeodae‐gil Seodaemun‐gu Seoul 03760 Republic of Korea
| | - Seo Young Jo
- Division of Chemical Engineering and Materials ScienceEwha Womans University 52 Ewhayeodae‐gil Seodaemun‐gu Seoul 03760 Republic of Korea
| | - Hye Min Song
- Division of Chemical Engineering and Materials ScienceEwha Womans University 52 Ewhayeodae‐gil Seodaemun‐gu Seoul 03760 Republic of Korea
| | - Se Young Park
- Division of Chemical Engineering and Materials ScienceEwha Womans University 52 Ewhayeodae‐gil Seodaemun‐gu Seoul 03760 Republic of Korea
| | - Su Kyeong Park
- Division of Chemical Engineering and Materials ScienceEwha Womans University 52 Ewhayeodae‐gil Seodaemun‐gu Seoul 03760 Republic of Korea
| | - Jiwon Pyo
- Division of Chemical Engineering and Materials ScienceEwha Womans University 52 Ewhayeodae‐gil Seodaemun‐gu Seoul 03760 Republic of Korea
| | - Hyun Gil Cha
- Bio‐based Chemistry Research Center, Advanced Convergent Chemistry DivisionKorea Research Institute of Chemical Technology (KRICT) Ulsan 44429 Republic of Korea
| | - Hoyong Kim
- Bio‐based Chemistry Research Center, Advanced Convergent Chemistry DivisionKorea Research Institute of Chemical Technology (KRICT) Ulsan 44429 Republic of Korea
| | - Jeong‐Geol Na
- Department of Chemical and Biomolecular EngineeringSogang University 35 Baekbumro Mapo‐gu Seoul 04107 Republic of Korea
| | - Chulhwan Park
- Department of Chemical EngineeringKwangwoon University 98‐2, Seokgye‐ro Nowon‐gu Seoul Republic of Korea
| | - Jong‐Il Choi
- Department of Biotechnology and Engineering, Interdisciplinary Program of Bioenergy and BiomaterialsChonnam National University Gwangju 61186 Republic of Korea
| | - Jeong Chan Joo
- Biobased Chemistry Research Center, Advanced Convergent Chemistry DivisionKorea Research Institute of Chemical Technology P.O.Box 107, 141 Gajeong‐ro, Yuseong‐gu Daejeon 34114 Republic of Korea
| | - Si Jae Park
- Division of Chemical Engineering and Materials ScienceEwha Womans University 52 Ewhayeodae‐gil Seodaemun‐gu Seoul 03760 Republic of Korea
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18
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Stress-tolerant non-conventional microbes enable next-generation chemical biosynthesis. Nat Chem Biol 2020; 16:113-121. [DOI: 10.1038/s41589-019-0452-x] [Citation(s) in RCA: 45] [Impact Index Per Article: 11.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2019] [Accepted: 12/11/2019] [Indexed: 12/13/2022]
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19
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Kwak S, Yun EJ, Lane S, Oh EJ, Kim KH, Jin YS. Redirection of the Glycolytic Flux Enhances Isoprenoid Production in Saccharomyces cerevisiae. Biotechnol J 2019; 15:e1900173. [PMID: 31466140 DOI: 10.1002/biot.201900173] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2019] [Revised: 08/08/2019] [Indexed: 01/07/2023]
Abstract
Sufficient supply of reduced nicotinamide adenine dinucleotide phosphate (NADPH) is a prerequisite of the overproduction of isoprenoids and related bioproducts in Saccharomyces cerevisiae. Although S. cerevisiae highly depends on the oxidative pentose phosphate (PP) pathway to produce NADPH, its metabolic flux toward the oxidative PP pathway is limited due to the rigid glycolysis flux. To maximize NADPH supply for the isoprenoid production in yeast, upper glycolytic metabolic fluxes are reduced by introducing mutations into phosphofructokinase (PFK) along with overexpression of ZWF1 encoding glucose-6-phosphate (G6P) dehydrogenase. The PFK mutations (Pfk1 S724D and Pfk2 S718D) result in less glycerol production and more accumulation of G6P, which is a gateway metabolite toward the oxidative PP pathway. When combined with the PFK mutations, overexpression of ZWF1 caused substantial increases of [NADPH]/[NADP+ ] ratios whereas the effect of ZWF1 overexpression alone in the wild-type strain is not noticeable. Also, the introduction of ZWF1 overexpression and the PFK mutations into engineered yeast overexpressing acetyl-CoA C-acetyltransferase (ERG10), truncated HMG-CoA reductase isozyme 1 (tHMG1), and amorphadiene synthase (ADS) leads to a titer of 497 mg L-1 of amorphadiene (3.7-fold over the parental strain). These results suggest that perturbation of upper glycolytic fluxes, in addition to ZWF1 overexpression, is necessary for efficient NADPH supply through the oxidative PP pathway and enhanced production of isoprenoids by engineered S. cerevisiae.
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Affiliation(s)
- Suryang Kwak
- 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
| | - Eun Ju Yun
- Carl R. Woese Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, IL, 61801, USA.,Department of Biotechnology, Korea University, Seoul, 02841, Republic of Korea
| | - Stephan Lane
- 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
| | - Eun Joong Oh
- 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
| | - Kyoung Heon Kim
- Department of Biotechnology, Korea University, Seoul, 02841, Republic of Korea
| | - 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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20
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Kim JE, Jang IS, Sung BH, Kim SC, Lee JY. Rerouting of NADPH synthetic pathways for increased protopanaxadiol production in Saccharomyces cerevisiae. Sci Rep 2018; 8:15820. [PMID: 30361526 PMCID: PMC6202386 DOI: 10.1038/s41598-018-34210-3] [Citation(s) in RCA: 38] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/13/2018] [Accepted: 10/11/2018] [Indexed: 11/17/2022] Open
Abstract
Ginseng (Panax ginseng) and its bioactive components, ginsenosides, are popular medicinal herbal products, exhibiting various pharmacological effects. Despite their advocated use for medication, the long cultivation periods of ginseng roots and their low ginsenoside content prevent mass production of this compound. Yeast Saccharomyces cerevisiae was engineered for production of protopanaxadiol (PPD), a type of aglycone characterizing ginsenoside. PPD-producing yeast cell factory was further engineered by obtaining a balance between enzyme expressions and altering cofactor availability. Different combinations of promoters (PGPD, PCCW12, and PADH2) were utilized to construct the PPD biosynthetic pathway. Rerouting the redox metabolism to improve NADPH availability in the engineered S. cerevisiae also increased PPD production. Combining these approaches resulted in more than an 11-fold increase in PPD titer over the initially constructed strain. The series of metabolic engineering strategies of this study provides a feasible approach for the microbial production of PPD and development of microbial platforms producing other industrially-relevant terpenoids.
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Affiliation(s)
- Jae-Eung Kim
- Center for Bio-based Chemistry, Korea Research Institute of Chemical Technology (KRICT), 406-30, Jongga-ro, Jung-gu, Ulsan, 44429, Republic of Korea
| | - In-Seung Jang
- Center for Bio-based Chemistry, Korea Research Institute of Chemical Technology (KRICT), 406-30, Jongga-ro, Jung-gu, Ulsan, 44429, Republic of Korea
| | - Bong Hyun Sung
- Cell Factory Research Center, Korea Research Institute of Bioscience and Biotechnology (KRIBB), Daejeon, 34141, Republic of Korea
| | - Sun Chang Kim
- Department of Biological Sciences, Korea Advanced Institute of Science and Technology (KAIST), Daejeon, 34141, Republic of Korea.
| | - Ju Young Lee
- Center for Bio-based Chemistry, Korea Research Institute of Chemical Technology (KRICT), 406-30, Jongga-ro, Jung-gu, Ulsan, 44429, Republic of Korea.
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21
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Microbial conversion of xylose into useful bioproducts. Appl Microbiol Biotechnol 2018; 102:9015-9036. [PMID: 30141085 DOI: 10.1007/s00253-018-9294-9] [Citation(s) in RCA: 30] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2018] [Revised: 08/03/2018] [Accepted: 08/06/2018] [Indexed: 02/06/2023]
Abstract
Microorganisms can produce a number of different bioproducts from the sugars in plant biomass. One challenge is devising processes that utilize all of the sugars in lignocellulosic hydrolysates. D-xylose is the second most abundant sugar in these hydrolysates. The microbial conversion of D-xylose to ethanol has been studied extensively; only recently, however, has conversion to bioproducts other than ethanol been explored. Moreover, in the case of yeast, D-xylose may provide a better feedstock for the production of bioproducts other than ethanol, because the relevant pathways are not subject to glucose-dependent repression. In this review, we discuss how different microorganisms are being used to produce novel bioproducts from D-xylose. We also discuss how D-xylose could be potentially used instead of glucose for the production of value-added bioproducts.
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Park HJ, Bae J, Ko H, Lee S, Sung BH, Han J, Sohn J. Low‐pH production of
d
‐lactic acid using newly isolated acid tolerant yeast
Pichia kudriavzevii
NG7. Biotechnol Bioeng 2018; 115:2232-2242. [DOI: 10.1002/bit.26745] [Citation(s) in RCA: 35] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2018] [Revised: 05/03/2018] [Accepted: 06/08/2018] [Indexed: 01/27/2023]
Affiliation(s)
- Hyun Joo Park
- Department of Civil and Environmental EngineeringKorea Advanced Institute of Science and Technology (KAIST) Daejeon Republic of Korea
- Cell Factory Research CenterKorea Research Institute of Bioscience and Biotechnology (KRIBB) Daejeon Republic of Korea
| | - Jung‐Hoon Bae
- Cell Factory Research CenterKorea Research Institute of Bioscience and Biotechnology (KRIBB) Daejeon Republic of Korea
| | - Hyeok‐Jin Ko
- Cell Factory Research CenterKorea Research Institute of Bioscience and Biotechnology (KRIBB) Daejeon Republic of Korea
| | - Sun‐Hee Lee
- Cell Factory Research CenterKorea Research Institute of Bioscience and Biotechnology (KRIBB) Daejeon Republic of Korea
| | - Bong Hyun Sung
- Cell Factory Research CenterKorea Research Institute of Bioscience and Biotechnology (KRIBB) Daejeon Republic of Korea
| | - Jong‐In Han
- Department of Civil and Environmental EngineeringKorea Advanced Institute of Science and Technology (KAIST) Daejeon Republic of Korea
| | - Jung‐Hoon Sohn
- Cell Factory Research CenterKorea Research Institute of Bioscience and Biotechnology (KRIBB) Daejeon Republic of Korea
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Engineering of Saccharomyces cerevisiae for enhanced production of L-lactic acid by co-expression of acid-stable glycolytic enzymes from Picrophilus torridus. KOREAN J CHEM ENG 2018. [DOI: 10.1007/s11814-018-0069-x] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/28/2022]
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Eş I, Mousavi Khaneghah A, Barba FJ, Saraiva JA, Sant'Ana AS, Hashemi SMB. Recent advancements in lactic acid production - a review. Food Res Int 2018; 107:763-770. [DOI: 10.1016/j.foodres.2018.01.001] [Citation(s) in RCA: 93] [Impact Index Per Article: 15.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2017] [Revised: 12/31/2017] [Accepted: 01/03/2018] [Indexed: 10/18/2022]
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Novy V, Brunner B, Nidetzky B. L-Lactic acid production from glucose and xylose with engineered strains of Saccharomyces cerevisiae: aeration and carbon source influence yields and productivities. Microb Cell Fact 2018; 17:59. [PMID: 29642896 PMCID: PMC5894196 DOI: 10.1186/s12934-018-0905-z] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2017] [Accepted: 03/31/2018] [Indexed: 12/21/2022] Open
Abstract
BACKGROUND Saccharomyces cerevisiae, engineered for L-lactic acid production from glucose and xylose, is a promising production host for lignocellulose-to-lactic acid processes. However, the two principal engineering strategies-pyruvate-to-lactic acid conversion with and without disruption of the competing pyruvate-to-ethanol pathway-have not yet resulted in strains that combine high lactic acid yields (YLA) and productivities (QLA) on both sugar substrates. Limitations seemingly arise from a dependency on the carbon source and the aeration conditions, but the underlying effects are poorly understood. We have recently presented two xylose-to-lactic acid converting strains, IBB14LA1 and IBB14LA1_5, which have the L-lactic acid dehydrogenase from Plasmodium falciparum (pfLDH) integrated at the pdc1 (pyruvate decarboxylase) locus. IBB14LA1_5 additionally has its pdc5 gene knocked out. In this study, the influence of carbon source and oxygen on YLA and QLA in IBB14LA1 and IBB14LA1_5 was investigated. RESULTS In anaerobic fermentation IBB14LA1 showed a higher YLA on xylose (0.27 g g Xyl-1 ) than on glucose (0.18 g g Glc-1 ). The ethanol yields (YEtOH, 0.15 g g Xyl-1 and 0.32 g g Glc-1 ) followed an opposite trend. In IBB14LA1_5, the effect of the carbon source on YLA was less pronounced (~ 0.80 g g Xyl-1 , and 0.67 g g Glc-1 ). Supply of oxygen accelerated glucose conversions significantly in IBB14LA1 (QLA from 0.38 to 0.81 g L-1 h-1) and IBB14LA1_5 (QLA from 0.05 to 1.77 g L-1 h-1) at constant YLA (IBB14LA1 ~ 0.18 g g Glc-1 ; IBB14LA1_5 ~ 0.68 g g Glc-1 ). In aerobic xylose conversions, however, lactic acid production ceased completely in IBB14LA1 and decreased drastically in IBB14LA1_5 (YLA aerobic ≤ 0.25 g g Xyl-1 and anaerobic ~ 0.80 g g Xyl-1 ) at similar QLA (~ 0.04 g L-1 h-1). Switching from aerobic to microaerophilic conditions (pO2 ~ 2%) prevented lactic acid metabolization, observed for fully aerobic conditions, and increased QLA and YLA up to 0.11 g L-1 h-1 and 0.38 g g Xyl-1 , respectively. The pfLDH and PDC activities in IBB14LA1 were measured and shown to change drastically dependent on carbon source and oxygen. CONCLUSION Evidence from conversion time courses together with results of activity measurements for pfLDH and PDC show that in IBB14LA1 the distribution of fluxes at the pyruvate branching point is carbon source and oxygen dependent. Comparison of the performance of strain IBB14LA1 and IBB14LA1_5 in conversions under different aeration conditions (aerobic, anaerobic, and microaerophilic) further suggest that xylose, unlike glucose, does not repress the respiratory response in both strains. This study proposes new genetic engineering targets for rendering genetically engineering S. cerevisiae better suited for lactic acid biorefineries.
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Affiliation(s)
- Vera Novy
- Institute of Biotechnology and Biochemical Engineering, NAWI Graz, Graz University of Technology, Petersgasse 12/I, 8010, Graz, Austria
| | - Bernd Brunner
- Institute of Biotechnology and Biochemical Engineering, NAWI Graz, Graz University of Technology, Petersgasse 12/I, 8010, Graz, Austria
| | - Bernd Nidetzky
- Institute of Biotechnology and Biochemical Engineering, NAWI Graz, Graz University of Technology, Petersgasse 12/I, 8010, Graz, Austria. .,Austrian Centre of Industrial Biotechnology, Graz, Austria.
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Jang IS, Yu BJ, Jang JY, Jegal J, Lee JY. Improving the efficiency of homologous recombination by chemical and biological approaches in Yarrowia lipolytica. PLoS One 2018; 13:e0194954. [PMID: 29566071 PMCID: PMC5864075 DOI: 10.1371/journal.pone.0194954] [Citation(s) in RCA: 30] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2018] [Accepted: 03/13/2018] [Indexed: 11/18/2022] Open
Abstract
Gene targeting is a challenge in Yarrowia lipolytica (Y. lipolytica) where non-homologous end-joining (NHEJ) is predominant over homologous recombination (HR). To improve the frequency and efficiency of HR in Y. lipolytica, the ku70 gene responsible for a double stand break (DSB) repair in the NHEJ pathway was disrupted, and the cell cycle was synchronized to the S-phase with hydroxyurea, respectively. Consequently, the HR frequency was over 46% with very short homology regions (50 bp): the pex10 gene was accurately deleted at a frequency of 60% and the β-carotene biosynthetic genes were integrated at the correct locus at an average frequency of 53%. For repeated use, the URA3 marker gene was also excised and deleted at a frequency of 100% by HR between the 100 bp homology regions flanking the URA3 gene. It was shown that appropriate combination of these chemical and biological approaches was very effective to promote HR and construct genetically modified Y. lipolytica strains for biotechnological applications.
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Affiliation(s)
- In-Seung Jang
- Center for Bio-based Chemistry, Korea Research Institute of Chemical Technology (KRICT), Jongga-ro, Jung-gu, Ulsan, Republic of Korea
- Intelligent Sustainable Materials R&D Group, Research Institute of Sustainable Manufacturing System, Korea Institute of Industrial Technology (KITECH), Yandaegiro-gil, Ipjang-myeon, Seobuk-gu, Cheonan-si, Chungcheongnam-do, Republic of Korea
| | - Byung Jo Yu
- Intelligent Sustainable Materials R&D Group, Research Institute of Sustainable Manufacturing System, Korea Institute of Industrial Technology (KITECH), Yandaegiro-gil, Ipjang-myeon, Seobuk-gu, Cheonan-si, Chungcheongnam-do, Republic of Korea
| | - Ji Yeon Jang
- Intelligent Sustainable Materials R&D Group, Research Institute of Sustainable Manufacturing System, Korea Institute of Industrial Technology (KITECH), Yandaegiro-gil, Ipjang-myeon, Seobuk-gu, Cheonan-si, Chungcheongnam-do, Republic of Korea
| | - Jonggeon Jegal
- Center for Bio-based Chemistry, Korea Research Institute of Chemical Technology (KRICT), Jongga-ro, Jung-gu, Ulsan, Republic of Korea
| | - Ju Young Lee
- Center for Bio-based Chemistry, Korea Research Institute of Chemical Technology (KRICT), Jongga-ro, Jung-gu, Ulsan, Republic of Korea
- * E-mail:
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27
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Zhao EM, Zhang Y, Mehl J, Park H, Lalwani MA, Toettcher JE, Avalos JL. Optogenetic regulation of engineered cellular metabolism for microbial chemical production. Nature 2018; 555:683-687. [PMID: 29562237 PMCID: PMC5876151 DOI: 10.1038/nature26141] [Citation(s) in RCA: 216] [Impact Index Per Article: 36.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2017] [Accepted: 02/13/2018] [Indexed: 12/29/2022]
Abstract
The optimization of engineered metabolic pathways requires careful control over the levels and timing of metabolic enzyme expression1-4. Optogenetic tools are ideal for achieving such precise control, as light can be applied and removed instantly without complex media changes. Here we show that light-controlled transcription can be used to enhance the biosynthesis of valuable products in engineered Saccharomyces cerevisiae. We introduce new optogenetic circuits to shift cells from a light-induced growth phase to a darkness-induced production phase, which allows us to control fermentation purely with light. Furthermore, optogenetic control of engineered pathways enables a new mode of bioreactor operation using periodic light pulses to tune enzyme expression during the production phase of fermentation to increase yields. Using these advances, we control the mitochondrial isobutanol pathway to produce up to 8.49 ± 0.31 g/L of isobutanol and 2.38 ± 0.06 g/L of 2-methyl-1-butanol micro-aerobically from glucose. These results make a compelling case for the application of optogenetics to metabolic engineering for valuable products.
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Affiliation(s)
- Evan M Zhao
- Department of Chemical and Biological Engineering, Hoyt Laboratory, Princeton University, 25 William Street, Princeton, New Jersey 08544, USA
| | - Yanfei Zhang
- Department of Chemical and Biological Engineering, Hoyt Laboratory, Princeton University, 25 William Street, Princeton, New Jersey 08544, USA
| | - Justin Mehl
- Department of Chemical and Biological Engineering, Hoyt Laboratory, Princeton University, 25 William Street, Princeton, New Jersey 08544, USA
| | - Helen Park
- Department of Chemical and Biological Engineering, Hoyt Laboratory, Princeton University, 25 William Street, Princeton, New Jersey 08544, USA
| | - Makoto A Lalwani
- Department of Chemical and Biological Engineering, Hoyt Laboratory, Princeton University, 25 William Street, Princeton, New Jersey 08544, USA
| | - Jared E Toettcher
- Department of Molecular Biology, 140 Lewis Thomas Laboratory, Washington Road, Princeton, New Jersey 08544, USA
| | - José L Avalos
- Department of Chemical and Biological Engineering, Hoyt Laboratory, Princeton University, 25 William Street, Princeton, New Jersey 08544, USA.,The Andlinger Center for Energy and the Environment, Princeton University, 86 Olden Street, Princeton, New Jersey 08544, USA
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28
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Xue G, Lai S, Li X, Zhang W, You J, Chen H, Qian Y, Gao P, Liu Z, Liu Y. Efficient bioconversion of organic wastes to high optical activity of l-lactic acid stimulated by cathode in mixed microbial consortium. WATER RESEARCH 2018; 131:1-10. [PMID: 29253664 DOI: 10.1016/j.watres.2017.12.024] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/28/2017] [Revised: 11/27/2017] [Accepted: 12/12/2017] [Indexed: 06/07/2023]
Abstract
Lactic acid is one of the emerging top biomass derived platform chemicals that can be fermented from organic wastes. This study evaluated the potential of Cathodic Electro-Fermentation (CEF) as a novel approach to enhance the yield of high optical activity (OA) of l-lactic acid from organic wastes using mixed microbial consortium. The fermentation process was stimulated through the cathode applied with -100 mV versus standard hydrogen electrode (SHE), which contributed to 4.73 times higher lactic acid productivity (0.6578 g L-1 h-1) compared to that in the open circuit control (0.1392 g L-1 h-1), and an improved OA of l-lactic acid was also observed (42.3% vs. 3.6% of the open circuit control). The study elucidated that the optimal voltage at -100 mV promoted the conversion of pyruvate to l-lactate by 77.9% compared to the Blank, which triggered the generation of l-lactic acid to occur rapidly even at low concentration of pyruvate. The significant variation of microbial community in family- and genus-level distributions were observed in CEF system. Furthermore, the open-circuit operation test demonstrated that the cathode providing in-situ electron supply was essential to achieve high efficient bioconversion of organic wastes to lactic acid. Our work highlights the feasibility of CEF to steer high value-added fermentation products deriving from organic wastes by the mixed microbial consortium.
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Affiliation(s)
- Gang Xue
- College of Environmental Science and Engineering, Donghua University, 2999 North Renmin Road, Shanghai 201620, China
| | - Sizhou Lai
- College of Environmental Science and Engineering, Donghua University, 2999 North Renmin Road, Shanghai 201620, China
| | - Xiang Li
- College of Environmental Science and Engineering, Donghua University, 2999 North Renmin Road, Shanghai 201620, China.
| | - Wenjuan Zhang
- College of Environmental Science and Engineering, Donghua University, 2999 North Renmin Road, Shanghai 201620, China
| | - Jiguang You
- College of Environmental Science and Engineering, Donghua University, 2999 North Renmin Road, Shanghai 201620, China
| | - Hong Chen
- College of Environmental Science and Engineering, Donghua University, 2999 North Renmin Road, Shanghai 201620, China
| | - Yajie Qian
- College of Environmental Science and Engineering, Donghua University, 2999 North Renmin Road, Shanghai 201620, China
| | - Pin Gao
- College of Environmental Science and Engineering, Donghua University, 2999 North Renmin Road, Shanghai 201620, China
| | - Zhenhong Liu
- College of Environmental Science and Engineering, Donghua University, 2999 North Renmin Road, Shanghai 201620, China
| | - Yanan Liu
- College of Environmental Science and Engineering, Donghua University, 2999 North Renmin Road, Shanghai 201620, China
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Effect of Pyruvate Decarboxylase Knockout on Product Distribution Using Pichia pastoris (Komagataella phaffii) Engineered for Lactic Acid Production. Bioengineering (Basel) 2018; 5:bioengineering5010017. [PMID: 29462904 PMCID: PMC5874883 DOI: 10.3390/bioengineering5010017] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/02/2018] [Revised: 02/11/2018] [Accepted: 02/12/2018] [Indexed: 01/06/2023] Open
Abstract
Lactic acid is the monomer unit of the bioplastic poly-lactic acid (PLA). One candidate organism for lactic acid production is Pichia pastoris, a yeast widely used for heterologous protein production. Nevertheless, this yeast has a poor fermentative capability that can be modulated by controlling oxygen levels. In a previous study, lactate dehydrogenase (LDH) activity was introduced into P. pastoris, enabling this yeast to produce lactic acid. The present study aimed to increase the flow of pyruvate towards the production of lactic acid in P. pastoris. To this end, a strain designated GLp was constructed by inserting the bovine lactic acid dehydrogenase gene (LDHb) concomitantly with the interruption of the gene encoding pyruvate decarboxylase (PDC). Aerobic fermentation, followed by micro-aerophilic culture two-phase fermentations, showed that the GLp strain achieved a lactic acid yield of 0.65 g/g. The distribution of fermentation products demonstrated that the acetate titer was reduced by 20% in the GLp strain with a concomitant increase in arabitol production: arabitol increased from 0.025 g/g to 0.174 g/g when compared to the GS115 strain. Taken together, the results show a significant potential for P. pastoris in producing lactic acid. Moreover, for the first time, physiological data regarding co-product formation have indicated the redox balance limitations of this yeast.
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30
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31
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Salusjärvi L, Toivari M, Vehkomäki ML, Koivistoinen O, Mojzita D, Niemelä K, Penttilä M, Ruohonen L. Production of ethylene glycol or glycolic acid from D-xylose in Saccharomyces cerevisiae. Appl Microbiol Biotechnol 2017; 101:8151-8163. [PMID: 29038973 DOI: 10.1007/s00253-017-8547-3] [Citation(s) in RCA: 43] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2017] [Revised: 09/05/2017] [Accepted: 09/17/2017] [Indexed: 11/26/2022]
Abstract
The important platform chemicals ethylene glycol and glycolic acid were produced via the oxidative D-xylose pathway in the yeast Saccharomyces cerevisiae. The expression of genes encoding D-xylose dehydrogenase (XylB) and D-xylonate dehydratase (XylD) from Caulobacter crescentus and YagE or YjhH aldolase and aldehyde dehydrogenase AldA from Escherichia coli enabled glycolic acid production from D-xylose up to 150 mg/L. In strains expressing only xylB and xylD, 29 mg/L 2-keto-3-deoxyxylonic acid [(S)-4,5-dihydroxy-2-oxopentanoic acid] (2K3DXA) was produced and D-xylonic acid accumulated to ca. 9 g/L. A significant amount of D-xylonic acid (ca. 14%) was converted to 3-deoxypentonic acid (3DPA), and also, 3,4-dihydroxybutyric acid was formed. 2K3DXA was further converted to glycolaldehyde when genes encoding by either YagE or YjhH aldolase from E. coli were expressed. Reduction of glycolaldehyde to ethylene glycol by an endogenous aldo-keto reductase activity resulted further in accumulation of ethylene glycol of 14 mg/L. The possibility of simultaneous production of lactic and glycolic acids was evaluated by expression of gene encoding lactate dehydrogenase ldhL from Lactobacillus helveticus together with aldA. Interestingly, this increased the accumulation of glycolic acid to 1 g/L. The D-xylonate dehydratase activity in yeast was notably low, possibly due to inefficient Fe-S cluster synthesis in the yeast cytosol, and leading to D-xylonic acid accumulation. The dehydratase activity was significantly improved by targeting its expression to mitochondria or by altering the Fe-S cluster metabolism of the cells with FRA2 deletion.
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Affiliation(s)
- Laura Salusjärvi
- VTT Technical Research Centre of Finland Ltd., Solutions for Natural Resources and Environment, Tietotie 2, P.O. Box 1000, FI-02044 VTT, Espoo, Finland.
| | - Mervi Toivari
- VTT Technical Research Centre of Finland Ltd., Solutions for Natural Resources and Environment, Tietotie 2, P.O. Box 1000, FI-02044 VTT, Espoo, Finland
| | - Maija-Leena Vehkomäki
- VTT Technical Research Centre of Finland Ltd., Solutions for Natural Resources and Environment, Tietotie 2, P.O. Box 1000, FI-02044 VTT, Espoo, Finland
| | - Outi Koivistoinen
- VTT Technical Research Centre of Finland Ltd., Solutions for Natural Resources and Environment, Tietotie 2, P.O. Box 1000, FI-02044 VTT, Espoo, Finland
| | - Dominik Mojzita
- VTT Technical Research Centre of Finland Ltd., Solutions for Natural Resources and Environment, Tietotie 2, P.O. Box 1000, FI-02044 VTT, Espoo, Finland
| | - Klaus Niemelä
- VTT Technical Research Centre of Finland Ltd., Solutions for Natural Resources and Environment, Tietotie 2, P.O. Box 1000, FI-02044 VTT, Espoo, Finland
| | - Merja Penttilä
- VTT Technical Research Centre of Finland Ltd., Solutions for Natural Resources and Environment, Tietotie 2, P.O. Box 1000, FI-02044 VTT, Espoo, Finland
| | - Laura Ruohonen
- VTT Technical Research Centre of Finland Ltd., Solutions for Natural Resources and Environment, Tietotie 2, P.O. Box 1000, FI-02044 VTT, Espoo, Finland
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Ozaki A, Konishi R, Otomo C, Kishida M, Takayama S, Matsumoto T, Tanaka T, Kondo A. Metabolic engineering of Schizosaccharomyces pombe via CRISPR-Cas9 genome editing for lactic acid production from glucose and cellobiose. Metab Eng Commun 2017; 5:60-67. [PMID: 29188185 PMCID: PMC5699526 DOI: 10.1016/j.meteno.2017.08.002] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2017] [Revised: 08/18/2017] [Accepted: 08/20/2017] [Indexed: 12/14/2022] Open
Abstract
Modification of the Schizosaccharomyces pombe genome is often laborious, time consuming due to the lower efficiency of homologous recombination. Here, we constructed metabolically engineered S. pombe strains using a CRISPR-Cas9 system and also demonstrated D-lactic acid (D-LA) production from glucose and cellobiose. Genes encoding two separate pyruvate decarboxylases (PDCs), an L-lactic acid dehydrogenase (L-LDH), and a minor alcohol dehydrogenase (SPBC337.11) were disrupted, thereby attenuating ethanol production. To increase the cellular supply of acetyl-CoA, an important metabolite for growth, we introduced genes encoding bacterial acetylating acetaldehyde dehydrogenase enzymes (Escherichia coli MhpF and EutE). D-LA production by the resulting strain was achieved by expressing a Lactobacillus plantarum gene encoding D-lactate dehydrogenase. The engineered strain efficiently consumed glucose and produced D-LA at 25.2 g/L from 35.5 g/L of consumed glucose with a yield of 0.71 g D-LA / g glucose. We further modified this strain by expressing beta-glucosidase by cell surface display; the resulting strain produced D-LA at 24.4 g/L from 30 g/L of cellobiose in minimal medium, with a yield of 0.68 g D-LA / g glucose. To our knowledge, this study represents the first report of a S. pombe strain that was metabolically engineered using a CRISPR-Cas9 system, and demonstrates the possibility of engineering S. pombe for the production of value-added chemicals. Schizosaccharomyces pombe were metabolically engineered using a CRISPR-Cas9 system. D-lactic acid (D-LA) producing Schizosaccharomyces pombe strains were constructed. 25.2 g/L of D-LA was produced with a yield of 0.71 g-D-LA / g-glucose. Beta-glucosidase was expressed on this engineered S. pombe strain. D-LA was produced at 24.4 g/L from 30 g/L of cellobiose directly.
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Affiliation(s)
- Aiko Ozaki
- Department of Chemical Science and Engineering, Graduate School of Engineering, Kobe University, 1-1, Rokkodaicho, Nada, Kobe 657-8501, Japan
| | - Rie Konishi
- Graduate School of Science, Technology and Innovation, Kobe University, 1-1 Rokkodaicho, Nada, Kobe 657-8501, Japan
| | - Chisako Otomo
- Graduate School of Science, Technology and Innovation, Kobe University, 1-1 Rokkodaicho, Nada, Kobe 657-8501, Japan
| | - Mayumi Kishida
- Graduate School of Science, Technology and Innovation, Kobe University, 1-1 Rokkodaicho, Nada, Kobe 657-8501, Japan
| | - Seiya Takayama
- Department of Chemical Science and Engineering, Graduate School of Engineering, Kobe University, 1-1, Rokkodaicho, Nada, Kobe 657-8501, Japan
| | - Takuya Matsumoto
- Graduate School of Science, Technology and Innovation, Kobe University, 1-1 Rokkodaicho, Nada, Kobe 657-8501, Japan
| | - Tsutomu Tanaka
- Department of Chemical Science and Engineering, Graduate School of Engineering, Kobe University, 1-1, Rokkodaicho, Nada, Kobe 657-8501, Japan
| | - Akihiko Kondo
- Graduate School of Science, Technology and Innovation, Kobe University, 1-1 Rokkodaicho, Nada, Kobe 657-8501, Japan
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Baek S, Kwon EY, Bae S, Cho B, Kim S, Hahn J. Improvement of
d
‐Lactic Acid Production in
Saccharomyces cerevisiae
Under Acidic Conditions by Evolutionary and Rational Metabolic Engineering. Biotechnol J 2017; 12. [DOI: 10.1002/biot.201700015] [Citation(s) in RCA: 50] [Impact Index Per Article: 7.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2017] [Revised: 07/11/2017] [Indexed: 01/12/2023]
Affiliation(s)
- Seung‐Ho Baek
- School of Chemical and Biological EngineeringInstitute of Chemical ProcessesSeoul National UniversitySeoulRepublic of Korea
| | - Eunice Y. Kwon
- School of Chemical and Biological EngineeringInstitute of Chemical ProcessesSeoul National UniversitySeoulRepublic of Korea
| | - Sang‐Jeong Bae
- School of Chemical and Biological EngineeringInstitute of Chemical ProcessesSeoul National UniversitySeoulRepublic of Korea
| | - Bo‐Ram Cho
- School of Chemical and Biological EngineeringInstitute of Chemical ProcessesSeoul National UniversitySeoulRepublic of Korea
| | - Seon‐Young Kim
- Personalized Genomic Medicine Research CenterKRIBBDaejeonRepublic of Korea
| | - Ji‐Sook Hahn
- School of Chemical and Biological EngineeringInstitute of Chemical ProcessesSeoul National UniversitySeoulRepublic of Korea
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Weusthuis RA, Mars AE, Springer J, Wolbert EJH, van der Wal H, de Vrije TG, Levisson M, Leprince A, Houweling-Tan G, PHA Moers A, Hendriks SNA, Mendes O, Griekspoor Y, Werten MWT, Schaap PJ, van der Oost J, Eggink G. Monascus ruber as cell factory for lactic acid production at low pH. Metab Eng 2017; 42:66-73. [DOI: 10.1016/j.ymben.2017.05.005] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2016] [Revised: 05/16/2017] [Accepted: 05/30/2017] [Indexed: 10/19/2022]
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Yamada R, Wakita K, Mitsui R, Ogino H. Enhanced d
-lactic acid production by recombinant Saccharomyces cerevisiae
following optimization of the global metabolic pathway. Biotechnol Bioeng 2017; 114:2075-2084. [DOI: 10.1002/bit.26330] [Citation(s) in RCA: 35] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2017] [Revised: 04/14/2017] [Accepted: 04/30/2017] [Indexed: 11/07/2022]
Affiliation(s)
- Ryosuke Yamada
- Department of Chemical Engineering; Osaka Prefecture University; 1-1 Gakuen-cho, Naka-ku Sakai Osaka 599-8531 Japan
| | - Kazuki Wakita
- Department of Chemical Engineering; Osaka Prefecture University; 1-1 Gakuen-cho, Naka-ku Sakai Osaka 599-8531 Japan
| | - Ryosuke Mitsui
- Department of Chemical Engineering; Osaka Prefecture University; 1-1 Gakuen-cho, Naka-ku Sakai Osaka 599-8531 Japan
| | - Hiroyasu Ogino
- Department of Chemical Engineering; Osaka Prefecture University; 1-1 Gakuen-cho, Naka-ku Sakai Osaka 599-8531 Japan
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Chen Y, Zhou H, Wang M, Tan T. Control of ATP concentration in Escherichia coli using an ATP-sensing riboswitch for enhanced S-adenosylmethionine production. RSC Adv 2017. [DOI: 10.1039/c7ra02538f] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
Abstract
We proposed an ATP-sensing riboswitch-based strategy which could be applied to regulate the intracellular ATP concentration dynamically inE. coli. This strategy will be most beneficial for enhancing the production of the ATP-driven metabolites.
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Affiliation(s)
- Yawei Chen
- College of Chemical and Pharmaceutical Engineering
- Henan University of Science and Technology
- Luoyang 471023
- PR China
| | - Huiyun Zhou
- College of Chemical and Pharmaceutical Engineering
- Henan University of Science and Technology
- Luoyang 471023
- PR China
| | - Meng Wang
- National Energy R&D Center for Biorefinery
- College of Life Science and Technology
- Beijing University of Chemical Technology
- Beijing 100029
- PR China
| | - Tianwei Tan
- National Energy R&D Center for Biorefinery
- College of Life Science and Technology
- Beijing University of Chemical Technology
- Beijing 100029
- PR China
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Ju SY, Kim JH, Lee PC. Long-term adaptive evolution of Leuconostoc mesenteroides for enhancement of lactic acid tolerance and production. BIOTECHNOLOGY FOR BIOFUELS 2016; 9:240. [PMID: 27843489 PMCID: PMC5103595 DOI: 10.1186/s13068-016-0662-3] [Citation(s) in RCA: 35] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/25/2016] [Accepted: 11/04/2016] [Indexed: 05/24/2023]
Abstract
BACKGROUND Lactic acid has been approved by the United States Food and Drug Administration as Generally Regarded As Safe (GRAS) and is commonly used in the cosmetics, pharmaceutical, and food industries. Applications of lactic acid have also emerged in the plastics industry. Lactic acid bacteria (LAB), such as Leuconostoc and Lactobacillus, are widely used as lactic acid producers for food-related and biotechnological applications. Nonetheless, industrial mass production of lactic acid in LAB is a challenge mainly because of growth inhibition caused by the end product, lactic acid. Thus, it is important to improve acid tolerance of LAB to achieve balanced cell growth and a high titer of lactic acid. Recently, adaptive evolution has been employed as one of the strategies to improve the fitness and to induce adaptive changes in bacteria under specific growth conditions, such as acid stress. RESULTS Wild-type Leuconostoc mesenteroides was challenged long term with exogenously supplied lactic acid, whose concentration was increased stepwise (for enhancement of lactic acid tolerance) during 1 year. In the course of the adaptive evolution at 70 g/L lactic acid, three mutants (LMS50, LMS60, and LMS70) showing high specific growth rates and lactic acid production were isolated and characterized. Mutant LMS70, isolated at 70 g/L lactic acid, increased d-lactic acid production up to 76.8 g/L, which was twice that in the wild type (37.8 g/L). Proteomic, genomic, and physiological analyses revealed that several possible factors affected acid tolerance, among which a mutation of ATPase ε subunit (involved in the regulation of intracellular pH) and upregulation of intracellular ammonia, as a buffering system, were confirmed to contribute to the observed enhancement of tolerance and production of d-lactic acid. CONCLUSIONS During adaptive evolution under lethal stress conditions, the fitness of L. mesenteroides gradually increased to accumulate beneficial mutations according to the stress level. The enhancement of acid tolerance in the mutants contributed to increased production of d-lactic acid. The observed genetic and physiological changes may systemically help remove protons and retain viability at high lactic acid concentrations.
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Affiliation(s)
- Si Yeon Ju
- Department of Molecular Science and Technology, Ajou University, Woncheon-dong, Yeongtong-gu, Suwon, 443-749 South Korea
- Department of Applied Chemistry and Biological Engineering, Ajou University, Woncheon-dong, Yeongtong-gu, Suwon, 443-749 South Korea
| | - Jin Ho Kim
- Department of Molecular Science and Technology, Ajou University, Woncheon-dong, Yeongtong-gu, Suwon, 443-749 South Korea
- Department of Applied Chemistry and Biological Engineering, Ajou University, Woncheon-dong, Yeongtong-gu, Suwon, 443-749 South Korea
| | - Pyung Cheon Lee
- Department of Molecular Science and Technology, Ajou University, Woncheon-dong, Yeongtong-gu, Suwon, 443-749 South Korea
- Department of Applied Chemistry and Biological Engineering, Ajou University, Woncheon-dong, Yeongtong-gu, Suwon, 443-749 South Korea
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Abdel-Rahman MA, Sonomoto K. Opportunities to overcome the current limitations and challenges for efficient microbial production of optically pure lactic acid. J Biotechnol 2016; 236:176-92. [DOI: 10.1016/j.jbiotec.2016.08.008] [Citation(s) in RCA: 114] [Impact Index Per Article: 14.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2016] [Accepted: 08/11/2016] [Indexed: 10/21/2022]
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Cordova LT, Alper HS. Central metabolic nodes for diverse biochemical production. Curr Opin Chem Biol 2016; 35:37-42. [PMID: 27607733 DOI: 10.1016/j.cbpa.2016.08.025] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2016] [Revised: 08/24/2016] [Accepted: 08/25/2016] [Indexed: 12/25/2022]
Abstract
Central carbon metabolism is conserved among all organisms for cellular function and energy generation. The connectivity of this metabolic map gives rises to key metabolite nodes. Five of these nodes in particular, pyruvate, citric acid, tyrosine and aspartate, acetyl-CoA, serve as critical starting points for the generation of a broad class of relevant chemical molecules with ranging applications from fuels, pharmaceuticals and polymer precursors. This review highlights recent progress in converting these metabolite nodes into valuable products. In particular, acetyl-CoA, the most well-connected node, serves as the building block for several classes of molecules including fatty acids and terpenes. Systematic metabolic engineering efforts focused on these metabolic building blocks has enabled the production of industrially-relevant, biobased compounds.
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Affiliation(s)
- Lauren T Cordova
- Institute for Cellular and Molecular Biology, The University of Texas at Austin, 2500 Speedway Avenue, Austin, TX 78712, United States
| | - Hal S Alper
- Institute for Cellular and Molecular Biology, The University of Texas at Austin, 2500 Speedway Avenue, Austin, TX 78712, United States; McKetta Department of Chemical Engineering, The University of Texas at Austin, 200 E Dean Keeton St. Stop C0400, Austin, TX 78712, United States.
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40
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Novy V, Brunner B, Müller G, Nidetzky B. Toward "homolactic" fermentation of glucose and xylose by engineered Saccharomyces cerevisiae harboring a kinetically efficient l-lactate dehydrogenase within pdc1-pdc5 deletion background. Biotechnol Bioeng 2016; 114:163-171. [PMID: 27426989 DOI: 10.1002/bit.26048] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2016] [Revised: 06/20/2016] [Accepted: 07/14/2016] [Indexed: 10/21/2022]
Abstract
l-Lactic acid is an important platform chemical and its production from the lignocellulosic sugars glucose and xylose is, therefore, of high interest. Tolerance to low pH and a generally high robustness make Saccharomyces cerevisiae a promising host for l-lactic acid fermentation but strain development for effective utilization of both sugars is an unsolved problem. The herein used S. cerevisiae strain IBB10B05 incorporates a NADH-dependent pathway for oxidoreductive xylose assimilation within CEN.PK113-7D background and was additionally evolved for accelerated xylose-to-ethanol fermentation. Selecting the Plasmodium falciparum l-lactate dehydrogenase (pfLDH) for its high kinetic efficiency, strain IBB14LA1 was derived from IBB10B05 by placing the pfldh gene at the pdc1 locus under control of the pdc1 promotor. Strain IBB14LA1_5 additionally had the pdc5 gene disrupted. With both strains, continued l-lactic acid formation from glucose or xylose, each at 50 g/L, necessitated stabilization of pH. Using calcium carbonate (11 g/L), anaerobic shaken bottle fermentations at pH ≥ 5 resulted in l-lactic acid yields (YLA ) of 0.67 g/g glucose and 0.80 g/g xylose for strain IBB14LA1_5. Only little xylitol was formed (≤0.08 g/g) and no ethanol. In pH stabilized aerobic conversions of glucose, strain IBB14LA1_5 further showed excellent l-lactic acid productivities (1.8 g/L/h) without losses in YLA (0.69 g/g glucose). In strain IBB14LA1, the YLA was lower (≤0.18 g/g glucose; ≤0.27 g/g xylose) due to ethanol as well as xylitol formation. Therefore, this study shows that a S. cerevisiae strain originally optimized for xylose-to-ethanol fermentation was useful to implement l-lactic acid production from glucose and xylose; and with the metabolic engineering strategy applied, advance toward homolactic fermentation of both sugars was made. Biotechnol. Bioeng. 2017;114: 163-171. © 2016 Wiley Periodicals, Inc.
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Affiliation(s)
- Vera Novy
- Graz University of Technology, Institute of Biotechnology and Biochemical Engineering, NAWI Graz, Petersgasse 12/I, 8010 Graz, Austria
| | - Bernd Brunner
- Graz University of Technology, Institute of Biotechnology and Biochemical Engineering, NAWI Graz, Petersgasse 12/I, 8010 Graz, Austria
| | - Gerdt Müller
- Graz University of Technology, Institute of Biotechnology and Biochemical Engineering, NAWI Graz, Petersgasse 12/I, 8010 Graz, Austria
| | - Bernd Nidetzky
- Graz University of Technology, Institute of Biotechnology and Biochemical Engineering, NAWI Graz, Petersgasse 12/I, 8010 Graz, Austria.,Austrian Centre of Industrial Biotechnology, Graz, Austria
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41
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Liu CG, Hao XM, Lin YH, Bai FW. Redox potential driven aeration during very-high-gravity ethanol fermentation by using flocculating yeast. Sci Rep 2016; 6:25763. [PMID: 27161047 PMCID: PMC4861961 DOI: 10.1038/srep25763] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2015] [Accepted: 04/21/2016] [Indexed: 11/09/2022] Open
Abstract
Ethanol fermentation requires oxygen to maintain high biomass and cell viability, especially under very-high-gravity (VHG) condition. In this work, fermentation redox potential (ORP) was applied to drive the aeration process at low dissolved oxygen (DO) levels, which is infeasible to be regulated by a DO sensor. The performance and characteristics of flocculating yeast grown under 300 and 260 g glucose/L conditions were subjected to various aeration strategies including: no aeration; controlled aeration at -150, -100 and -50 mV levels; and constant aeration at 0.05 and 0.2 vvm. The results showed that anaerobic fermentation produced the least ethanol and had the highest residual glucose after 72 h of fermentation. Controlled aerations, depending on the real-time oxygen demand, led to higher cell viability than the no-aeration counterpart. Constant aeration triggered a quick biomass formation, and fast glucose utilization. However, over aeration at 0.2 vvm caused a reduction of final ethanol concentration. The controlled aeration driven by ORP under VHG conditions resulted in the best fermentation performance. Moreover, the controlled aeration could enhance yeast flocculating activity, promote an increase of flocs size, and accelerate yeast separation near the end of fermentation.
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Affiliation(s)
- Chen-Guang Liu
- School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai 200240, China.,School of Life Science and Biotechnology, Dalian University of Technology, Dalian 116023, China
| | - Xue-Mi Hao
- School of Life Science and Biotechnology, Dalian University of Technology, Dalian 116023, China
| | - Yen-Han Lin
- Department of Chemical and Biological Engineering, University of Saskatchewan, Saskatoon SK S7N 5A9, Canada
| | - Feng-Wu Bai
- School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai 200240, China.,School of Life Science and Biotechnology, Dalian University of Technology, Dalian 116023, China
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Kim S, Bae SJ, Hahn JS. Redirection of pyruvate flux toward desired metabolic pathways through substrate channeling between pyruvate kinase and pyruvate-converting enzymes in Saccharomyces cerevisiae. Sci Rep 2016; 6:24145. [PMID: 27052099 PMCID: PMC4823786 DOI: 10.1038/srep24145] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2016] [Accepted: 03/21/2016] [Indexed: 11/08/2022] Open
Abstract
Spatial organization of metabolic enzymes allows substrate channeling, which accelerates processing of intermediates. Here, we investigated the effect of substrate channeling on the flux partitioning at a metabolic branch point, focusing on pyruvate metabolism in Saccharomyces cerevisiae. As a platform strain for the channeling of pyruvate flux, PYK1-Coh-Myc strain was constructed in which PYK1 gene encoding pyruvate kinase is tagged with cohesin domain. By using high-affinity cohesin-dockerin interaction, the pyruvate-forming enzyme Pyk1 was tethered to heterologous pyruvate-converting enzymes, lactate dehydrogenase and α-acetolactate synthase, to produce lactic acid and 2,3-butanediol, respectively. Pyruvate flux was successfully redirected toward desired pathways, with a concomitant decrease in ethanol production even without genetic attenuation of the ethanol-producing pathway. This pyruvate channeling strategy led to an improvement of 2,3-butanediol production by 38%, while showing a limitation in improving lactic acid production due to a reduced activity of lactate dehydrogenase by dockerin tagging.
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Affiliation(s)
- Sujin Kim
- School of Chemical and Biological Engineering, Seoul National University, Institute of Chemical Processes, 1 Gwanak-ro, Gwanak-gu, Seoul 08826, Republic of Korea
| | - Sang-Jeong Bae
- School of Chemical and Biological Engineering, Seoul National University, Institute of Chemical Processes, 1 Gwanak-ro, Gwanak-gu, Seoul 08826, Republic of Korea
| | - Ji-Sook Hahn
- School of Chemical and Biological Engineering, Seoul National University, Institute of Chemical Processes, 1 Gwanak-ro, Gwanak-gu, Seoul 08826, Republic of Korea
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43
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Becker-Kettern J, Paczia N, Conrotte JF, Kay DP, Guignard C, Jung PP, Linster CL. Saccharomyces cerevisiae Forms D-2-Hydroxyglutarate and Couples Its Degradation to D-Lactate Formation via a Cytosolic Transhydrogenase. J Biol Chem 2016; 291:6036-58. [PMID: 26774271 DOI: 10.1074/jbc.m115.704494] [Citation(s) in RCA: 46] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2015] [Indexed: 12/23/2022] Open
Abstract
The D or L form of 2-hydroxyglutarate (2HG) accumulates in certain rare neurometabolic disorders, and high D-2-hydroxyglutarate (D-2HG) levels are also found in several types of cancer. Although 2HG has been detected in Saccharomyces cerevisiae, its metabolism in yeast has remained largely unexplored. Here, we show that S. cerevisiae actively forms the D enantiomer of 2HG. Accordingly, the S. cerevisiae genome encodes two homologs of the human D-2HG dehydrogenase: Dld2, which, as its human homolog, is a mitochondrial protein, and the cytosolic protein Dld3. Intriguingly, we found that a dld3Δ knock-out strain accumulates millimolar levels of D-2HG, whereas a dld2Δ knock-out strain displayed only very moderate increases in D-2HG. Recombinant Dld2 and Dld3, both currently annotated as D-lactate dehydrogenases, efficiently oxidized D-2HG to α-ketoglutarate. Depletion of D-lactate levels in the dld3Δ, but not in the dld2Δ mutant, led to the discovery of a new type of enzymatic activity, carried by Dld3, to convert D-2HG to α-ketoglutarate, namely an FAD-dependent transhydrogenase activity using pyruvate as a hydrogen acceptor. We also provide evidence that Ser3 and Ser33, which are primarily known for oxidizing 3-phosphoglycerate in the main serine biosynthesis pathway, in addition reduce α-ketoglutarate to D-2HG using NADH and represent major intracellular sources of D-2HG in yeast. Based on our observations, we propose that D-2HG is mainly formed and degraded in the cytosol of S. cerevisiae cells in a process that couples D-2HG metabolism to the shuttling of reducing equivalents from cytosolic NADH to the mitochondrial respiratory chain via the D-lactate dehydrogenase Dld1.
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Affiliation(s)
- Julia Becker-Kettern
- From the Luxembourg Centre for Systems Biomedicine, University of Luxembourg, L-4367 Belvaux and
| | - Nicole Paczia
- From the Luxembourg Centre for Systems Biomedicine, University of Luxembourg, L-4367 Belvaux and
| | - Jean-François Conrotte
- From the Luxembourg Centre for Systems Biomedicine, University of Luxembourg, L-4367 Belvaux and
| | - Daniel P Kay
- From the Luxembourg Centre for Systems Biomedicine, University of Luxembourg, L-4367 Belvaux and
| | - Cédric Guignard
- the Luxembourg Institute of Science and Technology, 41 Rue du Brill, L-4422 Belvaux, Luxembourg
| | - Paul P Jung
- From the Luxembourg Centre for Systems Biomedicine, University of Luxembourg, L-4367 Belvaux and
| | - Carole L Linster
- From the Luxembourg Centre for Systems Biomedicine, University of Luxembourg, L-4367 Belvaux and
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44
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Chen Y, Nielsen J. Biobased organic acids production by metabolically engineered microorganisms. Curr Opin Biotechnol 2015; 37:165-172. [PMID: 26748037 DOI: 10.1016/j.copbio.2015.11.004] [Citation(s) in RCA: 93] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2015] [Revised: 10/26/2015] [Accepted: 11/03/2015] [Indexed: 12/30/2022]
Abstract
Bio-based production of organic acids via microbial fermentation has been traditionally used in food industry. With the recent desire to develop more sustainable bioprocesses for production of fuels, chemicals and materials, the market for microbial production of organic acids has been further expanded as organic acids constitute a key group among top building block chemicals that can be produced from renewable resources. Here we review the current status for production of citric acid and lactic acid, and we highlight the use of modern metabolic engineering technologies to develop high performance microbes for production of succinic acid and 3-hydroxypropionic acid. Also, the key limitations and challenges in microbial organic acids production are discussed.
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Affiliation(s)
- Yun Chen
- Department of Biology & Biological Engineering, Chalmers University of Technology, SE412 96 Gothenburg, Sweden; Novo Nordisk Foundation Center for Biosustainability, Chalmers University of Technology, SE412 96 Gothenburg, Sweden
| | - Jens Nielsen
- Department of Biology & Biological Engineering, Chalmers University of Technology, SE412 96 Gothenburg, Sweden; Novo Nordisk Foundation Center for Biosustainability, Chalmers University of Technology, SE412 96 Gothenburg, Sweden; Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, DK2970 Hørsholm, Denmark.
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45
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Improvement of lactic acid production in Saccharomyces cerevisiae by a deletion of ssb1. J Ind Microbiol Biotechnol 2015; 43:87-96. [PMID: 26660479 DOI: 10.1007/s10295-015-1713-7] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2015] [Accepted: 11/23/2015] [Indexed: 10/22/2022]
Abstract
Polylactic acid (PLA) is an important renewable polymer, but current processes for producing its precursor, lactic acid, suffer from process inefficiencies related to the use of bacterial hosts. Therefore, improving the capacity of Saccharomyces cerevisiae to produce lactic acid is a promising approach to improve industrial production of lactic acid. As one such improvement required, the lactic acid tolerance of yeast must be significantly increased. To enable improved tolerance, we employed an RNAi-mediated genome-wide expression knockdown approach as a means to rapidly identify potential genetic targets. In this approach, several gene knockdown targets were identified which confer increased acid tolerance to S. cerevisiae BY4741, of which knockdown of the ribosome-associated chaperone SSB1 conferred the highest increase (52%). This target was then transferred into a lactic acid-overproducing strain of S. cerevisiae CEN.PK in the form of a knockout and the resulting strain demonstrated up to 33% increased cell growth, 58% increased glucose consumption, and 60% increased L-lactic acid production. As SSB1 contains a close functional homolog SSB2 in yeast, this result was counterintuitive and may point to as-yet-undefined functional differences between SSB1 and SSB2 related to lactic acid production. The final strain produced over 50 g/L of lactic acid in under 60 h of fermentation.
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46
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Baek SH, Kwon EY, Kim YH, Hahn JS. Metabolic engineering and adaptive evolution for efficient production of D-lactic acid in Saccharomyces cerevisiae. Appl Microbiol Biotechnol 2015; 100:2737-48. [PMID: 26596574 DOI: 10.1007/s00253-015-7174-0] [Citation(s) in RCA: 72] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2015] [Revised: 10/23/2015] [Accepted: 11/10/2015] [Indexed: 12/01/2022]
Abstract
There is an increasing demand for microbial production of lactic acid (LA) as a monomer of biodegradable poly lactic acid (PLA). Both optical isomers, D-LA and L-LA, are required to produce stereocomplex PLA with improved properties. In this study, we developed Saccharomyces cerevisiae strains for efficient production of D-LA. D-LA production was achieved by expressing highly stereospecific D-lactate dehydrogenase gene (ldhA, LEUM_1756) from Leuconostoc mesenteroides subsp. mesenteroides ATCC 8293 in S. cerevisiae lacking natural LA production activity. D-LA consumption after glucose depletion was inhibited by deleting DLD1 encoding D-lactate dehydrogenase and JEN1 encoding monocarboxylate transporter. In addition, ethanol production was reduced by deleting PDC1 and ADH1 genes encoding major pyruvate decarboxylase and alcohol dehydrogenase, respectively, and glycerol production was eliminated by deleting GPD1 and GPD2 genes encoding glycerol-3-phosphate dehydrogenase. LA tolerance of the engineered D-LA-producing strain was enhanced by adaptive evolution and overexpression of HAA1 encoding a transcriptional activator involved in weak acid stress response, resulting in effective D-LA production up to 48.9 g/L without neutralization. In a flask fed-batch fermentation under neutralizing condition, our evolved strain produced 112.0 g/L D-LA with a yield of 0.80 g/g glucose and a productivity of 2.2 g/(L · h).
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Affiliation(s)
- Seung-Ho Baek
- School of Chemical and Biological Engineering, Seoul National University, 1 Gwanak-ro, Gwanak-gu, Seoul, 08826, Republic of Korea
| | - Eunice Y Kwon
- School of Chemical and Biological Engineering, Seoul National University, 1 Gwanak-ro, Gwanak-gu, Seoul, 08826, Republic of Korea
| | - Yong Hwan Kim
- Department of Chemical Engineering, Kwangwoon University, 20 Gwangun-ro, Nowon-gu, Seoul, 01897, Republic of Korea
| | - Ji-Sook Hahn
- School of Chemical and Biological Engineering, Seoul National University, 1 Gwanak-ro, Gwanak-gu, Seoul, 08826, Republic of Korea.
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47
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Zeldes BM, Keller MW, Loder AJ, Straub CT, Adams MWW, Kelly RM. Extremely thermophilic microorganisms as metabolic engineering platforms for production of fuels and industrial chemicals. Front Microbiol 2015; 6:1209. [PMID: 26594201 PMCID: PMC4633485 DOI: 10.3389/fmicb.2015.01209] [Citation(s) in RCA: 111] [Impact Index Per Article: 12.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2015] [Accepted: 10/19/2015] [Indexed: 01/06/2023] Open
Abstract
Enzymes from extremely thermophilic microorganisms have been of technological interest for some time because of their ability to catalyze reactions of industrial significance at elevated temperatures. Thermophilic enzymes are now routinely produced in recombinant mesophilic hosts for use as discrete biocatalysts. Genome and metagenome sequence data for extreme thermophiles provide useful information for putative biocatalysts for a wide range of biotransformations, albeit involving at most a few enzymatic steps. However, in the past several years, unprecedented progress has been made in establishing molecular genetics tools for extreme thermophiles to the point that the use of these microorganisms as metabolic engineering platforms has become possible. While in its early days, complex metabolic pathways have been altered or engineered into recombinant extreme thermophiles, such that the production of fuels and chemicals at elevated temperatures has become possible. Not only does this expand the thermal range for industrial biotechnology, it also potentially provides biodiverse options for specific biotransformations unique to these microorganisms. The list of extreme thermophiles growing optimally between 70 and 100°C with genetic toolkits currently available includes archaea and bacteria, aerobes and anaerobes, coming from genera such as Caldicellulosiruptor, Sulfolobus, Thermotoga, Thermococcus, and Pyrococcus. These organisms exhibit unusual and potentially useful native metabolic capabilities, including cellulose degradation, metal solubilization, and RuBisCO-free carbon fixation. Those looking to design a thermal bioprocess now have a host of potential candidates to choose from, each with its own advantages and challenges that will influence its appropriateness for specific applications. Here, the issues and opportunities for extremely thermophilic metabolic engineering platforms are considered with an eye toward potential technological advantages for high temperature industrial biotechnology.
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Affiliation(s)
- Benjamin M Zeldes
- Department of Chemical and Biomolecular Engineering, North Carolina State University Raleigh, NC, USA
| | - Matthew W Keller
- Department of Biochemistry and Molecular Biology, University of Georgia Athens, GA, USA
| | - Andrew J Loder
- Department of Chemical and Biomolecular Engineering, North Carolina State University Raleigh, NC, USA
| | - Christopher T Straub
- Department of Chemical and Biomolecular Engineering, North Carolina State University Raleigh, NC, USA
| | - Michael W W Adams
- Department of Biochemistry and Molecular Biology, University of Georgia Athens, GA, USA
| | - Robert M Kelly
- Department of Chemical and Biomolecular Engineering, North Carolina State University Raleigh, NC, USA
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