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Zhou S, Ding N, Han R, Deng Y. Metabolic engineering and fermentation optimization strategies for producing organic acids of the tricarboxylic acid cycle by microbial cell factories. BIORESOURCE TECHNOLOGY 2023; 379:128986. [PMID: 37001700 DOI: 10.1016/j.biortech.2023.128986] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/22/2023] [Revised: 03/26/2023] [Accepted: 03/27/2023] [Indexed: 05/03/2023]
Abstract
The organic acids of the tricarboxylic acid (TCA) pathway are important platform compounds and are widely used in many areas. The high-productivity strains and high-efficient and low-cost fermentation are required to satisfy a huge market size. The high metabolic flux of the TCA pathway endows microorganisms potential to produce high titers of these organic acids. Coupled with metabolic engineering and fermentation optimization, the titer of the organic acids has been significantly improved in recent years. Herein, we discuss and compare the recent advances in synthetic pathway engineering, cofactor engineering, transporter engineering, and fermentation optimization strategies to maximize the biosynthesis of organic acids. Such engineering strategies were mainly based on the TCA pathway and glyoxylate pathway. Furthermore, organic-acid-secretion enhancement and renewable-substrate-based fermentation are often performed to assist the biosynthesis of organic acids. Further strategies are also discussed to construct high-productivity and acid-resistant strains for industrial large-scale production.
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Affiliation(s)
- Shenghu Zhou
- National Engineering Research Center for Cereal Fermentation and Food Biomanufacturing, Jiangnan University, 1800 Lihu Road, Wuxi, Jiangsu 214122, China; Jiangsu Provincial Research Center for Bioactive Product Processing Technology, Jiangnan University, 1800 Lihu Road, Wuxi, Jiangsu 214122, China
| | - Nana Ding
- College of Food and Health, Zhejiang A&F University, Hangzhou 311300, China
| | - Runhua Han
- McKetta Department of Chemical Engineering, The University of Texas at Austin, Austin, TX, United States
| | - Yu Deng
- National Engineering Research Center for Cereal Fermentation and Food Biomanufacturing, Jiangnan University, 1800 Lihu Road, Wuxi, Jiangsu 214122, China; Jiangsu Provincial Research Center for Bioactive Product Processing Technology, Jiangnan University, 1800 Lihu Road, Wuxi, Jiangsu 214122, China.
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Enhancement of α-Ketoglutaric Acid Production by Yarrowia lipolytica Grown on Mixed Renewable Carbon Sources through Adjustment of Culture Conditions. Catalysts 2022. [DOI: 10.3390/catal13010014] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022] Open
Abstract
α-Ketoglutaric acid (KGA) is a valuable compound with a wide range of applications, e.g., in the cosmetics, pharmaceutical, chemical and food industries. The present study aimed to enhance the efficiency of KGA production by Yarrowia lipolytica CBS146773 from renewable carbon sources. In the investigation, various factors that may potentially affect KGA biosynthesis were examined in bioreactor cultures performed on a simple medium containing glycerol (20 g/L) and fed with four portions of a substrate mixture (15 + 15 g/L of glycerol and rapeseed oil). It was found that the process may be stimulated by regulation of the medium pH and aeration, application of selected neutralizing agents, supplementation with thiamine and addition of sorbitan monolaurate, whereas presence of biotin and iron ions had no positive effect on KGA biosynthesis. Adjustment of the parameters improved the process efficiency and allowed 82.4 g/L of KGA to be obtained, corresponding to productivity of 0.57 g/L h and yield of 0.59 g/g. In addition, the production of KGA was characterized by a low level (≤6.3 g/L) of by-products, i.e., citric and pyruvic acids. The results confirmed the high potential of renewable carbon sources (glycerol + rapeseed oil) for effective KGA biosynthesis by Yarrowia lipolytica.
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3
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Chopra M, Kumar V, Singh M, Aggarwal NK. An overview about the approaches used in the production of alpha-ketoglutaric acid with their applications. PHYSICAL SCIENCES REVIEWS 2022. [DOI: 10.1515/psr-2022-0162] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022]
Abstract
Abstract
Alpha ketoglutaric acid is a biological compound found naturally in the human body. It plays an important role in the cell metabolism and has a role in various metabolic pathways including Kreb’s cycle, protein metabolism and so on. Keto glutaric acid is chemically prepared from succinic acid and oxalic acid. It is a direct precursor of glutamic acid and triazines. It can be produced by oxidative decarboxylation of isocitrate by isocitrate dehydrogenase. The yeast Yarrowia lipolytica is used as a prospective producer of alpha ketoglutaric acid from ethanol. The capability to synthesize Keto glutaric acid has so far been investigated for many microorganisms such as Pseudomonas fluoroscens
, Bacillus subtilis
etc. P. fluoroscens have the ability to synthesize a huge amount of alpha ketoglutaric acid in a glycerol medium supplemented with manganese (Mn). The Mangnese has a significant impact on glycerol metabolism resulting in the buildup of alpha ketoglutaric acid. The metabolism of succinate may result in the production of alpha ketoglutarate. Despite its importance in TCA cycle, alpha ketoglutaric acid buildup as an intermediate product of bacterial glucose oxidation. Along with chemical synthesis and microbial fermentation, enzymatic transformation can also be used to produce alpha ketoglutaric acid. Biodiesel waste is considered as cheap and renewable carbon source for the development of alpha ketoglutaric acid. Alpha ketoglutarate is used for kidney disease, intestinal and stomach disorders and many other conditions. It also plays an important role in the food industry as food and nutrient enhancers. The review is covering all the aspects related with the Alpha ketoglutaric acid production, utilization and product recovery.
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Affiliation(s)
- Monika Chopra
- Department of Biotechnology , Maharishi Markandeshwar (Deemed to be University), Mullana , Ambala , 133207 , India
| | - Vikas Kumar
- Department of Biotechnology , Maharishi Markandeshwar (Deemed to be University), Mullana , Ambala , 133207 , India
| | - Manoj Singh
- Department of Biotechnology , Maharishi Markandeshwar (Deemed to be University), Mullana , Ambala , 133207 , India
| | - Neeraj K. Aggarwal
- Department of Microbiology , Kurukshetra University , Kurukshetra , 136119 , India
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4
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Selection of Producer of α-Ketoglutaric Acid from Ethanol-Containing Wastes and Impact of Cultivation Conditions. FERMENTATION 2022. [DOI: 10.3390/fermentation8080362] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022] Open
Abstract
Ester–aldehyde fraction (EAF) is a by-product of ethyl-alcohol-producing companies whose purification requires an expensive process. The results of this study illustrate the environmentally friendly and alternative possibility of using EAF to increase their value as substrate to produce α-ketoglutaric acid (KGA) using different yeasts. It was found that some species of the genera Babjeviella, Diutina, Moesziomyces, Pichia, Saturnispora, Sugiyamaella, Yarrowia and Zygoascus grown under thiamine deficiency accumulate KGA in the medium with an EAF as the sole carbon source. The strain Y. lipolytica VKM Y-2412 was selected as the producer. To reach the maximum production of KGA, the cultivation medium should contain 0.3 µg/L thiamine during cultivation in flasks and 2 µg/L in the fermentor; the concentration of (NH4)2SO4 should range from 3 to 6 g/L; and the optimal concentrations of Zn2+, Fe2+ and Cu2+ ions should be 1.2, 0.6 and 0.05 mg/L, respectively. EAF concentration should not exceed 1.5 g/L in the growth phase and 3 g/L in the KGA synthesis phase. At higher EAF concentrations, acetic acid was accumulated and inhibited yeast growth and KGA production. Under optimal conditions, the producer accumulated 53.8 g/L KGA with a yield (Yp/s) of 0.68 g/g substrate consumed.
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Swietalski P, Hetzel F, Klaiber I, Pross E, Seitl I, Fischer L. Orotic acid production by Yarrowia lipolytica under conditions of limited pyrimidine. Yeast 2021; 39:230-240. [PMID: 34648204 DOI: 10.1002/yea.3673] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2021] [Revised: 10/07/2021] [Accepted: 10/12/2021] [Indexed: 11/08/2022] Open
Abstract
Orotic acid (OA) is an intermediate of the pyrimidine biosynthesis with high industrial relevance due to its use as precursor for production of biochemical pyrimidines or its use as carrier molecule in drug formulations. It can be produced by fermentation of microorganisms with engineered pyrimidine metabolism. In this study, we surprisingly discovered the yeast Yarrowia lipolytica as a powerful producer of OA. The overproduction of OA in the Y. lipolytica strain PO1f was found to be caused by the deletion of the URA3 gene which prevents the irreversible decarboxylation of OA to uridine monophosphate. It was shown that the lack of orotidine-5'-phosphate decarboxylase was the reason for the accumulation of OA inside the cell since a rescue mutant of the URA3 deletion in Y. lipolytica PO1f completely prevented the OA secretion into the medium. In addition, pyrimidine limitation in the cell massively enhanced the OA accumulation followed by secretion due to intense overflow metabolism during bioreactor cultivations. Accordingly, supplementation of the medium with 200 mg/L uracil drastically decreased the OA overproduction by 91%. OA productivity was further enhanced in fed-batch cultivation with glucose and ammonium sulfate feed to a maximal yield of 9.62 ± 0.21 g/L. Y. lipolytica is one of three OA overproducing yeasts described in the literature so far, and in this study, the highest productivity was shown. This work demonstrates the potential of Y. lipolytica as a possible production organism for OA and provides a basis for further metabolic pathway engineering to optimize OA productivity.
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Affiliation(s)
- Paul Swietalski
- Institute of Food Science and Biotechnology, Department of Biotechnology and Enzyme Science, University of Hohenheim, Stuttgart, Germany
| | - Frank Hetzel
- Institute of Food Science and Biotechnology, Department of Biotechnology and Enzyme Science, University of Hohenheim, Stuttgart, Germany
| | - Iris Klaiber
- Core Facility Hohenheim, University of Hohenheim, Stuttgart, Germany
| | - Eva Pross
- Institute of Food Science and Biotechnology, Department of Biotechnology and Enzyme Science, University of Hohenheim, Stuttgart, Germany
| | - Ines Seitl
- Institute of Food Science and Biotechnology, Department of Biotechnology and Enzyme Science, University of Hohenheim, Stuttgart, Germany
| | - Lutz Fischer
- Institute of Food Science and Biotechnology, Department of Biotechnology and Enzyme Science, University of Hohenheim, Stuttgart, Germany
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Tomaszewska-Hetman L, Rywińska A, Lazar Z, Juszczyk P, Rakicka-Pustułka M, Janek T, Kuźmińska-Bajor M, Rymowicz W. Application of a New Engineered Strain of Yarrowia lipolytica for Effective Production of Calcium Ketoglutarate Dietary Supplements. Int J Mol Sci 2021; 22:7577. [PMID: 34299193 PMCID: PMC8304598 DOI: 10.3390/ijms22147577] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2021] [Revised: 07/09/2021] [Accepted: 07/12/2021] [Indexed: 01/02/2023] Open
Abstract
The present study aimed to develop a technology for the production of dietary supplements based on yeast biomass and α-ketoglutaric acid (KGA), produced by a new transformant of Yarrowia lipolytica with improved KGA biosynthesis ability, as well to verify the usefulness of the obtained products for food and feed purposes. Transformants of Y. lipolytica were constructed to overexpress genes encoding glycerol kinase, methylcitrate synthase and mitochondrial organic acid transporter. The strains were compared in terms of growth ability in glycerol- and oil-based media as well as their suitability for KGA biosynthesis in mixed glycerol-oil medium. The impact of different C:N:P ratios on KGA production by selected strain was also evaluated. Application of the strain that overexpressed all three genes in the culture with a C:N:P ratio of 87:5:1 allowed us to obtain 53.1 g/L of KGA with productivity of 0.35 g/Lh and yield of 0.53 g/g. Finally, the possibility of obtaining three different products with desired nutritional and health-beneficial characteristics was demonstrated: (1) calcium α-ketoglutarate (CaKGA) with purity of 89.9% obtained by precipitation of KGA with CaCO3, (2) yeast biomass with very good nutritional properties, (3) fixed biomass-CaKGA preparation containing 87.2 μg/g of kynurenic acid, which increases the health-promoting value of the product.
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Affiliation(s)
- Ludwika Tomaszewska-Hetman
- Department of Biotechnology and Food Microbiology, Wrocław University of Environmental and Life Sciences, Chełmońskiego Street 37, 51-630 Wrocław, Poland; (A.R.); (Z.L.); (P.J.); (M.R.-P.); (T.J.); (M.K.-B.); (W.R.)
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7
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Yarrowia lipolytica Strains and Their Biotechnological Applications: How Natural Biodiversity and Metabolic Engineering Could Contribute to Cell Factories Improvement. J Fungi (Basel) 2021; 7:jof7070548. [PMID: 34356927 PMCID: PMC8307478 DOI: 10.3390/jof7070548] [Citation(s) in RCA: 38] [Impact Index Per Article: 12.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2021] [Revised: 07/01/2021] [Accepted: 07/05/2021] [Indexed: 11/20/2022] Open
Abstract
Among non-conventional yeasts of industrial interest, the dimorphic oleaginous yeast Yarrowia lipolytica appears as one of the most attractive for a large range of white biotechnology applications, from heterologous proteins secretion to cell factories process development. The past, present and potential applications of wild-type, traditionally improved or genetically modified Yarrowia lipolytica strains will be resumed, together with the wide array of molecular tools now available to genetically engineer and metabolically remodel this yeast. The present review will also provide a detailed description of Yarrowia lipolytica strains and highlight the natural biodiversity of this yeast, a subject little touched upon in most previous reviews. This work intends to fill this gap by retracing the genealogy of the main Yarrowia lipolytica strains of industrial interest, by illustrating the search for new genetic backgrounds and by providing data about the main publicly available strains in yeast collections worldwide. At last, it will focus on exemplifying how advances in engineering tools can leverage a better biotechnological exploitation of the natural biodiversity of Yarrowia lipolytica and of other yeasts from the Yarrowia clade.
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Yan C, Li X, Zhang G, Zhu Y, Bi J, Hao H, Hou H. Quorum Sensing-Mediated and Growth Phase-Dependent Regulation of Metabolic Pathways in Hafnia alvei H4. Front Microbiol 2021; 12:567942. [PMID: 33737914 PMCID: PMC7960787 DOI: 10.3389/fmicb.2021.567942] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2020] [Accepted: 01/26/2021] [Indexed: 11/13/2022] Open
Abstract
Quorum sensing (QS) is a widespread regulatory mechanism in bacteria used to coordinate target gene expression with cell density. Thus far, little is known about the regulatory relationship between QS and cell density in terms of metabolic pathways in Hafnia alvei H4. In this study, transcriptomics analysis was performed under two conditions to address this question. The comparative transcriptome of H. alvei H4 wild-type at high cell density (OD600 = 1.7) relative to low cell density (OD600 = 0.3) was considered as growth phase-dependent manner (GPDM), and the transcriptome profile of luxI/R deletion mutant (ΔluxIR) compared to the wild-type was considered as QS-mediated regulation. In all, we identified 206 differentially expressed genes (DEGs) mainly presented in chemotaxis, TCA cycle, two-component system, ABC transporters and pyruvate metabolism, co-regulated by the both density-dependent regulation, and the results were validated by qPCR and swimming phenotypic assays. Aside from the co-regulated DEGs, we also found that 59 DEGs, mediated by density-independent QS, function in pentose phosphate and histidine metabolism and that 2084 cell-density-dependent DEGs involved in glycolysis/gluconeogenesis and phenylalanine metabolism were influenced only by GPDM from significantly enriched analysis of transcriptome data. The findings provided new information about the interplay between two density-dependent metabolic regulation, which could assist with the formulation of control strategies for this opportunistic pathogen, especially at high cell density.
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Affiliation(s)
- Congyang Yan
- School of Food Science and Technology, Dalian Polytechnic University, Dalian, China.,Liaoning Key Lab for Aquatic Processing Quality and Safety, Dalian, China
| | - Xue Li
- School of Food Science and Technology, Dalian Polytechnic University, Dalian, China.,Liaoning Key Lab for Aquatic Processing Quality and Safety, Dalian, China
| | - Gongliang Zhang
- School of Food Science and Technology, Dalian Polytechnic University, Dalian, China.,Liaoning Key Lab for Aquatic Processing Quality and Safety, Dalian, China
| | - Yaolei Zhu
- School of Food Science and Technology, Dalian Polytechnic University, Dalian, China.,Liaoning Key Lab for Aquatic Processing Quality and Safety, Dalian, China
| | - Jingran Bi
- School of Food Science and Technology, Dalian Polytechnic University, Dalian, China.,Liaoning Key Lab for Aquatic Processing Quality and Safety, Dalian, China
| | - Hongshun Hao
- Liaoning Key Lab for Aquatic Processing Quality and Safety, Dalian, China
| | - Hongman Hou
- School of Food Science and Technology, Dalian Polytechnic University, Dalian, China.,Liaoning Key Lab for Aquatic Processing Quality and Safety, Dalian, China
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9
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Luo Z, Yu S, Zeng W, Zhou J. Comparative analysis of the chemical and biochemical synthesis of keto acids. Biotechnol Adv 2021; 47:107706. [PMID: 33548455 DOI: 10.1016/j.biotechadv.2021.107706] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2020] [Revised: 01/25/2021] [Accepted: 01/26/2021] [Indexed: 12/28/2022]
Abstract
Keto acids are essential organic acids that are widely applied in pharmaceuticals, cosmetics, food, beverages, and feed additives as well as chemical synthesis. Currently, most keto acids on the market are prepared via chemical synthesis. The biochemical synthesis of keto acids has been discovered with the development of metabolic engineering and applied toward the production of specific keto acids from renewable carbohydrates using different metabolic engineering strategies in microbes. In this review, we provide a systematic summary of the types and applications of keto acids, and then summarize and compare the chemical and biochemical synthesis routes used for the production of typical keto acids, including pyruvic acid, oxaloacetic acid, α-oxobutanoic acid, acetoacetic acid, ketoglutaric acid, levulinic acid, 5-aminolevulinic acid, α-ketoisovaleric acid, α-keto-γ-methylthiobutyric acid, α-ketoisocaproic acid, 2-keto-L-gulonic acid, 2-keto-D-gluconic acid, 5-keto-D-gluconic acid, and phenylpyruvic acid. We also describe the current challenges for the industrial-scale production of keto acids and further strategies used to accelerate the green production of keto acids via biochemical routes.
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Affiliation(s)
- Zhengshan Luo
- National Engineering Laboratory for Cereal Fermentation Technology, Jiangnan University, 1800 Lihu Road, Wuxi, Jiangsu 214122, China; State Key Laboratory of Materials-Oriented Chemical Engineering, College of Food Science and Light Industry, Nanjing Tech University, Nanjing 211816, China; Key Laboratory of Industrial Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, 1800 Lihu Road, Wuxi, Jiangsu 214122, China
| | - Shiqin Yu
- National Engineering Laboratory for Cereal Fermentation Technology, Jiangnan University, 1800 Lihu Road, Wuxi, Jiangsu 214122, China; Key Laboratory of Industrial Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, 1800 Lihu Road, Wuxi, Jiangsu 214122, China; Jiangsu Provisional Research Center for Bioactive Product Processing Technology, Jiangnan University, 1800 Lihu Road, Wuxi, Jiangsu 214122, China
| | - Weizhu Zeng
- Key Laboratory of Industrial Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, 1800 Lihu Road, Wuxi, Jiangsu 214122, China
| | - Jingwen Zhou
- National Engineering Laboratory for Cereal Fermentation Technology, Jiangnan University, 1800 Lihu Road, Wuxi, Jiangsu 214122, China; Key Laboratory of Industrial Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, 1800 Lihu Road, Wuxi, Jiangsu 214122, China; Jiangsu Provisional Research Center for Bioactive Product Processing Technology, Jiangnan University, 1800 Lihu Road, Wuxi, Jiangsu 214122, China.
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10
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Efficient Surface Display of L-glutamate Oxidase and L-amino Acid Oxidase on Pichia pastoris Using Multi-copy Expression Strains. BIOTECHNOL BIOPROC E 2020. [DOI: 10.1007/s12257-019-0370-5] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
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11
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Kamzolova SV, Morgunov IG. Optimization of medium composition and fermentation conditions for α-ketoglutaric acid production from biodiesel waste by Yarrowia lipolytica. Appl Microbiol Biotechnol 2020; 104:7979-7989. [PMID: 32749527 DOI: 10.1007/s00253-020-10805-7] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2020] [Revised: 07/21/2020] [Accepted: 07/30/2020] [Indexed: 12/12/2022]
Abstract
This work demonstrates the ability of the yeast Yarrowia lipolytica cultivated on biodiesel waste to synthesize α-ketoglutaric acid with a minimal content of pyruvic acid as the main byproduct. The key factor promoting the microbial production of α-ketoglutaric acid from the waste is a strong deficiency of thiamine in the cultivation medium. The production of α-ketoglutaric acid by the yeast can be regulated by changing the concentration of nitrogen, iron, zinc, copper, and manganese in the medium, as well as by pH medium and the aeration rate. The optimization of these parameters in flask experiments allowed us to increase the concentration of α-ketoglutaric acid in the medium by 2.6 times and to shift the α-ketoglutaric acid/pyruvic acid ratio from 5:1 to 30:1. During cultivation in a fermentor under optimized conditions, Y. lipolytica produced 80.4 g/L α-ketoglutaric acid with a process selectivity of 96.7% and the product yield (YKGA) equal to 1.01 g/g. KEY POINTS: • α-Ketoglutaric acid is commercially important biotechnological product. • Biosynthesis of α-ketoglutaric acid from biodiesel waste. • Optimization of cultivation medium and nutrition medium.
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Affiliation(s)
- Svetlana V Kamzolova
- Federal Research Center Pushchino Scientific Center for Biological Research of the Russian Academy of Sciences, G.K. Skryabin Institute of Biochemistry and Physiology of Microorganisms of the Russian Academy of Sciences, Prospect Nauki 5, Pushchino, Moscow Region, 142290, Russia
| | - Igor G Morgunov
- Federal Research Center Pushchino Scientific Center for Biological Research of the Russian Academy of Sciences, G.K. Skryabin Institute of Biochemistry and Physiology of Microorganisms of the Russian Academy of Sciences, Prospect Nauki 5, Pushchino, Moscow Region, 142290, Russia.
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12
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Alpha-Ketoglutaric Acid Production from a Mixture of Glycerol and Rapeseed Oil by Yarrowia lipolytica Using Different Substrate Feeding Strategies. SUSTAINABILITY 2020. [DOI: 10.3390/su12156109] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
Abstract
The microbiological biosynthesis of α-ketoglutaric acid (KGA) has recently captured the attention of many scientists as an alternative to its common chemical synthesis. The present study aimed to evaluate the effect of the feeding strategy of substrates, i.e., glycerol (G = 20 g·dm−3) and rapeseed oil (O = 20 g·dm−3), on yeast growth and the parameters of KGA biosynthesis by a wild strain Yarrowia lipolytica A-8 in fed-batch and repeated-batch cultures. The effectiveness of KGA biosynthesis was demonstrated to depend on thiamine concentration and the substrate feeding method. In the fed-batch culture incubated with 3 µg·dm−3 of thiamine and a substrate feeding variant 2G(_OGO), KGA was produced in the amount of 62.1 g·dm−3 at the volumetric production rate of 0.37 g·dm−3·h−1. These values of KGA production parameters were higher than these obtained in the control culture (with rapeseed oil only). During 10 cycles of the 1788-h repeated-batch culture carried out acc. to the feeding strategy 2G(_OGO), in the last 5 cycles the yeast produced from 55.6 to 58.2 g·dm−3 of KGA and maximally 2.9 g·dm−3 of the pyruvic acid as a by-product.
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13
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Legendre F, MacLean A, Appanna VP, Appanna VD. Biochemical pathways to α-ketoglutarate, a multi-faceted metabolite. World J Microbiol Biotechnol 2020; 36:123. [PMID: 32686016 DOI: 10.1007/s11274-020-02900-8] [Citation(s) in RCA: 38] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2020] [Accepted: 07/13/2020] [Indexed: 11/26/2022]
Abstract
α-Ketoglutarate (AKG) also known as 2-oxoglutarate is an essential metabolite in virtually all organisms as it participates in a variety of biological processes including anti-oxidative defence, energy production, signalling modules, and genetic modification. This keto-acid also possesses immense commercial value as it is utilized as a nutritional supplement, a therapeutic agent, and a precursor to a variety of value-added products such as ethylene and heterocyclic compounds. Hence, the generation of KG in a sustainable and environmentally-neutral manner is a major ongoing research endeavour. In this mini-review, the enzymatic systems and the metabolic networks mediating the synthesis of AKG will be described. The importance of such enzymes as isocitrate dehydrogenase (ICDH), glutamate dehydrogenase (GDH), succinate semialdehyde dehydrogenase (SSADH) and transaminases that directly contribute to the formation of KG will be emphasized. The efficacy of microbial systems in providing an effective platform to generate this moiety and the molecular strategies involving genetic manipulation, abiotic stress and nutrient supplementation that result in the optimal production of AKG will be evaluated. Microbial systems and their components acting via the metabolic networks and the resident enzymes are well poised to provide effective biotechnological tools that can supply renewable AKG globally.
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Affiliation(s)
- F Legendre
- Department of Chemistry and Biochemistry, Laurentian University, Sudbury, ON, P3E 2C6, Canada
| | - A MacLean
- Department of Chemistry and Biochemistry, Laurentian University, Sudbury, ON, P3E 2C6, Canada
| | - V P Appanna
- Department of Chemistry and Biochemistry, Laurentian University, Sudbury, ON, P3E 2C6, Canada
| | - V D Appanna
- Department of Chemistry and Biochemistry, Laurentian University, Sudbury, ON, P3E 2C6, Canada.
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14
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Chen X, Dong X, Liu J, Luo Q, Liu L. Pathway engineering of Escherichia coli for α-ketoglutaric acid production. Biotechnol Bioeng 2020; 117:2791-2801. [PMID: 32530489 DOI: 10.1002/bit.27456] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/29/2020] [Revised: 05/19/2020] [Accepted: 06/11/2020] [Indexed: 01/09/2023]
Abstract
α-Ketoglutaric acid (α-KG) is a multifunctional dicarboxylic acid in the tricarboxylic acid (TCA) cycle, but microbial engineering for α-KG production is not economically efficient, due to the intrinsic inefficiency of its biosynthetic pathway. In this study, pathway engineering was used to improve pathway efficiency for α-KG production in Escherichia coli. First, the TCA cycle was rewired for α-KG production starting from pyruvate, and the engineered strain E. coli W3110Δ4-PCAI produced 15.66 g/L α-KG. Then, the rewired TCA cycle was optimized by designing various strengths of pyruvate carboxylase and isocitrate dehydrogenase expression cassettes, resulting in a large increase in α-KG production (24.66 g/L). Furthermore, acetyl coenzyme A (acetyl-CoA) availability was improved by overexpressing acetyl-CoA synthetase, leading to α-KG production up to 28.54 g/L. Finally, the engineered strain E. coli W3110Δ4-P(H) CAI(H) A was able to produce 32.20 g/L α-KG in a 5-L fed-batch bioreactor. This strategy described here paves the way to the development of an efficient pathway for microbial production of α-KG.
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Affiliation(s)
- 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.,International Joint Laboratory on Food Safety, Jiangnan University, Wuxi, China
| | - Xiaoxiang Dong
- State Key Laboratory of Food Science and Technology, Jiangnan University, Wuxi, China.,Key Laboratory of Industrial Biotechnology, Ministry of Education, Jiangnan University, Wuxi, China.,International Joint Laboratory on Food Safety, Jiangnan University, Wuxi, China
| | - Jia Liu
- State Key Laboratory of Food Science and Technology, Jiangnan University, Wuxi, China.,Key Laboratory of Industrial Biotechnology, Ministry of Education, Jiangnan University, Wuxi, China.,International Joint Laboratory on Food Safety, Jiangnan University, Wuxi, China
| | - Qiuling Luo
- State Key Laboratory of Food Science and Technology, Jiangnan University, Wuxi, China.,Wuxi Chenming Biotechnology Co., Ltd., Wuxi, China
| | - Liming Liu
- State Key Laboratory of Food Science and Technology, Jiangnan University, Wuxi, China.,Key Laboratory of Industrial Biotechnology, Ministry of Education, Jiangnan University, Wuxi, China.,International Joint Laboratory on Food Safety, Jiangnan University, Wuxi, China
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15
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Biovalorisation of crude glycerol and xylose into xylitol by oleaginous yeast Yarrowia lipolytica. Microb Cell Fact 2020; 19:121. [PMID: 32493445 PMCID: PMC7271524 DOI: 10.1186/s12934-020-01378-1] [Citation(s) in RCA: 25] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2020] [Accepted: 05/25/2020] [Indexed: 11/29/2022] Open
Abstract
Background Xylitol is a commercially important chemical with multiple applications in the food and pharmaceutical industries. According to the US Department of Energy, xylitol is one of the top twelve platform chemicals that can be produced from biomass. The chemical method for xylitol synthesis is however, expensive and energy intensive. In contrast, the biological route using microbial cell factories offers a potential cost-effective alternative process. The bioprocess occurs under ambient conditions and makes use of biocatalysts and biomass which can be sourced from renewable carbon originating from a variety of cheap waste feedstocks. Result In this study, biotransformation of xylose to xylitol was investigated using Yarrowia lipolytica, an oleaginous yeast which was firstly grown on a glycerol/glucose for screening of co-substrate, followed by media optimisation in shake flask, scale up in bioreactor and downstream processing of xylitol. A two-step medium optimization was employed using central composite design and artificial neural network coupled with genetic algorithm. The yeast amassed a concentration of 53.2 g/L xylitol using pure glycerol (PG) and xylose with a bioconversion yield of 0.97 g/g. Similar results were obtained when PG was substituted with crude glycerol (CG) from the biodiesel industry (titer: 50.5 g/L; yield: 0.92 g/g). Even when xylose from sugarcane bagasse hydrolysate was used as opposed to pure xylose, a xylitol yield of 0.54 g/g was achieved. Xylitol was successfully crystallized from PG/xylose and CG/xylose fermentation broths with a recovery of 39.5 and 35.3%, respectively. Conclusion To the best of the author’s knowledge, this study demonstrates for the first time the potential of using Y. lipolytica as a microbial cell factory for xylitol synthesis from inexpensive feedstocks. The results obtained are competitive with other xylitol producing organisms.![]()
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16
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Fickers P, Cheng H, Sze Ki Lin C. Sugar Alcohols and Organic Acids Synthesis in Yarrowia lipolytica: Where Are We? Microorganisms 2020; 8:E574. [PMID: 32326622 PMCID: PMC7232202 DOI: 10.3390/microorganisms8040574] [Citation(s) in RCA: 39] [Impact Index Per Article: 9.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2020] [Revised: 04/09/2020] [Accepted: 04/13/2020] [Indexed: 01/01/2023] Open
Abstract
Sugar alcohols and organic acids that derive from the metabolism of certain microorganisms have a panoply of applications in agro-food, chemical and pharmaceutical industries. The main challenge in their production is to reach a productivity threshold that allow the process to be profitable. This relies on the construction of efficient cell factories by metabolic engineering and on the development of low-cost production processes by using industrial wastes or cheap and widely available raw materials as feedstock. The non-conventional yeast Yarrowia lipolytica has emerged recently as a potential producer of such metabolites owing its low nutritive requirements, its ability to grow at high cell densities in a bioreactor and ease of genome edition. This review will focus on current knowledge on the synthesis of the most important sugar alcohols and organic acids in Y. lipolytica.
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Affiliation(s)
- Patrick Fickers
- Microbial Process and Interactions, TERRA Teaching and Research Centre, University of Liege—Gembloux Agro-Bio Tech, 5030 Gembloux, Belgium
| | - Hairong Cheng
- State Key Laboratory of Microbial Metabolism, School of Life Sciences & Biotechnology, Shanghai Jiao Tong University, Shanghai 200240, China;
| | - Carol Sze Ki Lin
- School of Energy and Environment, City University of Hong Kong, Tat Chee Avenue, Kowloon, Hong Kong;
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17
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Draft Genome Assemblies of Ionic Liquid-Resistant Yarrowia lipolytica PO1f and Its Superior Evolved Strain, YlCW001. Microbiol Resour Announc 2020; 9:9/9/e01356-19. [PMID: 32107299 PMCID: PMC7046820 DOI: 10.1128/mra.01356-19] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022] Open
Abstract
Adaptive laboratory evolution of Yarrowia lipolytica PO1f in the benchmark ionic liquid (IL; 1-ethyl-3-methylimidazolium acetate) produced a superior IL-tolerant microorganism, strain YlCW001. Here, we report the genome sequences of PO1f and YlCW001 to study the robustness of Y. lipolytica and its potential use as a microbial platform for producing fuels and chemicals.
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18
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Hamilton M, Consiglio AL, MacEwen K, Shaw AJ, Tsakraklides V. Identification of a Yarrowia lipolytica acetamidase and its use as a yeast genetic marker. Microb Cell Fact 2020; 19:22. [PMID: 32024536 PMCID: PMC7003347 DOI: 10.1186/s12934-020-1292-9] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2019] [Accepted: 01/22/2020] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Yarrowia lipolytica is an oleaginous yeast that can be genetically engineered to produce lipid and non-lipid biochemicals from a variety of feedstocks. Metabolic engineering of this organism usually requires genetic markers in order to select for modified cells. The potential to combine multiple genetic manipulations depends on the availability of multiple or recyclable selectable markers. RESULTS We found that Y. lipolytica has the ability to utilize acetamide as the sole nitrogen source suggesting that the genome contains an acetamidase gene. Two potential Y. lipolytica acetamidase gene candidates were identified by homology to the A. nidulans acetamidase amdS. These genes were deleted in the wild-type Y. lipolytica strain YB-392, and deletion strains were evaluated for acetamide utilization. One deletion strain was unable to grow on acetamide and a putative acetamidase gene YlAMD1 was identified. Transformation of YlAMD1 followed by selection on acetamide media and counterselection on fluoroacetamide media showed that YlAMD1 can be used as a recyclable genetic marker in Saccharomyces cerevisiae and Ylamd1Δ Y. lipolytica. CONCLUSIONS These findings add to our understanding of Y. lipolytica nitrogen utilization and expand the set of genetic tools available for engineering this organism, as well as S. cerevisiae.
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Affiliation(s)
| | | | - Kyle MacEwen
- Novogy, Inc., 85 Bolton Street, Cambridge, MA, 02140, USA
| | - A Joe Shaw
- Novogy, Inc., 85 Bolton Street, Cambridge, MA, 02140, USA
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19
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Czajka JJ, Kambhampati S, Tang YJ, Wang Y, Allen DK. Application of Stable Isotope Tracing to Elucidate Metabolic Dynamics During Yarrowia lipolytica α-Ionone Fermentation. iScience 2020; 23:100854. [PMID: 32058965 PMCID: PMC7005465 DOI: 10.1016/j.isci.2020.100854] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2019] [Revised: 12/19/2019] [Accepted: 01/15/2020] [Indexed: 11/15/2022] Open
Abstract
Targeted metabolite analysis in combination with 13C-tracing is a convenient strategy to determine pathway activity in biological systems; however, metabolite analysis is limited by challenges in separating and detecting pathway intermediates with current chromatographic methods. Here, a hydrophilic interaction chromatography tandem mass spectrometry approach was developed for improved metabolite separation, isotopologue analysis, and quantification. The physiological responses of a Yarrowia lipolytica strain engineered to produce ∼400 mg/L α-ionone and temporal changes in metabolism were quantified (e.g., mevalonate secretion, then uptake) indicating bottleneck shifts in the engineered pathway over the course of fermentation. Dynamic labeling results indicated limited tricarboxylic acid cycle label incorporation and, combined with a measurable ATP shortage during the high ionone production phase, suggested that electron transport and oxidative phosphorylation may limit energy supply and strain performance. The results provide insights into terpenoid pathway metabolic dynamics of non-model yeasts and offer guidelines for sensor development and modular engineering. A HILIC method is demonstrated for efficient separation of 57 cellular metabolites Production of α-ionone was ∼400 mg/L in bench-top bioreactors Engineered Y. lipolytica secreted then consumed mevalonate during fermentation Oxidative phosphorylation may limit performance in high-cell-density fermentations
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Affiliation(s)
- Jeffrey J Czajka
- Department of Energy, Environmental and Chemical Engineering, Washington University, St. Louis, MO, USA
| | | | - Yinjie J Tang
- Department of Energy, Environmental and Chemical Engineering, Washington University, St. Louis, MO, USA.
| | - Yechun Wang
- Arch Innotek, LLC, 4320 Forest Park Avenue, St Louis, MO, USA.
| | - Doug K Allen
- Donald Danforth Plant Science Center, St. Louis, MO, USA; United States Department of Agriculture, Agricultural Research Service, St. Louis, MO, USA.
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20
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Navarrete C, L. Martínez J. Non-conventional yeasts as superior production platforms for sustainable fermentation based bio-manufacturing processes. AIMS BIOENGINEERING 2020. [DOI: 10.3934/bioeng.2020024] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022] Open
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21
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Expression and Characterization of a New L-amino Acid Oxidase AAO Producing α-ketoglutaric Acid from L-glutamic Acid. BIOTECHNOL BIOPROC E 2019. [DOI: 10.1007/s12257-019-0182-7] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
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22
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Gallo M, Passannanti F, D'Apolito E, Nigro F, Salameh D, Nigro R. Biotechnological production of natural sweeteners and preservatives on tomato paste. J FOOD PROCESS ENG 2019. [DOI: 10.1111/jfpe.13327] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Affiliation(s)
- Marianna Gallo
- DICMAPIUniversity of Naples Federico II Naples Italy
- Engineering DepartmentUniversity of Rome Niccolò Cusano Rome Italy
| | | | | | - Federica Nigro
- Engineering DepartmentUniversity of Rome Niccolò Cusano Rome Italy
| | - Dana Salameh
- DICMAPIUniversity of Naples Federico II Naples Italy
| | - Roberto Nigro
- DICMAPIUniversity of Naples Federico II Naples Italy
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23
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Bae S, Park BG, Kim B, Hahn J. Multiplex Gene Disruption by Targeted Base Editing ofYarrowia lipolyticaGenome Using Cytidine Deaminase Combined with the CRISPR/Cas9 System. Biotechnol J 2019; 15:e1900238. [DOI: 10.1002/biot.201900238] [Citation(s) in RCA: 27] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2019] [Revised: 10/18/2019] [Indexed: 12/21/2022]
Affiliation(s)
- Sang‐Jeong Bae
- School of Chemical and Biological EngineeringInstitute of Chemical ProcessesSeoul National University 1 Gwanak‐ro Gwanak‐gu Seoul 08826 Republic of Korea
| | - Beom Gi Park
- School of Chemical and Biological EngineeringInstitute of Chemical ProcessesSeoul National University 1 Gwanak‐ro Gwanak‐gu Seoul 08826 Republic of Korea
| | - Byung‐Gee Kim
- School of Chemical and Biological EngineeringInstitute of Chemical ProcessesSeoul National University 1 Gwanak‐ro Gwanak‐gu Seoul 08826 Republic of Korea
| | - Ji‐Sook Hahn
- School of Chemical and Biological EngineeringInstitute of Chemical ProcessesSeoul National University 1 Gwanak‐ro Gwanak‐gu Seoul 08826 Republic of Korea
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24
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Alhasawi AA, Thomas SC, Tharmalingam S, Legendre F, Appanna VD. Isocitrate Lyase and Succinate Semialdehyde Dehydrogenase Mediate the Synthesis of α-Ketoglutarate in Pseudomonas fluorescens. Front Microbiol 2019; 10:1929. [PMID: 31507554 PMCID: PMC6716453 DOI: 10.3389/fmicb.2019.01929] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2019] [Accepted: 08/05/2019] [Indexed: 01/04/2023] Open
Abstract
Glycerol is an important by-product of the biodiesel industry and its transformation into value-added products like keto acids is being actively pursued in order to improve the efficacy of this renewable energy sector. Here, we report that the enhanced production of α-ketoglutarate (KG) effected by Pseudomonas fluorescens in a mineral medium supplemented with manganese (Mn) is propelled by the increased activities of succinate semialdehyde dehydrogenase (SSADH), γ-aminobutyric acid aminotransaminase (GABAT), and isocitrate lyase (ICL). The latter generates glyoxylate and succinate two key metabolites involved in this process. Fumarate reductase (FRD) also aids in augmenting the pool of succinate, a precursor of succinate semialdehyde (SSA). The latter is then carboxylated to KG with the assistance of α-ketoglutarate decarboxylase (KDC). These enzymes work in tandem to ensure copious secretion of the keto acid. When incubated with glycerol in the presence of bicarbonate (HCO3−), cell-free extracts readily produce KG with a metabolite fingerprint attributed to glutamate, γ-aminobutyric acid (GABA), succinate and succinate semialdehyde. Further targeted metabolomic and functional proteomic studies with high-performance liquid chromatography (HPLC), nuclear magnetic resonance (NMR) and gel electrophoresis techniques provided molecular insights into this KG-generating machinery. Real-time quantitative polymerase chain reaction (RT-qPCR) analyses revealed the transcripts responsible for ICL and SSADH were elevated in the Mn-supplemented cultures. This hitherto unreported metabolic network where ICL and SSADH orchestrate the enhanced production of KG from glycerol, provides an elegant means of converting an industrial waste into a keto acid with wide-ranging application in the medical, cosmetic, and chemical sectors.
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Affiliation(s)
- Azhar A Alhasawi
- Department of Chemistry and Biochemistry, Laurentian University, Sudbury, ON, Canada
| | - Sean C Thomas
- Department of Chemistry and Biochemistry, Laurentian University, Sudbury, ON, Canada
| | - Sujeethar Tharmalingam
- Department of Chemistry and Biochemistry, Laurentian University, Sudbury, ON, Canada.,Department of Biology, Laurentian University, Sudbury, ON, Canada.,Biomolecular Sciences Program, Laurentian University, Sudbury, ON, Canada.,Northern Ontario School of Medicine, Laurentian University, Sudbury, ON, Canada
| | - Felix Legendre
- Department of Chemistry and Biochemistry, Laurentian University, Sudbury, ON, Canada
| | - Vasu D Appanna
- Department of Chemistry and Biochemistry, Laurentian University, Sudbury, ON, Canada
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25
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Do DTH, Theron CW, Fickers P. Organic Wastes as Feedstocks for Non-Conventional Yeast-Based Bioprocesses. Microorganisms 2019; 7:E229. [PMID: 31370226 PMCID: PMC6722544 DOI: 10.3390/microorganisms7080229] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2019] [Revised: 07/26/2019] [Accepted: 07/29/2019] [Indexed: 12/22/2022] Open
Abstract
Non-conventional yeasts are efficient cell factories for the synthesis of value-added compounds such as recombinant proteins, intracellular metabolites, and/or metabolic by-products. Most bioprocess, however, are still designed to use pure, ideal sugars, especially glucose. In the quest for the development of more sustainable processes amid concerns over the future availability of resources for the ever-growing global population, the utilization of organic wastes or industrial by-products as feedstocks to support cell growth is a crucial approach. Indeed, vast amounts of industrial and commercial waste simultaneously represent an environmental burden and an important reservoir for recyclable or reusable material. These alternative feedstocks can provide microbial cell factories with the required metabolic building blocks and energy to synthesize value-added compounds, further representing a potential means of reduction of process costs as well. This review highlights recent strategies in this regard, encompassing knowledge on catabolic pathways and metabolic engineering solutions developed to endow cells with the required metabolic capabilities, and the connection of these to the synthesis of value-added compounds. This review focuses primarily, but not exclusively, on Yarrowia lipolytica as a yeast cell factory, owing to its broad range of naturally metabolizable carbon sources, together with its popularity as a non-conventional yeast.
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Affiliation(s)
- Diem T Hoang Do
- Microbial Processes and Interactions, TERRA Teaching and Research Centre, University of Liège - Gembloux AgroBio Tech, Av. de la Faculté, 2B. B-5030 Gembloux, Belgium
| | - Chrispian W Theron
- Microbial Processes and Interactions, TERRA Teaching and Research Centre, University of Liège - Gembloux AgroBio Tech, Av. de la Faculté, 2B. B-5030 Gembloux, Belgium
| | - Patrick Fickers
- Microbial Processes and Interactions, TERRA Teaching and Research Centre, University of Liège - Gembloux AgroBio Tech, Av. de la Faculté, 2B. B-5030 Gembloux, Belgium.
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26
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Baghban R, Farajnia S, Rajabibazl M, Ghasemi Y, Mafi A, Hoseinpoor R, Rahbarnia L, Aria M. Yeast Expression Systems: Overview and Recent Advances. Mol Biotechnol 2019; 61:365-384. [PMID: 30805909 DOI: 10.1007/s12033-019-00164-8] [Citation(s) in RCA: 98] [Impact Index Per Article: 19.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
Yeasts are outstanding hosts for the production of functional recombinant proteins with industrial or medical applications. Great attention has been emerged on yeast due to the inherent advantages and new developments in this host cell. For the production of each specific product, the most appropriate expression system should be identified and optimized both on the genetic and fermentation levels, considering the features of the host, vector and expression strategies. Currently, several new systems are commercially available; some of them are private and need licensing. The potential for secretory expression of heterologous proteins in yeast proposed this system as a candidate for the production of complex eukaryotic proteins. The common yeast expression hosts used for recombinant proteins' expression include Saccharomyces cerevisiae, Pichia pastoris, Hansenula polymorpha, Yarrowia lipolytica, Arxula adeninivorans, Kluyveromyces lactis, and Schizosaccharomyces pombe. This review is dedicated to discuss on significant characteristics of the most common methylotrophic and non-methylotrophic yeast expression systems with an emphasis on their advantages and new developments.
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Affiliation(s)
- Roghayyeh Baghban
- Medical Biotechnology Department, Faculty of Advanced Medical Science, Tabriz University of Medical Sciences, Tabriz, Iran.,Research Committee, Tabriz University of Medical Sciences, Tabriz, Iran.,Biotechnology Research Center, Tabriz University of Medical Sciences, Daneshgah Ave, Tabriz, Iran
| | - Safar Farajnia
- Biotechnology Research Center, Tabriz University of Medical Sciences, Daneshgah Ave, Tabriz, Iran. .,Drug Applied Research Center, Tabriz University of Medical Sciences, Tabriz, Iran.
| | - Masoumeh Rajabibazl
- Department of Clinical Biochemistry, Faculty of Medicine, Shahid Beheshti University of Medical Sciences, Velenjak, Arabi Ave, Tehran, Iran. .,Department of Biotechnology, School of Advanced Technologies in Medicine, Shahid Beheshti University of Medical Sciences, Tehran, Iran.
| | - Younes Ghasemi
- Department of Pharmaceutical Biotechnology, Faculty of Pharmacy and Pharmaceutical Sciences Research Center, Shiraz University of Medical Science, Shiraz, Iran
| | - AmirAli Mafi
- Anesthesiology Research Center, Shahid Beheshti University of Medical Sciences, Tehran, Iran
| | - Reyhaneh Hoseinpoor
- Department of Biotechnology, School of Advanced Technologies in Medicine, Shahid Beheshti University of Medical Sciences, Tehran, Iran
| | - Leila Rahbarnia
- Infectious and Tropical Diseases Research Center, Tabriz University of Medical Sciences, Tabriz, Iran
| | - Maryam Aria
- Biotechnology Research Center, Tabriz University of Medical Sciences, Daneshgah Ave, Tabriz, Iran
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27
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Genome Sequence of the Oleaginous Yeast Yarrowia lipolytica H222. Microbiol Resour Announc 2019; 8:MRA01547-18. [PMID: 30701247 PMCID: PMC6346196 DOI: 10.1128/mra.01547-18] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2018] [Accepted: 12/18/2018] [Indexed: 11/29/2022] Open
Abstract
Here, we report the genome sequence of the oleaginous yeast Yarrowia lipolytica H222. De novo genome assembly shows three main chromosomal rearrangements compared to that of strain E150/CLIB122. Here, we report the genome sequence of the oleaginous yeast Yarrowia lipolytica H222. De novo genome assembly shows three main chromosomal rearrangements compared to that of strain E150/CLIB122. This genomic resource will help integrate intraspecies diversity into synthetic biology projects that utilize Yarrowia as a biotechnological chassis for value-added chemical productions.
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28
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Synthetic biology tools for engineering Yarrowia lipolytica. Biotechnol Adv 2018; 36:2150-2164. [PMID: 30315870 PMCID: PMC6261845 DOI: 10.1016/j.biotechadv.2018.10.004] [Citation(s) in RCA: 93] [Impact Index Per Article: 15.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2018] [Revised: 09/11/2018] [Accepted: 10/07/2018] [Indexed: 12/15/2022]
Abstract
The non-conventional oleaginous yeast Yarrowia lipolytica shows great industrial promise. It naturally produces certain compounds of interest but can also artificially generate non-native metabolites, thanks to an engineering process made possible by the significant expansion of a dedicated genetic toolbox. In this review, we present recently developed synthetic biology tools that facilitate the manipulation of Y. lipolytica, including 1) DNA assembly techniques, 2) DNA parts for constructing expression cassettes, 3) genome-editing techniques, and 4) computational tools. Due to its metabolic features, Y. lipolytica is a promising cell factory for producing compounds of biotechnological interest. Fast and efficient synthetic biology tools have been developed, which has boosted engineering strategies for Y. lipolytica. This review describes the latest advances in synthetic biology for Y. lipolytica. DNA assembly tools, DNA parts for expression cassettes, genome-editing techniques, and computational tools are covered here.
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29
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Draft Genome Assemblies of Five Robust Yarrowia lipolytica Strains Exhibiting High Lipid Production, Pentose Sugar Utilization, and Sugar Alcohol Secretion from Undetoxified Lignocellulosic Biomass Hydrolysates. Microbiol Resour Announc 2018; 7:MRA01040-18. [PMID: 30533660 PMCID: PMC6256683 DOI: 10.1128/mra.01040-18] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2018] [Accepted: 09/04/2018] [Indexed: 11/24/2022] Open
Abstract
Screening the genetic diversity of 45 Yarrowia lipolytica strains identified five candidates with unique metabolic capability and robustness in undetoxified switchgrass hydrolysates, including superior lipid production and efficient pentose sugar utilization. Here, we report the genome sequences of these strains to study their robustness and potential to produce fuels and chemicals. Screening the genetic diversity of 45 Yarrowia lipolytica strains identified five candidates with unique metabolic capability and robustness in undetoxified switchgrass hydrolysates, including superior lipid production and efficient pentose sugar utilization. Here, we report the genome sequences of these strains to study their robustness and potential to produce fuels and chemicals.
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30
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Abdel-Mawgoud AM, Markham KA, Palmer CM, Liu N, Stephanopoulos G, Alper HS. Metabolic engineering in the host Yarrowia lipolytica. Metab Eng 2018; 50:192-208. [PMID: 30056205 DOI: 10.1016/j.ymben.2018.07.016] [Citation(s) in RCA: 109] [Impact Index Per Article: 18.2] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2018] [Revised: 07/23/2018] [Accepted: 07/24/2018] [Indexed: 12/21/2022]
Abstract
The nonconventional, oleaginous yeast, Yarrowia lipolytica is rapidly emerging as a valuable host for the production of a variety of both lipid and nonlipid chemical products. While the unique genetics of this organism pose some challenges, many new metabolic engineering tools have emerged to facilitate improved genetic manipulation in this host. This review establishes a case for Y. lipolytica as a premier metabolic engineering host based on innate metabolic capacity, emerging synthetic tools, and engineering examples. The metabolism underlying the lipid accumulation phenotype of this yeast as well as high flux through acyl-CoA precursors and the TCA cycle provide a favorable metabolic environment for expression of relevant heterologous pathways. These properties allow Y. lipolytica to be successfully engineered for the production of both native and nonnative lipid, organic acid, sugar and acetyl-CoA derived products. Finally, this host has unique metabolic pathways enabling growth on a wide range of carbon sources, including waste products. The expansion of carbon sources, together with the improvement of tools as highlighted here, have allowed this nonconventional organism to act as a cellular factory for valuable chemicals and fuels.
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Affiliation(s)
- Ahmad M Abdel-Mawgoud
- Department of Chemical Engineering, Massachusetts Institute of Technology, 77 Massachusetts Avenue, Cambridge, MA 02139, United States
| | - Kelly A Markham
- McKetta Department of Chemical Engineering, The University of Texas at Austin, 200 E Dean Keeton St. Stop C0400, Austin, TX 78712, United States
| | - Claire M Palmer
- Institute for Cellular and Molecular Biology, The University of Texas at Austin, 2500 Speedway Avenue, Austin, TX 78712, United States
| | - Nian Liu
- Department of Chemical Engineering, Massachusetts Institute of Technology, 77 Massachusetts Avenue, Cambridge, MA 02139, United States
| | - Gregory Stephanopoulos
- Department of Chemical Engineering, Massachusetts Institute of Technology, 77 Massachusetts Avenue, Cambridge, MA 02139, United States.
| | - Hal S Alper
- McKetta Department of Chemical Engineering, The University of Texas at Austin, 200 E Dean Keeton St. Stop C0400, Austin, TX 78712, United States; Institute for Cellular and Molecular Biology, The University of Texas at Austin, 2500 Speedway Avenue, Austin, TX 78712, United States.
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31
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Zeng W, Xu S, Du G, Liu S, Zhou J. Separation and purification of α-ketoglutarate and pyruvate from the fermentation broth of Yarrowia lipolytica. Bioprocess Biosyst Eng 2018; 41:1519-1527. [PMID: 29998382 DOI: 10.1007/s00449-018-1979-z] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2018] [Accepted: 07/05/2018] [Indexed: 11/26/2022]
Abstract
A strategy to achieve the efficient co-production of α-ketoglutarate (KGA) and pyruvate (PYR) via Yarrowia lipolytica fermentation was established in our previous work. The next big challenge is to achieve an efficient separation of the two keto acids. A strategy for simultaneously separating and purifying KGA and PYR based on their different boiling points was established, leading to the efficient separation and purification of the two keto acids from the fermentation broth of Y. lipolytica. The purity and yield of KGA/PYR reached 99.3/99.5 and 79.8/80.6%, respectively. Application of the separation method on industrial scale could further decrease the cost of the production of the two keto acids by biotechnological routes.
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Affiliation(s)
- Weizhu Zeng
- Key Laboratory of Industrial Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, 1800 Lihu Road, Wuxi, 214122, Jiangsu, China
- National Engineering Laboratory for Cereal Fermentation Technology, Jiangnan University, 1800 Lihu Road, Wuxi, 214122, Jiangsu, China
- Jiangsu Provisional Research Center for Bioactive Product Processing Technology, Jiangnan University, 1800 Lihu Road, Wuxi, 214122, Jiangsu, China
| | - Sha Xu
- Key Laboratory of Industrial Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, 1800 Lihu Road, Wuxi, 214122, Jiangsu, China
- National Engineering Laboratory for Cereal Fermentation Technology, Jiangnan University, 1800 Lihu Road, Wuxi, 214122, Jiangsu, China
| | - Guocheng Du
- Key Laboratory of Industrial Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, 1800 Lihu Road, Wuxi, 214122, Jiangsu, China
- The Key Laboratory of Carbohydrate Chemistry and Biotechnology, Ministry of Education, Jiangnan University, 1800 Lihu Road, Wuxi, 214122, Jiangsu, China
| | - Song Liu
- Key Laboratory of Industrial Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, 1800 Lihu Road, Wuxi, 214122, Jiangsu, China
- National Engineering Laboratory for Cereal Fermentation Technology, Jiangnan University, 1800 Lihu Road, Wuxi, 214122, Jiangsu, China
- Jiangsu Provisional Research Center for Bioactive Product Processing Technology, Jiangnan University, 1800 Lihu Road, Wuxi, 214122, Jiangsu, China
| | - Jingwen Zhou
- Key Laboratory of Industrial Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, 1800 Lihu Road, Wuxi, 214122, Jiangsu, China.
- National Engineering Laboratory for Cereal Fermentation Technology, Jiangnan University, 1800 Lihu Road, Wuxi, 214122, Jiangsu, China.
- Jiangsu Provisional Research Center for Bioactive Product Processing Technology, Jiangnan University, 1800 Lihu Road, Wuxi, 214122, Jiangsu, China.
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Engineering Yarrowia lipolytica for Use in Biotechnological Applications: A Review of Major Achievements and Recent Innovations. Mol Biotechnol 2018; 60:621-635. [DOI: 10.1007/s12033-018-0093-4] [Citation(s) in RCA: 49] [Impact Index Per Article: 8.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/14/2023]
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Increased flux through the TCA cycle enhances bacitracin production by Bacillus licheniformis DW2. Appl Microbiol Biotechnol 2018; 102:6935-6946. [PMID: 29911294 DOI: 10.1007/s00253-018-9133-z] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2018] [Revised: 05/07/2018] [Accepted: 05/23/2018] [Indexed: 11/27/2022]
Abstract
The dodecapeptide antibiotic bacitracin, produced by several strains of Bacillus licheniformis and Bacillus subtilis, is widely used as an antibacterial animal feed additive. Several genetic strategies were explored to enhance its production. The availability of building block amino acids for bacitracin production was found to play an important role in its synthesis. In this study, the TCA cycle in the industrial strain B. licheniformis DW2 was strengthened by overexpression of the key enzymes citrate synthase and isocitrate dehydrogenase (ICDH). As the central metabolic pathway, the TCA cycle is a major source for energy supply and intermediates for anabolism. By enhancing flux through the TCA cycle, more energy and precursors were generated for amino acid biosynthesis and uptake, resulting in enlarged intracellular pool of bacitracin-containing amino acids for bacitracin production. This study unveiled the metabolic responses of the increased TCA cycle flux in B. licheniformis and provided a novel strategy for enhancing bacitracin production.
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Promoter engineering of cascade biocatalysis for α-ketoglutaric acid production by coexpressing l-glutamate oxidase and catalase. Appl Microbiol Biotechnol 2018; 102:4755-4764. [DOI: 10.1007/s00253-018-8975-8] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2017] [Revised: 03/22/2018] [Accepted: 03/28/2018] [Indexed: 01/13/2023]
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Understanding Functional Roles of Native Pentose-Specific Transporters for Activating Dormant Pentose Metabolism in Yarrowia lipolytica. Appl Environ Microbiol 2018; 84:AEM.02146-17. [PMID: 29150499 DOI: 10.1128/aem.02146-17] [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: 09/29/2017] [Accepted: 11/02/2017] [Indexed: 01/08/2023] Open
Abstract
Pentoses, including xylose and arabinose, are the second most prevalent sugars in lignocellulosic biomass that can be harnessed for biological conversion. Although Yarrowia lipolytica has emerged as a promising industrial microorganism for production of high-value chemicals and biofuels, its native pentose metabolism is poorly understood. Our previous study demonstrated that Y. lipolytica (ATCC MYA-2613) has endogenous enzymes for d-xylose assimilation, but inefficient xylitol dehydrogenase causes Y. lipolytica to assimilate xylose poorly. In this study, we investigated the functional roles of native sugar-specific transporters for activating the dormant pentose metabolism in Y. lipolytica By screening a comprehensive set of 16 putative pentose-specific transporters, we identified two candidates, YALI0C04730p and YALI0B00396p, that enhanced xylose assimilation. The engineered mutants YlSR207 and YlSR223, overexpressing YALI0C04730p and YALI0B00396p, respectively, improved xylose assimilation approximately 23% and 50% in comparison to YlSR102, a parental engineered strain overexpressing solely the native xylitol dehydrogenase gene. Further, we activated and elucidated a widely unknown native l-arabinose assimilation pathway in Y. lipolytica through transcriptomic and metabolic analyses. We discovered that Y. lipolytica can coconsume xylose and arabinose, where arabinose utilization shares transporters and metabolic enzymes of some intermediate steps of the xylose assimilation pathway. Arabinose assimilation is synergistically enhanced in the presence of xylose, while xylose assimilation is competitively inhibited by arabinose. l-Arabitol dehydrogenase is the rate-limiting step responsible for poor arabinose utilization in Y. lipolytica Overall, this study sheds light on the cryptic pentose metabolism of Y. lipolytica and, further, helps guide strain engineering of Y. lipolytica for enhanced assimilation of pentose sugars.IMPORTANCE The oleaginous yeast Yarrowia lipolytica is a promising industrial-platform microorganism for production of high-value chemicals and fuels. For decades since its isolation, Y. lipolytica has been known to be incapable of assimilating pentose sugars, xylose and arabinose, that are dominantly present in lignocellulosic biomass. Through bioinformatic, transcriptomic, and enzymatic studies, we have uncovered the dormant pentose metabolism of Y. lipolytica Remarkably, unlike most yeast strains, which share the same transporters for importing hexose and pentose sugars, we discovered that Y. lipolytica possesses the native pentose-specific transporters. By overexpressing these transporters together with the rate-limiting d-xylitol and l-arabitol dehydrogenases, we activated the dormant pentose metabolism of Y. lipolytica Overall, this study provides a fundamental understanding of the dormant pentose metabolism of Y. lipolytica and guides future metabolic engineering of Y. lipolytica for enhanced conversion of pentose sugars to high-value chemicals and fuels.
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Liu Q, Ma X, Cheng H, Xu N, Liu J, Ma Y. Co-expression of l-glutamate oxidase and catalase in Escherichia coli to produce α-ketoglutaric acid by whole-cell biocatalyst. Biotechnol Lett 2017; 39:913-919. [DOI: 10.1007/s10529-017-2314-5] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2016] [Accepted: 02/23/2017] [Indexed: 11/28/2022]
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In vitro metabolic engineering for the production of α-ketoglutarate. Metab Eng 2017; 40:5-13. [PMID: 28238759 DOI: 10.1016/j.ymben.2017.02.011] [Citation(s) in RCA: 48] [Impact Index Per Article: 6.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/30/2016] [Revised: 02/16/2017] [Accepted: 02/21/2017] [Indexed: 11/23/2022]
Abstract
α-Ketoglutarate (aKG) represents a central intermediate of cell metabolism. It is used for medical treatments and as a chemical building block. Enzymatic cascade reactions have the potential to sustainably synthesize this natural product. Here we report a systems biocatalysis approach for an in vitro reaction set-up to produce aKG from glucuronate using the oxidative pathway of uronic acids. Because of two dehydrations, a decarboxylation, and reaction conditions favoring oxidation, the pathway is driven thermodynamically towards complete product formation. The five enzymes (including one for cofactor recycling) were first investigated individually to define optimal reaction conditions for the cascade reaction. Then, the kinetic parameters were determined under these conditions and the inhibitory effects of substrate, intermediates, and product were evaluated. As cofactor supply is critical for the cascade reaction, various set-ups were tested: increasing concentrations of the recycling enzyme, different initial NAD+ concentrations, as well as the use of a bubble reactor for faster oxygen diffusion. Finally, we were able to convert 10gL-1 glucuronate with 92% yield of aKG within 5h. The maximum productivity of 2.8gL-1 h-1 is the second highest reported in the biotechnological synthesis of aKG.
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Luo Z, Zeng W, Du G, Liu S, Fang F, Zhou J, Chen J. A high-throughput screening procedure for enhancing pyruvate production in Candida glabrata by random mutagenesis. Bioprocess Biosyst Eng 2017; 40:693-701. [DOI: 10.1007/s00449-017-1734-x] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2016] [Accepted: 01/07/2017] [Indexed: 12/30/2022]
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YaPing W, Ben R, Hong Y, Rui H, Li L, Ping'an L, Lixin M. High-level expression of l-glutamate oxidase in Pichia pastoris using multi-copy expression strains and high cell density cultivation. Protein Expr Purif 2017; 129:108-114. [DOI: 10.1016/j.pep.2016.09.014] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2016] [Revised: 09/18/2016] [Accepted: 09/26/2016] [Indexed: 10/20/2022]
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Mirończuk AM, Biegalska A, Dobrowolski A. Functional overexpression of genes involved in erythritol synthesis in the yeast Yarrowia lipolytica. BIOTECHNOLOGY FOR BIOFUELS 2017; 10:77. [PMID: 28352301 PMCID: PMC5366165 DOI: 10.1186/s13068-017-0772-6] [Citation(s) in RCA: 64] [Impact Index Per Article: 9.1] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/19/2017] [Accepted: 03/22/2017] [Indexed: 05/07/2023]
Abstract
BACKGROUND Erythritol, a four-carbon polyol synthesized by microorganisms as an osmoprotectant, is a natural sweetener produced on an industrial scale for decades. Despite the fact that the yeast Yarrowia lipolytica has been reported since the 1970s as an erythritol producer, the metabolic pathway of this polyol has never been characterized. It was shown that erythritol synthesis in yeast occurs via the pentose phosphate pathway (PPP). The oleaginous yeast Y. lipolytica is a good host for converting inexpensive glycerol into a value-added product such as erythritol. Glycerol is a renewable feedstock which is produced on a large scale as a waste product by many branches of industry. RESULTS In this study, we functionally overexpressed four genes involved in the pentose phosphate pathway (PPP): gene YALI0E06479g encoding transketolase (TKL1), gene YALI0F15587g encoding transaldolase (TAL1), gene YALI0E22649g encoding glucose-6-phosphate dehydrogenase (ZWF1), and gene YALI0B15598g encoding 6-phosphogluconate dehydrogenase (GND1). Here, we show that the crucial gene for erythritol synthesis in Y. lipolytica is transketolase. Overexpression of this gene results in a twofold improvement in erythritol synthesis during a shake-flask experiment (58 g/L). Moreover, overexpression of TKL1 allows for efficient production of erythritol independently from the supplied dissolved oxygen. Fermentation conducted in a 5-L bioreactor at low agitation results in almost 70% higher titer of erythritol over the control strain. CONCLUSION This work presents the importance of the PPP in erythritol synthesis and the feasibility for economic production of erythritol from glycerol by the yeast Y. lipolytica.
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Affiliation(s)
- Aleksandra M. Mirończuk
- Department of Biotechnology and Food Microbiology, Wroclaw University of Environmental and Life Sciences, Chełmońskiego 37, 51-630 Wrocław, Poland
| | - Anna Biegalska
- Department of Biotechnology and Food Microbiology, Wroclaw University of Environmental and Life Sciences, Chełmońskiego 37, 51-630 Wrocław, Poland
| | - Adam Dobrowolski
- Department of Biotechnology and Food Microbiology, Wroclaw University of Environmental and Life Sciences, Chełmońskiego 37, 51-630 Wrocław, Poland
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Applying pathway engineering to enhance production of alpha-ketoglutarate in Yarrowia lipolytica. Appl Microbiol Biotechnol 2016; 100:9875-9884. [DOI: 10.1007/s00253-016-7913-x] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2016] [Revised: 09/27/2016] [Accepted: 09/29/2016] [Indexed: 12/29/2022]
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Production of valuable compounds by molds and yeasts. J Antibiot (Tokyo) 2016; 70:347-360. [PMID: 27731337 PMCID: PMC7094691 DOI: 10.1038/ja.2016.121] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2016] [Revised: 08/31/2016] [Accepted: 09/01/2016] [Indexed: 11/30/2022]
Abstract
We are pleased to dedicate this paper to Dr Julian E Davies. Julian is a giant among microbial biochemists. He began his professional career as an organic chemistry PhD student at Nottingham University, moved on to a postdoctoral fellowship at Columbia University, then became a lecturer at the University of Manchester, followed by a fellowship in microbial biochemistry at Harvard Medical School. In 1965, he studied genetics at the Pasteur Institute, and 2 years later joined the University of Wisconsin in the Department of Biochemistry. He later became part of Biogen as Research Director and then President. After Biogen, Julian became Chair of the Department of Microbiology at the University of British Columbia in Vancouver, Canada, where he has contributed in a major way to the reputation of this department for many years. He also served as an Adjunct Professor at the University of Geneva. Among Julian’s areas of study and accomplishment are fungal toxins including α-sarcin, chemical synthesis of triterpenes, mode of action of streptomycin and other aminoglycoside antibiotics, biochemical mechanisms of antibiotic resistance in clinical isolates of bacteria harboring resistance plasmids, their origins and evolution, secondary metabolism of microorganisms, structure and function of bacterial ribosomes, antibiotic resistance mutations in yeast ribosomes, cloning of resistance genes from an antibiotic-producing microbe, gene cloning for industrial purposes, engineering of herbicide resistance in useful crops, bleomycin-resistance gene in clinical isolates of Staphylococcus aureus and many other topics. He has been an excellent teacher, lecturing in both English and French around the world, and has organized international courses. Julian has also served on the NIH study sections, as Editor for several international journals, and was one of the founders of the journal Plasmid. We expect the impact of Julian’s accomplishments to continue into the future.
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Zeng W, Fang F, Liu S, Du G, Chen J, Zhou J. Comparative genomics analysis of a series of Yarrowia lipolytica WSH-Z06 mutants with varied capacity for α-ketoglutarate production. J Biotechnol 2016; 239:76-82. [PMID: 27732868 DOI: 10.1016/j.jbiotec.2016.10.008] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2016] [Revised: 09/16/2016] [Accepted: 10/07/2016] [Indexed: 01/23/2023]
Abstract
Yarrowia lipolytica is one of the most intensively investigated α-ketoglutaric acid (α-KG) producers, and metabolic engineering has proven effective for enhancing production. However, regulation of α-KG metabolism remains poorly understood. Genetic engineering of new strains is accompanied by potential safety concerns in some countries and regions. A series of mutants with varied capacity for α-KG production were obtained using random mutagenesis of Y. lipolytica WSH-Z06. Comparative genomics analysis was implemented to identify genes candidates associated with α-KG production. Manipulation of genes regulating mitochondrial biogenesis and energy metabolism could improve α-KG production, while genes involved in regulating transformation between keto acids and amino acids may decrease production. One gene associated with cell cycle control well represented in all mutants, whereas this gene involved in cell concentration do not appear to influence α-KG production. The results shed light on α-KG production in eukaryotic cells, and pave the way for a high-throughput screening and random mutagenesis method for enhancing α-KG production.
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Affiliation(s)
- Weizhu Zeng
- School of Biotechnology and Key Laboratory of Industrial Biotechnology, Ministry of Education, Jiangnan University, 1800 Lihu Road, Wuxi, Jiangsu 214122, China
| | - Fang Fang
- School of Biotechnology and Key Laboratory of Industrial Biotechnology, Ministry of Education, Jiangnan University, 1800 Lihu Road, Wuxi, Jiangsu 214122, China; Synergetic Innovation Center of Food Safety and Nutrition, 1800 Lihu Road, Wuxi, Jiangsu 214122, China
| | - Song Liu
- School of Biotechnology and Key Laboratory of Industrial Biotechnology, Ministry of Education, Jiangnan University, 1800 Lihu Road, Wuxi, Jiangsu 214122, China; Synergetic Innovation Center of Food Safety and Nutrition, 1800 Lihu Road, Wuxi, Jiangsu 214122, China
| | - Guocheng Du
- School of Biotechnology and Key Laboratory of Industrial Biotechnology, Ministry of Education, Jiangnan University, 1800 Lihu Road, Wuxi, Jiangsu 214122, China; Synergetic Innovation Center of Food Safety and Nutrition, 1800 Lihu Road, Wuxi, Jiangsu 214122, China
| | - Jian Chen
- School of Biotechnology and Key Laboratory of Industrial Biotechnology, Ministry of Education, Jiangnan University, 1800 Lihu Road, Wuxi, Jiangsu 214122, China; Synergetic Innovation Center of Food Safety and Nutrition, 1800 Lihu Road, Wuxi, Jiangsu 214122, China
| | - Jingwen Zhou
- School of Biotechnology and Key Laboratory of Industrial Biotechnology, Ministry of Education, Jiangnan University, 1800 Lihu Road, Wuxi, Jiangsu 214122, China; Synergetic Innovation Center of Food Safety and Nutrition, 1800 Lihu Road, Wuxi, Jiangsu 214122, China.
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Guo H, Wan H, Chen H, Fang F, Liu S, Zhou J. Proteomic analysis of the response of α-ketoglutarate-producer Yarrowia lipolytica WSH-Z06 to environmental pH stimuli. Appl Microbiol Biotechnol 2016; 100:8829-41. [PMID: 27535241 DOI: 10.1007/s00253-016-7775-2] [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: 05/22/2016] [Revised: 07/25/2016] [Accepted: 08/02/2016] [Indexed: 11/25/2022]
Abstract
During bioproduction of short-chain carboxylates, a shift in pH is a common strategy for enhancing the biosynthesis of target products. Based on two-dimensional gel electrophoresis, comparative proteomics analysis of general and mitochondrial protein samples was used to investigate the cellular responses to environmental pH stimuli in the α-ketoglutarate overproducer Yarrowia lipolytica WSH-Z06. The lower environmental pH stimuli tensioned intracellular acidification and increased the level of reactive oxygen species (ROS). A total of 54 differentially expressed protein spots were detected, and 11 main cellular processes were identified to be involved in the cellular response to environmental pH stimuli. Slight decrease in cytoplasmic pH enhanced the cellular acidogenicity by elevating expression level of key enzymes in tricarboxylic acid cycle (TCA cycle). Enhanced energy biosynthesis, ROS elimination, and membrane potential homeostasis processes were also employed as cellular defense strategies to compete with environmental pH stimuli. Owing to its antioxidant role of α-ketoglutarate, metabolic flux shifted to α-ketoglutarate under lower pH by Y. lipolytica in response to acidic pH stimuli. The identified differentially expressed proteins provide clues for understanding the mechanisms of the cellular responses and for enhancing short-chain carboxylate production through metabolic engineering or process optimization strategies in combination with manipulation of environmental conditions.
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Affiliation(s)
- Hongwei Guo
- Department of Biotechnology and Bioengineering, School of Chemical Engineering and Key Laboratory of Fujian Province for Biological Chemical Engineering, Huaqiao University, 668 Jimei Road, Amoy, Fujian, 361021, China.,School of Biotechnology and Key Laboratory of Industrial Biotechnology, Ministry of Education, Jiangnan University, 1800 Lihu Road, Wuxi, Jiangsu, 214122, China
| | - Hui Wan
- School of Biotechnology and Key Laboratory of Industrial Biotechnology, Ministry of Education, Jiangnan University, 1800 Lihu Road, Wuxi, Jiangsu, 214122, China
| | - Hongwen Chen
- Department of Biotechnology and Bioengineering, School of Chemical Engineering and Key Laboratory of Fujian Province for Biological Chemical Engineering, Huaqiao University, 668 Jimei Road, Amoy, Fujian, 361021, China
| | - Fang Fang
- School of Biotechnology and Key Laboratory of Industrial Biotechnology, Ministry of Education, Jiangnan University, 1800 Lihu Road, Wuxi, Jiangsu, 214122, China
| | - Song Liu
- School of Biotechnology and Key Laboratory of Industrial Biotechnology, Ministry of Education, Jiangnan University, 1800 Lihu Road, Wuxi, Jiangsu, 214122, China
| | - Jingwen Zhou
- School of Biotechnology and Key Laboratory of Industrial Biotechnology, Ministry of Education, Jiangnan University, 1800 Lihu Road, Wuxi, Jiangsu, 214122, China.
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Jian X, Zhou S, Zhang C, Hua Q. In silico identification of gene amplification targets based on analysis of production and growth coupling. Biosystems 2016; 145:1-8. [DOI: 10.1016/j.biosystems.2016.05.002] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2015] [Revised: 05/03/2016] [Accepted: 05/04/2016] [Indexed: 11/16/2022]
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Dobrowolski A, Mituła P, Rymowicz W, Mirończuk AM. Efficient conversion of crude glycerol from various industrial wastes into single cell oil by yeast Yarrowia lipolytica. BIORESOURCE TECHNOLOGY 2016; 207:237-43. [PMID: 26890799 DOI: 10.1016/j.biortech.2016.02.039] [Citation(s) in RCA: 99] [Impact Index Per Article: 12.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/06/2016] [Revised: 02/08/2016] [Accepted: 02/09/2016] [Indexed: 05/07/2023]
Abstract
In this study, crude glycerol from various industries was used to produce lipids via wild type Yarrowia lipolytica A101. We tested samples without any prior purification from five different waste products; each contained various concentrations of glycerol (42-87%) as the sole carbon source. The best results for lipid production were obtained for medium containing glycerol from fat saponification. This reached 1.69gL(-1) (25% of total cell dry weight) with a biomass yield of 0.17gg(-1) in the flasks experiment. The batch cultivation in a bioreactor resulted in enhanced lipid production-it achieved 4.72gL(-1) with a biomass yield 0.21gg(-1). Moreover, the properly selected batch of crude glycerol provides a defined fatty acid composition. In summary, this paper shows that crude glycerol from soap production could be efficiently converted to single cell oil without any prior purification.
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Affiliation(s)
- Adam Dobrowolski
- Department of Biotechnology and Food Microbiology, Wrocław University of Environmental and Life Sciences, Chełmońskiego 37, Wrocław 51-630, Poland
| | - Paweł Mituła
- Institute of Environmental Engineering, Wrocław University of Environmental and Life Sciences, Grunwaldzki Sq 24, Wrocław 50-363, Poland
| | - Waldemar Rymowicz
- Department of Biotechnology and Food Microbiology, Wrocław University of Environmental and Life Sciences, Chełmońskiego 37, Wrocław 51-630, Poland
| | - Aleksandra M Mirończuk
- Department of Biotechnology and Food Microbiology, Wrocław University of Environmental and Life Sciences, Chełmońskiego 37, Wrocław 51-630, Poland.
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Synthetic biology and molecular genetics in non-conventional yeasts: Current tools and future advances. Fungal Genet Biol 2016; 89:126-136. [DOI: 10.1016/j.fgb.2015.12.001] [Citation(s) in RCA: 135] [Impact Index Per Article: 16.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2015] [Revised: 11/18/2015] [Accepted: 12/05/2015] [Indexed: 12/16/2022]
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Fan X, Chen R, Chen L, Liu L. Enhancement of alpha-ketoglutaric acid production from l-glutamic acid by high-cell-density cultivation. ACTA ACUST UNITED AC 2016. [DOI: 10.1016/j.molcatb.2016.01.009] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
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49
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A. Alhasawi A, D. Appanna V. Manganese orchestrates a metabolic shift leading to the increased bioconversion of glycerol into α-ketoglutarate. AIMS BIOENGINEERING 2016. [DOI: 10.3934/bioeng.2017.1.12] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
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Gao C, Yang X, Wang H, Rivero CP, Li C, Cui Z, Qi Q, Lin CSK. Robust succinic acid production from crude glycerol using engineered Yarrowia lipolytica. BIOTECHNOLOGY FOR BIOFUELS 2016; 9:179. [PMID: 27579143 PMCID: PMC5004273 DOI: 10.1186/s13068-016-0597-8] [Citation(s) in RCA: 97] [Impact Index Per Article: 12.1] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/03/2016] [Accepted: 08/19/2016] [Indexed: 05/02/2023]
Abstract
BACKGROUND Integrating waste management with fuels and chemical production is considered to address the food waste problem and oil crisis. Approximately, 600 million tonnes crude glycerol is produced from the biodiesel industry annually, which is a top renewable feedstock for succinic acid production. To meet the increasing demand for succinic acid production, the development of more efficient and cost-effective production methods is urgently needed. Herein, we have proposed a new strategy for integration of both biodiesel and SA production in a biorefinery unit by construction of an aerobic yeast Yarrowia lipolytica with a deletion in the gene coding succinate dehydrogenase subunit 5. RESULTS Robust succinic acid production by an engineered yeast Y. lipolytica from crude glycerol without pre-treatment was demonstrated. Diversion of metabolic flow from tricarboxylic acid cycle led to the success in generating a succinic acid producer Y. lipolytica PGC01003. The fermentation media and conditions were optimized, which resulted in 43 g L(-1) succinic acid production from crude glycerol. Using the fed-batch strategy in 2.5 L fermenter, up to 160 g L(-1) SA was yielded, indicating the great industrial potential. CONCLUSIONS Inactivation of SDH5 in Y. lipolytica Po1f led to succinic acid accumulation and secretion significantly. To our best knowledge, this is the highest titer obtained in fermentation on succinic acid production. In addition, the performance of batch and fed-batch fermentation showed high tolerance and yield on biodiesel by-product crude glycerol. All these results indicated that PGC01003 is a promising microbial factorial cell for the highly efficient strategy solving the environmental problem in connection with the production of value-added product.
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Affiliation(s)
- Cuijuan Gao
- School of Energy and Environment, City University of Hong Kong, Tat Chee Avenue, Kowloon, Hong Kong
- State Key Laboratory of Microbial Technology, Shandong University, Jinan, 250100 People’s Republic of China
- School of Life Science, Linyi University, Linyi, 276005 People’s Republic of China
| | - Xiaofeng Yang
- School of Energy and Environment, City University of Hong Kong, Tat Chee Avenue, Kowloon, Hong Kong
- School of Bioscience and Bioengineering, South China University of Technology, Guangzhou, 510006 People’s Republic of China
| | - Huaimin Wang
- School of Energy and Environment, City University of Hong Kong, Tat Chee Avenue, Kowloon, Hong Kong
| | - Cristina Perez Rivero
- School of Chemical Engineering and Analytical Science, The University of Manchester, Manchester, UK
| | - Chong Li
- School of Energy and Environment, City University of Hong Kong, Tat Chee Avenue, Kowloon, Hong Kong
| | - Zhiyong Cui
- State Key Laboratory of Microbial Technology, Shandong University, Jinan, 250100 People’s Republic of China
| | - Qingsheng Qi
- State Key Laboratory of Microbial Technology, Shandong University, Jinan, 250100 People’s Republic of China
| | - Carol Sze Ki Lin
- School of Energy and Environment, City University of Hong Kong, Tat Chee Avenue, Kowloon, Hong Kong
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