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Jovanovic Gasovic S, Dietrich D, Gläser L, Cao P, Kohlstedt M, Wittmann C. Multi-omics view of recombinant Yarrowia lipolytica: Enhanced ketogenic amino acid catabolism increases polyketide-synthase-driven docosahexaenoic production to high selectivity at the gram scale. Metab Eng 2023; 80:45-65. [PMID: 37683719 DOI: 10.1016/j.ymben.2023.09.003] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2023] [Revised: 09/04/2023] [Accepted: 09/04/2023] [Indexed: 09/10/2023]
Abstract
DHA is a marine PUFA of commercial value, given its multiple health benefits. The worldwide emerging shortage in DHA supply has increased interest in microbial cell factories that can provide the compound de novo. In this regard, the present work aimed to improve DHA production in the oleaginous yeast strain Y. lipolytica Af4, which synthetized the PUFA via a heterologous myxobacterial polyketide synthase (PKS)-like gene cluster. As starting point, we used transcriptomics, metabolomics, and 13C-based metabolic pathway profiling to study the cellular dynamics of Y. lipolytica Af4. The shift from the growth to the stationary DHA-production phase was associated with fundamental changes in carbon core metabolism, including a strong upregulation of the PUFA gene cluster, as well as an increase in citrate and fatty acid degradation. At the same time, the intracellular levels of the two DHA precursors acetyl-CoA and malonyl-CoA dropped by up to 98% into the picomolar range. Interestingly, the degradation pathways for the ketogenic amino acids l-lysine, l-leucine, and l-isoleucine were transcriptionally activated, presumably to provide extra acetyl-CoA. Supplementation with small amounts of these amino acids at the beginning of the DHA production phase beneficially increased the intracellular CoA-ester pools and boosted the DHA titer by almost 40%. Isotopic 13C-tracer studies revealed that the supplements were efficiently directed toward intracellular CoA-esters and DHA. Hereby, l-lysine was found to be most efficient, as it enabled long-term activation, due to storage within the vacuole and continuous breakdown. The novel strategy enabled DHA production in Y. lipolytica at the gram scale for the first time. DHA was produced at a high selectivity (27% of total fatty acids) and free of the structurally similar PUFA DPA, which facilitates purification for high-value medical applications that require API-grade DHA. The assembled multi-omics picture of the central metabolism of Y. lipolytica provides valuable insights into this important yeast. Beyond our work, the enhanced catabolism of ketogenic amino acids seems promising for the overproduction of other compounds in Y. lipolytica, whose synthesis is limited by the availability of CoA ester precursors.
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Affiliation(s)
| | - Demian Dietrich
- Institute of Systems Biotechnology, Saarland University, Germany
| | - Lars Gläser
- Institute of Systems Biotechnology, Saarland University, Germany
| | - Peng Cao
- Institute of Systems Biotechnology, Saarland University, Germany
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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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3
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Enhanced In Vitro Cascade Catalysis of Glycerol into Pyruvate and Acetoin by Integration with Dihydroxy Acid Dehydratase from Paralcaligenes ureilyticus. Catalysts 2021. [DOI: 10.3390/catal11111282] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/11/2023] Open
Abstract
Recently, an in vitro enzymatic cascade was constructed to transform glycerol into the high-value platform chemical pyruvate. However, the low activity of dihydroxy acid dehydratase from Sulfolobus solfataricus (SsDHAD) limited the efficiency. In this study, the enzymatic reduction of pyruvate catalyzed by d-lactate dehydrogenase from Pseudomonas aeruginosa PAO1 was used to assay the activities of dihydroxy acid dehydratases. Dihydroxy acid dehydratase from Paralcaligenes ureilyticus (PuDHT) was identified as the most efficient candidate for glycerate dehydration. After the optimization of the catalytic temperature for the enzymatic cascade, comprising alditol oxidase from Streptomyces coelicolor A3, PuDHT, and catalase from Aspergillus niger, 20.50 ± 0.27 mM of glycerol was consumed in 4 h to produce 18.95 ± 0.97 mM of pyruvate with a productivity 12.15-fold higher than the previous report using SsDHAD. The enzymatic cascade was further coupled with the pyruvate decarboxylase from Zymomonas mobile for the production of another platform compound, acetoin. Acetoin at a concentration of 8.52 ± 0.12 mM was produced from 21.62 ± 0.19 mM of glycerol with a productivity of 1.42 ± 0.02 mM h−1.
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Li B, Cai D, Chen S. Metabolic Engineering of Central Carbon Metabolism of Bacillus licheniformis for Enhanced Production of Poly-γ-glutamic Acid. Appl Biochem Biotechnol 2021; 193:3540-3552. [PMID: 34312784 DOI: 10.1007/s12010-021-03619-4] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2021] [Accepted: 07/12/2021] [Indexed: 01/17/2023]
Abstract
Poly-γ-glutamic acid (γ-PGA) is an anionic polymer with wide-ranging applications in the areas of medicine, light chemical industry, wastewater treatment, and agriculture. However, the production cost of γ-PGA is high for the requirement of adding the expensive precursor L-glutamic acid during fermentation, which hinders its widespread application. In this study, in order to improve γ-PGA yield, central carbon metabolism was engineered to enhance the carbon flux of tricarboxylic acid (TCA) cycle and glutamic acid synthesis in a γ-PGA production strain Bacillus licheniformis WX-02. Firstly, pyruvate dehydrogenase (PdhABCD) and citrate synthase (CitA) were overexpressed to strengthen the flux of pyruvate into TCA cycle, resulting in 34.93% and 11.14% increase of γ-PGA yield in B. licheniformis WX-02, respectively. Secondly, the carbon flux to glyoxylate shunt was rewired via varying the expression of isocitrate lyase (AceA), and a 23.24% increase of γ-PGA yield was obtained in AceA down-regulated strain WXPbacAaceBA. Thirdly, deletion of pyruvate formate-lyase gene pflB led to a 30.70% increase of γ-PGA yield. Finally, combinatorial metabolic engineering was applied, and γ-PGA titer was enhanced to 12.02 g/L via overexpressing pdhABCD and citA, repressing aceA, and deleting pflB, with a 69.30% improvement compared to WX-02. Collectively, metabolic engineering of central carbon metabolism is an effective strategy for enhanced γ-PGA production in B. licheniformis, and this research provided a promising strain for industrial production of γ-PGA.
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Affiliation(s)
- Bichan Li
- Fujian Provincial Key Laboratory of Eco-Industrial Green Technology, College of Ecological and Resource Engineering, Wuyi University, Wuyishan, 354300, People's Republic of China.,State Key Laboratory of Agricultural Microbiology, College of Life Science and Technology, Huazhong Agricultural University, Wuhan, 430070, Hubei, People's Republic of China
| | - Dongbo Cai
- State Key Laboratory of Biocatalysis and Enzyme Engineering, Environmental Microbial Technology Center of Hubei Province, College of Life Sciences, Hubei University, Wuhan, 430062, People's Republic of China
| | - Shouwen Chen
- Fujian Provincial Key Laboratory of Eco-Industrial Green Technology, College of Ecological and Resource Engineering, Wuyi University, Wuyishan, 354300, People's Republic of China. .,State Key Laboratory of Biocatalysis and Enzyme Engineering, Environmental Microbial Technology Center of Hubei Province, College of Life Sciences, Hubei University, Wuhan, 430062, People's Republic of China.
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Yu B, Sun W, Huang Z, Sun G, Li L, Gu J, Zheng M, Li X, Chun C, Hui Q, Wang X. Large-Scale Preparation of Highly Stable Recombinant Human Acidic Fibroblast Growth Factor in Escherichia coli BL21(DE3) plysS Strain. Front Bioeng Biotechnol 2021; 9:641505. [PMID: 33912546 PMCID: PMC8072344 DOI: 10.3389/fbioe.2021.641505] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2020] [Accepted: 03/24/2021] [Indexed: 12/02/2022] Open
Abstract
In this study, the optimum human aFGF gene encoding haFGF135 was cloned in pET3c and transferred to Escherichia coli BL21(DE3) plysS. To enhance the yield of fermentation and the expression level of the target protein, the fermentation parameters, including temperature, pH, dissolved oxygen, glucose concentration, ammonium chloride concentration, induction time, and inducer (IPTG) concentration, were optimized. The optimized fermentation parameters were used in large-scale fermentation (30 L). Ion-exchange and heparin-affinity column chromatography techniques were used for separation and purification of rhaFGF135 protein. HPLC, isoelectric focusing electrophoresis, and mass spectrometry were used to detect the purity, isoelectric point, and molecular weight and peptide map of rhaFGF135 protein, respectively. Mitogenic activity of rhaFGF135 protein was detected in NIH-3T3 cells and a full-thickness injury wound diabetic rat model. The production and expression level of rhaFGF135 in the 30-L scale fermentation reached 80.4 ± 2.7 g/L culture and 37.8% ± 1.8%, respectively. The RP-HPLC and SDS-PAGE purity of the final rhaFGF135 product almost reached 100%, and the final pure protein yield was 158.6 ± 6.8 mg/L culture. Finally, the cell and animal experiments showed that rhaFGF135 retained a potent mitogenic activity. The large-scale process of rhaFGF135 production reported herein is relatively stable and time-saving, and thus, it can be used as an efficient and economic strategy for the synthesis of rhaFGF135 at the industrial level.
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Affiliation(s)
- Bingjieu Yu
- Wenzhou Medical University, Chashan University Park, Wenzhou, China
| | - Wenzhe Sun
- Wenzhou Medical University, Chashan University Park, Wenzhou, China
| | - Zhen Huang
- Wenzhou Medical University, Chashan University Park, Wenzhou, China
| | - Gang Sun
- Wenzhou Medical University, Chashan University Park, Wenzhou, China
| | - Le Li
- Wenzhou Medical University, Chashan University Park, Wenzhou, China
| | - Jiawei Gu
- Wenzhou Medical University, Chashan University Park, Wenzhou, China
| | - Mengying Zheng
- Wenzhou Medical University, Chashan University Park, Wenzhou, China
| | - Xiaokun Li
- Wenzhou Medical University, Chashan University Park, Wenzhou, China.,Engineering Laboratory of Zhejiang Province for Pharmaceutical Development of Growth Factors, Biomedical Collaborative Innovation Center of Wenzhou, Wenzhou, China
| | - ChangJu Chun
- Research Institute of Pharmaceutical Sciences, College of Pharmacy, Chonnam National University, Gwangju, South Korea
| | - Qi Hui
- Wenzhou Medical University, Chashan University Park, Wenzhou, China.,Engineering Laboratory of Zhejiang Province for Pharmaceutical Development of Growth Factors, Biomedical Collaborative Innovation Center of Wenzhou, Wenzhou, China
| | - Xiaojie Wang
- Wenzhou Medical University, Chashan University Park, Wenzhou, China.,Engineering Laboratory of Zhejiang Province for Pharmaceutical Development of Growth Factors, Biomedical Collaborative Innovation Center of Wenzhou, Wenzhou, China
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6
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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: 35] [Impact Index Per Article: 8.8] [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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7
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Li Y, Yang S, Ma D, Song W, Gao C, Liu L, Chen X. Microbial engineering for the production of C 2-C 6 organic acids. Nat Prod Rep 2021; 38:1518-1546. [PMID: 33410446 DOI: 10.1039/d0np00062k] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
Covering: up to the end of 2020Organic acids, as building block compounds, have been widely used in food, pharmaceutical, plastic, and chemical industries. Until now, chemical synthesis is still the primary method for industrial-scale organic acid production. However, this process encounters some inevitable challenges, such as depletable petroleum resources, harsh reaction conditions and complex downstream processes. To solve these problems, microbial cell factories provide a promising approach for achieving the sustainable production of organic acids. However, some key metabolites in central carbon metabolism are strictly regulated by the network of cellular metabolism, resulting in the low productivity of organic acids. Thus, multiple metabolic engineering strategies have been developed to reprogram microbial cell factories to produce organic acids, including monocarboxylic acids, hydroxy carboxylic acids, amino carboxylic acids, dicarboxylic acids and monomeric units for polymers. These strategies mainly center on improving the catalytic efficiency of the enzymes to increase the conversion rate, balancing the multi-gene biosynthetic pathways to reduce the byproduct formation, strengthening the metabolic flux to promote the product biosynthesis, optimizing the metabolic network to adapt the environmental conditions and enhancing substrate utilization to broaden the substrate spectrum. Here, we describe the recent advances in producing C2-C6 organic acids by metabolic engineering strategies. In addition, we provide new insights as to when, what and how these strategies should be taken. Future challenges are also discussed in further advancing microbial engineering and establishing efficient biorefineries.
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Affiliation(s)
- Yang Li
- State Key Laboratory of Food Science and Technology, Jiangnan University, 1800 Lihu Road, Wuxi 214122, China.
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Synthesis of high-titer alka(e)nes in Yarrowia lipolytica is enabled by a discovered mechanism. Nat Commun 2020; 11:6198. [PMID: 33273473 PMCID: PMC7713262 DOI: 10.1038/s41467-020-19995-0] [Citation(s) in RCA: 29] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2020] [Accepted: 11/08/2020] [Indexed: 12/12/2022] Open
Abstract
Alka(e)nes are ideal fuel components for aviation, long-distance transport, and shipping. They are typically derived from fossil fuels and accounting for 24% of difficult-to-eliminate greenhouse gas emissions. The synthesis of alka(e)nes in Yarrowia lipolytica from CO2-neutral feedstocks represents an attractive alternative. Here we report that the high-titer synthesis of alka(e)nes in Yarrowia lipolytica harboring a fatty acid photodecarboxylase (CvFAP) is enabled by a discovered pathway. We find that acyl-CoAs, rather than free fatty acids (FFAs), are the preferred substrate for CvFAP. This finding allows us to debottleneck the pathway and optimize fermentation conditions so that we are able to redirect 89% of acyl-CoAs from the synthesis of neutral lipids to alka(e)nes and reach titers of 1.47 g/L from glucose. Two other CO2-derived substrates, wheat straw and acetate, are also demonstrated to be effective in producing alka(e)nes. Overall, our technology could advance net-zero emissions by providing CO2-neutral and energy-dense liquid biofuels. Alka(e)nes with chain lengths in C5-C23 range are ideal fuel components. Here, the authors report that high-titer production of alak(e)nes in pathway engineered Yarrowia lipolytica, which is enabled by the finding that acyl-CoA is another substrate of fatty acid photodecarboxylase (FAP).
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Wang Y, Zhang Z, Lu X, Zong H, Zhuge B. Genetic engineering of an industrial yeast Candida glycerinogenes for efficient production of 2-phenylethanol. Appl Microbiol Biotechnol 2020; 104:10481-10491. [PMID: 33180170 DOI: 10.1007/s00253-020-10991-4] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2020] [Revised: 10/23/2020] [Accepted: 10/31/2020] [Indexed: 10/23/2022]
Abstract
Microbial cell factories offer an economic approach for synthesizing "natural'" aromatic flavor compounds. During their fermentation process, the inefficient synthesis pathway and product cytotoxicity are the major barriers to the high-level production. This study combined metabolic engineering and tolerance engineering strategies to maximize the valuable rose-smell 2-phenylethanol (2-PE) production in Candida glycerinogenes, a GRAS diploid industrial yeast. Firstly, 2-PE metabolic networks involved in Ehrlich pathway were stepwise rewired using metabolic engineering, including the following: (1) overexpressing L-phenylalanine permease Aap9 enhanced precursor uptake; (2) overexpressing enzymes (aminotransferase Aro9 and decarboxylase Aro10) of Ehrlich pathway increased catalytic efficiency; and (3) disrupting the formation of by-product phenylacetate catalyzed by Ald2 and Ald3 maximized the metabolic flux toward 2-PE. Then, tolerance engineering was applied by overexpression of a stress-inducible gene SLC1 in the metabolically engineered strain to further enhance 2-PE production. Combining these two approaches finally resulted in 5.0 g/L 2-PE in shake flasks, with productivity reaching 0.21 g/L/h, which were increased by 38.9% and 177% compared with those of the non-engineered strain, respectively. The 2-PE yield of this engineered strain was 0.71 g/g L-phenylalanine, corresponding to 95.9% of theoretical yield. This study provides a reference to efficiently engineering of microbial cell factories for other valuable aromatic compounds. KEY POINTS: • Metabolic engineering improved 2-PE biosynthesis. • Tolerance engineering alleviated product inhibition, contributing to 2-PE production. • The best strain produced 5.0 g/L 2-PE with 0.959 mol/mol yield and high productivity.
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Affiliation(s)
- Yuqin Wang
- The Key Laboratory of Industrial Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, Wuxi, China.,The Key Laboratory of Carbohydrate Chemistry and Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, Wuxi, China.,Research Centre of Industrial Microbiology, School of Biotechnology, Jiangnan University, Wuxi, China
| | - Zhongyuan Zhang
- The Key Laboratory of Industrial Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, Wuxi, China.,The Key Laboratory of Carbohydrate Chemistry and Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, Wuxi, China.,Research Centre of Industrial Microbiology, School of Biotechnology, Jiangnan University, Wuxi, China
| | - Xinyao Lu
- The Key Laboratory of Industrial Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, Wuxi, China. .,The Key Laboratory of Carbohydrate Chemistry and Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, Wuxi, China. .,Research Centre of Industrial Microbiology, School of Biotechnology, Jiangnan University, Wuxi, China.
| | - Hong Zong
- The Key Laboratory of Industrial Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, Wuxi, China.,The Key Laboratory of Carbohydrate Chemistry and Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, Wuxi, China.,Research Centre of Industrial Microbiology, School of Biotechnology, Jiangnan University, Wuxi, China
| | - Bin Zhuge
- The Key Laboratory of Industrial Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, Wuxi, China. .,The Key Laboratory of Carbohydrate Chemistry and Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, Wuxi, China. .,Research Centre of Industrial Microbiology, School of Biotechnology, Jiangnan University, Wuxi, China.
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10
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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: 1.0] [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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11
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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: 1.2] [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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12
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Li N, Zeng W, Xu S, Zhou J. Toward fine-tuned metabolic networks in industrial microorganisms. Synth Syst Biotechnol 2020; 5:81-91. [PMID: 32542205 PMCID: PMC7283098 DOI: 10.1016/j.synbio.2020.05.002] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/26/2019] [Revised: 03/30/2020] [Accepted: 05/06/2020] [Indexed: 12/11/2022] Open
Abstract
There are numerous microorganisms in nature capable of synthesizing diverse useful compounds; however, these natural microorganisms are generally inefficient in the production of target products on an industrial scale, relative to either chemical synthesis or extraction methods. To achieve industrial production of useful compounds, these natural microorganisms must undergo a certain degree of mutation or effective fine-tuning strategies. This review describes how to achieve an ideal metabolic fine-tuned process, including static control strategies and dynamic control strategies. The static control strategies mainly focus on various matabolic engineering strategies, including protein engineering, upregulation/downregulation, and combinatrorial control of these metabolic engineering strategies, to enhance the flexibility of their application in fine-tuned metabolic metworks. Then, we focus on the dynamic control strategies for fine-tuned metabolic metworks. The design principles derived would guide us to construct microbial cell factories for various useful compounds.
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Affiliation(s)
- Ning Li
- Key Laboratory of Industrial Biotechnology, Ministry of Education and School of Biotechnology, Jiangnan University, 1800 Lihu Road, Wuxi, Jiangsu, 214122, China.,National Engineering Laboratory for Cereal Fermentation Technology, 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 and School of Biotechnology, Jiangnan University, 1800 Lihu Road, Wuxi, Jiangsu, 214122, China.,National Engineering Laboratory for Cereal Fermentation Technology, 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
| | - Sha Xu
- Key Laboratory of Industrial Biotechnology, Ministry of Education and School of Biotechnology, Jiangnan University, 1800 Lihu Road, Wuxi, Jiangsu, 214122, China.,National Engineering Laboratory for Cereal Fermentation Technology, 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
| | - Jingwen Zhou
- Key Laboratory of Industrial Biotechnology, Ministry of Education and School of Biotechnology, Jiangnan University, 1800 Lihu Road, Wuxi, Jiangsu, 214122, China.,National Engineering Laboratory for Cereal Fermentation Technology, 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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13
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Park YK, Ledesma-Amaro R, Nicaud JM. De novo Biosynthesis of Odd-Chain Fatty Acids in Yarrowia lipolytica Enabled by Modular Pathway Engineering. Front Bioeng Biotechnol 2020; 7:484. [PMID: 32039184 PMCID: PMC6987463 DOI: 10.3389/fbioe.2019.00484] [Citation(s) in RCA: 37] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2019] [Accepted: 12/27/2019] [Indexed: 01/21/2023] Open
Abstract
Microbial oils are regarded as promising alternatives to fossil fuels as concerns over environmental issues and energy production systems continue to mount. Odd-chain fatty acids (FAs) are a type of valuable lipid with various applications: they can serve as biomarkers, intermediates in the production of flavor and fragrance compounds, fuels, and plasticizers. Microorganisms naturally produce FAs, but such FAs are primarily even-chain; only negligible amounts of odd-chain FAs are generated. As a result, studies using microorganisms to produce odd-chain FAs have had limited success. Here, our objective was to biosynthesize odd-chain FAs de novo in Yarrowia lipolytica using inexpensive carbon sources, namely glucose, without any propionate supplementation. To achieve this goal, we constructed a modular metabolic pathway containing seven genes. In the engineered strain expressing this pathway, the percentage of odd-chain FAs out of total FAs was higher than in the control strain (3.86 vs. 0.84%). When this pathway was transferred into an obese strain, which had been engineered to accumulate large amounts of lipids, odd-chain fatty acid production was 7.2 times greater than in the control (0.05 vs. 0.36 g/L). This study shows that metabolic engineering research is making progress toward obtaining efficient cell factories that produce odd-chain FAs.
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Affiliation(s)
- Young-Kyoung Park
- Université Paris-Saclay, INRAE, AgroParisTech, Micalis Institute, Jouy-en-Josas, France
| | - Rodrigo Ledesma-Amaro
- Imperial College Centre for Synthetic Biology and Department of Bioengineering, Imperial College London, London, United Kingdom
| | - Jean-Marc Nicaud
- Université Paris-Saclay, INRAE, AgroParisTech, Micalis Institute, Jouy-en-Josas, France
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14
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Kamzolova SV, Morgunov IG. Biosynthesis of pyruvic acid from glycerol-containing substrates and its regulation in the yeast Yarrowia lipolytica. BIORESOURCE TECHNOLOGY 2018; 266:125-133. [PMID: 29960242 DOI: 10.1016/j.biortech.2018.06.071] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/24/2018] [Revised: 06/19/2018] [Accepted: 06/20/2018] [Indexed: 06/08/2023]
Abstract
The ability of different yeasts to synthesize pyruvic acid (PA) from glycerol-containing substrates has been studied. The selected strain Yarrowia lipolytica VKM Y-2378 synthesized PA with α-ketoglutaric acid (KGA) as a byproduct. The content of KGA greatly depended on cultivation conditions. The minimal formation of the byproduct was provided by the limitation of yeast growth by thiamine (0.6 µg/g biomass); the use of ammonium sulfate (0.6%) as a nitrogen source; addition of glycerol to cultivation medium in 20 g/L portions; maintaining the cultivation temperature at 28 °C, pH of the cultivation medium at 4.5, and medium aeration between 55 and 60% of saturation; the optimal cultivation time was 48 h. The selected strain cultivated under such conditions in a fermenter with a waste glycerol from biodiesel production process synthesized 41 g/L PA with a yield of 0.82 g/g. The mechanism of PA production from glycerol-containing substrates in Y. lipolytica is discussed.
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Affiliation(s)
- Svetlana V Kamzolova
- G.K. Skryabin Institute of Biochemistry and Physiology of Microorganisms, Russian Academy of Sciences, Pushchino 142290, Russia
| | - Igor G Morgunov
- G.K. Skryabin Institute of Biochemistry and Physiology of Microorganisms, Russian Academy of Sciences, Pushchino 142290, Russia.
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15
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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: 127] [Impact Index Per Article: 18.1] [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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16
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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: 0.7] [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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17
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Lu Q, Chen P, Addy M, Zhang R, Deng X, Ma Y, Cheng Y, Hussain F, Chen C, Liu Y, Ruan R. Carbon-dependent alleviation of ammonia toxicity for algae cultivation and associated mechanisms exploration. BIORESOURCE TECHNOLOGY 2018; 249:99-107. [PMID: 29040866 DOI: 10.1016/j.biortech.2017.09.175] [Citation(s) in RCA: 61] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/01/2017] [Revised: 09/24/2017] [Accepted: 09/25/2017] [Indexed: 06/07/2023]
Abstract
Ammonia toxicity in wastewater is one of the factors that limit the application of algae technology in wastewater treatment. This work explored the correlation between carbon sources and ammonia assimilation and applied a glucose-assisted nitrogen starvation method to alleviate ammonia toxicity. In this study, ammonia toxicity to Chlorella sp. was observed when NH3-N concentration reached 28.03mM in artificial wastewater. Addition of alpha-ketoglutarate in wastewater promoted ammonia assimilation, but low utilization efficiency and high cost of alpha-ketoglutarate limits its application in wastewater treatment. Comparison of three common carbon sources, glucose, citric acid, and sodium bicarbonate, indicates that in terms of ammonia assimilation, glucose is the best carbon source. Experimental results suggest that organic carbon with good ability of generating energy and hydride donor may be critical to ammonia assimilation. Nitrogen starvation treatment assisted by glucose increased ammonia removal efficiencies and algal viabilities.
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Affiliation(s)
- Qian Lu
- Center for Biorefining, and Department of Bioproducts and Biosystems Engineering, University of Minnesota, Saint Paul, MN 55108, USA
| | - Paul Chen
- Center for Biorefining, and Department of Bioproducts and Biosystems Engineering, University of Minnesota, Saint Paul, MN 55108, USA
| | - Min Addy
- Center for Biorefining, and Department of Bioproducts and Biosystems Engineering, University of Minnesota, Saint Paul, MN 55108, USA
| | - Renchuan Zhang
- Center for Biorefining, and Department of Bioproducts and Biosystems Engineering, University of Minnesota, Saint Paul, MN 55108, USA
| | - Xiangyuan Deng
- Center for Biorefining, and Department of Bioproducts and Biosystems Engineering, University of Minnesota, Saint Paul, MN 55108, USA
| | - Yiwei Ma
- Department of Food Science and Nutrition, University of Minnesota, Saint Paul, MN 55108, USA
| | - Yanling Cheng
- Center for Biorefining, and Department of Bioproducts and Biosystems Engineering, University of Minnesota, Saint Paul, MN 55108, USA
| | - Fida Hussain
- Faculty of Science and Technology, Qurtuba University of Science and Technology, Peshawar, KP, Pakistan
| | - Chi Chen
- Department of Food Science and Nutrition, University of Minnesota, Saint Paul, MN 55108, USA
| | - Yuhuan Liu
- MOE Biomass Energy Research Center and State Key Laboratory of Food Science, Nanchang University, Nanchang 330000, China
| | - Roger Ruan
- Center for Biorefining, and Department of Bioproducts and Biosystems Engineering, University of Minnesota, Saint Paul, MN 55108, USA; Department of Food Science and Nutrition, University of Minnesota, Saint Paul, MN 55108, USA; MOE Biomass Energy Research Center and State Key Laboratory of Food Science, Nanchang University, Nanchang 330000, China.
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18
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Luo Z, Liu S, Du G, Xu S, Zhou J, Chen J. Enhanced pyruvate production in Candida glabrata
by carrier engineering. Biotechnol Bioeng 2017; 115:473-482. [DOI: 10.1002/bit.26477] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2017] [Revised: 10/09/2017] [Accepted: 10/11/2017] [Indexed: 12/25/2022]
Affiliation(s)
- Zhengshan Luo
- Key Laboratory of Industrial Biotechnology; Ministry of Education, School of Biotechnology; Jiangnan University; Wuxi Jiangsu China
| | - Song Liu
- Key Laboratory of Industrial Biotechnology; Ministry of Education, School of Biotechnology; Jiangnan University; Wuxi Jiangsu China
| | - Guocheng Du
- Key Laboratory of Industrial Biotechnology; Ministry of Education, School of Biotechnology; Jiangnan University; Wuxi Jiangsu China
- The Key Laboratory of Carbohydrate Chemistry and Biotechnology, Ministry of Education; Jiangnan University; Wuxi Jiangsu China
| | - Sha Xu
- Key Laboratory of Industrial Biotechnology; Ministry of Education, School of Biotechnology; Jiangnan University; Wuxi Jiangsu China
- The Key Laboratory of Carbohydrate Chemistry and Biotechnology, Ministry of Education; Jiangnan University; Wuxi Jiangsu China
| | - Jingwen Zhou
- Key Laboratory of Industrial Biotechnology; Ministry of Education, School of Biotechnology; Jiangnan University; Wuxi Jiangsu China
| | - Jian Chen
- Key Laboratory of Industrial Biotechnology; Ministry of Education, School of Biotechnology; Jiangnan University; Wuxi Jiangsu China
- National Engineering Laboratory for Cereal Fermentation Technology; Jiangnan University; Wuxi Jiangsu China
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19
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Lu Q, Li J, Wang J, Li K, Li J, Han P, Chen P, Zhou W. Exploration of a mechanism for the production of highly unsaturated fatty acids in Scenedesmus sp. at low temperature grown on oil crop residue based medium. BIORESOURCE TECHNOLOGY 2017; 244:542-551. [PMID: 28803104 DOI: 10.1016/j.biortech.2017.08.005] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/04/2017] [Revised: 08/01/2017] [Accepted: 08/02/2017] [Indexed: 06/07/2023]
Abstract
The ability of algae to produce lipids comprising of unsaturated fatty acids varies with strains and culture conditions. This study investigates the effect of temperature on the production of unsaturated fatty acids in Scenedesmus sp. grown on oil crop residue based medium. At low temperature (10°C), synthesis of lipids compromising of high contents of unsaturated fatty acids took place primarily in the early stage while protein accumulation mainly occurred in the late stage. This stepwise lipid-protein synthesis process was found to be associated with the contents of acetyl-CoA and α-KG in the algal cells. A mechanism was proposed and tested through simulation experiments which quantified the carbon flux allocation in algal cells at different cultivation stages. It is concluded that low culture temperature such as 10°C is suitable for the production of lipids comprising of unsaturated fatty acids.
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Affiliation(s)
- Qian Lu
- School of Resources, Environmental & Chemical Engineering and Key Laboratory of Poyang Lake Environment and Resource Utilization, Nanchang University, Nanchang, China
| | - Jun Li
- School of Resources, Environmental & Chemical Engineering and Key Laboratory of Poyang Lake Environment and Resource Utilization, Nanchang University, Nanchang, China
| | - Jinghan Wang
- Environmental Simulation and Pollution Control State Key Joint Laboratory, State Environmental Protection Key Laboratory of Microorganism Application and Risk Control (SMARC), School of Environment, Tsinghua University, Beijing, China
| | - Kun Li
- School of Resources, Environmental & Chemical Engineering and Key Laboratory of Poyang Lake Environment and Resource Utilization, Nanchang University, Nanchang, China
| | - Jingjing Li
- School of Resources, Environmental & Chemical Engineering and Key Laboratory of Poyang Lake Environment and Resource Utilization, Nanchang University, Nanchang, China
| | - Pei Han
- School of Resources, Environmental & Chemical Engineering and Key Laboratory of Poyang Lake Environment and Resource Utilization, Nanchang University, Nanchang, China
| | - Paul Chen
- Center for Biorefining, Bioproducts and Biosystems Engineering Department, University of Minnesota, Saint Paul, United States
| | - Wenguang Zhou
- School of Resources, Environmental & Chemical Engineering and Key Laboratory of Poyang Lake Environment and Resource Utilization, Nanchang University, Nanchang, China.
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20
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Rational modular design of metabolic network for efficient production of plant polyphenol pinosylvin. Sci Rep 2017; 7:1459. [PMID: 28469159 PMCID: PMC5431097 DOI: 10.1038/s41598-017-01700-9] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2016] [Accepted: 03/29/2017] [Indexed: 11/08/2022] Open
Abstract
Efficient biosynthesis of the plant polyphenol pinosylvin, which has numerous applications in nutraceuticals and pharmaceuticals, is necessary to make biological production economically viable. To this end, an efficient Escherichia coli platform for pinosylvin production was developed via a rational modular design approach. Initially, different candidate pathway enzymes were screened to construct de novo pinosylvin pathway directly from D-glucose. A comparative analysis of pathway intermediate pools identified that this initial construct led to the intermediate cinnamic acid accumulation. The pinosylvin synthetic pathway was then divided into two new modules separated at cinnamic acid. Combinatorial optimization of transcriptional and translational levels of these two modules resulted in a 16-fold increase in pinosylvin titer. To further improve the concentration of the limiting precursor malonyl-CoA, the malonyl-CoA synthesis module based on clustered regularly interspaced short palindromic repeats interference was assembled and optimized with other two modules. The final pinosylvin titer was improved to 281 mg/L, which was the highest pinosylvin titer even directly from D-glucose without any additional precursor supplementation. The rational modular design approach described here could bolster our capabilities in synthetic biology for value-added chemical production.
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21
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Wu J, Zhang X, Xia X, Dong M. A systematic optimization of medium chain fatty acid biosynthesis via the reverse beta-oxidation cycle in Escherichia coli. Metab Eng 2017; 41:115-124. [PMID: 28392294 DOI: 10.1016/j.ymben.2017.03.012] [Citation(s) in RCA: 53] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2016] [Revised: 02/15/2017] [Accepted: 03/30/2017] [Indexed: 12/24/2022]
Abstract
Medium-chain fatty acids (MCFAs, 6-10 carbons) are valuable precursors to many industrial biofuels and chemicals, recently engineered reversal of the β-oxidation (r-BOX) cycle has been proposed as a potential platform for efficient synthesis of MCFAs. Previous studies have made many exciting achievements on functionally characterizing four core enzymes of this r-BOX cycle. However, the information about bottleneck nodes in this cycle is elusive. Here, a quantitative assessment of the inherent limitations of this cycle was conducted to capitalize on its potential. The selection of the core β-oxidation reversal enzymes in conjunction with acetyl-CoA synthetase endowed the ability to synthesize about 1g/L MCFAs. Furthermore, a gene dosage experiment was developed to identify two rate-limiting enzymes (acetyl-CoA synthetase and thiolase). The de novo pathway was then separated into two modules at thiolase and MCFA production titer increased to 2.8g/L after evaluating different construct environments. Additionally, the metabolism of host organism was reprogrammed to the desired biochemical product by the clustered regularly interspaced short palindromic repeats interference system, resulted in a final MCFA production of 3.8g/L. These findings described here identified the inherent limitations of r-BOX cycle and further unleashed the lipogenic potential of this cycle, thus paving the way for the development of a bacterial platform for microbial production of high-value oleo-chemicals from low-value carbons in a sustainable and environmentally friendly manner.
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Affiliation(s)
- Junjun Wu
- College of Food Science and Technology, Nanjing Agricultural University, 1 Weigang Road, Nanjing, Jiangsu 210095, China
| | - Xia Zhang
- College of Food Science and Technology, Nanjing Agricultural University, 1 Weigang Road, Nanjing, Jiangsu 210095, China
| | - Xiudong Xia
- Institute of Agro-Product Processing, Jiangsu Academy of Agricultural Sciences, Nanjing, Jiangsu 210095, China
| | - Mingsheng Dong
- College of Food Science and Technology, Nanjing Agricultural University, 1 Weigang Road, Nanjing, Jiangsu 210095, China.
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22
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Xu N, Ye C, Chen X, Liu J, Liu L. Genome-scale metabolic modelling common cofactors metabolism in microorganisms. J Biotechnol 2017; 251:1-13. [PMID: 28385592 DOI: 10.1016/j.jbiotec.2017.04.004] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2017] [Revised: 04/02/2017] [Accepted: 04/03/2017] [Indexed: 12/20/2022]
Abstract
The common cofactors ATP/ADP, NAD(P)(H), and acetyl-CoA/CoA are indispensable participants in biochemical reactions in industrial microbes. To systematically explore the effects of these cofactors on cell growth and metabolic phenotypes, the first genome-scale cofactor metabolic model, icmNX6434, including 6434 genes, 1782 metabolites, and 6877 reactions, was constructed from 14 genome-scale metabolic models of 14 industrial strains. The origin, consumption, and interactions of these common cofactors in microbial cells were elucidated by the icmNX6434 model, and they played important roles in cell growth. The essential cofactor modules contained 2480 genes and 2948 reactions; therefore, improving cofactor biosynthesis, directing these cofactors into essential metabolic pathways, as well as avoiding cofactor utilization during byproduct biosynthesis and futile cycles, are three ways to increase cell growth. The effects of these common cofactors on the distribution and rate of the carbon flux in four universal modes, as well as an optimized metabolic flux, could be obtained by manipulating cofactor availability and balance. Significant changes in the ATP, NAD(H), NADP(H), or acetyl-CoA concentrations triggered relevant metabolic responses to acidic, oxidative, heat, and osmotic stress. Globally, the model icmNX6434 provides a comprehensive platform to elucidate the physiological effects of these cofactors on cell growth, metabolic flux, and industrial robustness. Moreover, the results of this study are a further example of using a consensus genome-scale metabolic model to increase our understanding of key biological processes.
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Affiliation(s)
- Nan Xu
- State Key Laboratory of Food Science and Technology, Jiangnan University, 1800 Lihu Road, Wuxi, Jiangsu 214122, China; College of Bioscience and Biotechnology, Yangzhou University, Yangzhou, Jiangsu 225009, China; The Laboratory of Food Microbial-Manufacturing Engineering, Jiangnan University, Wuxi 214122, China
| | - Chao Ye
- State Key Laboratory of Food Science and 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; The Laboratory of Food Microbial-Manufacturing Engineering, Jiangnan University, Wuxi 214122, China
| | - Xiulai Chen
- State Key Laboratory of Food Science and 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; The Laboratory of Food Microbial-Manufacturing Engineering, Jiangnan University, Wuxi 214122, China
| | - Jia Liu
- State Key Laboratory of Food Science and 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; The Laboratory of Food Microbial-Manufacturing Engineering, Jiangnan University, Wuxi 214122, China
| | - Liming Liu
- State Key Laboratory of Food Science and 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; The Laboratory of Food Microbial-Manufacturing Engineering, Jiangnan University, Wuxi 214122, China.
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23
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Wu J, Zhou P, Zhang X, Dong M. Efficient de novo synthesis of resveratrol by metabolically engineered Escherichia coli. J Ind Microbiol Biotechnol 2017; 44:1083-1095. [PMID: 28324236 DOI: 10.1007/s10295-017-1937-9] [Citation(s) in RCA: 48] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2017] [Accepted: 03/12/2017] [Indexed: 12/18/2022]
Abstract
Resveratrol has been the subject of numerous scientific investigations due to its health-promoting activities against a variety of diseases. However, developing feasible and efficient microbial processes remains challenging owing to the requirement of supplementing expensive phenylpropanoic precursors. Here, various metabolic engineering strategies were developed for efficient de novo biosynthesis of resveratrol. A recombinant malonate assimilation pathway from Rhizobium trifolii was introduced to increase the supply of the key precursor malonyl-CoA and simultaneously, the clustered regularly interspaced short palindromic repeats interference system was explored to down-regulate fatty acid biosynthesis pathway to inactivate the malonyl-CoA consumption pathway. Down-regulation of fabD, fabH, fabB, fabF, fabI increased resveratrol production by 80.2, 195.6, 170.3, 216.5 and 123.7%, respectively. Furthermore, the combined effect of these genetic perturbations was investigated, which increased the resveratrol titer to 188.1 mg/L. Moreover, the efficiency of this synthetic pathway was improved by optimizing the expression level of the rate-limiting enzyme TAL based on reducing mRNA structure of 5' region. This further increased the final resveratrol titer to 304.5 mg/L. The study described here paves the way to the development of a simple and economical process for microbial production of resveratrol.
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Affiliation(s)
- Junjun Wu
- College of Food Science and Technology, Nanjing Agricultural University, 1 Weigang Road, Nanjing, Jiangsu, People's Republic of China.,Institute of Agro-Product Processing, Jiangsu Academy of Agricultural Sciences, Nanjing, 210095, Jiangsu, People's Republic of China
| | - Peng Zhou
- College of Food Science and Technology, Nanjing Agricultural University, 1 Weigang Road, Nanjing, Jiangsu, People's Republic of China.,Institute of Agro-Product Processing, Jiangsu Academy of Agricultural Sciences, Nanjing, 210095, Jiangsu, People's Republic of China
| | - Xia Zhang
- College of Food Science and Technology, Nanjing Agricultural University, 1 Weigang Road, Nanjing, Jiangsu, People's Republic of China.,Institute of Agro-Product Processing, Jiangsu Academy of Agricultural Sciences, Nanjing, 210095, Jiangsu, People's Republic of China
| | - Mingsheng Dong
- College of Food Science and Technology, Nanjing Agricultural University, 1 Weigang Road, Nanjing, Jiangsu, People's Republic of China. .,Institute of Agro-Product Processing, Jiangsu Academy of Agricultural Sciences, Nanjing, 210095, Jiangsu, People's Republic of China.
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24
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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: 6.0] [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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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: 1.8] [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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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: 1.4] [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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Wu J, Zhang X, Zhou J, Dong M. Efficient biosynthesis of (2S)-pinocembrin from d-glucose by integrating engineering central metabolic pathways with a pH-shift control strategy. BIORESOURCE TECHNOLOGY 2016; 218:999-1007. [PMID: 27450982 DOI: 10.1016/j.biortech.2016.07.066] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/18/2016] [Revised: 07/14/2016] [Accepted: 07/15/2016] [Indexed: 05/06/2023]
Abstract
Microbial fermentations promise to revolutionize the conventional extraction of (2S)-pinocembrin from natural plant sources. Previously an Escherichia coli fermentation system was developed for one-step (2S)-pinocembrin production. However, this fermentation platform need supplementation of expensive malonyl-CoA precursor malonate and requires morpholinopropane sulfonate to provide buffering capacity. Here, a clustered regularly interspaced short palindromic repeats interference was constructed to efficiently channel carbon flux toward malonyl-CoA. By exploring the effects of different culture pH on microbial fermentation, it was found that high pH values favored upstream pathway catalysis, while low pH values favored downstream pathway catalysis. Based on this theory, a two-stage pH control strategy was proposed. The pH was controlled at 7.0 during 0-10h, and was shifted to 6.5 after 10h. Finally, the (2S)-pinocembrin titers increased to 525.8mg/L. These results were attained in minimal medium without additional precursor supplementation, thus offering opportunities for industrial scale low-cost production of flavonoids.
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Affiliation(s)
- Junjun Wu
- College of Food Science and Technology, Nanjing Agricultural University, Nanjing, Jiangsu 210095, China; Institute of Agro-Product Processing, Jiangsu Academy of Agricultural Sciences, Nanjing, Jiangsu 210095, China
| | - Xia Zhang
- College of Food Science and Technology, Nanjing Agricultural University, Nanjing, Jiangsu 210095, China; Institute of Agro-Product Processing, Jiangsu Academy of Agricultural Sciences, Nanjing, Jiangsu 210095, China
| | - Jingwen Zhou
- Key Laboratory of Industrial Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, 1800 Lihu Road, Wuxi, Jiangsu 214122, China
| | - Mingsheng Dong
- College of Food Science and Technology, Nanjing Agricultural University, Nanjing, Jiangsu 210095, China; Institute of Agro-Product Processing, Jiangsu Academy of Agricultural Sciences, Nanjing, Jiangsu 210095, 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: 0.8] [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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Stepwise modular pathway engineering of Escherichia coli for efficient one-step production of (2S)-pinocembrin. J Biotechnol 2016; 231:183-192. [DOI: 10.1016/j.jbiotec.2016.06.007] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2016] [Revised: 05/26/2016] [Accepted: 06/09/2016] [Indexed: 12/17/2022]
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30
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Biosynthesis of pyruvic acid from glucose by Blastobotrys adeninivorans. Appl Microbiol Biotechnol 2016; 100:7689-97. [DOI: 10.1007/s00253-016-7618-1] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2016] [Revised: 04/27/2016] [Accepted: 05/05/2016] [Indexed: 10/21/2022]
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31
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Liu L, Guan N, Li J, Shin HD, Du G, Chen J. Development of GRAS strains for nutraceutical production using systems and synthetic biology approaches: advances and prospects. Crit Rev Biotechnol 2015; 37:139-150. [PMID: 26699901 DOI: 10.3109/07388551.2015.1121461] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Nutraceuticals are food substances with medical and health benefits for humans. Limited by complicated procedures, high cost, low yield, insufficient raw materials, resource waste, and environment pollution, chemical synthesis and extraction are being replaced by microbial synthesis of nutraceuticals. Many microbial strains that are generally regarded as safe (GRAS) have been identified and developed for the synthesis of nutraceuticals, and significant nutraceutical production by these strains has been achieved. In this review, we systematically summarize recent advances in nutraceutical research in terms of physiological effects on health, potential applications, drawbacks of traditional production processes, characteristics of production strains, and progress in microbial fermentation. Recent advances in systems and synthetic biology techniques have enabled comprehensive understanding of GRAS strains and its wider applications. Thus, these microbial strains are promising cell factories for the commercial production of nutraceuticals.
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Affiliation(s)
- Long Liu
- a Key Laboratory of Carbohydrate Chemistry and Biotechnology and.,b Key Laboratory of Industrial Biotechnology, Ministry of Education, Jiangnan University , Wuxi , China.,c Synergetic Innovation of Center of Food Safety and Nutrition, Jiangnan University , Wuxi , China , and
| | - Ningzi Guan
- a Key Laboratory of Carbohydrate Chemistry and Biotechnology and.,c Synergetic Innovation of Center of Food Safety and Nutrition, Jiangnan University , Wuxi , China , and
| | - Jianghua Li
- a Key Laboratory of Carbohydrate Chemistry and Biotechnology and.,b Key Laboratory of Industrial Biotechnology, Ministry of Education, Jiangnan University , Wuxi , China
| | - Hyun-Dong Shin
- d School of Chemical and Biomolecular Engineering, Georgia Institute of Technology , Atlanta , GA , USA
| | - Guocheng Du
- a Key Laboratory of Carbohydrate Chemistry and Biotechnology and.,b Key Laboratory of Industrial Biotechnology, Ministry of Education, Jiangnan University , Wuxi , China.,c Synergetic Innovation of Center of Food Safety and Nutrition, Jiangnan University , Wuxi , China , and
| | - Jian Chen
- a Key Laboratory of Carbohydrate Chemistry and Biotechnology and.,b Key Laboratory of Industrial Biotechnology, Ministry of Education, Jiangnan University , Wuxi , China.,c Synergetic Innovation of Center of Food Safety and Nutrition, Jiangnan University , Wuxi , China , and
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Shi S, Ji H, Siewers V, Nielsen J. Improved production of fatty acids bySaccharomyces cerevisiaethrough screening a cDNA library from the oleaginous yeastYarrowia lipolytica. FEMS Yeast Res 2015; 16:fov108. [DOI: 10.1093/femsyr/fov108] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 12/09/2015] [Indexed: 12/19/2022] Open
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33
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Liu HH, Ji XJ, Huang H. Biotechnological applications of Yarrowia lipolytica: Past, present and future. Biotechnol Adv 2015; 33:1522-46. [DOI: 10.1016/j.biotechadv.2015.07.010] [Citation(s) in RCA: 128] [Impact Index Per Article: 12.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2014] [Revised: 07/13/2015] [Accepted: 07/29/2015] [Indexed: 01/01/2023]
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34
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Yin X, Li J, Shin HD, Du G, Liu L, Chen J. Metabolic engineering in the biotechnological production of organic acids in the tricarboxylic acid cycle of microorganisms: Advances and prospects. Biotechnol Adv 2015; 33:830-41. [DOI: 10.1016/j.biotechadv.2015.04.006] [Citation(s) in RCA: 103] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2015] [Revised: 04/08/2015] [Accepted: 04/11/2015] [Indexed: 01/15/2023]
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35
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A high-throughput screening procedure for enhancing α-ketoglutaric acid production in Yarrowia lipolytica by random mutagenesis. Process Biochem 2015. [DOI: 10.1016/j.procbio.2015.06.011] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
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36
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Guo H, Madzak C, Du G, Zhou J. Mutagenesis of conserved active site residues of dihydrolipoamide succinyltransferase enhances the accumulation of α-ketoglutarate in Yarrowia lipolytica. Appl Microbiol Biotechnol 2015; 100:649-59. [PMID: 26428234 DOI: 10.1007/s00253-015-6995-1] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/06/2015] [Revised: 08/30/2015] [Accepted: 09/08/2015] [Indexed: 11/30/2022]
Abstract
α-Ketoglutarate (α-KG) is an important intermediate in the tricarboxylic acid cycle and has broad applications. The mitochondrial ketoglutarate dehydrogenase (KGDH) complex catalyzes the oxidation of α-KG to succinyl-CoA. Disruption of KGDH, which may enhance the accumulation of α-KG theoretically, was found to be lethal to obligate aerobic cells. In this study, individual overexpression of dihydrolipoamide succinyltransferase (DLST), which serves as the inner core of KGDH, decreased overall activity of the enzyme complex. Furthermore, two conserved active site residues of DLST, His419, and Asp423 were identified. In order to determine whether these residues are engaged in enzyme reaction or not, these two conserved residues were individually mutated. Analysis of the kinetic parameters of the enzyme variants provided evidence that the catalytic reaction of DLST depended on residues His419 and Asp423. Overexpression of mutated DLST not only impaired balanced assembly of KGDH, but also disrupted the catalytic integrity of the enzyme complex. Replacement of the Asp423 residue by glutamate increased extracellular α-KG by 40 % to 50 g L(-1) in mutant strain. These observations uncovered catalytic roles of two conserved active site residues of DLST and provided clues for effective metabolic strategies for rational carbon flux control for the enhanced production of α-KG and related bioproducts.
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Affiliation(s)
- Hongwei Guo
- School of Biotechnology and Key Laboratory of Industrial Biotechnology, Ministry of Education, Jiangnan University, 1800 Lihu Road, Wuxi, 214122, Jiangsu, China.,Synergetic Innovation Center of Food Safety and Nutrition, 1800 Lihu Road, Wuxi, 214122, Jiangsu, China
| | - Catherine Madzak
- UMR1238 Microbiologie et Génétique Moléculaire, INRA/CNRS/AgroPan's Tech, CBAI, BP 01, 78850, Thiverval-Grignon, France
| | - Guocheng Du
- School of Biotechnology and Key Laboratory of Industrial Biotechnology, Ministry of Education, Jiangnan University, 1800 Lihu Road, Wuxi, 214122, Jiangsu, China.,Synergetic Innovation Center of Food Safety and Nutrition, 1800 Lihu Road, Wuxi, 214122, Jiangsu, China
| | - Jingwen Zhou
- School of Biotechnology and Key Laboratory of Industrial Biotechnology, Ministry of Education, Jiangnan University, 1800 Lihu Road, Wuxi, 214122, Jiangsu, China. .,Synergetic Innovation Center of Food Safety and Nutrition, 1800 Lihu Road, Wuxi, 214122, Jiangsu, China.
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Yarrowia lipolytica: recent achievements in heterologous protein expression and pathway engineering. Appl Microbiol Biotechnol 2015; 99:4559-77. [PMID: 25947247 DOI: 10.1007/s00253-015-6624-z] [Citation(s) in RCA: 153] [Impact Index Per Article: 15.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2015] [Revised: 04/17/2015] [Accepted: 04/18/2015] [Indexed: 12/13/2022]
Abstract
The oleaginous yeast Yarrowia lipolytica has become a recognized system for expression/secretion of heterologous proteins. This non-conventional yeast is currently being developed as a workhorse for biotechnology by several research groups throughout the world, especially for single-cell oil production, whole cell bioconversion and upgrading of industrial wastes. This mini-review presents established tools for protein expression in Y. lipolytica and highlights novel developments in the areas of promoter design, surface display, and host strain or metabolic pathway engineering. An overview of the industrial and commercial biotechnological applications of Y. lipolytica is also presented.
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Guo H, Liu P, Madzak C, Du G, Zhou J, Chen J. Identification and application of keto acids transporters in Yarrowia lipolytica. Sci Rep 2015; 5:8138. [PMID: 25633653 PMCID: PMC4311248 DOI: 10.1038/srep08138] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2014] [Accepted: 01/08/2015] [Indexed: 01/18/2023] Open
Abstract
Production of organic acids by microorganisms is of great importance for obtaining building-block chemicals from sustainable biomass. Extracellular accumulation of organic acids involved a series of transporters, which play important roles in the accumulation of specific organic acid while lack of systematic demonstration in eukaryotic microorganisms. To circumvent accumulation of by-product, efforts have being orchestrated to carboxylate transport mechanism for potential clue in Yarrowia lipolytica WSH-Z06. Six endogenous putative transporter genes, YALI0B19470g, YALI0C15488g, YALI0C21406g, YALI0D24607g, YALI0D20108g and YALI0E32901g, were identified. Transport characteristics and substrate specificities were further investigated using a carboxylate-transport-deficient Saccharomyces cerevisiae strain. These transporters were expressed in Y. lipolytica WSH-Z06 to assess their roles in regulating extracellular keto acids accumulation. In a Y. lipolytica T1 line over expressing YALI0B19470g, α-ketoglutarate accumulated to 46.7 g·L−1, whereas the concentration of pyruvate decreased to 12.3 g·L−1. Systematic identification of these keto acids transporters would provide clues to further improve the accumulation of specific organic acids with higher efficiency in eukaryotic microorganisms.
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Affiliation(s)
- Hongwei Guo
- 1] School of Biotechnology and Key Laboratory of Industrial Biotechnology, Ministry of Education, Jiangnan University, 1800 Lihu Road, Wuxi, Jiangsu 214122, China [2] Synergetic Innovation Center of Food Safety and Nutrition, 1800 Lihu Road, Wuxi, Jiangsu 214122, China
| | - Peiran Liu
- School of Biotechnology and Key Laboratory of Industrial Biotechnology, Ministry of Education, Jiangnan University, 1800 Lihu Road, Wuxi, Jiangsu 214122, China
| | - Catherine Madzak
- UMR1238 Microbiologie et Génétique Moléculaire, INRA/CNRS/AgroPan's Tech, CBAI, BP 01, 78850 Thiverval-Grignon, France
| | - Guocheng Du
- 1] School of Biotechnology and Key Laboratory of Industrial Biotechnology, Ministry of Education, Jiangnan University, 1800 Lihu Road, Wuxi, Jiangsu 214122, China [2] Synergetic Innovation Center of Food Safety and Nutrition, 1800 Lihu Road, Wuxi, Jiangsu 214122, China
| | - Jingwen Zhou
- 1] School of Biotechnology and Key Laboratory of Industrial Biotechnology, Ministry of Education, Jiangnan University, 1800 Lihu Road, Wuxi, Jiangsu 214122, China [2] Synergetic Innovation Center of Food Safety and Nutrition, 1800 Lihu Road, Wuxi, Jiangsu 214122, China
| | - Jian Chen
- 1] School of Biotechnology and Key Laboratory of Industrial Biotechnology, Ministry of Education, Jiangnan University, 1800 Lihu Road, Wuxi, Jiangsu 214122, China [2] Synergetic Innovation Center of Food Safety and Nutrition, 1800 Lihu Road, Wuxi, Jiangsu 214122, China
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