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Wang LH, Qu WH, Xu YN, Xia SG, Xue QQ, Jiang XM, Liu HY, Xue CH, Wen YQ. Developing a High-Umami, Low-Salt Soy Sauce through Accelerated Moromi Fermentation with Corynebacterium and Lactiplantibacillus Strains. Foods 2024; 13:1386. [PMID: 38731757 PMCID: PMC11083161 DOI: 10.3390/foods13091386] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2024] [Revised: 04/09/2024] [Accepted: 04/14/2024] [Indexed: 05/13/2024] Open
Abstract
The traditional fermentation process of soy sauce employs a hyperhaline model and has a long fermentation period. A hyperhaline model can improve fermentation speed, but easily leads to the contamination of miscellaneous bacteria and fermentation failure. In this study, after the conventional koji and moromi fermentation, the fermentation broth was pasteurized and diluted, and then inoculated with three selected microorganisms including Corynebacterium glutamicum, Corynebacterium ammoniagenes, and Lactiplantibacillus plantarum for secondary fermentation. During this ten-day fermentation, the pH, free amino acids, organic acids, nucleotide acids, fatty acids, and volatile compounds were analyzed. The fermentation group inoculated with C. glutamicum accumulated the high content of amino acid nitrogen of 0.92 g/100 mL and glutamic acid of 509.4 mg/100 mL. The C. ammoniagenes group and L. plantarum group were rich in nucleotide and organic acid, respectively. The fermentation group inoculated with three microorganisms exhibited the best sensory attributes, showing the potential to develop a suitable fermentation method. The brewing speed of the proposed process in this study was faster than that of the traditional method, and the umami substances could be significantly accumulated in this low-salt fermented model (7% w/v NaCl). This study provides a reference for the low-salt and rapid fermentation of seasoning.
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Affiliation(s)
- Li-Hao Wang
- College of Food Science and Engineering, Ocean University of China, 1299 Sansha Road, Qingdao 266400, China; (L.-H.W.); (W.-H.Q.); (Y.-N.X.); (S.-G.X.); (Q.-Q.X.); (X.-M.J.); (C.-H.X.)
| | - Wen-Hui Qu
- College of Food Science and Engineering, Ocean University of China, 1299 Sansha Road, Qingdao 266400, China; (L.-H.W.); (W.-H.Q.); (Y.-N.X.); (S.-G.X.); (Q.-Q.X.); (X.-M.J.); (C.-H.X.)
| | - Ya-Nan Xu
- College of Food Science and Engineering, Ocean University of China, 1299 Sansha Road, Qingdao 266400, China; (L.-H.W.); (W.-H.Q.); (Y.-N.X.); (S.-G.X.); (Q.-Q.X.); (X.-M.J.); (C.-H.X.)
| | - Song-Gang Xia
- College of Food Science and Engineering, Ocean University of China, 1299 Sansha Road, Qingdao 266400, China; (L.-H.W.); (W.-H.Q.); (Y.-N.X.); (S.-G.X.); (Q.-Q.X.); (X.-M.J.); (C.-H.X.)
| | - Qian-Qian Xue
- College of Food Science and Engineering, Ocean University of China, 1299 Sansha Road, Qingdao 266400, China; (L.-H.W.); (W.-H.Q.); (Y.-N.X.); (S.-G.X.); (Q.-Q.X.); (X.-M.J.); (C.-H.X.)
| | - Xiao-Ming Jiang
- College of Food Science and Engineering, Ocean University of China, 1299 Sansha Road, Qingdao 266400, China; (L.-H.W.); (W.-H.Q.); (Y.-N.X.); (S.-G.X.); (Q.-Q.X.); (X.-M.J.); (C.-H.X.)
- Qingdao Institute of Marine Bioresources for Nutrition & Health Innovation, Qingdao 266109, China
| | - Hong-Ying Liu
- Ocean College, Hebei Agriculture University, Qinhuangdao 066000, China;
| | - Chang-Hu Xue
- College of Food Science and Engineering, Ocean University of China, 1299 Sansha Road, Qingdao 266400, China; (L.-H.W.); (W.-H.Q.); (Y.-N.X.); (S.-G.X.); (Q.-Q.X.); (X.-M.J.); (C.-H.X.)
- Qingdao Institute of Marine Bioresources for Nutrition & Health Innovation, Qingdao 266109, China
| | - Yun-Qi Wen
- College of Food Science and Engineering, Ocean University of China, 1299 Sansha Road, Qingdao 266400, China; (L.-H.W.); (W.-H.Q.); (Y.-N.X.); (S.-G.X.); (Q.-Q.X.); (X.-M.J.); (C.-H.X.)
- Qingdao Institute of Marine Bioresources for Nutrition & Health Innovation, Qingdao 266109, China
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Kou M, Cui Z, Fu J, Dai W, Wang Z, Chen T. Metabolic engineering of Corynebacterium glutamicum for efficient production of optically pure (2R,3R)-2,3-butanediol. Microb Cell Fact 2022; 21:150. [PMID: 35879766 PMCID: PMC9310479 DOI: 10.1186/s12934-022-01875-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2022] [Accepted: 07/07/2022] [Indexed: 11/24/2022] Open
Abstract
Background 2,3-butanediol is an important platform compound which has a wide range of applications, involving in medicine, chemical industry, food and other fields. Especially the optically pure (2R,3R)-2,3-butanediol can be employed as an antifreeze agent and as the precursor for producing chiral compounds. However, some (2R,3R)-2,3-butanediol overproducing strains are pathogenic such as Enterobacter cloacae and Klebsiella oxytoca. Results In this study, a (3R)-acetoin overproducing C. glutamicum strain, CGS9, was engineered to produce optically pure (2R,3R)-2,3-butanediol efficiently. Firstly, the gene bdhA from B. subtilis 168 was integrated into strain CGS9 and its expression level was further enhanced by using a strong promoter Psod and ribosome binding site (RBS) with high translation initiation rate, and the (2R,3R)-2,3-butanediol titer of the resulting strain was increased by 33.9%. Then the transhydrogenase gene udhA from E. coli was expressed to provide more NADH for 2,3-butanediol synthesis, which reduced the accumulation of the main byproduct acetoin by 57.2%. Next, a mutant atpG was integrated into strain CGK3, which increased the glucose consumption rate by 10.5% and the 2,3-butanediol productivity by 10.9% in shake-flask fermentation. Through fermentation engineering, the most promising strain CGK4 produced a titer of 144.9 g/L (2R,3R)-2,3-butanediol with a yield of 0.429 g/g glucose and a productivity of 1.10 g/L/h in fed-batch fermentation. The optical purity of the resulting (2R,3R)-2,3-butanediol surpassed 98%. Conclusions To the best of our knowledge, this is the highest titer of optically pure (2R,3R)-2,3-butanediol achieved by GRAS strains, and the result has demonstrated that C. glutamicum is a competitive candidate for (2R,3R)-2,3-butanediol production. Supplementary Information The online version contains supplementary material available at 10.1186/s12934-022-01875-5.
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Kataoka N, Matsutani M, Matsushita K, Yakushi T. Stepwise metabolic engineering of Corynebacterium glutamicum for the production of phenylalanine. J GEN APPL MICROBIOL 2022. [PMID: 35989300 DOI: 10.2323/jgam.2022.08.002] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/03/2022]
Abstract
Corynebacterium glutamicum was metabolically engineered to produce phenylalanine, a valuable aromatic amino acid that can be used as a raw material in the food and pharmaceutical industries. First, a starting phenylalanine-producer was constructed by overexpressing tryptophan-sensitive 3-deoxy-D-arabino-heptulosonate-7-phosphate synthase and phenylalanine- and tyrosine-insensitive bifunctional enzyme chorismate mutase prephenate dehydratase from Escherichia coli, followed by the inactivation of enzymes responsible for the formation of dihydroxyacetone and the consumption of shikimate pathway-related compounds. Second, redirection of the carbon flow from tyrosine to phenylalanine was attempted by deleting of the tyrA gene encoding prephenate dehydrogenase, which catalyzes the committed step for tyrosine biosynthesis from prephenate. However, suppressor mutants were generated, and two mutants were isolated and examined for phenylalanine production and genome sequencing. The suppressor mutant harboring an amino acid exchange (L180R) on RNase J, which was experimentally proven to lead to a loss of function of the enzyme, showed significantly enhanced production of phenylalanine. Finally, modifications of phosphoenolpyruvate-pyruvate metabolism were investigated, revealing that the inactivation of either phosphoenolpyruvate carboxylase or pyruvate carboxylase, which are enzymes of the anaplerotic pathway, is an effective means for improving phenylalanine production. The resultant strain, harboring a phosphoenolpyruvate carboxylase deficiency, synthesized 50.7 mM phenylalanine from 444 mM glucose. These results not only provided new insights into the practical mutations in constructing a phenylalanine-producing C. glutamicum but also demonstrated the creation of a potential strain for the biosynthesis of phenylalanine-derived compounds represented by plant secondary metabolites.
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Affiliation(s)
- Naoya Kataoka
- Division of Agricultural Sciences, Graduate School of Sciences and Technology for Innovation, Yamaguchi University.,Department of Biological Science, Faculty of Agriculture, Yamaguchi University.,Research Center for Thermotolerant Microbial Resources, Yamaguchi University
| | | | - Kazunobu Matsushita
- Division of Agricultural Sciences, Graduate School of Sciences and Technology for Innovation, Yamaguchi University.,Department of Biological Science, Faculty of Agriculture, Yamaguchi University.,Research Center for Thermotolerant Microbial Resources, Yamaguchi University
| | - Toshiharu Yakushi
- Division of Agricultural Sciences, Graduate School of Sciences and Technology for Innovation, Yamaguchi University.,Department of Biological Science, Faculty of Agriculture, Yamaguchi University.,Research Center for Thermotolerant Microbial Resources, Yamaguchi University
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Liu J, Liu M, Shi T, Sun G, Gao N, Zhao X, Guo X, Ni X, Yuan Q, Feng J, Liu Z, Guo Y, Chen J, Wang Y, Zheng P, Sun J. CRISPR-assisted rational flux-tuning and arrayed CRISPRi screening of an L-proline exporter for L-proline hyperproduction. Nat Commun 2022; 13:891. [PMID: 35173152 PMCID: PMC8850433 DOI: 10.1038/s41467-022-28501-7] [Citation(s) in RCA: 34] [Impact Index Per Article: 17.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2021] [Accepted: 01/24/2022] [Indexed: 02/07/2023] Open
Abstract
Development of hyperproducing strains is important for biomanufacturing of biochemicals and biofuels but requires extensive efforts to engineer cellular metabolism and discover functional components. Herein, we optimize and use the CRISPR-assisted editing and CRISPRi screening methods to convert a wild-type Corynebacterium glutamicum to a hyperproducer of L-proline, an amino acid with medicine, feed, and food applications. To facilitate L-proline production, feedback-deregulated variants of key biosynthetic enzyme γ-glutamyl kinase are screened using CRISPR-assisted single-stranded DNA recombineering. To increase the carbon flux towards L-proline biosynthesis, flux-control genes predicted by in silico analysis are fine-tuned using tailored promoter libraries. Finally, an arrayed CRISPRi library targeting all 397 transporters is constructed to discover an L-proline exporter Cgl2622. The final plasmid-, antibiotic-, and inducer-free strain produces L-proline at the level of 142.4 g/L, 2.90 g/L/h, and 0.31 g/g. The CRISPR-assisted strain development strategy can be used for engineering industrial-strength strains for efficient biomanufacturing.
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Affiliation(s)
- Jiao Liu
- Key Laboratory of Systems Microbial Biotechnology, Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin, 300308, China.,National Technology Innovation Center of Synthetic Biology, Tianjin, 300308, China
| | - Moshi Liu
- Key Laboratory of Systems Microbial Biotechnology, Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin, 300308, China.,National Technology Innovation Center of Synthetic Biology, Tianjin, 300308, China.,University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Tuo Shi
- Key Laboratory of Systems Microbial Biotechnology, Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin, 300308, China.,National Technology Innovation Center of Synthetic Biology, Tianjin, 300308, China
| | - Guannan Sun
- Key Laboratory of Systems Microbial Biotechnology, Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin, 300308, China.,National Technology Innovation Center of Synthetic Biology, Tianjin, 300308, China.,University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Ning Gao
- Key Laboratory of Systems Microbial Biotechnology, Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin, 300308, China.,National Technology Innovation Center of Synthetic Biology, Tianjin, 300308, China.,University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Xiaojia Zhao
- Key Laboratory of Systems Microbial Biotechnology, Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin, 300308, China.,National Technology Innovation Center of Synthetic Biology, Tianjin, 300308, China.,University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Xuan Guo
- Key Laboratory of Systems Microbial Biotechnology, Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin, 300308, China.,National Technology Innovation Center of Synthetic Biology, Tianjin, 300308, China
| | - Xiaomeng Ni
- Key Laboratory of Systems Microbial Biotechnology, Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin, 300308, China.,National Technology Innovation Center of Synthetic Biology, Tianjin, 300308, China
| | - Qianqian Yuan
- Key Laboratory of Systems Microbial Biotechnology, Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin, 300308, China.,National Technology Innovation Center of Synthetic Biology, Tianjin, 300308, China
| | - Jinhui Feng
- Key Laboratory of Systems Microbial Biotechnology, Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin, 300308, China.,National Technology Innovation Center of Synthetic Biology, Tianjin, 300308, China
| | - Zhemin Liu
- Key Laboratory of Systems Microbial Biotechnology, Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin, 300308, China.,National Technology Innovation Center of Synthetic Biology, Tianjin, 300308, China
| | - Yanmei Guo
- Key Laboratory of Systems Microbial Biotechnology, Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin, 300308, China.,National Technology Innovation Center of Synthetic Biology, Tianjin, 300308, China
| | - Jiuzhou Chen
- Key Laboratory of Systems Microbial Biotechnology, Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin, 300308, China.,National Technology Innovation Center of Synthetic Biology, Tianjin, 300308, China
| | - Yu Wang
- Key Laboratory of Systems Microbial Biotechnology, Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin, 300308, China. .,National Technology Innovation Center of Synthetic Biology, Tianjin, 300308, China. .,University of Chinese Academy of Sciences, Beijing, 100049, China.
| | - Ping Zheng
- Key Laboratory of Systems Microbial Biotechnology, Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin, 300308, China. .,National Technology Innovation Center of Synthetic Biology, Tianjin, 300308, China. .,University of Chinese Academy of Sciences, Beijing, 100049, China.
| | - Jibin Sun
- Key Laboratory of Systems Microbial Biotechnology, Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin, 300308, China.,National Technology Innovation Center of Synthetic Biology, Tianjin, 300308, China.,University of Chinese Academy of Sciences, Beijing, 100049, China
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Lin K, Han S, Zheng S. Application of Corynebacterium glutamicum engineering display system in three generations of biorefinery. Microb Cell Fact 2022; 21:14. [PMID: 35090458 PMCID: PMC8796525 DOI: 10.1186/s12934-022-01741-4] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2021] [Accepted: 01/09/2022] [Indexed: 11/29/2022] Open
Abstract
The fermentation production of platform chemicals in biorefineries is a sustainable alternative to the current petroleum refining process. The natural advantages of Corynebacterium glutamicum in carbon metabolism have led to C. glutamicum being used as a microbial cell factory that can use various biomass to produce value-added platform chemicals and polymers. In this review, we discussed the use of C. glutamicum surface display engineering bacteria in the three generations of biorefinery resources, and analyzed the C. glutamicum engineering display system in degradation, transport, and metabolic network reconstruction models. These engineering modifications show that the C. glutamicum engineering display system has great potential to become a cell refining factory based on sustainable biomass, and further optimizes the inherent properties of C. glutamicum as a whole-cell biocatalyst. This review will also provide a reference for the direction of future engineering transformation.
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Affiliation(s)
- Kerui Lin
- Guangdong Key Laboratory of Fermentation and Enzyme Engineering, School of Biology and Biological Engineering, South China University of Technology, Guangzhou, 510006, People's Republic of China.,Guangdong Research Center of Industrial Enzyme and Green Manufacturing Technology, School of Biology and Biological Engineering, South China University of Technology, Guangzhou, 510006, People's Republic of China
| | - Shuangyan Han
- Guangdong Key Laboratory of Fermentation and Enzyme Engineering, School of Biology and Biological Engineering, South China University of Technology, Guangzhou, 510006, People's Republic of China.,Guangdong Research Center of Industrial Enzyme and Green Manufacturing Technology, School of Biology and Biological Engineering, South China University of Technology, Guangzhou, 510006, People's Republic of China
| | - Suiping Zheng
- Guangdong Key Laboratory of Fermentation and Enzyme Engineering, School of Biology and Biological Engineering, South China University of Technology, Guangzhou, 510006, People's Republic of China. .,Guangdong Research Center of Industrial Enzyme and Green Manufacturing Technology, School of Biology and Biological Engineering, South China University of Technology, Guangzhou, 510006, People's Republic of China.
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Wang Y, Xu J, Jin Z, Xia X, Zhang W. Improvement of acetyl-CoA supply and glucose utilization increases l-leucine production in Corynebacterium glutamicum. Biotechnol J 2021; 17:e2100349. [PMID: 34870372 DOI: 10.1002/biot.202100349] [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: 07/05/2021] [Revised: 12/02/2021] [Accepted: 12/03/2021] [Indexed: 11/11/2022]
Abstract
BACKGROUND l-Leucine is one of important essential amino acids with multiple industrial applications, whose market requirements cannot be met because of the lower productivity. MAIN METHODS AND MAJOR RESULTS In this study, a strain of Corynebacterium glutamicum with high l-leucine yield was constructed to enhance its acetyl-CoA supply and glucose utilization. One copy of leuA under the control of a strong promoter was incorporated into the C. glutamicum genome. Then, acetyl-CoA supply was increased by the integration of a terminator in front of gltA and by the heterogeneous overexpression of acetyl-CoA synthetase (Acs) and deacetylase (CobB) derived from Escherichia coli. Next, the transcriptional regulator SugR was deleted to enhance glucose uptake via a phosphotransferase-mediated route. In fed-batch fermentation performed in a 5-L reactor, l-leucine production of 40.11±0.73 g/L was achieved under the optimized conditions, with the l-leucine yield and productivity of 0.25 g/g glucose and 0.59 g/L/h, respectively. CONCLUSIONS AND IMPLICATIONS These results represent a significant improvement in the l-leucine titer of C. glutamicum, indicating that the process possesses highly potential for industrial application. These strategies can be also expanded to enable the production of other value-added biochemicals derived from the intermediates of central carbon metabolism. This article is protected by copyright. All rights reserved.
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Affiliation(s)
- Yingyu Wang
- State Key Laboratory of Food Science and Technology, School of Food Science and Technology, Jiangnan University, WuXi, 214122, China.,The Key Laboratory of Industrial Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, WuXi, 214122, China
| | - Jianzhong Xu
- The Key Laboratory of Industrial Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, WuXi, 214122, China
| | - Zhengyu Jin
- State Key Laboratory of Food Science and Technology, School of Food Science and Technology, Jiangnan University, WuXi, 214122, China
| | - Xiaole Xia
- The Key Laboratory of Industrial Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, WuXi, 214122, China
| | - Weiguo Zhang
- The Key Laboratory of Industrial Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, WuXi, 214122, China
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Yang Y, Li L, Sun H, Li Z, Qi Z, Liu X. Improving CoQ 10 productivity by strengthening glucose transmembrane of Rhodobacter sphaeroides. Microb Cell Fact 2021; 20:207. [PMID: 34717624 PMCID: PMC8557541 DOI: 10.1186/s12934-021-01695-z] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2021] [Accepted: 10/18/2021] [Indexed: 02/01/2023] Open
Abstract
Background Several Rhodobacter sphaeroides have been widely applied in commercial CoQ10 production, but they have poor glucose use. Strategies for enhancing glucose use have been widely exploited in R. sphaeroides. Nevertheless, little research has focused on the role of glucose transmembrane in the improvement of production. Results There are two potential glucose transmembrane pathways in R. sphaeroides ATCC 17023: the fructose specific-phosphotransferase system (PTSFru, fruAB) and non-PTS that relied on glucokinase (glk). fruAB mutation revealed two effects on bacterial growth: inhibition at the early cultivation phase (12–24 h) and promotion since 36 h. Glucose metabolism showed a corresponding change in characteristic vs. the growth. For ΔfruAΔfruB, maximum biomass (Biomax) was increased by 44.39% and the CoQ10 content was 27.08% more than that of the WT. glk mutation caused a significant decrease in growth and glucose metabolism. Over-expressing a galactose:H+ symporter (galP) in the ΔfruAΔfruB relieved the inhibition and enhanced the growth further. Finally, a mutant with rapid growth and high CoQ10 titer was constructed (ΔfruAΔfruB/tac::galPOP) using several glucose metabolism modifications and was verified by fermentation in 1 L fermenters. Conclusions The PTSFru mutation revealed two effects on bacterial growth: inhibition at the early cultivation phase and promotion later. Additionally, biomass yield to glucose (Yb/glc) and CoQ10 synthesis can be promoted using fruAB mutation, and glk plays a key role in glucose metabolism. Strengthening glucose transmembrane via non-PTS improves the productivity of CoQ10 fermentation. Supplementary Information The online version contains supplementary material available at 10.1186/s12934-021-01695-z.
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Affiliation(s)
- Yuying Yang
- Key Laboratory of Shandong Microbial Engineering, College of Bioengineering, Qilu University of Technology (Shandong Academy of Sciences), Jinan, Shandong, People's Republic of China.,State Key Laboratory of Bio-Based Material and Green Papermaking (LBMP), Qilu University of Technology (Shandong Academy of Sciences), Jinan, Shandong, People's Republic of China
| | - Lu Li
- Key Laboratory of Shandong Microbial Engineering, College of Bioengineering, Qilu University of Technology (Shandong Academy of Sciences), Jinan, Shandong, People's Republic of China.,State Key Laboratory of Bio-Based Material and Green Papermaking (LBMP), Qilu University of Technology (Shandong Academy of Sciences), Jinan, Shandong, People's Republic of China
| | - Haoyu Sun
- Key Laboratory of Shandong Microbial Engineering, College of Bioengineering, Qilu University of Technology (Shandong Academy of Sciences), Jinan, Shandong, People's Republic of China.,State Key Laboratory of Bio-Based Material and Green Papermaking (LBMP), Qilu University of Technology (Shandong Academy of Sciences), Jinan, Shandong, People's Republic of China
| | - Zhen Li
- Key Laboratory of Shandong Microbial Engineering, College of Bioengineering, Qilu University of Technology (Shandong Academy of Sciences), Jinan, Shandong, People's Republic of China.,State Key Laboratory of Bio-Based Material and Green Papermaking (LBMP), Qilu University of Technology (Shandong Academy of Sciences), Jinan, Shandong, People's Republic of China
| | - Zhengliang Qi
- Key Laboratory of Shandong Microbial Engineering, College of Bioengineering, Qilu University of Technology (Shandong Academy of Sciences), Jinan, Shandong, People's Republic of China.
| | - Xinli Liu
- Key Laboratory of Shandong Microbial Engineering, College of Bioengineering, Qilu University of Technology (Shandong Academy of Sciences), Jinan, Shandong, People's Republic of China. .,State Key Laboratory of Bio-Based Material and Green Papermaking (LBMP), Qilu University of Technology (Shandong Academy of Sciences), Jinan, Shandong, People's Republic of China.
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Hoffmann SL, Kohlstedt M, Jungmann L, Hutter M, Poblete-Castro I, Becker J, Wittmann C. Cascaded valorization of brown seaweed to produce l-lysine and value-added products using Corynebacterium glutamicum streamlined by systems metabolic engineering. Metab Eng 2021; 67:293-307. [PMID: 34314893 DOI: 10.1016/j.ymben.2021.07.010] [Citation(s) in RCA: 25] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2020] [Revised: 06/23/2021] [Accepted: 07/22/2021] [Indexed: 12/15/2022]
Abstract
Seaweeds emerge as promising third-generation renewable for sustainable bioproduction. In the present work, we valorized brown seaweed to produce l-lysine, the world's leading feed amino acid, using Corynebacterium glutamicum, which was streamlined by systems metabolic engineering. The mutant C. glutamicum SEA-1 served as a starting point for development because it produced small amounts of l-lysine from mannitol, a major seaweed sugar, because of the deletion of its arabitol repressor AtlR and its engineered l-lysine pathway. Starting from SEA-1, we systematically optimized the microbe to redirect excess NADH, formed on the sugar alcohol, towards NADPH, required for l-lysine synthesis. The mannitol dehydrogenase variant MtlD D75A, inspired by 3D protein homology modelling, partly generated NADPH during the oxidation of mannitol to fructose, leading to a 70% increased l-lysine yield in strain SEA-2C. Several rounds of strain engineering further increased NADPH supply and l-lysine production. The best strain, SEA-7, overexpressed the membrane-bound transhydrogenase pntAB together with codon-optimized gapN, encoding NADPH-dependent glyceraldehyde 3-phosphate dehydrogenase, and mak, encoding fructokinase. In a fed-batch process, SEA-7 produced 76 g L-1l-lysine from mannitol at a yield of 0.26 mol mol-1 and a maximum productivity of 2.1 g L-1 h-1. Finally, SEA-7 was integrated into seaweed valorization cascades. Aqua-cultured Laminaria digitata, a major seaweed for commercial alginate, was extracted and hydrolyzed enzymatically, followed by recovery and clean-up of pure alginate gum. The residual sugar-based mixture was converted to l-lysine at a yield of 0.27 C-mol C-mol-1 using SEA-7. Second, stems of the wild-harvested seaweed Durvillaea antarctica, obtained as waste during commercial processing of the blades for human consumption, were extracted using acid treatment. Fermentation of the hydrolysate using SEA-7 provided l-lysine at a yield of 0.40 C-mol C-mol-1. Our findings enable improvement of the efficiency of seaweed biorefineries using tailor-made C. glutamicum strains.
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Affiliation(s)
- Sarah Lisa Hoffmann
- Institute of Systems Biotechnology, Saarland University, Saarbrücken, Germany
| | - Michael Kohlstedt
- Institute of Systems Biotechnology, Saarland University, Saarbrücken, Germany
| | - Lukas Jungmann
- Institute of Systems Biotechnology, Saarland University, Saarbrücken, Germany
| | - Michael Hutter
- Centre for Bioinformatics, Saarland University, Saarbrücken, Germany
| | | | - Judith Becker
- Institute of Systems Biotechnology, Saarland University, Saarbrücken, Germany
| | - Christoph Wittmann
- Institute of Systems Biotechnology, Saarland University, Saarbrücken, Germany.
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Krahn I, Bonder D, Torregrosa-Barragán L, Stoppel D, Krause JP, Rosenfeldt N, Meiswinkel TM, Seibold GM, Wendisch VF, Lindner SN. Evolving a New Efficient Mode of Fructose Utilization for Improved Bioproduction in Corynebacterium glutamicum. Front Bioeng Biotechnol 2021; 9:669093. [PMID: 34124022 PMCID: PMC8193941 DOI: 10.3389/fbioe.2021.669093] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2021] [Accepted: 04/14/2021] [Indexed: 11/13/2022] Open
Abstract
Fructose utilization in Corynebacterium glutamicum starts with its uptake and concomitant phosphorylation via the phosphotransferase system (PTS) to yield intracellular fructose 1-phosphate, which enters glycolysis upon ATP-dependent phosphorylation to fructose 1,6-bisphosphate by 1-phosphofructokinase. This is known to result in a significantly reduced oxidative pentose phosphate pathway (oxPPP) flux on fructose (∼10%) compared to glucose (∼60%). Consequently, the biosynthesis of NADPH demanding products, e.g., L-lysine, by C. glutamicum is largely decreased when fructose is the only carbon source. Previous works reported that fructose is partially utilized via the glucose-specific PTS presumably generating fructose 6-phosphate. This closer proximity to the entry point of the oxPPP might increase oxPPP flux and, consequently, NADPH availability. Here, we generated deletion strains lacking either the fructose-specific PTS or 1-phosphofructokinase activity. We used these strains in short-term evolution experiments on fructose minimal medium and isolated mutant strains, which regained the ability of fast growth on fructose as a sole carbon source. In these fructose mutants, the deletion of the glucose-specific PTS as well as the 6-phosphofructokinase gene, abolished growth, unequivocally showing fructose phosphorylation via glucose-specific PTS to fructose 6-phosphate. Gene sequencing revealed three independent amino acid substitutions in PtsG (M260V, M260T, and P318S). These three PtsG variants mediated faster fructose uptake and utilization compared to native PtsG. In-depth analysis of the effects of fructose utilization via these PtsG variants revealed significantly increased ODs, reduced side-product accumulation, and increased L-lysine production by 50%.
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Affiliation(s)
- Irene Krahn
- Chair of Genetics of Prokaryotes, Faculty of Biology and CeBiTec, Bielefeld University, Bielefeld, Germany
| | - Daniel Bonder
- Systems and Synthetic Metabolism, Max Planck Institute of Molecular Plant Physiology, Potsdam-Golm, Germany
| | - Lucía Torregrosa-Barragán
- Systems and Synthetic Metabolism, Max Planck Institute of Molecular Plant Physiology, Potsdam-Golm, Germany
| | - Dominik Stoppel
- Chair of Genetics of Prokaryotes, Faculty of Biology and CeBiTec, Bielefeld University, Bielefeld, Germany
| | - Jens P Krause
- Chair of Genetics of Prokaryotes, Faculty of Biology and CeBiTec, Bielefeld University, Bielefeld, Germany
| | | | - Tobias M Meiswinkel
- Chair of Genetics of Prokaryotes, Faculty of Biology and CeBiTec, Bielefeld University, Bielefeld, Germany
| | - Gerd M Seibold
- Institute of Biochemistry, University of Cologne, Cologne, Germany.,Department of Biotechnology and Biomedicine, Technical University of Denmark, Lyngby, Denmark
| | - Volker F Wendisch
- Chair of Genetics of Prokaryotes, Faculty of Biology and CeBiTec, Bielefeld University, Bielefeld, Germany
| | - Steffen N Lindner
- Chair of Genetics of Prokaryotes, Faculty of Biology and CeBiTec, Bielefeld University, Bielefeld, Germany.,Systems and Synthetic Metabolism, Max Planck Institute of Molecular Plant Physiology, Potsdam-Golm, Germany
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10
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Chen G, An X, Li H, Lai F, Yuan E, Xia X, Zhang Q. Detoxification of azo dye Direct Black G by thermophilic Anoxybacillus sp. PDR2 and its application potential in bioremediation. ECOTOXICOLOGY AND ENVIRONMENTAL SAFETY 2021; 214:112084. [PMID: 33640726 DOI: 10.1016/j.ecoenv.2021.112084] [Citation(s) in RCA: 23] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/25/2020] [Revised: 02/01/2021] [Accepted: 02/17/2021] [Indexed: 06/12/2023]
Abstract
Direct Black G (DBG) is a highly toxic synthetic azo dye which is difficult to degrade. Biological treatment seems to be a promising option for the treatment of azo dye containing effluent. A thermophilic bacterial strain (Anoxybacillus sp. PDR2) previously isolated from the soil can effectively remove DBG. However, the molecular underpinnings of DBG degradation and the microbial detoxification ability remains unknown. In the present study, the genetic background of PDR2 for the efficient degradation of DBG and its adaptation to azo dye-contaminated environments was revealed by bioinformatics. Moreover, the possible biodegradation pathways were speculated based on the UV-vis spectral analysis, FTIR, and intermediates identified by LC-MS. Additionally, phytotoxicity and the comet experiment studies clearly indicated that PDR2 converts toxic azo dye (DBG) into low toxicity metabolites. The combination of biodegradation pathways and detoxification analysis were utilized to explore the molecular degradation mechanism and bioremediation of azo dye for future applications. These findings will provide a valuable theoretical basis for the practical treatment of azo dye wastewater.
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Affiliation(s)
- Guotao Chen
- College of Bioscience and Biotechnology, Jiangxi Agricultural University, Jiangxi Engineering Laboratory for the Development and Utilization of Agricultural Microbial Resources, Nanchang 330045, PR China
| | - Xuejiao An
- College of Bioscience and Biotechnology, Jiangxi Agricultural University, Jiangxi Engineering Laboratory for the Development and Utilization of Agricultural Microbial Resources, Nanchang 330045, PR China
| | - Hanguang Li
- College of Bioscience and Biotechnology, Jiangxi Agricultural University, Jiangxi Engineering Laboratory for the Development and Utilization of Agricultural Microbial Resources, Nanchang 330045, PR China
| | - Fenju Lai
- College of Bioscience and Biotechnology, Jiangxi Agricultural University, Jiangxi Engineering Laboratory for the Development and Utilization of Agricultural Microbial Resources, Nanchang 330045, PR China
| | - En Yuan
- College of Pharmacy, Jiangxi University of Traditional Chinese Medicine, Nanchang 330045, PR China
| | - Xiang Xia
- College of Bioscience and Biotechnology, Jiangxi Agricultural University, Jiangxi Engineering Laboratory for the Development and Utilization of Agricultural Microbial Resources, Nanchang 330045, PR China
| | - Qinghua Zhang
- College of Bioscience and Biotechnology, Jiangxi Agricultural University, Jiangxi Engineering Laboratory for the Development and Utilization of Agricultural Microbial Resources, Nanchang 330045, PR China.
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11
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Pinheiro B, Petrov DP, Guo L, Martins GB, Bramkamp M, Jung K. Elongation factor P is required for EII Glc translation in Corynebacterium glutamicum due to an essential polyproline motif. Mol Microbiol 2020; 115:320-331. [PMID: 33012080 DOI: 10.1111/mmi.14618] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2020] [Revised: 09/25/2020] [Indexed: 12/22/2022]
Abstract
Translating ribosomes require elongation factor P (EF-P) to incorporate consecutive prolines (XPPX) into nascent peptide chains. The proteome of Corynebacterium glutamicum ATCC 13032 contains a total of 1,468 XPPX motifs, many of which are found in proteins involved in primary and secondary metabolism. We show here that synthesis of EIIGlc , the glucose-specific permease of the phosphoenolpyruvate (PEP): sugar phosphotransferase system (PTS) encoded by ptsG, is strongly dependent on EF-P, as an efp deletion mutant grows poorly on glucose as sole carbon source. The amount of EIIGlc is strongly reduced in this mutant, which consequently results in a lower rate of glucose uptake. Strikingly, the XPPX motif is essential for the activity of EIIGlc , and substitution of the prolines leads to inactivation of the protein. Finally, translation of GntR2, a transcriptional activator of ptsG, is also dependent on EF-P. However, its reduced amount in the efp mutant can be compensated for by other regulators. These results reveal for the first time a translational bottleneck involving production of the major glucose transporter EIIGlc , which has implications for future strain engineering strategies.
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Affiliation(s)
- Bruno Pinheiro
- Department of Biology I, Microbiology, Ludwig-Maximilians-Universität München, Martinsried, Germany
| | - Dimitar Plamenov Petrov
- Department of Biology I, Microbiology, Ludwig-Maximilians-Universität München, Martinsried, Germany
| | - Lingyun Guo
- Department of Biology I, Microbiology, Ludwig-Maximilians-Universität München, Martinsried, Germany
| | | | - Marc Bramkamp
- Institute for General Microbiology, Faculty of Mathematics and Natural Sciences, Christian-Albrechts-Universität zu Kiel, Kiel, Germany
| | - Kirsten Jung
- Department of Biology I, Microbiology, Ludwig-Maximilians-Universität München, Martinsried, Germany
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12
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Ruan H, Yu H, Xu J. The glucose uptake systems in Corynebacterium glutamicum: a review. World J Microbiol Biotechnol 2020; 36:126. [PMID: 32712859 DOI: 10.1007/s11274-020-02898-z] [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: 03/09/2020] [Accepted: 07/12/2020] [Indexed: 11/29/2022]
Abstract
The phosphoenolpyruvate-dependent glucose phosphotransferase system (PTSGlc) is the major uptake system responsible for transporting glucose, and is involved in glucose translocation and phosphorylation in Corynebacterium glutamicum. For the longest time, the PTSGlc was considered as the only uptake system for glucose. However, some PTS-independent glucose uptake systems (non-PTSGlc) were discovered in recent years, such as the coupling system of inositol permeases and glucokinases (IPGS) and the coupling system of β-glucoside-PTS permease and glucokinases (GPGS). The products (e.g. lysine, phenylalanine and leucine) will be increased because of the increasing intracellular level of phosphoenolpyruvate (PEP), while some by-products (e.g. lactic acid, alanine and acetic acid) will be reduced when this system become the main uptake pathway for glucose. In this review, we survey the uptake systems for glucose in C. glutamicum and their composition. Furthermore, we summarize the latest research of the regulatory mechanisms among these glucose uptake systems. Detailed strategies to manipulate glucose uptake system are addressed based on this knowledge.
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Affiliation(s)
- Haozhe Ruan
- The Key Laboratory of Industrial Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, 1800# Lihu Road, Wuxi, 214122, People's Republic of China
| | - Haibo Yu
- The Key Laboratory of Industrial Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, 1800# Lihu Road, Wuxi, 214122, People's Republic of China
| | - Jianzhong Xu
- The Key Laboratory of Industrial Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, 1800# Lihu Road, Wuxi, 214122, People's Republic of China.
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13
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Fermentative N-Methylanthranilate Production by Engineered Corynebacterium glutamicum. Microorganisms 2020; 8:microorganisms8060866. [PMID: 32521697 PMCID: PMC7356990 DOI: 10.3390/microorganisms8060866] [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: 05/22/2020] [Revised: 06/02/2020] [Accepted: 06/05/2020] [Indexed: 12/20/2022] Open
Abstract
The N-functionalized amino acid N-methylanthranilate is an important precursor for bioactive compounds such as anticancer acridone alkaloids, the antinociceptive alkaloid O-isopropyl N-methylanthranilate, the flavor compound O-methyl-N-methylanthranilate, and as a building block for peptide-based drugs. Current chemical and biocatalytic synthetic routes to N-alkylated amino acids are often unprofitable and restricted to low yields or high costs through cofactor regeneration systems. Amino acid fermentation processes using the Gram-positive bacterium Corynebacterium glutamicum are operated industrially at the million tons per annum scale. Fermentative processes using C. glutamicum for N-alkylated amino acids based on an imine reductase have been developed, while N-alkylation of the aromatic amino acid anthranilate with S-adenosyl methionine as methyl-donor has not been described for this bacterium. After metabolic engineering for enhanced supply of anthranilate by channeling carbon flux into the shikimate pathway, preventing by-product formation and enhancing sugar uptake, heterologous expression of the gene anmt encoding anthranilate N-methyltransferase from Ruta graveolens resulted in production of N-methylanthranilate (NMA), which accumulated in the culture medium. Increased SAM regeneration by coexpression of the homologous adenosylhomocysteinase gene sahH improved N-methylanthranilate production. In a test bioreactor culture, the metabolically engineered C. glutamicum C1* strain produced NMA to a final titer of 0.5 g·L−1 with a volumetric productivity of 0.01 g·L−1·h−1 and a yield of 4.8 mg·g−1 glucose.
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14
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Andriiash GS, Sekan OS, Tigunova OO, Blume YB, Shulga SM. Metabolic Engineering of Lysine Producing Corynebacterium glutamicum Strains. CYTOL GENET+ 2020. [DOI: 10.3103/s0095452720020024] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
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15
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Xu JZ, Ruan HZ, Yu HB, Liu LM, Zhang W. Metabolic engineering of carbohydrate metabolism systems in Corynebacterium glutamicum for improving the efficiency of L-lysine production from mixed sugar. Microb Cell Fact 2020; 19:39. [PMID: 32070345 PMCID: PMC7029506 DOI: 10.1186/s12934-020-1294-7] [Citation(s) in RCA: 24] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2019] [Accepted: 01/23/2020] [Indexed: 01/08/2023] Open
Abstract
The efficiency of industrial fermentation process mainly depends on carbon yield, final titer and productivity. To improve the efficiency of l-lysine production from mixed sugar, we engineered carbohydrate metabolism systems to enhance the effective use of sugar in this study. A functional metabolic pathway of sucrose and fructose was engineered through introduction of fructokinase from Clostridium acetobutylicum. l-lysine production was further increased through replacement of phosphoenolpyruvate-dependent glucose and fructose uptake system (PTSGlc and PTSFru) by inositol permeases (IolT1 and IolT2) and ATP-dependent glucokinase (ATP-GlK). However, the shortage of intracellular ATP has a significantly negative impact on sugar consumption rate, cell growth and l-lysine production. To overcome this defect, the recombinant strain was modified to co-express bifunctional ADP-dependent glucokinase (ADP-GlK/PFK) and NADH dehydrogenase (NDH-2) as well as to inactivate SigmaH factor (SigH), thus reducing the consumption of ATP and increasing ATP regeneration. Combination of these genetic modifications resulted in an engineered C. glutamicum strain K-8 capable of producing 221.3 ± 17.6 g/L l-lysine with productivity of 5.53 g/L/h and carbon yield of 0.71 g/g glucose in fed-batch fermentation. As far as we know, this is the best efficiency of l-lysine production from mixed sugar. This is also the first report for improving the efficiency of l-lysine production by systematic modification of carbohydrate metabolism systems.
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Affiliation(s)
- Jian-Zhong Xu
- The Key Laboratory of Industrial Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, 1800# Lihu Road, Wuxi, 214122, China.
| | - Hao-Zhe Ruan
- The Key Laboratory of Industrial Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, 1800# Lihu Road, Wuxi, 214122, China
| | - Hai-Bo Yu
- The Key Laboratory of Industrial Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, 1800# Lihu Road, Wuxi, 214122, China
| | - Li-Ming Liu
- State Key Laboratory of Food Science and Technology, School of Biotechnology, Jiangnan University, 1800# Lihu Road, Wuxi, 214122, China
| | - Weiguo Zhang
- The Key Laboratory of Industrial Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, 1800# Lihu Road, Wuxi, 214122, China
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16
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Xu JZ, Yu HB, Han M, Liu LM, Zhang WG. Metabolic engineering of glucose uptake systems in Corynebacterium glutamicum for improving the efficiency of l-lysine production. ACTA ACUST UNITED AC 2019; 46:937-949. [DOI: 10.1007/s10295-019-02170-w] [Citation(s) in RCA: 20] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/26/2018] [Accepted: 03/27/2019] [Indexed: 11/25/2022]
Abstract
Abstract
Traditional amino acid producers typically exhibit the low glucose uptake rate and growth deficiency, resulting in a long fermentation time because of the accumulation of side mutations in breeding of strains. In this study, we demonstrate that the efficiency of l-lysine production in traditional l-lysine producer Corynebacterium glutamicum ZL-9 can be improved by rationally engineering glucose uptake systems. To do this, different bypasses for glucose uptake were investigated to reveal the best glucose uptake system for l-lysine production in traditional l-lysine producer. This study showed that overexpression of the key genes in PTSGlc or non-PTSGlc increased the glucose consumption, growth rate, and l-lysine production. However, increasing the function of PTSGlc in glucose uptake led to the increase of by-products, especially for plasmid-mediated expression system. Increasing the participation of non-PTSGlc in glucose utilization showed the best glucose uptake system for l-lysine production. The final strain ZL-92 with increasing the expression level of iolT1, iolT2 and ppgK could produce 201.6 ± 13.8 g/L of l-lysine with a productivity of 5.04 g/L/h and carbon yield of 0.65 g/(g glucose) in fed-batch culture. This is the first report of a rational modification of glucose uptake systems that improve the efficiency of l-lysine production through increasing the participation of non-PTSGlc in glucose utilization in traditional l-lysine producer. Similar strategies can be also used for producing other amino acids or their derivatives.
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Affiliation(s)
- Jian-Zhong Xu
- 0000 0001 0708 1323 grid.258151.a The Key Laboratory of Industrial Biotechnology, Ministry of Education, School of Biotechnology Jiangnan University 1800 Lihu Road 214122 Wuxi People’s Republic of China
| | - Hai-Bo Yu
- 0000 0001 0708 1323 grid.258151.a The Key Laboratory of Industrial Biotechnology, Ministry of Education, School of Biotechnology Jiangnan University 1800 Lihu Road 214122 Wuxi People’s Republic of China
| | - Mei Han
- 0000 0004 0431 6539 grid.469163.f Shanghai Business School 2271 Zhongsha West-Road 200235 Shanghai People’s Republic of China
| | - Li-Ming Liu
- 0000 0001 0708 1323 grid.258151.a State Key Laboratory of Food Science and Technology, School of Biotechnology Jiangnan University 1800 Lihu Road 214122 Wuxi People’s Republic of China
| | - Wei-Guo Zhang
- 0000 0001 0708 1323 grid.258151.a The Key Laboratory of Industrial Biotechnology, Ministry of Education, School of Biotechnology Jiangnan University 1800 Lihu Road 214122 Wuxi People’s Republic of China
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Matsuura R, Kishida M, Konishi R, Hirata Y, Adachi N, Segawa S, Imao K, Tanaka T, Kondo A. Metabolic engineering to improve 1,5‐diaminopentane production from cellobiose using β‐glucosidase‐secreting
Corynebacterium glutamicum. Biotechnol Bioeng 2019; 116:2640-2651. [DOI: 10.1002/bit.27082] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2019] [Revised: 05/27/2019] [Accepted: 06/05/2019] [Indexed: 12/15/2022]
Affiliation(s)
- Rena Matsuura
- Department of Chemical Science and Engineering, Graduate School of Engineering Kobe University Kobe Japan
| | - Mayumi Kishida
- Department of Chemical Science and Engineering, Graduate School of Engineering Kobe University Kobe Japan
| | - Rie Konishi
- Department of Chemical Science and Engineering, Graduate School of Engineering Kobe University Kobe Japan
| | - Yuuki Hirata
- Department of Chemical Science and Engineering, Graduate School of Engineering Kobe University Kobe Japan
| | - Noriko Adachi
- Department of Chemical Science and Engineering, Graduate School of Engineering Kobe University Kobe Japan
| | - Shota Segawa
- Department of Chemical Science and Engineering, Graduate School of Engineering Kobe University Kobe Japan
| | - Kenta Imao
- Department of Chemical Science and Engineering, Graduate School of Engineering Kobe University Kobe Japan
| | - Tsutomu Tanaka
- Department of Chemical Science and Engineering, Graduate School of Engineering Kobe University Kobe Japan
| | - Akihiko Kondo
- Graduate School of Science, Technology and Innovation Kobe University Kobe Japan
- Center for Sustainable Resource Science RIKEN Wako Saitama Japan
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Wang Z, Liu J, Chen L, Zeng AP, Solem C, Jensen PR. Alterations in the transcription factors GntR1 and RamA enhance the growth and central metabolism of Corynebacterium glutamicum. Metab Eng 2018; 48:1-12. [DOI: 10.1016/j.ymben.2018.05.004] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2018] [Accepted: 05/07/2018] [Indexed: 12/30/2022]
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Santos AS, Ramos RT, Silva A, Hirata R, Mattos-Guaraldi AL, Meyer R, Azevedo V, Felicori L, Pacheco LGC. Searching whole genome sequences for biochemical identification features of emerging and reemerging pathogenic Corynebacterium species. Funct Integr Genomics 2018; 18:593-610. [PMID: 29752561 DOI: 10.1007/s10142-018-0610-3] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2017] [Revised: 03/28/2018] [Accepted: 04/16/2018] [Indexed: 12/24/2022]
Abstract
Biochemical tests are traditionally used for bacterial identification at the species level in clinical microbiology laboratories. While biochemical profiles are generally efficient for the identification of the most important corynebacterial pathogen Corynebacterium diphtheriae, their ability to differentiate between biovars of this bacterium is still controversial. Besides, the unambiguous identification of emerging human pathogenic species of the genus Corynebacterium may be hampered by highly variable biochemical profiles commonly reported for these species, including Corynebacterium striatum, Corynebacterium amycolatum, Corynebacterium minutissimum, and Corynebacterium xerosis. In order to identify the genomic basis contributing for the biochemical variabilities observed in phenotypic identification methods of these bacteria, we combined a comprehensive literature review with a bioinformatics approach based on reconstruction of six specific biochemical reactions/pathways in 33 recently released whole genome sequences. We used data retrieved from curated databases (MetaCyc, PathoSystems Resource Integration Center (PATRIC), The SEED, TransportDB, UniProtKB) associated with homology searches by BLAST and profile Hidden Markov Models (HMMs) to detect enzymes participating in the various pathways and performed ab initio protein structure modeling and molecular docking to confirm specific results. We found a differential distribution among the various strains of genes that code for some important enzymes, such as beta-phosphoglucomutase and fructokinase, and also for individual components of carbohydrate transport systems, including the fructose-specific phosphoenolpyruvate-dependent sugar phosphotransferase (PTS) and the ribose-specific ATP-binging cassette (ABC) transporter. Horizontal gene transfer plays a role in the biochemical variability of the isolates, as some genes needed for sucrose fermentation were seen to be present in genomic islands. Noteworthy, using profile HMMs, we identified an enzyme with putative alpha-1,6-glycosidase activity only in some specific strains of C. diphtheriae and this may aid to understanding of the differential abilities to utilize glycogen and starch between the biovars.
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Affiliation(s)
- André S Santos
- Bioinformatics Post-Graduate Program, Institute of Biological Sciences, Federal University of Minas Gerais (UFMG), Belo Horizonte, MG, Brazil
- Institute of Health Sciences, Federal University of Bahia (UFBA), Salvador, BA, Brazil
| | - Rommel T Ramos
- Institute of Biological Sciences, Federal University of Pará (UFPA), Belém, PA, Brazil
| | - Artur Silva
- Institute of Biological Sciences, Federal University of Pará (UFPA), Belém, PA, Brazil
| | - Raphael Hirata
- Faculty of Medical Sciences, Rio de Janeiro State University (UERJ), Rio de Janeiro, RJ, Brazil
| | - Ana L Mattos-Guaraldi
- Faculty of Medical Sciences, Rio de Janeiro State University (UERJ), Rio de Janeiro, RJ, Brazil
| | - Roberto Meyer
- Institute of Health Sciences, Federal University of Bahia (UFBA), Salvador, BA, Brazil
| | - Vasco Azevedo
- Bioinformatics Post-Graduate Program, Institute of Biological Sciences, Federal University of Minas Gerais (UFMG), Belo Horizonte, MG, Brazil
| | - Liza Felicori
- Bioinformatics Post-Graduate Program, Institute of Biological Sciences, Federal University of Minas Gerais (UFMG), Belo Horizonte, MG, Brazil
| | - Luis G C Pacheco
- Institute of Health Sciences, Federal University of Bahia (UFBA), Salvador, BA, Brazil.
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Shin WS, Lee D, Lee SJ, Chun GT, Choi SS, Kim ES, Kim S. Characterization of a non-phosphotransferase system for cis,cis-muconic acid production in Corynebacterium glutamicum. Biochem Biophys Res Commun 2018; 499:279-284. [DOI: 10.1016/j.bbrc.2018.03.146] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2018] [Accepted: 03/19/2018] [Indexed: 01/19/2023]
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21
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Kitade Y, Hashimoto R, Suda M, Hiraga K, Inui M. Production of 4-Hydroxybenzoic Acid by an Aerobic Growth-Arrested Bioprocess Using Metabolically Engineered Corynebacterium glutamicum. Appl Environ Microbiol 2018; 84:e02587-17. [PMID: 29305513 PMCID: PMC5835730 DOI: 10.1128/aem.02587-17] [Citation(s) in RCA: 53] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2017] [Accepted: 12/14/2017] [Indexed: 12/22/2022] Open
Abstract
Corynebacterium glutamicum was metabolically engineered to produce 4-hydroxybenzoic acid (4-HBA), a valuable aromatic compound used as a raw material for the production of liquid crystal polymers and paraben. C. glutamicum was found to have a higher tolerance to 4-HBA toxicity than previously reported hosts used for the production of genetically engineered 4-HBA. To obtain higher titers of 4-HBA, we employed a stepwise overexpression of all seven target genes in the shikimate pathway in C. glutamicum Specifically, multiple chromosomal integrations of a mutated aroG gene from Escherichia coli, encoding a 3-deoxy-d-arabinoheptulosonic acid 7-phosphate (DAHP) synthase, and wild-type aroCKB from C. glutamicum, encoding chorismate synthase, shikimate kinase, and 3-dehydroquinate synthase, were effective in increasing product titers. The last step of the 4-HBA biosynthesis pathway was recreated in C. glutamicum by expressing a highly 4-HBA-resistant chorismate pyruvate-lyase (UbiC) from the intestinal bacterium Providencia rustigianii To enhance the yield of 4-HBA, we reduced the formation of by-products, such as 1,3-dihydroxyacetone and pyruvate, by deleting hdpA, a gene coding for a haloacid dehalogenase superfamily phosphatase, and pyk, a gene coding for a pyruvate kinase, from the bacterial chromosome. The maximum concentration of 4-HBA produced by the resultant strain was 36.6 g/liter, with a yield of 41% (mol/mol) glucose after incubation for 24 h in minimal medium in an aerobic growth-arrested bioprocess using a jar fermentor. To our knowledge, this is the highest concentration of 4-HBA produced by a metabolically engineered microorganism ever reported.IMPORTANCE Since aromatic compound 4-HBA has been chemically produced from petroleum-derived phenol for a long time, eco-friendly bioproduction of 4-HBA from biomass resources is desired in order to address environmental issues. In microbial chemical production, product toxicity often causes problems, but we confirmed that wild-type C. glutamicum has high tolerance to the target 4-HBA. A growth-arrested bioprocess using this microorganism has been successfully used for the production of various compounds, such as biofuels, organic acids, and amino acids. However, no production method has been applied for aromatic compounds to date. In this study, we screened for a novel final reaction enzyme possessing characteristics superior to those in previously employed microbial 4-HBA production. We demonstrated that the use of the highly 4-HBA-resistant UbiC from the intestinal bacterium P. rustigianii is very effective in increasing 4-HBA production.
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Affiliation(s)
- Yukihiro Kitade
- Molecular Microbiology and Biotechnology Group, Research Institute of Innovative Technology for the Earth (RITE), Kizugawa, Kyoto, Japan
- Green Phenol Development Co., Ltd., Kizugawa, Kyoto, Japan
| | | | - Masako Suda
- Molecular Microbiology and Biotechnology Group, Research Institute of Innovative Technology for the Earth (RITE), Kizugawa, Kyoto, Japan
- Green Phenol Development Co., Ltd., Kizugawa, Kyoto, Japan
| | - Kazumi Hiraga
- Molecular Microbiology and Biotechnology Group, Research Institute of Innovative Technology for the Earth (RITE), Kizugawa, Kyoto, Japan
- Green Phenol Development Co., Ltd., Kizugawa, Kyoto, Japan
| | - Masayuki Inui
- Molecular Microbiology and Biotechnology Group, Research Institute of Innovative Technology for the Earth (RITE), Kizugawa, Kyoto, Japan
- Green Phenol Development Co., Ltd., Kizugawa, Kyoto, Japan
- Graduate School of Biological Sciences, Nara Institute of Science and Technology, Ikoma, Nara, Japan
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Wang X, Khushk I, Xiao Y, Gao Q, Bao J. Tolerance improvement of Corynebacterium glutamicum on lignocellulose derived inhibitors by adaptive evolution. Appl Microbiol Biotechnol 2017; 102:377-388. [DOI: 10.1007/s00253-017-8627-4] [Citation(s) in RCA: 38] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2017] [Revised: 10/24/2017] [Accepted: 11/06/2017] [Indexed: 01/09/2023]
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Zhang X, Lai L, Xu G, Zhang X, Shi J, Xu Z. Effects of pyruvate kinase on the growth of Corynebacterium glutamicum and L-serine accumulation. Process Biochem 2017. [DOI: 10.1016/j.procbio.2017.01.028] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
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Enhancement of fructose utilization from sucrose in the cell for improved l-serine production in engineered Corynebacterium glutamicum. Biochem Eng J 2017. [DOI: 10.1016/j.bej.2016.11.021] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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Enhanced Glucose Consumption and Organic Acid Production by Engineered Corynebacterium glutamicum Based on Analysis of a pfkB1 Deletion Mutant. Appl Environ Microbiol 2017; 83:AEM.02638-16. [PMID: 27881414 DOI: 10.1128/aem.02638-16] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2016] [Accepted: 11/17/2016] [Indexed: 02/08/2023] Open
Abstract
In the analysis of a carbohydrate metabolite pathway, we found interesting phenotypes in a mutant strain of Corynebacterium glutamicum deficient in pfkB1, which encodes fructose-1-phosphate kinase. After being aerobically cultivated with fructose as a carbon source, this mutant consumed glucose and produced organic acid, predominantly l-lactate, at a level more than 2-fold higher than that of the wild-type grown with glucose under conditions of oxygen deprivation. This considerably higher fermentation capacity was unique for the combination of pfkB1 deletion and cultivation with fructose. In the metabolome and transcriptome analyses of this strain, marked intracellular accumulation of fructose-1-phosphate and significant upregulation of several genes related to the phosphoenolpyruvate:carbohydrate phosphotransferase system, glycolysis, and organic acid synthesis were identified. We then examined strains overexpressing several of the identified genes and demonstrated enhanced glucose consumption and organic acid production by these engineered strains, whose values were found to be comparable to those of the model pfkB1 deletion mutant grown with fructose. l-Lactate production by the ppc deletion mutant of the engineered strain was 2,390 mM (i.e., 215 g/liter) after 48 h under oxygen deprivation, which was a 2.7-fold increase over that of the wild-type strain with a deletion of ppc IMPORTANCE: Enhancement of glycolytic flux is important for improving microbiological production of chemicals, but overexpression of glycolytic enzymes has often resulted in little positive effect. That is presumably because the central carbon metabolism is under the complex and strict regulation not only transcriptionally but also posttranscriptionally, for example, by the ATP/ADP ratio. In contrast, we studied a mutant strain of Corynebacterium glutamicum that showed markedly enhanced glucose consumption and organic acid production and, based on the findings, identified several genes whose overexpression was effective in enhancing glycolytic flux under conditions of oxygen deprivation. These results will further understanding of the regulatory mechanisms of glycolytic flux and can be widely applied to the improvement of the microbial production of useful chemicals.
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Affiliation(s)
- Volker F. Wendisch
- Bielefeld University; Genetics of Prokaryotes, Faculty of Biology and CeBiTec; Postfach 100131 33501 Bielefeld Germany
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Kogure T, Kubota T, Suda M, Hiraga K, Inui M. Metabolic engineering of Corynebacterium glutamicum for shikimate overproduction by growth-arrested cell reaction. Metab Eng 2016; 38:204-216. [DOI: 10.1016/j.ymben.2016.08.005] [Citation(s) in RCA: 75] [Impact Index Per Article: 9.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2016] [Revised: 08/16/2016] [Accepted: 08/18/2016] [Indexed: 11/30/2022]
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Elucidation of the regulatory role of the fructose operon reveals a novel target for enhancing the NADPH supply in Corynebacterium glutamicum. Metab Eng 2016; 38:344-357. [PMID: 27553884 DOI: 10.1016/j.ymben.2016.08.004] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2016] [Revised: 08/05/2016] [Accepted: 08/18/2016] [Indexed: 11/21/2022]
Abstract
The performance of Corynebacterium glutamicum cell factories producing compounds which rely heavily on NADPH has been reported to depend on the sugar being metabolized. While some aspects of this phenomenon have been elucidated, there are still many unresolved questions as to how sugar metabolism is linked to redox and to the general metabolism. We here provide new insights into the regulation of the metabolism of this important platform organism by systematically characterizing mutants carrying various lesions in the fructose operon. Initially, we found that a strain where the dedicated fructose uptake system had been inactivated (KO-ptsF) was hampered in growth on sucrose minimal medium, and suppressor mutants appeared readily. Comparative genomic analysis in conjunction with enzymatic assays revealed that suppression was linked to inactivation of the pfkB gene, encoding a fructose-1-phosphate kinase. Detailed characterization of KO-ptsF, KO-pfkB and double knock-out (DKO) derivatives revealed a strong role for sugar-phosphates, especially fructose-1-phosphate (F1P), in governing sugar as well as redox metabolism due to effects on transcriptional regulation of key genes. These findings allowed us to propose a simple model explaining the correlation between sugar phosphate concentration, gene expression and ultimately the observed phenotype. To guide us in our analysis and help us identify bottlenecks in metabolism we debugged an existing genome-scale model onto which we overlaid the transcriptome data. Based on the results obtained we managed to enhance the NADPH supply and transform the wild-type strain into delivering the highest yield of lysine ever obtained on sucrose and fructose, thus providing a good example of how regulatory mechanisms can be harnessed for bioproduction.
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Lemoine A, Limberg MH, Kästner S, Oldiges M, Neubauer P, Junne S. Performance loss ofCorynebacterium glutamicumcultivations under scale-down conditions using complex media. Eng Life Sci 2016. [DOI: 10.1002/elsc.201500144] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022] Open
Affiliation(s)
- Anja Lemoine
- Bioprocess Engineering; TU Berlin; Berlin Germany
| | - Michael H. Limberg
- Research Centre Juelich; Institute of Bio- and Geosciences-IBG-1: Biotechnology; Juelich Germany
| | | | - Marco Oldiges
- Research Centre Juelich; Institute of Bio- and Geosciences-IBG-1: Biotechnology; Juelich Germany
| | | | - Stefan Junne
- Bioprocess Engineering; TU Berlin; Berlin Germany
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Lysine Fermentation: History and Genome Breeding. ADVANCES IN BIOCHEMICAL ENGINEERING/BIOTECHNOLOGY 2016; 159:73-102. [DOI: 10.1007/10_2016_27] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
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Becker J, Gießelmann G, Hoffmann SL, Wittmann C. Corynebacterium glutamicum for Sustainable Bioproduction: From Metabolic Physiology to Systems Metabolic Engineering. ADVANCES IN BIOCHEMICAL ENGINEERING/BIOTECHNOLOGY 2016; 162:217-263. [DOI: 10.1007/10_2016_21] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
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Visser M, Stams AJM, Frutschi M, Bernier-Latmani R. Phylogenetic comparison of Desulfotomaculum species of subgroup 1a and description of Desulfotomaculum reducens sp. nov. Int J Syst Evol Microbiol 2015; 66:762-767. [PMID: 26597812 DOI: 10.1099/ijsem.0.000786] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/14/2023] Open
Abstract
A genome and physiological comparison was made of the type strains of Desulfotomaculum species belonging to subgroup 1a and of 'Desulfotomaculum reducens' strain MI-1. Phenotypically, 'Desulfotomaculum reducens' strain MI-1 can be distinguished from the other described Desulfotomaculum species of subgroup 1a by its ability to grow with propionate and butyrate. In addition, the strain is able to use a variety of metals as electron acceptors. Metal reduction has not been tested in the other species, but seems likely based on our genome analysis. Phylogenetic 16S rRNA gene sequence analysis and the average nucleotide identity between the genomes of the species of subgroup 1a show that strain MI-1 represents a novel species within the Desulfotomaculum 1a subgroup, Desulfotomaculum reducens sp. nov. The type strain is MI-1T.
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Affiliation(s)
- Michael Visser
- Laboratory of Microbiology, Wageningen University, Stippeneng 4, 6708 WE Wageningen, The Netherlands
| | - Alfons J M Stams
- Laboratory of Microbiology, Wageningen University, Stippeneng 4, 6708 WE Wageningen, The Netherlands.,CEB-Centre of Biological Engineering, University of Minho, Campus de Gualtar, 4710-057 Braga, Portugal
| | - Manon Frutschi
- Environmental Microbiology Laboratory, École Polytechnique Fédérale de Lausanne, CH A1 375 Station 6, Lausanne CH-1015, Switzerland
| | - Rizlan Bernier-Latmani
- Environmental Microbiology Laboratory, École Polytechnique Fédérale de Lausanne, CH A1 375 Station 6, Lausanne CH-1015, Switzerland
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Xu G, Zhu Q, Luo Y, Zhang X, Guo W, Dou W, Li H, Xu H, Zhang X, Xu Z. Enhanced production of l-serine by deleting sdaA combined with modifying and overexpressing serA in a mutant of Corynebacterium glutamicum SYPS-062 from sucrose. Biochem Eng J 2015. [DOI: 10.1016/j.bej.2015.06.009] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/28/2023]
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Rees MA, Stinear TP, Goode RJA, Coppel RL, Smith AI, Kleifeld O. Changes in protein abundance are observed in bacterial isolates from a natural host. Front Cell Infect Microbiol 2015; 5:71. [PMID: 26528441 PMCID: PMC4604328 DOI: 10.3389/fcimb.2015.00071] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2015] [Accepted: 09/25/2015] [Indexed: 11/23/2022] Open
Abstract
Bacterial proteomic studies frequently use strains cultured in synthetic liquid media over many generations. It is uncertain whether bacterial proteins expressed under these conditions will be the same as the repertoire found in natural environments, or when bacteria are infecting a host organism. Thus, genomic and proteomic characterization of bacteria derived from the host environment in comparison to reference strains grown in the lab, should aid understanding of pathogenesis. Isolates of Corynebacterium pseudotuberculosis were obtained from the lymph nodes of three naturally infected sheep and compared to a laboratory reference strain using bottom-up proteomics, after whole genome sequencing of each of the field isolates. These comparisons were performed following growth in liquid media that allowed us to reach the required protein amount for proteomic analysis. Over 1350 proteins were identified in the isolated strains, from which unique proteome features were revealed. Several of the identified proteins demonstrated a significant abundance difference in the field isolates compared to the reference strain even though there were no obvious differences in the DNA sequence of the corresponding gene or in nearby non-coding DNA. Higher abundance in the field isolates was observed for proteins related to hypoxia and nutrient deficiency responses as well as to thiopeptide biosynthesis.
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Affiliation(s)
- Megan A Rees
- Coppel Laboratory, Department of Microbiology, Monash University Clayton, VIC, Australia ; Monash Biomedical Proteomics Facility, Department of Biochemistry and Molecular Biology, Monash University Clayton, VIC, Australia
| | - Timothy P Stinear
- Stinear Laboratory, Department of Microbiology and Immunology, University of Melbourne Parkville, VIC, Australia
| | - Robert J A Goode
- Monash Biomedical Proteomics Facility, Department of Biochemistry and Molecular Biology, Monash University Clayton, VIC, Australia
| | - Ross L Coppel
- Coppel Laboratory, Department of Microbiology, Monash University Clayton, VIC, Australia
| | - Alexander I Smith
- Monash Biomedical Proteomics Facility, Department of Biochemistry and Molecular Biology, Monash University Clayton, VIC, Australia
| | - Oded Kleifeld
- Monash Biomedical Proteomics Facility, Department of Biochemistry and Molecular Biology, Monash University Clayton, VIC, Australia
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Sawada K, Wada M, Hagiwara T, Zen-In S, Imai K, Yokota A. Effect of pyruvate kinase gene deletion on the physiology of Corynebacterium glutamicum ATCC13032 under biotin-sufficient non-glutamate-producing conditions: Enhanced biomass production. Metab Eng Commun 2015; 2:67-75. [PMID: 34150510 PMCID: PMC8193254 DOI: 10.1016/j.meteno.2015.07.001] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2014] [Revised: 04/21/2015] [Accepted: 07/02/2015] [Indexed: 11/17/2022] Open
Abstract
The effect of pyruvate kinase gene (pyk) deletion on the physiology of Corynebacterium glutamicum ATCC13032 was investigated under biotin-sufficient, non-glutamate-producing conditions. In a complex medium containing 100 g/L glucose, a defined pyk deletion mutant, strain D1, exhibited 35% enhancement in glucose consumption rate, 37% increased growth and a 57% reduction in respiration rate compared to the wild-type parent. Significant upregulation of phosphoenolpyruvate (PEP) carboxylase and downregulation of PEP carboxykinase activities were observed in the D1 mutant, which may have prevented over-accumulation of PEP caused by the pyk deletion. Moreover, we found a dramatic 63% reduction in the activity of malate:quinone oxidoreductase (MQO) in the D1 mutant. MQO, a TCA cycle enzyme that converts malate to oxaloacetate (OAA), constitutes a major primary gate to the respiratory chain in C. glutamicum, thus explaining the reduced respiration rate in the mutant. Additionally, pyruvate carboxylase gene expression was downregulated in the mutant. These changes seemed to prevent OAA over-accumulation caused by the activity changes of PEP carboxylase/PEP carboxykinase. Intrinsically the same alterations were observed in the cultures conducted in a minimal medium containing 20 g/L glucose. Despite these responses in the mutant, metabolic distortion caused by pyk deletion under non-glutamate-producing conditions required amelioration by increased biomass production, as metabolome analysis revealed increased intracellular concentrations of several precursor metabolites for building block formation associated with pyk deletion. These fermentation profiles and metabolic alterations observed in the mutant reverted completely to the wild-type phenotypes in the pyk-complemented strain, suggesting the observed metabolic changes were caused by the pyk deletion. These results demonstrated multilateral strategies to overcome metabolic disturbance caused by pyk deletion in this bacterium. The effect of pyk-deletion was investigated under non-glutamate-producing conditions. Pyk-deletion induced enhanced growth, glucose consumption, and reduced respiration. Metabolic changes that suppressed PEP/OAA over-accumulation led to enhanced growth. MQO was proposed as a key controller regulating OAA formation and respiration.
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Affiliation(s)
- Kazunori Sawada
- Laboratory of Microbial Physiology, Research Faculty of Agriculture, Hokkaido University, Kita-9 Nishi-9, Kita-ku, Sapporo 060-8589, Japan
| | - Masaru Wada
- Laboratory of Microbial Physiology, Research Faculty of Agriculture, Hokkaido University, Kita-9 Nishi-9, Kita-ku, Sapporo 060-8589, Japan
| | - Takuya Hagiwara
- Laboratory of Microbial Physiology, Research Faculty of Agriculture, Hokkaido University, Kita-9 Nishi-9, Kita-ku, Sapporo 060-8589, Japan
| | - Susumu Zen-In
- Laboratory of Microbial Physiology, Research Faculty of Agriculture, Hokkaido University, Kita-9 Nishi-9, Kita-ku, Sapporo 060-8589, Japan
| | - Keita Imai
- Laboratory of Microbial Physiology, Research Faculty of Agriculture, Hokkaido University, Kita-9 Nishi-9, Kita-ku, Sapporo 060-8589, Japan
| | - Atsushi Yokota
- Laboratory of Microbial Physiology, Research Faculty of Agriculture, Hokkaido University, Kita-9 Nishi-9, Kita-ku, Sapporo 060-8589, Japan
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Increasing succinic acid production using the PTS-independent glucose transport system in a Corynebacterium glutamicum PTS-defective mutant. ACTA ACUST UNITED AC 2015; 42:1073-82. [DOI: 10.1007/s10295-015-1630-9] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2014] [Accepted: 04/28/2015] [Indexed: 12/29/2022]
Abstract
Abstract
Succinic acid synthesized from glucose shows potential as a bio-based platform chemical. However, the need for a high glucose concentration, and the accompanying low yields, limit its industrial applications. Despite efficient glucose uptake by the phosphotransferase system (PTS), 1 mol of phosphoenolpyruvate is required for each mole of internalized glucose. Therefore, a PTS-defective Corynebacterium glutamicum mutant was constructed to increase phosphoenolpyruvate availability for succinic acid synthesis, resulting in a lower glucose utilization rate and slower growth. The transcriptional regulator iolR was also deleted to enable the PTS-defective mutant to utilize glucose via iolT-mediated glucose transport. Deletion of iolR and overexpression of iolT1 and ppgk (polyphosphate glucokinase) in the PTS-deficient C. glutamicum strain completely restored glucose utilization, increasing production by 11.6 % and yield by 32.4 % compared with the control. This study revealed for the first time that iolR represses the expression of the two glucokinase genes (glk and ppgk).
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A third glucose uptake bypass in Corynebacterium glutamicum ATCC 31833. Appl Microbiol Biotechnol 2014; 99:2741-50. [PMID: 25549619 DOI: 10.1007/s00253-014-6323-1] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2014] [Revised: 12/09/2014] [Accepted: 12/12/2014] [Indexed: 10/24/2022]
Abstract
In Corynebacterium glutamicum, the phosphoenolpyruvate-dependent sugar phosphotransferase system (PTS) has long been the only known glucose uptake system, but we recently found suppressor mutants emerging from a PTS-negative strain of C. glutamicum ATCC 31833 on glucose agar plates, and identified two alternative potential glucose uptake systems, the myo-inositol transporters encoded by iolT1 and iolT2. The expression of either gene renders the PTS-negative strain WTΔptsH capable of growing on glucose. In the present study, we found a suppressor strain that still grew on glucose even after the iolT1 and iolT2 genes were both disrupted under the PTS-negative background. Whole-genome sequencing of the suppressor strain SPH1 identified a G-to-T exchange at 134 bp upstream of the bglF gene encoding an EII component of the β-glucoside-PTS, which is found in limited wild-type strains of C. glutamicum. Introduction of the mutation into strain WTΔptsH allowed the PTS-negative strain to grow on glucose. Reverse transcription-quantitative PCR analysis revealed that the mutation upregulates the bglF gene by approximately 11-fold. Overexpression of bglF under the gapA promoter in strain WTΔptsH rendered the strain capable of growing on glucose, and deletion of bglF in strain SPH1 abolished the growth again, proving that bglF is responsible for glucose uptake in the suppressor strain. Simultaneous disruption of three glucokinase genes, glk (Cgl2185, NCgl2105), ppgK (Cgl1910, NCgl1835), and Cgl2647 (NCgl2558), in strain SPH1 resulted in no growth on glucose. Plasmid-mediated expression of any of the three genes in the triple-knockout mutant restored the growth on glucose. These results indicate that C. glutamicum ATCC 31833 has an additional non-PTS glucose uptake route consisting of the bglF-specified EII permease and native glucokinases.
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Peters-Wendisch P, Götker S, Heider S, Komati Reddy G, Nguyen A, Stansen K, Wendisch V. Engineering biotin prototrophic Corynebacterium glutamicum strains for amino acid, diamine and carotenoid production. J Biotechnol 2014; 192 Pt B:346-54. [DOI: 10.1016/j.jbiotec.2014.01.023] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2013] [Revised: 12/21/2013] [Accepted: 01/03/2014] [Indexed: 11/17/2022]
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Zhou Z, Wang C, Chen Y, Zhang K, Xu H, Cai H, Chen Z. Increasing available NADH supply during succinic acid production by Corynebacterium glutamicum. Biotechnol Prog 2014; 31:12-9. [PMID: 25311136 DOI: 10.1002/btpr.1998] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/11/2014] [Revised: 10/09/2014] [Indexed: 11/06/2022]
Abstract
A critical factor in the biotechnological production of succinic acid with Corynebacterium glutamicum is the sufficient supply of NADH. It is conceivable that cofactor availability and the proportion of cofactor in the active form may play an important role in dictating the succinic acid yield. PntAB genes from Escherichia coli can directly catalyze the reversible hydride transfer and adjust the dynamic balance between NADP(H) and NAD(H). Hence, we studied the physiological effect of coenzyme systems by expressing the membrane-bound transhydrogenase pntAB genes. We have shown experimentally that the pntAB genes could function as an alternative source of NADH. In an anaerobic fermentation with C. glutamicum NC-3-pntAB, a 16% higher succinic acid yield and a 57% higher production from glucose were obtained by pntAB expression. Moreover, the formation of by-products was significantly decreased. The concomitant increase in the consumption of intracellular NADPH from 0.6 to 1.2 mmol/g CDW and the increased NADH/NAD(+) ratio resulted from introduction of pntAB, suggesting that the membrane-bound transhydrogenase converted excess NADPH to NADH for succinic acid production. Finally, we explored whether the transhydrogenase had different effects on the succinic acid formation on different carbon sources. The succinic acid yield was increased in the presence of pntAB by 16% on glucose, 7% on sucrose, and without large influence on fructose and xylose. The results of this study demonstrated that the effectiveness of cofactor manipulation could be a promising strategy applied in metabolic engineering.
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Affiliation(s)
- Zhihui Zhou
- College of Biotechnology and Pharmaceutical Engineering, Nanjing University of Technology, Nanjing, 211816, China
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40
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Succinate production from CO₂-grown microalgal biomass as carbon source using engineered Corynebacterium glutamicum through consolidated bioprocessing. Sci Rep 2014; 4:5819. [PMID: 25056811 PMCID: PMC4108913 DOI: 10.1038/srep05819] [Citation(s) in RCA: 33] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2014] [Accepted: 07/08/2014] [Indexed: 02/05/2023] Open
Abstract
The potential for production of chemicals from microalgal biomass has been considered as an alternative route for CO2 mitigation and establishment of biorefineries. This study presents the development of consolidated bioprocessing for succinate production from microalgal biomass using engineered Corynebacterium glutamicum. Starch-degrading and succinate-producing C. glutamicum strains produced succinate (0.16 g succinate/g total carbon source) from a mixture of starch and glucose as a model microalgal biomass. Subsequently, the engineered C. glutamicum strains were able to produce succinate (0.28 g succinate/g of total sugars including starch) from pretreated microalgal biomass of CO2-grown Chlamydomonas reinhardtii. For the first time, this work shows succinate production from CO2 via sequential fermentations of CO2-grown microalgae and engineered C. glutamicum. Therefore, consolidated bioprocessing based on microalgal biomass could be useful to promote variety of biorefineries.
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Woo HM, Park JB. Recent progress in development of synthetic biology platforms and metabolic engineering of Corynebacterium glutamicum. J Biotechnol 2014; 180:43-51. [DOI: 10.1016/j.jbiotec.2014.03.003] [Citation(s) in RCA: 43] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/24/2013] [Revised: 02/08/2014] [Accepted: 03/03/2014] [Indexed: 01/21/2023]
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Vogt M, Haas S, Klaffl S, Polen T, Eggeling L, van Ooyen J, Bott M. Pushing product formation to its limit: Metabolic engineering of Corynebacterium glutamicum for l-leucine overproduction. Metab Eng 2014; 22:40-52. [DOI: 10.1016/j.ymben.2013.12.001] [Citation(s) in RCA: 95] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2013] [Revised: 10/31/2013] [Accepted: 12/03/2013] [Indexed: 11/29/2022]
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43
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Vasco-Cárdenas MF, Baños S, Ramos A, Martín JF, Barreiro C. Proteome response of Corynebacterium glutamicum to high concentration of industrially relevant C₄ and C₅ dicarboxylic acids. J Proteomics 2013; 85:65-88. [PMID: 23624027 DOI: 10.1016/j.jprot.2013.04.019] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2012] [Revised: 03/05/2013] [Accepted: 04/09/2013] [Indexed: 12/11/2022]
Abstract
UNLABELLED More than fifty years of industrial and scientific developments on the amino acid-producer strain Corynebacterium glutamicum has generated an extremely huge knowledge highly applicable to the development of new products. Despite the production of dicarboxylic acids has already been engineered in C. glutamicum, the effect caused by these acids at competitive industrial levels has not yet been described. Thus, aspartic, fumaric, itaconic, malic and succinic acids have been tested on the growth of C. glutamicum to obtain their minimal inhibitory concentrations and their intracellular effects analyzed by 2D-DIGE. This analysis showed the modification of the central metabolism of C. glutamicum, the cross-regulation between malic acid and glucose as well as the aspartic acid utilization as nitrogen source. The analysis of the transcriptional regulators involved in the control of the detected proteins pointed to the ramB gene as a candidate for strain improvement. The analysis of the ΔramB mutant demonstrated its function as an enhancer of the growth speed or resistance level against aspartic, fumaric, itaconic and malic acids in C. glutamicum. BIOLOGICAL SIGNIFICANCE The effect of dicarboxylic acids addition to the C. glutamicum culture broth has been described. This proteome response is detailed and the deletion of a global regulator (ramB) has been described as a possible improving method for industrial strains. In addition, the consumption of aspartic acid as nitrogen source has been described for the first time in C. glutamicum, as well as, the cross-regulation between malic acid and glucose through the F0F1 respiratory system.
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Affiliation(s)
- María F Vasco-Cárdenas
- Área de Microbiología, Departamento de Biología Molecular, Universidad de León, Campus de Vegazana s/n, 24071 León, Spain
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