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Mao J, Zhang H, Chen Y, Wei L, Liu J, Nielsen J, Chen Y, Xu N. Relieving metabolic burden to improve robustness and bioproduction by industrial microorganisms. Biotechnol Adv 2024; 74:108401. [PMID: 38944217 DOI: 10.1016/j.biotechadv.2024.108401] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2024] [Revised: 05/04/2024] [Accepted: 06/25/2024] [Indexed: 07/01/2024]
Abstract
Metabolic burden is defined by the influence of genetic manipulation and environmental perturbations on the distribution of cellular resources. The rewiring of microbial metabolism for bio-based chemical production often leads to a metabolic burden, followed by adverse physiological effects, such as impaired cell growth and low product yields. Alleviating the burden imposed by undesirable metabolic changes has become an increasingly attractive approach for constructing robust microbial cell factories. In this review, we provide a brief overview of metabolic burden engineering, focusing specifically on recent developments and strategies for diminishing the burden while improving robustness and yield. A variety of examples are presented to showcase the promise of metabolic burden engineering in facilitating the design and construction of robust microbial cell factories. Finally, challenges and limitations encountered in metabolic burden engineering are discussed.
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Affiliation(s)
- Jiwei Mao
- Department of Life Sciences, Chalmers University of Technology, SE412 96 Gothenburg, Sweden
| | - Hongyu Zhang
- Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin 300308, PR China; College of Life Sciences, University of Chinese Academy of Sciences, Beijing, 100049, PR China
| | - Yu Chen
- Key Laboratory of Quantitative Synthetic Biology, Shenzhen Institute of Synthetic Biology, Shenzhen Institute of Advanced Technology, Chinese Academy of Sciences, Shenzhen 518055, PR China
| | - Liang Wei
- Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin 300308, PR China
| | - Jun Liu
- Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin 300308, PR China; Key Laboratory of Engineering Biology for Low-Carbon Manufacturing, Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin 300308, PR China
| | - Jens Nielsen
- Department of Life Sciences, Chalmers University of Technology, SE412 96 Gothenburg, Sweden; BioInnovation Institute, Ole Maaløes Vej 3, DK2200 Copenhagen, Denmark.
| | - Yun Chen
- Department of Life Sciences, Chalmers University of Technology, SE412 96 Gothenburg, Sweden; Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, DK2800 Kongens Lyngby, Denmark.
| | - Ning Xu
- Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin 300308, PR China; College of Life Sciences, University of Chinese Academy of Sciences, Beijing, 100049, PR China; Key Laboratory of Engineering Biology for Low-Carbon Manufacturing, Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin 300308, PR China.
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Qiao Y, Yin B, Zhou W, Wang M, Chang Z, Zhou J, Yue M, Chen J, Liu F, Feng Z. Nutrient consumption patterns of Lactobacillus acidophilus. JOURNAL OF THE SCIENCE OF FOOD AND AGRICULTURE 2024; 104:5982-5990. [PMID: 38427028 DOI: 10.1002/jsfa.13424] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/13/2023] [Revised: 02/17/2024] [Accepted: 03/01/2024] [Indexed: 03/02/2024]
Abstract
BACKGROUND One of the greatest challenges in using Lactobacillus acidophilus as a probiotic is acid stress. The current research aimed to identify substances that help L. acidophilus resist acid stress; this was achieved through assessing its nutrient consumption patterns under various pH conditions. RESULTS The consumption rates of alanine, uracil, adenine, guanine, niacin, and manganese were consistently higher than 60% for L. acidophilus LA-5 cultured at pH 5.8, 4.9, and 4.4. The consumption rates of glutamic acid + glutamine and thiamine increased with decreasing pH and were higher than 60% at pH 4.9 and 4.4. The viable counts of L. acidophilus LA-5 were significantly increased under the corresponding acidic stress conditions (pH 4.9 and 4.4) through the appropriate addition of either alanine (3.37 and 2.81 mmol L-1), glutamic acid + glutamine (4.77 mmol L-1), guanine (0.13 and 0.17 mmol L-1), niacin (0.02 mmol L-1), thiamine (0.009 mmol L-1), or manganese (0.73 and 0.64 mmol L-1) (P < 0.05). The viable counts of L. acidophilus LA-5 cultured in a medium supplemented with combined nutritional factors was 1.02-1.03-fold of the counts observed in control medium under all acid conditions (P < 0.05). CONCLUSION Alanine, glutamic acid + glutamine, guanine, niacin, thiamine, and manganese can improve the growth of L. acidophilus LA-5 in an acidic environment in the present study. The results will contribute to optimizing strategies to enhance the acid resistance of L. acidophilus and expand its application in the fermentation industry. © 2024 Society of Chemical Industry.
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Affiliation(s)
- Yali Qiao
- Key Laboratory of Dairy Science, Ministry of Education, College of Food Science, Northeast Agricultural University, Harbin, China
| | - Boxing Yin
- Yangzhou Yangda Kangyuan Dairy Co., Ltd, Yangzhou, China
| | - Wei Zhou
- Yangzhou Yangda Kangyuan Dairy Co., Ltd, Yangzhou, China
| | - Mengrui Wang
- Key Laboratory of Dairy Science, Ministry of Education, College of Food Science, Northeast Agricultural University, Harbin, China
| | - Ziqing Chang
- Key Laboratory of Dairy Science, Ministry of Education, College of Food Science, Northeast Agricultural University, Harbin, China
| | - Junping Zhou
- Key Laboratory of Dairy Science, Ministry of Education, College of Food Science, Northeast Agricultural University, Harbin, China
| | - Mingzhe Yue
- Key Laboratory of Dairy Science, Ministry of Education, College of Food Science, Northeast Agricultural University, Harbin, China
| | - Junxia Chen
- Key Laboratory of Dairy Science, Ministry of Education, College of Food Science, Northeast Agricultural University, Harbin, China
| | - Fei Liu
- Key Laboratory of Dairy Science, Ministry of Education, College of Food Science, Northeast Agricultural University, Harbin, China
| | - Zhen Feng
- Yangzhou Yangda Kangyuan Dairy Co., Ltd, Yangzhou, China
- Spice and Beverage Research Institute, Chinese Academy of Tropical Agricultural Sciences, Wanning, China
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Ding N, Yuan Z, Sun L, Yin L. Dynamic and Static Regulation of Nicotinamide Adenine Dinucleotide Phosphate: Strategies, Challenges, and Future Directions in Metabolic Engineering. Molecules 2024; 29:3687. [PMID: 39125091 PMCID: PMC11314019 DOI: 10.3390/molecules29153687] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2024] [Revised: 07/30/2024] [Accepted: 07/31/2024] [Indexed: 08/12/2024] Open
Abstract
Reduced nicotinamide adenine dinucleotide phosphate (NADPH) is a crucial cofactor in metabolic networks. The efficient regeneration of NADPH is one of the limiting factors for productivity in biotransformation processes. To date, many metabolic engineering tools and static regulation strategies have been developed to regulate NADPH regeneration. However, traditional static regulation methods often lead to the NADPH/NADP+ imbalance, causing disruptions in cell growth and production. These methods also fail to provide real-time monitoring of intracellular NADP(H) or NADPH/NADP+ levels. In recent years, various biosensors have been developed for the detection, monitoring, and dynamic regulate of the intracellular NADP(H) levels or the NADPH/NADP+ balance. These NADPH-related biosensors are mainly used in the cofactor engineering of bacteria, yeast, and mammalian cells. This review analyzes and summarizes the NADPH metabolic regulation strategies from both static and dynamic perspectives, highlighting current challenges and potential solutions, and discusses future directions for the advanced regulation of the NADPH/NADP+ balance.
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Affiliation(s)
- Nana Ding
- State Key Laboratory of Subtropical Silviculture, Zhejiang A&F University, Hangzhou 311300, China; (Z.Y.); (L.S.)
- Zhejiang Provincial Key Laboratory of Resources Protection and Innovation of Traditional Chinese Medicine, Zhejiang A&F University, Hangzhou 311300, China
| | - Zenan Yuan
- State Key Laboratory of Subtropical Silviculture, Zhejiang A&F University, Hangzhou 311300, China; (Z.Y.); (L.S.)
- Zhejiang Provincial Key Laboratory of Resources Protection and Innovation of Traditional Chinese Medicine, Zhejiang A&F University, Hangzhou 311300, China
| | - Lei Sun
- State Key Laboratory of Subtropical Silviculture, Zhejiang A&F University, Hangzhou 311300, China; (Z.Y.); (L.S.)
- Zhejiang Provincial Key Laboratory of Resources Protection and Innovation of Traditional Chinese Medicine, Zhejiang A&F University, Hangzhou 311300, China
| | - Lianghong Yin
- State Key Laboratory of Subtropical Silviculture, Zhejiang A&F University, Hangzhou 311300, China; (Z.Y.); (L.S.)
- Zhejiang Provincial Key Laboratory of Resources Protection and Innovation of Traditional Chinese Medicine, Zhejiang A&F University, Hangzhou 311300, China
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Song F, Qin Z, Qiu K, Huang Z, Wang L, Zhang H, Shan X, Meng H, Liu X, Zhou J. Development of a vitamin B 5 hyperproducer in Escherichia coli by multiple metabolic engineering. Metab Eng 2024; 84:158-168. [PMID: 38942195 DOI: 10.1016/j.ymben.2024.06.006] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2024] [Revised: 06/06/2024] [Accepted: 06/14/2024] [Indexed: 06/30/2024]
Abstract
Vitamin B5 [D-pantothenic acid (D-PA)] is an essential water-soluble vitamin that is widely used in the food and feed industries. Currently, the relatively low fermentation efficiency limits the industrial application of D-PA. Here, a plasmid-free D-PA hyperproducer was constructed using systematic metabolic engineering strategies. First, pyruvate was enriched by deleting the non-phosphotransferase system, inhibiting pyruvate competitive branches, and dynamically controlling the TCA cycle. Next, the (R)-pantoate pathway was enhanced by screening the rate-limiting enzyme PanBC and regulating the other enzymes of this pathway one by one. Then, to enhance NADPH sustainability, NADPH regeneration was achieved through the novel "PEACES" system by (1) expressing the NAD + kinase gene ppnk from Clostridium glutamicum and the NADP + -dependent gapCcae from Clostridium acetobutyricum and (2) knocking-out the endogenous sthA gene, which interacts with ilvC and panE in the D-PA biosynthesis pathway. Combined with transcriptome analysis, it was found that the membrane proteins OmpC and TolR promoted D-PA efflux by increasing membrane fluidity. Strain PA132 produced a D-PA titer of 83.26 g/L by two-stage fed-batch fermentation, which is the highest D-PA titer reported so far. This work established competitive producers for the industrial production of D-PA and provided an effective strategy for the production of related products.
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Affiliation(s)
- Fuqiang Song
- Science Center for Future Foods, Jiangnan University, 1800 Lihu Road, Wuxi, Jiangsu, 214122, China; Engineering Research Center of Ministry of Education on Food Synthetic Biotechnology, Jiangnan University, 1800 Lihu Road, Wuxi, Jiangsu, 214122, China; Jiangsu Province Engineering Research Center of Food Synthetic Biotechnology, Jiangnan University, Wuxi, 214122, China
| | - Zhijie Qin
- Science Center for Future Foods, Jiangnan University, 1800 Lihu Road, Wuxi, Jiangsu, 214122, China; Engineering Research Center of Ministry of Education on Food Synthetic Biotechnology, Jiangnan University, 1800 Lihu Road, Wuxi, Jiangsu, 214122, China
| | - Kun Qiu
- Science Center for Future Foods, Jiangnan University, 1800 Lihu Road, Wuxi, Jiangsu, 214122, China; Engineering Research Center of Ministry of Education on Food Synthetic Biotechnology, Jiangnan University, 1800 Lihu Road, Wuxi, Jiangsu, 214122, China
| | - Zhongshi Huang
- Science Center for Future Foods, Jiangnan University, 1800 Lihu Road, Wuxi, Jiangsu, 214122, China; Engineering Research Center of Ministry of Education on Food Synthetic Biotechnology, Jiangnan University, 1800 Lihu Road, Wuxi, Jiangsu, 214122, China
| | - Lian Wang
- Science Center for Future Foods, Jiangnan University, 1800 Lihu Road, Wuxi, Jiangsu, 214122, China; Engineering Research Center of Ministry of Education on Food Synthetic Biotechnology, Jiangnan University, 1800 Lihu Road, Wuxi, Jiangsu, 214122, China
| | - Heng Zhang
- Science Center for Future Foods, Jiangnan University, 1800 Lihu Road, Wuxi, Jiangsu, 214122, China; Engineering Research Center of Ministry of Education on Food Synthetic Biotechnology, Jiangnan University, 1800 Lihu Road, Wuxi, Jiangsu, 214122, China
| | - Xiaoyu Shan
- Science Center for Future Foods, Jiangnan University, 1800 Lihu Road, Wuxi, Jiangsu, 214122, China; Engineering Research Center of Ministry of Education on Food Synthetic Biotechnology, Jiangnan University, 1800 Lihu Road, Wuxi, Jiangsu, 214122, China
| | - Hao Meng
- Hunan Chengda Biotechnology Co., Ltd., Malukou, Anhua, Hunan, 413506, China
| | - Xirong Liu
- Hunan Chengda Biotechnology Co., Ltd., Malukou, Anhua, Hunan, 413506, China
| | - Jingwen Zhou
- Science Center for Future Foods, Jiangnan University, 1800 Lihu Road, Wuxi, Jiangsu, 214122, China; Engineering Research Center of Ministry of Education on Food Synthetic Biotechnology, Jiangnan University, 1800 Lihu Road, Wuxi, Jiangsu, 214122, China; Jiangsu Province Engineering Research Center of Food Synthetic Biotechnology, Jiangnan University, Wuxi, 214122, China.
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Han T, Miao G. Strategies, Achievements, and Potential Challenges of Plant and Microbial Chassis in the Biosynthesis of Plant Secondary Metabolites. Molecules 2024; 29:2106. [PMID: 38731602 PMCID: PMC11085123 DOI: 10.3390/molecules29092106] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2024] [Revised: 04/27/2024] [Accepted: 04/27/2024] [Indexed: 05/13/2024] Open
Abstract
Diverse secondary metabolites in plants, with their rich biological activities, have long been important sources for human medicine, food additives, pesticides, etc. However, the large-scale cultivation of host plants consumes land resources and is susceptible to pest and disease problems. Additionally, the multi-step and demanding nature of chemical synthesis adds to production costs, limiting their widespread application. In vitro cultivation and the metabolic engineering of plants have significantly enhanced the synthesis of secondary metabolites with successful industrial production cases. As synthetic biology advances, more research is focusing on heterologous synthesis using microorganisms. This review provides a comprehensive comparison between these two chassis, evaluating their performance in the synthesis of various types of secondary metabolites from the perspectives of yield and strategies. It also discusses the challenges they face and offers insights into future efforts and directions.
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Affiliation(s)
- Taotao Han
- Department of Bioengineering, Huainan Normal University, Huainan 232038, China;
| | - Guopeng Miao
- Department of Bioengineering, Huainan Normal University, Huainan 232038, China;
- Key Laboratory of Bioresource and Environmental Biotechnology of Anhui Higher Education Institutes, Huainan Normal University, Huainan 232038, China
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Yang H, He Y, Zhou S, Deng Y. Dynamic regulation and cofactor engineering of escherichia coli to enhance production of glycolate from corn stover hydrolysate. BIORESOURCE TECHNOLOGY 2024; 398:130531. [PMID: 38447620 DOI: 10.1016/j.biortech.2024.130531] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/27/2023] [Revised: 02/24/2024] [Accepted: 03/03/2024] [Indexed: 03/08/2024]
Abstract
Glycolic acid is widely employed in chemical cleaning, the production of polyglycolic acid-lactic acid, and polyglycolic acid. Currently, the bottleneck of glycolate biosynthesis lies on the imbalance of metabolic flux and the deficiency of NADPH. In this study, a dynamic regulation system was developed and optimized to enhance the metabolic flux from glucose to glycolate. Additionally, the knockout of transhydrogenase (sthA), along with the overexpression of pyridine nucleotide transhydrogenase (pntAB) and the implementation of the Entner-Doudoroff pathway, were performed to further increase the production of the NADPH, thereby increasing the titer of glycolate to 5.6 g/L. To produce glycolate from corn stover hydrolysate, carbon catabolite repression was alleviated and glucose utilization was accelerated. The final strain, E. coli Mgly10-245, is inducer-free, achieving a glycolate titer of 46.1 g/L using corn stover hydrolysate (77.1 % of theoretical yield). These findings will contribute to the advancement of industrial glycolate production.
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Affiliation(s)
- Haining Yang
- National Engineering Research Center of Cereal Fermentation and Food Biomanufacturing, Jiangnan University, 1800 Lihu Road, Wuxi, Jiangsu 214122, China
| | - Yucai He
- State Key Laboratory of Biocatalysis and Enzyme Engineering, School of Life Sciences, Hubei University, China, 430062
| | - Shenghu Zhou
- National Engineering Research Center of Cereal Fermentation and Food Biomanufacturing, Jiangnan University, 1800 Lihu Road, Wuxi, Jiangsu 214122, China; Jiangsu Provincial Research Center for Bioactive Product Processing Technology, Jiangnan University, 1800 Lihu Road, Wuxi, Jiangsu 214122, China.
| | - Yu Deng
- National Engineering Research Center of Cereal Fermentation and Food Biomanufacturing, Jiangnan University, 1800 Lihu Road, Wuxi, Jiangsu 214122, China; Jiangsu Provincial Research Center for Bioactive Product Processing Technology, Jiangnan University, 1800 Lihu Road, Wuxi, Jiangsu 214122, China.
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Hao Y, Pan X, You J, Li G, Xu M, Rao Z. Microbial production of branched chain amino acids: Advances and perspectives. BIORESOURCE TECHNOLOGY 2024; 397:130502. [PMID: 38417463 DOI: 10.1016/j.biortech.2024.130502] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/25/2023] [Revised: 02/23/2024] [Accepted: 02/25/2024] [Indexed: 03/01/2024]
Abstract
Branched-chain amino acids (BCAAs) such as L-valine, L-leucine, and L-isoleucine are widely used in food and feed. To comply with sustainable development goals, commercial production of BCAAs has been completely replaced with microbial fermentation. However, the efficient production of BCAAs by microorganisms remains a serious challenge due to their staggered metabolic networks and cell growth. To overcome these difficulties, systemic metabolic engineering has emerged as an effective and feasible strategy for the biosynthesis of BCAA. This review firstly summarizes the research advances in the microbial synthesis of BCAAs and representative engineering strategies. Second, systematic methods, such as high-throughput screening, adaptive laboratory evolution, and omics analysis, can be used to analyses the synthesis of BCAAs at the whole-cell level and further improve the titer of target chemicals. Finally, new tools and engineering strategies that may increase the production output and development direction of the microbial production of BCAAs are discussed.
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Affiliation(s)
- Yanan Hao
- Key Laboratory of Industrial Biotechnology of the Ministry of Education, Laboratory of Applied Microorganisms and Metabolic Engineering, School of Biotechnology, Jiangnan University, Wuxi 214122, China
| | - Xuewei Pan
- Key Laboratory of Industrial Biotechnology of the Ministry of Education, Laboratory of Applied Microorganisms and Metabolic Engineering, School of Biotechnology, Jiangnan University, Wuxi 214122, China
| | - Jiajia You
- Key Laboratory of Industrial Biotechnology of the Ministry of Education, Laboratory of Applied Microorganisms and Metabolic Engineering, School of Biotechnology, Jiangnan University, Wuxi 214122, China
| | - Guomin Li
- Key Laboratory of Industrial Biotechnology of the Ministry of Education, Laboratory of Applied Microorganisms and Metabolic Engineering, School of Biotechnology, Jiangnan University, Wuxi 214122, China
| | - Meijuan Xu
- Key Laboratory of Industrial Biotechnology of the Ministry of Education, Laboratory of Applied Microorganisms and Metabolic Engineering, School of Biotechnology, Jiangnan University, Wuxi 214122, China
| | - Zhiming Rao
- Key Laboratory of Industrial Biotechnology of the Ministry of Education, Laboratory of Applied Microorganisms and Metabolic Engineering, School of Biotechnology, Jiangnan University, Wuxi 214122, China.
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Zou S, Zhang B, Han Y, Liu J, Zhao K, Xue Y, Zheng Y. Design of a cofactor self-sufficient whole-cell biocatalyst for enzymatic asymmetric reduction via engineered metabolic pathways and multi-enzyme cascade. Biotechnol J 2024; 19:e2300744. [PMID: 38509791 DOI: 10.1002/biot.202300744] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/27/2023] [Revised: 02/22/2024] [Accepted: 03/03/2024] [Indexed: 03/22/2024]
Abstract
NAD(P)H-dependent oxidoreductases are crucial biocatalysts for synthesizing chiral compounds. Yet, the industrial implementation of enzymatic redox reactions is often hampered by an insufficient supply of expensive nicotinamide cofactors. Here, a cofactor self-sufficient whole-cell biocatalyst was developed for the enzymatic asymmetric reduction of 2-oxo-4-[(hydroxy)(-methyl)phosphinyl] butyric acid (PPO) to L-phosphinothricin (L-PPT). The endogenous NADP+ pool was significantly enhanced by regulating Preiss-Handler pathway toward NAD(H) synthesis and, in the meantime, introducing NAD kinase to phosphorylate NAD(H) toward NADP+. The intracellular NADP(H) concentration displayed a 2.97-fold increase with the strategy compared with the wild-type strain. Furthermore, a recombinant multi-enzyme cascade biocatalytic system was constructed based on the Escherichia coli chassis. In order to balance multi-enzyme co-expression levels, the strategy of modulating rate-limiting enzyme PmGluDH by RBS strengths regulation successfully increased the catalytic efficiency of PPO conversion. Finally, the cofactor self-sufficient whole-cell biocatalyst effectively converted 300 mM PPO to L-PPT in 2 h without the need to add exogenous cofactors, resulting in a 2.3-fold increase in PPO conversion (%) from 43% to 100%, with a high space-time yield of 706.2 g L-1 d-1 and 99.9% ee. Overall, this work demonstrates a technological example for constructing a cofactor self-sufficient system for NADPH-dependent redox biocatalysis.
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Affiliation(s)
- Shuping Zou
- Key Laboratory of Bioorganic Synthesis of Zhejiang Province, College of Biotechnology and Bioengineering, Zhejiang University of Technology, Hangzhou, China
- Engineering Research Center of Bioconversion and Biopurification of Ministry of Education, Zhejiang University of Technology, Hangzhou, China
| | - Bing Zhang
- Key Laboratory of Bioorganic Synthesis of Zhejiang Province, College of Biotechnology and Bioengineering, Zhejiang University of Technology, Hangzhou, China
- Engineering Research Center of Bioconversion and Biopurification of Ministry of Education, Zhejiang University of Technology, Hangzhou, China
| | - Yuyue Han
- Key Laboratory of Bioorganic Synthesis of Zhejiang Province, College of Biotechnology and Bioengineering, Zhejiang University of Technology, Hangzhou, China
- Engineering Research Center of Bioconversion and Biopurification of Ministry of Education, Zhejiang University of Technology, Hangzhou, China
| | - Jinlong Liu
- Key Laboratory of Bioorganic Synthesis of Zhejiang Province, College of Biotechnology and Bioengineering, Zhejiang University of Technology, Hangzhou, China
- Engineering Research Center of Bioconversion and Biopurification of Ministry of Education, Zhejiang University of Technology, Hangzhou, China
| | - Kuo Zhao
- Key Laboratory of Bioorganic Synthesis of Zhejiang Province, College of Biotechnology and Bioengineering, Zhejiang University of Technology, Hangzhou, China
- Engineering Research Center of Bioconversion and Biopurification of Ministry of Education, Zhejiang University of Technology, Hangzhou, China
| | - Yaping Xue
- Key Laboratory of Bioorganic Synthesis of Zhejiang Province, College of Biotechnology and Bioengineering, Zhejiang University of Technology, Hangzhou, China
- Engineering Research Center of Bioconversion and Biopurification of Ministry of Education, Zhejiang University of Technology, Hangzhou, China
| | - Yuguo Zheng
- Key Laboratory of Bioorganic Synthesis of Zhejiang Province, College of Biotechnology and Bioengineering, Zhejiang University of Technology, Hangzhou, China
- Engineering Research Center of Bioconversion and Biopurification of Ministry of Education, Zhejiang University of Technology, Hangzhou, China
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Jaroensuk J, Sutthaphirom C, Phonbuppha J, Chinantuya W, Kesornpun C, Akeratchatapan N, Kittipanukul N, Phatinuwat K, Atichartpongkul S, Fuangthong M, Pongtharangkul T, Hollmann F, Chaiyen P. A versatile in situ cofactor enhancing system for meeting cellular demands for engineered metabolic pathways. J Biol Chem 2024; 300:105598. [PMID: 38159859 PMCID: PMC10850783 DOI: 10.1016/j.jbc.2023.105598] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2023] [Revised: 12/02/2023] [Accepted: 12/18/2023] [Indexed: 01/03/2024] Open
Abstract
Cofactor imbalance obstructs the productivities of metabolically engineered cells. Herein, we employed a minimally perturbing system, xylose reductase and lactose (XR/lactose), to increase the levels of a pool of sugar phosphates which are connected to the biosynthesis of NAD(P)H, FAD, FMN, and ATP in Escherichia coli. The XR/lactose system could increase the amounts of the precursors of these cofactors and was tested with three different metabolically engineered cell systems (fatty alcohol biosynthesis, bioluminescence light generation, and alkane biosynthesis) with different cofactor demands. Productivities of these cells were increased 2-4-fold by the XR/lactose system. Untargeted metabolomic analysis revealed different metabolite patterns among these cells, demonstrating that only metabolites involved in relevant cofactor biosynthesis were altered. The results were also confirmed by transcriptomic analysis. Another sugar reducing system (glucose dehydrogenase) could also be used to increase fatty alcohol production but resulted in less yield enhancement than XR. This work demonstrates that the approach of increasing cellular sugar phosphates can be a generic tool to increase in vivo cofactor generation upon cellular demand for synthetic biology.
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Affiliation(s)
- Juthamas Jaroensuk
- School of Biomolecular Science and Engineering, Vidyasirimedhi Institute of Science and Technology (VISTEC), Rayong, Thailand
| | - Chalermroj Sutthaphirom
- School of Biomolecular Science and Engineering, Vidyasirimedhi Institute of Science and Technology (VISTEC), Rayong, Thailand
| | - Jittima Phonbuppha
- School of Biomolecular Science and Engineering, Vidyasirimedhi Institute of Science and Technology (VISTEC), Rayong, Thailand
| | - Wachirawit Chinantuya
- School of Biomolecular Science and Engineering, Vidyasirimedhi Institute of Science and Technology (VISTEC), Rayong, Thailand; Faculty of Science, Department of Biochemistry and Center for Excellence in Protein and Enzyme Technology, Mahidol University, Bangkok, Thailand
| | - Chatchai Kesornpun
- School of Biomolecular Science and Engineering, Vidyasirimedhi Institute of Science and Technology (VISTEC), Rayong, Thailand
| | - Nattanon Akeratchatapan
- School of Biomolecular Science and Engineering, Vidyasirimedhi Institute of Science and Technology (VISTEC), Rayong, Thailand
| | - Narongyot Kittipanukul
- School of Biomolecular Science and Engineering, Vidyasirimedhi Institute of Science and Technology (VISTEC), Rayong, Thailand
| | - Kamonwan Phatinuwat
- Program in Applied Biological Sciences, Chulabhorn Graduate Institute, Bangkok, Thailand
| | | | - Mayuree Fuangthong
- Program in Applied Biological Sciences, Chulabhorn Graduate Institute, Bangkok, Thailand; Laboratory of Biotechnology, Chulabhorn Research Institute, Bangkok, Thailand
| | | | - Frank Hollmann
- Department of Biotechnology, Delft University of Technology, Delft, Netherlands
| | - Pimchai Chaiyen
- School of Biomolecular Science and Engineering, Vidyasirimedhi Institute of Science and Technology (VISTEC), Rayong, Thailand.
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Ma X, Sun C, Xian M, Guo J, Zhang R. Progress in research on the biosynthesis of 1,2,4-butanetriol by engineered microbes. World J Microbiol Biotechnol 2024; 40:68. [PMID: 38200399 DOI: 10.1007/s11274-024-03885-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2023] [Accepted: 01/05/2024] [Indexed: 01/12/2024]
Abstract
1,2,4-butanetriol (BT) is a polyol with unique chemical properties, which has a stereocenter and can be divided into D-BT (the S-enantiomer) and L-BT (the R-enantiomer). BT can be used for the synthesis of 1,2,4-butanetriol trinitrate, 3-hydroxytetrahydrofuran, polyurethane, and other chemicals. It is widely used in the military industry, medicine, tobacco, polymer. At present, the BT is mainly synthesized by chemical methods, which are accompanied by harsh reaction conditions, poor selectivity, many by-products, and environmental pollution. Therefore, BT biosynthesis methods with the advantages of mild reaction conditions and green sustainability have become a current research hotspot. In this paper, the research status of microbial synthesis of BT was summarized from the following three aspects: (1) the biosynthetic pathway establishment for BT from xylose; (2) metabolic engineering strategies employed for improving BT production from xylose; (3) other substrates for BT production. Finally, the challenges and prospects of biosynthetic BT were discussed for future methods to improve competitiveness for industrial production.
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Affiliation(s)
- Xiangyu Ma
- CAS Key Laboratory of Bio-Based Materials, Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, Qingdao, 266101, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Chao Sun
- CAS Key Laboratory of Bio-Based Materials, Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, Qingdao, 266101, China
- Shandong Energy Institute, Qingdao, 266101, China
- Qingdao New Energy Shandong Laboratory, Qingdao, 266101, China
| | - Mo Xian
- CAS Key Laboratory of Bio-Based Materials, Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, Qingdao, 266101, China
- Shandong Energy Institute, Qingdao, 266101, China
- Qingdao New Energy Shandong Laboratory, Qingdao, 266101, China
| | - Jing Guo
- CAS Key Laboratory of Bio-Based Materials, Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, Qingdao, 266101, China.
- Shandong Energy Institute, Qingdao, 266101, China.
- Qingdao New Energy Shandong Laboratory, Qingdao, 266101, China.
| | - Rubing Zhang
- CAS Key Laboratory of Bio-Based Materials, Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, Qingdao, 266101, China.
- Shandong Energy Institute, Qingdao, 266101, China.
- Qingdao New Energy Shandong Laboratory, Qingdao, 266101, China.
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11
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Zhao K, Tang H, Zhang B, Zou S, Liu Z, Zheng Y. Microbial production of vitamin B5: current status and prospects. Crit Rev Biotechnol 2023; 43:1172-1192. [PMID: 36210178 DOI: 10.1080/07388551.2022.2104690] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2021] [Accepted: 07/01/2022] [Indexed: 11/03/2022]
Abstract
Vitamin B5, also called D-pantothenic acid (D-PA), is a necessary micronutrient that plays an essential role in maintaining the physiological function of an organism. It is widely used in: food, medicine, feed, cosmetics, and other fields. Currently, the production of D-PA in industry heavily relies on chemical processes and enzymatic catalysis. With an increasing demand on the market, replacing chemical-based production of D-PA with microbial fermentation utilizing renewable resources is necessary. In this review, the physiological role and applications of D-PA were firstly introduced, after which the biosynthesis pathways and enzymes will be summarized. Subsequently, a series of cell factory development strategies for excessive D-PA production are analyzed and discussed. Finally, the prospect of microbial production of D-PA production has been prospected.
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Affiliation(s)
- Kuo Zhao
- National and Local Joint Engineering Research Center for Biomanufacturing of Chiral Chemicals, Zhejiang University of Technology, Hangzhou, PR China
- College of Biotechnology and Bioengineering, Key Laboratory of Bioorganic Synthesis of Zhejiang Province, Zhejiang University of Technology, Hangzhou, PR China
| | - Heng Tang
- National and Local Joint Engineering Research Center for Biomanufacturing of Chiral Chemicals, Zhejiang University of Technology, Hangzhou, PR China
- College of Biotechnology and Bioengineering, Key Laboratory of Bioorganic Synthesis of Zhejiang Province, Zhejiang University of Technology, Hangzhou, PR China
| | - Bo Zhang
- National and Local Joint Engineering Research Center for Biomanufacturing of Chiral Chemicals, Zhejiang University of Technology, Hangzhou, PR China
- College of Biotechnology and Bioengineering, Key Laboratory of Bioorganic Synthesis of Zhejiang Province, Zhejiang University of Technology, Hangzhou, PR China
| | - Shuping Zou
- National and Local Joint Engineering Research Center for Biomanufacturing of Chiral Chemicals, Zhejiang University of Technology, Hangzhou, PR China
- College of Biotechnology and Bioengineering, Key Laboratory of Bioorganic Synthesis of Zhejiang Province, Zhejiang University of Technology, Hangzhou, PR China
| | - Zhiqiang Liu
- National and Local Joint Engineering Research Center for Biomanufacturing of Chiral Chemicals, Zhejiang University of Technology, Hangzhou, PR China
- College of Biotechnology and Bioengineering, Key Laboratory of Bioorganic Synthesis of Zhejiang Province, Zhejiang University of Technology, Hangzhou, PR China
| | - Yuguo Zheng
- National and Local Joint Engineering Research Center for Biomanufacturing of Chiral Chemicals, Zhejiang University of Technology, Hangzhou, PR China
- College of Biotechnology and Bioengineering, Key Laboratory of Bioorganic Synthesis of Zhejiang Province, Zhejiang University of Technology, Hangzhou, PR China
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12
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Zhang B, Lingga C, De Groot H, Hackmann TJ. The oxidoreductase activity of Rnf balances redox cofactors during fermentation of glucose to propionate in Prevotella. Sci Rep 2023; 13:16429. [PMID: 37777597 PMCID: PMC10542786 DOI: 10.1038/s41598-023-43282-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2023] [Accepted: 09/21/2023] [Indexed: 10/02/2023] Open
Abstract
Propionate is a microbial metabolite formed in the gastrointestinal tract, and it affects host physiology as a source of energy and signaling molecule. Despite the importance of propionate, the biochemical pathways responsible for its formation are not clear in all microbes. For the succinate pathway used during fermentation, a key enzyme appears to be missing-one that oxidizes ferredoxin and reduces NAD. Here we show that Rnf [ferredoxin-NAD+ oxidoreductase (Na+-transporting)] is this key enzyme in two abundant bacteria of the rumen (Prevotella brevis and Prevotella ruminicola). We found these bacteria form propionate, succinate, and acetate with the classic succinate pathway. Without ferredoxin:NAD+ oxidoreductase, redox cofactors would be unbalanced; it would produce almost equal excess amounts of reduced ferredoxin and oxidized NAD. By combining growth experiments, genomics, proteomics, and enzyme assays, we point to the possibility that these bacteria solve this problem by oxidizing ferredoxin and reducing NAD with Rnf [ferredoxin-NAD+ oxidoreductase (Na+-transporting)]. Genomic and phenotypic data suggest many bacteria may use Rnf similarly. This work shows the ferredoxin:NAD+ oxidoreductase activity of Rnf is important to propionate formation in Prevotella species and other bacteria from the environment, and it provides fundamental knowledge for manipulating fermentative propionate production.
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Affiliation(s)
- Bo Zhang
- Department of Animal Science, University of California, Davis, CA, USA
| | | | - Hannah De Groot
- Department of Animal Science, University of California, Davis, CA, USA
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13
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Wang HD, Xu JZ, Zhang WG. Reduction of acetate synthesis, enhanced arginine export, and supply of precursors, cofactors, and energy for improved synthesis of L-arginine by Escherichia coli. Appl Microbiol Biotechnol 2023; 107:3593-3603. [PMID: 37097502 DOI: 10.1007/s00253-023-12532-1] [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: 01/24/2023] [Revised: 03/27/2023] [Accepted: 03/30/2023] [Indexed: 04/26/2023]
Abstract
L-arginine (L-Arg) is a semi-essential amino acid with many important physiological functions. However, achieving efficient manufacture of L-Arg on an industrial scale using Escherichia coli (E. coli) remains a major challenge. In previous studies, we constructed a strain of E. coli A7, which had good L-Arg production capacity. In this study, E. coli A7 was further modified, and E. coli A21 with more efficient L-Arg production capacity was obtained. Firstly, we reduced the acetate accumulation of strain A7 by weakening the poxB gene and overexpressing acs gene. Secondly, we improved the L-Arg transport efficiency of strains by overexpressing the lysE gene from Corynebacterium glutamicum (C. glutamicum). Finally, we enhanced the supplies of precursors for the synthesis of L-Arg and optimized the supplies of cofactor NADPH and energy ATP in strain. After fermentation in a 5-L bioreactor, the L-Arg titer of strain A21 was found to be 89.7 g/L. The productivity was 1.495 g/(L·h) and the glucose yield was 0.377 g/g. Our study further narrowed the titer gap between E. coli and C. glutamicum in the synthesis of L-Arg. In all recent studies on the L-Arg production by E. coli, this was the highest titer recorded. In conclusion, our study further promotes the efficient mass synthesis of L-Arg by E. coli. KEY POINTS: • The acetate accumulation of starting strain A7 was decreased. • Overexpression of gene lysE of C. glutamicum enhanced L-Arg transport in strain A10. • Enhance the supplies of precursors for the synthesis of L-Arg and optimize the supplies of cofactor NADPH and energy ATP. Finally, Strain A21 was detected to have an L-Arg titer of 89.7 g/L in a 5-L bioreactor.
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Affiliation(s)
- Hai-De Wang
- The Key Laboratory of Industrial Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, 1800# Lihu Road, Wuxi, 214122, People's Republic of China.
| | - Jian-Zhong 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
| | - Wei-Guo Zhang
- 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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14
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Zou S, Lu J, Zhang B, Li X, Jiang Z, Xue Y, Zheng Y. A combination fermentation strategy for simultaneously increasing cellular NADP(H) level, biomass, and enzymatic activity of glufosinate dehydrogenase in Escherichia coli. Bioprocess Biosyst Eng 2023; 46:867-878. [PMID: 37022468 DOI: 10.1007/s00449-023-02871-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2023] [Accepted: 03/26/2023] [Indexed: 04/07/2023]
Abstract
Oxidoreductase is one of the most important biocatalysts for the synthesis of various chiral compounds. However, their whole-cell activity is frequently affected by an insufficient supply of expensive nicotinamide cofactors. This study aimed to overcome such shortcomings by developing a combination fermentation strategy for simultaneously increasing intracellular NADP(H) level, biomass, and glufosinate dehydrogenase activity in E. coli. The results showed that the feeding mode of NAD(H) synthesis precursor and lactose inducer had essential effects on the accumulation level of intracellular NADPH. Adding 40 mg L-1 of L-aspartic acid to the medium increased the intracellular NADP(H) concentration by 36.3%. Under the pH-stat feeding mode and adding 0.4 g L-1 h-1 lactose, the NADP(H) concentration, biomass, and GluDH activity in the 5-L fermenter reached 445.7 μmol L-1, 21.7 gDCW L-1, and 8569.3 U L-1, respectively. As far as we know, this is the highest reported activity of GluDH in the fermentation broth. Finally, the 5000-L fermenter was successfully scaled up to use this fermentation approach. The combination fermentation strategy might serve as a useful approach for the high-activity fermentation of other NADPH-dependent oxidoreductases.
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Affiliation(s)
- Shuping Zou
- Key Laboratory of Bioorganic Synthesis of Zhejiang Province, College of Biotechnology and Bioengineering, Zhejiang University of Technology, Hangzhou, 310014, China
- Engineering Research Center of Bioconversion and Biopurification of Ministry of Education, Zhejiang University of Technology, Hangzhou, 310014, China
| | - Jiawei Lu
- Key Laboratory of Bioorganic Synthesis of Zhejiang Province, College of Biotechnology and Bioengineering, Zhejiang University of Technology, Hangzhou, 310014, China
- Engineering Research Center of Bioconversion and Biopurification of Ministry of Education, Zhejiang University of Technology, Hangzhou, 310014, China
| | - Bing Zhang
- Key Laboratory of Bioorganic Synthesis of Zhejiang Province, College of Biotechnology and Bioengineering, Zhejiang University of Technology, Hangzhou, 310014, China
- Engineering Research Center of Bioconversion and Biopurification of Ministry of Education, Zhejiang University of Technology, Hangzhou, 310014, China
| | - Xia Li
- Key Laboratory of Bioorganic Synthesis of Zhejiang Province, College of Biotechnology and Bioengineering, Zhejiang University of Technology, Hangzhou, 310014, China
- Engineering Research Center of Bioconversion and Biopurification of Ministry of Education, Zhejiang University of Technology, Hangzhou, 310014, China
| | - Zhentao Jiang
- Key Laboratory of Bioorganic Synthesis of Zhejiang Province, College of Biotechnology and Bioengineering, Zhejiang University of Technology, Hangzhou, 310014, China
- Engineering Research Center of Bioconversion and Biopurification of Ministry of Education, Zhejiang University of Technology, Hangzhou, 310014, China
| | - Yaping Xue
- Key Laboratory of Bioorganic Synthesis of Zhejiang Province, College of Biotechnology and Bioengineering, Zhejiang University of Technology, Hangzhou, 310014, China.
- Engineering Research Center of Bioconversion and Biopurification of Ministry of Education, Zhejiang University of Technology, Hangzhou, 310014, China.
| | - Yuguo Zheng
- Key Laboratory of Bioorganic Synthesis of Zhejiang Province, College of Biotechnology and Bioengineering, Zhejiang University of Technology, Hangzhou, 310014, China
- Engineering Research Center of Bioconversion and Biopurification of Ministry of Education, Zhejiang University of Technology, Hangzhou, 310014, China
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15
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Using oils and fats to replace sugars as feedstocks for biomanufacturing: Challenges and opportunities for the yeast Yarrowia lipolytica. Biotechnol Adv 2023; 65:108128. [PMID: 36921878 DOI: 10.1016/j.biotechadv.2023.108128] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/07/2023] [Revised: 03/08/2023] [Accepted: 03/10/2023] [Indexed: 03/16/2023]
Abstract
More than 200 million tons of plant oils and animal fats are produced annually worldwide from oil, crops, and the rendered animal fat industry. Triacylglycerol, an abundant energy-dense compound, is the major form of lipid in oils and fats. While oils or fats are very important raw materials and functional ingredients for food or related products, a significant portion is currently diverted to or recovered as waste. To significantly increase the value of waste oils or fats and expand their applications with a minimal environmental footprint, microbial biomanufacturing is presented as an effective strategy for adding value. Though both bacteria and yeast can be engineered to use oils or fats as the biomanufacturing feedstocks, the yeast Yarrowia lipolytica is presented as one of the most attractive platforms. Y. lipolytica is oleaginous, generally regarded as safe, demonstrated as a promising industrial producer, and has unique capabilities for efficient catabolism and bioconversion of lipid substrates. This review summarizes the major challenges and opportunities for Y. lipolytica as a new biomanufacturing platform for the production of value-added products from oils and fats. This review also discusses relevant cellular and metabolic engineering strategies such as fatty acid transport, fatty acid catabolism and bioconversion, redox balances and energy yield, cell morphology and stress response, and bioreaction engineering. Finally, this review highlights specific product classes including long-chain diacids, wax esters, terpenes, and carotenoids with unique synthesis opportunities from oils and fats in Y. lipolytica.
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16
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Nielsen JR, Weusthuis RA, Huang WE. Growth-coupled enzyme engineering through manipulation of redox cofactor regeneration. Biotechnol Adv 2023; 63:108102. [PMID: 36681133 DOI: 10.1016/j.biotechadv.2023.108102] [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: 09/01/2022] [Revised: 01/11/2023] [Accepted: 01/15/2023] [Indexed: 01/20/2023]
Abstract
Enzymes need to be efficient, robust, and highly specific for their effective use in commercial bioproduction. These properties can be introduced using various enzyme engineering techniques, with random mutagenesis and directed evolution (DE) often being chosen when there is a lack of structural information -or mechanistic understanding- of the enzyme. The screening or selection step of DE is the limiting part of this process, since it must ideally be (ultra)-high throughput, specifically target the catalytic activity of the enzyme and have an accurately quantifiable metric for said activity. Growth-coupling selection strategies involve coupling a desired enzyme activity to cellular metabolism and therefore growth, where growth (rate) becomes the output metric. Redox cofactors (NAD+/NADH and NADP+/NADPH) have recently been identified as promising target molecules for growth coupling, owing to their essentiality for cellular metabolism and ubiquitous nature. Redox cofactor oxidation or reduction can be disrupted through metabolic engineering and the use of specific culturing conditions, rendering the cell inviable unless a 'rescue' reaction complements the imposed metabolic deficiency. Using this principle, enzyme variants displaying improved cofactor oxidation or reduction rates can be selected for through an increased growth rate of the cell. In recent years, several E. coli strains have been developed that are deficient in the oxidation or reduction of NAD+/NADH and NADP+/NADPH pairs, and of non-canonical redox cofactor pairs NMN+/NMNH and NCD+/NCDH, which provides researchers with a versatile toolbox of enzyme engineering platforms. A range of redox cofactor dependent enzymes have since been engineered using a variety of these strains, demonstrating the power of using this growth-coupling technique for enzyme engineering. This review aims to summarize the metabolic engineering involved in creating strains auxotrophic for the reduced or oxidized state of redox cofactors, and the resulting successes in using them for enzyme engineering. Perspectives on the unique features and potential future applications of this technique are also presented.
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Affiliation(s)
- Jochem R Nielsen
- Department of Engineering Science, University of Oxford, Oxford OX1 3PJ, United Kingdom.
| | - Ruud A Weusthuis
- Department of Bioprocess Engineering, Wageningen University & Research, Wageningen 6700AA, the Netherlands.
| | - Wei E Huang
- Department of Engineering Science, University of Oxford, Oxford OX1 3PJ, United Kingdom.
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17
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Sun Y, Zhang T, Lu B, Li X, Jiang L. Application of cofactors in the regulation of microbial metabolism: A state of the art review. Front Microbiol 2023; 14:1145784. [PMID: 37113222 PMCID: PMC10126289 DOI: 10.3389/fmicb.2023.1145784] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2023] [Accepted: 03/15/2023] [Indexed: 04/29/2023] Open
Abstract
Cofactors are crucial chemicals that maintain cellular redox balance and drive the cell to do synthetic and catabolic reactions. They are involved in practically all enzymatic activities that occur in live cells. It has been a hot research topic in recent years to manage their concentrations and forms in microbial cells by using appropriate techniques to obtain more high-quality target products. In this review, we first summarize the physiological functions of common cofactors, and give a brief overview of common cofactors acetyl coenzyme A, NAD(P)H/NAD(P)+, and ATP/ADP; then we provide a detailed introduction of intracellular cofactor regeneration pathways, review the regulation of cofactor forms and concentrations by molecular biological means, and review the existing regulatory strategies of microbial cellular cofactors and their application progress, to maximize and rapidly direct the metabolic flux to target metabolites. Finally, we speculate on the future of cofactor engineering applications in cell factories. Graphical Abstract.
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Affiliation(s)
- Yang Sun
- State Key Laboratory of Materials-Oriented Chemical Engineering, College of Food Science and Light Industry, Nanjing Tech University, Nanjing, China
| | - Ting Zhang
- State Key Laboratory of Materials-Oriented Chemical Engineering, College of Food Science and Light Industry, Nanjing Tech University, Nanjing, China
| | - Bingqian Lu
- State Key Laboratory of Materials-Oriented Chemical Engineering, College of Food Science and Light Industry, Nanjing Tech University, Nanjing, China
| | - Xiangfei Li
- Engineering Laboratory for Industrial Microbiology Molecular Beeding of Anhui Province, College of Biologic and Food Engineering, Anhui Polytechnic University, Wuhu, China
- *Correspondence: Xiangfei Li,
| | - Ling Jiang
- State Key Laboratory of Materials-Oriented Chemical Engineering, College of Food Science and Light Industry, Nanjing Tech University, Nanjing, China
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18
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Huo J, Bai Y, Fan TP, Zheng X, Cai Y. Hydroxytyrosol production from l-DOPA by engineered Escherichia coli co-expressing l-amino acid deaminase, α-keto acid decarboxylase, aldehyde reductase and glucose dehydrogenase with NADH regeneration. Process Biochem 2022. [DOI: 10.1016/j.procbio.2022.09.008] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 10/31/2022]
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19
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Yuan SF, Nair PH, Borbon D, Coleman SM, Fan PH, Lin WL, Alper HS. Metabolic engineering of E. coli for β-alanine production using a multi-biosensor enabled approach. Metab Eng 2022; 74:24-35. [PMID: 36067877 DOI: 10.1016/j.ymben.2022.08.012] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/06/2022] [Revised: 07/18/2022] [Accepted: 08/30/2022] [Indexed: 10/31/2022]
Abstract
β-alanine is an important biomolecule used in nutraceuticals, pharmaceuticals, and chemical synthesis. The relatively eco-friendly bioproduction of β-alanine has recently attracted more interest than petroleum-based chemical synthesis. In this work, we developed two types of in vivo high-throughput screening platforms, wherein one was utilized to identify a novel target ribonuclease E (encoded by rne) as well as a redox-cofactor balancing module that can enhance de novo β-alanine biosynthesis from glucose, and the other was employed for screening fermentation conditions. When combining these approaches with rational upstream and downstream module engineering, an engineered E. coli producer was developed that exhibited 3.4- and 6.6-fold improvement in β-alanine yield (0.85 mol β-alanine/mole glucose) and specific β-alanine production (0.74 g/L/OD600), respectively, compared to the parental strain in a minimal medium. Across all of the strains constructed, the best yielding strain exhibited 1.08 mol β-alanine/mole glucose (equivalent to 81.2% of theoretic yield). The final engineered strain produced 6.98 g/L β-alanine in a batch-mode bioreactor and 34.8 g/L through a whole-cell catalysis. This approach demonstrates the utility of biosensor-enabled high-throughput screening for the production of β-alanine.
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Affiliation(s)
- Shuo-Fu Yuan
- Institute for Cellular and Molecular Biology, The University of Texas at Austin, Austin, TX, USA
| | - Priya H Nair
- McKetta Department of Chemical Engineering, The University of Texas at Austin, Austin, TX, USA
| | - Dominic Borbon
- Biology, College of Natural Sciences, The University of Texas at Austin, Austin, TX, USA
| | - Sarah M Coleman
- McKetta Department of Chemical Engineering, The University of Texas at Austin, Austin, TX, USA
| | - Po-Hsun Fan
- Department of Chemistry, College of Pharmacy, The University of Texas at Austin, Austin, TX, USA
| | - Wen-Ling Lin
- Institute for Cellular and Molecular Biology, The University of Texas at Austin, Austin, TX, USA
| | - Hal S Alper
- Institute for Cellular and Molecular Biology, The University of Texas at Austin, Austin, TX, USA; McKetta Department of Chemical Engineering, The University of Texas at Austin, Austin, TX, USA.
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20
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Wang J, Yang J, Shi G, Li W, Ju Y, Wei L, Liu J, Xu N. Transcriptome profiles of high-lysine adaptation reveal insights into osmotic stress response in Corynebacterium glutamicum. Front Bioeng Biotechnol 2022; 10:933325. [PMID: 36017356 PMCID: PMC9395588 DOI: 10.3389/fbioe.2022.933325] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2022] [Accepted: 07/06/2022] [Indexed: 12/05/2022] Open
Abstract
Corynebacterium glutamicum has been widely and effectively used for fermentative production of l-lysine on an industrial scale. However, high-level accumulation of end products inevitably leads to osmotic stress and hinders further increase of l-lysine production. At present, the underlying mechanism by which C. glutamicum cells adapt to high-lysine-induced osmotic stress is still unclear. In this study, we conducted a comparative transcriptomic analysis by RNA-seq to determine gene expression profiles under different high-lysine stress conditions. The results indicated that the increased expression of some metabolic pathways such as sulfur metabolism and specific amino acid biosynthesis might offer favorable benefits for high-lysine adaptation. Functional assays of 18 representative differentially expressed genes showed that the enhanced expression of multiple candidate genes, especially grpE chaperon, conferred high-lysine stress tolerance in C. glutamicum. Moreover, DNA repair component MutT and energy-transducing NADH dehydrogenase Ndh were also found to be important for protecting cells against high-lysine-induced osmotic stress. Taken together, these aforementioned findings provide broader views of transcriptome profiles and promising candidate targets of C. glutamicum for the adaptation of high-lysine stress during fermentation.
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Affiliation(s)
- Jian Wang
- College of Biological and Agricultural Engineering, Jilin University, Changchun, China
| | - Jian Yang
- College of Biological and Agricultural Engineering, Jilin University, Changchun, China
| | - Guoxin Shi
- College of Biological and Agricultural Engineering, Jilin University, Changchun, China
| | - Weidong Li
- College of Biological and Agricultural Engineering, Jilin University, Changchun, China
| | - Yun Ju
- School of Food Engineering and Biotechnology, Tianjin University of Science and Technology, Tianjin, China
| | - Liang Wei
- Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin, China
| | - Jun Liu
- Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin, China
- Key Laboratory of Systems Microbial Biotechnology, Chinese Academy of Sciences, Tianjin, China
| | - Ning Xu
- Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin, China
- Key Laboratory of Systems Microbial Biotechnology, Chinese Academy of Sciences, Tianjin, China
- *Correspondence: Ning Xu,
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21
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Partipilo M, Yang G, Mascotti ML, Wijma HJ, Slotboom DJ, Fraaije MW. A conserved sequence motif in the E. coli soluble FAD-containing pyridine nucleotide transhydrogenase is important for reaction efficiency. J Biol Chem 2022; 298:102304. [PMID: 35933012 PMCID: PMC9460512 DOI: 10.1016/j.jbc.2022.102304] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2022] [Revised: 07/20/2022] [Accepted: 07/21/2022] [Indexed: 11/06/2022] Open
Abstract
Soluble pyridine nucleotide transhydrogenases (STHs) are flavoenzymes involved in the redox homeostasis of the essential cofactors NAD(H) and NADP(H). They catalyze the reversible transfer of reducing equivalents between the two nicotinamide cofactors. The soluble transhydrogenase from Escherichia coli (SthA) has found wide use in both in vivo and in vitro applications to steer reducing equivalents toward NADPH-requiring reactions. However, mechanistic insight into SthA function is still lacking. In this work, we present a biochemical characterization of SthA, focusing for the first time on the reactivity of the flavoenzyme with molecular oxygen. We report on oxidase activity of SthA that takes place both during transhydrogenation and in the absence of an oxidized nicotinamide cofactor as an electron acceptor. We find that this reaction produces the reactive oxygen species hydrogen peroxide and superoxide anion. Furthermore, we explore the evolutionary significance of the well-conserved CXXXXT motif that distinguishes STHs from the related family of flavoprotein disulfide reductases in which a CXXXXC motif is conserved. Our mutational analysis revealed the cysteine and threonine combination in SthA leads to better coupling efficiency of transhydrogenation and reduced reactive oxygen species release compared to enzyme variants with mutated motifs. These results expand our mechanistic understanding of SthA by highlighting reactivity with molecular oxygen and the importance of the evolutionarily conserved sequence motif.
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Affiliation(s)
- Michele Partipilo
- Membrane Enzymology Group, Groningen Institute of Biomolecular Sciences & Biotechnology, University of Groningen, Nijenborgh 4, 9747 AG Groningen, The Netherlands
| | - Guang Yang
- Molecular Enzymology Group, Groningen Institute of Biomolecular Sciences & Biotechnology, University of Groningen, Nijenborgh 4, 9747 AG Groningen, The Netherlands
| | - Maria Laura Mascotti
- Molecular Enzymology Group, Groningen Institute of Biomolecular Sciences & Biotechnology, University of Groningen, Nijenborgh 4, 9747 AG Groningen, The Netherlands; IMIBIO-SL CONICET, Facultad de Química Bioquímica y Farmacia, Universidad Nacional de San Luis, Ejercito de los Andes 950, D5700HHW, San Luis, Argentina
| | - Hein J Wijma
- Molecular Enzymology Group, Groningen Institute of Biomolecular Sciences & Biotechnology, University of Groningen, Nijenborgh 4, 9747 AG Groningen, The Netherlands
| | - Dirk Jan Slotboom
- Membrane Enzymology Group, Groningen Institute of Biomolecular Sciences & Biotechnology, University of Groningen, Nijenborgh 4, 9747 AG Groningen, The Netherlands.
| | - Marco W Fraaije
- Molecular Enzymology Group, Groningen Institute of Biomolecular Sciences & Biotechnology, University of Groningen, Nijenborgh 4, 9747 AG Groningen, The Netherlands.
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22
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Zhou S, Alper HS, Zhou J, Deng Y. Intracellular biosensor-based dynamic regulation to manipulate gene expression at the spatiotemporal level. Crit Rev Biotechnol 2022; 43:646-663. [PMID: 35450502 DOI: 10.1080/07388551.2022.2040415] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
The use of intracellular, biosensor-based dynamic regulation strategies to regulate and improve the production of useful compounds have progressed significantly over previous decades. By employing such an approach, it is possible to simultaneously realize high productivity and optimum growth states. However, industrial fermentation conditions contain a mixture of high- and low-performance non-genetic variants, as well as young and aged cells at all growth phases. Such significant individual variations would hinder the precise controlling of metabolic flux at the single-cell level to achieve high productivity at the macroscopic population level. Intracellular biosensors, as the regulatory centers of metabolic networks, can real-time sense intra- and extracellular conditions and, thus, could be synthetically adapted to balance the biomass formation and overproduction of compounds by individual cells. Herein, we highlight advances in the designing and engineering approaches to intracellular biosensors. Then, the spatiotemporal properties of biosensors associated with the distribution of inducers are compared. Also discussed is the use of such biosensors to dynamically control the cellular metabolic flux. Such biosensors could achieve single-cell regulation or collective regulation goals, depending on whether or not the inducer distribution is only intracellular.
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Affiliation(s)
- Shenghu Zhou
- National Engineering Laboratory for Cereal Fermentation Technology (NELCF), Jiangnan University, Wuxi, Jiangsu, China.,Jiangsu Provincial Research Center for Bioactive Product Processing Technology, Jiangnan University, Wuxi, Jiangsu, China
| | - Hal S Alper
- Institute for Cellular and Molecular Biology, The University of Texas at Austin, Austin, TX, USA.,McKetta Department of Chemical Engineering, The University of Texas at Austin, Austin, TX, USA
| | - Jingwen Zhou
- National Engineering Laboratory for Cereal Fermentation Technology (NELCF), Jiangnan University, Wuxi, Jiangsu, China.,Jiangsu Provincial Research Center for Bioactive Product Processing Technology, Jiangnan University, Wuxi, Jiangsu, China
| | - Yu Deng
- National Engineering Laboratory for Cereal Fermentation Technology (NELCF), Jiangnan University, Wuxi, Jiangsu, China.,Jiangsu Provincial Research Center for Bioactive Product Processing Technology, Jiangnan University, Wuxi, Jiangsu, China
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23
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Hai-De W, Shuai L, Bing-Bing W, Jie L, Jian-Zhong X, Wei-Guo Z. Metabolic engineering of Escherichia coli for efficient production of l-arginine. ADVANCES IN APPLIED MICROBIOLOGY 2022; 122:127-150. [PMID: 37085192 DOI: 10.1016/bs.aambs.2022.11.002] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
As a semi-essential amino acid, l-arginine (l-Arg) plays an important role in food, health care, and medical treatment. At present, the main method of producing l-Arg is the use of microbial fermentation. Therefore, the selection and breeding of high-efficiency microbial strains is the top priority. To continuously improve the l-Arg production performance of the strains, a series of metabolic engineering strategies have been tried to transform the strains. The production of l-Arg by metabolically engineered Corynebacterium glutamicum (C. glutamicum) reached a relatively high level. Escherichia coli (E. coli), as a strain with great potential for l-Arg production, also has a large number of research strategies aimed at screening effective E. coli for producing l-Arg. E. coli also has a number of advantages over C. glutamicum in producing l-Arg. Therefore, it is of great significance to screen out excellent and stable E. coli to produce l-Arg. Here, based on recent research results, we review the metabolic pathways of l-Arg production in E. coli, the research progress of l-Arg production in E. coli, and various regulatory strategies implemented in E. coli.
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24
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Taymaz-Nikerel H, Lara AR. Vitreoscilla Haemoglobin: A Tool to Reduce Overflow Metabolism. Microorganisms 2021; 10:microorganisms10010043. [PMID: 35056491 PMCID: PMC8779101 DOI: 10.3390/microorganisms10010043] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2021] [Revised: 12/18/2021] [Accepted: 12/20/2021] [Indexed: 11/26/2022] Open
Abstract
Overflow metabolism is a phenomenon extended in nature, ranging from microbial to cancer cells. Accumulation of overflow metabolites pose a challenge for large-scale bioprocesses. Yet, the causes of overflow metabolism are not fully clarified. In this work, the underlying mechanisms, reasons and consequences of overflow metabolism in different organisms have been summarized. The reported effect of aerobic expression of Vitreoscilla haemoglobin (VHb) in different organisms are revised. The use of VHb to reduce overflow metabolism is proposed and studied through flux balance analysis in E. coli at a fixed maximum substrate and oxygen uptake rates. Simulations showed that the presence of VHb increases the growth rate, while decreasing acetate production, in line with the experimental measurements. Therefore, aerobic VHb expression is considered a potential tool to reduce overflow metabolism in cells.
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Affiliation(s)
- Hilal Taymaz-Nikerel
- Department of Genetics and Bioengineering, Istanbul Bilgi University, İstanbul 34060, Turkey;
| | - Alvaro R. Lara
- Departamento de Procesos y Tecnología, Universidad Autónoma Metropolitana, Mexico City 05348, Mexico
- Correspondence:
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25
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Identification and Characterization of a Novel Soluble Pyridine Nucleotide Transhydrogenase from Streptomyces avermitilis. Curr Microbiol 2021; 79:32. [PMID: 34931264 DOI: 10.1007/s00284-021-02727-y] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2021] [Accepted: 11/25/2021] [Indexed: 10/19/2022]
Abstract
Soluble pyridine nucleotide transhydrogenase (STH) transfers hydride between NADH and NADPH to maintain redox balance. In the present study, the sth gene from Gram-positive bacterium Streptomyces avermitilis (SaSTH) was expressed in Escherichia coli, and the recombinant STH protein was purified to homogeneity. Activity assays indicated that SaSTH was able to catalyze transhydrogenase reactions by using NADH or NADPH as reductants and thio-NAD+ as an oxidant. The apparent Km value for NADPH (74.5 μM) was lower than that for NADH (104.0 μM) and the apparent kcat/Km for NADPH (2704.7 mM-1 s-1) was higher than that for NADH (1129.8 mM-1 s-1). SaSTH showed optimal activity at 25 °C and at a pH of 6.2. Heat-inactivation studies revealed that SaSTH remained stable below 55 °C and that approximately 50% activity was preserved at 57 °C for 20 min. Analyses also showed that SaSTH activity was inhibited by divalent ions, particularly Co2+, Ni2+, and Zn2+. In addition, the transhydrogenase activity of SaSTH was inhibited by ATP and strongly stimulated by ADP and AMP. In summary, we characterized a recombinant enzyme exhibiting STH activity from Gram-positive bacteria for the first time. Our findings provide new options for cofactor engineering and industrial biocatalytic processes.
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26
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Kawai R, Toya Y, Miyoshi K, Murakami M, Niide T, Horinouchi T, Maeda T, Shibai A, Furusawa C, Shimizu H. Acceleration of target production in co-culture by enhancing intermediate consumption through adaptive laboratory evolution. Biotechnol Bioeng 2021; 119:936-945. [PMID: 34914093 DOI: 10.1002/bit.28007] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/04/2021] [Revised: 11/23/2021] [Accepted: 12/13/2021] [Indexed: 11/09/2022]
Abstract
Co-culture is a promising way to alleviate metabolic burden by dividing the metabolic pathways into several modules and sharing the conversion processes with multiple strains. Since an intermediate is passed from the donor to the recipient via the extracellular environment, it is inevitably diluted. Therefore, enhancing the intermediate consumption rate is important for increasing target productivity. In the present study, we demonstrated the enhancement of mevalonate consumption in Escherichia coli by adaptive laboratory evolution and applied the evolved strain to isoprenol production in an E. coli (upstream: glucose to mevalonate)-E. coli (downstream: mevalonate to isoprenol) co-culture. An engineered mevalonate auxotroph strain was repeatedly sub-cultured in a synthetic medium supplemented with mevalonate, where the mevalonate concentration was decreased stepwise from 100 to 20 µM. In five parallel evolution experiments, all growth rates gradually increased, resulting in five evolved strains. Whole-genome re-sequencing and reverse engineering identified three mutations involved in enhancing mevalonate consumption. After introducing nudF gene for producing isoprenol, the isoprenol-producing parental and evolved strains were respectively co-cultured with a mevalonate-producing strain. At an inoculation ratio of 1:3 (upstream:downstream), isoprenol production using the evolved strain was 3.3 times higher than that using the parental strain.
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Affiliation(s)
- Ryutaro Kawai
- Department of Bioinformatic Engineering, Graduate School of Information Science and Technology, Osaka University, Suita, Osaka, Japan
| | - Yoshihiro Toya
- Department of Bioinformatic Engineering, Graduate School of Information Science and Technology, Osaka University, Suita, Osaka, Japan
| | - Kenta Miyoshi
- Department of Bioinformatic Engineering, Graduate School of Information Science and Technology, Osaka University, Suita, Osaka, Japan
| | - Manami Murakami
- Department of Bioinformatic Engineering, Graduate School of Information Science and Technology, Osaka University, Suita, Osaka, Japan
| | - Teppei Niide
- Department of Bioinformatic Engineering, Graduate School of Information Science and Technology, Osaka University, Suita, Osaka, Japan
| | | | - Tomoya Maeda
- RIKEN Center for Biosystems Dynamics Research, Suita, Osaka, Japan
| | - Atsushi Shibai
- RIKEN Center for Biosystems Dynamics Research, Suita, Osaka, Japan
| | - Chikara Furusawa
- RIKEN Center for Biosystems Dynamics Research, Suita, Osaka, Japan.,Department of Physics, The University of Tokyo, Tokyo, Japan
| | - Hiroshi Shimizu
- Department of Bioinformatic Engineering, Graduate School of Information Science and Technology, Osaka University, Suita, Osaka, Japan
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27
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Gao C, Wang J, Guo L, Hu G, Liu J, Song W, Liu L, Chen X. Immobilization of Microbial Consortium for Glutaric Acid Production from Lysine. ChemCatChem 2021. [DOI: 10.1002/cctc.202101245] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Affiliation(s)
- Cong Gao
- State Key Laboratory of Food Science and Technology Jiangnan University Lihu Road 1800 Wuxi 214122 P. R. China
- International Joint Laboratory on Food Safety Jiangnan University Lihu Road 1800 Wuxi 214122 P. R. China
| | - Jiaping Wang
- State Key Laboratory of Food Science and Technology Jiangnan University Lihu Road 1800 Wuxi 214122 P. R. China
- International Joint Laboratory on Food Safety Jiangnan University Lihu Road 1800 Wuxi 214122 P. R. China
| | - Liang Guo
- State Key Laboratory of Food Science and Technology Jiangnan University Lihu Road 1800 Wuxi 214122 P. R. China
- International Joint Laboratory on Food Safety Jiangnan University Lihu Road 1800 Wuxi 214122 P. R. China
| | - Guipeng Hu
- School of Pharmaceutical Science Jiangnan University Lihu Road 1800 Wuxi 214122 P. R. China
| | - Jia Liu
- State Key Laboratory of Food Science and Technology Jiangnan University Lihu Road 1800 Wuxi 214122 P. R. China
- International Joint Laboratory on Food Safety Jiangnan University Lihu Road 1800 Wuxi 214122 P. R. China
| | - Wei Song
- School of Pharmaceutical Science Jiangnan University Lihu Road 1800 Wuxi 214122 P. R. China
| | - Liming Liu
- State Key Laboratory of Food Science and Technology Jiangnan University Lihu Road 1800 Wuxi 214122 P. R. China
- International Joint Laboratory on Food Safety Jiangnan University Lihu Road 1800 Wuxi 214122 P. R. China
| | - Xiulai Chen
- State Key Laboratory of Food Science and Technology Jiangnan University Lihu Road 1800 Wuxi 214122 P. R. China
- International Joint Laboratory on Food Safety Jiangnan University Lihu Road 1800 Wuxi 214122 P. R. China
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28
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Lv H, Zhang Y, Shao J, Liu H, Wang Y. Ferulic acid production by metabolically engineered Escherichia coli. BIORESOUR BIOPROCESS 2021; 8:70. [PMID: 38650224 PMCID: PMC10992898 DOI: 10.1186/s40643-021-00423-0] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2021] [Accepted: 07/28/2021] [Indexed: 11/10/2022] Open
Abstract
Ferulic acid (p-hydroxy-3-methoxycinnamic acid, FA) is a natural active substance present in plant cell walls, with antioxidant, anticancer, antithrombotic and other properties; it is widely used in medicine, food, and cosmetics. Production of FA by eco-friendly bioprocess is of great potential. In this study, FA was biosynthesized by metabolically engineered Escherichia coli. As the first step, the genes tal (encoding tyrosine ammonia-lyase, RsTAL) from Rhodobacter sphaeroides, sam5 (encoding p-coumarate 3-hydroxylase, SeSAM5) from Saccharothrix espanaensis and comt (encoding Caffeic acid O-methytransferase, TaCM) from Triticum aestivum were cloned in an operon on the pET plasmid backbone, E. coli strain containing this construction was proved to produce FA from L-tyrosine successfully, and confirmed the function of TaCM as caffeic acid O-methytransferase. Fermentation result revealed JM109(DE3) as a more suitable host cell for FA production than BL21(DE3). After that the genes expression strength of FA pathway were optimized by tuning of promoter strength (T7 promoter or T5 promoter) and copy number (pBR322 or p15A), and the combination p15a-T5 works best. To further improve FA production, E. coli native pntAB, encoding pyridine nucleotide transhydrogenase, was selected from five NADPH regeneration genes to supplement redox cofactor NADPH for converting p-coumaric acid into caffeic acid in FA biosynthesis process. Sequentially, to further convert caffeic acid into FA, a non-native methionine kinase (MetK from Streptomyces spectabilis) was also overexpressed. Based on the flask fermentation data which show that the engineered E. coli strain produced 212 mg/L of FA with 11.8 mg/L caffeic acid residue, it could be concluded that it is the highest yield of FA achieved by E. coli K-12 strains reported to the best of our knowledge.
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Affiliation(s)
- Huajun Lv
- CAS Key Laboratory of Synthetic Biology, CAS Center for Excellence in Molecular Plant Sciences, Shanghai Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, Shanghai, 200032, China
| | - Ying Zhang
- CAS Key Laboratory of Synthetic Biology, CAS Center for Excellence in Molecular Plant Sciences, Shanghai Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, Shanghai, 200032, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Jie Shao
- CAS Key Laboratory of Synthetic Biology, CAS Center for Excellence in Molecular Plant Sciences, Shanghai Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, Shanghai, 200032, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Haili Liu
- CAS Key Laboratory of Synthetic Biology, CAS Center for Excellence in Molecular Plant Sciences, Shanghai Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, Shanghai, 200032, China
| | - Yong Wang
- CAS Key Laboratory of Synthetic Biology, CAS Center for Excellence in Molecular Plant Sciences, Shanghai Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, Shanghai, 200032, China.
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29
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Improved production of D-pantothenic acid in Escherichia coli by integrated strain engineering and fermentation strategies. J Biotechnol 2021; 339:65-72. [PMID: 34352344 DOI: 10.1016/j.jbiotec.2021.07.014] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2021] [Revised: 07/26/2021] [Accepted: 07/29/2021] [Indexed: 11/23/2022]
Abstract
D-pantothenic acid (D-PA) is an essential vitamin that has been widely used in medicine, food, and animal feed. Microbial production of D-PA from natural renewable resources is attractive and challenging. In this study, both strain improvements and fermentation process strategies were applied to achieve high-level D-PA production in Escherichia coli. First, a D-PA-producing strain was developed through deletion of the aceF and mdh genes combined with the overexpression of the gene ppnk. The obtained engineered E. coli DPA02/pT-ppnk accumulated 6.89 ± 0.11 g/L of D-PA in shake flask fermentation, which was 79.9 % higher than the control strain. Moreover, the cultivation process contributed greatly to D-PA production with respect to titer and productivity by betaine supplementation and dissolved oxygen (DO)-feedback feeding framework. Under optimal conditions, 68.3 g/L of D-PA, the specific productivity of 0.794 g/L h and the yield of 0.36 g/g glucose in 5 L fermenter were achieved. Overall, this research successfully exploited advanced strategies to lay the foundation for bio-based D-PA production in industrial applications.
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30
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Alsiyabi A, Chowdhury NB, Long D, Saha R. Enhancing in silico strain design predictions through next generation metabolic modeling approaches. Biotechnol Adv 2021; 54:107806. [PMID: 34298108 DOI: 10.1016/j.biotechadv.2021.107806] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2021] [Revised: 06/22/2021] [Accepted: 07/15/2021] [Indexed: 02/06/2023]
Abstract
The reconstruction and analysis of metabolic models has garnered increasing attention due to the multitude of applications in which these have proven to be practical. The growing number of generated metabolic models has been accompanied by an exponentially expanding arsenal of tools used to analyze them. In this work, we discussed the biological relevance of a number of promising modeling frameworks, focusing on the questions and hypotheses each method is equipped to address. To this end, we critically analyzed the steady-state modeling approaches focusing on resource allocation and incorporation of thermodynamic considerations which produce promising results and aid in the generation and experimental validation of numerous predictions. For smaller networks involving more complex regulation, we addressed kinetic modeling techniques which show encouraging results in addressing questions outside the scope of steady-state modeling. Finally, we discussed the potential application of the discussed frameworks within the field of strain design. Adoption of such methodologies is believed to significantly enhance the accuracy of in silico predictions and hence decrease the number of design-build-test cycles required.
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Affiliation(s)
- Adil Alsiyabi
- Chemical and Biomolecular Engineering, University of Nebraska-Lincoln, United States of America
| | - Niaz Bahar Chowdhury
- Chemical and Biomolecular Engineering, University of Nebraska-Lincoln, United States of America
| | - Dianna Long
- Complex Biosystems, University of Nebraska-Lincoln, United States of America
| | - Rajib Saha
- Chemical and Biomolecular Engineering, University of Nebraska-Lincoln, United States of America; Complex Biosystems, University of Nebraska-Lincoln, United States of America.
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31
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Shen YP, Liao YL, Lu Q, He X, Yan ZB, Liu JZ. ATP and NADPH engineering of Escherichia coli to improve the production of 4-hydroxyphenylacetic acid using CRISPRi. BIOTECHNOLOGY FOR BIOFUELS 2021; 14:100. [PMID: 33879249 PMCID: PMC8056492 DOI: 10.1186/s13068-021-01954-6] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 12/23/2020] [Accepted: 04/11/2021] [Indexed: 06/12/2023]
Abstract
BACKGROUND 4-Hydroxyphenylacetic acid (4HPAA) is an important raw material for the synthesis of drugs, pesticides and biochemicals. Microbial biotechnology would be an attractive approach for 4HPAA production, and cofactors play an important role in biosynthesis. RESULTS We developed a novel strategy called cofactor engineering based on clustered regularly interspaced short palindromic repeat interference (CRISPRi) screening (CECRiS) for improving NADPH and/or ATP availability, enhancing the production of 4HPAA. All NADPH-consuming and ATP-consuming enzyme-encoding genes of E. coli were repressed through CRISPRi. After CRISPRi screening, 6 NADPH-consuming and 19 ATP-consuming enzyme-encoding genes were identified. The deletion of the NADPH-consuming enzyme-encoding gene yahK and the ATP-consuming enzyme-encoding gene fecE increased the production of 4HPAA from 6.32 to 7.76 g/L. Automatically downregulating the expression of the pabA gene using the Esa-PesaS quorum-sensing-repressing system further improved the production of 4HPAA. The final strain E. coli 4HPAA-∆yfp produced 28.57 g/L of 4HPAA with a yield of 27.64% (mol/mol) in 2-L bioreactor fed-batch fermentations. The titer and yield are the highest values to date. CONCLUSION This CECRiS strategy will be useful in engineering microorganisms for the high-level production of bioproducts.
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Affiliation(s)
- Yu-Ping Shen
- Institute of Synthetic Biology, Biomedical Center, Guangdong Province Key Laboratory of Improved Variety Reproduction in Aquatic Economic Animals, School of Life Sciences, Sun Yat-Sen University, Guangzhou, 510275 People’s Republic of China
- College of Chemistry and Bioengineering, Hunan University of Science and Engineering, Yongzhou, 425199 China
| | - Yu-Ling Liao
- Institute of Synthetic Biology, Biomedical Center, Guangdong Province Key Laboratory of Improved Variety Reproduction in Aquatic Economic Animals, School of Life Sciences, Sun Yat-Sen University, Guangzhou, 510275 People’s Republic of China
| | - Qian Lu
- Institute of Synthetic Biology, Biomedical Center, Guangdong Province Key Laboratory of Improved Variety Reproduction in Aquatic Economic Animals, School of Life Sciences, Sun Yat-Sen University, Guangzhou, 510275 People’s Republic of China
| | - Xin He
- Institute of Synthetic Biology, Biomedical Center, Guangdong Province Key Laboratory of Improved Variety Reproduction in Aquatic Economic Animals, School of Life Sciences, Sun Yat-Sen University, Guangzhou, 510275 People’s Republic of China
| | - Zhi-Bo Yan
- Institute of Synthetic Biology, Biomedical Center, Guangdong Province Key Laboratory of Improved Variety Reproduction in Aquatic Economic Animals, School of Life Sciences, Sun Yat-Sen University, Guangzhou, 510275 People’s Republic of China
| | - Jian-Zhong Liu
- Institute of Synthetic Biology, Biomedical Center, Guangdong Province Key Laboratory of Improved Variety Reproduction in Aquatic Economic Animals, School of Life Sciences, Sun Yat-Sen University, Guangzhou, 510275 People’s Republic of China
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32
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Liu Y, Guo X, Liu W, Wang J, Kent Zhao Z. Structural Insights into Malic Enzyme Variants Favoring an Unnatural Redox Cofactor. Chembiochem 2021; 22:1765-1768. [PMID: 33523590 DOI: 10.1002/cbic.202000800] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2020] [Revised: 01/27/2021] [Indexed: 01/07/2023]
Abstract
The use of nicotinamide cytosine dinucleotide (NCD), a biocompatible nicotinamide adenosine dinucleotide (NAD) analogue, is of great scientific and biotechnological interest. Several redox enzymes have been devised to favor NCD, and have been successfully applied in creating NCD-dependent redox systems. However, molecular interactions between cofactor and protein have still to be disclosed in order to guide further engineering efforts. Here we report the structural analysis of an NCD-favoring malic enzyme (ME) variant derived from Escherichia coli. The X-ray crystal structure data revealed that the residues located at position 346 and 401 in ME acted as the "gatekeepers" of the adenine moiety binding cavity. When Arg346 was substituted with either acidic or aromatic residues, the corresponding mutants showed substantially reduced NCD preference. Inspired by these observations, we generated Lactobacillus helveticus derived d-lactate dehydrogenase variants at Ile177, the counterpart to Arg346 in ME, and found a similar trend in terms of cofactor preference changes. As many NAD-dependent oxidoreductases share key structural features, our results provide guidance for protein engineering to obtain more NCD-favoring variants.
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Affiliation(s)
- Yuxue Liu
- College of Life Sciences, Henan Normal University, 46 East of Construction Road, Xinxiang, 453007, P. R. China.,Division of Biotechnology, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, 457 Zhongshan Road, Dalian, 116023, P. R. China
| | - Xiaojia Guo
- Division of Biotechnology, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, 457 Zhongshan Road, Dalian, 116023, P. R. China
| | - Wujun Liu
- Division of Biotechnology, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, 457 Zhongshan Road, Dalian, 116023, P. R. China.,Present address: Institute of Cancer Stem Cell, Dalian Medical University, Dalian, 116044, P. R. China
| | - Junting Wang
- Division of Biotechnology, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, 457 Zhongshan Road, Dalian, 116023, P. R. China
| | - Zongbao Kent Zhao
- Division of Biotechnology, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, 457 Zhongshan Road, Dalian, 116023, P. R. China.,State Key Laboratory of Catalysis, Dalian Institute of Chemical Physics, CAS, Dalian, 116023, P. R. China
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33
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Improving the production of NAD + via multi-strategy metabolic engineering in Escherichia coli. Metab Eng 2021; 64:122-133. [PMID: 33577950 DOI: 10.1016/j.ymben.2021.01.012] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2020] [Revised: 01/30/2021] [Accepted: 01/31/2021] [Indexed: 02/07/2023]
Abstract
Nicotinamide adenine dinucleotide (NAD+) is an essential coenzyme involved in numerous physiological processes. As an attractive product in the industrial field, NAD+ also plays an important role in oxidoreductase-catalyzed reactions, drug synthesis, and the treatment of diseases, such as dementia, diabetes, and vascular dysfunction. Currently, although the biotechnology to construct NAD+-overproducing strains has been developed, limited regulation and low productivity still hamper its use on large scales. Here, we describe multi-strategy metabolic engineering to address the NAD+-production bottleneck in E. coli. First, blocking the degradation pathway of NAD(H) increased the accumulation of NAD+ by 39%. Second, key enzymes involved in the Preiss-Handler pathway of NAD+ synthesis were overexpressed and led to a 221% increase in the NAD+ concentration. Third, the PRPP synthesis module and Preiss-Handler pathway were combined to strengthen the precursors supply, which resulted in enhancement of NAD+ content by 520%. Fourth, increasing the ATP content led to an increase in the concentration of NAD+ by 170%. Finally, with the combination of all above strategies, a strain with a high yield of NAD+ was constructed, with the intracellular NAD+ concentration reaching 26.9 μmol/g DCW, which was 834% that of the parent strain. This study presents an efficient design of an NAD+-producing strain through global regulation metabolic engineering.
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34
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Cao Z, Meng R, Wang P, Zhu G. Heterologous expression and enzymatic identification of two novel soluble pyridine nucleotide transhydrogenases from Acidobacteria bacterium KBS 146 and Nocardia jiangxiensis. BIOTECHNOL BIOTEC EQ 2021. [DOI: 10.1080/13102818.2021.1988708] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/19/2022] Open
Affiliation(s)
- Zhengyu Cao
- Anhui Provincial Key Laboratory of Molecular Enzymology and Mechanism of Major Diseases and Key Laboratory of Biomedicine in Gene Diseases and Health of Anhui Higher Education Institutes, College of Life Sciences, Anhui Normal University, Wuhu, Anhui, PR China
| | - Rui Meng
- Anhui Provincial Key Laboratory of Molecular Enzymology and Mechanism of Major Diseases and Key Laboratory of Biomedicine in Gene Diseases and Health of Anhui Higher Education Institutes, College of Life Sciences, Anhui Normal University, Wuhu, Anhui, PR China
| | - Peng Wang
- Anhui Provincial Key Laboratory of Molecular Enzymology and Mechanism of Major Diseases and Key Laboratory of Biomedicine in Gene Diseases and Health of Anhui Higher Education Institutes, College of Life Sciences, Anhui Normal University, Wuhu, Anhui, PR China
| | - Guoping Zhu
- Anhui Provincial Key Laboratory of Molecular Enzymology and Mechanism of Major Diseases and Key Laboratory of Biomedicine in Gene Diseases and Health of Anhui Higher Education Institutes, College of Life Sciences, Anhui Normal University, Wuhu, Anhui, PR China
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Kutscha R, Pflügl S. Microbial Upgrading of Acetate into Value-Added Products-Examining Microbial Diversity, Bioenergetic Constraints and Metabolic Engineering Approaches. Int J Mol Sci 2020; 21:ijms21228777. [PMID: 33233586 PMCID: PMC7699770 DOI: 10.3390/ijms21228777] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2020] [Revised: 10/29/2020] [Accepted: 11/18/2020] [Indexed: 01/20/2023] Open
Abstract
Ecological concerns have recently led to the increasing trend to upgrade carbon contained in waste streams into valuable chemicals. One of these components is acetate. Its microbial upgrading is possible in various species, with Escherichia coli being the best-studied. Several chemicals derived from acetate have already been successfully produced in E. coli on a laboratory scale, including acetone, itaconic acid, mevalonate, and tyrosine. As acetate is a carbon source with a low energy content compared to glucose or glycerol, energy- and redox-balancing plays an important role in acetate-based growth and production. In addition to the energetic challenges, acetate has an inhibitory effect on microorganisms, reducing growth rates, and limiting product concentrations. Moreover, extensive metabolic engineering is necessary to obtain a broad range of acetate-based products. In this review, we illustrate some of the necessary energetic considerations to establish robust production processes by presenting calculations of maximum theoretical product and carbon yields. Moreover, different strategies to deal with energetic and metabolic challenges are presented. Finally, we summarize ways to alleviate acetate toxicity and give an overview of process engineering measures that enable sustainable acetate-based production of value-added chemicals.
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Banerjee D, Eng T, Lau AK, Sasaki Y, Wang B, Chen Y, Prahl JP, Singan VR, Herbert RA, Liu Y, Tanjore D, Petzold CJ, Keasling JD, Mukhopadhyay A. Genome-scale metabolic rewiring improves titers rates and yields of the non-native product indigoidine at scale. Nat Commun 2020; 11:5385. [PMID: 33097726 PMCID: PMC7584609 DOI: 10.1038/s41467-020-19171-4] [Citation(s) in RCA: 46] [Impact Index Per Article: 11.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2020] [Accepted: 09/30/2020] [Indexed: 01/06/2023] Open
Abstract
High titer, rate, yield (TRY), and scalability are challenging metrics to achieve due to trade-offs between carbon use for growth and production. To achieve these metrics, we take the minimal cut set (MCS) approach that predicts metabolic reactions for elimination to couple metabolite production strongly with growth. We compute MCS solution-sets for a non-native product indigoidine, a sustainable pigment, in Pseudomonas putida KT2440, an emerging industrial microbe. From the 63 solution-sets, our omics guided process identifies one experimentally feasible solution requiring 14 simultaneous reaction interventions. We implement a total of 14 genes knockdowns using multiplex-CRISPRi. MCS-based solution shifts production from stationary to exponential phase. We achieve 25.6 g/L, 0.22 g/l/h, and ~50% maximum theoretical yield (0.33 g indigoidine/g glucose). These phenotypes are maintained from batch to fed-batch mode, and across scales (100-ml shake flasks, 250-ml ambr®, and 2-L bioreactors).
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Affiliation(s)
- Deepanwita Banerjee
- Joint BioEnergy Institute, Lawrence Berkeley National Laboratory, Emeryville, CA, 94608, USA
- Biological Systems and Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, CA, 94720, USA
| | - Thomas Eng
- Joint BioEnergy Institute, Lawrence Berkeley National Laboratory, Emeryville, CA, 94608, USA
- Biological Systems and Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, CA, 94720, USA
| | - Andrew K Lau
- Joint BioEnergy Institute, Lawrence Berkeley National Laboratory, Emeryville, CA, 94608, USA
- Biological Systems and Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, CA, 94720, USA
| | - Yusuke Sasaki
- Joint BioEnergy Institute, Lawrence Berkeley National Laboratory, Emeryville, CA, 94608, USA
- Biological Systems and Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, CA, 94720, USA
| | - Brenda Wang
- Joint BioEnergy Institute, Lawrence Berkeley National Laboratory, Emeryville, CA, 94608, USA
- Biological Systems and Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, CA, 94720, USA
| | - Yan Chen
- Joint BioEnergy Institute, Lawrence Berkeley National Laboratory, Emeryville, CA, 94608, USA
- Biological Systems and Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, CA, 94720, USA
| | - Jan-Philip Prahl
- Biological Systems and Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, CA, 94720, USA
- Advanced Biofuel and Bioproduct Process Development Unit, Lawrence Berkeley National Laboratory, Emeryville, CA, 94608, USA
| | - Vasanth R Singan
- Biological Systems and Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, CA, 94720, USA
- Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA, 94720, USA
| | - Robin A Herbert
- Joint BioEnergy Institute, Lawrence Berkeley National Laboratory, Emeryville, CA, 94608, USA
- Biological Systems and Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, CA, 94720, USA
| | - Yuzhong Liu
- Joint BioEnergy Institute, Lawrence Berkeley National Laboratory, Emeryville, CA, 94608, USA
- Biological Systems and Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, CA, 94720, USA
| | - Deepti Tanjore
- Biological Systems and Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, CA, 94720, USA
- Advanced Biofuel and Bioproduct Process Development Unit, Lawrence Berkeley National Laboratory, Emeryville, CA, 94608, USA
| | - Christopher J Petzold
- Joint BioEnergy Institute, Lawrence Berkeley National Laboratory, Emeryville, CA, 94608, USA
- Biological Systems and Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, CA, 94720, USA
| | - Jay D Keasling
- Joint BioEnergy Institute, Lawrence Berkeley National Laboratory, Emeryville, CA, 94608, USA
- Biological Systems and Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, CA, 94720, USA
- QB3 Institute, University of California-Berkeley, 5885 Hollis Street, 4th Floor, Emeryville, CA, 94608, USA
- Department of Chemical & Biomolecular Engineering, University of California, Berkeley, CA, 94720, USA
- Department of Bioengineering, University of California, Berkeley, CA, 94720, USA
- Novo Nordisk Foundation Center for Biosustainability, Technical University Denmark, 2970, Horsholm, Denmark
- Synthetic Biochemistry Center, Institute for Synthetic Biology, Shenzhen Institutes for Advanced Technologies, Shenzhen, China
| | - Aindrila Mukhopadhyay
- Joint BioEnergy Institute, Lawrence Berkeley National Laboratory, Emeryville, CA, 94608, USA.
- Biological Systems and Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, CA, 94720, USA.
- Environmental Genomics and Systems Biology Division, Lawrence Berkeley National Laboratory, Berkeley, CA, 94720, USA.
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Weusthuis RA, Folch PL, Pozo-Rodríguez A, Paul CE. Applying Non-canonical Redox Cofactors in Fermentation Processes. iScience 2020; 23:101471. [PMID: 32891057 PMCID: PMC7479625 DOI: 10.1016/j.isci.2020.101471] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2020] [Revised: 07/29/2020] [Accepted: 08/14/2020] [Indexed: 01/29/2023] Open
Abstract
Fermentation processes are used to sustainably produce chemicals and as such contribute to the transition to a circular economy. The maximum theoretical yield of a conversion can only be approached if all electrons present in the substrate end up in the product. Control over the electrons is therefore crucial. However, electron transfer via redox cofactors results in a diffuse distribution of electrons over metabolism. To overcome this challenge, we propose to apply non-canonical redox cofactors (NRCs) in metabolic networks: cofactors that channel electrons exclusively from substrate to product, forming orthogonal circuits for electron transfer.
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Affiliation(s)
- Ruud A. Weusthuis
- Bioprocess Engineering, Wageningen University & Research, Post Office Box 16, 6700 AA Wageningen, the Netherlands
| | - Pauline L. Folch
- Bioprocess Engineering, Wageningen University & Research, Post Office Box 16, 6700 AA Wageningen, the Netherlands
| | - Ana Pozo-Rodríguez
- Bioprocess Engineering, Wageningen University & Research, Post Office Box 16, 6700 AA Wageningen, the Netherlands
| | - Caroline E. Paul
- Biocatalysis, Department of Biotechnology, Delft University of Technology, Van der Maasweg 9, 2629 HZ Delft, the Netherlands
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Xie Y, Chen J, Wang B, Chen T, Chen J, Zhang Y, Liu X, Chen Q. Activation and enhancement of caerulomycin A biosynthesis in marine-derived Actinoalloteichus sp. AHMU CJ021 by combinatorial genome mining strategies. Microb Cell Fact 2020; 19:159. [PMID: 32762690 PMCID: PMC7412835 DOI: 10.1186/s12934-020-01418-w] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2020] [Accepted: 07/30/2020] [Indexed: 12/17/2022] Open
Abstract
Background Activation of silent biosynthetic gene clusters (BGCs) in marine-derived actinomycete strains is a feasible strategy to discover bioactive natural products. Actinoalloteichus sp. AHMU CJ021, isolated from the seashore, was shown to contain an intact but silent caerulomycin A (CRM A) BGC-cam in its genome. Thus, a genome mining work was preformed to activate the strain’s production of CRM A, an immunosuppressive drug lead with diverse bioactivities. Results To well activate the expression of cam, ribosome engineering was adopted to treat the wild type Actinoalloteichus sp. AHMU CJ021. The initial mutant strain XC-11G with gentamycin resistance and CRM A production titer of 42.51 ± 4.22 mg/L was selected from all generated mutant strains by gene expression comparison of the essential biosynthetic gene-camE. The titer of CRM A production was then improved by two strain breeding methods via UV mutagenesis and cofactor engineering-directed increase of intracellular riboflavin, which finally generated the optimal mutant strain XC-11GUR with a CRM A production titer of 113.91 ± 7.58 mg/L. Subsequently, this titer of strain XC-11GUR was improved to 618.61 ± 16.29 mg/L through medium optimization together with further adjustment derived from response surface methodology. In terms of this 14.6 folds increase in the titer of CRM A compared to the initial value, strain XC-GUR could be a well alternative strain for CRM A development. Conclusions Our results had constructed an ideal CRM A producer. More importantly, our efforts also had demonstrated the effectiveness of abovementioned combinatorial strategies, which is applicable to the genome mining of bioactive natural products from abundant actinomycetes strains.
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Affiliation(s)
- Yunchang Xie
- Key Laboratory of Functional Small Organic Molecule Ministry of Education and Jiangxi's Key Laboratory of Green Chemistry, Key Laboratory of Protection and Utilization of Subtropic Plant Resources of Jiangxi Province, College of Life Sciences, Jiangxi Normal University, Nanchang, 330022, China
| | - Jiawen Chen
- Key Laboratory of Functional Small Organic Molecule Ministry of Education and Jiangxi's Key Laboratory of Green Chemistry, Key Laboratory of Protection and Utilization of Subtropic Plant Resources of Jiangxi Province, College of Life Sciences, Jiangxi Normal University, Nanchang, 330022, China
| | - Bo Wang
- Guangdong Provincial Key Laboratory of Genome Read and Write, Shenzhen Engineering Laboratory for Innovative Molecular Diagnostics, Guangdong Provincial Academician Workstation of BGI Synthetic Genomics, BGI-Shenzhen, Beishan Industrial Zone, Shenzhen, 518083, China.,China National GeneBank, BGI-Shenzhen, Jinsha Road, Shenzhen, 518120, China
| | - Tai Chen
- Guangdong Provincial Key Laboratory of Genome Read and Write, Shenzhen Engineering Laboratory for Innovative Molecular Diagnostics, Guangdong Provincial Academician Workstation of BGI Synthetic Genomics, BGI-Shenzhen, Beishan Industrial Zone, Shenzhen, 518083, China.,China National GeneBank, BGI-Shenzhen, Jinsha Road, Shenzhen, 518120, China
| | - Junyu Chen
- Key Laboratory of Functional Small Organic Molecule Ministry of Education and Jiangxi's Key Laboratory of Green Chemistry, Key Laboratory of Protection and Utilization of Subtropic Plant Resources of Jiangxi Province, College of Life Sciences, Jiangxi Normal University, Nanchang, 330022, China
| | - Yuan Zhang
- School of Life Sciences, Anhui Medical University, Hefei, 230032, China
| | - Xiaoying Liu
- School of Life Sciences, Anhui Medical University, Hefei, 230032, China.
| | - Qi Chen
- School of Life Sciences, Anhui Medical University, Hefei, 230032, China.
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Verhagen KJA, van Gulik WM, Wahl SA. Dynamics in redox metabolism, from stoichiometry towards kinetics. Curr Opin Biotechnol 2020; 64:116-123. [DOI: 10.1016/j.copbio.2020.01.002] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2019] [Revised: 01/05/2020] [Accepted: 01/06/2020] [Indexed: 12/12/2022]
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Song HS, Jeon JM, Bhatia SK, Choi TR, Lee SM, Park SL, Lee HS, Yoon JJ, Ahn J, Lee H, Brigham CJ, Choi KY, Yang YH. Enhanced isobutanol production by co-production of polyhydroxybutyrate and cofactor engineering. J Biotechnol 2020; 320:66-73. [DOI: 10.1016/j.jbiotec.2020.06.017] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2019] [Revised: 05/29/2020] [Accepted: 06/18/2020] [Indexed: 01/17/2023]
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High-Efficient Production of ( S)-1-[3,5-Bis(trifluoromethyl)phenyl]ethanol via Whole-Cell Catalyst in Deep-Eutectic Solvent-Containing Micro-Aerobic Medium System. Molecules 2020; 25:molecules25081855. [PMID: 32316570 PMCID: PMC7221904 DOI: 10.3390/molecules25081855] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2020] [Revised: 04/09/2020] [Accepted: 04/15/2020] [Indexed: 01/12/2023] Open
Abstract
The ratio of substrate to catalyst (S/C) is a prime target for the application of asymmetric production of enantiomerically enriched intermediates by whole-cell biocatalyst. In the present study, an attractive increase in S/C was achieved in a natural deep-eutectic solvent (NADES) containing reaction system under microaerobic condition for high production of (S)-1-[3,5-bis(trifluoromethyl)phenyl]ethanol ((S)-3,5-BTPE) with Candida tropicalis 104. In PBS buffer (0.2 M, pH 8.0) at 200 rpm and 30 °C, 79.5 g (Dry Cell Weight, DCW)/L C. tropicalis 104 maintained the same yield of 73.7% for the bioreduction of 3,5-bis(trifluoromethyl)acetophenone (BTAP) under an oxygen-deficient environment compared with oxygen-sufficient conditions, while substrate load increased 4.0-fold (from 50 mM to 200 mM). Furthermore, when choline chloride:trehalose (ChCl:T, 1:1 molar ratio) was introduced into the reaction system for its versatility of increasing cell membrane permeability and declining BTAP cytotoxicity to biocatalyst, the yields were further increased to 86.2% under 200 mM BTAP, or 72.9% at 300 mM BTAP. After the optimization of various reaction parameters involved in the bioreduction, and the amount of biocatalyst and maltose co-substrate remained 79.5 g (DCW)/L and 50 g/L, the S/C for the reduction elevated 6.3 times (3.8 mM/g versus 0.6 mM/g). By altering the respiratory pattern of the whole-cell biocatalyst and exploiting the ChCl:T-containing reaction system, the developed strategy exhibits an attractive potential for enhancing catalytic efficiency of whole-cell-mediated reduction, and provides valuable insight for the development of whole-cell catalysis.
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Xu JJ, Fu LJ, Si KL, Yue TL, Guo CF. 3-phenyllactic acid production by free-whole-cells of Lactobacillus crustorum in batch and continuous fermentation systems. J Appl Microbiol 2020; 129:335-344. [PMID: 32009287 DOI: 10.1111/jam.14599] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2019] [Revised: 01/06/2020] [Accepted: 01/29/2020] [Indexed: 01/11/2023]
Abstract
AIM 3-Phenyllactic acid (3-PLA) has been widely used in food and material industries. Three Lactobacillus crustorum strains have shown greater 3-PLA production ability in our previous study. The objectives of this study were to further improve 3-PLA yields in batch and continuous fermentation systems using of free-whole-cells of the three L. crustorum strains. MATERIALS AND RESULTS The fermentation conditions of free-whole-cells of the three L. crustorum strains for 3-PLA production were optimized. Among these strains, L. crustorum NWAFU 1078 showed excellent reusability and significantly (P < 0·05) greater 3-PLA production ability than the other strains after 10th recycle. The strain possesses three l-lactate dehydrogenase and three d-lactate dehydrogenase catalysing 3-PLA production from phenylpyruvic acid (PPA). Under the optimal conditions, the strain produced 15·2 mmol l-1 3-PLA (76% PPA conversion rate) in a batch fermentation system and 6·5 mmol l-1 h-1 3-PLA (55% PPA conversion rate) in a continuous fermentation system using a 0·6 dilution rate. CONCLUSIONS Free-whole-cells of L. crustorum NWAFU 1078 showed excellent reusability and higher 3-PLA yields under optimal biotransformation conditions in both batch and continuous fermentation systems. SIGNIFICANCE AND IMPACT OF THE STUDY This study provides the possibility to use the free-whole-cells of L. crustorum NWAFU 1078 as a biocatalyst for effective production of 3-PLA.
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Affiliation(s)
- J-J Xu
- College of Food Science and Engineering, Northwest A&F University, Yangling, China
| | - L-J Fu
- College of Food Science and Engineering, Northwest A&F University, Yangling, China
| | - K-L Si
- College of Food Science and Engineering, Northwest A&F University, Yangling, China
| | - T-L Yue
- College of Food Science and Engineering, Northwest A&F University, Yangling, China
| | - C-F Guo
- College of Food Science and Engineering, Northwest A&F University, Yangling, China
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Shimizu K, Matsuoka Y. Redox rebalance against genetic perturbations and modulation of central carbon metabolism by the oxidative stress regulation. Biotechnol Adv 2019; 37:107441. [PMID: 31472206 DOI: 10.1016/j.biotechadv.2019.107441] [Citation(s) in RCA: 31] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2019] [Revised: 08/04/2019] [Accepted: 08/23/2019] [Indexed: 12/11/2022]
Abstract
The micro-aerophilic organisms and aerobes as well as yeast and higher organisms have evolved to gain energy through respiration (via oxidative phosphorylation), thereby enabling them to grow much faster than anaerobes. However, during respiration, reactive oxygen species (ROSs) are inherently (inevitably) generated, and threaten the cell's survival. Therefore, living organisms (or cells) must furnish the potent defense systems to keep such ROSs at harmless level, where the cofactor balance plays crucial roles. Namely, NADH is the source of energy generation (catabolism) in the respiratory chain reactions, through which ROSs are generated, while NADPH plays important roles not only for the cell synthesis (anabolism) but also for detoxifying ROSs. Therefore, the cell must rebalance the redox ratio by modulating the fluxes of the central carbon metabolism (CCM) by regulating the multi-level regulation machinery upon genetic perturbations and the change in the growth conditions. Here, we discuss about how aerobes accomplish such cofactor homeostasis against redox perturbations. In particular, we consider how single-gene mutants (including pgi, pfk, zwf, gnd and pyk mutants) modulate their metabolisms in relation to cofactor rebalance (and also by adaptive laboratory evolution). We also discuss about how the overproduction of NADPH (by the pathway gene mutation) can be utilized for the efficient production of useful value-added chemicals such as medicinal compounds, polyhydroxyalkanoates, and amino acids, all of which require NADPH in their synthetic pathways. We then discuss about the metabolic responses against oxidative stress, where αketoacids play important roles not only for the coordination between catabolism and anabolism, but also for detoxifying ROSs by non-enzymatic reactions, as well as for reducing the production of ROSs by repressing the activities of the TCA cycle and respiration (via carbon catabolite repression). Thus, we discuss about the mechanisms (basic strategies) that modulate the metabolism from respiration to respiro-fermentative metabolism causing overflow, based on the role of Pyk activity, affecting the NADPH production at the oxidative pentose phosphate (PP) pathway, and the roles of αketoacids for the change in the source of energy generation from the oxidative phosphorylation to the substrate level phosphorylation.
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Affiliation(s)
- Kazuyuki Shimizu
- Kyushu institute of Technology, Iizuka, Fukuoka 820-8502, Japan; Institute of Advanced Biosciences, Keio university, Tsuruoka, Yamagata 997-0017, Japan.
| | - Yu Matsuoka
- Kyushu institute of Technology, Iizuka, Fukuoka 820-8502, Japan.
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Lim HG, Kwak DH, Park S, Woo S, Yang JS, Kang CW, Kim B, Noh MH, Seo SW, Jung GY. Vibrio sp. dhg as a platform for the biorefinery of brown macroalgae. Nat Commun 2019; 10:2486. [PMID: 31171782 PMCID: PMC6554313 DOI: 10.1038/s41467-019-10371-1] [Citation(s) in RCA: 26] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2018] [Accepted: 05/08/2019] [Indexed: 12/14/2022] Open
Abstract
Although brown macroalgae holds potential as an alternative feedstock, its utilization by conventional microbial platforms has been limited due to the inability to metabolize one of the principal sugars, alginate. Here, we isolate Vibrio sp. dhg, a fast-growing bacterium that can efficiently assimilate alginate. Based on systematic characterization of the genomic information of Vibrio sp. dhg, we establish a genetic toolbox for its engineering. We also demonstrate its ability to rapidly produce ethanol, 2,3-butanediol, and lycopene from brown macroalgae sugar mixture with high productivities and yields. Collectively, Vibrio sp. dhg can be used as a platform for the efficient conversion of brown macroalgae sugars into diverse value-added biochemicals.
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Affiliation(s)
- Hyun Gyu Lim
- Department of Chemical Engineering, Pohang University of Science and Technology, 77 Cheongam-Ro, Nam-Gu, Pohang, Gyeongbuk, 37673, Korea
| | - Dong Hun Kwak
- School of Interdisciplinary Bioscience and Bioengineering, Pohang University of Science and Technology, 77 Cheongam-Ro, Nam-Gu, Pohang, Gyeongbuk, 37673, Korea
| | - Sungwoo Park
- School of Chemical and Biological Engineering, Institute of Chemical Process, Seoul National University, 1 Gwanak-Ro, Gwanak-Gu, Seoul, 08826, Korea
| | - Sunghwa Woo
- Department of Chemical Engineering, Pohang University of Science and Technology, 77 Cheongam-Ro, Nam-Gu, Pohang, Gyeongbuk, 37673, Korea
| | - Jae-Seong Yang
- Department of Chemical Engineering, Pohang University of Science and Technology, 77 Cheongam-Ro, Nam-Gu, Pohang, Gyeongbuk, 37673, Korea
| | - Chae Won Kang
- Department of Chemical Engineering, Pohang University of Science and Technology, 77 Cheongam-Ro, Nam-Gu, Pohang, Gyeongbuk, 37673, Korea
| | - Beomhee Kim
- School of Chemical and Biological Engineering, Institute of Chemical Process, Seoul National University, 1 Gwanak-Ro, Gwanak-Gu, Seoul, 08826, Korea
| | - Myung Hyun Noh
- Department of Chemical Engineering, Pohang University of Science and Technology, 77 Cheongam-Ro, Nam-Gu, Pohang, Gyeongbuk, 37673, Korea
| | - Sang Woo Seo
- School of Chemical and Biological Engineering, Institute of Chemical Process, Seoul National University, 1 Gwanak-Ro, Gwanak-Gu, Seoul, 08826, Korea.
| | - Gyoo Yeol Jung
- Department of Chemical Engineering, Pohang University of Science and Technology, 77 Cheongam-Ro, Nam-Gu, Pohang, Gyeongbuk, 37673, Korea.
- School of Interdisciplinary Bioscience and Bioengineering, Pohang University of Science and Technology, 77 Cheongam-Ro, Nam-Gu, Pohang, Gyeongbuk, 37673, Korea.
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Switching the substrate specificity from NADH to NADPH by a single mutation of NADH oxidase from Lactobacillus rhamnosus. Int J Biol Macromol 2019; 135:328-336. [PMID: 31128193 DOI: 10.1016/j.ijbiomac.2019.05.146] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2019] [Revised: 05/14/2019] [Accepted: 05/14/2019] [Indexed: 02/07/2023]
Abstract
Enzymatic NADP+ regeneration is a promising approach to produce valuable chemicals under economic conditions. Among all the enzymatic routes, using water-forming NADH oxidase is an ideal one because there is no by-product. However, most NADH oxidases have a low specific activity to NADPH. In this work, a thermostable NADH oxidase from Lactobacillus rhamnosus (LrNox) was rationally engineered to switch its specificity from NADH to NADPH. The results show that mutants D177A, G178R, D177A/G178R, D177A/G178R/L179S improved the NADPH activity by a factor of 4-6. The highest NADPH catalytic efficiency (Kcat/Km 223.71 S-1 μm-1, 47.6-fold higher than wild-type LrNox) and 51% of NADH activity retention were achieved by replacing the single amino acid Leu179 for serine (L179S) in LrNox. Modeling of L179S-NADPH complex reveals that the phosphate group of NADPH interacts with the hydroxyl of Ser179 with a strong hydrogen bond and several shorter hydrogen bonds with the amino group of Lys185 could stabilize the binding of NADPH in the L179S mutant. This work provides an efficient method for converting NAD(P)H specificity and shows that L179S mutant is a potential and efficient auxiliary enzyme for NADP+ regeneration.
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Liang J, Huang H, Wang S. Distribution, Evolution, Catalytic Mechanism, and Physiological Functions of the Flavin-Based Electron-Bifurcating NADH-Dependent Reduced Ferredoxin: NADP + Oxidoreductase. Front Microbiol 2019; 10:373. [PMID: 30881354 PMCID: PMC6405883 DOI: 10.3389/fmicb.2019.00373] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2018] [Accepted: 02/12/2019] [Indexed: 12/12/2022] Open
Abstract
NADH-dependent reduced ferredoxin:NADP+ oxidoreductase (Nfn) is an electron-bifurcating enzyme first discovered in the strict anaerobes Clostridium kluyveri and Moorella thermoacetica. In vivo, Nfn catalyzes the endergonic reduction of NADP+ with NADH coupled to the exergonic reduction of NADP+ with reduced ferredoxin. Most Nfn homologs consist of two subunits, although in certain species Nfn homologs are fused. In contrast to other electron-bifurcating enzymes, Nfn possess a simpler structure. Therefore, Nfn becomes a perfect model to determine the mechanism of flavin-based electron bifurcation, which is a novel energy coupling mode distributed among anaerobic bacteria and archaea. The crystal structures of Nfn from Thermotoga maritima and Pyrococcus furiosus are known, and studies have shown that the FAD molecule of the NfnB (b-FAD) is the site of electron bifurcation, and other cofactors, including a [2Fe2S] cluster, two [4Fe4S] clusters, and the FAD molecule on the NfnA subunit, contribute to electron transfer. Further, the short-lived anionic flavin semiquinone (ASQ) state of b-FAD is essential for electron bifurcation. Nfn homologs are widely distributed among microbes, including bacteria, archaea, and probably eukaryotes, most of which are anaerobes despite that certain species are facultative microbes and even aerobes. Moreover, potential evidence shows that lateral gene transfer may occur in the evolution of this enzyme. Nfn homologs present four different structural patterns, including the well-characterized NfnAB and three different kinds of fused Nfn homologs whose detailed properties have not been characterized. These findings indicate that gene fusion/fission and gene rearrangement may contribute to the evolution of this enzyme. Under physiological conditions, Nfn catalyzes the reduction of NADP+ with NADH and reduced ferredoxin, which is then used in certain NADPH-dependent reactions. Deletion of nfn in several microbes causes low growth and redox unbalance and may influence the distribution of fermentation products. It’s also noteworthy that different Nfn homologs perform different functions according to its circumstance. Physiological functions of Nfn indicate that it can be a potential tool in the metabolic engineering of industrial microorganisms, which can regulate the redox potential in vivo.
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Affiliation(s)
- Jiyu Liang
- State Key Laboratory of Microbial Technology, Microbial Technology Institute, Shandong University, Qingdao, China
| | - Haiyan Huang
- Institute of Basic Medicine, Shandong Academy of Medical Sciences, Jinan, China
| | - Shuning Wang
- State Key Laboratory of Microbial Technology, Microbial Technology Institute, Shandong University, Qingdao, China
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47
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Chen L, Cao C, Wang S, Varcoe JR, Slade RCT, Avignone-Rossa C, Zhao F. Electron Communication of Bacillus subtilis in Harsh Environments. iScience 2019; 12:260-269. [PMID: 30711749 PMCID: PMC6360405 DOI: 10.1016/j.isci.2019.01.020] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2018] [Revised: 01/11/2019] [Accepted: 01/16/2019] [Indexed: 12/24/2022] Open
Abstract
Elucidating the effect of harsh environments on the activities of microorganisms is important in revealing how microbes withstand unfavorable conditions or evolve mechanisms to counteract those effects, many of which involve electron transfer phenomena. Here we show that the non-acidophilic and non-thermophilic Bacillus subtilis is able to maintain activity after being subjected to extreme temperatures (100°C for up to 8 h) and acidic environments (pH = 1.50 for over 2 years). In the process, our results suggest that B. subtilis utilizes an extracellular electron transfer as an electron communication pathway between B. subtilis and the environment that involves the cofactor nicotinamide adenine dinucleotide as an essential participant to maintain viability. Elucidation of the capability of the non-acidophilic and non-thermophilic strain to maintain viability under these extreme conditions could aid in understanding the cell responses to different environments from the perspective of energy conservation pathways.
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Affiliation(s)
- Lixiang Chen
- CAS Key Laboratory of Urban Pollutant Conversion, Institute of Urban Environment, Chinese Academy of Sciences, Xiamen 361021, P.R.China; University of Chinese Academy of Sciences, Beijing 100049, P.R.China
| | - Changli Cao
- Ningbo Urban Environment Observation and Research Station, Chinese Academy of Sciences, Ningbo 315830, P.R. China
| | - Shuhua Wang
- CAS Key Laboratory of Urban Pollutant Conversion, Institute of Urban Environment, Chinese Academy of Sciences, Xiamen 361021, P.R.China; University of Chinese Academy of Sciences, Beijing 100049, P.R.China
| | - John R Varcoe
- Department of Chemistry, University of Surrey, Guildford GU2 7XH, UK
| | - Robert C T Slade
- Department of Chemistry, University of Surrey, Guildford GU2 7XH, UK
| | | | - Feng Zhao
- CAS Key Laboratory of Urban Pollutant Conversion, Institute of Urban Environment, Chinese Academy of Sciences, Xiamen 361021, P.R.China.
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48
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Cabulong RB, Valdehuesa KNG, Bañares AB, Ramos KRM, Nisola GM, Lee WK, Chung WJ. Improved cell growth and biosynthesis of glycolic acid by overexpression of membrane-bound pyridine nucleotide transhydrogenase. J Ind Microbiol Biotechnol 2018; 46:159-169. [PMID: 30554290 DOI: 10.1007/s10295-018-2117-2] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2018] [Accepted: 11/27/2018] [Indexed: 01/07/2023]
Abstract
The non-conventional D-xylose metabolism called the Dahms pathway which only requires the expression of at least three enzymes to produce pyruvate and glycolaldehyde has been previously engineered in Escherichia coli. Strains that rely on this pathway exhibit lower growth rates which were initially attributed to the perturbed redox homeostasis as evidenced by the lower intracellular NADPH concentrations during exponential growth phase. NADPH-regenerating systems were then tested to restore the redox homeostasis. The membrane-bound pyridine nucleotide transhydrogenase, PntAB, was overexpressed and resulted to a significant increase in biomass and glycolic acid titer and yield. Furthermore, expression of PntAB in an optimized glycolic acid-producing strain improved the growth and product titer significantly. This work demonstrated that compensating for the NADPH demand can be achieved by overexpression of PntAB in E. coli strains assimilating D-xylose through the Dahms pathway. Consequently, increase in biomass accumulation and product concentration was also observed.
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Affiliation(s)
- Rhudith B Cabulong
- Department of Energy Science and Technology (DEST), Energy and Environment Fusion Technology Center (E2FTC), Myongji University, Myongji-ro 116, Cheoin-gu, Yongin, Gyeonggi-do, 170-58, South Korea
| | - Kris Niño G Valdehuesa
- Department of Energy Science and Technology (DEST), Energy and Environment Fusion Technology Center (E2FTC), Myongji University, Myongji-ro 116, Cheoin-gu, Yongin, Gyeonggi-do, 170-58, South Korea
| | - Angelo B Bañares
- Department of Energy Science and Technology (DEST), Energy and Environment Fusion Technology Center (E2FTC), Myongji University, Myongji-ro 116, Cheoin-gu, Yongin, Gyeonggi-do, 170-58, South Korea
| | - Kristine Rose M Ramos
- Department of Energy Science and Technology (DEST), Energy and Environment Fusion Technology Center (E2FTC), Myongji University, Myongji-ro 116, Cheoin-gu, Yongin, Gyeonggi-do, 170-58, South Korea
| | - Grace M Nisola
- Department of Energy Science and Technology (DEST), Energy and Environment Fusion Technology Center (E2FTC), Myongji University, Myongji-ro 116, Cheoin-gu, Yongin, Gyeonggi-do, 170-58, South Korea
| | - Won-Keun Lee
- Division of Bioscience and Bioinformatics, Myongji University, Myongji-ro 116, Cheoin-gu, Yongin, Gyeonggi-do, 170-58, South Korea.
| | - Wook-Jin Chung
- Department of Energy Science and Technology (DEST), Energy and Environment Fusion Technology Center (E2FTC), Myongji University, Myongji-ro 116, Cheoin-gu, Yongin, Gyeonggi-do, 170-58, South Korea.
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49
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Liu J, Li H, Xiong H, Xie X, Chen N, Zhao G, Caiyin Q, Zhu H, Qiao J. Two-stage carbon distribution and cofactor generation for improving l-threonine production of Escherichia coli. Biotechnol Bioeng 2018; 116:110-120. [PMID: 30252940 DOI: 10.1002/bit.26844] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2018] [Revised: 09/09/2018] [Accepted: 09/21/2018] [Indexed: 12/14/2022]
Abstract
L-Threonine, a kind of essential amino acid, has numerous applications in food, pharmaceutical, and aquaculture industries. Fermentative l-threonine production from glucose has been achieved in Escherichia coli. However, there are still several limiting factors hindering further improvement of l-threonine productivity, such as the conflict between cell growth and production, byproduct accumulation, and insufficient availability of cofactors (adenosine triphosphate, NADH, and NADPH). Here, a metabolic modification strategy of two-stage carbon distribution and cofactor generation was proposed to address the above challenges in E. coli THRD, an l-threonine producing strain. The glycolytic fluxes towards tricarboxylic acid cycle were increased in growth stage through heterologous expression of pyruvate carboxylase, phosphoenolpyruvate carboxykinase, and citrate synthase, leading to improved glucose utilization and growth performance. In the production stage, the carbon flux was redirected into l-threonine synthetic pathway via a synthetic genetic circuit. Meanwhile, to sustain the transaminase reaction for l-threonine production, we developed an l-glutamate and NADPH generation system through overexpression of glutamate dehydrogenase, formate dehydrogenase, and pyridine nucleotide transhydrogenase. This strategy not only exhibited 2.02- and 1.21-fold increase in l-threonine production in shake flask and bioreactor fermentation, respectively, but had potential to be applied in the production of many other desired oxaloacetate derivatives, especially those involving cofactor reactions.
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Affiliation(s)
- Jiaheng Liu
- Key Laboratory of Systems Bioengineering (Ministry of Education), Tianjin University, Tianjin, China.,School of Chemical Engineering and Technology, Tianjin University, Tianjin, China.,SynBio Research Platform, Collaborative Innovation Center of Chemical Science and Engineering (Tianjin) Tianjin University, Tianjin, China
| | - Huiling Li
- Key Laboratory of Systems Bioengineering (Ministry of Education), Tianjin University, Tianjin, China.,School of Chemical Engineering and Technology, Tianjin University, Tianjin, China.,SynBio Research Platform, Collaborative Innovation Center of Chemical Science and Engineering (Tianjin) Tianjin University, Tianjin, China
| | - Hui Xiong
- Key Laboratory of Systems Bioengineering (Ministry of Education), Tianjin University, Tianjin, China.,School of Chemical Engineering and Technology, Tianjin University, Tianjin, China.,SynBio Research Platform, Collaborative Innovation Center of Chemical Science and Engineering (Tianjin) Tianjin University, Tianjin, China
| | - Xixian Xie
- National and Local United Engineering Lab of Metabolic Control Fermentation Technology, Tianjin University of Science and Technology, Tianjin, China
| | - Ning Chen
- National and Local United Engineering Lab of Metabolic Control Fermentation Technology, Tianjin University of Science and Technology, Tianjin, China
| | - Guangrong Zhao
- Key Laboratory of Systems Bioengineering (Ministry of Education), Tianjin University, Tianjin, China.,School of Chemical Engineering and Technology, Tianjin University, Tianjin, China.,SynBio Research Platform, Collaborative Innovation Center of Chemical Science and Engineering (Tianjin) Tianjin University, Tianjin, China
| | - Qinggele Caiyin
- Key Laboratory of Systems Bioengineering (Ministry of Education), Tianjin University, Tianjin, China.,School of Chemical Engineering and Technology, Tianjin University, Tianjin, China
| | - Hongji Zhu
- Key Laboratory of Systems Bioengineering (Ministry of Education), Tianjin University, Tianjin, China.,School of Chemical Engineering and Technology, Tianjin University, Tianjin, China
| | - Jianjun Qiao
- Key Laboratory of Systems Bioengineering (Ministry of Education), Tianjin University, Tianjin, China.,School of Chemical Engineering and Technology, Tianjin University, Tianjin, China.,SynBio Research Platform, Collaborative Innovation Center of Chemical Science and Engineering (Tianjin) Tianjin University, Tianjin, China
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50
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Goldbeck O, Eck AW, Seibold GM. Real Time Monitoring of NADPH Concentrations in Corynebacterium glutamicum and Escherichia coli via the Genetically Encoded Sensor mBFP. Front Microbiol 2018; 9:2564. [PMID: 30405597 PMCID: PMC6207642 DOI: 10.3389/fmicb.2018.02564] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2018] [Accepted: 10/08/2018] [Indexed: 12/16/2022] Open
Abstract
Analyses of intracellular NADPH concentrations are prerequisites for the design of microbial production strains and process optimization. mBFP was described as metagenomics derived, blue fluorescent protein showing NADPH-dependent fluorescence. Characterization of mBFP showed a high specificity for binding of NADPH (KD 0.64 mM) and no binding of NADH, the protein exclusively amplified fluorescence of NADPH. mBFP catalyzed the NADPH-dependent reduction of benzaldehyde and further aldehydes, which fits to its classification as short chain dehydrogenase. For in vivo NADPH analyses a codon-optimized gene for mBFP was introduced into Corynebacterium glutamicum WT and the phosphoglucoisomerase-deficient strain C. glutamicum Δpgi, which accumulates high levels of NADPH. For determination of intracellular NADPH concentrations by mBFP a calibration method with permeabilized cells was developed. By this means an increase of intracellular NADPH concentrations within seconds after the addition of glucose to nutrient-starved cells of both C. glutamicum WT and C. glutamicum Δpgi was observed; as expected the internal NADPH concentration was significantly higher for C. glutamicum Δpgi (0.31 mM) when compared to C. glutamicum WT (0.19 mM). Addition of paraquat to E. coli cells carrying mBFP led as expected to an immediate decrease of intracellular NADPH concentrations, showing the versatile use of mBFP as intracellular sensor.
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Affiliation(s)
- Oliver Goldbeck
- Institute of Microbiology and Biotechnology, Ulm University, Ulm, Germany
| | - Alexander W Eck
- Institute for Biochemistry, University of Cologne, Cologne, Germany
| | - Gerd M Seibold
- Institute of Microbiology and Biotechnology, Ulm University, Ulm, Germany.,Institute for Biochemistry, University of Cologne, Cologne, Germany
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