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Zhou H, Zhang Y, Long CP, Xia X, Xue Y, Ma Y, Antoniewicz MR, Tao Y, Lin B. A citric acid cycle-deficient Escherichia coli as an efficient chassis for aerobic fermentations. Nat Commun 2024; 15:2372. [PMID: 38491007 PMCID: PMC10943122 DOI: 10.1038/s41467-024-46655-4] [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: 04/21/2023] [Accepted: 03/05/2024] [Indexed: 03/18/2024] Open
Abstract
Tricarboxylic acid cycle (TCA cycle) plays an important role for aerobic growth of heterotrophic bacteria. Theoretically, eliminating TCA cycle would decrease carbon dissipation and facilitate chemicals biosynthesis. Here, we construct an E. coli strain without a functional TCA cycle that can serve as a versatile chassis for chemicals biosynthesis. We first use adaptive laboratory evolution to recover aerobic growth in minimal medium of TCA cycle-deficient E. coli. Inactivation of succinate dehydrogenase is a key event in the evolutionary trajectory. Supply of succinyl-CoA is identified as the growth limiting factor. By replacing endogenous succinyl-CoA dependent enzymes, we obtain an optimized TCA cycle-deficient E. coli strain. As a proof of concept, the strain is engineered for high-yield production of four separate products. This work enhances our understanding of the role of the TCA cycle in E. coli metabolism and demonstrates the advantages of using TCA cycle-deficient E. coli strain for biotechnological applications.
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Affiliation(s)
- Hang Zhou
- CAS Key Laboratory of Microbial Physiological and Metabolic Engineering, State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, 100101, Beijing, China
- University of Chinese Academy of Sciences, 100049, Beijing, China
| | - Yiwen Zhang
- CAS Key Laboratory of Microbial Physiological and Metabolic Engineering, State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, 100101, Beijing, China
- University of Chinese Academy of Sciences, 100049, Beijing, China
| | - Christopher P Long
- Department of Chemical and Biomolecular Engineering, Metabolic Engineering and Systems Biology Laboratory, University of Delaware, Newark, DE, 19716, USA
| | - Xuesen Xia
- School of Biology and Biological Engineering, South China University of Technology, Guangzhou, 510006, China
| | - Yanfen Xue
- CAS Key Laboratory of Microbial Physiological and Metabolic Engineering, State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, 100101, Beijing, China
| | - Yanhe Ma
- CAS Key Laboratory of Microbial Physiological and Metabolic Engineering, State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, 100101, Beijing, China.
| | - Maciek R Antoniewicz
- Department of Chemical and Biomolecular Engineering, Metabolic Engineering and Systems Biology Laboratory, University of Delaware, Newark, DE, 19716, USA.
- Department of Chemical Engineering, University of Michigan, Ann Arbor, MI, USA.
| | - Yong Tao
- CAS Key Laboratory of Microbial Physiological and Metabolic Engineering, State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, 100101, Beijing, China.
- University of Chinese Academy of Sciences, 100049, Beijing, China.
| | - Baixue Lin
- CAS Key Laboratory of Microbial Physiological and Metabolic Engineering, State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, 100101, Beijing, China.
- University of Chinese Academy of Sciences, 100049, Beijing, China.
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Li C, Sun P, Wei G, Zhu Y, Li J, Liu Y, Chen J, Deng Y. Efficient biosynthesis of creatine by whole-cell catalysis from guanidinoacetic acid in Corynebacterium glutamicum. Synth Syst Biotechnol 2024; 9:99-107. [PMID: 38288444 PMCID: PMC10823089 DOI: 10.1016/j.synbio.2024.01.003] [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: 10/10/2023] [Revised: 12/10/2023] [Accepted: 01/05/2024] [Indexed: 01/31/2024] Open
Abstract
Creatine is a naturally occurring derivative of an amino acid commonly utilized in functional foods and pharmaceuticals. Nevertheless, the current industrial synthesis of creatine relies on chemical processes, which may hinder its utilization in certain applications. Therefore, a biological approach was devised that employs whole-cell biocatalysis in the bacterium Corynebacterium glutamicum, which is considered safe for use in food production, to produce safe-for-consumption creatine. The objective of this study was to identify a guanidinoacetate N-methyltransferase (GAMT) with superior catalytic activity for creatine production. Through employing whole-cell biocatalysis, a gamt gene from Mus caroli (Mcgamt) was cloned and expressed in C. glutamicum ATCC 13032, resulting in a creatine titer of 3.37 g/L. Additionally, the study employed a promoter screening strategy that utilized nine native strong promoters in C. glutamicum to enhance the expression level of GAMT. The highest titer was achieved using the P1676 promoter, reaching 4.14 g/L. The conditions of whole-cell biocatalysis were further optimized, resulting in a creatine titer of 5.42 g/L. This is the first report of successful secretory creatine expression in C. glutamicum, which provides a safer and eco-friendly approach for the industrial production of creatine.
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Affiliation(s)
- Chunjian Li
- College of Food Science and Engineering, Qingdao Agricultural University, Qingdao 266109, China
- Key Laboratory of Special Food Processing (Co-construction by Ministry and Province), Ministry of Agriculture Rural Affairs, Qingdao Agricultural University, Qingdao 266109, China
- Shandong Technology Innovation Center of Special Food, Qingdao 266109, China
- Qingdao Special Food Research Institute, Qingdao 266109, China
- Qingdao Nuoan Baite Biotechnology Co., Ltd., Qingdao 266109, China
| | - Pengdong Sun
- College of Food Science and Engineering, Qingdao Agricultural University, Qingdao 266109, China
- Key Laboratory of Special Food Processing (Co-construction by Ministry and Province), Ministry of Agriculture Rural Affairs, Qingdao Agricultural University, Qingdao 266109, China
- Shandong Technology Innovation Center of Special Food, Qingdao 266109, China
- Qingdao Special Food Research Institute, Qingdao 266109, China
| | - Guoqing Wei
- College of Food Science and Engineering, Qingdao Agricultural University, Qingdao 266109, China
- Key Laboratory of Special Food Processing (Co-construction by Ministry and Province), Ministry of Agriculture Rural Affairs, Qingdao Agricultural University, Qingdao 266109, China
- Shandong Technology Innovation Center of Special Food, Qingdao 266109, China
- Qingdao Special Food Research Institute, Qingdao 266109, China
| | - Yuqi Zhu
- College of Food Science and Engineering, Qingdao Agricultural University, Qingdao 266109, China
- Key Laboratory of Special Food Processing (Co-construction by Ministry and Province), Ministry of Agriculture Rural Affairs, Qingdao Agricultural University, Qingdao 266109, China
- Shandong Technology Innovation Center of Special Food, Qingdao 266109, China
- Qingdao Special Food Research Institute, Qingdao 266109, China
| | - Jingyuan Li
- College of Food Science and Engineering, Qingdao Agricultural University, Qingdao 266109, China
- Key Laboratory of Special Food Processing (Co-construction by Ministry and Province), Ministry of Agriculture Rural Affairs, Qingdao Agricultural University, Qingdao 266109, China
- Shandong Technology Innovation Center of Special Food, Qingdao 266109, China
- Qingdao Special Food Research Institute, Qingdao 266109, China
| | - Yanfeng Liu
- Qingdao Special Food Research Institute, Qingdao 266109, China
- Science Center for Future Foods, Engineering Research Center of Ministry of Education on Food Synthetic Biotechnology, and Jiangsu Province Engineering Research Center of Food Synthetic Biotechnology, Jiangnan University, Wuxi 214122, China
- Key Laboratory of Carbohydrate Chemistry and Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, Wuxi 214122, China
| | - Jian Chen
- Qingdao Special Food Research Institute, Qingdao 266109, China
- Science Center for Future Foods, Engineering Research Center of Ministry of Education on Food Synthetic Biotechnology, and Jiangsu Province Engineering Research Center of Food Synthetic Biotechnology, Jiangnan University, Wuxi 214122, China
- Key Laboratory of Carbohydrate Chemistry and Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, Wuxi 214122, China
| | - Yang Deng
- College of Food Science and Engineering, Qingdao Agricultural University, Qingdao 266109, China
- Key Laboratory of Special Food Processing (Co-construction by Ministry and Province), Ministry of Agriculture Rural Affairs, Qingdao Agricultural University, Qingdao 266109, China
- Shandong Technology Innovation Center of Special Food, Qingdao 266109, China
- Qingdao Special Food Research Institute, Qingdao 266109, China
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Wang S, Meng S, Yang X, Zhang B, Zhang JH, Bai ZK, Song MX. The mechanism of acid resistance by ornithine decarboxylase in Trichinella spiralis. Exp Parasitol 2023; 249:108503. [PMID: 36925097 DOI: 10.1016/j.exppara.2023.108503] [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: 09/16/2022] [Revised: 03/05/2023] [Accepted: 03/08/2023] [Indexed: 03/17/2023]
Abstract
Trichinella spiralis is a zoonotic parasite with worldwide distribution that can seriously harm human health and animal husbandry. Ornithine decarboxylase is a component of the acid resistance (AR) system in Escherichia coli. The aim of this study was to investigate the role that T. spiralis ornithine decarboxylase (TsODC) plays in the acid resistance mechanism of T. spiralis. This study involved assessing the transcription and expression of TsODC in worms under acidic conditions. According to mRNA sequences published by NCBI and the results of molecular biology experiments, the complete TsODC sequence was cloned and expressed. rTsODC had good immunogenicity, and immunofluorescence analysis revealed that TsODC was principally localized on the surface tissues of the nematode, especially at the head and tail. qRT‒PCR and Western blotting analysis indicated that the relative expression levels of TsODC mRNA and protein were highest when cultured at pH 2.5 for 2 h. The muscle larvae (ML) of T. spiralis were treated with curcumin and rapamycin, as well as arginine and TsODC polyantisera. The expression levels of TsODC mRNA and protein were significantly increased by arginine and suppressed by curcumin and rapamycin. After reducing the amount of TsODC, the relative expression of TsODC mRNA and the survival rate of T. spiralis ML were both reduced when compared to these values in the phosphate-buffered saline (PBS) group. The results indicated that TsODC is a member of the T. spiralis AR system and different treatments on TsODC have different effects; thus, these treatments might be a new way to prevent T. spiralis infection.
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Affiliation(s)
- Shuang Wang
- Heilongjiang Key Laboratory for Zoonosis, College of Veterinary Medicine, Northeast Agricultural University, 600 Changjiang Street, Harbin, 150030, China
| | - Shi Meng
- Heilongjiang Key Laboratory for Zoonosis, College of Veterinary Medicine, Northeast Agricultural University, 600 Changjiang Street, Harbin, 150030, China
| | - Xiao Yang
- Heilongjiang Key Laboratory for Zoonosis, College of Veterinary Medicine, Northeast Agricultural University, 600 Changjiang Street, Harbin, 150030, China
| | - Bohan Zhang
- Heilongjiang Key Laboratory for Zoonosis, College of Veterinary Medicine, Northeast Agricultural University, 600 Changjiang Street, Harbin, 150030, China
| | - Jian Hui Zhang
- Heilongjiang Key Laboratory for Zoonosis, College of Veterinary Medicine, Northeast Agricultural University, 600 Changjiang Street, Harbin, 150030, China
| | - Zhi Kun Bai
- Heilongjiang Key Laboratory for Zoonosis, College of Veterinary Medicine, Northeast Agricultural University, 600 Changjiang Street, Harbin, 150030, China.
| | - Ming Xin Song
- Heilongjiang Key Laboratory for Zoonosis, College of Veterinary Medicine, Northeast Agricultural University, 600 Changjiang Street, Harbin, 150030, China.
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Abstract
Guanidinoacetate (GAA) is a naturally occurring amino acid derivative and the direct precursor of creatine, which is widely used in feed additives and the pharmaceutical industry. The current industrial synthesis of GAA is based on chemical methods, which limits the application of GAA. Here, a biological approach is developed for food safety GAA production via whole-cell biocatalysis by the generally regarded as safe (GRAS) bacterium Bacillus subtilis. First, we introduced a heterologous arginine: glycine amidinotransferase (AgaT) from Amycolatopsis kentuckyensis into B. subtilis and optimized its expression level using strategies including: promoter optimization, ribosome binding site (RBS) and N-terminal coding sequence (NCS) screening. In order to alleviate the waste of arginine and the inhibition of AgaT by ornithine, we optimized the natural ornithine cycle in B. subtilis. At the same time, the first gene in the glycine degradation pathway was knocked out. After optimization using these strategies, the titer of GAA was 4.26 g/L with a productivity of 0.21 g/L/h in 20 h, which provides a new method for the biosynthesis of GAA.
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Yang F, Xu J, Zhu Y, Wang Y, Xu M, Rao Z. High-level production of the agmatine in engineered Corynebacterium crenatum with the inhibition-releasing arginine decarboxylase. Microb Cell Fact 2022; 21:16. [PMID: 35101042 PMCID: PMC8805389 DOI: 10.1186/s12934-022-01742-3] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2021] [Accepted: 01/12/2022] [Indexed: 01/11/2023] Open
Abstract
Abstract
Background
Agmatine is a member of biogenic amines and is an important medicine which is widely used to regulate body balance and neuroprotective effects. At present, the industrial production of agmatine mainly depends on the chemical method, but it is often accompanied by problems including cumbersome processes, harsh reaction conditions, toxic substances production and heavy environmental pollution. Therefore, to tackle the above issues, arginine decarboxylase was overexpressed heterologously and rationally designed in Corynebacterium crenatum to produce agmatine from glucose by one-step fermentation.
Results
In this study, we report the development in the Generally Regarded as Safe (GRAS) l-arginine-overproducing C. crenatum for high-titer agmatine biosynthesis through overexpressing arginine decarboxylase based on metabolic engineering. Then, arginine decarboxylase was mutated to release feedback inhibition and improve catalytic activity. Subsequently, the specific enzyme activity and half-inhibitory concentration of I534D mutant were increased 35.7% and 48.1%, respectively. The agmatine production of the whole-cell bioconversion with AGM3 was increased by 19.3% than the AGM2. Finally, 45.26 g/L agmatine with the yield of 0.31 g/g glucose was achieved by one-step fermentation of the engineered C. crenatum with overexpression of speAI534D.
Conclusions
The engineered C. crenatum strain AGM3 in this work was proved as an efficient microbial cell factory for the industrial fermentative production of agmatine. Based on the insights from this work, further producing other valuable biochemicals derived from l-arginine by Corynebacterium crenatum is feasible.
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