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Zhou M, Wei L, Wu C, Chen W, Tang Z. Systematic Engineering of Escherichia coli for Efficient Production of Cytidine 5'-Monophosphate. ACS OMEGA 2024; 9:6663-6668. [PMID: 38371780 PMCID: PMC10870394 DOI: 10.1021/acsomega.3c07713] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/04/2023] [Revised: 01/05/2024] [Accepted: 01/19/2024] [Indexed: 02/20/2024]
Abstract
Cytidine 5'-monophosphate (CMP) was widely applied in the food and pharmaceutical industries. Currently, CMP is mainly produced by enzyme catalysis. However, the starting materials for enzyme catalysis were relatively expensive. Therefore, seeking a low-cost production process for CMP was attractive. In this study, Escherichia coli (E. coli) was systematically modified to produce CMP. First, a the cytidine-producing strain was constructed by deleting cdd, rihA, rihB, and rihC. Second, the genes involved in the pyrimidine precursor competing pathway and negative regulation were deleted to increase cyti dine biosynthesis. Third, the deletion of the genes that caused the loss of CMP phosphatase activity led to the accumulation of CMP, and the overexpression of the rate-limiting step genes and feedback inhibition resistance genes greatly increased the yield of CMP. The yield of CMP was further increased to 1013.6 mg/L by blocking CMP phosphorylation. Ultimately, the yield of CMP reached 15.3 g/L in a 50 L bioreactor. Overall, the engineered E. coli with a high yield of CMP was successfully constructed and showed the potential for industrial production.
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Affiliation(s)
- Min Zhou
- Institute
of Biopharmaceuticals, School of Pharmaceutical Sciences, Taizhou University, Taizhou 318000, China
| | - Liyuan Wei
- Institute
of Biopharmaceuticals, School of Pharmaceutical Sciences, Taizhou University, Taizhou 318000, China
| | - Chongzhi Wu
- Institute
of Biopharmaceuticals, School of Pharmaceutical Sciences, Taizhou University, Taizhou 318000, China
| | - Wei Chen
- Hangzhou
Hizyme Biotech Co., Ltd., Hangzhou 310011, China
| | - Zhengju Tang
- Taizhou
Central Hospital (Taizhou University Hospital), Taizhou 318000, China
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2
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Teng F, Wang L, Hu M, Tao Y. Cell-free regeneration of ATP based on polyphosphate kinase 2 facilitates cytidine 5'-monophosphate production. Enzyme Microb Technol 2023; 165:110211. [PMID: 36804179 DOI: 10.1016/j.enzmictec.2023.110211] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2022] [Revised: 02/02/2023] [Accepted: 02/08/2023] [Indexed: 02/13/2023]
Abstract
Cytidine 5'-monophosphate (5'-CMP), a key intermediate for the production of nucleotide derivatives, has been extensively used in food, agriculture, and medicine industries. Compared to RNA degradation and chemical synthesis, the biosynthesis of 5'-CMP has attracted wide attention due to its relatively low cost and eco-friendliness. In this study, we developed a cell-free regeneration of ATP based on polyphosphate kinase 2 (PPK2) to manufacture 5'-CMP from cytidine (CR). McPPK2 from Meiothermus cerbereus exhibited high specific activity (128.5 U/mg) and was used to accomplish ATP regeneration. McPPK2 and LhUCK (a uridine-cytidine kinase from Lactobacillus helveticus) were combined to convert CR to 5'-CMP. Further, the degradation of CR was inhibited by knocking out cdd from the Escherichia coli genome to enhance 5'-CMP production. Finally, the cell-free system based on ATP regeneration maximized the titer of 5'-CMP up to 143.5 mM. The wider applicability of this cell-free system was demonstrated in the synthesis of deoxycytidine 5'-monophosphate (5'-dCMP) from deoxycytidine (dCR) by incorporating McPPK2 and BsdCK (a deoxycytidine kinase from Bacillus subtilis). This study suggests that the cell-free regeneration of ATP based on PPK2 has the advantage of great flexibility for producing 5'-(d)CMP and other (deoxy)nucleotides.
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Affiliation(s)
- Fei Teng
- Chinese Academy of Sciences Key Laboratory of Microbial Physiological and Metabolic Engineering, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, China; College of Life Science, University of Chinese Academy of Sciences, Beijing 100049, China
| | - Lei Wang
- Chinese Academy of Sciences Key Laboratory of Microbial Physiological and Metabolic Engineering, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, China; College of Life Science, University of Chinese Academy of Sciences, Beijing 100049, China.
| | - Meirong Hu
- College of Life Science, University of Chinese Academy of Sciences, Beijing 100049, China
| | - Yong Tao
- Chinese Academy of Sciences Key Laboratory of Microbial Physiological and Metabolic Engineering, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, China; College of Life Science, University of Chinese Academy of Sciences, Beijing 100049, China.
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Han B, Dai Z, Li Z. Computer-Based Design of a Cell Factory for High-Yield Cytidine Production. ACS Synth Biol 2022; 11:4123-4133. [PMID: 36442151 DOI: 10.1021/acssynbio.2c00431] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Pyrimidine ribonucleotide de novo biosynthesis pathway (PRdnBP) is an important pathway to produce pyrimidine nucleosides. We attempted to systematically investigate PRdnBP in Escherichia coli with genome-scale metabolic models and utilized the models to guide strain design. The balance of central carbon metabolism and PRdnBP affected the production of cytidine from glucose. Using Bayesian metabolic flux analysis, the effect of modified PRdnBP on the metabolic network was analyzed. The acetate overflow became coupled with PRdnBP flux, while they were originally independent under oxygen-sufficient conditions. The coupling between cytidine production and acetate secretion in the modified strain was weakened by arcA deletion, which resulted in further improving the efficient accumulation of cytidine. In total, 1.28 g/L of cytidine with a yield of 0.26 g/g glucose was produced. The yield of cytidine produced by E. coli is higher than previous reports. Our strategy provides an effective attempt to find metabolic bottlenecks in genetically engineered bacteria by using flux coupling analysis.
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Affiliation(s)
- Bin Han
- State Key Laboratory of Bioreactor Engineering, East China University of Science and Technology, 130 Meilong Road, Shanghai200237, China
| | - Zeyu Dai
- State Key Laboratory of Bioreactor Engineering, East China University of Science and Technology, 130 Meilong Road, Shanghai200237, China
| | - Zhimin Li
- State Key Laboratory of Bioreactor Engineering, East China University of Science and Technology, 130 Meilong Road, Shanghai200237, China.,Shanghai Collaborative Innovation Center for Biomanufacturing Technology, 130 Meilong Road, Shanghai200237, China
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The Effect of E. coli Uridine-Cytidine Kinase Gene Deletion on Cytidine Synthesis and Transcriptome Analysis. FERMENTATION-BASEL 2022. [DOI: 10.3390/fermentation8110586] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
Cytidine is an antiviral and anticancer drug intermediate, its primary method of manufacture being fermentation. Uridine-cytidine kinase (UCK) catalyzes the reverse process of phosphorylation of cytidine to produce cytidylic acid, which influences cytidine accumulation in the Escherichia coli cytidine biosynthesis pathway. The cytidine-producing strain E. coli NXBG-11 was used as the starting strain in this work; the udk gene coding UCK was knocked out of the chromosomal genome using clustered regularly interspaced short palindromic repeats (CRISPR)/Cas9 technology. The mutant strain E. coli NXBG-12 was obtained; its transcriptomics were studied to see how udk gene deletion affected cytidine synthesis and cell-wide transcription. The mutant strain E. coli NXBG-12 generated 1.28 times more cytidine than the original strain E. coli NXBG-11 after 40 h of shake-flask fermentation at 37 °C. The udk gene was knocked out, and transcriptome analysis showed that there were 1168 differentially expressed genes between the mutant and original strains, 559 upregulated genes and 609 downregulated genes. It was primarily shown that udk gene knockout has a positive impact on the cytidine synthesis network because genes involved in cytidine synthesis were significantly upregulated (p < 0.05) and genes related to the cytidine precursor PRPP and cofactor NADPH were upregulated in the PPP and TCA pathways. These results principally demonstrate that udk gene deletion has a favorable impact on the cytidine synthesis network. The continual improvement of cytidine synthesis and metasynthesis is made possible by this information, which is also useful for further converting microorganisms that produce cytidine.
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Zhang H, Liang Z, Zhao M, Ma Y, Luo Z, Li S, Xu H. Metabolic Engineering of Escherichia coli for Ectoine Production With a Fermentation Strategy of Supplementing the Amino Donor. Front Bioeng Biotechnol 2022; 10:824859. [PMID: 35145959 PMCID: PMC8822159 DOI: 10.3389/fbioe.2022.824859] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2021] [Accepted: 01/04/2022] [Indexed: 11/13/2022] Open
Abstract
Ectoine, an osmotic pressure-compensated solute, is used in the food, agriculture, medicine, and cosmetics industries due to its ability to protect macromolecules. In this study, an ectoine-producing variant of Escherichia coli, ET08, was genetically constructed by introducing the ectABC gene cluster and eliminating metabolic pathways involving lysine and pyruvate. Medium optimization enhanced ectoine production from 1.87 to 10.2 g/L. Analysis of the transcriptional levels revealed that supplementation with ammonium sulfate enhanced the metabolic flux towards the biosynthesis of ectoine. Furthermore, by optimizing the copy number of ectA, ectB, and ectC, the recombinant E. coli ET11 (ectA:ectB:ectC = 1:2:1) produced 12.9 g/L ectoine in the shake flask and 53.2 g/L ectoine in a fed-batch fermenter, representing the highest ectoine titer produced by E. coli, which has great industrial prospects.
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Affiliation(s)
- Hao Zhang
- State Key Laboratory of Materials-Oriented Chemical Engineering, Nanjing Tech University, Nanjing, China
- College of Food Science and Light Industry, Nanjing Tech University, Nanjing, China
| | - Zhong Liang
- State Key Laboratory of Materials-Oriented Chemical Engineering, Nanjing Tech University, Nanjing, China
- College of Food Science and Light Industry, Nanjing Tech University, Nanjing, China
| | - Ming Zhao
- State Key Laboratory of Materials-Oriented Chemical Engineering, Nanjing Tech University, Nanjing, China
- College of Food Science and Light Industry, Nanjing Tech University, Nanjing, China
| | - Yanqin Ma
- State Key Laboratory of Materials-Oriented Chemical Engineering, Nanjing Tech University, Nanjing, China
- College of Food Science and Light Industry, Nanjing Tech University, Nanjing, China
| | - Zhengshan Luo
- State Key Laboratory of Materials-Oriented Chemical Engineering, Nanjing Tech University, Nanjing, China
- College of Food Science and Light Industry, Nanjing Tech University, Nanjing, China
| | - Sha Li
- State Key Laboratory of Materials-Oriented Chemical Engineering, Nanjing Tech University, Nanjing, China
- College of Food Science and Light Industry, Nanjing Tech University, Nanjing, China
- *Correspondence: Sha Li, ; Hong Xu,
| | - Hong Xu
- State Key Laboratory of Materials-Oriented Chemical Engineering, Nanjing Tech University, Nanjing, China
- College of Food Science and Light Industry, Nanjing Tech University, Nanjing, China
- Jiangsu National Synergetic Innovation Center for Advanced Materials, Nanjing Tech University, Nanjing, China
- *Correspondence: Sha Li, ; Hong Xu,
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Ma R, Fang H, Liu H, Pan L, Wang H, Zhang H. Overexpression of uracil permease and nucleoside transporter from Bacillus amyloliquefaciens improves cytidine production in Escherichia coli. Biotechnol Lett 2021; 43:1211-1219. [PMID: 33646457 DOI: 10.1007/s10529-021-03103-3] [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: 08/08/2020] [Accepted: 02/08/2021] [Indexed: 11/28/2022]
Abstract
Cytidine is an important raw material for nucleic acid health food and genetic engineering research. In recent years, it has shown irreplaceable effects in anti-virus, anti-tumor, and AIDS drugs. Its biosynthetic pathway is complex and highly regulated. In this study, overexpression of uracil permease and a nucleoside transporter from Bacillus amyloliquefaciens related to cell membrane transport in Escherichia coli strain BG-08 was found to increase cytidine production in shake flask cultivation by 1.3-fold (0.91 ± 0.03 g/L) and 1.8-fold (1.26 ± 0.03 g/L) relative to that of the original strain (0.70 ± 0.03 g/L), respectively. Co-overexpression of uracil permease and a nucleoside transporter further increased cytidine yield by 2.7-fold (1.59 ± 0.05 g/L) compared with that of the original strain. These results indicate that the overexpressed uracil permease and nucleoside transporter can promote the accumulation of cytidine, and the two proteins play a synergistic role in the secretion of cytidine in Escherichia coli.
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Affiliation(s)
- Ruoshuang Ma
- Ningxia Key Laboratory for Food Microbial-Applications Technology and Safety Control, School of Agriculture, Ningxia University, Yinchuan, 750021, China
| | - Haitian Fang
- Ningxia Key Laboratory for Food Microbial-Applications Technology and Safety Control, School of Agriculture, Ningxia University, Yinchuan, 750021, China
| | - Huiyan Liu
- Ningxia Key Laboratory for Food Microbial-Applications Technology and Safety Control, School of Agriculture, Ningxia University, Yinchuan, 750021, China.
| | - Lin Pan
- Ningxia Key Laboratory for Food Microbial-Applications Technology and Safety Control, School of Agriculture, Ningxia University, Yinchuan, 750021, China
| | - Hongyan Wang
- Ningxia Key Laboratory for Food Microbial-Applications Technology and Safety Control, School of Agriculture, Ningxia University, Yinchuan, 750021, China
| | - Heng Zhang
- Ningxia Key Laboratory for Food Microbial-Applications Technology and Safety Control, School of Agriculture, Ningxia University, Yinchuan, 750021, China
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7
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Yang K, Li Z. Multistep construction of metabolically engineered Escherichia coli for enhanced cytidine biosynthesis. Biochem Eng J 2020. [DOI: 10.1016/j.bej.2019.107433] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
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