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Zhang X, Niu P, Liu H, Fang H. Production of pyrimidine nucleosides in microbial systems via metabolic engineering: Theoretical analysis research and prospects. Biotechnol Adv 2024; 75:108419. [PMID: 39053562 DOI: 10.1016/j.biotechadv.2024.108419] [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: 05/10/2024] [Revised: 06/26/2024] [Accepted: 07/22/2024] [Indexed: 07/27/2024]
Abstract
Pyrimidine nucleosides, as intermediate materials of significant commercial value, find extensive applications in the pharmaceutical industry. However, the current production of pyrimidine nucleosides largely relies on chemical synthesis, creating environmental problems that do not align with sustainable development goals. Recent progress in systemic metabolic engineering and synthetic biology has enabled the synthesis of natural products like pyrimidine nucleosides through microbial fermentation, offering a more sustainable alternative. Nevertheless, the intricate and tightly regulated biosynthetic pathways involved in the microbial production of pyrimidine nucleosides pose a formidable challenge. This study focuses on metabolic engineering and synthetic biology strategies aimed at enhancing pyrimidine nucleoside production. These strategies include gene modification, transcriptional regulation, metabolic flux analysis, cofactor balance optimization, and transporter engineering. Finally, this research highlights the challenges involved in the further development of pyrimidine nucleoside-producing strains and offers potential solutions in order to provide theoretical guidance for future research endeavors in this field.
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Affiliation(s)
- Xiangjun Zhang
- School of Life Science, Ningxia University, Yinchuan, Ningxia 750021, China
| | - Pilian Niu
- School of Life Science, Ningxia University, Yinchuan, Ningxia 750021, China
| | - Huiyan Liu
- School of Food Science and Engineering, Ningxia Key Laboratory for Food Microbial-Applications Technology and Safety Control, Ningxia University, Yinchuan, Ningxia 750021, China.
| | - Haitian Fang
- School of Food Science and Engineering, Ningxia Key Laboratory for Food Microbial-Applications Technology and Safety Control, Ningxia University, Yinchuan, Ningxia 750021, China.
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Zhang K, Qin M, Hou Y, Zhang W, Wang Z, Wang H. Efficient production of guanosine in Escherichia coli by combinatorial metabolic engineering. Microb Cell Fact 2024; 23:182. [PMID: 38898430 PMCID: PMC11186194 DOI: 10.1186/s12934-024-02452-8] [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: 04/22/2024] [Accepted: 06/06/2024] [Indexed: 06/21/2024] Open
Abstract
BACKGROUND Guanosine is a purine nucleoside that is widely used as a raw material for food additives and pharmaceutical products. Microbial fermentation is the main production method of guanosine. However, the guanosine-producing strains possess multiple metabolic pathway interactions and complex regulatory mechanisms. The lack of strains with efficiently producing-guanosine greatly limited industrial application. RESULTS We attempted to efficiently produce guanosine in Escherichia coli using systematic metabolic engineering. First, we overexpressed the purine synthesis pathway from Bacillus subtilis and the prs gene, and deleted three genes involved in guanosine catabolism to increase guanosine accumulation. Subsequently, we attenuated purA expression and eliminated feedback and transcription dual inhibition. Then, we modified the metabolic flux of the glycolysis and Entner-Doudoroff (ED) pathways and performed redox cofactors rebalancing. Finally, transporter engineering and enhancing the guanosine synthesis pathway further increased the guanosine titre to 134.9 mg/L. After 72 h of the fed-batch fermentation in shake-flask, the guanosine titre achieved 289.8 mg/L. CONCLUSIONS Our results reveal that the guanosine synthesis pathway was successfully optimized by combinatorial metabolic engineering, which could be applicable to the efficient synthesis of other nucleoside products.
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Affiliation(s)
- Kun Zhang
- Henan Province Engineering Laboratory for Bioconversion Technology of Functional Microbes, College of Life Sciences, Henan Normal University, Xinxiang, 453007, China
| | - Mengxing Qin
- Henan Province Engineering Laboratory for Bioconversion Technology of Functional Microbes, College of Life Sciences, Henan Normal University, Xinxiang, 453007, China
| | - Yu Hou
- Henan Province Engineering Laboratory for Bioconversion Technology of Functional Microbes, College of Life Sciences, Henan Normal University, Xinxiang, 453007, China
| | - Wenwen Zhang
- Henan Province Engineering Laboratory for Bioconversion Technology of Functional Microbes, College of Life Sciences, Henan Normal University, Xinxiang, 453007, China
| | - Zhenyu Wang
- Henan Province Engineering Laboratory for Bioconversion Technology of Functional Microbes, College of Life Sciences, Henan Normal University, Xinxiang, 453007, China
| | - Hailei Wang
- Henan Province Engineering Laboratory for Bioconversion Technology of Functional Microbes, College of Life Sciences, Henan Normal University, Xinxiang, 453007, China.
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Zhang X, Liu L, Ma C, Zhang H, Liu H, Fang H. Improving the level of the cytidine biosynthesis in E. coli through atmospheric room temperature plasma mutagenesis and metabolic engineering. J Appl Microbiol 2024; 135:lxae133. [PMID: 38830792 DOI: 10.1093/jambio/lxae133] [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: 03/21/2024] [Revised: 05/09/2024] [Accepted: 06/01/2024] [Indexed: 06/05/2024]
Abstract
AIMS Cytidine, as an important commercial precursor in the chemical synthesis of antiviral and antitumor drugs, is in great demand in the market. Therefore, the purpose of this study is to build a microbial cell factory with high cytidine production. METHODS AND RESULTS A mutant E. coli NXBG-11-F34 with high tolerance to uridine monophosphate structural analogs and good genetic stability was obtained by atmospheric room temperature plasma (ARTP) mutagenesis combined with high-throughput screening. Then, the udk and rihA genes involved in cytidine catabolism were knocked out by CRISPR/Cas9 gene editing technology, and the recombinant strain E. coli NXBG-13 was constructed. The titer, yield, and productivity of cytidine fermented in a 5 l bioreactor were 15.7 g l-1, 0.164 g g-1, and 0.327 g l-1 h-1, respectively. Transcriptome analysis of the original strain and the recombinant strain E. coli NXBG-13 showed that the gene expression profiles of the two strains changed significantly, and the cytidine de novo pathway gene of the recombinant strain was up-regulated significantly. CONCLUSIONS ARTP mutagenesis combined with metabolic engineering is an effective method to construct cytidine-producing strains.
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Affiliation(s)
- Xiangjun Zhang
- School of Life Science, Ningxia University, Yinchuan 750021, China
| | - Lu Liu
- Ningxia Key Laboratory for Food Microbial-Applications Technology and Safety Control, School of Food Science and Engineering, Ningxia University, Yinchuan 750021, China
| | - Cong Ma
- Ningxia Key Laboratory for Food Microbial-Applications Technology and Safety Control, School of Food Science and Engineering, Ningxia University, Yinchuan 750021, China
| | - Haojie Zhang
- Ningxia Key Laboratory for Food Microbial-Applications Technology and Safety Control, School of Food Science and Engineering, Ningxia University, Yinchuan 750021, China
| | - Huiyan Liu
- Ningxia Key Laboratory for Food Microbial-Applications Technology and Safety Control, School of Food Science and Engineering, Ningxia University, Yinchuan 750021, China
| | - Haitian Fang
- Ningxia Key Laboratory for Food Microbial-Applications Technology and Safety Control, School of Food Science and Engineering, Ningxia University, Yinchuan 750021, China
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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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Zhou M, Tang R, Wei L, Wang J, Qi H. Metabolic Engineering of Escherichia coli for Efficient Production of Pseudouridine. ACS OMEGA 2023; 8:36386-36392. [PMID: 37810737 PMCID: PMC10552469 DOI: 10.1021/acsomega.3c05219] [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: 07/19/2023] [Accepted: 09/06/2023] [Indexed: 10/10/2023]
Abstract
Pseudouridine-incorporated mRNA vaccines can enhance protein expression and reduce immunogenicity, leading to a high demand for pseudouridine to be used in mRNA drug production. To achieve the low-cost production of pseudouridine, Escherichia coli was systematically modified to utilize inexpensive raw materials to efficiently produce pseudouridine. First, in the pyrimidine biosynthesis pathway, genes related to the precursor competing pathway and the negative regulator were deleted, which increased pseudouridine production. Second, two critical genes, pseudouridine-5'-phosphate glycosidase (psuG) and phosphatase genes from different bacteria, were screened and employed in various genetic constructs, and the pseudouridine yield of the optical strain increased to 599 mg/L. The accumulation of pseudouridine was further increased by the deletion of pseudouridine catabolism-related genes. Ultimately, the pseudouridine titer in a 5 L bioreactor reached 7.9 g/L, and the yield of pseudouridine on glucose was 0.15 g/g. Overall, a cell factory producing pseudouridine was successfully constructed and showed potential for industrial production.
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Affiliation(s)
- Min Zhou
- Institute
of Biopharmaceuticals, School of Pharmaceutical Sciences, Taizhou University, Taizhou 318000, China
| | - Ruyu Tang
- 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
| | - Jidong Wang
- Key
Laboratory of Vector Biology and Pathogen Control of Zhejiang Province,
College of Life Science, Huzhou University, Huzhou 313000, China
| | - Huan Qi
- Key
Laboratory of Vector Biology and Pathogen Control of Zhejiang Province,
College of Life Science, Huzhou University, Huzhou 313000, 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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Ren Y, Liu Q, Liu H, Zhou X, Zhang Y, Cai M. High-level living cell production of cytidine-5'-diphosphocholine in metabolically engineered yeast. J Biotechnol 2021; 341:129-136. [PMID: 34536458 DOI: 10.1016/j.jbiotec.2021.08.013] [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: 05/20/2021] [Revised: 08/17/2021] [Accepted: 08/24/2021] [Indexed: 10/20/2022]
Abstract
Industrial production of neuroprotective drug CDP-choline is accomplished via permeabilized or lysed cell biotransformation because of the inefficient penetration of substrates into intact cells. We previously proposed a novel one-step living cell method for CDP-choline production by engineered yeast, but obtained low titer and molar yield. This study develops a high-production strain with improved molar yield by metabolic engineering strategies. The selective markers previously integrated into host cell were recovered for facilitating genetic modification, which however resulted a strain with improved CDP-choline titer and molar yield to CMP. Knockout of 5'-NT or CDA in CMP sinking pathway but not APY in CTP sinking pathway further improved CDP-choline titer and molar yield to CMP. However, overexpression of seven enzymes in CTP synthetic pathway showed no positive functions. Finally, optimization of CMP and choline phosphate levels for the optimized recombinant strains achieved a high-level CDP-choline of ~30 g/L, which was enhanced by 400% compared to the previous work. Also, the molar yield of CDP-choline to CMP increased from 40% to 84.7%. The titer and molar yield are comparable to the reported permeabilized or lysed cell based biotransformation methods. It represents a novel and competitive paradigm for the potential industrial production of CDP-choline.
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Affiliation(s)
- Yanna Ren
- State Key Laboratory of Bioreactor Engineering, East China University of Science and Technology, 130 Meilong Road, Shanghai 200237, China
| | - Qi Liu
- State Key Laboratory of Bioreactor Engineering, East China University of Science and Technology, 130 Meilong Road, Shanghai 200237, China
| | - Haifeng Liu
- China Resources Angde Biotech Pharma Co., Ltd., 78 E-jiao Street, Liaocheng, China
| | - Xiangshan Zhou
- China Resources Angde Biotech Pharma Co., Ltd., 78 E-jiao Street, Liaocheng, China; China Resources Biopharmaceutical Co., Ltd., 1301-84 Sightseeing Road, Shenzhen, China
| | - Yuanxing Zhang
- Shanghai Collaborative Innovation Center for Biomanufacturing, 130 Meilong Road, Shanghai 200237, China
| | - Menghao Cai
- State Key Laboratory of Bioreactor Engineering, East China University of Science and Technology, 130 Meilong Road, Shanghai 200237, China.
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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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