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Cai DS, Yang XY, Yang YQ, Gao F, Cheng XH, Zhao YJ, Qi R, Zhang YZ, Lu JH, Lin XY, Liu YJ, Xu B, Wang PL, Lei HM. Design and synthesis of novel anti-multidrug-resistant staphylococcus aureus derivatives of glycyrrhetinic acid by blocking arginine biosynthesis, metabolic and H 2S biogenesis. Bioorg Chem 2023; 131:106337. [PMID: 36603244 DOI: 10.1016/j.bioorg.2022.106337] [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: 08/03/2022] [Revised: 12/12/2022] [Accepted: 12/22/2022] [Indexed: 12/31/2022]
Abstract
With the soaring number of multidrug-resistant bacteria, it is imperative to develop novel efficient antibacterial agents and discovery new antibacterial pathways. Herein, we designed and synthesized a series of structurally novel glycyrrhetinic acid (GA) derivatives against multidrug-resistant Staphylococcus aureus (MRSA). The in vitro antibacterial activity of these compounds was evaluated using the microbroth dilution method, agar plate coating experiments and real-time growth curves, respectively. Most of the target derivatives showed moderate antibacterial activity against Staphylococcus aureus (S. aureus) and MRSA (MIC = 3.125-25 μM), but inactivity against Escherichia coli (E. Coli) and Pseudomonas aeruginosa (P. aeruginosa) (MIC > 200 μM). Among them, compound 11 had the strongest antibacterial activity against MRSA, with an MIC value of 3.125 μM, which was 32 times and 64 times than the first-line antibiotics penicillin and norfloxacin, respectively. Additionally, transcriptomic (RNA-seq) and quantitative polymerase chain reaction (qPCR) analysis revealed that the antibacterial mechanism of compound 11 was through blocking the arginine biosynthesis and metabolic and the H2S biogenesis. Importantly, compound 11 was confirmed to have good biocompatibility through the in vitro hemolysis tests, cytotoxicity assays and the in vivo quail chicken chorioallantoic membrane (qCAM) experiments. Current study provided new potential antibacterial candidates from glycyrrhetinic acid derivatives for clinical treatment of MRSA infections.
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Affiliation(s)
- De-Sheng Cai
- School of Chinese Pharmacy, Beijing University of Chinese Medicine, Beijing 102488, PR China
| | - Xiao-Yun Yang
- School of Chinese Pharmacy, Beijing University of Chinese Medicine, Beijing 102488, PR China
| | - Yu-Qin Yang
- School of Chinese Pharmacy, Beijing University of Chinese Medicine, Beijing 102488, PR China
| | - Feng Gao
- School of Chinese Pharmacy, Beijing University of Chinese Medicine, Beijing 102488, PR China
| | - Xue-Hao Cheng
- School of Chinese Pharmacy, Beijing University of Chinese Medicine, Beijing 102488, PR China
| | - Ya-Juan Zhao
- School of Chinese Pharmacy, Beijing University of Chinese Medicine, Beijing 102488, PR China
| | - Rui Qi
- School of Chinese Pharmacy, Beijing University of Chinese Medicine, Beijing 102488, PR China
| | - Yao-Zhi Zhang
- School of Chinese Pharmacy, Beijing University of Chinese Medicine, Beijing 102488, PR China
| | - Ji-Hui Lu
- School of Chinese Pharmacy, Beijing University of Chinese Medicine, Beijing 102488, PR China
| | - Xiao-Yu Lin
- School of Chinese Pharmacy, Beijing University of Chinese Medicine, Beijing 102488, PR China
| | - Yi-Jing Liu
- School of Chinese Pharmacy, Beijing University of Chinese Medicine, Beijing 102488, PR China
| | - Bing Xu
- School of Chinese Pharmacy, Beijing University of Chinese Medicine, Beijing 102488, PR China.
| | - Peng-Long Wang
- School of Chinese Pharmacy, Beijing University of Chinese Medicine, Beijing 102488, PR China.
| | - Hai-Min Lei
- School of Chinese Pharmacy, Beijing University of Chinese Medicine, Beijing 102488, PR China.
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Wu K, Mao Z, Mao Y, Niu J, Cai J, Yuan Q, Yun L, Liao X, Wang Z, Ma H. ecBSU1: A Genome-Scale Enzyme-Constrained Model of Bacillus subtilis Based on the ECMpy Workflow. Microorganisms 2023; 11:microorganisms11010178. [PMID: 36677469 PMCID: PMC9864840 DOI: 10.3390/microorganisms11010178] [Citation(s) in RCA: 9] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2022] [Revised: 12/24/2022] [Accepted: 01/05/2023] [Indexed: 01/13/2023] Open
Abstract
Genome-scale metabolic models (GEMs) play an important role in the phenotype prediction of microorganisms, and their accuracy can be further improved by integrating other types of biological data such as enzyme concentrations and kinetic coefficients. Enzyme-constrained models (ecModels) have been constructed for several species and were successfully applied to increase the production of commodity chemicals. However, there was still no genome-scale ecModel for the important model organism Bacillus subtilis prior to this study. Here, we integrated enzyme kinetic and proteomic data to construct the first genome-scale ecModel of B. subtilis (ecBSU1) using the ECMpy workflow. We first used ecBSU1 to simulate overflow metabolism and explore the trade-off between biomass yield and enzyme usage efficiency. Next, we simulated the growth rate on eight previously published substrates and found that the simulation results of ecBSU1 were in good agreement with the literature. Finally, we identified target genes that enhance the yield of commodity chemicals using ecBSU1, most of which were consistent with the experimental data, and some of which may be potential novel targets for metabolic engineering. This work demonstrates that the integration of enzymatic constraints is an effective method to improve the performance of GEMs. The ecModel can predict overflow metabolism more precisely and can be used for the identification of target genes to guide the rational design of microbial cell factories.
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Affiliation(s)
- Ke Wu
- Key Laboratory of Systems Bioengineering (Ministry of Education), Frontier Science Center for Synthetic Biology (Ministry of Education), Department of Biochemical Engineering, School of Chemical Engineering and Technology, Tianjin University, Tianjin 300072, China
- Biodesign Center, Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin 300308, China
- National Technology Innovation Center of Synthetic Biology, Tianjin 300308, China
| | - Zhitao Mao
- Biodesign Center, Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin 300308, China
- National Technology Innovation Center of Synthetic Biology, Tianjin 300308, China
| | - Yufeng Mao
- Biodesign Center, Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin 300308, China
- National Technology Innovation Center of Synthetic Biology, Tianjin 300308, China
| | - Jinhui Niu
- Biodesign Center, Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin 300308, China
- National Technology Innovation Center of Synthetic Biology, Tianjin 300308, China
| | - Jingyi Cai
- Biodesign Center, Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin 300308, China
- National Technology Innovation Center of Synthetic Biology, Tianjin 300308, China
| | - Qianqian Yuan
- Biodesign Center, Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin 300308, China
- National Technology Innovation Center of Synthetic Biology, Tianjin 300308, China
| | - Lili Yun
- Tianjin Medical Laboratory, BGI-Tianjin, BGI-Shenzhen, Tianjin 300308, China
| | - Xiaoping Liao
- Biodesign Center, Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin 300308, China
- National Technology Innovation Center of Synthetic Biology, Tianjin 300308, China
| | - Zhiwen Wang
- Key Laboratory of Systems Bioengineering (Ministry of Education), Frontier Science Center for Synthetic Biology (Ministry of Education), Department of Biochemical Engineering, School of Chemical Engineering and Technology, Tianjin University, Tianjin 300072, China
- Correspondence: (Z.W.); (H.M.)
| | - Hongwu Ma
- Biodesign Center, Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin 300308, China
- National Technology Innovation Center of Synthetic Biology, Tianjin 300308, China
- Correspondence: (Z.W.); (H.M.)
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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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Wang C, Xu J, Ban R. Metabolic engineering of Bacillus subtilis for high-level production of uridine from glucose. Lett Appl Microbiol 2022; 75:824-830. [PMID: 35657030 DOI: 10.1111/lam.13754] [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: 02/11/2022] [Revised: 05/26/2022] [Accepted: 05/27/2022] [Indexed: 11/28/2022]
Abstract
As an intermediate in drug synthesis, uridine has practical applications in the pharmaceutical field. Bacillus subtilis is used as a host to boost uridine yield by manipulating its uridine biosynthesis pathway. In this study, we engineered a high-uridine-producing strain of B. subtilis by modifying its metabolic pathways in vivo. Overexpression of the aspartate ammonia-lyase (ansB) gene increased the relative transcriptional level of ansB in B. subtilis TD320 by 13.18 times and improved uridine production to 15.13 g L-1 after 72-h fermentation. Overexpression of the putative 6-phosphogluconolactonase (ykgB) gene increased uridine production by the derivative strain TD325 to 15.43 g L-1 . Reducing the translation of the amido phosphoribosyl transferase (purF) gene and inducing expression of the subtilisin E (aprE) gene resulted in a 1.99-fold increase in uridine production after 24 h shaking. Finally, uridine production in the optimal strain B. subtilis TD335, which exhibited reduced urease expression, reached 17.9 g L-1 with a yield of 314 mg of uridine g-1 glucose. To our knowledge, this is the first study to obtain high-yield uridine-producing B. subtilis in a medium containing only three components (80 g L-1 glucose, 20 g L-1 yeast powder, and 20 g L-1 urea).
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Affiliation(s)
- Chen Wang
- Department of Biochemical Engineering, School of Chemical Engineering and Technology, Tianjin University, Tianjin 300072, People's Republic of China
| | - Jingyu Xu
- Department of Biochemical Engineering, School of Chemical Engineering and Technology, Tianjin University, Tianjin 300072, People's Republic of China
| | - Rui Ban
- Department of Biochemical Engineering, School of Chemical Engineering and Technology, Tianjin University, Tianjin 300072, People's Republic of China
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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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Zhang X, Wang C, Liu L, Ban R. Improve uridine production by modifying related metabolic pathways in Bacillus subtilis. Biotechnol Lett 2020; 42:551-555. [PMID: 31993847 DOI: 10.1007/s10529-020-02820-5] [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: 08/12/2019] [Accepted: 12/09/2019] [Indexed: 10/25/2022]
Abstract
OBJECTIVES The metabolic pathway related to uridine production was modified in Bacillus subtilis in order to increase the production of uridine. RESULTS Decreasing the relative transcriptional level of pur operon in Bacillus subtilis TD300 to 80%, and the production of the derived strain TD312 was increased to 11.81 g uridine/l and the yield was increased to 270 mg uridine/g glucose. The expression of pucR gene in situ by PccpA resulting in a 194.01-fold increase in the relative transcriptional level of pucR gene and 349.71-fold increase in the relative transcriptional level of ure operon, respectively. Furthermore, the production of TD314 reached 13.06 g uridine/l, while the yield reached 250 mg uridine/g glucose. CONCLUSION This is the first report that more than 13 g uridine/l with a yield of 250 mg uridine/g glucose is produced in shake flask fermentation of genetically engineered Bacillus subtilis.
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Affiliation(s)
- Xueting Zhang
- Department of Biochemical Engineering, School of Chemical Engineering and Technology, Tianjin University, Tianjin, 300072, People's Republic of China
| | - Chen Wang
- Department of Biochemical Engineering, School of Chemical Engineering and Technology, Tianjin University, Tianjin, 300072, People's Republic of China
| | - Lu Liu
- Department of Biochemical Engineering, School of Chemical Engineering and Technology, Tianjin University, Tianjin, 300072, People's Republic of China
| | - Rui Ban
- Department of Biochemical Engineering, School of Chemical Engineering and Technology, Tianjin University, Tianjin, 300072, People's Republic of China. .,Key Laboratory of Systems Bioengineering (Tianjin University), Ministry of Education, Tianjin University, Tianjin, 300072, People's Republic of China.
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Cai D, Rao Y, Zhan Y, Wang Q, Chen S. EngineeringBacillusfor efficient production of heterologous protein: current progress, challenge and prospect. J Appl Microbiol 2019; 126:1632-1642. [DOI: 10.1111/jam.14192] [Citation(s) in RCA: 42] [Impact Index Per Article: 8.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2018] [Revised: 12/13/2018] [Accepted: 12/28/2018] [Indexed: 12/18/2022]
Affiliation(s)
- D. Cai
- State Key Laboratory of Biocatalysis and Enzyme Engineering, Environmental Microbial Technology Center of Hubei Province Hubei Collaborative Innovation Center for Green Transformation of Bio‐Resources, College of Life Sciences, Hubei University Wuhan PR China
| | - Y. Rao
- State Key Laboratory of Biocatalysis and Enzyme Engineering, Environmental Microbial Technology Center of Hubei Province Hubei Collaborative Innovation Center for Green Transformation of Bio‐Resources, College of Life Sciences, Hubei University Wuhan PR China
| | - Y. Zhan
- State Key Laboratory of Biocatalysis and Enzyme Engineering, Environmental Microbial Technology Center of Hubei Province Hubei Collaborative Innovation Center for Green Transformation of Bio‐Resources, College of Life Sciences, Hubei University Wuhan PR China
| | - Q. Wang
- State Key Laboratory of Biocatalysis and Enzyme Engineering, Environmental Microbial Technology Center of Hubei Province Hubei Collaborative Innovation Center for Green Transformation of Bio‐Resources, College of Life Sciences, Hubei University Wuhan PR China
| | - S. Chen
- State Key Laboratory of Biocatalysis and Enzyme Engineering, Environmental Microbial Technology Center of Hubei Province Hubei Collaborative Innovation Center for Green Transformation of Bio‐Resources, College of Life Sciences, Hubei University Wuhan PR China
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Wu H, Li Y, Ma Q, Li Q, Jia Z, Yang B, Xu Q, Fan X, Zhang C, Chen N, Xie X. Metabolic engineering of Escherichia coli for high-yield uridine production. Metab Eng 2018; 49:248-256. [PMID: 30189293 DOI: 10.1016/j.ymben.2018.09.001] [Citation(s) in RCA: 40] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2018] [Revised: 08/22/2018] [Accepted: 09/01/2018] [Indexed: 01/14/2023]
Abstract
Uridine is a kind of pyrimidine nucleoside that has been widely applied in the pharmaceutical industry. Although microbial fermentation is a promising method for industrial production of uridine, an efficient microbial cell factory is still lacking. In this study, we constructed a metabolically engineered Escherichia coli capable of high-yield uridine production. First, we developed a CRISPR/Cas9-mediated chromosomal integration strategy to integrate large DNA into the E. coli chromosome, and a 9.7 kb DNA fragment including eight genes in the pyrimidine operon of Bacillus subtilis F126 was integrated into the yghX locus of E. coli W3110. The resultant strain produced 3.3 g/L uridine and 4.5 g/L uracil in shake flask culture for 32 h. Subsequently, five genes involved in uridine catabolism were knocked out, and the uridine titer increased to 7.8 g/L. As carbamyl phosphate, aspartate, and 5'-phosphoribosyl pyrophosphate are important precursors for uridine synthesis, we further modified several metabolism-related genes and synergistically improved the supply of these precursors, leading to a 76.9% increase in uridine production. Finally, nupC and nupG encoding nucleoside transport proteins were deleted, and the extracellular uridine accumulation increased to 14.5 g/L. After 64 h of fed-batch fermentation, the final engineered strain UR6 produced 70.3 g/L uridine with a yield and productivity of 0.259 g/g glucose and 1.1 g/L/h, respectively. To the best of our knowledge, this is the highest uridine titer and productivity ever reported for the fermentative production of uridine.
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Affiliation(s)
- Heyun Wu
- National and Local United Engineering Lab of Metabolic Control Fermentation Technology, Tianjin University of Science and Technology, Tianjin 300457, China; College of Biotechnology, Tianjin University of Science and Technology, Tianjin 300457, China
| | - Yanjun Li
- National and Local United Engineering Lab of Metabolic Control Fermentation Technology, Tianjin University of Science and Technology, Tianjin 300457, China; College of Biotechnology, Tianjin University of Science and Technology, Tianjin 300457, China
| | - Qian Ma
- National and Local United Engineering Lab of Metabolic Control Fermentation Technology, Tianjin University of Science and Technology, Tianjin 300457, China; College of Biotechnology, Tianjin University of Science and Technology, Tianjin 300457, China
| | - Qiang Li
- National and Local United Engineering Lab of Metabolic Control Fermentation Technology, Tianjin University of Science and Technology, Tianjin 300457, China; College of Biotechnology, Tianjin University of Science and Technology, Tianjin 300457, China
| | - Zifan Jia
- National and Local United Engineering Lab of Metabolic Control Fermentation Technology, Tianjin University of Science and Technology, Tianjin 300457, China; College of Biotechnology, Tianjin University of Science and Technology, Tianjin 300457, China
| | - Bo Yang
- The Institute of Seawater Desalination and Multipurpose Utilization, SOA, Tianjin 300192, China
| | - Qingyang Xu
- National and Local United Engineering Lab of Metabolic Control Fermentation Technology, Tianjin University of Science and Technology, Tianjin 300457, China; College of Biotechnology, Tianjin University of Science and Technology, Tianjin 300457, China
| | - Xiaoguang Fan
- National and Local United Engineering Lab of Metabolic Control Fermentation Technology, Tianjin University of Science and Technology, Tianjin 300457, China; College of Biotechnology, Tianjin University of Science and Technology, Tianjin 300457, China
| | - Chenglin Zhang
- National and Local United Engineering Lab of Metabolic Control Fermentation Technology, Tianjin University of Science and Technology, Tianjin 300457, China; College of Biotechnology, Tianjin University of Science and Technology, Tianjin 300457, China
| | - Ning Chen
- National and Local United Engineering Lab of Metabolic Control Fermentation Technology, Tianjin University of Science and Technology, Tianjin 300457, China; College of Biotechnology, Tianjin University of Science and Technology, Tianjin 300457, China.
| | - Xixian Xie
- National and Local United Engineering Lab of Metabolic Control Fermentation Technology, Tianjin University of Science and Technology, Tianjin 300457, China; College of Biotechnology, Tianjin University of Science and Technology, Tianjin 300457, China.
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Fan X, Wu H, Jia Z, Li G, Li Q, Chen N, Xie X. Metabolic engineering of Bacillus subtilis for the co-production of uridine and acetoin. Appl Microbiol Biotechnol 2018; 102:8753-8762. [DOI: 10.1007/s00253-018-9316-7] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2018] [Revised: 07/31/2018] [Accepted: 08/08/2018] [Indexed: 01/19/2023]
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