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Zhang H, Wang P, Zhang J, Sun Q, He Q, He X, Chen H, Ji H. Boosting the Catalase-Like Activity of SAzymes via Facile Tuning of the Distances between Neighboring Atoms in Single-Iron Sites. Angew Chem Int Ed Engl 2024; 63:e202316779. [PMID: 38100508 DOI: 10.1002/anie.202316779] [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: 11/05/2023] [Revised: 12/04/2023] [Accepted: 12/15/2023] [Indexed: 12/17/2023]
Abstract
A nanozyme with neighboring single-iron sites (Fe2 -SAzyme) was introduced as a bioinspired catalase mimic, featuring excellent activity under varied conditions, twice as high as that of random Fe1 -SAzyme and ultrahigh H2 O2 affinity as that of bioenzymes. Surprisingly, the interatomic spacing tuning between adjacent iron sites also suppressed the competitive peroxidase pathway, remarkably increasing the catalase/peroxidase selectivity up to ~6 times compared to Fe1 -SAzyme. This dramatically switched the catalytic activity of Fe-SAzymes from generating (i.e. Fe1 -SAzymes, preferably mimicking peroxidase) to scavenging ROS (i.e. Fe2 -SAzymes, dominantly mimicking catalase). Theoretical and experimental investigations suggested that the pairwise single-iron sites may serve as a robust molecular tweezer to efficiently trap and decompose H2 O2 into O2 , via cooperative hydrogen-bonding induced end-bridge adsorption. The versatile mechano-assisted in situ MOF capsulation strategy enabled facile access to neighboring M2 -SAzyme (M=Fe, Ir, Pt), even up to a 1000 grams scale, but with no obvious scale-up effect for both structures and performances.
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Affiliation(s)
- Hao Zhang
- Key Laboratory of Bioinorganic and Synthetic Chemistry of Ministry of Education, Fine Chemical Industry Research Institute, School of Chemistry, Sun Yat-sen University, Guangzhou, 510275, P. R. China
| | - Pengbo Wang
- School of Light Industry and Food Engineering, Guangxi University, Nanning, 530004, P. R. China
| | - Jingru Zhang
- School of Light Industry and Food Engineering, Guangxi University, Nanning, 530004, P. R. China
| | - Qingdi Sun
- Key Laboratory of Bioinorganic and Synthetic Chemistry of Ministry of Education, Fine Chemical Industry Research Institute, School of Chemistry, Sun Yat-sen University, Guangzhou, 510275, P. R. China
| | - Qian He
- School of Light Industry and Food Engineering, Guangxi University, Nanning, 530004, P. R. China
| | - Xiaohui He
- Key Laboratory of Bioinorganic and Synthetic Chemistry of Ministry of Education, Fine Chemical Industry Research Institute, School of Chemistry, Sun Yat-sen University, Guangzhou, 510275, P. R. China
| | - Hongyu Chen
- School of Light Industry and Food Engineering, Guangxi University, Nanning, 530004, P. R. China
| | - Hongbing Ji
- Key Laboratory of Bioinorganic and Synthetic Chemistry of Ministry of Education, Fine Chemical Industry Research Institute, School of Chemistry, Sun Yat-sen University, Guangzhou, 510275, P. R. China
- State Key Laboratory Breeding Base of Green-Chemical Synthesis Technology, Institute of Green Petroleum Processing and Light Hydrocarbon Conversion, College of Chemical Engineering, Zhejiang University of Technology, Hangzhou, 310014, P. R. China
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2
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Tong Y, Wei Y, Ju Y, Li P, Zhang Y, Li L, Gao L, Liu S, Liu D, Hu Y, Li Z, Yu H, Luo Y, Wang J, Wang Y, Zhang Y. Anaerobic purinolytic enzymes enable dietary purine clearance by engineered gut bacteria. Cell Chem Biol 2023; 30:1104-1114.e7. [PMID: 37164019 DOI: 10.1016/j.chembiol.2023.04.008] [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: 01/06/2023] [Revised: 03/08/2023] [Accepted: 04/17/2023] [Indexed: 05/12/2023]
Abstract
Uric acid, the end product of purine degradation, causes hyperuricemia and gout, afflicting hundreds of millions of people. The debilitating effects of gout are exacerbated by dietary purine intake, and thus a potential therapeutic strategy is to enhance purine degradation in the gut microbiome. Aerobic purine degradation involves oxidative dearomatization of uric acid catalyzed by the O2-dependent uricase. The enzymes involved in purine degradation in strictly anaerobic bacteria remain unknown. Here we report the identification and characterization of these enzymes, which include four hydrolases belonging to different enzyme families, and a prenyl-flavin mononucleotide-dependent decarboxylase. Introduction of the first two hydrolases to Escherichia coli Nissle 1917 enabled its anaerobic growth on xanthine as the sole nitrogen source. Oral supplementation of these engineered probiotics ameliorated hyperuricemia in a Drosophila melanogaster model, including the formation of renal uric acid stones and a shortened lifespan, providing a route toward the development of purinolytic probiotics.
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Affiliation(s)
- Yang Tong
- Tianjin Key Laboratory for Modern Drug Delivery & High-Efficiency, Collaborative Innovation Center of Chemical Science and Engineering, School of Pharmaceutical Science and Technology, Tianjin University, Tianjin 300072, China; Frontiers Science Center for Synthetic Biology (Ministry of Education), Tianjin University, Tianjin 300072, China; Key Laboratory of Systems Bioengineering (Ministry of Education), School of Chemical Engineering and Technology, Tianjin University, Tianjin 300072, China; Department of Chemistry, Tianjin University, Tianjin 300072, P.R. China
| | - Yifeng Wei
- Singapore Institute of Food and Biotechnology Innovation, Agency for Science, Technology and Research (A∗STAR), Singapore 138669, Singapore
| | - Yingjie Ju
- Tianjin Key Laboratory for Modern Drug Delivery & High-Efficiency, Collaborative Innovation Center of Chemical Science and Engineering, School of Pharmaceutical Science and Technology, Tianjin University, Tianjin 300072, China
| | - Peishan Li
- Tianjin Key Laboratory for Modern Drug Delivery & High-Efficiency, Collaborative Innovation Center of Chemical Science and Engineering, School of Pharmaceutical Science and Technology, Tianjin University, Tianjin 300072, China; Frontiers Science Center for Synthetic Biology (Ministry of Education), Tianjin University, Tianjin 300072, China
| | - Yumin Zhang
- Tianjin Key Laboratory of Radiation Medicine and Molecular Nuclear Medicine, Institute of Radiation Medicine, Chinese Academy of Medical Sciences & Peking Union Medical College, Tianjin 300192, P.R. China
| | - Liqin Li
- Tianjin Speerise Challenge Biotechnology Co., Ltd., Zhangjiawo Industrial Park, No. 16 Huiyuan Road, Zhangjiawo Town, Xiqing District, Tianjin 300380, China
| | - Lujuan Gao
- Tianjin Key Laboratory for Modern Drug Delivery & High-Efficiency, Collaborative Innovation Center of Chemical Science and Engineering, School of Pharmaceutical Science and Technology, Tianjin University, Tianjin 300072, China
| | - Shengnan Liu
- Tianjin Key Laboratory for Modern Drug Delivery & High-Efficiency, Collaborative Innovation Center of Chemical Science and Engineering, School of Pharmaceutical Science and Technology, Tianjin University, Tianjin 300072, China; Frontiers Science Center for Synthetic Biology (Ministry of Education), Tianjin University, Tianjin 300072, China
| | - Dazhi Liu
- Tianjin Key Laboratory for Modern Drug Delivery & High-Efficiency, Collaborative Innovation Center of Chemical Science and Engineering, School of Pharmaceutical Science and Technology, Tianjin University, Tianjin 300072, China; Meining Pharma Inc, 2-401-1, Bldg 8, Huiying Industrial Park, No. 86 West Zhonghuan Road, Tianjin Pilot Free Trade Zone, Tianjin 300308, China
| | - Yiling Hu
- Tianjin Key Laboratory for Modern Drug Delivery & High-Efficiency, Collaborative Innovation Center of Chemical Science and Engineering, School of Pharmaceutical Science and Technology, Tianjin University, Tianjin 300072, China; Frontiers Science Center for Synthetic Biology (Ministry of Education), Tianjin University, Tianjin 300072, China
| | - Zhi Li
- Tianjin Key Laboratory for Modern Drug Delivery & High-Efficiency, Collaborative Innovation Center of Chemical Science and Engineering, School of Pharmaceutical Science and Technology, Tianjin University, Tianjin 300072, China; Frontiers Science Center for Synthetic Biology (Ministry of Education), Tianjin University, Tianjin 300072, China
| | - Hongbin Yu
- Department of Hematology, West China Hospital, Sichuan University, Chengdu 610041, China
| | - Yunzi Luo
- Frontiers Science Center for Synthetic Biology (Ministry of Education), Tianjin University, Tianjin 300072, China; Key Laboratory of Systems Bioengineering (Ministry of Education), School of Chemical Engineering and Technology, Tianjin University, Tianjin 300072, China
| | - Jian Wang
- Tianjin Speerise Challenge Biotechnology Co., Ltd., Zhangjiawo Industrial Park, No. 16 Huiyuan Road, Zhangjiawo Town, Xiqing District, Tianjin 300380, China
| | - Yiwen Wang
- Tianjin Key Laboratory for Modern Drug Delivery & High-Efficiency, Collaborative Innovation Center of Chemical Science and Engineering, School of Pharmaceutical Science and Technology, Tianjin University, Tianjin 300072, China.
| | - Yan Zhang
- Tianjin Key Laboratory for Modern Drug Delivery & High-Efficiency, Collaborative Innovation Center of Chemical Science and Engineering, School of Pharmaceutical Science and Technology, Tianjin University, Tianjin 300072, China; Frontiers Science Center for Synthetic Biology (Ministry of Education), Tianjin University, Tianjin 300072, China; Key Laboratory of Systems Bioengineering (Ministry of Education), School of Chemical Engineering and Technology, Tianjin University, Tianjin 300072, China; Department of Chemistry, Tianjin University, Tianjin 300072, P.R. China.
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Jiang Z, Wang C, Wu Z, Chen K, Yang W, Deng H, Song H, Zhou X. Enzymatic deamination of the epigenetic nucleoside N6-methyladenosine regulates gene expression. Nucleic Acids Res 2021; 49:12048-12068. [PMID: 34850126 PMCID: PMC8643624 DOI: 10.1093/nar/gkab1124] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2021] [Revised: 10/20/2021] [Accepted: 11/16/2021] [Indexed: 12/26/2022] Open
Abstract
N6-methyladenosine (m6A) modification is the most extensively studied epigenetic modification due to its crucial role in regulating an array of biological processes. Herein, Bsu06560, formerly annotated as an adenine deaminase derived from Bacillus subtilis 168, was recognized as the first enzyme capable of metabolizing the epigenetic nucleoside N6-methyladenosine. A model of Bsu06560 was constructed, and several critical residues were putatively identified via mutational screening. Two mutants, F91L and Q150W, provided a superiorly enhanced conversion ratio of adenosine and N6-methyladenosine. The CRISPR-Cas9 system generated Bsu06560-knockout, F91L, and Q150W mutations from the B. subtilis 168 genome. Transcriptional profiling revealed a higher global gene expression level in BS-F91L and BS-Q150W strains with enhanced N6-methyladenosine deaminase activity. The differentially expressed genes were categorized using GO, COG, KEGG and verified through RT-qPCR. This study assessed the crucial roles of Bsu06560 in regulating adenosine and N6-methyladenosine metabolism, which influence a myriad of biological processes. This is the first systematic research to identify and functionally annotate an enzyme capable of metabolizing N6-methyladenosine and highlight its significant roles in regulation of bacterial metabolism. Besides, this study provides a novel method for controlling gene expression through the mutations of critical residues.
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Affiliation(s)
- Zhuoran Jiang
- The Institute of Advanced Studies, and Key Laboratory of Biomedical Polymers-Ministry of Education, College of Chemistry and Molecular Sciences, Wuhan University, 40072 Wuhan, P.R. China
| | - Chao Wang
- The Institute of Advanced Studies, and Key Laboratory of Biomedical Polymers-Ministry of Education, College of Chemistry and Molecular Sciences, Wuhan University, 40072 Wuhan, P.R. China
| | - Zixin Wu
- The Institute of Advanced Studies, and Key Laboratory of Biomedical Polymers-Ministry of Education, College of Chemistry and Molecular Sciences, Wuhan University, 40072 Wuhan, P.R. China
| | - Kun Chen
- The Institute of Advanced Studies, and Key Laboratory of Biomedical Polymers-Ministry of Education, College of Chemistry and Molecular Sciences, Wuhan University, 40072 Wuhan, P.R. China
| | - Wei Yang
- The Institute of Advanced Studies, and Key Laboratory of Biomedical Polymers-Ministry of Education, College of Chemistry and Molecular Sciences, Wuhan University, 40072 Wuhan, P.R. China
| | - Hexiang Deng
- The Institute of Advanced Studies, and Key Laboratory of Biomedical Polymers-Ministry of Education, College of Chemistry and Molecular Sciences, Wuhan University, 40072 Wuhan, P.R. China
| | - Heng Song
- The Institute of Advanced Studies, and Key Laboratory of Biomedical Polymers-Ministry of Education, College of Chemistry and Molecular Sciences, Wuhan University, 40072 Wuhan, P.R. China
| | - Xiang Zhou
- The Institute of Advanced Studies, and Key Laboratory of Biomedical Polymers-Ministry of Education, College of Chemistry and Molecular Sciences, Wuhan University, 40072 Wuhan, P.R. China
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Mahor D, Prasad GS. Biochemical Characterization of Kluyveromyces lactis Adenine Deaminase and Guanine Deaminase and Their Potential Application in Lowering Purine Content in Beer. Front Bioeng Biotechnol 2018; 6:180. [PMID: 30555824 PMCID: PMC6281700 DOI: 10.3389/fbioe.2018.00180] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2018] [Accepted: 11/12/2018] [Indexed: 11/13/2022] Open
Abstract
Excess amounts of uric acid in humans leads to hyperuricemia, which is a biochemical precursor of gout and is also associated with various other disorders. Gout is termed as crystallization of uric acid, predominantly within joints. The burden of hyperuricemia and gout has increased worldwide due to lifestyle changes, obesity, and consumption of purine-rich foods, fructose-containing drinks, and alcoholic beverages. Some of the therapies available to cure gout are associated with unwanted side-effects and antigenicity. We propose an attractive and safe strategy to reduce purine content in beverages using enzymatic application of purine degrading enzymes such as adenine deaminase (ADA) and guanine deaminase (GDA) that convert adenine and guanine into hypoxanthine and xanthine, respectively. We cloned, expressed, purified, and biochemically characterized both adenine deaminase (ADA) and guanine deaminase (GDA) enzymes that play important roles in the purine degradation pathway of Kluyveromyces lactis, and demonstrate their application in lowering purine content in a beverage. The popular beverage beer has been selected as an experimental sample as it confers higher risks of hyperuricemia and gout. Quantification of purine content in 16 different beers from the Indian market showed varying concentrations of different purines. Enzymatic treatment of beer samples with ADA and GDA showed a reduction of adenine and guanine content, respectively. These enzymes in combination with other purine degrading enzymes showed marked reduction in purine content in beer samples. Both enzymes can work at 5.0–8.0 pH range and retain >50% activity at 40°C, making them good candidates for industrial applications.
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Affiliation(s)
- Durga Mahor
- Microbial Type Culture Collection and Gene Bank, CSIR-Institute of Microbial Technology, Chandigarh, India
| | - Gandham S Prasad
- Microbial Type Culture Collection and Gene Bank, CSIR-Institute of Microbial Technology, Chandigarh, India
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Ran S, Liu B, Jiang W, Sun Z, Liang J. Transcriptome analysis of Enterococcus faecalis in response to alkaline stress. Front Microbiol 2015; 6:795. [PMID: 26300863 PMCID: PMC4528170 DOI: 10.3389/fmicb.2015.00795] [Citation(s) in RCA: 36] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2015] [Accepted: 07/22/2015] [Indexed: 11/13/2022] Open
Abstract
Enterococcus faecalis is the most commonly isolated species from endodontic failure root canals; its persistence in treated root canals has been attributed to its ability to resist high pH stress. The goal of this study was to characterize the E. faecalis transcriptome and to identify candidate genes for response and resistance to alkaline stress using Illumina HiSeq 2000 sequencing. We found that E. faecalis could survive and form biofilms in a pH 10 environment and that alkaline stress had a great impact on the transcription of many genes in the E. faecalis genome. The transcriptome sequencing results revealed that 613 genes were differentially expressed (DEGs) for E. faecalis grown in pH 10 medium; 211 genes were found to be differentially up-regulated and 402 genes differentially down-regulated. Many of the down-regulated genes found are involved in cell energy production and metabolism and carbohydrate and amino acid metabolism, and the up-regulated genes are mostly related to nucleotide transport and metabolism. The results presented here reveal that cultivation of E. faecalis in alkaline stress has a profound impact on its transcriptome. The observed regulation of genes and pathways revealed that E. faecalis reduced its carbohydrate and amino acid metabolism and increased nucleotide synthesis to adapt and grow in alkaline stress. A number of the regulated genes may be useful candidates for the development of new therapeutic approaches for the treatment of E. faecalis infections.
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Affiliation(s)
- Shujun Ran
- Shanghai Key Laboratory of Stomatology, Department of Endodontics and Operative Dentistry, School of Medicine, Ninth People's Hospital, Shanghai Jiao Tong University Shanghai, China
| | - Bin Liu
- Shanghai Key Laboratory of Stomatology, Department of Endodontics and Operative Dentistry, School of Medicine, Ninth People's Hospital, Shanghai Jiao Tong University Shanghai, China
| | - Wei Jiang
- Shanghai Key Laboratory of Stomatology, Department of Endodontics and Operative Dentistry, School of Medicine, Ninth People's Hospital, Shanghai Jiao Tong University Shanghai, China
| | - Zhe Sun
- Shanghai Key Laboratory of Stomatology, Department of Endodontics and Operative Dentistry, School of Medicine, Ninth People's Hospital, Shanghai Jiao Tong University Shanghai, China
| | - Jingping Liang
- Shanghai Key Laboratory of Stomatology, Department of Endodontics and Operative Dentistry, School of Medicine, Ninth People's Hospital, Shanghai Jiao Tong University Shanghai, China
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