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Liu J, Huo R, Fu H, Chen S, Qiao X, Xu B, Zhang Z, Wu J, Su L. High-efficient preparation of β-nicotinamide mononucleotides by crude enzymes cascade catalytic reaction. Enzyme Microb Technol 2024; 180:110482. [PMID: 39059289 DOI: 10.1016/j.enzmictec.2024.110482] [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: 04/07/2024] [Revised: 06/27/2024] [Accepted: 07/14/2024] [Indexed: 07/28/2024]
Abstract
β-nicotinamide mononucleotide (β-NMN) is a key precursor of nicotinamide adenine dinucleotide, and becomes attractive in the nutrition and health care fields, but its enzymatic synthesis is expensive. In this study, a six-enzyme cascade catalytic system was constructed to produce β-NMN. Using D-ribose and nicotinamide as substrates, the β-NMN yield reached 97.5 % catalyzed by purified enzymes. Then, after knocking out the genes encoding proteins that consume β-NMN in E. coli BL21(DE3), the similar β-NMN yield, 97.2 %, using the crude enzymes could be also obtained. After that, β-NMN synthesis was performed under increased substrate concentration, and 'modular' crude enzymes cascade catalytic reaction system was proposed to reduce the inhibition of polyphosphate on ribose-phosphate diphosphokinase activity, and the β-NMN yield reached 78.4 % at 10 mM D-ribose, which is 1.82 times of that in 'one-pot' reaction and represents the highest β-NMN preparation level with phosphoribosylpyrophosphate as the core reported till now.
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Affiliation(s)
- Jiehu Liu
- Key Laboratory of Industrial Biotechnology Ministry of Education and School of Biotechnology, Jiangnan University, 1800 Lihu Avenue, Wuxi 214122, China; State Key Laboratory of Food Science and Resources, Jiangnan University, 1800 Lihu Avenue, Wuxi 214122, China
| | - Runtian Huo
- Key Laboratory of Industrial Biotechnology Ministry of Education and School of Biotechnology, Jiangnan University, 1800 Lihu Avenue, Wuxi 214122, China; State Key Laboratory of Food Science and Resources, Jiangnan University, 1800 Lihu Avenue, Wuxi 214122, China
| | - Huixian Fu
- Key Laboratory of Industrial Biotechnology Ministry of Education and School of Biotechnology, Jiangnan University, 1800 Lihu Avenue, Wuxi 214122, China; State Key Laboratory of Food Science and Resources, Jiangnan University, 1800 Lihu Avenue, Wuxi 214122, China
| | - Shiheng Chen
- Key Laboratory of Industrial Biotechnology Ministry of Education and School of Biotechnology, Jiangnan University, 1800 Lihu Avenue, Wuxi 214122, China; State Key Laboratory of Food Science and Resources, Jiangnan University, 1800 Lihu Avenue, Wuxi 214122, China
| | - Xueyi Qiao
- Zhengzhou Tobacco Research Institute of CNTC, Zhengzhou 450001, China
| | - Bo Xu
- Zhengzhou Tobacco Research Institute of CNTC, Zhengzhou 450001, China
| | - Zhaoyuan Zhang
- Key Laboratory of Industrial Biotechnology Ministry of Education and School of Biotechnology, Jiangnan University, 1800 Lihu Avenue, Wuxi 214122, China; State Key Laboratory of Food Science and Resources, Jiangnan University, 1800 Lihu Avenue, Wuxi 214122, China
| | - Jing Wu
- Key Laboratory of Industrial Biotechnology Ministry of Education and School of Biotechnology, Jiangnan University, 1800 Lihu Avenue, Wuxi 214122, China; State Key Laboratory of Food Science and Resources, Jiangnan University, 1800 Lihu Avenue, Wuxi 214122, China
| | - Lingqia Su
- Key Laboratory of Industrial Biotechnology Ministry of Education and School of Biotechnology, Jiangnan University, 1800 Lihu Avenue, Wuxi 214122, China; State Key Laboratory of Food Science and Resources, Jiangnan University, 1800 Lihu Avenue, Wuxi 214122, China.
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2
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Zou S, Zhang B, Han Y, Liu J, Zhao K, Xue Y, Zheng Y. Design of a cofactor self-sufficient whole-cell biocatalyst for enzymatic asymmetric reduction via engineered metabolic pathways and multi-enzyme cascade. Biotechnol J 2024; 19:e2300744. [PMID: 38509791 DOI: 10.1002/biot.202300744] [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: 12/27/2023] [Revised: 02/22/2024] [Accepted: 03/03/2024] [Indexed: 03/22/2024]
Abstract
NAD(P)H-dependent oxidoreductases are crucial biocatalysts for synthesizing chiral compounds. Yet, the industrial implementation of enzymatic redox reactions is often hampered by an insufficient supply of expensive nicotinamide cofactors. Here, a cofactor self-sufficient whole-cell biocatalyst was developed for the enzymatic asymmetric reduction of 2-oxo-4-[(hydroxy)(-methyl)phosphinyl] butyric acid (PPO) to L-phosphinothricin (L-PPT). The endogenous NADP+ pool was significantly enhanced by regulating Preiss-Handler pathway toward NAD(H) synthesis and, in the meantime, introducing NAD kinase to phosphorylate NAD(H) toward NADP+. The intracellular NADP(H) concentration displayed a 2.97-fold increase with the strategy compared with the wild-type strain. Furthermore, a recombinant multi-enzyme cascade biocatalytic system was constructed based on the Escherichia coli chassis. In order to balance multi-enzyme co-expression levels, the strategy of modulating rate-limiting enzyme PmGluDH by RBS strengths regulation successfully increased the catalytic efficiency of PPO conversion. Finally, the cofactor self-sufficient whole-cell biocatalyst effectively converted 300 mM PPO to L-PPT in 2 h without the need to add exogenous cofactors, resulting in a 2.3-fold increase in PPO conversion (%) from 43% to 100%, with a high space-time yield of 706.2 g L-1 d-1 and 99.9% ee. Overall, this work demonstrates a technological example for constructing a cofactor self-sufficient system for NADPH-dependent redox biocatalysis.
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Affiliation(s)
- Shuping Zou
- Key Laboratory of Bioorganic Synthesis of Zhejiang Province, College of Biotechnology and Bioengineering, Zhejiang University of Technology, Hangzhou, China
- Engineering Research Center of Bioconversion and Biopurification of Ministry of Education, Zhejiang University of Technology, Hangzhou, China
| | - Bing Zhang
- Key Laboratory of Bioorganic Synthesis of Zhejiang Province, College of Biotechnology and Bioengineering, Zhejiang University of Technology, Hangzhou, China
- Engineering Research Center of Bioconversion and Biopurification of Ministry of Education, Zhejiang University of Technology, Hangzhou, China
| | - Yuyue Han
- Key Laboratory of Bioorganic Synthesis of Zhejiang Province, College of Biotechnology and Bioengineering, Zhejiang University of Technology, Hangzhou, China
- Engineering Research Center of Bioconversion and Biopurification of Ministry of Education, Zhejiang University of Technology, Hangzhou, China
| | - Jinlong Liu
- Key Laboratory of Bioorganic Synthesis of Zhejiang Province, College of Biotechnology and Bioengineering, Zhejiang University of Technology, Hangzhou, China
- Engineering Research Center of Bioconversion and Biopurification of Ministry of Education, Zhejiang University of Technology, Hangzhou, China
| | - Kuo Zhao
- Key Laboratory of Bioorganic Synthesis of Zhejiang Province, College of Biotechnology and Bioengineering, Zhejiang University of Technology, Hangzhou, China
- Engineering Research Center of Bioconversion and Biopurification of Ministry of Education, Zhejiang University of Technology, Hangzhou, China
| | - Yaping Xue
- Key Laboratory of Bioorganic Synthesis of Zhejiang Province, College of Biotechnology and Bioengineering, Zhejiang University of Technology, Hangzhou, China
- Engineering Research Center of Bioconversion and Biopurification of Ministry of Education, Zhejiang University of Technology, Hangzhou, China
| | - Yuguo Zheng
- Key Laboratory of Bioorganic Synthesis of Zhejiang Province, College of Biotechnology and Bioengineering, Zhejiang University of Technology, Hangzhou, China
- Engineering Research Center of Bioconversion and Biopurification of Ministry of Education, Zhejiang University of Technology, Hangzhou, China
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3
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Huang Z, Wang X, Li N, Song F, Zhou J. Systematic engineering of Escherichia coli for efficient production of nicotinamide riboside from nicotinamide and 3-cyanopyridine. BIORESOURCE TECHNOLOGY 2023; 377:128953. [PMID: 36963699 DOI: 10.1016/j.biortech.2023.128953] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/23/2023] [Revised: 03/17/2023] [Accepted: 03/21/2023] [Indexed: 06/18/2023]
Abstract
Nicotinamide riboside (NR), a key biosynthetic precursor of NAD+, is receiving increasing attention because of its role. In this study, a whole-cell catalysis method to efficiently synthesize NR was established. First, the performance of 5'-nucleotidase (UshA) from Escherichia coli was confirmed to have high catalytic activity to synthesize NR. Then, the endogenous NR degradation pathway was detected, and the genes (rihA, rihB, and rihC) involved in NR degradation were knocked out, which enabled NR biosynthesis. In addition, the important role of the signal peptide of UshA in NR transport had been confirmed. Subsequently, nitrile hydratase was introduced to achieve the conversion of 3-cyanopyridine to NR. Finally, the NR titer reached 25.6 and 29.8 g/L with nicotinamide and 3-cyanopyridine, respectively, as substrates in a 5-L bioreactor, the efficient biosynthesis of NR in E. coli by using nicotinamide and 3-cyanopyridine.
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Affiliation(s)
- Zhongshi Huang
- Science Center for Future Foods, Jiangnan University, 1800 Lihu Road, Wuxi, Jiangsu 214122, China; Key Laboratory of Industrial Biotechnology, Ministry of Education and School of Biotechnology, Jiangnan University, 1800 Lihu Road, Wuxi, Jiangsu 214122, China; Engineering Research Center of Ministry of Education on Food Synthetic Biotechnology, Jiangnan University, 1800 Lihu Road, Wuxi, Jiangsu 214122, China; Jiangsu Province Engineering Research Center of Food Synthetic Biotechnology, Jiangnan University, Wuxi 214122, China
| | - Xinglong Wang
- Science Center for Future Foods, Jiangnan University, 1800 Lihu Road, Wuxi, Jiangsu 214122, China; Key Laboratory of Industrial Biotechnology, Ministry of Education and School of Biotechnology, Jiangnan University, 1800 Lihu Road, Wuxi, Jiangsu 214122, China
| | - Ning Li
- Science Center for Future Foods, Jiangnan University, 1800 Lihu Road, Wuxi, Jiangsu 214122, China; Key Laboratory of Industrial Biotechnology, Ministry of Education and School of Biotechnology, Jiangnan University, 1800 Lihu Road, Wuxi, Jiangsu 214122, China
| | - Fuqiang Song
- Science Center for Future Foods, Jiangnan University, 1800 Lihu Road, Wuxi, Jiangsu 214122, China; Key Laboratory of Industrial Biotechnology, Ministry of Education and School of Biotechnology, Jiangnan University, 1800 Lihu Road, Wuxi, Jiangsu 214122, China
| | - Jingwen Zhou
- Science Center for Future Foods, Jiangnan University, 1800 Lihu Road, Wuxi, Jiangsu 214122, China; Key Laboratory of Industrial Biotechnology, Ministry of Education and School of Biotechnology, Jiangnan University, 1800 Lihu Road, Wuxi, Jiangsu 214122, China; Engineering Research Center of Ministry of Education on Food Synthetic Biotechnology, Jiangnan University, 1800 Lihu Road, Wuxi, Jiangsu 214122, China; Jiangsu Province Engineering Research Center of Food Synthetic Biotechnology, Jiangnan University, Wuxi 214122, China.
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4
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Nishiyama T, Hoshino R, Ueda K. Characterization of 5'-nucleotidases secreted from Streptomyces. Appl Microbiol Biotechnol 2023; 107:2289-2302. [PMID: 36820897 DOI: 10.1007/s00253-023-12426-2] [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: 11/07/2022] [Revised: 01/26/2023] [Accepted: 02/01/2023] [Indexed: 02/24/2023]
Abstract
To study the ability of Streptomyces to utilize environmental nucleotides, we screened for strains exhibiting extracellular 5'-inosine monophosphate (IMP)-dephosphorylating activity in our collection of soil isolates and obtained two producers: NE5-10 and Y2F8-2. The enzyme responsible for the activity was purified from the culture supernatant of each strain, and its mass spectral data were used to identify the coding sequence. The gene was successfully identified in the whole genome sequence of each strain; it was located in a conserved gene cluster of phosphate-related functions and encoded an approximately 600-amino acid long protein containing an N-terminal secretion signal. The mature part of the protein exhibited similarity to a known bacterial 5'-nucleotidase. The locus of the 5'-nucleotidase gene contained genes encoding proteins involved in phosphate utilization. The conserved gene arrangement of the locus in various Streptomyces genomes suggested the genetic region to be involved in phosphate-scavenging in this group of bacteria. Phylogenetic analysis demonstrated that the isolated Streptomyces enzymes represent an uncharacterized group of bacterial 5'-nucleotidases. Enzymatic characterization of the two Streptomyces enzymes demonstrated that both enzymes exhibited 5'-nucleotidase activity but differed in terms of optimal temperature and pH, dependence on divalent cations, and substrate specificity. The Km and Vmax values of the 5'-IMP-dephosphorylating activity were 0.239 mM and 9.47 U/mg, respectively, for NE5-10 and 0.221 mM and 38.17 U/mg, respectively, for Y2F8-2. Enzyme activity in the culture broth of the two Streptomyces producers occurred in a phosphate-limitation-dependent manner, supporting their involvement in the acquisition of phosphorus. KEY POINTS: • We purified and characterized nucleotidases from two Streptomyces. • Two nucleotidases were presumed to be involved in phosphate acquisition. • It showed diversity in phosphate acquisition among microorganisms.
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Affiliation(s)
- Tatsuya Nishiyama
- Life Science Research Center, College of Bioresource Sciences, Nihon University, 1866 Kameino, 252-0880, Fujisawa, Japan.
| | - Rio Hoshino
- Life Science Research Center, College of Bioresource Sciences, Nihon University, 1866 Kameino, 252-0880, Fujisawa, Japan
| | - Kenji Ueda
- Life Science Research Center, College of Bioresource Sciences, Nihon University, 1866 Kameino, 252-0880, Fujisawa, Japan
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Genotoxins: The Mechanistic Links between Escherichia coli and Colorectal Cancer. Cancers (Basel) 2023; 15:cancers15041152. [PMID: 36831495 PMCID: PMC9954437 DOI: 10.3390/cancers15041152] [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: 12/27/2022] [Revised: 02/06/2023] [Accepted: 02/09/2023] [Indexed: 02/16/2023] Open
Abstract
Emerging evidence indicates bacterial infections contribute to the formation of cancers. Bacterial genotoxins are effectors that cause DNA damage by introducing single- and double-strand DNA breaks in the host cells. The first bacterial genotoxin cytolethal distending toxin (CDT) was a protein identified in 1987 in a pathogenic strain in Escherichia coli (E. coli) isolated from a young patient. The peptide-polyketide genotoxin colibactin is produced by the phylogenetic group B2 of E. coli. Recently, a protein produced by attaching/effacing (A/E) pathogens, including enteropathogenic and enterohemorrhagic E. coli (EPEC and EHEC) and their murine equivalent Citrobacter rodentium (CR), has been reported as a novel protein genotoxin, being injected via the type III secretion system (T3SS) into host cells and harboring direct DNA digestion activity with a catalytic histidine-aspartic acid dyad. These E. coli-produced genotoxins impair host DNA, which results in senescence or apoptosis of the target cells if the damage is beyond repair. Conversely, host cells can survive and proliferate if the genotoxin-induced DNA damage is not severe enough to kill them. The surviving cells may accumulate genomic instability and acquire malignant traits. This review presents the cellular responses of infection with the genotoxins-producing E. coli and discusses the current knowledge of the tumorigenic potential of these toxins.
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6
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Surface display of (R)-carbonyl reductase on Escherichia coli as biocatalyst for recycling biotransformation of 2-hydroxyacetophenone. Biochem Eng J 2022. [DOI: 10.1016/j.bej.2022.108686] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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7
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Jing X, Gong Y, Pan H, Meng Y, Ren Y, Diao Z, Mu R, Xu T, Zhang J, Ji Y, Li Y, Wang C, Qu L, Cui L, Ma B, Xu J. Single-cell Raman-activated sorting and cultivation (scRACS-Culture) for assessing and mining in situ phosphate-solubilizing microbes from nature. ISME COMMUNICATIONS 2022; 2:106. [PMID: 37938284 PMCID: PMC9723661 DOI: 10.1038/s43705-022-00188-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/13/2022] [Revised: 10/05/2022] [Accepted: 10/06/2022] [Indexed: 01/25/2023]
Abstract
Due to the challenges in detecting in situ activity and cultivating the not-yet-cultured, functional assessment and mining of living microbes from nature has typically followed a 'culture-first' paradigm. Here, employing phosphate-solubilizing microbes (PSM) as model, we introduce a 'screen-first' strategy that is underpinned by a precisely one-cell-resolution, complete workflow of single-cell Raman-activated Sorting and Cultivation (scRACS-Culture). Directly from domestic sewage, individual cells were screened for in-situ organic-phosphate-solubilizing activity via D2O intake rate, sorted by the function via Raman-activated Gravity-driven Encapsulation (RAGE), and then cultivated from precisely one cell. By scRACS-Culture, pure cultures of strong organic PSM including Comamonas spp., Acinetobacter spp., Enterobacter spp. and Citrobacter spp., were derived, whose phosphate-solubilizing activities in situ are 90-200% higher than in pure culture, underscoring the importance of 'screen-first' strategy. Moreover, employing scRACS-Seq for post-RACS cells that remain uncultured, we discovered a previously unknown, low-abundance, strong organic-PSM of Cutibacterium spp. that employs secretary metallophosphoesterase (MPP), cell-wall-anchored 5'-nucleotidase (encoded by ushA) and periplasmic-membrane located PstSCAB-PhoU transporter system for efficient solubilization and scavenging of extracellular phosphate in sewage. Therefore, scRACS-Culture and scRACS-Seq provide an in situ function-based, 'screen-first' approach for assessing and mining microbes directly from the environment.
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Affiliation(s)
- Xiaoyan Jing
- Single-Cell Center, CAS Key Laboratory of Biofuels, Shandong Key Laboratory of Energy Genetics, Qingdao Institute of BioEnergy and Bioprocess Technology, Chinese Academy of Sciences, Qingdao, Shandong, China
- University of Chinese Academy of Sciences, Beijing, China
- Shandong Energy Institute, Qingdao, Shandong, China
- Qingdao New Energy Shandong Laboratory, Qingdao, Shandong, China
| | - Yanhai Gong
- Single-Cell Center, CAS Key Laboratory of Biofuels, Shandong Key Laboratory of Energy Genetics, Qingdao Institute of BioEnergy and Bioprocess Technology, Chinese Academy of Sciences, Qingdao, Shandong, China
- University of Chinese Academy of Sciences, Beijing, China
- Shandong Energy Institute, Qingdao, Shandong, China
- Qingdao New Energy Shandong Laboratory, Qingdao, Shandong, China
| | - Huihui Pan
- Single-Cell Center, CAS Key Laboratory of Biofuels, Shandong Key Laboratory of Energy Genetics, Qingdao Institute of BioEnergy and Bioprocess Technology, Chinese Academy of Sciences, Qingdao, Shandong, China
- University of Chinese Academy of Sciences, Beijing, China
- Shandong Energy Institute, Qingdao, Shandong, China
- Qingdao New Energy Shandong Laboratory, Qingdao, Shandong, China
| | - Yu Meng
- Single-Cell Center, CAS Key Laboratory of Biofuels, Shandong Key Laboratory of Energy Genetics, Qingdao Institute of BioEnergy and Bioprocess Technology, Chinese Academy of Sciences, Qingdao, Shandong, China
- University of Chinese Academy of Sciences, Beijing, China
- Shandong Energy Institute, Qingdao, Shandong, China
- Qingdao New Energy Shandong Laboratory, Qingdao, Shandong, China
| | - Yishang Ren
- Single-Cell Center, CAS Key Laboratory of Biofuels, Shandong Key Laboratory of Energy Genetics, Qingdao Institute of BioEnergy and Bioprocess Technology, Chinese Academy of Sciences, Qingdao, Shandong, China
- University of Chinese Academy of Sciences, Beijing, China
- Shandong Energy Institute, Qingdao, Shandong, China
- Qingdao New Energy Shandong Laboratory, Qingdao, Shandong, China
| | - Zhidian Diao
- Single-Cell Center, CAS Key Laboratory of Biofuels, Shandong Key Laboratory of Energy Genetics, Qingdao Institute of BioEnergy and Bioprocess Technology, Chinese Academy of Sciences, Qingdao, Shandong, China
- University of Chinese Academy of Sciences, Beijing, China
- Shandong Energy Institute, Qingdao, Shandong, China
- Qingdao New Energy Shandong Laboratory, Qingdao, Shandong, China
| | - Runzhi Mu
- Qingdao Zhang Cun River Water Co., Ltd, Qingdao, Shandong, China
| | - Teng Xu
- Single-Cell Center, CAS Key Laboratory of Biofuels, Shandong Key Laboratory of Energy Genetics, Qingdao Institute of BioEnergy and Bioprocess Technology, Chinese Academy of Sciences, Qingdao, Shandong, China
- University of Chinese Academy of Sciences, Beijing, China
- Shandong Energy Institute, Qingdao, Shandong, China
- Qingdao New Energy Shandong Laboratory, Qingdao, Shandong, China
| | - Jia Zhang
- Single-Cell Center, CAS Key Laboratory of Biofuels, Shandong Key Laboratory of Energy Genetics, Qingdao Institute of BioEnergy and Bioprocess Technology, Chinese Academy of Sciences, Qingdao, Shandong, China
- University of Chinese Academy of Sciences, Beijing, China
- Shandong Energy Institute, Qingdao, Shandong, China
- Qingdao New Energy Shandong Laboratory, Qingdao, Shandong, China
| | - Yuetong Ji
- Single-Cell Center, CAS Key Laboratory of Biofuels, Shandong Key Laboratory of Energy Genetics, Qingdao Institute of BioEnergy and Bioprocess Technology, Chinese Academy of Sciences, Qingdao, Shandong, China
- Shandong Energy Institute, Qingdao, Shandong, China
- Qingdao New Energy Shandong Laboratory, Qingdao, Shandong, China
- Qingdao Single-Cell Biotechnology Co., Ltd, Qingdao, Shandong, China
| | - Yuandong Li
- Single-Cell Center, CAS Key Laboratory of Biofuels, Shandong Key Laboratory of Energy Genetics, Qingdao Institute of BioEnergy and Bioprocess Technology, Chinese Academy of Sciences, Qingdao, Shandong, China
- University of Chinese Academy of Sciences, Beijing, China
- Shandong Energy Institute, Qingdao, Shandong, China
- Qingdao New Energy Shandong Laboratory, Qingdao, Shandong, China
| | - Chen Wang
- Single-Cell Center, CAS Key Laboratory of Biofuels, Shandong Key Laboratory of Energy Genetics, Qingdao Institute of BioEnergy and Bioprocess Technology, Chinese Academy of Sciences, Qingdao, Shandong, China
- University of Chinese Academy of Sciences, Beijing, China
- Shandong Energy Institute, Qingdao, Shandong, China
- Qingdao New Energy Shandong Laboratory, Qingdao, Shandong, China
| | - Lingyun Qu
- The First Institute of Oceanography, Ministry of Natural Resources, Qingdao, Shandong, China
| | - Li Cui
- Key Laboratory of Urban Environment and Health, Institute of Urban Environment, Chinese Academy of Sciences, Xiamen, Fujian, China
| | - Bo Ma
- Single-Cell Center, CAS Key Laboratory of Biofuels, Shandong Key Laboratory of Energy Genetics, Qingdao Institute of BioEnergy and Bioprocess Technology, Chinese Academy of Sciences, Qingdao, Shandong, China.
- University of Chinese Academy of Sciences, Beijing, China.
- Shandong Energy Institute, Qingdao, Shandong, China.
- Qingdao New Energy Shandong Laboratory, Qingdao, Shandong, China.
| | - Jian Xu
- Single-Cell Center, CAS Key Laboratory of Biofuels, Shandong Key Laboratory of Energy Genetics, Qingdao Institute of BioEnergy and Bioprocess Technology, Chinese Academy of Sciences, Qingdao, Shandong, China.
- University of Chinese Academy of Sciences, Beijing, China.
- Shandong Energy Institute, Qingdao, Shandong, China.
- Qingdao New Energy Shandong Laboratory, Qingdao, Shandong, China.
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8
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Huang Z, Li N, Yu S, Zhang W, Zhang T, Zhou J. Systematic Engineering of Escherichia coli for Efficient Production of Nicotinamide Mononucleotide From Nicotinamide. ACS Synth Biol 2022; 11:2979-2988. [PMID: 35977419 DOI: 10.1021/acssynbio.2c00100] [Citation(s) in RCA: 15] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/24/2023]
Abstract
Research studies on NAD+ have proven its crucial role in aging and disease. Nicotinamide mononucleotide (NMN), as the key intermediate of NAD+, plays a significant role in supplying and maintaining NAD+ levels. In the present study, a biocatalytic method for the efficient synthesis of NMN was established. First, Escherichia coli was systematically modified to make it more conducive to the biosynthesis and accumulation of NMN. Next, the performance of nicotinamide phosphoribosyltransferase from Vibrio bacteriophage KVP40 (VpNadV) was determined, which has the best catalytic activity to produce NMN from nicotinamide. The accumulation of extracellular NMN was further increased after the introduction of an NMN transporter. Fine-tuning of gene expression and copy number led to the synthesis of NMN at the yield of 2.6 g/L at the shake flask level. The introduction of a nicotinamide transporter, BcniaP, could not obviously increase the production of NMN at the shake flask level, but it decreased the production of NMN at the bioreactor level. Finally, the titer of NMN reached 16.2 g/L with a conversion ratio of 97.0% from nicotinamide, both of which are highest according to currently available reports. The fed-batch fermentation with direct supplementation of nicotinamide could facilitate the industrial-scale production of NMN compared to that achieved by the whole-cell catalysis process. These results also represent the highest reported yield of NMN synthesized from nicotinamide in E. coli.
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Affiliation(s)
- Zhongshi Huang
- Science Center for Future Foods, Jiangnan University, 1800 Lihu Road, Wuxi, Jiangsu 214122, China.,Key Laboratory of Industrial Biotechnology, Ministry of Education and School of Biotechnology, Jiangnan University, 1800 Lihu Road, Wuxi, Jiangsu 214122, China
| | - Ning Li
- Science Center for Future Foods, Jiangnan University, 1800 Lihu Road, Wuxi, Jiangsu 214122, China.,Key Laboratory of Industrial Biotechnology, Ministry of Education and School of Biotechnology, Jiangnan University, 1800 Lihu Road, Wuxi, Jiangsu 214122, China
| | - Shiqin Yu
- Science Center for Future Foods, Jiangnan University, 1800 Lihu Road, Wuxi, Jiangsu 214122, China.,Key Laboratory of Industrial Biotechnology, Ministry of Education and School of Biotechnology, Jiangnan University, 1800 Lihu Road, Wuxi, Jiangsu 214122, China.,Engineering Research Center of Ministry of Education on Food Synthetic Biotechnology, Jiangnan University, 1800 Lihu Road, Wuxi, Jiangsu 214122, China.,Jiangsu Province Engineering Research Center of Food Synthetic Biotechnology, Jiangnan University, Wuxi 214122, China
| | - Weiping Zhang
- Bloomage Biotechnology Corporation Limited, 678 Tianchen Street, Jinan, Shandong 250101, China
| | - Tianmeng Zhang
- Bloomage Biotechnology Corporation Limited, 678 Tianchen Street, Jinan, Shandong 250101, China
| | - Jingwen Zhou
- Science Center for Future Foods, Jiangnan University, 1800 Lihu Road, Wuxi, Jiangsu 214122, China.,Key Laboratory of Industrial Biotechnology, Ministry of Education and School of Biotechnology, Jiangnan University, 1800 Lihu Road, Wuxi, Jiangsu 214122, China.,Engineering Research Center of Ministry of Education on Food Synthetic Biotechnology, Jiangnan University, 1800 Lihu Road, Wuxi, Jiangsu 214122, China.,Jiangsu Province Engineering Research Center of Food Synthetic Biotechnology, Jiangnan University, Wuxi 214122, China
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9
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Stancheva SG, Frömbling J, Sassu EL, Hennig-Pauka I, Ladinig A, Gerner W, Grunert T, Ehling-Schulz M. Proteomic and immunoproteomic insights into the exoproteome of Actinobacillus pleuropneumoniae, the causative agent of porcine pleuropneumonia. Microb Pathog 2022; 172:105759. [PMID: 36087692 DOI: 10.1016/j.micpath.2022.105759] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2022] [Revised: 08/26/2022] [Accepted: 08/30/2022] [Indexed: 10/31/2022]
Abstract
Porcine pleuropneumonia caused by Actinobacillus pleuropneumoniae affects pig health status and the swine industry worldwide. Despite the extensive number of studies focused on A. pleuropneumoniae infection and vaccine development, a thorough analysis of the A. pleuropneumoniae exoproteome is still missing. Using a complementary approach of quantitative proteomics and immunoproteomics we gained an in-depth insight into the A. pleuropneumoniae serotype 2 exoproteome, which provides the basis for future functional studies. Label-free liquid chromatography-tandem mass spectrometry (LC-MS/MS) revealed 593 exoproteins, of which 104 were predicted to be virulence factors. The RTX toxins ApxIIA and ApxIIIA -were found to be the most abundant proteins in the A. pleuropneumoniae serotype 2 exoproteome. Furthermore, the ApxIVA toxin was one of the proteins showing the highest abundance, although ApxIVA is commonly assumed to be expressed exclusively in vivo. Our study revealed several antigens, including proteins with moonlight functions, such as the elongation factor (EF)-Tu, and proteins linked to specific metabolic traits, such as the maltodextrin-binding protein MalE, that warrant future functional characterization and might present potential targets for novel therapeutics and vaccines. Our Ig-classes specific serological proteome analysis (SERPA) approach allowed us to explore the development of the host humoral immune response over the course of the infection. These SERPAs pinpointed proteins that might play a key role in virulence and persistence and showed that the immune response to the different Apx toxins is distinct. For instance, our results indicate that the ApxIIIA toxin has properties of a thymus-independent antigen, which should be studied in more detail.
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Affiliation(s)
- Stelli G Stancheva
- Institute of Microbiology, Department for Pathobiology, University of Veterinary Medicine Vienna, Austria
| | - Janna Frömbling
- Institute of Microbiology, Department for Pathobiology, University of Veterinary Medicine Vienna, Austria
| | - Elena L Sassu
- University Clinic for Swine, Department for Farm Animals and Veterinary Public Health, University of Veterinary Medicine Vienna, Austria
| | - Isabel Hennig-Pauka
- Field Station for Epidemiology, University of Veterinary Medicine Hannover, Bakum, Germany
| | - Andrea Ladinig
- University Clinic for Swine, Department for Farm Animals and Veterinary Public Health, University of Veterinary Medicine Vienna, Austria
| | - Wilhelm Gerner
- Institute of Immunology, Department of Pathobiology, University of Veterinary Medicine Vienna, Vienna, Austria
| | - Tom Grunert
- Institute of Microbiology, Department for Pathobiology, University of Veterinary Medicine Vienna, Austria
| | - Monika Ehling-Schulz
- Institute of Microbiology, Department for Pathobiology, University of Veterinary Medicine Vienna, Austria.
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10
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Oral Administration with Live Attenuated Citrobacter rodentium Protects Immunocompromised Mice from Lethal Infection. Infect Immun 2022; 90:e0019822. [PMID: 35861565 PMCID: PMC9302154 DOI: 10.1128/iai.00198-22] [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: 01/07/2023] Open
Abstract
Enteropathogenic Escherichia coli (EPEC) and enterohemorrhagic E. coli (EHEC) are important causative agents for foodborne diseases worldwide. Besides antibiotic treatment, vaccination has been deemed as the most effective strategy for preventing EPEC- and EHEC-caused foodborne illnesses. Despite substantial progress made in identifying promising antigens and efficacious vaccines, no vaccines against EPEC or EHEC have yet been licensed. Mice are inherently resistant to EPEC and EHEC infections; infection with Citrobacter rodentium (CR), the murine equivalent of EPEC and EHEC, in mice has been widely used as a model to study bacterial pathogenesis and develop novel vaccine strategies. Mirroring the severe outcomes of EPEC and EHEC infections in immunocompromised populations, immunocompromised mouse strains such as interleukin-22 knockout (Il22-/-) are susceptible to CR infection with severe clinical symptoms and mortality. Live attenuated bacterial vaccine strategies have been scarcely investigated for EPEC and EHEC infections, in particular in immunocompromised populations associated with severe outcomes. Here we examined whether live attenuated CR strain with rational genetic manipulation generates protective immunity against lethal CR infection in the susceptible Il22-/- mice. Our results demonstrate that oral administration of live ΔespFΔushA strain promotes efficient systemic and humoral immunity against a wide range of CR virulence determinants, thus protecting otherwise lethal CR infection, even in immunocompromised Il22-/- mice. This provides a proof of concept of live attenuated vaccination strategy for preventing CR infection in immunocompromised hosts associated with more severe symptoms and lethality.
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11
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Liu Y, Xie N, Yu B. De Novo Biosynthesis of D- p-Hydroxyphenylglycine by a Designed Cofactor Self-Sufficient Route and Co-culture Strategy. ACS Synth Biol 2022; 11:1361-1372. [PMID: 35244401 DOI: 10.1021/acssynbio.2c00007] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
d-p-Hydroxyphenylglycine (D-HPG) is an important intermediate for the synthesis of β-lactam antibiotics with an annual market demand of thousands of tons. Currently, the main production processes are via chemical approaches. Although enzymatic conversion has been investigated for D-HPG production, synthesis of the substrate DL-hydroxyphenylhydantoin is still chemically based, which suffers from high pollution and harsh reaction conditions. In this study, one cofactor self-sufficient route for D-HPG production from l-phenylalanine was newly designed and the artificial pathway was functionalized by selecting suitable enzymes and adjusting their expressions in strain Pseudomonas putida KT2440. Notably, a new R-mandelate dehydrogenase from Lactococcus lactis with relatively high activity under pH neutral conditions was successfully mined to demonstrate the biosynthetic pathway in vivo. The performance of the engineered P. putida strain was further increased by enhancing cellular NAD availability and blocking l-phenylalanine consumption. Coupled with the l-phenylalanine producer, Escherichia coli strain ATCC 31884, a stable and interactive co-culture process was also developed by engineering a "cross-link auxotrophic" system to produce D-HPG directly from glucose. Thus, this study is the first approach for the de novo biosynthesis of D-HPG by engineering a non-natural pathway and lays the foundation for further improving the efficiency of D-HPG production via a green and sustainable route.
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Affiliation(s)
- Yang Liu
- CAS Key Laboratory of Microbial Physiological and Metabolic Engineering, State Key Laboratory of Mycology, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Nengzhong Xie
- National Engineering Research Center for Non-Food Biorefinery, State Key Laboratory of Non-Food Biomass and Enzyme Technology, Guangxi Biomass Engineering Technology Research Center, Guangxi Key Laboratory of Bio-refinery, Guangxi Academy of Sciences, Nanning 530007, China
| | - Bo Yu
- CAS Key Laboratory of Microbial Physiological and Metabolic Engineering, State Key Laboratory of Mycology, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, China
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12
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Wang J, Guo X, Wan L, Liu Y, Xue H, Zhao ZK. Engineering formaldehyde dehydrogenase from Pseudomonas putida to favor nicotinamide cytosine dinucleotide. Chembiochem 2022; 23:e202100697. [PMID: 35146861 DOI: 10.1002/cbic.202100697] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2021] [Revised: 02/09/2022] [Indexed: 11/05/2022]
Abstract
The enzyme formaldehyde dehydrogenase (FalDH) from Pseudomonas putida is of particular interest for biotechnological applications as it catalyses the oxidation of formaldehyde independent of glutathione. However, the consumption of a stoichiometric amount of nicotinamide adenine dinucleotide (NAD) can be challenging at the metabolic level as this may affect many other NAD-linked processes. A potential solution is to engineer FalDH to utilize non-natural cofactors. Here we devised FalDH variants to favor nicotinamide cytosine dinucleotide (NCD) by structure-guided modification of the binding pocket for the adenine moiety of NAD. Several mutants were obtained and the best one FalDH 9B2 had over 150-fold higher preference for NCD than NAD. Molecular docking analysis indicated that the cofactor binding pocket shrinked to better fit NCD, a smaller-sized cofactor. FalDH 9B2 together with other NCD-linked enzymes offer opportunities to assemble orthogonal pathways for biological conversion of C1 molecules.
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Affiliation(s)
- Junting Wang
- Dalian Institute of Chemical Physics, Laboratory of Biotechnology, CHINA
| | - Xiaojia Guo
- Dalian Institute of Chemical Physics, Laboratory of Biotechnology, CHINA
| | - Li Wan
- Dalian Institute of Chemical Physics, Laboratory of Biotechnology, CHINA
| | - Yuxue Liu
- Dalian Institute of Chemical Physics, Laboratory of Biotechnology, CHINA
| | - Haizhao Xue
- Dalian Institute of Chemical Physics, Laboratory of Biotechnology, CHINA
| | - Zongbao Kent Zhao
- Dalian Institute of Chemical Physics, Division of Biotechnology, 457 Zhongshan Road, 116023, Dalian, CHINA
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13
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Zakataeva NP. Microbial 5'-nucleotidases: their characteristics, roles in cellular metabolism, and possible practical applications. Appl Microbiol Biotechnol 2021; 105:7661-7681. [PMID: 34568961 PMCID: PMC8475336 DOI: 10.1007/s00253-021-11547-w] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2021] [Revised: 08/21/2021] [Accepted: 08/24/2021] [Indexed: 11/25/2022]
Abstract
5′-Nucleotidases (EC 3.1.3.5) are enzymes that catalyze the hydrolytic dephosphorylation of 5′-ribonucleotides and 5′-deoxyribonucleotides to their respective nucleosides and phosphate. Most 5′-nucleotidases have broad substrate specificity and are multifunctional enzymes capable of cleaving phosphorus from not only mononucleotide phosphate molecules but also a variety of other phosphorylated metabolites. 5′-Nucleotidases are widely distributed throughout all kingdoms of life and found in different cellular locations. The well-studied vertebrate 5′-nucleotidases play an important role in cellular metabolism. These enzymes are involved in purine and pyrimidine salvage pathways, nucleic acid repair, cell-to-cell communication, signal transduction, control of the ribo- and deoxyribonucleotide pools, etc. Although the first evidence of microbial 5′-nucleotidases was obtained almost 60 years ago, active studies of genetic control and the functions of microbial 5′-nucleotidases started relatively recently. The present review summarizes the current knowledge about microbial 5′-nucleotidases with a focus on their diversity, cellular localizations, molecular structures, mechanisms of catalysis, physiological roles, and activity regulation and approaches to identify new 5′-nucleotidases. The possible applications of these enzymes in biotechnology are also discussed. Key points • Microbial 5′-nucleotidases differ in molecular structure, hydrolytic mechanism, and cellular localization. • 5′-Nucleotidases play important and multifaceted roles in microbial cells. • Microbial 5′-nucleotidases have wide range of practical applications.
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Affiliation(s)
- Natalia P Zakataeva
- Ajinomoto-Genetika Research Institute, 1st Dorozhny Proezd, b.1-1, Moscow, 117545, Russia.
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14
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Liu Y, Fu K, Wier EM, Lei Y, Hodgson A, Xu D, Xia X, Zheng D, Ding H, Sears CL, Yang J, Wan F. Bacterial genotoxin accelerates transient infection-driven murine colon tumorigenesis. Cancer Discov 2021; 12:236-249. [PMID: 34479870 DOI: 10.1158/2159-8290.cd-21-0912] [Citation(s) in RCA: 24] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2021] [Revised: 08/19/2021] [Accepted: 08/24/2021] [Indexed: 12/24/2022]
Abstract
Chronic and low-grade inflammation associated with persistent bacterial infections has been linked to colon tumor development; however, the impact of transient and self-limited infections in bacterially-driven colon tumorigenesis has remained enigmatic. Here we report that UshA is a novel genotoxin in attaching/effacing (A/E) pathogens, which includes the human pathogens enteropathogenic Escherichia coli (EPEC), enterohemorrhagic E. coli (EHEC), and their murine equivalent Citrobacter rodentium (CR). UshA harbors direct DNA digestion activity with a catalytic histidine-aspartic acid dyad. Injected via the Type III Secretion System (T3SS) into host cells, UshA triggers DNA damage and initiates tumorigenic transformation during infections in vitro and in vivo. Moreover, UshA plays an indispensable role in CR infection-accelerated colon tumorigenesis in genetically susceptible ApcMinΔ716/+ mice. Collectively, our results reveal that UshA, functioning as a bacterial T3SS-dependant genotoxin, plays a critical role in prompting transient and noninvasive bacterial infection-accelerated colon tumorigenesis in mice.
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Affiliation(s)
- Yue Liu
- Biochemistry and Molecular Biology, Johns Hopkins Bloomberg School of Public Health
| | - Kai Fu
- Biochemistry and Molecular Biology, Johns Hopkins Bloomberg School of Public Health
| | - Eric M Wier
- Biochemistry and Molecular Biology, Johns Hopkins Bloomberg School of Public Health
| | - Yifan Lei
- Biochemistry and Molecular Biology, Johns Hopkins Bloomberg School of Public Health
| | - Andrea Hodgson
- Biochemistry and Molecular Biology, Johns Hopkins Bloomberg School of Public Health
| | - Dongqing Xu
- Biochemistry and Molecular Biology, Johns Hopkins Bloomberg School of Public Health
| | - Xue Xia
- Biochemistry and Molecular Biology, Johns Hopkins Bloomberg School of Public Health
| | - Dandan Zheng
- Chinese Academy of Medical Sciences and Peking Union Medical College
| | - Hua Ding
- Johns Hopkins Bloomberg School of Public Health
| | | | - Jian Yang
- Chinese Academy of Medical Sciences and Peking Union Medical College
| | - Fengyi Wan
- Biochemistry and Molecular Biology, Johns Hopkins Bloomberg School of Public Health
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15
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Improving the production of NAD + via multi-strategy metabolic engineering in Escherichia coli. Metab Eng 2021; 64:122-133. [PMID: 33577950 DOI: 10.1016/j.ymben.2021.01.012] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2020] [Revised: 01/30/2021] [Accepted: 01/31/2021] [Indexed: 02/07/2023]
Abstract
Nicotinamide adenine dinucleotide (NAD+) is an essential coenzyme involved in numerous physiological processes. As an attractive product in the industrial field, NAD+ also plays an important role in oxidoreductase-catalyzed reactions, drug synthesis, and the treatment of diseases, such as dementia, diabetes, and vascular dysfunction. Currently, although the biotechnology to construct NAD+-overproducing strains has been developed, limited regulation and low productivity still hamper its use on large scales. Here, we describe multi-strategy metabolic engineering to address the NAD+-production bottleneck in E. coli. First, blocking the degradation pathway of NAD(H) increased the accumulation of NAD+ by 39%. Second, key enzymes involved in the Preiss-Handler pathway of NAD+ synthesis were overexpressed and led to a 221% increase in the NAD+ concentration. Third, the PRPP synthesis module and Preiss-Handler pathway were combined to strengthen the precursors supply, which resulted in enhancement of NAD+ content by 520%. Fourth, increasing the ATP content led to an increase in the concentration of NAD+ by 170%. Finally, with the combination of all above strategies, a strain with a high yield of NAD+ was constructed, with the intracellular NAD+ concentration reaching 26.9 μmol/g DCW, which was 834% that of the parent strain. This study presents an efficient design of an NAD+-producing strain through global regulation metabolic engineering.
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16
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Zhang Q, Huang Q, Fang Q, Li H, Tang H, Zou G, Wang D, Li S, Bei W, Chen H, Li L, Zhou R. Identification of genes regulated by the two-component system response regulator NarP of Actinobacillus pleuropneumoniae via DNA-affinity-purified sequencing. Microbiol Res 2019; 230:126343. [PMID: 31539852 DOI: 10.1016/j.micres.2019.126343] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2019] [Revised: 09/08/2019] [Accepted: 09/09/2019] [Indexed: 01/21/2023]
Abstract
Identifying the direct target genes of response regulators (RRs) of a bacterial two-component system (TCS) is critical to understand the roles of TCS in bacterial environmental adaption and pathogenesis. Actinobacillus pleuropneumoniae is an important respiratory bacterial pathogen that causes considerable economic losses to swine industry worldwide. The targets of A. pleuropneumoniae NarP (nitrate/nitrite RR), which is the cognate RR of the nitrate/nitrite sensor histidine kinase NarQ, are still unknown. In the present study, a DNA-affinity-purified sequencing (DAP-Seq) approach was established. The upstream regions of a total of 131 candidate genes from the genome of A. pleuropneumoniae were co-purified with the activated NarP protein. Electrophoretic mobility shift assay (EMSA) results confirmed the interactions of NarP with the promoter regions of five selected target genes, including dmsA, pgaA, ftpA, cstA and ushA. The EMSA-confirmed target genes were significantly up-regulated in the narP-deleted mutant in the presence of additional nitrate, whilst the transcriptional changes were restored in the complemented strain. The NarP binding motif in the upstream regions of the target genes dmsA and ftpA were further identified and confirmed by EMSA using the truncated binding motif. The NarP binding sites were present in a total of 25.2% of the DNA fragments captured by DAP-Seq. These results demonstrated that the established DAP-Seq method is effective for exploring the direct targets of RRs of bacterial TCSs and that the A. pleuropneumoniae NarP could be a repressor in response to nitrate.
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Affiliation(s)
- Qiuhong Zhang
- State Key Laboratory of Agricultural Microbiology, College of Veterinary Medicine, Huazhong Agricultural University, Wuhan, Hubei, 430070, China; Key Laboratory of Preventive Veterinary Medicine in Hubei Province, The Cooperative Innovation Center for Sustainable Pig Production, Wuhan, Hubei, 430070, China
| | - Qi Huang
- State Key Laboratory of Agricultural Microbiology, College of Veterinary Medicine, Huazhong Agricultural University, Wuhan, Hubei, 430070, China; Key Laboratory of Preventive Veterinary Medicine in Hubei Province, The Cooperative Innovation Center for Sustainable Pig Production, Wuhan, Hubei, 430070, China
| | - Qiong Fang
- State Key Laboratory of Agricultural Microbiology, College of Veterinary Medicine, Huazhong Agricultural University, Wuhan, Hubei, 430070, China; Key Laboratory of Preventive Veterinary Medicine in Hubei Province, The Cooperative Innovation Center for Sustainable Pig Production, Wuhan, Hubei, 430070, China
| | - Haotian Li
- State Key Laboratory of Agricultural Microbiology, College of Veterinary Medicine, Huazhong Agricultural University, Wuhan, Hubei, 430070, China; Key Laboratory of Preventive Veterinary Medicine in Hubei Province, The Cooperative Innovation Center for Sustainable Pig Production, Wuhan, Hubei, 430070, China
| | - Hao Tang
- State Key Laboratory of Agricultural Microbiology, College of Veterinary Medicine, Huazhong Agricultural University, Wuhan, Hubei, 430070, China; Key Laboratory of Preventive Veterinary Medicine in Hubei Province, The Cooperative Innovation Center for Sustainable Pig Production, Wuhan, Hubei, 430070, China
| | - Geng Zou
- State Key Laboratory of Agricultural Microbiology, College of Veterinary Medicine, Huazhong Agricultural University, Wuhan, Hubei, 430070, China; Key Laboratory of Preventive Veterinary Medicine in Hubei Province, The Cooperative Innovation Center for Sustainable Pig Production, Wuhan, Hubei, 430070, China
| | - Dong Wang
- State Key Laboratory of Agricultural Microbiology, College of Veterinary Medicine, Huazhong Agricultural University, Wuhan, Hubei, 430070, China; Key Laboratory of Preventive Veterinary Medicine in Hubei Province, The Cooperative Innovation Center for Sustainable Pig Production, Wuhan, Hubei, 430070, China
| | - Siqi Li
- State Key Laboratory of Agricultural Microbiology, College of Veterinary Medicine, Huazhong Agricultural University, Wuhan, Hubei, 430070, China; Key Laboratory of Preventive Veterinary Medicine in Hubei Province, The Cooperative Innovation Center for Sustainable Pig Production, Wuhan, Hubei, 430070, China
| | - Weicheng Bei
- State Key Laboratory of Agricultural Microbiology, College of Veterinary Medicine, Huazhong Agricultural University, Wuhan, Hubei, 430070, China; Key Laboratory of Preventive Veterinary Medicine in Hubei Province, The Cooperative Innovation Center for Sustainable Pig Production, Wuhan, Hubei, 430070, China; Key Laboratory of Development of Veterinary Diagnostic Products, Ministry of Agriculture and Rural Affairs of the People's Republic of China, Wuhan, Hubei, 430070, China; International Research Center for Animal Disease, Ministry of Science and Technology of the People's Republic of China, Wuhan, Hubei, 430070, China
| | - Huanchun Chen
- State Key Laboratory of Agricultural Microbiology, College of Veterinary Medicine, Huazhong Agricultural University, Wuhan, Hubei, 430070, China; Key Laboratory of Preventive Veterinary Medicine in Hubei Province, The Cooperative Innovation Center for Sustainable Pig Production, Wuhan, Hubei, 430070, China; Key Laboratory of Development of Veterinary Diagnostic Products, Ministry of Agriculture and Rural Affairs of the People's Republic of China, Wuhan, Hubei, 430070, China; International Research Center for Animal Disease, Ministry of Science and Technology of the People's Republic of China, Wuhan, Hubei, 430070, China
| | - Lu Li
- State Key Laboratory of Agricultural Microbiology, College of Veterinary Medicine, Huazhong Agricultural University, Wuhan, Hubei, 430070, China; Key Laboratory of Preventive Veterinary Medicine in Hubei Province, The Cooperative Innovation Center for Sustainable Pig Production, Wuhan, Hubei, 430070, China; Key Laboratory of Development of Veterinary Diagnostic Products, Ministry of Agriculture and Rural Affairs of the People's Republic of China, Wuhan, Hubei, 430070, China; International Research Center for Animal Disease, Ministry of Science and Technology of the People's Republic of China, Wuhan, Hubei, 430070, China.
| | - Rui Zhou
- State Key Laboratory of Agricultural Microbiology, College of Veterinary Medicine, Huazhong Agricultural University, Wuhan, Hubei, 430070, China; Key Laboratory of Preventive Veterinary Medicine in Hubei Province, The Cooperative Innovation Center for Sustainable Pig Production, Wuhan, Hubei, 430070, China; Key Laboratory of Development of Veterinary Diagnostic Products, Ministry of Agriculture and Rural Affairs of the People's Republic of China, Wuhan, Hubei, 430070, China; International Research Center for Animal Disease, Ministry of Science and Technology of the People's Republic of China, Wuhan, Hubei, 430070, China.
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17
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Wang L, Liu B, Liu Y, Sun Y, Liu W, Yu D, Zhao ZK. Escherichia coli Strain Designed for Characterizing in Vivo Functions of Nicotinamide Adenine Dinucleotide Analogues. Org Lett 2019; 21:3218-3222. [PMID: 30995052 DOI: 10.1021/acs.orglett.9b00935] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/28/2023]
Abstract
An Escherichia coli strain was constructed for the efficient import of nicotinamide adenine dinucleotide (NAD) analogues into cells by limiting extracellular degradation while expressing an efficient NAD importer. In vivo functions of three NAD analogues were characterized. Nicotinamide hypoxanthine dinucleotide was identified as an inhibitor of NAD synthesis. Nicotinamide cytosine dinucleotide had excellent biocompatibility and was used for characterizing a growth-dependent degradation of in vivo nicotinamide cofactors.
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Affiliation(s)
- Lei Wang
- School of Chemical Engineering , Northeast Electric Power University , Jilin 132012 , China
| | - Bin Liu
- School of Chemical Engineering , Northeast Electric Power University , Jilin 132012 , China
| | - Yuxue Liu
- Division of Biotechnology , Dalian Institute of Chemical Physics , CAS, Dalian 116023 , China
| | - Yue Sun
- School of Chemical Engineering , Northeast Electric Power University , Jilin 132012 , China
| | - Wujun Liu
- Institute of Cancer Stem Cell , Dalian Medical University , Dalian 116044 , China
| | - Dayu Yu
- School of Chemical Engineering , Northeast Electric Power University , Jilin 132012 , China
| | - Zongbao K Zhao
- Division of Biotechnology , Dalian Institute of Chemical Physics , CAS, Dalian 116023 , China
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18
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Han Q, Eiteman MA. Enhancement of NAD(H) pool for formation of oxidized biochemicals in Escherichia coli. J Ind Microbiol Biotechnol 2018; 45:939-950. [PMID: 30159648 DOI: 10.1007/s10295-018-2072-y] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2018] [Accepted: 08/13/2018] [Indexed: 10/28/2022]
Abstract
The NAD+/NADH ratio and the total NAD(H) play important roles for whole-cell biochemical redox transformations. After the carbon source is exhausted, the degradation of NAD(H) could contribute to a decline in the rate of a desired conversion. In this study, methods to slow the native rate of NAD(H) degradation were examined using whole-cell Escherichia coli with two model oxidative NAD+-dependent biotransformations. A high phosphate concentration (50 mM) was observed to slow NAD(H) degradation. We also constructed E. coli strains with deletions in genes coding several enzymes involved in NAD+ degradation. In shake-flask experiments, the total NAD(H) concentration positively correlated with conversion of xylitol to L-xylulose by xylitol 4-dehydrogenase, and the greatest conversion (80%) was observed using MG1655 nadR nudC mazG/pZE12-xdh/pCS27-nox. Controlled 1-L batch processes comparing E. coli nadR nudC mazG with a wild-type background strain demonstrated a 30% increase in final L-xylulose concentration (5.6 vs. 7.9 g/L) and a 25% increase in conversion (0.53 vs. 0.66 g/g). MG1655 nadR nudC mazG was also examined for the conversion of galactitol to L-tagatose by galactitol 2-dehydrogenase. A batch process using 15 g/L glycerol and 10 g/L galactitol generated over 9.4 g/L L-tagatose, corresponding to 90% conversion and a yield of 0.95 g L-tagatose/g galactitol consumed. The results demonstrate the value of minimizing NAD(H) degradation as a means to improve NAD+-dependent biotransformations.
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Affiliation(s)
- Qi Han
- School of Chemical Materials and Biomedical Engineering, University of Georgia, Athens, GA, 30602, USA
| | - Mark A Eiteman
- School of Chemical Materials and Biomedical Engineering, University of Georgia, Athens, GA, 30602, USA.
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19
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Microbial cell factories for the sustainable manufacturing of B vitamins. Curr Opin Biotechnol 2018; 56:18-29. [PMID: 30138794 DOI: 10.1016/j.copbio.2018.07.006] [Citation(s) in RCA: 67] [Impact Index Per Article: 11.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2018] [Revised: 07/20/2018] [Accepted: 07/23/2018] [Indexed: 12/16/2022]
Abstract
Vitamins are essential compounds in human and animal diets. Their demand is increasing globally in food, feed, cosmetics, chemical and pharmaceutical industries. Most current production methods are unsustainable because they use non-renewable sources and often generate hazardous waste. Many microorganisms produce vitamins naturally, but their corresponding metabolic pathways are tightly regulated since vitamins are needed only in catalytic amounts. Metabolic engineering is accelerating the development of microbial cell factories for vitamins that could compete with chemical methods that have been optimized over decades, but scientific hurdles remain. Additional technological and regulatory issues need to be overcome for innovative bioprocesses to reach the market. Here, we review the current state of development and challenges for fermentative processes for the B vitamin group.
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20
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Wang L, Ji D, Liu Y, Wang Q, Wang X, Zhou YJ, Zhang Y, Liu W, Zhao ZK. Synthetic Cofactor-Linked Metabolic Circuits for Selective Energy Transfer. ACS Catal 2017. [DOI: 10.1021/acscatal.6b03579] [Citation(s) in RCA: 34] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Affiliation(s)
- Lei Wang
- Division
of Biotechnology, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian 116023, China
- Dalian
National Laboratory for Clean Energy, Dalian Institute of Chemical
Physics, Chinese Academy of Sciences, Dalian 116023, China
- Institute
of Green Conversion of Biological Bioresource and Metabolic Engineering,
College of Chemical Engineering, Northeast Electric Power University, Jilin 132012, China
| | - Debin Ji
- Division
of Biotechnology, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian 116023, China
| | - Yuxue Liu
- Division
of Biotechnology, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian 116023, China
| | - Qian Wang
- Division
of Biotechnology, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian 116023, China
- Dalian
National Laboratory for Clean Energy, Dalian Institute of Chemical
Physics, Chinese Academy of Sciences, Dalian 116023, China
| | - Xueying Wang
- Division
of Biotechnology, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian 116023, China
| | - Yongjin J. Zhou
- Division
of Biotechnology, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian 116023, China
| | - Yixin Zhang
- Division
of Biotechnology, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian 116023, China
| | - Wujun Liu
- Division
of Biotechnology, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian 116023, China
- Dalian
National Laboratory for Clean Energy, Dalian Institute of Chemical
Physics, Chinese Academy of Sciences, Dalian 116023, China
| | - Zongbao K. Zhao
- Division
of Biotechnology, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian 116023, China
- Dalian
National Laboratory for Clean Energy, Dalian Institute of Chemical
Physics, Chinese Academy of Sciences, Dalian 116023, China
- State Key
Laboratory of Catalysis, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian 116023, China
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21
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Zakataeva NP, Romanenkov DV, Yusupova YR, Skripnikova VS, Asahara T, Gronskiy SV. Identification, Heterologous Expression, and Functional Characterization of Bacillus subtilis YutF, a HAD Superfamily 5'-Nucleotidase with Broad Substrate Specificity. PLoS One 2016; 11:e0167580. [PMID: 27907199 PMCID: PMC5132288 DOI: 10.1371/journal.pone.0167580] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2016] [Accepted: 11/16/2016] [Indexed: 11/25/2022] Open
Abstract
5'-nucleotidases (EC 3.1.3.5) catalyze the hydrolytic dephosphorylation of 5'-ribonucleotides and 5'-deoxyribonucleotides as well as complex nucleotides, such as uridine 5'-diphosphoglucose (UDP-glucose), nicotinamide adenine dinucleotide and flavin adenine dinucleotide, to their corresponding nucleosides plus phosphate. These enzymes have been found in diverse species in intracellular and membrane-bound, surface-localized forms. Soluble forms of 5'-nucleotidases belong to the ubiquitous haloacid dehalogenase superfamily (HADSF) and have been shown to be involved in the regulation of nucleotide, nucleoside and nicotinamide adenine dinucleotide (NAD+) pools. Despite the important role of 5'-nucleotidases in cellular metabolism, only a few of these enzymes have been characterized in the Gram-positive bacterium Bacillus subtilis, the workhorse industrial microorganism included in the Food and Drug Administration’s GRAS (generally regarded as safe) list. In the present study, we report the identification of a novel 5'-nucleotidase gene from B. subtilis, yutF, which comprises 771 bp encoding a 256-amino-acid protein belonging to the IIA subfamily of the HADSF. The gene product is responsible for the major p-nitrophenyl phosphatase activity in B. subtilis. The yutF gene was overexpressed in Escherichia coli, and its product fused to a polyhistidine tag was purified and biochemically characterized as a soluble 5'-nucleotidase with broad substrate specificity. The recombinant YutF protein was found to hydrolyze various purine and pyrimidine 5'-nucleotides, showing preference for 5'-nucleoside monophosphates and, specifically, 5'-XMP. Recombinant YutF also exhibited phosphohydrolase activity toward nucleotide precursors, ribose-5-phosphate and 5-phosphoribosyl-1-pyrophosphate. Determination of the kinetic parameters of the enzyme revealed a low substrate specificity (Km values in the mM concentration range) and modest catalytic efficiencies with respect to substrates. An initial study of the regulation of yutF expression showed that the yutF gene is a component of the yutDEF transcription unit and that YutF overproduction positively influences yutDEF expression.
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Affiliation(s)
| | | | | | | | - Takayuki Asahara
- Research Institute for Bioscience Products & Fine Chemicals, Ajinomoto Co., Inc, Kawasaki, Kanagawa, Japan
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Sun Y, Ye Q, Wu M, Wu Y, Zhang C, Yan W. High yields and soluble expression of superoxide dismutases in Escherichia coli due to the HIV-1 Tat peptide via increases in mRNA transcription. Exp Mol Med 2016; 48:e264. [PMID: 27741225 PMCID: PMC5099423 DOI: 10.1038/emm.2016.91] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2016] [Revised: 04/18/2016] [Accepted: 04/21/2016] [Indexed: 11/29/2022] Open
Abstract
This study aimed to validate the high yield and soluble expression of proteins carrying the transactivator of transcription (Tat) peptide tag, and further explored the potential mechanism by which the Tat tag increases expression. Escherichia coli superoxide dismutase (SOD) proteins, including SodA, SodB and SodC, were selected for analysis. As expected, the yields and the solubility of Tat-tagged proteins were higher than those of Tat-free proteins, and similar results were observed for the total SOD enzyme activity. Bacterial cells that overexpressed Tat-tagged proteins exhibited increased anti-paraquat activity compared with those expressing Tat-free proteins that manifested as SodA>SodC>SodB. When compared with an MG1655 wild-type strain, the growth of a ΔSodA mutant strain was found to be inhibited after paraquat treatment; the growth of ΔSodB and ΔSodC mutant strains was also slightly inhibited. The mRNA transcript level of genes encoding Tat-tagged proteins was higher than that of genes encoding Tat-free proteins. Furthermore, the α-helix and turn of Tat-tagged proteins were higher than those of Tat-free proteins, but the β-sheet and random coil content was lower. These results indicated that the incorporation of the Tat core peptide as a significant basic membrane transduction peptide in fusion proteins could increase mRNA transcripts and promote the high yield and soluble expression of heterologous proteins in E. coli.
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Affiliation(s)
- Yangdong Sun
- Department of Biological Engineering, College of Pharmacy, Jilin University, Changchun, China
| | - Qiao Ye
- Beijing Institute of Radiation Medicine, State Key Laboratory of Proteomics, Cognitive and Mental Health Research Center, Beijing, China
| | - Min Wu
- Institute of Protein Research, Tongji University, Shanghai, China
| | - Yonghong Wu
- Beijing Institute of Radiation Medicine, State Key Laboratory of Proteomics, Cognitive and Mental Health Research Center, Beijing, China
| | - Chenggang Zhang
- Beijing Institute of Radiation Medicine, State Key Laboratory of Proteomics, Cognitive and Mental Health Research Center, Beijing, China
| | - Weiqun Yan
- Department of Biological Engineering, College of Pharmacy, Jilin University, Changchun, China
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Ali TH, El-Ghonemy DH. Purification and characterization of the enzymes involved in nicotinamide adenine dinucleotide degradation by Penicillium brevicompactum NRC 829. 3 Biotech 2016; 6:34. [PMID: 28330104 PMCID: PMC4722047 DOI: 10.1007/s13205-015-0349-7] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2015] [Accepted: 08/07/2015] [Indexed: 10/26/2022] Open
Abstract
The present study was conducted to investigate a new pathway for the degradation of nicotinamide adenine dinucleotide (NAD) by Penicillium brevicompactum NRC 829 extracts. Enzymes involved in the hydrolysis of NAD, i.e. alkaline phosphatase, aminohydrolase and glycohydrolase were determined. Alkaline phosphatase was found to catalyse the sequential hydrolysis of two phosphate moieties of NAD molecule to nicotinamide riboside plus adenosine. Adenosine was then deaminated by aminohydrolase to inosine and ammonia. While glycohydrolase catalyzed the hydrolysis of the nicotinamide-ribosidic bond of NAD+ to produce nicotinamide and ADP-ribose in equimolar amounts, enzyme purification through a 3-step purification procedure revealed the existence of two peaks of alkaline phosphatases, and one peak contained deaminase and glycohydrolase activities. NAD deaminase was purified to homogeneity as estimated by sodium dodecyl sulphate-polyacrylamide gel electrophoresis with an apparent molecular mass of 91 kDa. Characterization and determination of some of NAD aminohydrolase kinetic properties were conducted due to its biological role in the regulation of cellular NAD level. The results also revealed that NAD did not exert its feedback control on nicotinamide amidase produced by P. brevicompactum.
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Abstract
Calcineurin-like metallophosphoesterases (MPEs) form a large superfamily of binuclear metal-ion-centre-containing enzymes that hydrolyse phosphomono-, phosphodi- or phosphotri-esters in a metal-dependent manner. The MPE domain is found in Mre11/SbcD DNA-repair enzymes, mammalian phosphoprotein phosphatases, acid sphingomyelinases, purple acid phosphatases, nucleotidases and bacterial cyclic nucleotide phosphodiesterases. Despite this functional diversity, MPEs show a remarkably similar structural fold and active-site architecture. In the present review, we summarize the available structural, biochemical and functional information on these proteins. We also describe how diversification and specialization of the core MPE fold in various MPEs is achieved by amino acid substitution in their active sites, metal ions and regulatory effects of accessory domains. Finally, we discuss emerging roles of these proteins as non-catalytic protein-interaction scaffolds. Thus we view the MPE superfamily as a set of proteins with a highly conserved structural core that allows embellishment to result in dramatic and niche-specific diversification of function.
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