1
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Wohlgemuth R. Selective Biocatalytic Defunctionalization of Raw Materials. CHEMSUSCHEM 2022; 15:e202200402. [PMID: 35388636 DOI: 10.1002/cssc.202200402] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/24/2022] [Revised: 04/05/2022] [Indexed: 06/14/2023]
Abstract
Biobased raw materials, such as carbohydrates, amino acids, nucleotides, or lipids contain valuable functional groups with oxygen and nitrogen atoms. An abundance of many functional groups of the same type, such as primary or secondary hydroxy groups in carbohydrates, however, limits the synthetic usefulness if similar reactivities cannot be differentiated. Therefore, selective defunctionalization of highly functionalized biobased starting materials to differentially functionalized compounds can provide a sustainable access to chiral synthons, even in case of products with fewer functional groups. Selective defunctionalization reactions, without affecting other functional groups of the same type, are of fundamental interest for biocatalytic reactions. Controlled biocatalytic defunctionalizations of biobased raw materials are attractive for obtaining valuable platform chemicals and building blocks. The biocatalytic removal of functional groups, an important feature of natural metabolic pathways, can also be utilized in a systemic strategy for sustainable metabolite synthesis.
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Affiliation(s)
- Roland Wohlgemuth
- Institute of Molecular and Industrial Biotechnology, Lodz University of Technology Łódź, 90-537, Lodz, Poland
- Swiss Coordination Committee Biotechnology (SKB), 8002, Zurich, Switzerland
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2
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Vogel U, Beerens K, Desmet T. Nucleotide sugar dehydratases: Structure, mechanism, substrate specificity, and application potential. J Biol Chem 2022; 298:101809. [PMID: 35271853 PMCID: PMC8987622 DOI: 10.1016/j.jbc.2022.101809] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2021] [Revised: 02/24/2022] [Accepted: 02/28/2022] [Indexed: 11/14/2022] Open
Abstract
Nucleotide sugar (NS) dehydratases play a central role in the biosynthesis of deoxy and amino sugars, which are involved in a variety of biological functions in all domains of life. Bacteria are true masters of deoxy sugar biosynthesis as they can produce a wide range of highly specialized monosaccharides. Indeed, deoxy and amino sugars play important roles in the virulence of gram-positive and gram-negative pathogenic species and are additionally involved in the biosynthesis of diverse macrolide antibiotics. The biosynthesis of deoxy sugars relies on the activity of NS dehydratases, which can be subdivided into three groups based on their structure and reaction mechanism. The best-characterized NS dehydratases are the 4,6-dehydratases that, together with the 5,6-dehydratases, belong to the NS-short-chain dehydrogenase/reductase superfamily. The other two groups are the less abundant 2,3-dehydratases that belong to the Nudix hydrolase superfamily and 3-dehydratases, which are related to aspartame aminotransferases. 4,6-Dehydratases catalyze the first step in all deoxy sugar biosynthesis pathways, converting nucleoside diphosphate hexoses to nucleoside diphosphate-4-keto-6-deoxy hexoses, which in turn are further deoxygenated by the 2,3- and 3-dehydratases to form dideoxy and trideoxy sugars. In this review, we give an overview of the NS dehydratases focusing on the comparison of their structure and reaction mechanisms, thereby highlighting common features, and investigating differences between closely related members of the same superfamilies.
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Affiliation(s)
- Ulrike Vogel
- Centre for Synthetic Biology (CSB) - Unit for Biocatalysis and Enzyme Engineering, Faculty of Bioscience Engineering, Ghent University, Gent, Belgium
| | - Koen Beerens
- Centre for Synthetic Biology (CSB) - Unit for Biocatalysis and Enzyme Engineering, Faculty of Bioscience Engineering, Ghent University, Gent, Belgium
| | - Tom Desmet
- Centre for Synthetic Biology (CSB) - Unit for Biocatalysis and Enzyme Engineering, Faculty of Bioscience Engineering, Ghent University, Gent, Belgium.
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3
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Calcium-Phosphate Combination Enhances Spinosad Production in Saccharopolyspora spinosa via Regulation of Fatty Acid Metabolism. Appl Biochem Biotechnol 2022; 194:2528-2541. [PMID: 35166996 DOI: 10.1007/s12010-022-03799-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 12/31/2021] [Indexed: 11/02/2022]
Abstract
Phosphate concentration above 10 mM reduces the production of many secondary metabolites; however, the phenomenon is not mechanistically understood yet. Specifically, the problem of phosphorus limitation in antibiotic production remains unresolved. This study investigates the phosphorus inhibition effect on spinosad production and alleviates it by calcium and phosphate supplementation to fermentation media. Furthermore, we examined the mechanism of fatty acids-induced increase in polyketides production. Four phosphates that were supplemented into the fermentation media include NaH2PO4, Na2HPO4, KH2PO4, and K2HPO4 and NaH2PO4 was found to be the most effective phosphate. Under the optimal phosphate condition of supplementing 20 mM NaH2PO4 on the fourth day and 5 g/L CaCO3, the maximal spinosad production reached 520 mg/L, showing a 1.65-fold increase over the control treatment. In the NaH2PO4-CaCO3 system, the de novo fatty acid biosynthesis was significantly downregulated while spinosad biosynthesis and β-oxidation were upregulated. The coordination of de novo fatty acid biosynthesis and β-oxidation promoted intracellular acetyl-CoA concentration. The results demonstrate that NaH2PO4-CaCO3 combined addition is a simple and effective strategy to alleviate phosphorus inhibition effect through the regulation of fatty acid metabolism and accumulation of immediate precursors. This information improves our understanding of phosphates' influence on the large-scale production of polyketides.
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4
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An Z, Tao H, Wang Y, Xia B, Zou Y, Fu S, Fang F, Sun X, Huang R, Xia Y, Deng Z, Liu R, Liu T. Increasing the heterologous production of spinosad in Streptomyces albus J1074 by regulating biosynthesis of its polyketide skeleton. Synth Syst Biotechnol 2021; 6:292-301. [PMID: 34584996 PMCID: PMC8453208 DOI: 10.1016/j.synbio.2021.09.008] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2021] [Revised: 08/27/2021] [Accepted: 09/13/2021] [Indexed: 11/18/2022] Open
Abstract
Spinosyns are natural broad-spectrum biological insecticides with a double glycosylated polyketide structure that are produced by aerobic fermentation of the actinomycete, Saccharopolyspora spinosa. However, their large-scale overproduction is hindered by poorly understood bottlenecks in optimizing the original strain, and poor adaptability of the heterologous strain to the production of spinosyn. In this study, we genetically engineered heterologous spinosyn-producer Streptomyces albus J1074 and optimized the fermentation to improve the production of spinosad (spinosyn A and spinosyn D) based on our previous work. We systematically investigated the result of overexpressing polyketide synthase genes (spnA, B, C, D, E) using a constitutive promoter on the spinosad titer in S. albus J1074. The supply of polyketide synthase precursors was then increased to further improve spinosad production. Finally, increasing or replacing the carbon source of the culture medium resulted in a final spinosad titer of ∼70 mg/L, which is the highest titer of spinosad achieved in heterologous Streptomyces species. This research provides useful strategies for efficient heterologous production of natural products.
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Key Words
- 2-[2-hydroxy-1,1-bis(hydroxymethyl)ethyl)amino]ethanesulfonic acid, (TES)
- HPLC-high resolution mass spectrometer, (HPLC-HRMS)
- Heterologous production
- Luria−Bertani, (LB)
- Polyketide
- Polyketide synthase
- Spinosad
- Spinosyn
- Streptomyces
- acetyl-CoA carboxylase, (ACC)
- acetyl-CoA synthetase, (AcsA)
- biosynthetic gene cluster, (BGC)
- high-performance liquid chromatography, (HPLC)
- limit of detection, (LoD)
- overlap extension-polymerase chain reaction, (OE-PCR)
- polyketide synthase, (PKS)
- propionyl-CoA carboxylase, (PCC)
- soya flour mannitol, (SFM)
- β and ε subunits of Acc, (AccBE)
- β and ε subunits of PCC, (PccBE)
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Affiliation(s)
- Ziheng An
- Key Laboratory of Combinatorial Biosynthesis and Drug Discovery, Ministry of Education and Wuhan University School of Pharmaceutical Sciences, Wuhan, 430071, PR China
| | - Hui Tao
- Key Laboratory of Combinatorial Biosynthesis and Drug Discovery, Ministry of Education and Wuhan University School of Pharmaceutical Sciences, Wuhan, 430071, PR China
| | - Yong Wang
- Key Laboratory of Combinatorial Biosynthesis and Drug Discovery, Ministry of Education and Wuhan University School of Pharmaceutical Sciences, Wuhan, 430071, PR China
| | - Bingqing Xia
- Key Laboratory of Combinatorial Biosynthesis and Drug Discovery, Ministry of Education and Wuhan University School of Pharmaceutical Sciences, Wuhan, 430071, PR China
| | - Yang Zou
- Key Laboratory of Combinatorial Biosynthesis and Drug Discovery, Ministry of Education and Wuhan University School of Pharmaceutical Sciences, Wuhan, 430071, PR China
| | - Shuai Fu
- Key Laboratory of Combinatorial Biosynthesis and Drug Discovery, Ministry of Education and Wuhan University School of Pharmaceutical Sciences, Wuhan, 430071, PR China
| | - Fang Fang
- Key Laboratory of Combinatorial Biosynthesis and Drug Discovery, Ministry of Education and Wuhan University School of Pharmaceutical Sciences, Wuhan, 430071, PR China
| | - Xiao Sun
- Key Laboratory of Combinatorial Biosynthesis and Drug Discovery, Ministry of Education and Wuhan University School of Pharmaceutical Sciences, Wuhan, 430071, PR China
| | - Renqiong Huang
- Key Laboratory of Combinatorial Biosynthesis and Drug Discovery, Ministry of Education and Wuhan University School of Pharmaceutical Sciences, Wuhan, 430071, PR China
| | - Yao Xia
- Key Laboratory of Combinatorial Biosynthesis and Drug Discovery, Ministry of Education and Wuhan University School of Pharmaceutical Sciences, Wuhan, 430071, PR China
| | - Zixin Deng
- Key Laboratory of Combinatorial Biosynthesis and Drug Discovery, Ministry of Education and Wuhan University School of Pharmaceutical Sciences, Wuhan, 430071, PR China
| | - Ran Liu
- Key Laboratory of Combinatorial Biosynthesis and Drug Discovery, Ministry of Education and Wuhan University School of Pharmaceutical Sciences, Wuhan, 430071, PR China
- CAS Key Laboratory of Quantitative Engineering Biology, Shenzhen Institute of Synthetic Biology, Shenzhen Institute of Advanced Technology, Chinese Academy of Sciences, Shenzhen, 518055, PR China
| | - Tiangang Liu
- Key Laboratory of Combinatorial Biosynthesis and Drug Discovery, Ministry of Education and Wuhan University School of Pharmaceutical Sciences, Wuhan, 430071, PR China
- Hubei Engineering Laboratory for Synthetic Microbiology, Wuhan Institute of Biotechnology, Wuhan, 430075, PR China
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5
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Nie QY, Ji ZY, Hu Y, Tang GL. Characterization of Highly Reductive Modification of Tetracycline D-Ring Reveals Enzymatic Conversion of Enone to Alkane. ACS Catal 2021. [DOI: 10.1021/acscatal.1c01226] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023]
Affiliation(s)
- Qiu-Yue Nie
- State Key Laboratory of Bioorganic and Natural Products Chemistry, Center for Excellence in Molecular Synthesis, Shanghai Institute of Organic Chemistry, University of Chinese Academy of Sciences, Chinese Academy of Sciences, 345 Lingling Road, Shanghai 200032, People’s Republic of China
| | - Zhen-Yu Ji
- State Key Laboratory of Bioorganic and Natural Products Chemistry, Center for Excellence in Molecular Synthesis, Shanghai Institute of Organic Chemistry, University of Chinese Academy of Sciences, Chinese Academy of Sciences, 345 Lingling Road, Shanghai 200032, People’s Republic of China
| | - Yu Hu
- State Key Laboratory of Bioorganic and Natural Products Chemistry, Center for Excellence in Molecular Synthesis, Shanghai Institute of Organic Chemistry, University of Chinese Academy of Sciences, Chinese Academy of Sciences, 345 Lingling Road, Shanghai 200032, People’s Republic of China
| | - Gong-Li Tang
- State Key Laboratory of Bioorganic and Natural Products Chemistry, Center for Excellence in Molecular Synthesis, Shanghai Institute of Organic Chemistry, University of Chinese Academy of Sciences, Chinese Academy of Sciences, 345 Lingling Road, Shanghai 200032, People’s Republic of China
- School of Chemistry and Materials Science Hangzhou Institute for Advanced Study, University of Chinese Academy of Sciences, 1 Sub-lane Xiangshan, Hangzhou 310024, People’s Republic of China
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6
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Yeh YC, Kim HJ, Liu HW. Mechanistic Investigation of 1,2-Diol Dehydration of Paromamine Catalyzed by the Radical S-Adenosyl-l-methionine Enzyme AprD4. J Am Chem Soc 2021; 143:5038-5043. [PMID: 33784078 DOI: 10.1021/jacs.1c00076] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
AprD4 is a radical S-adenosyl-l-methionine (SAM) enzyme catalyzing C3'-deoxygenation of paromamine to form 4'-oxo-lividamine. It is the only 1,2-diol dehydratase in the radical SAM enzyme superfamily that has been identified and characterized in vitro. The AprD4 catalyzed 1,2-diol dehydration is a key step in the biosynthesis of several C3'-deoxy-aminoglycosides. While the regiochemistry of the hydrogen atom abstraction catalyzed by AprD4 has been established, the mechanism of the subsequent chemical transformation remains not fully understood. To investigate the mechanism, several substrate analogues were synthesized and their fates upon incubation with AprD4 were analyzed. The results support a mechanism involving formation of a ketyl radical intermediate followed by direct elimination of the C3'-hydroxyl group rather than that of a gem-diol intermediate generated via 1,2-migration of the C3'-hydroxyl group to C4'. The stereochemistry of hydrogen atom incorporation after radical-mediated dehydration was also established.
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Affiliation(s)
- Yu-Cheng Yeh
- Department of Chemistry, University of Texas at Austin, Austin, Texas 78712, United States
| | - Hak Joong Kim
- Department of Chemistry, University of Texas at Austin, Austin, Texas 78712, United States
| | - Hung-Wen Liu
- Department of Chemistry, University of Texas at Austin, Austin, Texas 78712, United States.,Division of Chemical Biology and Medicinal Chemistry, College of Pharmacy, University of Texas at Austin, Austin, Texas 78712, United States
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7
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Zhou S, Chen X, Ni X, Liu Y, Zhang H, Dong M, Xia H. Pyridoxal-5'-phosphate-dependent enzyme GenB3 Catalyzes C-3',4'-dideoxygenation in gentamicin biosynthesis. Microb Cell Fact 2021; 20:65. [PMID: 33750386 PMCID: PMC7941887 DOI: 10.1186/s12934-021-01558-7] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2020] [Accepted: 03/03/2021] [Indexed: 11/20/2022] Open
Abstract
Background The C-3′,4′-dideoxygenation structure in gentamicin can prevent deactivation by aminoglycoside 3′-phosphotransferase (APH(3′)) in drug-resistant pathogens. However, the enzyme catalyzing the dideoxygenation step in the gentamicin biosynthesis pathway remains unknown. Results Here, we report that GenP catalyzes 3′ phosphorylation of the gentamicin biosynthesis intermediates JI-20A, JI-20Ba, and JI-20B. We further demonstrate that the pyridoxal-5′-phosphate (PLP)-dependent enzyme GenB3 uses these phosphorylated substrates to form 3′,4′-dideoxy-4′,5′-ene-6′-oxo products. The following C-6′-transamination and the GenB4-catalyzed reduction of 4′,5′-olefin lead to the formation of gentamicin C. To the best of our knowledge, GenB3 is the first PLP-dependent enzyme catalyzing dideoxygenation in aminoglycoside biosynthesis. Conclusions This discovery solves a long-standing puzzle in gentamicin biosynthesis and enriches our knowledge of the chemistry of PLP-dependent enzymes. Interestingly, these results demonstrate that to evade APH(3′) deactivation by pathogens, the gentamicin producers evolved a smart strategy, which utilized their own APH(3′) to activate hydroxyls as leaving groups for the 3′,4′-dideoxygenation in gentamicin biosynthesis. Supplementary Information The online version contains supplementary material available at 10.1186/s12934-021-01558-7.
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Affiliation(s)
- Shaotong Zhou
- School of Life Science and Biopharmaceutics, Shenyang Pharmaceutical University, Benxi, 117004, China
| | - Xiaotang Chen
- School of Life Science and Biopharmaceutics, Shenyang Pharmaceutical University, Benxi, 117004, China
| | - Xianpu Ni
- School of Life Science and Biopharmaceutics, Shenyang Pharmaceutical University, Benxi, 117004, China.
| | - Yu Liu
- School of Life Science and Biopharmaceutics, Shenyang Pharmaceutical University, Benxi, 117004, China
| | - Hui Zhang
- School of Life Science and Biopharmaceutics, Shenyang Pharmaceutical University, Benxi, 117004, China
| | - Min Dong
- Frontiers Science Center for Synthetic Biology, Key Laboratory of Systems Bioengineering (MOE), School of Chemical Engineering and Technology, Tianjin University, Tianjin, 300072, China.
| | - Huanzhang Xia
- School of Life Science and Biopharmaceutics, Shenyang Pharmaceutical University, Benxi, 117004, China.
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8
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Mo J, Ye J, Chen H, Hou B, Wu H, Zhang H. Cloning and identification of the Frigocyclinone biosynthetic gene cluster from Streptomyces griseus strain NTK 97. Biosci Biotechnol Biochem 2019; 83:2082-2089. [PMID: 31303144 DOI: 10.1080/09168451.2019.1638755] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/08/2022]
Abstract
Frigocyclinone is a novel antibiotic with antibacterial and anticancer activities. It is produced by both Antarctica-derived Streptomyces griseus NTK 97 and marine sponge-associated Streptomyces sp. M7_15. Here, we first report the biosynthetic gene cluster of frigocyclinone in the S. griseus NTK 97. The frigocyclinone gene cluster spans a DNA region of 33-kb which consists of 30 open reading frames (ORFs), encoding minimal type II polyketide synthase, aromatase and cyclase, redox tailoring enzymes, sugar biosynthesis-related enzymes, C-glycosyltransferase, a resistance protein, and three regulatory proteins. Based on the bioinformatic analysis, a biosynthetic pathway for frigocyclinone was proposed. Second, to verify the cloned gene cluster, CRISPR-Cpf1 mediated gene disruption was conducted. Mutant with the disruption of beta-ketoacyl synthase encoding gene frig20 fully loses the ability of producing frigocyclinone, while inactivating the glycosyltransferase gene frig1 leads to the production of key intermediate of anti-MRSA anthraquinone tetrangomycin.
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Affiliation(s)
- Jian Mo
- State Key Laboratory of Bioreactor Engineering, East China University of Science and Technology , Shanghai , China.,Department of Applied Biology, East China University of Science and Technology , Shanghai , China
| | - Jiang Ye
- State Key Laboratory of Bioreactor Engineering, East China University of Science and Technology , Shanghai , China.,Department of Applied Biology, East China University of Science and Technology , Shanghai , China
| | - Haozhe Chen
- State Key Laboratory of Bioreactor Engineering, East China University of Science and Technology , Shanghai , China.,Department of Applied Biology, East China University of Science and Technology , Shanghai , China
| | - Bingbing Hou
- State Key Laboratory of Bioreactor Engineering, East China University of Science and Technology , Shanghai , China.,Department of Applied Biology, East China University of Science and Technology , Shanghai , China
| | - Haizhen Wu
- State Key Laboratory of Bioreactor Engineering, East China University of Science and Technology , Shanghai , China.,Department of Applied Biology, East China University of Science and Technology , Shanghai , China
| | - Huizhan Zhang
- State Key Laboratory of Bioreactor Engineering, East China University of Science and Technology , Shanghai , China.,Department of Applied Biology, East China University of Science and Technology , Shanghai , China
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9
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Tao H, Zhang Y, Deng Z, Liu T. Strategies for Enhancing the Yield of the Potent Insecticide Spinosad in Actinomycetes. Biotechnol J 2018; 14:e1700769. [DOI: 10.1002/biot.201700769] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2018] [Revised: 05/19/2018] [Indexed: 01/20/2023]
Affiliation(s)
- Hui Tao
- Key Laboratory of Combinatorial Biosynthesis and Drug Discovery; Ministry of Education and Wuhan University School of Pharmaceutical Sciences; Wuhan 430071 P. R. China
| | - Yuchen Zhang
- Key Laboratory of Combinatorial Biosynthesis and Drug Discovery; Ministry of Education and Wuhan University School of Pharmaceutical Sciences; Wuhan 430071 P. R. China
| | - Zixin Deng
- Key Laboratory of Combinatorial Biosynthesis and Drug Discovery; Ministry of Education and Wuhan University School of Pharmaceutical Sciences; Wuhan 430071 P. R. China
- Hubei Engineering Laboratory for Synthetic Microbiology; Wuhan Institute of Biotechnology; Wuhan 430075 P. R. China
- State Key Laboratory of Microbial Metabolism, and School of Life Sciences and Biotechnology; Shanghai Jiao Tong University; Shanghai 200240 P. R. China
| | - Tiangang Liu
- Key Laboratory of Combinatorial Biosynthesis and Drug Discovery; Ministry of Education and Wuhan University School of Pharmaceutical Sciences; Wuhan 430071 P. R. China
- Hubei Engineering Laboratory for Synthetic Microbiology; Wuhan Institute of Biotechnology; Wuhan 430075 P. R. China
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10
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Tan GY, Deng K, Liu X, Tao H, Chang Y, Chen J, Chen K, Sheng Z, Deng Z, Liu T. Heterologous Biosynthesis of Spinosad: An Omics-Guided Large Polyketide Synthase Gene Cluster Reconstitution in Streptomyces. ACS Synth Biol 2017; 6:995-1005. [PMID: 28264562 DOI: 10.1021/acssynbio.6b00330] [Citation(s) in RCA: 66] [Impact Index Per Article: 9.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
With the advent of the genomics era, heterologous gene expression has been used extensively as a means of accessing natural products (NPs) from environmental DNA samples. However, the heterologous production of NPs often has very low efficiency or is unable to produce targeted NPs. Moreover, due to the complicated transcriptional and metabolic regulation of NP biosynthesis in native producers, especially in the cases of genome mining, it is also difficult to rationally and systematically engineer synthetic pathways to improved NPs biosynthetic efficiency. In this study, various strategies ranging from heterologous production of a NP to subsequent application of omics-guided synthetic modules optimization for efficient biosynthesis of NPs with complex structure have been developed. Heterologous production of spinosyn in Streptomyces spp. has been demonstrated as an example of the application of these approaches. Combined with the targeted omics approach, several rate-limiting steps of spinosyn heterologous production in Streptomyces spp. have been revealed. Subsequent engineering work overcame three of selected rate-limiting steps, and the production of spinosad was increased step by step and finally reached 1460 μg/L, which is about 1000-fold higher than the original strain S. albus J1074 (C4I6-M). These results indicated that the omics platform developed in this work was a powerful tool for guiding the rational refactoring of heterologous biosynthetic pathway in Streptomyces host. Additionally, this work lays the foundation for further studies aimed at the more efficient production of spinosyn in a heterologous host. And the strategy developed in this study is expected to become readily adaptable to highly efficient heterologous production of other NPs with complex structure.
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Affiliation(s)
- Gao-Yi Tan
- Key
Laboratory of Combinatorial Biosynthesis and Drug Discovery (Wuhan
University), Ministry of Education, and Wuhan University School of Pharmaceutical Sciences, Wuhan 430071, China
- State
Key Laboratory of Bioreactor Engineering, School of Bioengineering, East China University of Science and Technology, 130 Meilong Road, Shanghai 200237, China
| | - Kunhua Deng
- Key
Laboratory of Combinatorial Biosynthesis and Drug Discovery (Wuhan
University), Ministry of Education, and Wuhan University School of Pharmaceutical Sciences, Wuhan 430071, China
- Hubei
Engineering Laboratory for Synthetic Microbiology, Wuhan Institute of Biotechnology, Wuhan 430075, China
| | - Xinhua Liu
- Key
Laboratory of Combinatorial Biosynthesis and Drug Discovery (Wuhan
University), Ministry of Education, and Wuhan University School of Pharmaceutical Sciences, Wuhan 430071, China
- Hubei
Engineering Laboratory for Synthetic Microbiology, Wuhan Institute of Biotechnology, Wuhan 430075, China
| | - Hui Tao
- Key
Laboratory of Combinatorial Biosynthesis and Drug Discovery (Wuhan
University), Ministry of Education, and Wuhan University School of Pharmaceutical Sciences, Wuhan 430071, China
- Hubei
Engineering Laboratory for Synthetic Microbiology, Wuhan Institute of Biotechnology, Wuhan 430075, China
| | - Yingying Chang
- Key
Laboratory of Combinatorial Biosynthesis and Drug Discovery (Wuhan
University), Ministry of Education, and Wuhan University School of Pharmaceutical Sciences, Wuhan 430071, China
- Hubei
Engineering Laboratory for Synthetic Microbiology, Wuhan Institute of Biotechnology, Wuhan 430075, China
| | - Jia Chen
- Key
Laboratory of Combinatorial Biosynthesis and Drug Discovery (Wuhan
University), Ministry of Education, and Wuhan University School of Pharmaceutical Sciences, Wuhan 430071, China
- Hubei
Engineering Laboratory for Synthetic Microbiology, Wuhan Institute of Biotechnology, Wuhan 430075, China
| | - Kai Chen
- Shenyang Research Institute of Chemical Industry Ltd., Co., SINOCHEM Group, Shengyang 110021, China
| | - Zhi Sheng
- Shenyang Research Institute of Chemical Industry Ltd., Co., SINOCHEM Group, Shengyang 110021, China
| | - Zixin Deng
- Key
Laboratory of Combinatorial Biosynthesis and Drug Discovery (Wuhan
University), Ministry of Education, and Wuhan University School of Pharmaceutical Sciences, Wuhan 430071, China
- Hubei
Engineering Laboratory for Synthetic Microbiology, Wuhan Institute of Biotechnology, Wuhan 430075, China
- State Key Laboratory of Microbial Metabolism, and School of Life Sciences & Biotechnology, Shanghai Jiao Tong University, 800 Dongchuan Road, Shanghai 200240, China
| | - Tiangang Liu
- Key
Laboratory of Combinatorial Biosynthesis and Drug Discovery (Wuhan
University), Ministry of Education, and Wuhan University School of Pharmaceutical Sciences, Wuhan 430071, China
- Hubei
Engineering Laboratory for Synthetic Microbiology, Wuhan Institute of Biotechnology, Wuhan 430075, China
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11
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Tan GY, Liu T. Rational synthetic pathway refactoring of natural products biosynthesis in actinobacteria. Metab Eng 2017; 39:228-236. [DOI: 10.1016/j.ymben.2016.12.006] [Citation(s) in RCA: 47] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2016] [Revised: 10/31/2016] [Accepted: 12/05/2016] [Indexed: 11/28/2022]
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12
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Bai Y, Zhou PP, Fan P, Zhu YM, Tong Y, Wang HB, Yu LJ. Four-stage dissolved oxygen strategy based on multi-scale analysis for improving spinosad yield by Saccharopolyspora spinosa ATCC49460. Microb Biotechnol 2015; 8:561-8. [PMID: 25808914 PMCID: PMC4408188 DOI: 10.1111/1751-7915.12264] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/03/2014] [Revised: 11/24/2014] [Accepted: 12/26/2014] [Indexed: 11/29/2022] Open
Abstract
Dissolved oxygen (DO) is an important influencing factor in the process of aerobic microbial fermentation. Spinosad is an aerobic microbial-derived secondary metabolite. In our study, spinosad was used as an example to establish a DO strategy by multi-scale analysis, which included a reactor, cell and gene scales. We changed DO conditions that are related to the characteristics of cell metabolism (glucose consumption rate, biomass accumulation and spinosad production). Consequently, cell growth was promoted by maintaining DO at 40% in the first 24 h and subsequently increasing DO to 50% in 24 h to 96 h. In an in-depth analysis of the key enzyme genes (gtt, spn A, spn K and spn O), expression of spinosad and specific Adenosine Triphosphate (ATP), the spinosad yield was increased by regulating DO to 30% within 96 h to 192 h and then changing it to 25% in 192 h to 240 h. Under the four-phase DO strategy, spinosad yield increased by 652.1%, 326.1%, 546.8%, and 781.4% compared with the yield obtained under constant DO control at 50%, 40%, 30%, and 20% respectively. The proposed method provides a novel way to develop a precise DO strategy for fermentation.
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Affiliation(s)
- Yun Bai
- Institute of Resource Biology and Biotechnology, Department of Biotechnology, College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan, 430074, China; Key Laboratory of Molecular Biophysics Ministry of Education, Huazhong University of Science and Technology, Wuhan, 430074, China
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Kim HJ, Choi SH, Jeon BS, Kim N, Pongdee R, Wu Q, Liu HW. Chemoenzymatic synthesis of spinosyn A. Angew Chem Int Ed Engl 2014; 53:13553-7. [PMID: 25287333 PMCID: PMC4266379 DOI: 10.1002/anie.201407806] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2014] [Indexed: 11/11/2022]
Abstract
Following the biosynthesis of polyketide backbones by polyketide synthases (PKSs), post-PKS modifications result in a significantly elevated level of structural complexity that renders the chemical synthesis of these natural products challenging. We report herein a total synthesis of the widely used polyketide insecticide spinosyn A by exploiting the prowess of both chemical and enzymatic methods. As more polyketide biosynthetic pathways are characterized, this chemoenzymatic approach is expected to become readily adaptable to streamlining the synthesis of other complex polyketides with more elaborate post-PKS modifications.
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Affiliation(s)
- Hak Joong Kim
- Division of Medicinal Chemistry, College of Pharmacy and Department of Chemistry, University of Texas at Austin, Austin, TX 78712 (USA); Department of Chemistry, Korea University (Republic of Korea)
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14
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Kim HJ, Choi SH, Jeon BS, Kim N, Pongdee R, Wu Q, Liu HW. Chemoenzymatic Synthesis of Spinosyn A. Angew Chem Int Ed Engl 2014. [DOI: 10.1002/ange.201407806] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022]
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15
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Yang Q, Ding X, Liu X, Liu S, Sun Y, Yu Z, Hu S, Rang J, He H, He L, Xia L. Differential proteomic profiling reveals regulatory proteins and novel links between primary metabolism and spinosad production in Saccharopolyspora spinosa. Microb Cell Fact 2014; 13:27. [PMID: 24555503 PMCID: PMC3936707 DOI: 10.1186/1475-2859-13-27] [Citation(s) in RCA: 33] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2013] [Accepted: 02/18/2014] [Indexed: 11/29/2022] Open
Abstract
Background Saccharopolyspora spinosa is an important producer of antibiotic spinosad with clarified biosynthesis pathway but its complex regulation networks associated with primary metabolism and secondary metabolites production almost have never been concerned or studied before. The proteomic analysis of a novel Saccharopolyspora spinosa CCTCC M206084 was performed and aimed to provide a global profile of regulatory proteins. Results Two-dimensional-liquid chromatography-tandem mass spectrometry (LC-MS/MS) identified 1090, 1166, 701, and 509 proteins from four phases respectively, i.e., the logarithmic growth phase (T1), early stationary phase (T2), late stationary phase (T3), and decline phase (T4). Among the identified proteins, 1579 were unique to the S. spinosa proteome, including almost all the enzymes for spinosad biosynthesis. Trends in protein expression over the various time phases were deduced from using the modified protein abundance index (PAI), revealed the importance of stress pathway proteins and other global regulatory network proteins during spinosad biosynthesis. Sodium dodecyl sulfate-polyacrylamide gel electrophoresis analysis followed by one-dimensional LC-MS/MS identification revealed similar trend of protein expression from four phases with the results of semi-quantification by PAI. qRT-PCR analysis revealed that 6 different expressed genes showed a positive correlation between changes at translational and transcriptional expression level. Expression of three proteins that likely promote spinosad biosynthesis, namely, 5-methyltetrahydropteroyltriglutamate-homocysteine S-methyltransferase (MHSM), glutamine synthetase (GS) and cyclic nucleotide-binding domain-containing protein (CNDP) was validated by western blot, which confirmed the results of proteomic analysis. Conclusions This study is the first systematic analysis of the S. spinosa proteome during fermentation and its valuable proteomic data of regulatory proteins may be used to enhance the production yield of spinosad in future studies.
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Affiliation(s)
| | - Xuezhi Ding
- Hunan Provincial Key Laboratory of Microbial Molecular Biology-State Key laboratory Breeding Base of Microbial Molecular Biology, College of life Science, Hunan Normal University, Changsha 410081, China.
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16
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Identification of the incednine biosynthetic gene cluster: characterization of novel β-glutamate-β-decarboxylase IdnL3. J Antibiot (Tokyo) 2013; 66:691-9. [DOI: 10.1038/ja.2013.76] [Citation(s) in RCA: 33] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2013] [Revised: 06/11/2013] [Accepted: 06/21/2013] [Indexed: 12/18/2022]
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Isiorho EA, Liu HW, Keatinge-Clay AT. Structural studies of the spinosyn rhamnosyltransferase, SpnG. Biochemistry 2012; 51:1213-22. [PMID: 22283226 DOI: 10.1021/bi201860q] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Spinosyns A and D (spinosad), like many other complex polyketides, are tailored near the end of their biosyntheses through the addition of sugars. SpnG, which catalyzes their 9-OH rhamnosylation, is also capable of adding other monosaccharides to the spinosyn aglycone (AGL) from TDP-sugars; however, the substitution of UDP-D-glucose for TDP-D-glucose as the donor substrate is known to result in a >60000-fold reduction in k(cat). Here, we report the structure of SpnG at 1.65 Å resolution, SpnG bound to TDP at 1.86 Å resolution, and SpnG bound to AGL at 1.70 Å resolution. The SpnG-TDP complex reveals how SpnG employs N202 to discriminate between TDP- and UDP-sugars. A conformational change of several residues in the active site is promoted by the binding of TDP. The SpnG-AGL complex shows that the binding of AGL is mediated via hydrophobic interactions and that H13, the potential catalytic base, is within 3 Å of the nucleophilic 9-OH group of AGL. A model for the Michaelis complex was constructed to reveal the features that allow SpnG to transfer diverse sugars; it also revealed that the rhamnosyl moiety is in a skew-boat conformation during the transfer reaction.
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Affiliation(s)
- Eta A Isiorho
- Division of Medicinal Chemistry, College of Pharmacy, The University of Texas at Austin, Austin, Texas 78712, United States
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18
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Characterization of the amicetin biosynthesis gene cluster from Streptomyces vinaceusdrappus NRRL 2363 implicates two alternative strategies for amide bond formation. Appl Environ Microbiol 2012; 78:2393-401. [PMID: 22267658 DOI: 10.1128/aem.07185-11] [Citation(s) in RCA: 35] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Amicetin, an antibacterial and antiviral agent, belongs to a group of disaccharide nucleoside antibiotics featuring an α-(1→4)-glycoside bond in the disaccharide moiety. In this study, the amicetin biosynthesis gene cluster was cloned from Streptomyces vinaceusdrappus NRRL 2363 and localized on a 37-kb contiguous DNA region. Heterologous expression of the amicetin biosynthesis gene cluster in Streptomyces lividans TK64 resulted in the production of amicetin and its analogues, thereby confirming the identity of the ami gene cluster. In silico sequence analysis revealed that 21 genes were putatively involved in amicetin biosynthesis, including 3 for regulation and transportation, 10 for disaccharide biosynthesis, and 8 for the formation of the amicetin skeleton by the linkage of cytosine, p-aminobenzoic acid (PABA), and the terminal (+)-α-methylserine moieties. The inactivation of the benzoate coenzyme A (benzoate-CoA) ligase gene amiL and the N-acetyltransferase gene amiF led to two mutants that accumulated the same two compounds, cytosamine and 4-acetamido-3-hydroxybenzoic acid. These data indicated that AmiF functioned as an amide synthethase to link cytosine and PABA. The inactivation of amiR, encoding an acyl-CoA-acyl carrier protein transacylase, resulted in the production of plicacetin and norplicacetin, indicating AmiR to be responsible for attachment of the terminal methylserine moiety to form another amide bond. These findings implicated two alternative strategies for amide bond formation in amicetin biosynthesis.
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Romo AJ, Liu HW. Mechanisms and structures of vitamin B(6)-dependent enzymes involved in deoxy sugar biosynthesis. BIOCHIMICA ET BIOPHYSICA ACTA 2011; 1814:1534-47. [PMID: 21315852 PMCID: PMC3115481 DOI: 10.1016/j.bbapap.2011.02.003] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/15/2010] [Revised: 01/08/2011] [Accepted: 02/01/2011] [Indexed: 10/18/2022]
Abstract
PLP is well-regarded for its role as a coenzyme in a number of diverse enzymatic reactions. Transamination, deoxygenation, and aldol reactions mediated by PLP-dependent enzymes enliven and enrich deoxy sugar biosynthesis, endowing these compounds with unique structures and contributing to their roles as determinants of biological activity in many natural products. The importance of deoxy aminosugars in natural product biosynthesis has spurred several recent structural investigations of sugar aminotransferases. The structure of a PMP-dependent enzyme catalyzing the C-3 deoxygenation reaction in the biosynthesis of ascarylose was also determined. These studies, and the crystal structures they have provided, offer a wealth of new insights regarding the enzymology of PLP/PMP-dependent enzymes in deoxy sugar biosynthesis. In this review, we consider these recent achievements in the structural biology of deoxy sugar biosynthetic enzymes and the important implications they hold for understanding enzyme catalysis and natural product biosynthesis in general. This article is part of a Special Issue entitled: Pyridoxal Phosphate Enzymology.
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Affiliation(s)
- Anthony J. Romo
- Division of Medicinal Chemistry, College of Pharmacy, and Department of Chemistry and Biochemistry, University of Texas at Austin, Austin, Texas 78712
| | - Hung-wen Liu
- Division of Medicinal Chemistry, College of Pharmacy, and Department of Chemistry and Biochemistry, University of Texas at Austin, Austin, Texas 78712
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Genome sequence of the Spinosyns-producing bacterium Saccharopolyspora spinosa NRRL 18395. J Bacteriol 2011; 193:3150-1. [PMID: 21478350 DOI: 10.1128/jb.00344-11] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Saccharopolyspora spinosa is a Gram-positive bacterium that produces spinosad, a well-known biodegradable insecticide that is used for agricultural pest control and has an excellent environmental and mammalian toxicological profile. Here, we present the first draft genome sequence of the type strain Saccharopolyspora spinosa NRRL 18395, which consists of 22 scaffolds.
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Sasaki E, Ogasawara Y, Liu HW. A biosynthetic pathway for BE-7585A, a 2-thiosugar-containing angucycline-type natural product. J Am Chem Soc 2010; 132:7405-17. [PMID: 20443562 DOI: 10.1021/ja1014037] [Citation(s) in RCA: 52] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Sulfur is an essential element found ubiquitously in living systems. However, there exist only a few sulfur-containing sugars in nature and their biosyntheses have not been studied. BE-7585A produced by Amycolatopsis orientalis subsp. vinearia BA-07585 has a 2-thiosugar and is a member of the angucycline class of compounds. We report herein the results of our initial efforts to study the biosynthesis of BE-7585A. Spectroscopic analyses verified the structure of BE-7585A, which is closely related to rhodonocardin A. Feeding experiments using (13)C-labeled acetate were carried out to confirm that the angucycline core is indeed polyketide-derived. The results indicated an unusual manner of angular tetracyclic ring construction, perhaps via a Baeyer-Villiger type rearrangement. Subsequent cloning and sequencing led to the identification of the bex gene cluster spanning approximately 30 kbp. A total of 28 open reading frames, which are likely involved in BE-7585A formation, were identified in the cluster. In view of the presence of a homologue of a thiazole synthase gene (thiG), bexX, in the bex cluster, the mechanism of sulfur incorporation into the 2-thiosugar moiety could resemble that found in thiamin biosynthesis. A glycosyltransferase homologue, BexG2, was heterologously expressed in Escherichia coli. The purified enzyme successfully catalyzed the coupling of 2-thioglucose 6-phosphate and UDP-glucose to produce 2-thiotrehalose 6-phosphate, which is the precursor of the disaccharide unit in BE-7585A. On the basis of these genetic and biochemical experiments, a biosynthetic pathway for BE-7585A can now be proposed. The combined results set the stage for future biochemical studies of 2-thiosugar biosynthesis and BE-7585A assembly.
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Affiliation(s)
- Eita Sasaki
- Division of Medicinal Chemistry, College of Pharmacy, and Department of Chemistry and Biochemistry, University of Texas at Austin, Austin, Texas 78712, USA
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22
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Kirst HA. The spinosyn family of insecticides: realizing the potential of natural products research. J Antibiot (Tokyo) 2010; 63:101-11. [DOI: 10.1038/ja.2010.5] [Citation(s) in RCA: 209] [Impact Index Per Article: 14.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
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Huang KX, Xia L, Zhang Y, Ding X, Zahn JA. Recent advances in the biochemistry of spinosyns. Appl Microbiol Biotechnol 2009; 82:13-23. [DOI: 10.1007/s00253-008-1784-8] [Citation(s) in RCA: 42] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2008] [Revised: 10/31/2008] [Accepted: 11/02/2008] [Indexed: 10/21/2022]
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Thibodeaux C, Melançon C, Liu HW. Biosynthese von Naturstoffzuckern und enzymatische Glycodiversifizierung. Angew Chem Int Ed Engl 2008. [DOI: 10.1002/ange.200801204] [Citation(s) in RCA: 40] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/10/2023]
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25
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Schmidt B, Biernat A. The Tandem Ring‐Closing Metathesis–Isomerization Approach to 6‐Deoxyglycals. Chemistry 2008; 14:6135-41. [DOI: 10.1002/chem.200800567] [Citation(s) in RCA: 45] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
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Hong L, Zhao Z, Melançon CE, Zhang H, Liu HW. In vitro characterization of the enzymes involved in TDP-D-forosamine biosynthesis in the spinosyn pathway of Saccharopolyspora spinosa. J Am Chem Soc 2008; 130:4954-67. [PMID: 18345667 DOI: 10.1021/ja0771383] [Citation(s) in RCA: 67] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Forosamine (4-dimethylamino)-2,3,4,6-tetradeoxy-beta-D-threo-hexopyranose) is a highly deoxygenated sugar component of several important natural products, including the potent yet environmentally benign insecticide spinosyns. To study D-forosamine biosynthesis, the five genes (spnO, N, Q, R, and S) from the spinosyn gene cluster thought to be involved in the conversion of TDP-4-keto-6-deoxy-D-glucose to TDP-D-forosamine were cloned and heterologously expressed, and the corresponding proteins were purified and their activities examined in vitro. Previous work demonstrated that SpnQ functions as a pyridoxamine 5'-monophosphate (PMP)-dependent 3-dehydrase which, in the presence of the cellular reductase pairs ferredoxin/ferredoxin reductase or flavodoxin/flavodoxin reductase, catalyzes C-3 deoxygenation of TDP-4-keto-2,6-dideoxy-D-glucose. It was also established that SpnR functions as a transaminase which converts the SpnQ product, TDP-4-keto-2,3,6-trideoxy-D-glucose, to TDP-4-amino-2,3,4,6-tetradeoxy-D-glucose. The results presented here provide a full account of the characterization of SpnR and SpnQ and reveal that SpnO and SpnN functions as a 2,3-dehydrase and a 3-ketoreductase, respectively. These two enzymes act sequentially to catalyze C-2 deoxygenation of TDP-4-keto-6-deoxy-D-glucose to form the SpnQ substrate, TDP-4-keto-2,6-dideoxy-D-glucose. Evidence has also been obtained to show that SpnS functions as the 4-dimethyltransferase that converts the SpnR product to TDP-D-forosamine. Thus, the biochemical functions of the five enzymes involved in TDP-D-forosamine formation have now been fully elucidated. The steady-state kinetic parameters for the SpnQ-catalyzed reaction have been determined, and the substrate specificities of SpnQ and SpnR have been explored. The implications of this work for natural product glycodiversification and comparative mechanistic analysis of SpnQ and related NDP-sugar 3-dehydrases E1 and ColD are discussed.
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Affiliation(s)
- Lin Hong
- Division of Medicinal Chemistry, College of Pharmacy, University of Texas at Austin, Austin, Texas 78712, USA
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Thibodeaux CJ, Melançon CE, Liu HW. Natural-product sugar biosynthesis and enzymatic glycodiversification. Angew Chem Int Ed Engl 2008; 47:9814-59. [PMID: 19058170 PMCID: PMC2796923 DOI: 10.1002/anie.200801204] [Citation(s) in RCA: 320] [Impact Index Per Article: 20.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Abstract
Many biologically active small-molecule natural products produced by microorganisms derive their activities from sugar substituents. Changing the structures of these sugars can have a profound impact on the biological properties of the parent compounds. This realization has inspired attempts to derivatize the sugar moieties of these natural products through exploitation of the sugar biosynthetic machinery. This approach requires an understanding of the biosynthetic pathway of each target sugar and detailed mechanistic knowledge of the key enzymes. Scientists have begun to unravel the biosynthetic logic behind the assembly of many glycosylated natural products and have found that a core set of enzyme activities is mixed and matched to synthesize the diverse sugar structures observed in nature. Remarkably, many of these sugar biosynthetic enzymes and glycosyltransferases also exhibit relaxed substrate specificity. The promiscuity of these enzymes has prompted efforts to modify the sugar structures and alter the glycosylation patterns of natural products through metabolic pathway engineering and enzymatic glycodiversification. In applied biomedical research, these studies will enable the development of new glycosylation tools and generate novel glycoforms of secondary metabolites with useful biological activity.
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Affiliation(s)
- Christopher J. Thibodeaux
- Division of Medicinal Chemistry, College of Pharmacy, and Department of Chemistry and Biochemistry, University of Texas at Austin, Austin, TX. (USA), 78712
| | - Charles E. Melançon
- Division of Medicinal Chemistry, College of Pharmacy, and Department of Chemistry and Biochemistry, University of Texas at Austin, Austin, TX. (USA), 78712
| | - Hung-wen Liu
- Division of Medicinal Chemistry, College of Pharmacy, and Department of Chemistry and Biochemistry, University of Texas at Austin, Austin, TX. (USA), 78712
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28
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Thibodeaux CJ, Melançon CE, Liu HW. Natural-product sugar biosynthesis and enzymatic glycodiversification. Angew Chem Int Ed Engl 2008. [PMID: 19058170 DOI: 10.1002/anie] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/13/2023]
Abstract
Many biologically active small-molecule natural products produced by microorganisms derive their activities from sugar substituents. Changing the structures of these sugars can have a profound impact on the biological properties of the parent compounds. This realization has inspired attempts to derivatize the sugar moieties of these natural products through exploitation of the sugar biosynthetic machinery. This approach requires an understanding of the biosynthetic pathway of each target sugar and detailed mechanistic knowledge of the key enzymes. Scientists have begun to unravel the biosynthetic logic behind the assembly of many glycosylated natural products and have found that a core set of enzyme activities is mixed and matched to synthesize the diverse sugar structures observed in nature. Remarkably, many of these sugar biosynthetic enzymes and glycosyltransferases also exhibit relaxed substrate specificity. The promiscuity of these enzymes has prompted efforts to modify the sugar structures and alter the glycosylation patterns of natural products through metabolic pathway engineering and enzymatic glycodiversification. In applied biomedical research, these studies will enable the development of new glycosylation tools and generate novel glycoforms of secondary metabolites with useful biological activity.
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Affiliation(s)
- Christopher J Thibodeaux
- Division of Medicinal Chemistry, College of Pharmacy and Department of Chemistry and Biochemistry, University of Texas at Austin, Austin, TX 78712, USA
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Zhang H, White-Phillip JA, Melançon CE, Kwon HJ, Yu WL, Liu HW. Elucidation of the kijanimicin gene cluster: insights into the biosynthesis of spirotetronate antibiotics and nitrosugars. J Am Chem Soc 2007; 129:14670-83. [PMID: 17985890 DOI: 10.1021/ja0744854] [Citation(s) in RCA: 113] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
The antibiotic kijanimicin produced by the actinomycete Actinomadura kijaniata has a broad spectrum of bioactivities as well as a number of interesting biosynthetic features. To understand the molecular basis for its formation and to develop a combinatorial biosynthetic system for this class of compounds, a 107.6 kb segment of the A. kijaniata chromosome containing the kijanimicin biosynthetic locus was identified, cloned, and sequenced. The complete pathway for the formation of TDP-l-digitoxose, one of the two sugar donors used in construction of kijanimicin, was elucidated through biochemical analysis of four enzymes encoded in the gene cluster. Sequence analysis indicates that the aglycone kijanolide is formed by the combined action of a modular Type-I polyketide synthase, a conserved set of enzymes involved in formation, attachment, and intramolecular cyclization of a glycerate-derived three-carbon unit, which forms the core of the spirotetronate moiety. The genes involved in the biosynthesis of the unusual deoxysugar d-kijanose [2,3,4,6-tetradeoxy-4-(methylcarbamyl)-3-C-methyl-3-nitro-d-xylo-hexopyranose], including one encoding a flavoenzyme predicted to catalyze the formation of the nitro group, have also been identified. This work has implications for the biosynthesis of other spirotetronate antibiotics and nitrosugar-bearing natural products, as well as for future mechanistic and biosynthetic engineering efforts.
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Affiliation(s)
- Hua Zhang
- Division of Medicinal Chemistry, College of Pharmacy, Institute of Cellular and Molecular Biology, Austin, Texas 78712, USA
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30
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Anthracycline Biosynthesis: Genes, Enzymes and Mechanisms. ANTHRACYCLINE CHEMISTRY AND BIOLOGY I 2007. [DOI: 10.1007/128_2007_14] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/03/2023]
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