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Huang S, Ji H, Zheng J. Structural and computational insights into the regioselectivity of SpnK involved in rhamnose methylation of spinosyn. Int J Biol Macromol 2023; 253:126763. [PMID: 37703985 DOI: 10.1016/j.ijbiomac.2023.126763] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2023] [Revised: 09/03/2023] [Accepted: 09/04/2023] [Indexed: 09/15/2023]
Abstract
Rhamnose methylation of spinosyn critical for insecticidal activity is orchestrated by substrate specificity of three S-adenosyl-L-methionine (SAM) dependent methyltransferases (MTs). Previous in vitro enzymatic assays indicate that 3'-O-MT SpnK accepts the rhamnosylated aglycone (RAGL) and 2'-O-methylated RAGL as substrates, but does not tolerate the presence of a methoxy moiety at the O-4' position of the rhamnose unit. Here we solved the crystal structures of apo and ligand-bound SpnK, and used molecular dynamic (MD) simulations to decipher the molecular basis of substrate specificity. SpnK assembles into a tetramer, with each set of three monomers forming an integrated substrate binding pocket. The MD simulations of SpnK complexed with RAGL or 2'-O-methylated RAGL revealed that the 4'-hydroxyl of the rhamnose unit formed a hydrogen bond with a conserved Asp299 of the catalytic center, which is disrupted in structures of SpnK complexed with 4'-O-methylated RAGL or 2',4'-di-O-methylated RAGL. Comparison with SpnI methylating the C2'-hydroxyl of RAGL reveals a correlation between a DLQT/DLWT motif and the selectivity of rhamnose O-MTs. Together, our structural and computational results revealed the structural basis of substrate specificity of rhamnose O-MTs and would potentially help the engineering of spinosyn derivatives.
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Affiliation(s)
- Shuxin Huang
- State Key Laboratory of Microbial Metabolism, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai 200240, China
| | - Huining Ji
- Joint International Research Laboratory of Metabolic & Developmental Sciences, Shanghai Jiao Tong University, Shanghai 200240, China
| | - Jianting Zheng
- State Key Laboratory of Microbial Metabolism, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai 200240, China; Joint International Research Laboratory of Metabolic & Developmental Sciences, Shanghai Jiao Tong University, Shanghai 200240, China.
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2
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Kazemzadeh K, Pelosi L, Chenal C, Chobert SC, Hajj Chehade M, Jullien M, Flandrin L, Schmitt W, He Q, Bouvet E, Jarzynka M, Varoquaux N, Junier I, Pierrel F, Abby SS. Diversification of Ubiquinone Biosynthesis via Gene Duplications, Transfers, Losses, and Parallel Evolution. Mol Biol Evol 2023; 40:msad219. [PMID: 37788637 PMCID: PMC10597321 DOI: 10.1093/molbev/msad219] [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: 05/26/2023] [Revised: 09/11/2023] [Accepted: 09/26/2023] [Indexed: 10/05/2023] Open
Abstract
The availability of an ever-increasing diversity of prokaryotic genomes and metagenomes represents a major opportunity to understand and decipher the mechanisms behind the functional diversification of microbial biosynthetic pathways. However, it remains unclear to what extent a pathway producing a specific molecule from a specific precursor can diversify. In this study, we focus on the biosynthesis of ubiquinone (UQ), a crucial coenzyme that is central to the bioenergetics and to the functioning of a wide variety of enzymes in Eukarya and Pseudomonadota (a subgroup of the formerly named Proteobacteria). UQ biosynthesis involves three hydroxylation reactions on contiguous carbon atoms. We and others have previously shown that these reactions are catalyzed by different sets of UQ-hydroxylases that belong either to the iron-dependent Coq7 family or to the more widespread flavin monooxygenase (FMO) family. Here, we combine an experimental approach with comparative genomics and phylogenetics to reveal how UQ-hydroxylases evolved different selectivities within the constrained framework of the UQ pathway. It is shown that the UQ-FMOs diversified via at least three duplication events associated with two cases of neofunctionalization and one case of subfunctionalization, leading to six subfamilies with distinct hydroxylation selectivity. We also demonstrate multiple transfers of the UbiM enzyme and the convergent evolution of UQ-FMOs toward the same function, which resulted in two independent losses of the Coq7 ancestral enzyme. Diversification of this crucial biosynthetic pathway has therefore occurred via a combination of parallel evolution, gene duplications, transfers, and losses.
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Affiliation(s)
- Katayoun Kazemzadeh
- Univ. Grenoble Alpes, CNRS, UMR 5525, VetAgro Sup, Grenoble INP, TIMC, 38000 Grenoble, France
| | - Ludovic Pelosi
- Univ. Grenoble Alpes, CNRS, UMR 5525, VetAgro Sup, Grenoble INP, TIMC, 38000 Grenoble, France
| | - Clothilde Chenal
- Univ. Grenoble Alpes, CNRS, UMR 5525, VetAgro Sup, Grenoble INP, TIMC, 38000 Grenoble, France
| | - Sophie-Carole Chobert
- Univ. Grenoble Alpes, CNRS, UMR 5525, VetAgro Sup, Grenoble INP, TIMC, 38000 Grenoble, France
| | - Mahmoud Hajj Chehade
- Univ. Grenoble Alpes, CNRS, UMR 5525, VetAgro Sup, Grenoble INP, TIMC, 38000 Grenoble, France
| | - Margaux Jullien
- Univ. Grenoble Alpes, CNRS, UMR 5525, VetAgro Sup, Grenoble INP, TIMC, 38000 Grenoble, France
| | - Laura Flandrin
- Univ. Grenoble Alpes, CNRS, UMR 5525, VetAgro Sup, Grenoble INP, TIMC, 38000 Grenoble, France
| | - William Schmitt
- Univ. Grenoble Alpes, CNRS, UMR 5525, VetAgro Sup, Grenoble INP, TIMC, 38000 Grenoble, France
| | - Qiqi He
- Univ. Grenoble Alpes, CNRS, UMR 5525, VetAgro Sup, Grenoble INP, TIMC, 38000 Grenoble, France
| | - Emma Bouvet
- Univ. Grenoble Alpes, CNRS, UMR 5525, VetAgro Sup, Grenoble INP, TIMC, 38000 Grenoble, France
| | - Manon Jarzynka
- Univ. Grenoble Alpes, CNRS, UMR 5525, VetAgro Sup, Grenoble INP, TIMC, 38000 Grenoble, France
| | - Nelle Varoquaux
- Univ. Grenoble Alpes, CNRS, UMR 5525, VetAgro Sup, Grenoble INP, TIMC, 38000 Grenoble, France
| | - Ivan Junier
- Univ. Grenoble Alpes, CNRS, UMR 5525, VetAgro Sup, Grenoble INP, TIMC, 38000 Grenoble, France
| | - Fabien Pierrel
- Univ. Grenoble Alpes, CNRS, UMR 5525, VetAgro Sup, Grenoble INP, TIMC, 38000 Grenoble, France
| | - Sophie S Abby
- Univ. Grenoble Alpes, CNRS, UMR 5525, VetAgro Sup, Grenoble INP, TIMC, 38000 Grenoble, France
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3
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Diab MK, Mead HM, Khedr MA, Nafie MS, Abu-Elsaoud AM, Hanora A, El-Shatoury SA. Endophytic actinobacteria from wild medicinal plants are a natural source of insecticide to control the African cotton leafworm (Spodoptera littoralis). AMB Express 2023; 13:47. [PMID: 37184816 DOI: 10.1186/s13568-023-01550-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2023] [Accepted: 04/20/2023] [Indexed: 05/16/2023] Open
Abstract
Insecticide resistance in agricultural pests has prompted the need to discover novel compounds with new modes of action. We investigated the potency of secondary metabolites from seventy endophytic actinobacteria against laboratory and field strains of Spodoptera littoralis (fourth instar), comparable to the bioinsecticide spinetoram (Radiant SC 12%). Endophytes from Artemisia herba-alba and A. judaica were highly effective. Chemical profiling of the most potent metabolite of the strain Streptomyces sp. ES2 was investigated using LC-QTOF-MS-MS technique, and the activity was validated through molecular docking studies. Metabolic extracts from actinobacteria belonging to Streptomyces, Nocardioides, and Pseudonocardia showed immediate and latent death to the Spodoptera littoralis fourth instar larvae. The metabolite from strain ES2 has shown the most promising and significant histopathological and inhibitory effects on the fourth instar larvae. ES2 metabolite caused lesions in the body wall cuticle, indicating a different mode of action than that of Radiant. Chemical profiling of ES2 showed the presence of cyromazine (molt inhibitor), 4-nitrophenol, and diazinon as key constituents. In conclusion, these findings suggest that secondary metabolites from endophytic actinobacteria inhabiting wild medicinal plants can be a sustainable source for promising natural biocontrol agents. This is the first illustration of the insecticidal activity of Artemisia spp. microbiome, and natural cyromazine synthesis by actinobacteria.
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Affiliation(s)
- Mohamed K Diab
- Agricultural Research Center, Pest Physiology Department, Plant Protection Research Institute, Giza, 12311, Egypt
| | - Hala M Mead
- Agricultural Research Center, Pest Physiology Department, Plant Protection Research Institute, Giza, 12311, Egypt
| | - Mohamad A Khedr
- Agricultural Research Center, Cotton Leafworm Department, Plant Protection Research Institute, Giza, 12311, Egypt
| | - Mohamed S Nafie
- Faculty of Science, Chemistry Department, Suez Canal University, Ismailia, 41522, Egypt
| | | | - Amro Hanora
- Faculty of Pharmacy, Microbiology Department, Suez Canal University, Ismailia, 41522, Egypt
| | - Sahar A El-Shatoury
- Faculty of Science, Botany & Microbiology Department, Suez Canal University, Ismailia, 41522, Egypt.
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4
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Wu X, Yuwen M, Pu Z, Zhao Z, Yu H, Zha J. Engineering of flavonoid 3'-O-methyltransferase for improved biosynthesis of chrysoeriol in Escherichia coli. Appl Microbiol Biotechnol 2023; 107:1663-1672. [PMID: 36719434 DOI: 10.1007/s00253-023-12403-9] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/03/2022] [Revised: 01/18/2023] [Accepted: 01/20/2023] [Indexed: 02/01/2023]
Abstract
O-Methylation catalyzed by O-methyltransferases (OMTs) is an important modification of flavonoids for improving the transport efficiency across membranes and metabolic stability in mammalian cells. Chrysoeriol, also known as 3'-O-methylated luteolin, is a methylated flavonoid compound with health-promoting activities. The generation of chrysoeriol from luteolin can be catalyzed by a rice-derived 3'-OMT named ROMT-9, which has a high regiospecificity and activity toward flavonoids in vitro. Herein, we explored the potential of ROMT-9 for in vivo biosynthesis of chrysoeriol in Escherichia coli and adopted semi-rational enzyme engineering guided by homology modeling and molecular docking to improve the bio-production. Two positive variants including L34Q and W284A were obtained which promoted chrysoeriol formation to more than 85 mg/L from 200 mg/L of luteolin in 24 h compared with a titer of 55 mg/L for the strain expressing the native enzyme. Further biochemical analysis confirmed that such improvement in production stemmed from a higher enzyme expression level for the L34Q variant and higher efficiency in substrate binding and catalysis for the W284A variant. This study provides some insights into the engineering of other flavonoid OMTs and will facilitate high-level biosynthesis of methylated flavonoids in engineered microorganisms. KEY POINTS: • Biosynthesis of chrysoeriol from luteolin in E. coli using ROMT-9 • Engineering of ROMT-9 for better bio-production • ROMT-9 variants promote production via better expression or better catalysis.
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Affiliation(s)
- Xia Wu
- School of Food and Biological Engineering, Shaanxi University of Science and Technology, Xi'an, 710021, Shaanxi, China
| | - Miaomiao Yuwen
- School of Food and Biological Engineering, Shaanxi University of Science and Technology, Xi'an, 710021, Shaanxi, China
| | - Zhongji Pu
- Hangzhou Global Scientific and Technological Innovation Center, Zhejiang University, Hangzhou, 311200, Zhejiang, China
| | - Zhen Zhao
- School of Food and Biological Engineering, Shaanxi University of Science and Technology, Xi'an, 710021, Shaanxi, China
| | - Haoran Yu
- Hangzhou Global Scientific and Technological Innovation Center, Zhejiang University, Hangzhou, 311200, Zhejiang, China. .,Institute of Bioengineering, College of Chemical and Biological Engineering, Zhejiang University, Hangzhou, 310027, Zhejiang, China.
| | - Jian Zha
- School of Food and Biological Engineering, Shaanxi University of Science and Technology, Xi'an, 710021, Shaanxi, China.
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5
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Yi JS, Kim JM, Ban YH, Yoon YJ. Modular polyketide synthase-derived insecticidal agents: from biosynthesis and metabolic engineering to combinatorial biosynthesis for their production. Nat Prod Rep 2023; 40:972-987. [PMID: 36691749 DOI: 10.1039/d2np00078d] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/25/2023]
Abstract
Covering: up to 2022Polyketides derived from actinomycetes are a valuable source of eco-friendly biochemical insecticides. The development of new insecticides is urgently required, as the number of insects resistant to more than one drug is rapidly increasing. Moreover, significant enhancement of the production of such biochemical insecticides is required for economical production. There has been considerable improvement in polyketide insecticidal agent production and development of new insecticides. However, most commercially important biochemical insecticides are synthesized by modular type I polyketide synthases (PKSs), and their structural complexities make chemical modification challenging. A detailed understanding of the biosynthetic mechanisms of potent polyketide insecticides and the structure-activity relationships of their analogs will provide insight into the comprehensive design of new insecticides with improved efficacies. Further metabolic engineering and combinatorial biosynthesis efforts, reinvigorated by synthetic biology, can eventually produce designed analogs in large quantities. This highlight reviews the biosynthesis of representative insecticides produced by modular type I PKSs, such as avermectin, spinosyn, and spectinabilin, and their insecticidal properties. Metabolic engineering and combinatorial biosynthetic strategies for the development of high-yield strains and analogs with insecticidal activities are emphasized, proposing a way to develop a next-generation insecticide.
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Affiliation(s)
- Jeong Sang Yi
- Natural Products Research Institute, College of Pharmacy, Seoul National University, Seoul, 08826, Republic of Korea.
| | - Jung Min Kim
- Natural Products Research Institute, College of Pharmacy, Seoul National University, Seoul, 08826, Republic of Korea.
| | - Yeon Hee Ban
- College of Biomedical Science, Kangwon National University, Chuncheon, 24341, Republic of Korea.
| | - Yeo Joon Yoon
- Natural Products Research Institute, College of Pharmacy, Seoul National University, Seoul, 08826, Republic of Korea.
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Li X, Guo R, Luan J, Fu J, Zhang Y, Wang H. Improving spinosad production by tuning expressions of the forosamine methyltransferase and the forosaminyl transferase to reduce undesired less active byproducts in the heterologous host Streptomyces albus J1074. Microb Cell Fact 2023; 22:15. [PMID: 36658647 PMCID: PMC9854174 DOI: 10.1186/s12934-023-02023-3] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2022] [Accepted: 01/12/2023] [Indexed: 01/21/2023] Open
Abstract
BACKGROUND Spinosad is a macrolide insecticide with the tetracyclic lactone backbone to which forosamine and tri-O-methylrhamnose are attached. Both the sugar moieties are essential for its insecticidal activity. In biosynthesis of spinosad, the amino group of forosamine is dimethylated by SpnS and then transferred onto the lactone backbone by SpnP. Because the spinosad native producer is difficult to genetically manipulate, we previously changed promoters, ribosome binding sites and start codons of 23 spinosad biosynthetic genes to construct an artificial gene cluster which resulted in a 328-fold yield improvement in the heterologous host Streptomyces albus J1074 compared with the native gene cluster. However, in fermentation of J1074 with the artificial gene cluster, the N-monodesmethyl spinosad with lower insecticidal activity was always produced with the same titer as spinosad. RESULTS By tuning expression of SpnS with an inducible promotor, we found that the undesired less active byproduct N-monodesmethyl spinosad was produced when SpnS was expressed at low level. Although N-monodesmethyl spinosad can be almost fully eliminated with high SpnS expression level, the titer of desired product spinosad was only increased by less than 38%. When the forosaminyl transferase SpnP was further overexpressed together with SpnS, the titer of spinosad was improved by 5.3 folds and the content of N-desmethyl derivatives was decreased by ~ 90%. CONCLUSION N-monodesmethyl spinosad was produced due to unbalanced expression of spnS and upstream biosynthetic genes in the refactored artificial gene cluster. The accumulated N-desmethyl forosamine was transferred onto the lactone backbone by SpnP. This study suggested that balanced expression of biosynthetic genes should be considered in the refactoring strategy to avoid accumulation of undesired intermediates or analogues which may affect optimal production of desired compounds.
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Affiliation(s)
- Xiaochen Li
- grid.27255.370000 0004 1761 1174State Key Laboratory of Microbial Technology, Institute of Microbial Technology, Helmholtz International Lab for Anti-infectives, Shandong University–Helmholtz Institute of Biotechnology, Shandong University, Binhai Rd 72, Qingdao, 266237 Shandong China
| | - Ruofei Guo
- grid.27255.370000 0004 1761 1174State Key Laboratory of Microbial Technology, Institute of Microbial Technology, Helmholtz International Lab for Anti-infectives, Shandong University–Helmholtz Institute of Biotechnology, Shandong University, Binhai Rd 72, Qingdao, 266237 Shandong China
| | - Ji Luan
- grid.27255.370000 0004 1761 1174State Key Laboratory of Microbial Technology, Institute of Microbial Technology, Helmholtz International Lab for Anti-infectives, Shandong University–Helmholtz Institute of Biotechnology, Shandong University, Binhai Rd 72, Qingdao, 266237 Shandong China
| | - Jun Fu
- grid.27255.370000 0004 1761 1174State Key Laboratory of Microbial Technology, Institute of Microbial Technology, Helmholtz International Lab for Anti-infectives, Shandong University–Helmholtz Institute of Biotechnology, Shandong University, Binhai Rd 72, Qingdao, 266237 Shandong China
| | - Youming Zhang
- grid.27255.370000 0004 1761 1174State Key Laboratory of Microbial Technology, Institute of Microbial Technology, Helmholtz International Lab for Anti-infectives, Shandong University–Helmholtz Institute of Biotechnology, Shandong University, Binhai Rd 72, Qingdao, 266237 Shandong China
| | - Hailong Wang
- grid.27255.370000 0004 1761 1174State Key Laboratory of Microbial Technology, Institute of Microbial Technology, Helmholtz International Lab for Anti-infectives, Shandong University–Helmholtz Institute of Biotechnology, Shandong University, Binhai Rd 72, Qingdao, 266237 Shandong China
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Kong L, Deng Z, You D. Chemistry and biosynthesis of bacterial polycyclic xanthone natural products. Nat Prod Rep 2022; 39:2057-2095. [PMID: 36083257 DOI: 10.1039/d2np00046f] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/22/2023]
Abstract
Covering: up to the end of 2021Bacterial polycyclic xanthone natural products (BPXNPs) are a growing family of natural xanthones featuring a pentangular architecture with various modifications to the tricyclic xanthone chromophore. Their structural diversities and various activities have fueled biosynthetic and chemical synthetic studies. Moreover, their more potent activities than the clinically used drugs make them potential candidates for the treatment of diseases. Future unraveling of structure activity relationships (SARs) will provide new options for the (bio)-synthesis of drug analogues with higher activities. This review summarizes the isolation, structural elucidation and biological activities and more importantly, the recent strategies for the microbial biosynthesis and chemical synthesis of BPXNPs. Regarding their biosynthesis, we discuss the recent progress in enzymes that synthesize tricyclic xanthone, the protein candidates for structural moieties (methylene dioxygen bridge and nitrogen heterocycle), tailoring enzymes for methylation and halogenation. The chemical synthesis part summarizes the recent methodology for the division synthesis and coupling construction of achiral molecular skeletons. Ultimately, perspectives on the biosynthetic study of BPXNPs are discussed.
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Affiliation(s)
- Lingxin Kong
- State Key Laboratory of Microbial Metabolism, Joint International Research Laboratory of Metabolic and Developmental Sciences, School of Life Sciences & Biotechnology, Shanghai Jiao Tong University, Shanghai 200240, China.
| | - Zixin Deng
- State Key Laboratory of Microbial Metabolism, Joint International Research Laboratory of Metabolic and Developmental Sciences, School of Life Sciences & Biotechnology, Shanghai Jiao Tong University, Shanghai 200240, China.
| | - Delin You
- State Key Laboratory of Microbial Metabolism, Joint International Research Laboratory of Metabolic and Developmental Sciences, School of Life Sciences & Biotechnology, Shanghai Jiao Tong University, Shanghai 200240, China.
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8
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Functional Characterization of a Regiospecific Sugar- O-Methyltransferase from Nocardia. Appl Environ Microbiol 2022; 88:e0075422. [PMID: 35703553 PMCID: PMC9275233 DOI: 10.1128/aem.00754-22] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Methyltransferases transfer a methyl group to a diverse group of natural products, thus providing structural diversity, stability, and altered pharmacological properties to the molecules. A limited number of regiospecific sugar-O-methyltransferases are functionally characterized. Thus, discovery of such an enzyme could solve the difficulties of biological production of methoxy derivatives of glycosylated molecules. In the current study, a regiospecific sugar-O-methyltransferase, ThnM1, belonging to the biosynthetic gene cluster (BGC) of 1-(α-L-(2-O-methyl)-6-deoxymannopyranosyloxy)-3,6,8-trimethoxynaphthalene produced by Nocardia sp. strain CS682, was analyzed and functionally characterized. ThnM1 demonstrated promiscuity to diverse chemical structures such as rhamnose-containing anthraquinones and flavonoids with regiospecific methylation at the 2′-hydroxyl group of the sugar moiety. Compared with other compounds, anthraquinone rhamnosides were found to be the preferred substrates for methylation. Thus, the enzyme was further employed for whole-cell biotransformation using engineered Escherichia coli to produce a methoxy-rhamnosyl derivative of quinizarin, an anthraquinone derivative. The structure of the newly generated derivative from Escherichia coli fermentation was elucidated by liquid chromatography-mass spectrometry and nuclear magnetic resonance spectroscopic analyses and identified as quinizarin-4-O-α-l-2-O-methylrhamnoside (QRM). Further, the biological impact of methylation was studied by comparing the cytotoxicity of QRM with that of quinizarin against the U87MG, SNU-1, and A375SM cancer cell lines. IMPORTANCE ThnM1 is a putative sugar-O-methyltransferase produced by the Nocardia sp. strain CS682 and is encoded by a gene belonging to the biosynthetic gene cluster (BGC) of 1-(α-l-(2-O-methyl)-6-deoxymannopyranosyloxy)-3,6,8-trimethoxynaphthalene. We demonstrated that ThnM1 is a promiscuous enzyme with regiospecific activity at the 2′-OH of rhamnose. As regiospecific methylation of sugars by chemical synthesis is a challenging step, ThnM1 may fill the gap in the potential diversification of natural products by methylating the rhamnose moiety attached to them.
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9
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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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10
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Comparative transcriptomic analysis of two Saccharopolyspora spinosa strains reveals the relationships between primary metabolism and spinosad production. Sci Rep 2021; 11:14779. [PMID: 34285307 PMCID: PMC8292330 DOI: 10.1038/s41598-021-94251-z] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2021] [Accepted: 07/06/2021] [Indexed: 11/23/2022] Open
Abstract
Saccharopolyspora spinosa is a well-known actinomycete for producing the secondary metabolites, spinosad, which is a potent insecticides possessing both efficiency and safety. In the previous researches, great efforts, including physical mutagenesis, fermentation optimization, genetic manipulation and other methods, have been employed to increase the yield of spinosad to hundreds of folds from the low-yield strain. However, the metabolic network in S. spinosa still remained un-revealed. In this study, two S. spinosa strains with different spinosad production capability were fermented and sampled at three fermentation periods. Then the total RNA of these samples was isolated and sequenced to construct the transcriptome libraries. Through transcriptomic analysis, large numbers of differentially expressed genes were identified and classified according to their different functions. According to the results, spnI and spnP were suggested as the bottleneck during spinosad biosynthesis. Primary metabolic pathways such as carbon metabolic pathways exhibited close relationship with spinosad formation, as pyruvate and phosphoenolpyruvic acid were suggested to accumulate in spinosad high-yield strain during fermentation. The addition of soybean oil in the fermentation medium activated the lipid metabolism pathway, enhancing spinosad production. Glutamic acid and aspartic acid were suggested to be the most important amino acids and might participate in spinosad biosynthesis.
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He H, Peng S, Yuan S, Tang J, Liu Z, Rang J, Xia Z, Hu J, Chen J, Ding X, Hu S, Sun Y, Xia L. Effects of lytS-L on the primary metabolism and butenyl-spinosyn biosynthesis in Saccharopolyspora pogona. Gene 2020; 766:145130. [PMID: 32911030 DOI: 10.1016/j.gene.2020.145130] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/27/2019] [Revised: 07/31/2020] [Accepted: 09/01/2020] [Indexed: 12/11/2022]
Abstract
The LytTR family two-component system widely exists in bacterial cells and plays an important role in metabolic regulation. The lytS-L gene that encodes for a LytTR family sensor kinase was knocked out to study its influence on the growth, phenotype, and the biosynthesis of the insecticidal polyketide butenyl-spinosyn in Saccharopolyspora pogona NRRL 30141 (S. pogona). High performance liquid chromatography (HPLC) results showed that the butenyl-spinosyn yield of the lytS-L knockout mutant decreased by 58.9% compared with that of the parental strain. This is manifested by a weak toxicity of the mutant against the insect Helicoverpa assulta (H. armigera). Comparative proteomic analysis revealed the expression characteristics of the proteins in S. pogona and S. pogona-ΔlytS-L: a total of 14 proteins involved in energy metabolism were down-regulated, 9 proteins related to carbon metabolism such as glycolysis, and tricarboxylic acid cycle (TCA) were up-regulated, while 13 proteins involved in the biosynthesis of butenyl-spinosyn were down-regulated (fold change >1.2 or< 0.83). The qRT-PCR (Quantitative Real-time PCR) analysis illustrated that the changes in the expression levels of transcription and translation of the identified genes were consistent. This study explores the function of the two-component system of the LytTR family in S. pogona and shows that the lytS-L gene has an important influence on regulating primary metabolism and butenyl-spinosyn biosynthesis of S. pogona.
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Affiliation(s)
- Haocheng He
- Hunan Provincial Key Laboratory for Microbial Molecular Biology, State Key Laboratory of Developmental Biology of Freshwater Fish, College of Life Science, Hunan Normal University, Changsha, China
| | - Shengnan Peng
- Hunan Provincial Key Laboratory for Microbial Molecular Biology, State Key Laboratory of Developmental Biology of Freshwater Fish, College of Life Science, Hunan Normal University, Changsha, China
| | - Shuangqin Yuan
- Hunan Provincial Key Laboratory for Microbial Molecular Biology, State Key Laboratory of Developmental Biology of Freshwater Fish, College of Life Science, Hunan Normal University, Changsha, China
| | - Jianli Tang
- Hunan Provincial Key Laboratory for Microbial Molecular Biology, State Key Laboratory of Developmental Biology of Freshwater Fish, College of Life Science, Hunan Normal University, Changsha, China
| | - Zhudong Liu
- Hunan Provincial Key Laboratory for Microbial Molecular Biology, State Key Laboratory of Developmental Biology of Freshwater Fish, College of Life Science, Hunan Normal University, Changsha, China
| | - Jie Rang
- Hunan Provincial Key Laboratory for Microbial Molecular Biology, State Key Laboratory of Developmental Biology of Freshwater Fish, College of Life Science, Hunan Normal University, Changsha, China
| | - Ziyuan Xia
- Hunan Provincial Key Laboratory for Microbial Molecular Biology, State Key Laboratory of Developmental Biology of Freshwater Fish, College of Life Science, Hunan Normal University, Changsha, China
| | - Jinjuan Hu
- Hunan Provincial Key Laboratory for Microbial Molecular Biology, State Key Laboratory of Developmental Biology of Freshwater Fish, College of Life Science, Hunan Normal University, Changsha, China
| | - Jianming Chen
- Hunan Provincial Key Laboratory for Microbial Molecular Biology, State Key Laboratory of Developmental Biology of Freshwater Fish, College of Life Science, Hunan Normal University, Changsha, China
| | - Xuezhi Ding
- Hunan Provincial Key Laboratory for Microbial Molecular Biology, State Key Laboratory of Developmental Biology of Freshwater Fish, College of Life Science, Hunan Normal University, Changsha, China
| | - Shengbiao Hu
- Hunan Provincial Key Laboratory for Microbial Molecular Biology, State Key Laboratory of Developmental Biology of Freshwater Fish, College of Life Science, Hunan Normal University, Changsha, China
| | - Yunjun Sun
- Hunan Provincial Key Laboratory for Microbial Molecular Biology, State Key Laboratory of Developmental Biology of Freshwater Fish, College of Life Science, Hunan Normal University, Changsha, China.
| | - Liqiu Xia
- Hunan Provincial Key Laboratory for Microbial Molecular Biology, State Key Laboratory of Developmental Biology of Freshwater Fish, College of Life Science, Hunan Normal University, Changsha, China.
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Kong L, Wang Q, Yang W, Shen J, Li Y, Zheng X, Wang L, Chu Y, Deng Z, Chooi YH, You D. Three Recently Diverging Duplicated Methyltransferases Exhibit Substrate-Dependent Regioselectivity Essential for Xantholipin Biosynthesis. ACS Chem Biol 2020; 15:2107-2115. [PMID: 32649177 DOI: 10.1021/acschembio.0c00296] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/22/2023]
Abstract
Polycyclic xanthones are characterized by highly oxygenated, angular hexacyclic frameworks and exhibit diverse biological activities. Although many of them have been isolated and chemically synthesized, the detailed biosynthetic machinery awaits discovery. Recently, xanthone construction in the xantholipin (1) pathway was shown to involve cryptic demethoxylation. This suggested a rationale for the existence of three O-methyltransferase (OMT) genes in the gene cluster, although there are only two O-methyl groups in the structure of 1. Here, in vivo and in vitro analysis have been used to show that the three paralogous OMTs, XanM1-M3, introduce individual methyl groups at specific points in the biosynthetic pathway. Each OMT can to some extent take over the role of the other OMTs, although they exhibit highly substrate-dependent regiospecificity. In addition, phylogenetic analysis suggests their evolution from a common ancestor. Four putative ancestral proteins were constructed, and one of them performed all the functions of XanM1-M3, while the others possessed more limited catalytic functions. The results suggest that a promiscuous common ancestor may have been able to catalyze all three reactions prior to gene duplication and functional divergence. The characterization of XanM1-M3 expands the enzyme inventory for polycyclic xanthone biosynthesis and suggests novel directed evolution approaches to diversifying natural product pathways.
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Affiliation(s)
- Lingxin Kong
- State Key Laboratory of Microbial Metabolism, Joint International Research Laboratory of Metabolic and Developmental Sciences, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai 200030, China
| | - Qing Wang
- State Key Laboratory of Microbial Metabolism, Joint International Research Laboratory of Metabolic and Developmental Sciences, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai 200030, China
| | - Weinan Yang
- State Key Laboratory of Microbial Metabolism, Joint International Research Laboratory of Metabolic and Developmental Sciences, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai 200030, China
| | - Jufang Shen
- State Key Laboratory of Microbial Metabolism, Joint International Research Laboratory of Metabolic and Developmental Sciences, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai 200030, China
| | - Yan Li
- State Key Laboratory of Microbial Metabolism, Joint International Research Laboratory of Metabolic and Developmental Sciences, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai 200030, China
| | - Xiaoqing Zheng
- State Key Laboratory of Microbial Metabolism, Joint International Research Laboratory of Metabolic and Developmental Sciences, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai 200030, China
| | - Lu Wang
- Sichuan Industrial Institute of Antibiotics, Chengdu University, Chengdu 610052, China
| | - Yiwen Chu
- Sichuan Industrial Institute of Antibiotics, Chengdu University, Chengdu 610052, China
| | - Zixin Deng
- State Key Laboratory of Microbial Metabolism, Joint International Research Laboratory of Metabolic and Developmental Sciences, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai 200030, China
| | - Yit-Heng Chooi
- School of Molecular Sciences, University of Western Australia, Perth, Western Australia 6009, Australia
| | - Delin You
- State Key Laboratory of Microbial Metabolism, Joint International Research Laboratory of Metabolic and Developmental Sciences, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai 200030, China
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Song C, Luan J, Cui Q, Duan Q, Li Z, Gao Y, Li R, Li A, Shen Y, Li Y, Stewart AF, Zhang Y, Fu J, Wang H. Enhanced Heterologous Spinosad Production from a 79-kb Synthetic Multioperon Assembly. ACS Synth Biol 2019; 8:137-147. [PMID: 30590919 DOI: 10.1021/acssynbio.8b00402] [Citation(s) in RCA: 32] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
Refactoring biosynthetic pathways for enhanced secondary metabolite production is a central challenge for synthetic biology. Here we applied advanced DNA assembly methods and a uniform overexpression logic using constitutive promoters to achieve efficient heterologous production of the complex insecticidal macrolide spinosad. We constructed a 79-kb artificial gene cluster in which 23 biosynthetic genes were grouped into 7 operons, each with a strong constitutive promoter. Compared with the original gene cluster, the artificial gene cluster resulted in a 328-fold enhanced spinosad production in Streptomyces albus J1074. To achieve this goal, we applied the ExoCET DNA assembly method to build a plasmid from 13 GC-rich fragments with high efficiency in one step. Together with our previous direct cloning and recombineering tools, we present new synthetic biology options for refactoring large gene clusters for diverse applications.
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Affiliation(s)
- Chaoyi Song
- Shandong University−Helmholtz Institute of Biotechnology, State Key Laboratory of Microbial Technology, School of Life Science, Shandong University, Binhai Road 72, 266237 Qingdao, People’s Republic of China
| | - Ji Luan
- Shandong University−Helmholtz Institute of Biotechnology, State Key Laboratory of Microbial Technology, School of Life Science, Shandong University, Binhai Road 72, 266237 Qingdao, People’s Republic of China
| | - Qingwen Cui
- Shandong University−Helmholtz Institute of Biotechnology, State Key Laboratory of Microbial Technology, School of Life Science, Shandong University, Binhai Road 72, 266237 Qingdao, People’s Republic of China
| | - Qiuyue Duan
- Shandong University−Helmholtz Institute of Biotechnology, State Key Laboratory of Microbial Technology, School of Life Science, Shandong University, Binhai Road 72, 266237 Qingdao, People’s Republic of China
| | - Zhen Li
- Shandong University−Helmholtz Institute of Biotechnology, State Key Laboratory of Microbial Technology, School of Life Science, Shandong University, Binhai Road 72, 266237 Qingdao, People’s Republic of China
| | - Yunsheng Gao
- Shandong University−Helmholtz Institute of Biotechnology, State Key Laboratory of Microbial Technology, School of Life Science, Shandong University, Binhai Road 72, 266237 Qingdao, People’s Republic of China
| | - Ruijuan Li
- Shandong University−Helmholtz Institute of Biotechnology, State Key Laboratory of Microbial Technology, School of Life Science, Shandong University, Binhai Road 72, 266237 Qingdao, People’s Republic of China
| | - Aiying Li
- Shandong University−Helmholtz Institute of Biotechnology, State Key Laboratory of Microbial Technology, School of Life Science, Shandong University, Binhai Road 72, 266237 Qingdao, People’s Republic of China
| | - Yuemao Shen
- Shandong University−Helmholtz Institute of Biotechnology, State Key Laboratory of Microbial Technology, School of Life Science, Shandong University, Binhai Road 72, 266237 Qingdao, People’s Republic of China
| | - Yuezhong Li
- Shandong University−Helmholtz Institute of Biotechnology, State Key Laboratory of Microbial Technology, School of Life Science, Shandong University, Binhai Road 72, 266237 Qingdao, People’s Republic of China
| | - A. Francis Stewart
- Genomics, Biotechnology Center, Technische Universität Dresden, Tatzberg 47-51, Dresden 01307, Germany
- GenArc GmbH, BioInnovationsZentrum, Tatzberg 47, Dresden 01307, Germany
| | - Youming Zhang
- Shandong University−Helmholtz Institute of Biotechnology, State Key Laboratory of Microbial Technology, School of Life Science, Shandong University, Binhai Road 72, 266237 Qingdao, People’s Republic of China
| | - Jun Fu
- Shandong University−Helmholtz Institute of Biotechnology, State Key Laboratory of Microbial Technology, School of Life Science, Shandong University, Binhai Road 72, 266237 Qingdao, People’s Republic of China
| | - Hailong Wang
- Shandong University−Helmholtz Institute of Biotechnology, State Key Laboratory of Microbial Technology, School of Life Science, Shandong University, Binhai Road 72, 266237 Qingdao, People’s Republic of China
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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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16
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Saccharopolyspora hattusasensis sp. nov., isolated from soil. Antonie Van Leeuwenhoek 2017; 110:1719-1727. [DOI: 10.1007/s10482-017-0921-8] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2017] [Accepted: 07/29/2017] [Indexed: 10/19/2022]
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17
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Dai P, Wang CX, Gao H, Wang QZ, Tang XL, Chen GD, Hong K, Hu D, Yao XS. Characterization of Methyltransferase AlmCII in Chalcomycin Biosynthesis: The First TylF Family O-Methyltransferase Works on a 4'-Deoxysugar. Chembiochem 2017; 18:1510-1517. [PMID: 28488816 DOI: 10.1002/cbic.201700216] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2017] [Indexed: 11/11/2022]
Abstract
Sugar O-methylation is a ubiquitous modification in natural products and plays diverse roles. This realization has inspired many attempts to search for novel methyltransferases. Chalcomycins are a group of 16-membered macrolides containing two methylated sugars that require three methyltransferases for their biosynthesis. Here, we identified that AlmCII, a sugar O-methyltransferase belonging to the TylF family that was previously only known to methylate sugars with a 4'-hydroxy group, can methylate a 4',6'-dideoxysugar during the biosynthesis of chalcomycins. An in vitro enzymatic assay revealed that AlmCII is divalent metal-dependent with an optimal pH of 8.0 and optimal temperature of 42 °C. Moreover, the 3'-O-demethylated chalcomycins exhibit less than 6 % of the antibacterial activity of their parent compounds. This is the first report demonstrating that a TylF family O-methyltransferase can use a 4'-deoxy sugar as a substrate and highlighting the importance of this methylation for the antibacterial activity of chalcomycins.
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Affiliation(s)
- Ping Dai
- Institute of Traditional Chinese Medicine and Natural Products, College of Pharmacy, Jinan University, No. 601 Huangpu Avenue, Guangzhou, 510632, P. R. China
| | - Chuan-Xi Wang
- Institute of Traditional Chinese Medicine and Natural Products, College of Pharmacy, Jinan University, No. 601 Huangpu Avenue, Guangzhou, 510632, P. R. China
| | - Hao Gao
- Institute of Traditional Chinese Medicine and Natural Products, College of Pharmacy, Jinan University, No. 601 Huangpu Avenue, Guangzhou, 510632, P. R. China
| | - Qiao-Zhen Wang
- Institute of Traditional Chinese Medicine and Natural Products, College of Pharmacy, Jinan University, No. 601 Huangpu Avenue, Guangzhou, 510632, P. R. China
| | - Xiao-Long Tang
- Institute of Traditional Chinese Medicine and Natural Products, College of Pharmacy, Jinan University, No. 601 Huangpu Avenue, Guangzhou, 510632, P. R. China
| | - Guo-Dong Chen
- Institute of Traditional Chinese Medicine and Natural Products, College of Pharmacy, Jinan University, No. 601 Huangpu Avenue, Guangzhou, 510632, P. R. China
| | - Kui Hong
- Key Laboratory of Combinatorial Biosynthesis and Drug Discovery, Ministry of Education, School of Pharmaceutical Sciences, Wuhan University, No. 185 Donghu Road, Wuhan, 430071, P. R. China
| | - Dan Hu
- Institute of Traditional Chinese Medicine and Natural Products, College of Pharmacy, Jinan University, No. 601 Huangpu Avenue, Guangzhou, 510632, P. R. China.,State Key Laboratory of Bioorganic and Natural Products Chemistry, Shanghai Institute of Organic Chemistry, University of Chinese Academy of Sciences, No.345 Lingling Road, Shanghai, 200032, P. R. China
| | - Xin-Sheng Yao
- Institute of Traditional Chinese Medicine and Natural Products, College of Pharmacy, Jinan University, No. 601 Huangpu Avenue, Guangzhou, 510632, P. R. China
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18
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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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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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Parajuli P, Pandey RP, Huyen Nguyen TT, Shrestha B, Yamaguchi T, Sohng JK. Biosynthesis of natural and non-natural genistein glycosides. RSC Adv 2017. [DOI: 10.1039/c6ra28145a] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/02/2023] Open
Abstract
Biosynthesis of various genistein glycopyranoside scaffolds using versatile GTs and SOMTs. Each compound was structurally characterized and biological activity assay was carried out.
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Affiliation(s)
- Prakash Parajuli
- Department of Life Science and Biochemical Engineering
- Sun Moon University
- Tangjeong-myeon Asan-Si
- Republic of Korea
| | - Ramesh Prasad Pandey
- Department of Life Science and Biochemical Engineering
- Sun Moon University
- Tangjeong-myeon Asan-Si
- Republic of Korea
- Department of BT-Convergent Pharmaceutical Engineering
| | - Trang Thi Huyen Nguyen
- Department of Life Science and Biochemical Engineering
- Sun Moon University
- Tangjeong-myeon Asan-Si
- Republic of Korea
| | - Biplav Shrestha
- Department of Life Science and Biochemical Engineering
- Sun Moon University
- Tangjeong-myeon Asan-Si
- Republic of Korea
| | - Tokutaro Yamaguchi
- Department of Life Science and Biochemical Engineering
- Sun Moon University
- Tangjeong-myeon Asan-Si
- Republic of Korea
- Department of BT-Convergent Pharmaceutical Engineering
| | - Jae Kyung Sohng
- Department of Life Science and Biochemical Engineering
- Sun Moon University
- Tangjeong-myeon Asan-Si
- Republic of Korea
- Department of BT-Convergent Pharmaceutical Engineering
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Genome mining of the sordarin biosynthetic gene cluster from Sordaria araneosa Cain ATCC 36386: characterization of cycloaraneosene synthase and GDP-6-deoxyaltrose transferase. J Antibiot (Tokyo) 2016; 69:541-8. [PMID: 27072286 DOI: 10.1038/ja.2016.40] [Citation(s) in RCA: 41] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2016] [Revised: 03/04/2016] [Accepted: 03/13/2016] [Indexed: 01/24/2023]
Abstract
Sordarin is a glycoside antibiotic with a unique tetracyclic diterpene aglycone structure called sordaricin. To understand its intriguing biosynthetic pathway that may include a Diels-Alder-type [4+2]cycloaddition, genome mining of the gene cluster from the draft genome sequence of the producer strain, Sordaria araneosa Cain ATCC 36386, was carried out. A contiguous 67 kb gene cluster consisting of 20 open reading frames encoding a putative diterpene cyclase, a glycosyltransferase, a type I polyketide synthase, and six cytochrome P450 monooxygenases were identified. In vitro enzymatic analysis of the putative diterpene cyclase SdnA showed that it catalyzes the transformation of geranylgeranyl diphosphate to cycloaraneosene, a known biosynthetic intermediate of sordarin. Furthermore, a putative glycosyltransferase SdnJ was found to catalyze the glycosylation of sordaricin in the presence of GDP-6-deoxy-d-altrose to give 4'-O-demethylsordarin. These results suggest that the identified sdn gene cluster is responsible for the biosynthesis of sordarin. Based on the isolated potential biosynthetic intermediates and bioinformatics analysis, a plausible biosynthetic pathway for sordarin is proposed.
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Natural product derived insecticides: discovery and development of spinetoram. ACTA ACUST UNITED AC 2016; 43:185-93. [DOI: 10.1007/s10295-015-1710-x] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2015] [Accepted: 11/02/2015] [Indexed: 12/23/2022]
Abstract
Abstract
This review highlights the importance of natural product research and industrial microbiology for product development in the agricultural industry, based on examples from Dow AgroSciences. It provides an overview of the discovery and development of spinetoram, a semisynthetic insecticide derived by a combination of a genetic block in a specific O-methylation of the rhamnose moiety of spinosad coupled with neural network-based QSAR and synthetic chemistry. It also emphasizes the key role that new technologies and multidisciplinary approaches play in the development of current spinetoram production strains.
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Zhao F, Zhang C, Yin J, Shen Y, Lu W. Coupling of Spinosad Fermentation and Separation Process via Two-Step Macroporous Resin Adsorption Method. Appl Biochem Biotechnol 2015; 176:2144-56. [PMID: 26077683 DOI: 10.1007/s12010-015-1704-1] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2015] [Accepted: 06/02/2015] [Indexed: 10/23/2022]
Abstract
In this paper, a two-step resin adsorption technology was investigated for spinosad production and separation as follows: the first step resin addition into the fermentor at early cultivation period to decrease the timely product concentration in the broth; the second step of resin addition was used after fermentation to adsorb and extract the spinosad. Based on this, a two-step macroporous resin adsorption-membrane separation process for spinosad fermentation, separation, and purification was established. Spinosad concentration in 5-L fermentor increased by 14.45 % after adding 50 g/L macroporous at the beginning of fermentation. The established two-step macroporous resin adsorption-membrane separation process got the 95.43 % purity and 87 % yield for spinosad, which were both higher than that of the conventional crystallization of spinosad from aqueous phase that were 93.23 and 79.15 % separately. The two-step macroporous resin adsorption method has not only carried out the coupling of spinosad fermentation and separation but also increased spinosad productivity. In addition, the two-step macroporous resin adsorption-membrane separation process performs better in spinosad yield and purity.
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Affiliation(s)
- Fanglong Zhao
- Department of Biological Engineering, School of Chemical Engineering and Technology, Tianjin University, Tianjin, 300072, People's Republic of China
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Bernard SM, Akey DL, Tripathi A, Park SR, Konwerski JR, Anzai Y, Li S, Kato F, Sherman DH, Smith JL. Structural basis of substrate specificity and regiochemistry in the MycF/TylF family of sugar O-methyltransferases. ACS Chem Biol 2015; 10:1340-51. [PMID: 25692963 DOI: 10.1021/cb5009348] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Abstract
Sugar moieties in natural products are frequently modified by O-methylation. In the biosynthesis of the macrolide antibiotic mycinamicin, methylation of a 6'-deoxyallose substituent occurs in a stepwise manner first at the 2'- and then the 3'-hydroxyl groups to produce the mycinose moiety in the final product. The timing and placement of the O-methylations impact final stage C-H functionalization reactions mediated by the P450 monooxygenase MycG. The structural basis of pathway ordering and substrate specificity is unknown. A series of crystal structures of MycF, the 3'-O-methyltransferase, including the free enzyme and complexes with S-adenosyl homocysteine (SAH), substrate, product, and unnatural substrates, show that SAM binding induces substantial ordering that creates the binding site for the natural substrate, and a bound metal ion positions the substrate for catalysis. A single amino acid substitution relaxed the 2'-methoxy specificity but retained regiospecificity. The engineered variant produced a new mycinamicin analog, demonstrating the utility of structural information to facilitate bioengineering approaches for the chemoenzymatic synthesis of complex small molecules containing modified sugars. Using the MycF substrate complex and the modeled substrate complex of a 4'-specific homologue, active site residues were identified that correlate with the 3' or 4' specificity of MycF family members and define the protein and substrate features that direct the regiochemistry of methyltransfer. This classification scheme will be useful in the annotation of new secondary metabolite pathways that utilize this family of enzymes.
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Affiliation(s)
- Steffen M. Bernard
- Chemical
Biology Doctoral Program, University of Michigan, Ann Arbor, Michigan 48109, United States
- Life
Sciences Institute, University of Michigan, Ann Arbor, Michigan 48109, United States
| | - David L. Akey
- Life
Sciences Institute, University of Michigan, Ann Arbor, Michigan 48109, United States
| | - Ashootosh Tripathi
- Life
Sciences Institute, University of Michigan, Ann Arbor, Michigan 48109, United States
| | - Sung Ryeol Park
- Life
Sciences Institute, University of Michigan, Ann Arbor, Michigan 48109, United States
| | - Jamie R. Konwerski
- Life
Sciences Institute, University of Michigan, Ann Arbor, Michigan 48109, United States
| | - Yojiro Anzai
- Faculty
of Pharmaceutical Sciences, Toho University, 2-2-1 Miyama, Funabashi, Chiba 274-8510, Japan
| | - Shengying Li
- Life
Sciences Institute, University of Michigan, Ann Arbor, Michigan 48109, United States
| | - Fumio Kato
- Faculty
of Pharmaceutical Sciences, Toho University, 2-2-1 Miyama, Funabashi, Chiba 274-8510, Japan
| | - David H. Sherman
- Life
Sciences Institute, University of Michigan, Ann Arbor, Michigan 48109, United States
- Departments of Medicinal Chemistry, Chemistry, and Microbiology & Immunology, University of Michigan, Ann Arbor, Michigan 48109, United States
| | - Janet L. Smith
- Life
Sciences Institute, University of Michigan, Ann Arbor, Michigan 48109, United States
- Department
of Biological Chemistry, University of Michigan, Ann Arbor, Michigan 48109, United States
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Chen JM, Shepherd MD, Horn J, Leggas M, Rohr J. Enzymatic methylation and structure-activity-relationship studies on polycarcin V, a gilvocarcin-type antitumor agent. Chembiochem 2014; 15:2729-35. [PMID: 25366963 PMCID: PMC4266428 DOI: 10.1002/cbic.201402426] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2014] [Indexed: 11/06/2022]
Abstract
Polycarcin V, a polyketide natural product of Streptomyces polyformus, was chosen to study structure-activity relationships of the gilvocarcin group of antitumor antibiotics due to a similar chemical structure and comparable bioactivity with gilvocarcin V, the principle compound of this group, and the feasibility of enzymatic modifications of its sugar moiety by auxiliary O-methyltransferases. Such enzymes were used to modify the interaction of the drug with histone H3, the biological target that interacts with the sugar moiety. Cytotoxicity assays revealed that a free 2'-OH group of the sugar moiety is essential to maintain the bioactivity of polycarcin V, apparently an important hydrogen bond donor for the interaction with histone H3, and converting 3'-OH into an OCH3 group improved the bioactivity. Bis-methylated polycarcin derivatives revealed weaker activity than the parent compound, indicating that at least two hydrogen bond donors in the sugar are necessary for optimal binding.
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Affiliation(s)
- Jhong-Min Chen
- Department of Pharmaceutical Sciences, College of Pharmacy, University of Kentucky, 789 South Limestone Street, Lexington, Kentucky 40536-0596, USA
| | - Micah D. Shepherd
- Department of Pharmaceutical Sciences, College of Pharmacy, University of Kentucky, 789 South Limestone Street, Lexington, Kentucky 40536-0596, USA
- ZuChem Inc., Next Innovation Center, 801 West Main Street, Peoria, Illinois 61606-1877, USA
| | - Jamie Horn
- Department of Pharmaceutical Sciences, College of Pharmacy, University of Kentucky, 789 South Limestone Street, Lexington, Kentucky 40536-0596, USA
| | - Markos Leggas
- Department of Pharmaceutical Sciences, College of Pharmacy, University of Kentucky, 789 South Limestone Street, Lexington, Kentucky 40536-0596, USA
- Center for Pharmaceutical Science and Innovation, College of Pharmacy, University of Kentucky, 789 South Limestone Street, Lexington, Kentucky 40536-0596, USA
| | - Jürgen Rohr
- Department of Pharmaceutical Sciences, College of Pharmacy, University of Kentucky, 789 South Limestone Street, Lexington, Kentucky 40536-0596, USA
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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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Jha AK, Pokhrel AR, Chaudhary AK, Park SW, Cho WJ, Sohng JK. Metabolic engineering of rational screened Saccharopolyspora spinosa for the enhancement of spinosyns A and D production. Mol Cells 2014; 37:727-33. [PMID: 25256218 PMCID: PMC4213763 DOI: 10.14348/molcells.2014.0168] [Citation(s) in RCA: 7] [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: 06/16/2014] [Revised: 08/19/2014] [Accepted: 08/19/2014] [Indexed: 12/04/2022] Open
Abstract
Spinosyns A and D are potent ingredient for insect control with exceptional safety to non-target organisms. It consists of a 21-carbon tetracyclic lactone with forosamine and tri-O-methylated rhamnose which are derived from S-adenosylmethionine. Although previous studies have revealed the involvement of metK1 (S-adenosylmethionine synthetase), rmbA (glucose-1-phosphate thymidylyltransferase), and rmbB (TDP-D-glucose-4, 6-dehydratase) in the biosynthesis of spinosad, expression of these genes into rational screened Saccharopolyspora spinosa (S. spinosa MUV) has not been elucidated till date. In the present study, S. spinosa MUV was developed to utilize for metabolic engineering. The yield of spinosyns A and D in S. spinosa MUV was 244 mg L(-1) and 129 mg L(-1), which was 4.88-fold and 4.77-fold higher than that in the wild-type (50 mg L(-1) and 27 mg L(-1)), respectively. To achieve the better production; positive regulator metK1-sp, rmbA and rmbB genes from Streptomyces peucetius, were expressed and co-expressed in S. spinosa MUV under the control of strong ermE* promoter, using an integration vector pSET152 and expression vector pIBR25, respectively. Herewith, the genetically engineered strain of S. spinosa MUV, produce spinosyns A and D up to 372/217 mg L(-1) that is 7.44/8.03-fold greater than that of wild type. This result demonstrates the use of metabolic engineering on rationally developed high producing natural variants for the production.
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Affiliation(s)
- Amit Kumar Jha
- Institute of Biomolecule Reconstruction (iBR), Department of Pharmaceutical Engineering, Sun Moon University, Asan 333-708,
Korea
| | - Anaya Raj Pokhrel
- Institute of Biomolecule Reconstruction (iBR), Department of Pharmaceutical Engineering, Sun Moon University, Asan 333-708,
Korea
| | - Amit Kumar Chaudhary
- Institute of Biomolecule Reconstruction (iBR), Department of Pharmaceutical Engineering, Sun Moon University, Asan 333-708,
Korea
| | | | | | - Jae Kyung Sohng
- Institute of Biomolecule Reconstruction (iBR), Department of Pharmaceutical Engineering, Sun Moon University, Asan 333-708,
Korea
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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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Draft Genome Sequence of Insecticidal
Streptomyces
sp. Strain PCS3-D2, Isolated from Mangrove Soil in Philippines. GENOME ANNOUNCEMENTS 2014; 2:2/3/e00448-14. [PMID: 24926046 PMCID: PMC4056289 DOI: 10.1128/genomea.00448-14] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
Abstract
A draft genome sequence of a Streptomyces sp. isolated from mangrove soil in Cebu, Philippines, is described here. This isolate produced compounds with contact insecticidal activity against important corn pests. The genome contains 7,479,793 bp (in 27 scaffolds), 6,297 predicted genes, and 29 secondary metabolite biosynthetic gene clusters.
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Wang X, Zhang C, Wang M, Lu W. Genome-scale metabolic network reconstruction of Saccharopolyspora spinosa for spinosad production improvement. Microb Cell Fact 2014; 13:41. [PMID: 24628959 PMCID: PMC4003821 DOI: 10.1186/1475-2859-13-41] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2013] [Accepted: 03/12/2014] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Spinosad is a macrolide antibiotic produced by Saccharopolyspora spinosa with aerobic fermentation. However, the wild strain has a low productivity. In this article, a computational guided engineering approach was adopted in order to improve the yield of spinosad in S. spinosa. RESULTS Firstly, a genome-scale metabolic network reconstruction (GSMR) for S.spinosa based on its genome information, literature data and experimental data was established. The model was consists of 1,577 reactions, 1,726 metabolites, and 733 enzymes after manually refined. Then, amino acids supplying experiments were performed in order to test the capabilities of the model, and the results showed a high consistency. Subsequently, transhydrogenase (PntAB, EC 1.6.1.2) was chosen as the potential target for spinosad yield improvement based on the in silico metabolic network models. Furthermore, the target gene was manipulated in the parent strain in order to validate the model predictions. At last, shake flask fermentation was carried out which led to spinosad production of 75.32 mg/L, 86.5% higher than the parent strain (40.39 mg/L). CONCLUSIONS Results confirmed the model had a high potential in engineering S. spinosa for spinosad production. It is the first GSMM for S.spinosa, it has significance for a better understanding of the comprehensive metabolism and guiding strain designing of Saccharopolyspora spinosa in the future.
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Affiliation(s)
| | | | | | - Wenyu Lu
- Department of Biological Engineering, School of Chemical Engineering and Technology, Tianjin University, Tianjin 300072, PR China.
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31
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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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Saccharopolyspora ghardaiensis sp. nov., an extremely halophilic actinomycete isolated from Algerian Saharan soil. J Antibiot (Tokyo) 2013; 67:299-303. [PMID: 24346634 DOI: 10.1038/ja.2013.136] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2013] [Revised: 10/23/2013] [Accepted: 11/15/2013] [Indexed: 11/08/2022]
Abstract
A novel halophilic actinomycete, strain designated H53(T), was isolated from a Saharan soil sample collected from Chaâbet Ntissa, Béni-isguen, Ghardaïa (South of Algeria) and was characterized taxonomically by means of polyphasic approach. Optimal growth was found to occur at 30-35 °C, pH 6-7 and in the presence of 15-25% (w/v) NaCl. The strain was observed to produce abundant aerial mycelium, which formed long chains of rod-shaped spores at maturity, and well developed and fragmented substrate mycelium. The cell wall was determined to contain meso-diaminopimelic acid; the diagnostic whole-cell sugars were arabinose and galactose. The predominant menaquinones were found to be MK-9(H₄) and MK-9(H₆). The predominant cellular fatty acids were determined to be iso- and anteiso-C17:0, iso-C15:0, and cis9 iso-C17:1. The diagnostic phospholipid detected was phosphatidylcholine. The morphological and chemotaxonomic characteristics of the strain were consistent with those of members of the genus Saccharopolyspora. Phylogenetic analyses on the basis of the 16S ribosomal RNA (rRNA) gene sequence showed that this strain formed a distinct phyletic line within the radiation of the genus Saccharopolyspora. The 16S rRNA sequence similarities between strain H53(T) and other members of the genus Saccharopolyspora ranged from 92.1 to 94.3%. The DNA G+C content of strain H53(T) was 72.6%. The genotypic and phenotypic data showed that the strain H53(T) represents a novel species of the genus Saccharopolyspora, for which the name Saccharopolyspora ghardaiensis sp. nov. is proposed, with the type strain H53(T) (=DSM 45606(T)=CCUG 63370(T)=CECT 8304(T)).
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A comparative metabolomics analysis of Saccharopolyspora spinosa WT, WH124, and LU104 revealed metabolic mechanisms correlated with increases in spinosad yield. Biosci Biotechnol Biochem 2013; 77:1661-8. [PMID: 23924726 DOI: 10.1271/bbb.130169] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/15/2023]
Abstract
Metabolomics analysis of three Saccharopolyspora spinosa strains (wild type strain WT, ultraviolet mutant strain WH124, and metabolic engineering strain LU104) with different spinosad producing levels was performed by liquid chromatograph coupled to mass spectrometry (LC-MS). The metabolite profiles were subjected to hierarchal clustering analysis (HCA) and principal component analysis (PCA). The results of HCA on a heat map revealed that the large numbers of primary metabolism detected were more abundant in WH124 and less abundant in LU104 during the early fermentation stage as compared to the WT strain. PCA separated the three strains clearly and suggested nine metabolites that contributed predominantly to the separation. These biomarkers were associated with central carbon metabolism (succinic acid, α-ketoglutarate, acetyl-CoA, and ATP), amino acid metabolism (glutamate, glutamine, and valine), and secondary metabolism (pseudoaglycone), etc. These findings provide insight into the metabolomic characteristics of the two high-yield strains and for further regulation of spinosad production.
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Singh S, Chang A, Helmich KE, Bingman CA, Wrobel RL, Beebe ET, Makino SI, Aceti DJ, Dyer K, Hura GL, Sunkara M, Morris AJ, Phillips GN, Thorson JS. Structural and functional characterization of CalS11, a TDP-rhamnose 3'-O-methyltransferase involved in calicheamicin biosynthesis. ACS Chem Biol 2013; 8:1632-9. [PMID: 23662776 PMCID: PMC3875630 DOI: 10.1021/cb400068k] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Sugar methyltransferases (MTs) are an important class of tailoring enzymes that catalyze the transfer of a methyl group from S-adenosyl-l-methionine to sugar-based N-, C- and O-nucleophiles. While sugar N- and C-MTs involved in natural product biosynthesis have been found to act on sugar nucleotide substrates prior to a subsequent glycosyltransferase reaction, corresponding sugar O-methylation reactions studied thus far occur after the glycosyltransfer reaction. Herein we report the first in vitro characterization using (1)H-(13)C-gHSQC with isotopically labeled substrates and the X-ray structure determination at 1.55 Å resolution of the TDP-3'-O-rhamnose-methyltransferase CalS11 from Micromonospora echinospora. This study highlights a unique NMR-based methyltransferase assay, implicates CalS11 to be a metal- and general acid/base-dependent O-methyltransferase, and as a first crystal structure for a TDP-hexose-O-methyltransferase, presents a new template for mechanistic studies and/or engineering.
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Affiliation(s)
- Shanteri Singh
- Center for Pharmaceutical Research and Innovation, University of Kentucky College of Pharmacy, 789 South Limestone Street, Lexington, KY 40536-0596, USA
| | - Aram Chang
- Department of Biochemistry, University of Wisconsin-Madison, Madison, Wisconsin 53706, USA
| | - Kate E. Helmich
- Department of Biochemistry, University of Wisconsin-Madison, Madison, Wisconsin 53706, USA
| | - Craig A. Bingman
- Department of Biochemistry, University of Wisconsin-Madison, Madison, Wisconsin 53706, USA
| | - Russel L. Wrobel
- Department of Biochemistry, University of Wisconsin-Madison, Madison, Wisconsin 53706, USA
| | - Emily T. Beebe
- Department of Biochemistry, University of Wisconsin-Madison, Madison, Wisconsin 53706, USA
| | - Shin-Ichi Makino
- Department of Biochemistry, University of Wisconsin-Madison, Madison, Wisconsin 53706, USA
| | - David J. Aceti
- Department of Biochemistry, University of Wisconsin-Madison, Madison, Wisconsin 53706, USA
| | - Kevin Dyer
- Physical Bioscience Division, Lawrence Berkeley National Laboratory, Berkeley CA 94720, USA
| | - Greg L. Hura
- Physical Bioscience Division, Lawrence Berkeley National Laboratory, Berkeley CA 94720, USA
| | - Manjula Sunkara
- Division of Cardiovascular Medicine, University of Kentucky, Lexington, KY 40536, USA
| | - Andrew J. Morris
- Division of Cardiovascular Medicine, University of Kentucky, Lexington, KY 40536, USA
| | - George N. Phillips
- Department of Biochemistry, University of Wisconsin-Madison, Madison, Wisconsin 53706, USA
- Department of Biochemistry and Cell Biology, Rice University, Houston, Texas 77005, USA
| | - Jon S. Thorson
- Center for Pharmaceutical Research and Innovation, University of Kentucky College of Pharmacy, 789 South Limestone Street, Lexington, KY 40536-0596, USA
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Xue C, Duan Y, Zhao F, Lu W. Stepwise increase of spinosad production in Saccharopolyspora spinosa by metabolic engineering. Biochem Eng J 2013. [DOI: 10.1016/j.bej.2013.01.007] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
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Xu F, Kong D, He X, Zhang Z, Han M, Xie X, Wang P, Cheng H, Tao M, Zhang L, Deng Z, Lin S. Characterization of streptonigrin biosynthesis reveals a cryptic carboxyl methylation and an unusual oxidative cleavage of a N-C bond. J Am Chem Soc 2013; 135:1739-48. [PMID: 23301954 DOI: 10.1021/ja3069243] [Citation(s) in RCA: 31] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Streptonigrin (STN, 1) is a highly functionalized aminoquinone alkaloid with broad and potent antitumor activity. Here, we reported the biosynthetic gene cluster of STN identified by genome scanning of a STN producer Streptomyces flocculus CGMCC4.1223. This cluster consists of 48 genes determined by a series of gene inactivations. On the basis of the structures of intermediates and shunt products accumulated from five specific gene inactivation mutants and feeding experiments, the biosynthetic pathway was proposed, and the sequence of tailoring steps was preliminarily determined. In this pathway, a cryptic methylation of lavendamycin was genetically and biochemically characterized to be catalyzed by a leucine carboxyl methyltransferase StnF2. A [2Fe-2S](2+) cluster-containing aromatic ring dioxygenase StnB1/B2 system was biochemically characterized to catalyze a regiospecific cleavage of the N-C8' bond of the indole ring of the methyl ester of lavendamycin. This work provides opportunities to illuminate the enzymology of novel reactions involved in this pathway and to create, using genetic and chemo-enzymatic methods, new streptonigrinoid analogues as potential therapeutic agents.
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Affiliation(s)
- Fei Xu
- State Key Laboratory of Microbial Metabolism, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, 800 Dongchuan Road, Shanghai 200240, China
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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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Bioactive Natural Products as Potential Candidates to Control Aedes aegypti, the Vector of Dengue. STUDIES IN NATURAL PRODUCTS CHEMISTRY VOLUME 37 2012. [DOI: 10.1016/b978-0-444-59514-0.00010-9] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/01/2023]
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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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Niu S, Hu T, Li S, Xiao Y, Ma L, Zhang G, Zhang H, Yang X, Ju J, Zhang C. Characterization of a sugar-O-methyltransferase TiaS5 affords new Tiacumicin analogues with improved antibacterial properties and reveals substrate promiscuity. Chembiochem 2011; 12:1740-8. [PMID: 21633995 DOI: 10.1002/cbic.201100129] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2011] [Indexed: 12/18/2022]
Abstract
The 18-membered macrocyclic glycoside tiacumicin B, an RNA polymerase inhibitor, is of great therapeutic significance in treating Clostridium difficile infections. The recent characterization of the tiacumicin B biosynthetic gene cluster from Dactylosporangium aurantiacum subsp. hamdenensis NRRL 18085 revealed the functions of two glycosyltransferases, a C-methyltransferase, an acyltransferase, two cytochrome P450s, and a tailoring dihalogenase in tiacumicin biosynthesis. Here we report the genetic confirmation and biochemical characterization of TiaS5 as a sugar-O-methyltransferase, requisite for tiacumicin B biosynthesis. The tiaS5-inactivation mutant is capable of producing 14 tiacumicin analogues (11 of which are new), all lacking the 2'-O-methyl group on the internal rhamnose moiety. Notably, two tiacumicin analogues exhibit improved antibacterial properties. We have also biochemically verified TiaS5 as an S-adenosyl-L-methionine-dependent O-methyltransferase, requiring divalent metal ions for activity. Substrate probing revealed TiaS5 to be a promiscuous enzyme, recognizing 12 tiacumicin analogues. These findings unequivocally establish that TiaS5 functions as a 2'-O-methyltransferase and provide direct biochemical evidence that TiaS5-catalyzed methylation is a tailoring step after glycosyl coupling in tiacumicin B biosynthesis.
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Affiliation(s)
- Siwen Niu
- CAS Key Laboratory of Marine Bio-resources Sustainable Utilization, RNAM Center for Marine Microbiology, Guangdong Key Laboratory of Marine Materia Medica, South China Sea Institute of Oceanology, Chinese Academy of Sciences, 164 West Xingang Road, Guangzhou 510301, China
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Enzyme-catalysed [4+2] cycloaddition is a key step in the biosynthesis of spinosyn A. Nature 2011; 473:109-12. [PMID: 21544146 PMCID: PMC3092164 DOI: 10.1038/nature09981] [Citation(s) in RCA: 235] [Impact Index Per Article: 18.1] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2010] [Accepted: 03/03/2011] [Indexed: 11/08/2022]
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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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