1
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Zhou W, Ding W, Wu X, Sun J, Bai W. Microbial synthesis of anthocyanins and pyranoanthocyanins: current bottlenecks and potential solutions. Crit Rev Food Sci Nutr 2024:1-18. [PMID: 38935054 DOI: 10.1080/10408398.2024.2369703] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/28/2024]
Abstract
Anthocyanins (ACNs) are secondary metabolites found in plants. Due to their impressive biological activities, ACNs have gained significant popularity and extensive application within the food, pharmaceutical, and nutraceutical industries. A derivative of ACNs: pyranoanthocyanins (PACNs) possesses more stable properties and interesting biological activities. However, conventional methods for the production of ACNs, including chemical synthesis and plant extraction, involve organic solvents. Microbial synthesis of ACNs from renewable biomass, such as amino acids or flavonoids, is considered a sustainable and environmentally friendly method for large-scale production of ACNs. Recently, the construction of microbial cell factories (MCFs) for the efficient biosynthesis of ACNs and PACNs has attracted much attention. In this review, we summarize the cases of microbial synthesis of ACNs, and analyze the bottlenecks in reconstructing the metabolic pathways for synthesizing PACNs in microorganisms. Consequently, there is an urgent need to investigate the mechanisms behind the development of MCFs for PACNs synthesis. Such research also holds significant promise for advancing the production of food pigments. Meanwhile, we propose potential solutions to the bottleneck problem based on metabolic engineering and enzyme engineering. Finally, the development prospects of natural food and biotechnology are discussed.
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Affiliation(s)
- Weijie Zhou
- Department of Food Science and Engineering, Institute of Food Safety and Nutrition, Guangdong Engineering Technology Center of Food Safety Molecular Rapid Detection, Jinan University, Guangdong, China
| | - Weiqiu Ding
- Institute of Microbial Biotechnology, Jinan University, Guangzhou, Guangdong, China
| | - Xingyuan Wu
- Department of Food Science and Engineering, Institute of Food Safety and Nutrition, Guangdong Engineering Technology Center of Food Safety Molecular Rapid Detection, Jinan University, Guangdong, China
| | - Jianxia Sun
- Department of Food Science and Engineering, School of Chemical Engineering and Light Industry, Guangdong University of Technology, Guangdong, China
| | - Weibin Bai
- Department of Food Science and Engineering, Institute of Food Safety and Nutrition, Guangdong Engineering Technology Center of Food Safety Molecular Rapid Detection, Jinan University, Guangdong, China
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2
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Jo WS, Curtis BJ, Rehan M, Adrover-Castellano ML, Sherman DH, Healy AR. N-to- S Acyl Transfer as an Enabling Strategy in Asymmetric and Chemoenzymatic Synthesis. JACS AU 2024; 4:2058-2066. [PMID: 38818054 PMCID: PMC11134368 DOI: 10.1021/jacsau.4c00257] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 03/20/2024] [Revised: 05/01/2024] [Accepted: 05/02/2024] [Indexed: 06/01/2024]
Abstract
The observation of thioester-mediated acyl transfer processes in nature has inspired the development of novel protein synthesis and functionalization methodologies. The chemoselective transfer of an acyl group from S-to-N is the basis of several powerful ligation strategies. In this work, we sought to apply the reverse process, the transfer of an acyl group from N-to-S, as a method to convert stable chiral amides into more reactive thioesters. To this end, we developed a novel cysteine-derived oxazolidinone that serves as both a chiral imide auxiliary and an acyl transfer agent. This auxiliary combines the desirable features of rigid chiral imides as templates for asymmetric transformations with the synthetic applicability of thioesters. We demonstrate that the auxiliary can be applied in a range of highly selective asymmetric transformations. Subsequent intramolecular N-to-S acyl transfer of the chiral product and in situ trapping of the resulting thioester provides access to diverse carboxylic acid derivatives under mild conditions. The oxazolidinone thioester products can also be isolated and used in Pd-mediated transformations to furnish highly valuable chiral scaffolds, such as noncanonical amino acids, cyclic ketones, tetrahydropyrones, and dihydroquinolinones. Finally, we demonstrate that the oxazolidinone thioesters can also serve as a surrogate for SNAC-thioesters, enabling their seamless use as non-native substrates in biocatalytic transformations.
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Affiliation(s)
- Woonkee S Jo
- Chemistry Program, New York University Abu Dhabi (NYUAD), Saadiyat Island, Abu Dhabi 129188, United Arab Emirates (UAE)
| | - Brian J Curtis
- Life Sciences Institute, University of Michigan, 210 Washtenaw Avenue, Ann Arbor, MI 48109, USA
| | - Mohammad Rehan
- Chemistry Program, New York University Abu Dhabi (NYUAD), Saadiyat Island, Abu Dhabi 129188, United Arab Emirates (UAE)
| | | | - David H Sherman
- Life Sciences Institute, University of Michigan, 210 Washtenaw Avenue, Ann Arbor, MI 48109, USA
- Departments of Medicinal Chemistry, Chemistry, and Microbiology & Immunology, University of Michigan, Ann Arbor, MI 48109USA
| | - Alan R Healy
- Chemistry Program, New York University Abu Dhabi (NYUAD), Saadiyat Island, Abu Dhabi 129188, United Arab Emirates (UAE)
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3
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Bowen JI, Zhong X, Gao K, Reed B, Crump MP, Wang L, Willis CL. Combining total synthesis and genetic engineering to probe dihydropyran formation in ambruticin biosynthesis. Chem Sci 2024; 15:5319-5326. [PMID: 38577359 PMCID: PMC10988584 DOI: 10.1039/d4sc00720d] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2024] [Accepted: 02/27/2024] [Indexed: 04/06/2024] Open
Abstract
The ambruticins are a family of potent antifungal polyketide derived natural products isolated from the myxobacterium Sorangium cellulosum. Their unusual structures include a trisubstituted cyclopropyl group and two oxygen heterocycles, a tetrahydropyran (THP) and dihydropyran (DHP). Herein we report a flexible modular approach for the total synthesis of ambruticins which is used to prepare ambruticins F and S as well as in the first total synthesis of 20,21-dihydroambruticin F. The flexible strategy unites 3 fragments via Julia-Kocienski olefinations and provides important standards for investigation of dihydropyran formation in ambruticin biosynthesis. Cultures of wild-type S. cellulosum So ce10 produce mainly ambruticin S and the VS series of metabolites. An efficient electroporation method enabled gene knockout experiments which revealed that the ΔambP-S mutant of S. cellulosum accumulated the bisTHP polyketide 20,21-dihydroambruticin F. In contrast, the ΔambN-S mutant gave ambruticin F with the 20,21-alkene as the major metabolite confirming that AmbP and AmbO (a Rieske enzyme and flavin-dependent monooxygenase respectively) are implicated in 20,21-alkene formation. The results of feeding studies to a Sorangium strain containing only ambP and ambO are in accord with formation of the 20,21-alkene occurring prior to generation of the C3 to C7 dihydroxylated tetrahydropyran in ambruticin biosynthesis.
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Affiliation(s)
- James I Bowen
- School of Chemistry, University of Bristol Bristol BS8 1TS UK
| | - Xiaotong Zhong
- Institute of Microbiology, Chinese Academy of Sciences No. 1 Beichen West Road, Chaoyang District Beijing 100101 China
| | - Kaining Gao
- Institute of Microbiology, Chinese Academy of Sciences No. 1 Beichen West Road, Chaoyang District Beijing 100101 China
- School of Life Sciences, Yunnan University Kunming 650500 China
| | - Benjamin Reed
- School of Chemistry, University of Bristol Bristol BS8 1TS UK
| | - Matthew P Crump
- School of Chemistry, University of Bristol Bristol BS8 1TS UK
| | - Luoyi Wang
- Institute of Microbiology, Chinese Academy of Sciences No. 1 Beichen West Road, Chaoyang District Beijing 100101 China
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4
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Guth FM, Lindner F, Rydzek S, Peil A, Friedrich S, Hauer B, Hahn F. Rieske Oxygenase-Catalyzed Oxidative Late-Stage Functionalization during Complex Antifungal Polyketide Biosynthesis. ACS Chem Biol 2023; 18:2450-2456. [PMID: 37948749 DOI: 10.1021/acschembio.3c00498] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2023]
Abstract
Rieske oxygenases (ROs) from natural product biosynthetic pathways are a poorly studied group of enzymes with significant potential as oxidative functionalization biocatalysts. A study on the ROs JerL, JerP, and AmbP from the biosynthetic pathways of jerangolid A and ambruticin VS-3 is described. Their activity was successfully reconstituted using whole-cell bioconversion systems coexpressing the ROs and their respective natural flavin-dependent reductase (FDR) partners. Feeding authentic biosynthetic intermediates and synthetic surrogates to these strains confirmed the involvement of the ROs in hydroxymethylpyrone and dihydropyran formation and revealed crucial information about the RO's substrate specificity. The pronounced dependence of JerL and JerP on the presence of a methylenolether allowed the precise temporal assignment of RO catalysis to the ultimate steps of jerangolid biosynthesis. JerP and AmbP stand out among the biosynthetic ROs studied so far for their ability to catalyze clean tetrahydropyran desaturation without further functionalizing the formed electron-rich double bonds. This work highlights the remarkable ability of ROs to highly selectively oxidize complex molecular scaffolds.
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Affiliation(s)
- Florian M Guth
- Professur für Organische Chemie (Lebensmittelchemie), Fakultät für Biologie, Chemie und Geowissenschaften, Department of Chemistry, Universität Bayreuth, 95447 Bayreuth, Germany
| | - Frederick Lindner
- Professur für Organische Chemie (Lebensmittelchemie), Fakultät für Biologie, Chemie und Geowissenschaften, Department of Chemistry, Universität Bayreuth, 95447 Bayreuth, Germany
| | - Simon Rydzek
- Professur für Organische Chemie (Lebensmittelchemie), Fakultät für Biologie, Chemie und Geowissenschaften, Department of Chemistry, Universität Bayreuth, 95447 Bayreuth, Germany
| | - Andreas Peil
- Professur für Organische Chemie (Lebensmittelchemie), Fakultät für Biologie, Chemie und Geowissenschaften, Department of Chemistry, Universität Bayreuth, 95447 Bayreuth, Germany
| | - Steffen Friedrich
- Professur für Organische Chemie (Lebensmittelchemie), Fakultät für Biologie, Chemie und Geowissenschaften, Department of Chemistry, Universität Bayreuth, 95447 Bayreuth, Germany
| | - Bernhard Hauer
- Institute of Technical Biochemistry, Universität Stuttgart, Allmandring 31, 70569 Stuttgart, Germany
| | - Frank Hahn
- Professur für Organische Chemie (Lebensmittelchemie), Fakultät für Biologie, Chemie und Geowissenschaften, Department of Chemistry, Universität Bayreuth, 95447 Bayreuth, Germany
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5
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Kim MC, Winter JM, Cullum R, Smith AJ, Fenical W. Expanding the Utility of Bioinformatic Data for the Full Stereostructural Assignments of Marinolides A and B, 24- and 26-Membered Macrolactones Produced by a Chemically Exceptional Marine-Derived Bacterium. Mar Drugs 2023; 21:367. [PMID: 37367692 DOI: 10.3390/md21060367] [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: 06/03/2023] [Revised: 06/15/2023] [Accepted: 06/16/2023] [Indexed: 06/28/2023] Open
Abstract
Marinolides A and B, two new 24- and 26-membered bacterial macrolactones, were isolated from the marine-derived actinobacterium AJS-327 and their stereostructures initially assigned by bioinformatic data analysis. Macrolactones typically possess complex stereochemistry, the assignments of which have been one of the most difficult undertakings in natural products chemistry, and in most cases, the use of X-ray diffraction methods and total synthesis have been the major methods of assigning their absolute configurations. More recently, however, it has become apparent that the integration of bioinformatic data is growing in utility to assign absolute configurations. Genome mining and bioinformatic analysis identified the 97 kb mld biosynthetic cluster harboring seven type I polyketide synthases. A detailed bioinformatic investigation of the ketoreductase and enoylreductase domains within the multimodular polyketide synthases, coupled with NMR and X-ray diffraction data, allowed for the absolute configurations of marinolides A and B to be determined. While using bioinformatics to assign the relative and absolute configurations of natural products has high potential, this method must be coupled with full NMR-based analysis to both confirm bioinformatic assignments as well as any additional modifications that occur during biosynthesis.
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Affiliation(s)
- Min Cheol Kim
- Center for Marine Biotechnology and Biomedicine, Scripps Institution of Oceanography, Skaggs School of Pharmacy and Pharmaceutical Sciences, Moores Comprehensive Cancer Center, University of California, La Jolla, San Diego, CA 92093, USA
| | - Jaclyn M Winter
- Department of Pharmacology and Toxicology, University of Utah, Salt Lake City, UT 84112, USA
| | - Reiko Cullum
- Center for Marine Biotechnology and Biomedicine, Scripps Institution of Oceanography, Skaggs School of Pharmacy and Pharmaceutical Sciences, Moores Comprehensive Cancer Center, University of California, La Jolla, San Diego, CA 92093, USA
| | - Alexander J Smith
- Center for Marine Biotechnology and Biomedicine, Scripps Institution of Oceanography, Skaggs School of Pharmacy and Pharmaceutical Sciences, Moores Comprehensive Cancer Center, University of California, La Jolla, San Diego, CA 92093, USA
| | - William Fenical
- Center for Marine Biotechnology and Biomedicine, Scripps Institution of Oceanography, Skaggs School of Pharmacy and Pharmaceutical Sciences, Moores Comprehensive Cancer Center, University of California, La Jolla, San Diego, CA 92093, USA
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6
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Du Z, Li Y, Liu Y, Shi T. Molecular Insights into Bifunctional Ambruticin DH3 for Substrate Specificity and Catalytic Mechanism. Chemistry 2023; 29:e202203420. [PMID: 36464909 DOI: 10.1002/chem.202203420] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2022] [Revised: 11/30/2022] [Accepted: 11/30/2022] [Indexed: 12/11/2022]
Abstract
Dehydratase (DH), a domain located at polyketide synthase (PKS) modules, commonly catalyzes the dehydration of β-hydroxy to an α,β-unsaturated acyl intermediate. As a unique bifunctional dehydratase, AmbDH3 (the DH domain of module 3 of the ambruticin PKS) is verified to be responsible for both dehydration and the following pyran-forming cyclization. Besides, in vitro studies showed that its catalytic efficiency varies with different chiral substrates. However, the detailed molecular mechanism of AmbDH3 remains unclear. In this work, the structural rationale for the substrate specificity (2R/2S- and 6R/6S-substrates) in AmbDH3 was elucidated and the complete reaction pathways including dehydration and cyclization were presented. Both MD simulations and binding free energy calculations indicated AmbDH3 had a stronger preference for 2R-substrates (2R6R-2, 2R6S-3) than 2S-substrates (2S6R-1), and residue H51 and G61 around the catalytic pocket were emphasized by forming stable hydrogen bonds with 2R-substrates. In addition, AmbDH3's mild tolerance at C6 was explained by comparison of substrate conformation and hydrogen bond network in 6S- and 6R-substrate systems. The QM/MM results supported a consecutive one-base dehydration and cyclization mechanism for 2R6S-3 substrate with the energy barrier of 25.2 kcal mol-1 and 24.5 kcal mol-1 , respectively. Our computational results uncover the substrate recognition and catalytic process of the first bifunctional dehydratase-cyclase AmbDH3, which will shed light on the application of multifunctional DH domains in PKSs for diverse natural product analogs and benefit the chemoenzymatic synthesis of stereoselective pyran-containing products.
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Affiliation(s)
- Zeqian Du
- 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, 200240, P. R. China
| | - Yongzhen 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, 200240, P. R. China
| | - Yihan Liu
- 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, 200240, P. R. China
| | - Ting Shi
- School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, No. 800 Dongchuan Rd., Shanghai, 200240, P. R. China
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7
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Magar RT, Pham VTT, Poudel PB, Nguyen HT, Bridget AF, Sohng JK. Biosynthetic pathway of peucemycin and identification of its derivative from Streptomyces peucetius. Appl Microbiol Biotechnol 2023; 107:1217-1231. [PMID: 36680588 DOI: 10.1007/s00253-023-12385-8] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2022] [Revised: 01/08/2023] [Accepted: 01/10/2023] [Indexed: 01/22/2023]
Abstract
Streptomyces peucetius ATCC 27952 is a well-known producer of important anticancer compounds, daunorubicin and doxorubicin. In this study, we successfully identified a new macrolide, 25-hydroxy peucemycin, that exhibited an antibacterial effect on some pathogens. Based on the structure of a newly identified compound and through the inactivation of a polyketide synthase gene, we successfully identified its biosynthetic gene cluster which was considered to be the cryptic biosynthetic gene cluster. The biosynthetic gene cluster spans 51 kb with 16 open reading frames. Five type I polyketide synthase (PKS) genes encode eight modules that synthesize the polyketide chain of peucemycin before undergoing post-PKS tailoring steps. In addition to the regular starter and extender units, some modules have specificity towards ethylmalonyl-CoA and unusual butylmalonyl-CoA. A credible explanation for the specificity of the unusual extender unit has been searched for. Moreover, the enzyme responsible for the final tailoring pathway was also identified. Based on all findings, a plausible biosynthetic pathway is here proposed. KEY POINTS: • Identification of a new macrolide, 25-hydroxy peucemycin. • An FMN-dependent monooxygenase is responsible for the hydroxylation of peucemycin. • The module encoded by peuC is unique to accept the butylmalonyl-CoA as an unusual extender unit.
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Affiliation(s)
- Rubin Thapa Magar
- Department of Life Science and Biochemical Engineering, Sun Moon University, 70 Sun Moon-Ro 221, Tangjeong-Myeon, Asan-Si, Chungnam, 31460, South Korea
| | - Van Thuy Thi Pham
- Department of Life Science and Biochemical Engineering, Sun Moon University, 70 Sun Moon-Ro 221, Tangjeong-Myeon, Asan-Si, Chungnam, 31460, South Korea
| | - Purna Bahadur Poudel
- Department of Life Science and Biochemical Engineering, Sun Moon University, 70 Sun Moon-Ro 221, Tangjeong-Myeon, Asan-Si, Chungnam, 31460, South Korea
| | - Hue Thi Nguyen
- Department of Life Science and Biochemical Engineering, Sun Moon University, 70 Sun Moon-Ro 221, Tangjeong-Myeon, Asan-Si, Chungnam, 31460, South Korea
| | - Adzemye Fovennso Bridget
- Department of Life Science and Biochemical Engineering, Sun Moon University, 70 Sun Moon-Ro 221, Tangjeong-Myeon, Asan-Si, Chungnam, 31460, South Korea
| | - Jae Kyung Sohng
- Department of Life Science and Biochemical Engineering, Sun Moon University, 70 Sun Moon-Ro 221, Tangjeong-Myeon, Asan-Si, Chungnam, 31460, South Korea.
- Department of Pharmaceutical Engineering and Biotechnology, Sun Moon University, 70 Sun Moon-Ro 221, Tangjeong-Myeon, Asan-Si, Chungnam, 31460, South Korea.
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8
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Wagner L, Stang J, Derra S, Hollmann T, Hahn F. Towards understanding oxygen heterocycle-forming biocatalysts: a selectivity study of the pyran synthase PedPS7. Org Biomol Chem 2022; 20:9645-9649. [PMID: 36412217 DOI: 10.1039/d2ob02064e] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
Intramolecular oxa-Michael addition-catalysing cyclases are widespread in polyketide biosynthetic pathways. Although they have significant potential in biotechnology and chemoenzymatic synthesis of chiral heterocycles, they have only scarcely been studied. Here, we present detailed investigations on the selectivity profile of the pyran synthase PedPS7 showing that it combines broad substrate tolerance with high selectivity for the formation of up to two new stereocentres and relaxed precursor stereoisomer discrimination. Two of the four possible tetrahydropyran stereoisomers are reliably accessible by this enzyme. The results indicate fundamental differences between the individual subtypes of intramolecular oxa-Michael addition-catalysing cyclases.
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Affiliation(s)
- Lisa Wagner
- Professur für Organische Chemie (Lebensmittelchemie), Fakultät für Biologie, Chemie und Geowissenschaften, Department of Chemistry, Universität Bayreuth, 95447 Bayreuth, Germany.
| | - Jörg Stang
- Professur für Organische Chemie (Lebensmittelchemie), Fakultät für Biologie, Chemie und Geowissenschaften, Department of Chemistry, Universität Bayreuth, 95447 Bayreuth, Germany.
| | - Sebastian Derra
- Professur für Organische Chemie (Lebensmittelchemie), Fakultät für Biologie, Chemie und Geowissenschaften, Department of Chemistry, Universität Bayreuth, 95447 Bayreuth, Germany.
| | - Tim Hollmann
- Professur für Organische Chemie (Lebensmittelchemie), Fakultät für Biologie, Chemie und Geowissenschaften, Department of Chemistry, Universität Bayreuth, 95447 Bayreuth, Germany.
| | - Frank Hahn
- Professur für Organische Chemie (Lebensmittelchemie), Fakultät für Biologie, Chemie und Geowissenschaften, Department of Chemistry, Universität Bayreuth, 95447 Bayreuth, Germany.
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9
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Hobson C, Jenner M, Jian X, Griffiths D, Roberts DM, Rey-Carrizo M, Challis GL. Diene incorporation by a dehydratase domain variant in modular polyketide synthases. Nat Chem Biol 2022; 18:1410-1416. [PMID: 36109649 PMCID: PMC7613849 DOI: 10.1038/s41589-022-01127-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2020] [Accepted: 07/27/2022] [Indexed: 11/09/2022]
Abstract
Modular polyketide synthases (PKSs) are biosynthetic assembly lines that construct structurally diverse natural products with wide-ranging applications in medicine and agriculture. Various mechanisms contribute to structural diversification during PKS-mediated chain assembly, including dehydratase (DH) domain-mediated elimination of water from R and S-configured 3-hydroxy-thioesters to introduce E- and Z-configured carbon-carbon double bonds, respectively. Here we report the discovery of a DH domain variant that catalyzes the sequential elimination of two molecules of water from a (3R, 5S)-3,5-dihydroxy thioester during polyketide chain assembly, introducing a conjugated E,Z-diene into various modular PKS products. We show that the reaction proceeds via a (2E, 5S)-2-enoyl-5-hydroxy-thioester intermediate and involves an additional universally conserved histidine residue that is absent from the active site of most conventional DH domains. These findings expand the diverse range of chemistries mediated by DH-like domains in modular PKSs, highlighting the catalytic versatility of the double hotdog fold.
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Affiliation(s)
- Christian Hobson
- Department of Chemistry, University of Warwick, Coventry, UK.,Willow Biosciences Inc., Vancouver, British Columbia, Canada
| | - Matthew Jenner
- Department of Chemistry, University of Warwick, Coventry, UK.,Warwick Integrative Synthetic Biology Centre, University of Warwick, Coventry, UK
| | - Xinyun Jian
- Department of Chemistry, University of Warwick, Coventry, UK.,Warwick Integrative Synthetic Biology Centre, University of Warwick, Coventry, UK.,Department of Biochemistry and Molecular Biology, Biomedicine Discovery Institute, Monash University, Clayton, Victoria, Australia
| | - Daniel Griffiths
- Department of Chemistry, University of Warwick, Coventry, UK.,Monash University Accident Research Centre, Clayton, Victoria, Australia
| | | | - Matias Rey-Carrizo
- Department of Chemistry, University of Warwick, Coventry, UK.,BCN Medical Writing, Sabadell, Spain
| | - Gregory L Challis
- Department of Chemistry, University of Warwick, Coventry, UK. .,Warwick Integrative Synthetic Biology Centre, University of Warwick, Coventry, UK. .,Department of Biochemistry and Molecular Biology, Biomedicine Discovery Institute, Monash University, Clayton, Victoria, Australia. .,ARC Centre of Excellence for Innovations in Peptide and Protein Science, Monash University, Clayton, Victoria, Australia.
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10
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Yin Z, Liebhart E, Stegmann E, Brötz-Oesterhelt H, Dickschat JS. An isotopic probe to follow the stereochemical course of dehydratase reactions in polyketide and fatty acid biosynthesis. Org Chem Front 2022. [DOI: 10.1039/d2qo00272h] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Four stereoisomeric and isotopically labelled probes that are suitable to easily follow the stereochemical course of dehydratases have been synthesised.
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Affiliation(s)
- Zhiyong Yin
- Kekulé-Institute of Organic Chemistry and Biochemistry, University of Bonn, Gerhard-Domagk-Strasse 1, 53121 Bonn, Germany
| | - Elisa Liebhart
- Interfaculty Institute of Microbiology and Infection Medicine, Deptartment of Microbial Bioactive Compounds, Auf der Morgenstelle 28, 72076 Tübingen, Germany
| | - Evi Stegmann
- Interfaculty Institute of Microbiology and Infection Medicine, Deptartment of Microbial Bioactive Compounds, Auf der Morgenstelle 28, 72076 Tübingen, Germany
| | - Heike Brötz-Oesterhelt
- Interfaculty Institute of Microbiology and Infection Medicine, Deptartment of Microbial Bioactive Compounds, Auf der Morgenstelle 28, 72076 Tübingen, Germany
| | - Jeroen S. Dickschat
- Kekulé-Institute of Organic Chemistry and Biochemistry, University of Bonn, Gerhard-Domagk-Strasse 1, 53121 Bonn, Germany
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11
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Bowen JI, Wang L, Crump MP, Willis CL. Ambruticins: tetrahydropyran ring formation and total synthesis. Org Biomol Chem 2021; 19:6210-6215. [PMID: 34190301 DOI: 10.1039/d1ob00883h] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
The ambruticins are a family of polyketide natural products which exhibit potent antifungal activity. Gene knockout experiments are in accord with the proposal that the tetrahydropyran ring of the ambruticins is formed via the AmbJ catalysed epoxidation of the unsaturated 3,5-dihydroxy acid, ambruticin J, followed by regioselective cyclisation to ambruticin F. Herein, a convergent approach to the total synthesis of ambruticin J is described as well as model studies involving epoxidation and cyclisations of unsaturated hydroxy esters to give tetrahydropyrans and tetrahydrofurans. The total synthesis involves preparation of three key fragments which were united via a Suzuki-Miyaura cross-coupling and Julia-Kocienski olefination to generate the required carbon framework. Global deprotection to a triol and selective oxidation of the primary alcohol gave, after hydrolysis of the lactone, ambruticin J.
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Affiliation(s)
- James I Bowen
- School of Chemistry, University of Bristol, Bristol, BS8 1TS, UK.
| | - Luoyi Wang
- Institute of Microbiology, Chinese Academy of Sciences, NO. 1 Beichen West Road, Chaoyang District, Beijing, 100101, China
| | - Matthew P Crump
- School of Chemistry, University of Bristol, Bristol, BS8 1TS, UK.
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12
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Wagner L, Roß T, Hollmann T, Hahn F. Cross-linking of a polyketide synthase domain leads to a recyclable biocatalyst for chiral oxygen heterocycle synthesis. RSC Adv 2021; 11:20248-20251. [PMID: 35479892 PMCID: PMC9033652 DOI: 10.1039/d1ra03692k] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2021] [Accepted: 05/26/2021] [Indexed: 12/17/2022] Open
Abstract
The potential of polyketide synthase (PKS) domains for chemoenzymatic synthesis can often not be tapped due to their low stability and activity in vitro. In this proof-of-principle study, the immobilisation of the heterocycle-forming PKS domain AmbDH3 as a cross-linked enzyme aggregate (CLEA) is described. The AmbDH3-CLEA showed good activity recovery, stability and recyclability. Repetitive reactions on the semi-preparative scale were performed with high conversion and isolated yield. Similar to that observed for the free enzyme, the aggregate retained substrate tolerance and the ability for kinetic resolution. This first example of a successful enzymatic PKS domain immobilisation demonstrates that cross-linking can in principle be applied to this type of enzyme to increase its applicability for chemoenzymatic synthesis. Cross-linking of the polyketide synthase domain AmbDH3 led to an active aggregate with improved properties for the chemoenzymatic synthesis of chiral oxygen heterocycles, such as recyclability and facile purification.![]()
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Affiliation(s)
- Lisa Wagner
- Department of Chemistry, Faculty of Biology, Chemistry and Earth Sciences, University of Bayreuth Universitätsstraße 30 95447 Bayreuth Germany
| | - Theresa Roß
- Department of Chemistry, Faculty of Biology, Chemistry and Earth Sciences, University of Bayreuth Universitätsstraße 30 95447 Bayreuth Germany
| | - Tim Hollmann
- Department of Chemistry, Faculty of Biology, Chemistry and Earth Sciences, University of Bayreuth Universitätsstraße 30 95447 Bayreuth Germany
| | - Frank Hahn
- Department of Chemistry, Faculty of Biology, Chemistry and Earth Sciences, University of Bayreuth Universitätsstraße 30 95447 Bayreuth Germany
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13
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Linne Y, Bonandi E, Tabet C, Geldsetzer J, Kalesse M. The Total Synthesis of Chondrochloren A. Angew Chem Int Ed Engl 2021. [DOI: 10.1002/ange.202016072] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Affiliation(s)
- Yannick Linne
- Institute for Organic Chemistry Gottfried Wilhelm Leibniz Universität Hannover Schneiderberg 1B 30167 Hannover Germany
| | - Elisa Bonandi
- Institute for Organic Chemistry Gottfried Wilhelm Leibniz Universität Hannover Schneiderberg 1B 30167 Hannover Germany
| | - Christopher Tabet
- Institute for Organic Chemistry Gottfried Wilhelm Leibniz Universität Hannover Schneiderberg 1B 30167 Hannover Germany
| | - Jan Geldsetzer
- Helmholtz Centre for Infection Research (HZI) Inhoffenstrasse 7 38124 Braunschweig Germany
| | - Markus Kalesse
- Institute for Organic Chemistry Gottfried Wilhelm Leibniz Universität Hannover Schneiderberg 1B 30167 Hannover Germany
- Centre of Biomolecular Drug Research (BMWZ) Gottfried Wilhelm Leibniz Universität Hannover Schneiderberg 38 30167 Hannover Germany
- Helmholtz Centre for Infection Research (HZI) Inhoffenstrasse 7 38124 Braunschweig Germany
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14
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Linne Y, Bonandi E, Tabet C, Geldsetzer J, Kalesse M. The Total Synthesis of Chondrochloren A. Angew Chem Int Ed Engl 2021; 60:6938-6942. [PMID: 33450788 PMCID: PMC8048958 DOI: 10.1002/anie.202016072] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2020] [Revised: 01/13/2021] [Indexed: 12/01/2022]
Abstract
The first total synthesis of chondrochloren A is accomplished using a 1,2‐metallate rearrangement addition as an alternative for the Nozaki‐Hiyama‐Kishi reaction. This transformation also avoids the inherent challenges of this polyketide segment and provides a new, unprecedented strategy to assemble polyketidal frameworks. The formation of the Z‐enamide is accomplished using a Z‐selective cross coupling of the corresponding amide to a Z‐vinyl bromide.
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Affiliation(s)
- Yannick Linne
- Institute for Organic Chemistry, Gottfried Wilhelm Leibniz Universität Hannover, Schneiderberg 1B, 30167, Hannover, Germany
| | - Elisa Bonandi
- Institute for Organic Chemistry, Gottfried Wilhelm Leibniz Universität Hannover, Schneiderberg 1B, 30167, Hannover, Germany
| | - Christopher Tabet
- Institute for Organic Chemistry, Gottfried Wilhelm Leibniz Universität Hannover, Schneiderberg 1B, 30167, Hannover, Germany
| | - Jan Geldsetzer
- Helmholtz Centre for Infection Research (HZI), Inhoffenstrasse 7, 38124, Braunschweig, Germany
| | - Markus Kalesse
- Institute for Organic Chemistry, Gottfried Wilhelm Leibniz Universität Hannover, Schneiderberg 1B, 30167, Hannover, Germany.,Centre of Biomolecular Drug Research (BMWZ), Gottfried Wilhelm Leibniz Universität Hannover, Schneiderberg 38, 30167, Hannover, Germany.,Helmholtz Centre for Infection Research (HZI), Inhoffenstrasse 7, 38124, Braunschweig, Germany
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15
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Liu L, Yu Q, Zhang H, Tao W, Wang R, Bai L, Zhao YL, Shi T. Theoretical study on substrate recognition and catalytic mechanisms of gephyronic acid dehydratase DH1. Catal Sci Technol 2021. [DOI: 10.1039/d0cy01776k] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
The bifunctional dehydratase GphF DH1 catalyzes both the dehydration of β-hydroxy and the double bond isomerization with the energy barrier of 27.0 kcal mol−1 and 17.2 kcal mol−1 respectively.
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Affiliation(s)
- Lei Liu
- 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 200240
| | - Qian Yu
- 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 200240
| | - Haoqing Zhang
- 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 200240
| | - Wentao Tao
- 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 200240
| | - Rufan 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 200240
| | - Linquan Bai
- 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 200240
| | - Yi-Lei Zhao
- 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 200240
| | - Ting Shi
- 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 200240
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16
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Hahn F, Guth FM. The ambruticins and jerangolids - chemistry, biology and chemoenzymatic synthesis of potent antifungal drug candidates. Nat Prod Rep 2020; 37:1300-1315. [PMID: 32420573 DOI: 10.1039/d0np00012d] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Covering: 1977 to 2020The ambruticins and jerangolids are myxobacterial reduced polyketides, which are produced via highly unusual biosynthetic pathways containing a plethora of non-canonical enzymatic transformations. Since the discovery of the first congeners in the late 1970s, they have been in the focus of drug development due to their good antifungal activity and low toxicity in mammals, which result from interaction with an unusual innercellular target in fungi. Despite significant efforts, which have led to the development of various total syntheses, their structural complexity has yet avoided full exploitation of their pharmacological potential. This article summarises biological, total and semisynthetic as well as biosynthetic studies on both compounds. An outlook on the biosynthesis-based approaches to them and their derivatives is presented. Due to the structural and biosynthetic characteristics of the ambruticins and jerangolids, chemoenzymatic processes that make use of their biosynthetic pathway enzymes are particularly promising to gain efficient access to derivative libraries for structure activity relationship studies.
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Affiliation(s)
- Frank Hahn
- Department of Chemistry, University of Bayreuth, 51427 Bayreuth, Germany.
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17
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Drufva EE, Hix EG, Bailey CB. Site directed mutagenesis as a precision tool to enable synthetic biology with engineered modular polyketide synthases. Synth Syst Biotechnol 2020; 5:62-80. [PMID: 32637664 PMCID: PMC7327777 DOI: 10.1016/j.synbio.2020.04.001] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2020] [Revised: 04/01/2020] [Accepted: 04/06/2020] [Indexed: 12/04/2022] Open
Abstract
Modular polyketide synthases (PKSs) are a multidomain megasynthase class of biosynthetic enzymes that have great promise for the development of new compounds, from new pharmaceuticals to high value commodity and specialty chemicals. Their colinear biosynthetic logic has been viewed as a promising platform for synthetic biology for decades. Due to this colinearity, domain swapping has long been used as a strategy to introduce molecular diversity. However, domain swapping often fails because it perturbs critical protein-protein interactions within the PKS. With our increased level of structural elucidation of PKSs, using judicious targeted mutations of individual residues is a more precise way to introduce molecular diversity with less potential for global disruption of the protein architecture. Here we review examples of targeted point mutagenesis to one or a few residues harbored within the PKS that alter domain specificity or selectivity, affect protein stability and interdomain communication, and promote more complex catalytic reactivity.
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Key Words
- ACP, acyl carrier protein
- AT, acyltransferase
- DEBS, 6-deoxyerthronolide B synthase
- DH, dehydratase
- EI, enoylisomerase
- ER, enoylreductase
- KR, ketoreductase
- KS, ketosynthase
- LM, loading module
- MT, methyltransferase
- Mod, module
- PKS, polyketide synthase
- PS, pyran synthase
- Polyketide synthase
- Protein engineering
- Rational design
- SNAC, N-acetyl cysteamine
- Saturation mutagenesis
- Site directed mutagenesis
- Synthetic biology
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Affiliation(s)
- Erin E. Drufva
- Department of Chemistry, University of Tennessee-Knoxville, Knoxville, TN, 37996, USA
| | - Elijah G. Hix
- Department of Chemistry, University of Tennessee-Knoxville, Knoxville, TN, 37996, USA
| | - Constance B. Bailey
- Department of Chemistry, University of Tennessee-Knoxville, Knoxville, TN, 37996, USA
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18
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Hollmann T, Berkhan G, Wagner L, Sung KH, Kolb S, Geise H, Hahn F. Biocatalysts from Biosynthetic Pathways: Enabling Stereoselective, Enzymatic Cycloether Formation on a Gram Scale. ACS Catal 2020. [DOI: 10.1021/acscatal.9b05071] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Affiliation(s)
- Tim Hollmann
- Professur für Organische Chemie (Lebensmittelchemie), Fakultät für Biologie, Chemie und Geowissenschaften, Department of Chemistry, Universität Bayreuth, Universitätsstraße 30, 95447 Bayreuth, Germany
| | - Gesche Berkhan
- Professur für Organische Chemie (Lebensmittelchemie), Fakultät für Biologie, Chemie und Geowissenschaften, Department of Chemistry, Universität Bayreuth, Universitätsstraße 30, 95447 Bayreuth, Germany
- Centre for Biomolecular Drug Research, Leibniz Universität Hannover, Schneiderberg 38, 30167 Hannover, Germany
| | - Lisa Wagner
- Professur für Organische Chemie (Lebensmittelchemie), Fakultät für Biologie, Chemie und Geowissenschaften, Department of Chemistry, Universität Bayreuth, Universitätsstraße 30, 95447 Bayreuth, Germany
| | - Kwang Hoon Sung
- Helmholtz-Zentrum für Infektionsforschung GmbH, Inhoffenstrasse 7, 38124 Braunschweig, Germany
- Institute of Biochemistry, Biotechnology and Bioinformatics, Technische Universität Braunschweig, Spielmannstrasse 7, 38106 Braunschweig, Germany
- Protein Facility, ILAb Co., Ltd. NP513, The Catholic University of Korea, 420-743 Bucheon, Republic of Korea
| | - Simon Kolb
- Professur für Organische Chemie (Lebensmittelchemie), Fakultät für Biologie, Chemie und Geowissenschaften, Department of Chemistry, Universität Bayreuth, Universitätsstraße 30, 95447 Bayreuth, Germany
| | - Hendrik Geise
- Centre for Biomolecular Drug Research, Leibniz Universität Hannover, Schneiderberg 38, 30167 Hannover, Germany
| | - Frank Hahn
- Professur für Organische Chemie (Lebensmittelchemie), Fakultät für Biologie, Chemie und Geowissenschaften, Department of Chemistry, Universität Bayreuth, Universitätsstraße 30, 95447 Bayreuth, Germany
- Centre for Biomolecular Drug Research, Leibniz Universität Hannover, Schneiderberg 38, 30167 Hannover, Germany
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19
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Abstract
Enzyme-mediated cascade reactions are widespread in biosynthesis. To facilitate comparison with the mechanistic categorizations of cascade reactions by synthetic chemists and delineate the common underlying chemistry, we discuss four types of enzymatic cascade reactions: those involving nucleophilic, electrophilic, pericyclic, and radical reactions. Two subtypes of enzymes that generate radical cascades exist at opposite ends of the oxygen abundance spectrum. Iron-based enzymes use O2 to generate high valent iron-oxo species to homolyze unactivated C-H bonds in substrates to initiate skeletal rearrangements. At anaerobic end, enzymes reversibly cleave S-adenosylmethionine (SAM) to generate the 5'-deoxyadenosyl radical as a powerful oxidant to initiate C-H bond homolysis in bound substrates. The latter enzymes are termed radical SAM enzymes. We categorize the former as "thwarted oxygenases".
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Affiliation(s)
- Christopher T Walsh
- Stanford University Chemistry, Engineering, and Medicine for Human Health (CheM-H), Stanford University, Stanford, CA, 94305, USA
| | - Bradley S Moore
- Center for Marine Biotechnology and Biomedicine, Scripps Institution of Oceanography, University of California, San Diego, La Jolla, CA, 92093, USA
- Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California, San Diego, La Jolla, CA, 92093, USA
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20
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Wu WJ, Li MM, Liu B, Wu Y. Racemization of α-Alkyl-β-Keto Esters and Enantioselective Total Synthesis of Two C-2′′′Epimers of Plant Glycerolipid Santinol C. European J Org Chem 2019. [DOI: 10.1002/ejoc.201900467] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Affiliation(s)
- Wen-Ju Wu
- State Key Laboratory of Bioorganic and Natural Products Chemistry; Center for Excellence in Molecular Synthesis; Shanghai Institute of Organic Chemistry, Chinese Academy of Sciences; 345 Lingling Road 200032 Shanghai China
- Key Laboratory of Green Chemical Technology of College of Heilongjiang Province; College of Chemical and Environmental Engineering; Harbin University of Science and Technology; 150040 Harbin China
| | - Mei-Mei Li
- State Key Laboratory of Bioorganic and Natural Products Chemistry; Center for Excellence in Molecular Synthesis; Shanghai Institute of Organic Chemistry, Chinese Academy of Sciences; 345 Lingling Road 200032 Shanghai China
- Key Laboratory of Green Chemical Technology of College of Heilongjiang Province; College of Chemical and Environmental Engineering; Harbin University of Science and Technology; 150040 Harbin China
| | - Bo Liu
- Key Laboratory of Green Chemical Technology of College of Heilongjiang Province; College of Chemical and Environmental Engineering; Harbin University of Science and Technology; 150040 Harbin China
| | - Yikang Wu
- State Key Laboratory of Bioorganic and Natural Products Chemistry; Center for Excellence in Molecular Synthesis; Shanghai Institute of Organic Chemistry, Chinese Academy of Sciences; 345 Lingling Road 200032 Shanghai China
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21
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He BB, Zhou T, Bu XL, Weng JY, Xu J, Lin S, Zheng JT, Zhao YL, Xu MJ. Enzymatic Pyran Formation Involved in Xiamenmycin Biosynthesis. ACS Catal 2019. [DOI: 10.1021/acscatal.9b01034] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Affiliation(s)
- Bei-Bei He
- Key Laboratory of Systems Biomedicine (Ministry of Education), Shanghai Center for Systems Biomedicine, Shanghai Jiao Tong University, Shanghai 200240, People’s Republic of China
- State Key Laboratory of Microbial Metabolism, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai 200240, People’s Republic of China
| | - Ting Zhou
- State Key Laboratory of Microbial Metabolism, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai 200240, People’s Republic of China
| | - Xu-Liang Bu
- State Key Laboratory of Microbial Metabolism, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai 200240, People’s Republic of China
| | - Jing-Yi Weng
- Key Laboratory of Systems Biomedicine (Ministry of Education), Shanghai Center for Systems Biomedicine, Shanghai Jiao Tong University, Shanghai 200240, People’s Republic of China
| | - Jun Xu
- State Key Laboratory of Microbial Metabolism, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai 200240, People’s Republic of China
- School of Oceanography, Shanghai Jiao Tong University, Shanghai 200240, People’s Republic of China
| | - Shuangjun Lin
- State Key Laboratory of Microbial Metabolism, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai 200240, People’s Republic of China
| | - Jian-Ting Zheng
- State Key Laboratory of Microbial Metabolism, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai 200240, People’s Republic of China
| | - Yi-Lei Zhao
- State Key Laboratory of Microbial Metabolism, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai 200240, People’s Republic of China
| | - Min-Juan Xu
- Key Laboratory of Systems Biomedicine (Ministry of Education), Shanghai Center for Systems Biomedicine, Shanghai Jiao Tong University, Shanghai 200240, People’s Republic of China
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22
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Affiliation(s)
- Christopher T. Walsh
- Stanford University Chemistry, Engineering, and Medicine for Human Health (CheM-H)Stanford University Stanford CA 94305 USA
| | - Bradley S. Moore
- Center for Marine Biotechnology and BiomedicineScripps Institution of OceanographyUniversity of California, San Diego La Jolla CA 92093 USA
- Skaggs School of Pharmacy and Pharmaceutical SciencesUniversity of California, San Diego La Jolla CA 92093 USA
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23
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Abstract
Enzymes that catalyze a Michael-type addition in polyketide biosynthesis are summarized and discussed.
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Affiliation(s)
- Akimasa Miyanaga
- Department of Chemistry
- Tokyo Institute of Technology
- Tokyo 152-8551
- Japan
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24
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Lindner F, Friedrich S, Hahn F. Total Synthesis of Complex Biosynthetic Late-Stage Intermediates and Bioconversion by a Tailoring Enzyme from Jerangolid Biosynthesis. J Org Chem 2018; 83:14091-14101. [DOI: 10.1021/acs.joc.8b02047] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Affiliation(s)
- Frederick Lindner
- Professur für Organische Chemie (Lebensmittelchemie), Department of Chemistry, Fakultät für Biologie, Chemie und Geowissenschaften, Universität Bayreuth, Universitätsstraße 30, 95447 Bayreuth, Germany
| | - Steffen Friedrich
- Professur für Organische Chemie (Lebensmittelchemie), Department of Chemistry, Fakultät für Biologie, Chemie und Geowissenschaften, Universität Bayreuth, Universitätsstraße 30, 95447 Bayreuth, Germany
| | - Frank Hahn
- Professur für Organische Chemie (Lebensmittelchemie), Department of Chemistry, Fakultät für Biologie, Chemie und Geowissenschaften, Universität Bayreuth, Universitätsstraße 30, 95447 Bayreuth, Germany
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25
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Dodge GJ, Ronnow D, Taylor RE, Smith JL. Molecular Basis for Olefin Rearrangement in the Gephyronic Acid Polyketide Synthase. ACS Chem Biol 2018; 13:2699-2707. [PMID: 30179448 PMCID: PMC6233718 DOI: 10.1021/acschembio.8b00645] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Polyketide synthases (PKS) are a rich source of natural products of varied chemical composition and biological significance. Here, we report the characterization of an atypical dehydratase (DH) domain from the PKS pathway for gephyronic acid, an inhibitor of eukaryotic protein synthesis. Using a library of synthetic substrate mimics, the reaction course, stereospecificity, and tolerance to non-native substrates of GphF DH1 are probed via LC-MS analysis. Taken together, the studies establish GphF DH1 as a dual-function dehydratase/isomerase that installs an odd-to-even double bond and yields a product consistent with the isobutenyl terminus of gephyronic acid. The studies also reveal an unexpected C2 epimerase function in catalytic turnover with the native substrate. A 1.55-Å crystal structure of GphF DH1 guided mutagenesis experiments to elucidate the roles of key amino acids in the multistep DH1 catalysis, identifying critical functions for leucine and tyrosine side chains. The mutagenesis results were applied to add a secondary isomerase functionality to a nonisomerizing DH in the first successful gain-of-function engineering of a PKS DH. Our studies of GphF DH1 catalysis highlight the versatility of the DH active site and adaptation for a specific catalytic outcome with a specific substrate.
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Affiliation(s)
- Greg J. Dodge
- Department of Biological Chemistry and Life Sciences Institute University of Michigan Ann Arbor, Michigan, 48109
| | - Danialle Ronnow
- Department of Chemistry and Biochemistry University of Notre Dame Notre Dame, Indiana 46556
| | - Richard E. Taylor
- Department of Chemistry and Biochemistry University of Notre Dame Notre Dame, Indiana 46556
| | - Janet L. Smith
- Department of Biological Chemistry and Life Sciences Institute University of Michigan Ann Arbor, Michigan, 48109
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26
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Sundaram S, Kim HJ, Bauer R, Thongkongkaew T, Heine D, Hertweck C. On-Line Polyketide Cyclization into Diverse Medium-Sized Lactones by a Specialized Ketosynthase Domain. Angew Chem Int Ed Engl 2018. [DOI: 10.1002/ange.201804991] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
Affiliation(s)
- Srividhya Sundaram
- Department of Biomolecular Chemistry; Leibniz Institute for Natural Product Research and Infection Biology-; Hans Knöll Institute; Beutenbergstrasse 11a 07745 Jena Germany
| | - Hak Joong Kim
- Department of Biomolecular Chemistry; Leibniz Institute for Natural Product Research and Infection Biology-; Hans Knöll Institute; Beutenbergstrasse 11a 07745 Jena Germany
| | - Ruth Bauer
- Department of Biomolecular Chemistry; Leibniz Institute for Natural Product Research and Infection Biology-; Hans Knöll Institute; Beutenbergstrasse 11a 07745 Jena Germany
| | - Tawatchai Thongkongkaew
- Department of Biomolecular Chemistry; Leibniz Institute for Natural Product Research and Infection Biology-; Hans Knöll Institute; Beutenbergstrasse 11a 07745 Jena Germany
| | - Daniel Heine
- Department of Biomolecular Chemistry; Leibniz Institute for Natural Product Research and Infection Biology-; Hans Knöll Institute; Beutenbergstrasse 11a 07745 Jena Germany
| | - Christian Hertweck
- Department of Biomolecular Chemistry; Leibniz Institute for Natural Product Research and Infection Biology-; Hans Knöll Institute; Beutenbergstrasse 11a 07745 Jena Germany
- Chair for Natural Product Chemistry; Friedrich Schiller University; Jena Germany
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27
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Meng S, Tang GL, Pan HX. Enzymatic Formation of Oxygen-Containing Heterocycles in Natural Product Biosynthesis. Chembiochem 2018; 19:2002-2022. [PMID: 30039582 DOI: 10.1002/cbic.201800225] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2018] [Indexed: 01/12/2023]
Abstract
Oxygen-containing heterocycles are widely encountered in natural products that display diverse pharmacological properties and have potential benefits to human health. The formation of O-heterocycles catalyzed by different types of enzymes in the biosynthesis of natural products not only contributes to the structural diversity of these compounds, but also enriches our understanding of nature's ability to construct complex molecules. This minireview focuses on the various modes of enzymatic O-heterocyclization identified in natural product biosynthesis and summarizes the possible mechanisms involved in ring closure.
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Affiliation(s)
- Song Meng
- State Key Laboratory of Bio-organic and Natural Products Chemistry, Shanghai Institute of Organic Chemistry, University of the Chinese Academy of Sciences, 345 Lingling Road, Shanghai, 200032, China
| | - Gong-Li Tang
- State Key Laboratory of Bio-organic and Natural Products Chemistry, Shanghai Institute of Organic Chemistry, University of the Chinese Academy of Sciences, 345 Lingling Road, Shanghai, 200032, China
| | - Hai-Xue Pan
- State Key Laboratory of Bio-organic and Natural Products Chemistry, Shanghai Institute of Organic Chemistry, University of the Chinese Academy of Sciences, 345 Lingling Road, Shanghai, 200032, China
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28
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Sundaram S, Kim HJ, Bauer R, Thongkongkaew T, Heine D, Hertweck C. On-Line Polyketide Cyclization into Diverse Medium-Sized Lactones by a Specialized Ketosynthase Domain. Angew Chem Int Ed Engl 2018; 57:11223-11227. [PMID: 29897642 DOI: 10.1002/anie.201804991] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2018] [Indexed: 12/15/2022]
Abstract
Ketosynthase (KS) domains of modular type I polyketide synthases (PKSs) typically catalyze the Claisen condensation of acyl and malonyl units to form linear chains. In stark contrast, the KS of the rhizoxin PKS branching module mediates a Michael addition, which sets the basis for a pharmacophoric δ-lactone moiety. The precise role of the KS was evaluated by site-directed mutagenesis, chemical probes, and biotransformations. Biochemical and kinetic analyses helped to dissect branching and lactonization reactions and unequivocally assign the entire sequence to the KS. Probing the range of accepted substrates with diverse synthetic surrogates in vitro, we found that the KS tolerates defined acyl chain lengths to produce five- to seven-membered lactones. These results show that the KS is multifunctional, as it catalyzes β-branching and lactonization. Information on the increased product portfolio of the unusual, TE-independent on-line cyclization is relevant for synthetic biology approaches.
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Affiliation(s)
- Srividhya Sundaram
- Department of Biomolecular Chemistry, Leibniz Institute for Natural Product Research and Infection Biology-, Hans Knöll Institute, Beutenbergstrasse 11a, 07745, Jena, Germany
| | - Hak Joong Kim
- Department of Biomolecular Chemistry, Leibniz Institute for Natural Product Research and Infection Biology-, Hans Knöll Institute, Beutenbergstrasse 11a, 07745, Jena, Germany
| | - Ruth Bauer
- Department of Biomolecular Chemistry, Leibniz Institute for Natural Product Research and Infection Biology-, Hans Knöll Institute, Beutenbergstrasse 11a, 07745, Jena, Germany
| | - Tawatchai Thongkongkaew
- Department of Biomolecular Chemistry, Leibniz Institute for Natural Product Research and Infection Biology-, Hans Knöll Institute, Beutenbergstrasse 11a, 07745, Jena, Germany
| | - Daniel Heine
- Department of Biomolecular Chemistry, Leibniz Institute for Natural Product Research and Infection Biology-, Hans Knöll Institute, Beutenbergstrasse 11a, 07745, Jena, Germany
| | - Christian Hertweck
- Department of Biomolecular Chemistry, Leibniz Institute for Natural Product Research and Infection Biology-, Hans Knöll Institute, Beutenbergstrasse 11a, 07745, Jena, Germany.,Chair for Natural Product Chemistry, Friedrich Schiller University, Jena, Germany
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29
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Abstract
Enzymes in biosynthetic pathways, especially in plant and microbial metabolism, generate structural and functional group complexity in small molecules by conversion of acyclic frameworks to cyclic scaffolds via short, efficient routes. The distinct chemical logic used by several distinct classes of cyclases, oxidative and non-oxidative, has recently been elucidated by genome mining, heterologous expression, and genetic and mechanistic analyses. These include enzymes performing pericyclic transformations, pyran synthases, tandem acting epoxygenases, and epoxide "hydrolases", as well as oxygenases and radical S-adenosylmethionine enzymes that involve rearrangements of substrate radicals under aerobic or anaerobic conditions.
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Affiliation(s)
- Christopher T. Walsh
- Stanford University Chemistry, Engineering, and Medicine for Human Health (ChEM-H), Stanford University, Stanford, CA
| | - Yi Tang
- Department of Chemical and Biomolecular Engineering and Department of Chemistry and Biochemistry, University of California, Los Angeles, CA
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30
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Wagner DT, Zhang Z, Meoded RA, Cepeda AJ, Piel J, Keatinge-Clay AT. Structural and Functional Studies of a Pyran Synthase Domain from a trans-Acyltransferase Assembly Line. ACS Chem Biol 2018; 13:975-983. [PMID: 29481043 DOI: 10.1021/acschembio.8b00049] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
trans-Acyltransferase assembly lines possess enzymatic domains often not observed in their better characterized cis-acyltransferase counterparts. Within this repertoire of largely unexplored biosynthetic machinery is a class of enzymes called the pyran synthases that catalyze the formation of five- and six-membered cyclic ethers from diverse polyketide chains. The 1.55 Å resolution crystal structure of a pyran synthase domain excised from the ninth module of the sorangicin assembly line highlights the similarity of this enzyme to the ubiquitous dehydratase domain and provides insight into the mechanism of ring formation. Functional assays of point mutants reveal the central importance of the active site histidine that is shared with the dehydratases as well as the supporting role of a neighboring semiconserved asparagine.
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Affiliation(s)
- Drew T. Wagner
- Department of Molecular Biosciences, The University of Texas at Austin, Austin, Texas 78712, United States
| | - Zhicheng Zhang
- Department of Chemistry, The University of Texas at Austin, Austin, Texas 78712, United States
| | - Roy A. Meoded
- Institut für Mikrobiologie, Eidgenössiche Technische Hochschule (ETH) Zürich, Vladimir-Prelog-Weg 4, 8093 Zürich, Switzerland
| | - Alexis J. Cepeda
- Department of Molecular Biosciences, The University of Texas at Austin, Austin, Texas 78712, United States
| | - Jörn Piel
- Institut für Mikrobiologie, Eidgenössiche Technische Hochschule (ETH) Zürich, Vladimir-Prelog-Weg 4, 8093 Zürich, Switzerland
| | - Adrian T. Keatinge-Clay
- Department of Molecular Biosciences, The University of Texas at Austin, Austin, Texas 78712, United States
- Department of Chemistry, The University of Texas at Austin, Austin, Texas 78712, United States
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31
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Hemmerling F, Lebe KE, Wunderlich J, Hahn F. An Unusual Fatty Acyl:Adenylate Ligase (FAAL)-Acyl Carrier Protein (ACP) Didomain in Ambruticin Biosynthesis. Chembiochem 2018. [DOI: 10.1002/cbic.201800084] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Affiliation(s)
- Franziska Hemmerling
- Professur für Organische Chemie (Lebensmittelchemie); Fakultät für Biologie, Chemie und Geowissenschaften; Universität Bayreuth; Universitätsstrasse 30 95447 Bayreuth Germany
- Biomolekulares Wirkstoffzentrum; Leibniz Universität Hannover; Schneiderberg 38 30167 Hannover Germany
| | - Karen E. Lebe
- Biomolekulares Wirkstoffzentrum; Leibniz Universität Hannover; Schneiderberg 38 30167 Hannover Germany
| | - Johannes Wunderlich
- Professur für Organische Chemie (Lebensmittelchemie); Fakultät für Biologie, Chemie und Geowissenschaften; Universität Bayreuth; Universitätsstrasse 30 95447 Bayreuth Germany
| | - Frank Hahn
- Professur für Organische Chemie (Lebensmittelchemie); Fakultät für Biologie, Chemie und Geowissenschaften; Universität Bayreuth; Universitätsstrasse 30 95447 Bayreuth Germany
- Biomolekulares Wirkstoffzentrum; Leibniz Universität Hannover; Schneiderberg 38 30167 Hannover Germany
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32
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Pandey RP, Sohng JK. In Vitro
Type I Modular Polyketide Synthase Catalysis for New Antibiotics. B KOREAN CHEM SOC 2018. [DOI: 10.1002/bkcs.11416] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
Affiliation(s)
- Ramesh Prasad Pandey
- Department of Life Science and Biochemical Engineering; and Department of BT-Convergent Pharmaceutical Engineering, Sun Moon University; Asan-si 31460 Republic of Korea
| | - Jae Kyung Sohng
- Department of Life Science and Biochemical Engineering; and Department of BT-Convergent Pharmaceutical Engineering, Sun Moon University; Asan-si 31460 Republic of Korea
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33
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Sung KH, Berkhan G, Hollmann T, Wagner L, Blankenfeldt W, Hahn F. Einblicke in die duale Aktivität einer bifunktionalen Dehydratase-Cyclase-Domäne. Angew Chem Int Ed Engl 2017. [DOI: 10.1002/ange.201707774] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Affiliation(s)
- Kwang Hoon Sung
- Helmholtz-Zentrum für Infektionsforschung GmbH; Inhoffenstraße 7 38124 Braunschweig Deutschland
- Institut für Biochemie, Biotechnologie und Bioinformatik; Technische Universität Braunschweig; Spielmannstraße 7 38106 Braunschweig Deutschland
| | - Gesche Berkhan
- Professur für Organische Chemie, Lebensmittelchemie, Fachgruppe Chemie, Fakultät für Biologie, Chemie und Geowissenschaften; Universität Bayreuth; Universitätsstraße 30 95447 Bayreuth Deutschland
- Zentrum für Biomolekulare Wirkstoffe, BMWZ; Leibniz Universität Hannover; Schneiderberg 38 30167 Hannover Deutschland
| | - Tim Hollmann
- Professur für Organische Chemie, Lebensmittelchemie, Fachgruppe Chemie, Fakultät für Biologie, Chemie und Geowissenschaften; Universität Bayreuth; Universitätsstraße 30 95447 Bayreuth Deutschland
| | - Lisa Wagner
- Professur für Organische Chemie, Lebensmittelchemie, Fachgruppe Chemie, Fakultät für Biologie, Chemie und Geowissenschaften; Universität Bayreuth; Universitätsstraße 30 95447 Bayreuth Deutschland
| | - Wulf Blankenfeldt
- Helmholtz-Zentrum für Infektionsforschung GmbH; Inhoffenstraße 7 38124 Braunschweig Deutschland
- Institut für Biochemie, Biotechnologie und Bioinformatik; Technische Universität Braunschweig; Spielmannstraße 7 38106 Braunschweig Deutschland
| | - Frank Hahn
- Professur für Organische Chemie, Lebensmittelchemie, Fachgruppe Chemie, Fakultät für Biologie, Chemie und Geowissenschaften; Universität Bayreuth; Universitätsstraße 30 95447 Bayreuth Deutschland
- Zentrum für Biomolekulare Wirkstoffe, BMWZ; Leibniz Universität Hannover; Schneiderberg 38 30167 Hannover Deutschland
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34
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Sung KH, Berkhan G, Hollmann T, Wagner L, Blankenfeldt W, Hahn F. Insights into the Dual Activity of a Bifunctional Dehydratase-Cyclase Domain. Angew Chem Int Ed Engl 2017; 57:343-347. [PMID: 29084363 DOI: 10.1002/anie.201707774] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2017] [Indexed: 01/12/2023]
Abstract
Oxygen-containing heterocycles are a common structural motif in polyketide natural products and contribute significantly to their biological activity. Here, we report structural and mechanistic investigations on AmbDH3, a polyketide synthase domain with dual activity as dehydratase (DH) and pyran-forming cyclase in ambruticin biosynthesis. AmbDH3 is similar to monofunctional DH domains, using H51 and D215 for dehydration. V173 was confirmed as a diagnostic residue for cyclization activity by a mutational study and enzymatic in vitro experiments. Similar motifs were observed in the seemingly monofunctional AmbDH2, which also shows an unexpected cyclase activity. Our results pave the way for mining of hidden cyclases in biosynthetic pathways. They also open interesting prospects for the generation of novel biocatalysts for chemoenzymatic synthesis and pyran-polyketides by combinatorial biosynthesis.
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Affiliation(s)
- Kwang Hoon Sung
- Helmholtz-Zentrum für Infektionsforschung GmbH, Inhoffenstrasse 7, 38124, Braunschweig, Germany.,Institute of Biochemistry, Biotechnology and Bioinformatics, Technische Universität Braunschweig, Spielmannstrasse 7, 38106, Braunschweig, Germany
| | - Gesche Berkhan
- Professur für Organische Chemie, Lebensmittelchemie, Department of Chemistry, Fakultät für Biologie, Chemie und Geowissenschaften, Universität Bayreuth, Universitätsstrasse 30, 95447, Bayreuth, Germany.,Centre for Biomolecular Drug Research, BMWZ, Leibniz Universität Hannover, Schneiderberg 38, 30167, Hannover, Germany
| | - Tim Hollmann
- Professur für Organische Chemie, Lebensmittelchemie, Department of Chemistry, Fakultät für Biologie, Chemie und Geowissenschaften, Universität Bayreuth, Universitätsstrasse 30, 95447, Bayreuth, Germany
| | - Lisa Wagner
- Professur für Organische Chemie, Lebensmittelchemie, Department of Chemistry, Fakultät für Biologie, Chemie und Geowissenschaften, Universität Bayreuth, Universitätsstrasse 30, 95447, Bayreuth, Germany
| | - Wulf Blankenfeldt
- Helmholtz-Zentrum für Infektionsforschung GmbH, Inhoffenstrasse 7, 38124, Braunschweig, Germany.,Institute of Biochemistry, Biotechnology and Bioinformatics, Technische Universität Braunschweig, Spielmannstrasse 7, 38106, Braunschweig, Germany
| | - Frank Hahn
- Professur für Organische Chemie, Lebensmittelchemie, Department of Chemistry, Fakultät für Biologie, Chemie und Geowissenschaften, Universität Bayreuth, Universitätsstrasse 30, 95447, Bayreuth, Germany.,Centre for Biomolecular Drug Research, BMWZ, Leibniz Universität Hannover, Schneiderberg 38, 30167, Hannover, Germany
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35
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Masschelein J, Jenner M, Challis GL. Antibiotics from Gram-negative bacteria: a comprehensive overview and selected biosynthetic highlights. Nat Prod Rep 2017. [PMID: 28650032 DOI: 10.1039/c7np00010c] [Citation(s) in RCA: 63] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
Covering: up to 2017The overwhelming majority of antibiotics in clinical use originate from Gram-positive Actinobacteria. In recent years, however, Gram-negative bacteria have become increasingly recognised as a rich yet underexplored source of novel antimicrobials, with the potential to combat the looming health threat posed by antibiotic resistance. In this article, we have compiled a comprehensive list of natural products with antimicrobial activity from Gram-negative bacteria, including information on their biosynthetic origin(s) and molecular target(s), where known. We also provide a detailed discussion of several unusual pathways for antibiotic biosynthesis in Gram-negative bacteria, serving to highlight the exceptional biocatalytic repertoire of this group of microorganisms.
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Affiliation(s)
- J Masschelein
- Department of Chemistry, University of Warwick, Gibbet Hill Road, Coventry, UK.
| | - M Jenner
- Department of Chemistry, University of Warwick, Gibbet Hill Road, Coventry, UK.
| | - G L Challis
- Department of Chemistry, University of Warwick, Gibbet Hill Road, Coventry, UK.
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36
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Dunbar KL, Scharf DH, Litomska A, Hertweck C. Enzymatic Carbon-Sulfur Bond Formation in Natural Product Biosynthesis. Chem Rev 2017; 117:5521-5577. [PMID: 28418240 DOI: 10.1021/acs.chemrev.6b00697] [Citation(s) in RCA: 348] [Impact Index Per Article: 49.7] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
Sulfur plays a critical role for the development and maintenance of life on earth, which is reflected by the wealth of primary metabolites, macromolecules, and cofactors bearing this element. Whereas a large body of knowledge has existed for sulfur trafficking in primary metabolism, the secondary metabolism involving sulfur has long been neglected. Yet, diverse sulfur functionalities have a major impact on the biological activities of natural products. Recent research at the genetic, biochemical, and chemical levels has unearthed a broad range of enzymes, sulfur shuttles, and chemical mechanisms for generating carbon-sulfur bonds. This Review will give the first systematic overview on enzymes catalyzing the formation of organosulfur natural products.
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Affiliation(s)
- Kyle L Dunbar
- Department of Biomolecular Chemistry, Leibniz Institute for Natural Product Research and Infection Biology (HKI) , Beutenbergstrasse 11a, 07745 Jena, Germany
| | - Daniel H Scharf
- Life Sciences Institute, University of Michigan , 210 Washtenaw Avenue, Ann Arbor, Michigan 48109-2216, United States
| | - Agnieszka Litomska
- Department of Biomolecular Chemistry, Leibniz Institute for Natural Product Research and Infection Biology (HKI) , Beutenbergstrasse 11a, 07745 Jena, Germany
| | - Christian Hertweck
- Department of Biomolecular Chemistry, Leibniz Institute for Natural Product Research and Infection Biology (HKI) , Beutenbergstrasse 11a, 07745 Jena, Germany.,Friedrich Schiller University , 07743 Jena, Germany
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37
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Abstract
The enzymology of 135 assembly lines containing primarily cis-acyltransferase modules is comprehensively analyzed, with greater attention paid to less common phenomena. Diverse online transformations, in which the substrate and/or product of the reaction is an acyl chain bound to an acyl carrier protein, are classified so that unusual reactions can be compared and underlying assembly-line logic can emerge. As a complement to the chemistry surrounding the loading, extension, and offloading of assembly lines that construct primarily polyketide products, structural aspects of the assembly-line machinery itself are considered. This review of assembly-line phenomena, covering the literature up to 2017, should thus be informative to the modular polyketide synthase novice and expert alike.
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Affiliation(s)
- Adrian T Keatinge-Clay
- Department of Molecular Biosciences, The University of Texas at Austin , Austin, Texas 78712, United States
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38
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Weissman KJ. Polyketide stereocontrol: a study in chemical biology. Beilstein J Org Chem 2017; 13:348-371. [PMID: 28326145 PMCID: PMC5331325 DOI: 10.3762/bjoc.13.39] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2016] [Accepted: 02/01/2017] [Indexed: 11/23/2022] Open
Abstract
The biosynthesis of reduced polyketides in bacteria by modular polyketide synthases (PKSs) proceeds with exquisite stereocontrol. As the stereochemistry is intimately linked to the strong bioactivity of these molecules, the origins of stereochemical control are of significant interest in attempts to create derivatives of these compounds by genetic engineering. In this review, we discuss the current state of knowledge regarding this key aspect of the biosynthetic pathways. Given that much of this information has been obtained using chemical biology tools, work in this area serves as a showcase for the power of this approach to provide answers to fundamental biological questions.
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Affiliation(s)
- Kira J Weissman
- UMR 7365, Ingénierie Moléculaire et Physiopathologie Articulaire (IMoPA), CNRS-Université de Lorraine, Biopôle de l’Université de Lorraine, Campus Biologie Santé, Avenue de la Forêt de Haye, BP 50184, 54505 Vandœuvre-lès-Nancy Cedex, France
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39
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Liddle E, Scott A, Han LC, Ivison D, Simpson TJ, Willis CL, Cox RJ. In vitro kinetic study of the squalestatin tetraketide synthase dehydratase reveals the stereochemical course of a fungal highly reducing polyketide synthase. Chem Commun (Camb) 2017; 53:1727-1730. [PMID: 28106181 DOI: 10.1039/c6cc10172k] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023]
Abstract
Six potential diketide substrates for the squalestatin tetraketide synthase (SQTKS) dehydratase (DH) domain were synthesised as N-acetyl cysteamine thiolesters (SNAC) and tested in kinetic assays as substrates with an isolated DH domain. 3R-3-hydroxybutyryl SNAC 3R-16 was turned over by the enzyme, but its enantiomer was not. Of the four 2-methyl substrates only 2R,3R-2-methyl-3-hydroxybutyryl SNAC 2R,3R-8 was a substrate. Combined with stereochemical information from the isolated SQTKS enoyl reductase (ER) domain, our results provide a near complete stereochemical description of the first cycle of beta-modification reactions of a fungal highly reducing polyketide synthase (HR-PKS). The results emphasise the close relationship between fungal HR-PKS and vertebrate fatty acid synthases (vFAS).
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Affiliation(s)
- Emma Liddle
- School of Chemistry, University of Bristol, Cantock's Close, Bristol, BS8 1TS, UK
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40
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The Draft Genome Sequence of Actinokineospora bangkokensis 44EHW T Reveals the Biosynthetic Pathway of the Antifungal Thailandin Compounds with Unusual Butylmalonyl-CoA Extender Units. Molecules 2016; 21:molecules21111607. [PMID: 27886115 PMCID: PMC6273641 DOI: 10.3390/molecules21111607] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2016] [Revised: 11/17/2016] [Accepted: 11/19/2016] [Indexed: 11/16/2022] Open
Abstract
We report the draft genome sequence of Actinokineospora bangkokensis 44EHWT, the producer of the antifungal polyene compounds, thailandins A and B. The sequence contains 7.45 Mb, 74.1% GC content and 35 putative gene clusters for the biosynthesis of secondary metabolites. There are three gene clusters encoding large polyketide synthases of type I. Annotation of the ORF functions and targeted gene disruption enabled us to identify the cluster for thailandin biosynthesis. We propose a plausible biosynthetic pathway for thailandin, where the unusual butylmalonyl-CoA extender unit is incorporated and results in an untypical side chain.
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41
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Berkhan G, Merten C, Holec C, Hahn F. Das Zusammenspiel zwischen einer multifunktionalen Dehydratase-Domäne und einer C-Methyltransferase bewirkt die Doppelbindungsverschiebung in der Ambruticin-Biosynthese. Angew Chem Int Ed Engl 2016. [DOI: 10.1002/ange.201607827] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Affiliation(s)
- Gesche Berkhan
- Professur für Organische Chemie (Lebensmittelchemie), Fakultät für Biologie, Chemie und Geowissenschaften; Universität Bayreuth; Universitätsstraße 30 95447 Bayreuth Deutschland
- Zentrum für Biomolekulare Wirkstoffe; Leibniz Universität Hannover; Schneiderberg 38 30167 Hannover Deutschland
| | - Christian Merten
- Ruhr-Universität Bochum; Organische Chemie 2; Universitätsstraße 150 44801 Bochum Deutschland
| | - Claudia Holec
- Institut für Bioorganische Chemie; Heinrich-Heine-Universität, Düsseldorf im Forschungszentrum Jülich; Stetternicher Forst, Geb. 15.8 52426 Jülich Deutschland
| | - Frank Hahn
- Professur für Organische Chemie (Lebensmittelchemie), Fakultät für Biologie, Chemie und Geowissenschaften; Universität Bayreuth; Universitätsstraße 30 95447 Bayreuth Deutschland
- Zentrum für Biomolekulare Wirkstoffe; Leibniz Universität Hannover; Schneiderberg 38 30167 Hannover Deutschland
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42
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Franke J, Hertweck C. Biomimetic Thioesters as Probes for Enzymatic Assembly Lines: Synthesis, Applications, and Challenges. Cell Chem Biol 2016; 23:1179-1192. [PMID: 27693058 DOI: 10.1016/j.chembiol.2016.08.014] [Citation(s) in RCA: 64] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2016] [Revised: 08/09/2016] [Accepted: 08/31/2016] [Indexed: 10/20/2022]
Abstract
Thioesters play essential roles in many biosynthetic pathways to fatty acids, esters, polyketides, and non-ribosomal peptides. Coenzyme A (CoA) and related phosphopantetheine thioesters are typically employed as activated acyl units for diverse C-C, C-O, and C-N coupling reactions. To study and control these enzymatic assembly lines in vitro and in vivo structurally simplified analogs such as N-acetylcysteamine (NAC) thioesters have been developed. This review gives an overview on experimental strategies enabled by synthetic NAC thioesters, such as the elucidation of complex biosynthetic pathways and enzyme mechanisms as well as precursor-directed biosynthesis and mutasynthesis. The review also summarizes synthetic protocols and protection group strategies to access these versatile synthetic tools, which are reactive and often unstable compounds. In addition, alternative phosphopantetheine thioester mimics are presented that can be used as protein tags or suicide inhibitors for protein crosslinking and off-loading probes to elucidate polyketide intermediates.
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Affiliation(s)
- Jakob Franke
- Department of Biomolecular Chemistry, Leibniz Institute for Natural Product Research and Infection Biology (HKI), Beutenbergstraße 11a, 07745 Jena, Germany
| | - Christian Hertweck
- Department of Biomolecular Chemistry, Leibniz Institute for Natural Product Research and Infection Biology (HKI), Beutenbergstraße 11a, 07745 Jena, Germany; Friedrich Schiller University, 07743 Jena, Germany.
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43
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Berkhan G, Merten C, Holec C, Hahn F. The Interplay between a Multifunctional Dehydratase Domain and a C-Methyltransferase Effects Olefin Shift in Ambruticin Biosynthesis. Angew Chem Int Ed Engl 2016; 55:13589-13592. [DOI: 10.1002/anie.201607827] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2016] [Indexed: 01/27/2023]
Affiliation(s)
- Gesche Berkhan
- Professur für Organische Chemie (Lebensmittelchemie), Fakultät für Biologie, Chemie und Geowissenschaften; Universität Bayreuth; Universitätsstrasse 30 95447 Bayreuth Germany
- Zentrum für Biomolekulare Wirkstoffe; Leibniz Universität Hannover; Schneiderberg 38 30167 Hannover Germany
| | - Christian Merten
- Ruhr Universität Bochum; Organische Chemie 2; Universitätsstrasse 150 44801 Bochum Germany
| | - Claudia Holec
- Institut für Bioorganische Chemie; Heinrich-Heine-Universität Düsseldorf im Forschungszentrum Jülich; Stetternicher Forst, Geb. 15.8 52426 Jülich Germany
| | - Frank Hahn
- Professur für Organische Chemie (Lebensmittelchemie), Fakultät für Biologie, Chemie und Geowissenschaften; Universität Bayreuth; Universitätsstrasse 30 95447 Bayreuth Germany
- Zentrum für Biomolekulare Wirkstoffe; Leibniz Universität Hannover; Schneiderberg 38 30167 Hannover Germany
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44
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Hemmerling F, Hahn F. Biosynthesis of oxygen and nitrogen-containing heterocycles in polyketides. Beilstein J Org Chem 2016; 12:1512-50. [PMID: 27559404 PMCID: PMC4979870 DOI: 10.3762/bjoc.12.148] [Citation(s) in RCA: 42] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2016] [Accepted: 06/22/2016] [Indexed: 01/01/2023] Open
Abstract
This review highlights the biosynthesis of heterocycles in polyketide natural products with a focus on oxygen and nitrogen-containing heterocycles with ring sizes between 3 and 6 atoms. Heterocycles are abundant structural elements of natural products from all classes and they often contribute significantly to their biological activity. Progress in recent years has led to a much better understanding of their biosynthesis. In this context, plenty of novel enzymology has been discovered, suggesting that these pathways are an attractive target for future studies.
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Affiliation(s)
- Franziska Hemmerling
- Institut für Organische Chemie and Zentrum für Biomolekulare Wirkstoffe, Gottfried Wilhelm Leibniz Universität Hannover, Schneiderberg 38, 30167 Hannover, Germany; Fakultät für Biologie, Chemie und Geowissenschaften, Universität Bayreuth, Universitätsstraße 30, 95440 Bayreuth, Germany
| | - Frank Hahn
- Institut für Organische Chemie and Zentrum für Biomolekulare Wirkstoffe, Gottfried Wilhelm Leibniz Universität Hannover, Schneiderberg 38, 30167 Hannover, Germany; Fakultät für Biologie, Chemie und Geowissenschaften, Universität Bayreuth, Universitätsstraße 30, 95440 Bayreuth, Germany
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45
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Pang B, Wang M, Liu W. Cyclization of polyketides and non-ribosomal peptides on and off their assembly lines. Nat Prod Rep 2016; 33:162-73. [PMID: 26604034 DOI: 10.1039/c5np00095e] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Modular polyketide synthases (PKSs) and non-ribosomal peptide synthetases (NRPSs) are multifunctional megaenzymes that serve as templates to program the assembly of short carboxylic acids and amino acids in a primarily co-linear manner. The variation, combination, permutation and evolution of their functional units (e.g., modules, domains and proteins) along with their association with external enzymes have resulted in the generation of numerous versions of templates, the roles of which have not been fully recognized in the structural diversification of polyketides, non-ribosomal peptides and their hybrids present in nature. In this Highlight, we focus on the assembly-line enzymology and associated chemistry by providing examples of some newly characterized cyclization reactions that occur on and off the assembly lines during and after chain elongation for the purpose of elucidating the template effects of PKSs and NRPSs. A fundamental understanding of the underlying biosynthetic logic would facilitate the elucidation of chemical information contained within the PKS or NRPS templates and benefit the development of strategies for genome mining, biosynthesis-inspired chemical synthesis and combinatorial biosynthesis.
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Affiliation(s)
- Bo Pang
- State Key Laboratory of Bioorganic and Natural Products Chemistry, Shanghai Institute of Organic Chemistry, Chinese Academy of Sciences, 345 Lingling Road, Shanghai 200032, China.
| | - Min Wang
- State Key Laboratory of Bioorganic and Natural Products Chemistry, Shanghai Institute of Organic Chemistry, Chinese Academy of Sciences, 345 Lingling Road, Shanghai 200032, China.
| | - Wen Liu
- State Key Laboratory of Bioorganic and Natural Products Chemistry, Shanghai Institute of Organic Chemistry, Chinese Academy of Sciences, 345 Lingling Road, Shanghai 200032, China. and Huzhou Center of Bio-Synthetic Innovation, 1366 Hongfeng Road, Huzhou 313000, China
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46
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Yang L, Lin Z, Huang SH, Hong R. Stereodivergent Synthesis of Functionalized Tetrahydropyrans Accelerated by Mechanism-Based Allylboration and Bioinspired Oxa-Michael Cyclization. Angew Chem Int Ed Engl 2016. [DOI: 10.1002/ange.201600558] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
Affiliation(s)
- Lin Yang
- CAS Key Laboratory of Synthetic Chemistry of Natural Substances; Shanghai Institute of Organic Chemistry (CAS); 345 Lingling Road Shanghai 200032 China
| | - Zuming Lin
- CAS Key Laboratory of Synthetic Chemistry of Natural Substances; Shanghai Institute of Organic Chemistry (CAS); 345 Lingling Road Shanghai 200032 China
| | - Sha-Hua Huang
- CAS Key Laboratory of Synthetic Chemistry of Natural Substances; Shanghai Institute of Organic Chemistry (CAS); 345 Lingling Road Shanghai 200032 China
- School of Chemical and Environmental Engineering; Shanghai Institute of Technology; 100 Haiquan Road Shanghai 201418 China
| | - Ran Hong
- CAS Key Laboratory of Synthetic Chemistry of Natural Substances; Shanghai Institute of Organic Chemistry (CAS); 345 Lingling Road Shanghai 200032 China
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47
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Yang L, Lin Z, Huang SH, Hong R. Stereodivergent Synthesis of Functionalized Tetrahydropyrans Accelerated by Mechanism-Based Allylboration and Bioinspired Oxa-Michael Cyclization. Angew Chem Int Ed Engl 2016; 55:6280-4. [DOI: 10.1002/anie.201600558] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2016] [Revised: 02/23/2016] [Indexed: 11/06/2022]
Affiliation(s)
- Lin Yang
- CAS Key Laboratory of Synthetic Chemistry of Natural Substances; Shanghai Institute of Organic Chemistry (CAS); 345 Lingling Road Shanghai 200032 China
| | - Zuming Lin
- CAS Key Laboratory of Synthetic Chemistry of Natural Substances; Shanghai Institute of Organic Chemistry (CAS); 345 Lingling Road Shanghai 200032 China
| | - Sha-Hua Huang
- CAS Key Laboratory of Synthetic Chemistry of Natural Substances; Shanghai Institute of Organic Chemistry (CAS); 345 Lingling Road Shanghai 200032 China
- School of Chemical and Environmental Engineering; Shanghai Institute of Technology; 100 Haiquan Road Shanghai 201418 China
| | - Ran Hong
- CAS Key Laboratory of Synthetic Chemistry of Natural Substances; Shanghai Institute of Organic Chemistry (CAS); 345 Lingling Road Shanghai 200032 China
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48
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Sundaram S, Hertweck C. On-line enzymatic tailoring of polyketides and peptides in thiotemplate systems. Curr Opin Chem Biol 2016; 31:82-94. [DOI: 10.1016/j.cbpa.2016.01.012] [Citation(s) in RCA: 44] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2015] [Revised: 12/21/2015] [Accepted: 01/15/2016] [Indexed: 11/26/2022]
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49
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Liang S, Hammond GB, Xu B. Supported gold nanoparticles catalyzed cis-selective semihydrogenation of alkynes using ammonium formate as the reductant. Chem Commun (Camb) 2016; 52:6013-6. [DOI: 10.1039/c6cc01318j] [Citation(s) in RCA: 33] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/21/2023]
Abstract
TiO2 supported gold nanoparticles with a low loading (0.5 mol%) are able to semihydrogenate non-fluorinated and gem-difluorinated alkynes to cis-alkenes with high selectivity, using cost-effective and easy-to-handle ammonium formate as the reductant.
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Affiliation(s)
- Shengzong Liang
- Department of Chemistry
- University of Louisville
- Louisville
- USA
| | | | - Bo Xu
- College of Chemistry
- Chemical Engineering and Biotechnology
- Donghua University
- Shanghai 201620
- China
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50
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Cochrane RVK, Sanichar R, Lambkin GR, Reiz B, Xu W, Tang Y, Vederas JC. Production of New Cladosporin Analogues by Reconstitution of the Polyketide Synthases Responsible for the Biosynthesis of this Antimalarial Agent. Angew Chem Int Ed Engl 2015; 55:664-8. [PMID: 26783060 DOI: 10.1002/anie.201509345] [Citation(s) in RCA: 34] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2015] [Indexed: 11/10/2022]
Abstract
The antimalarial agent cladosporin is a nanomolar inhibitor of the Plasmodium falciparum lysyl-tRNA synthetase, and exhibits activity against both blood- and liver-stage infection. Cladosporin can be isolated from the fungus Cladosporium cladosporioides, where it is biosynthesized by a highly reducing (HR) and a non-reducing (NR) iterative type I polyketide synthase (PKS) pair. Genome sequencing of the host organism and subsequent heterologous expression of these enzymes in Saccharomyces cerevisiae produced cladosporin, confirming the identity of the putative gene cluster. Incorporation of a pentaketide intermediate analogue indicated a 5+3 assembly by the HR PKS Cla2 and the NR PKS Cla3 during cladosporin biosynthesis. Advanced-intermediate analogues were synthesized and incorporated by Cla3 to furnish new cladosporin analogues. A putative lysyl-tRNA synthetase resistance gene was identified in the cladosporin gene cluster. Analysis of the active site emphasizes key structural features thought to be important in resistance to cladosporin.
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Affiliation(s)
- Rachel V K Cochrane
- Department of Chemistry, University of Alberta, Edmonton, Alberta, T6G 2G2 (Canada)
| | - Randy Sanichar
- Department of Chemistry, University of Alberta, Edmonton, Alberta, T6G 2G2 (Canada)
| | - Gareth R Lambkin
- Department of Chemistry, University of Alberta, Edmonton, Alberta, T6G 2G2 (Canada)
| | - Béla Reiz
- Department of Chemistry, University of Alberta, Edmonton, Alberta, T6G 2G2 (Canada)
| | - Wei Xu
- Department of Chemical and Biomolecular Engineering and Department of Chemistry and Biochemistry, University of California, Los Angeles, CA 90095 (USA)
| | - Yi Tang
- Department of Chemical and Biomolecular Engineering and Department of Chemistry and Biochemistry, University of California, Los Angeles, CA 90095 (USA)
| | - John C Vederas
- Department of Chemistry, University of Alberta, Edmonton, Alberta, T6G 2G2 (Canada).
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