1
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Yan P, Wang G, Huang M, Liu Z, Dai C, Hu B, Gu M, Deng Z, Liu R, Wang X, Liu T. Combinatorial Biosynthesis Creates a Novel Aglycone Polyether with High Potency and Low Side Effects Against Bladder Cancer. ADVANCED SCIENCE (WEINHEIM, BADEN-WURTTEMBERG, GERMANY) 2024; 11:e2404668. [PMID: 38935027 PMCID: PMC11348059 DOI: 10.1002/advs.202404668] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/01/2024] [Revised: 06/11/2024] [Indexed: 06/28/2024]
Abstract
Polyethers play a crucial role in the development of anticancer drugs. To enhance the anticancer efficacy and reduce the toxicity of these compounds, thereby advancing their application in cancer treatment, herein, guided by the structure-activity relationships of aglycone polyethers, novel aglycone polyethers are rationally redesigned with potentially improved efficacy and reduced toxicity against tumors. To realize the biosynthesis of the novel aglycone polyethers, the gene clusters and the post-polyketide synthase tailoring pathways for aglycone polyethers endusamycin and lenoremycin are identified and subjected to combinatorial biosynthesis studies, resulting in the creation of a novel aglycone polyether termed End-16, which demonstrates significant potential for treating bladder cancer (BLCA). End-16 demonstrates the ability to suppress the proliferation, migration, invasion, and cellular protrusions formation of BLCA cells, as well as induce cell cycle arrest in the G1 phase in vitro. Notably, End-16 exhibits superior inhibitory activity and fewer side effects against BLCA compared to the frontline anti-BLCA drug cisplatin in vivo, thereby warranting further preclinical studies. This study highlights the significant potential of integrating combinatorial biosynthesis strategies with rational design to create unnatural products with enhanced pharmacological properties.
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Affiliation(s)
- Pan Yan
- Key Laboratory of Combinatorial Biosynthesis and Drug DiscoveryMinistry of Education and School of Pharmaceutical SciencesWuhan UniversityWuhan430071China
| | - Gang Wang
- Department of UrologyZhongnan Hospital of Wuhan UniversityWuhan430071China
- Department of Biological RepositoriesHuman Genetic Resource Preservation Center of Hubei ProvinceZhongnan Hospital of Wuhan UniversityWuhan430071China
- Medical Research InstituteFrontier Science Center of Immunology and MetabolismWuhan UniversityWuhan430071China
| | - Minjian Huang
- Key Laboratory of Combinatorial Biosynthesis and Drug DiscoveryMinistry of Education and School of Pharmaceutical SciencesWuhan UniversityWuhan430071China
- Wuhan Hesheng Technology Co., LtdWuhan430074China
| | - Zhen Liu
- Key Laboratory of Combinatorial Biosynthesis and Drug DiscoveryMinistry of Education and School of Pharmaceutical SciencesWuhan UniversityWuhan430071China
| | - Chong Dai
- Key Laboratory of Combinatorial Biosynthesis and Drug DiscoveryMinistry of Education and School of Pharmaceutical SciencesWuhan UniversityWuhan430071China
| | - Ben Hu
- Precision Cancer Diagnostic CenterZhongnan Hospital of Wuhan UniversityWuhan430071China
| | - Meijia Gu
- Key Laboratory of Combinatorial Biosynthesis and Drug DiscoveryMinistry of Education and School of Pharmaceutical SciencesWuhan UniversityWuhan430071China
| | - Zixin Deng
- State Key Laboratory of Microbial MetabolismSchool of Life Sciences and BiotechnologyShanghai Jiao Tong UniversityShanghai200240China
| | - Ran Liu
- State Key Laboratory of Microbial MetabolismSchool of Life Sciences and BiotechnologyShanghai Jiao Tong UniversityShanghai200240China
- Key Laboratory of Quantitative Synthetic BiologyShenzhen Institute of Synthetic BiologyShenzhen Institutes of Advanced TechnologyChinese Academy of SciencesShenzhen518055China
| | - Xinghuan Wang
- Department of UrologyZhongnan Hospital of Wuhan UniversityWuhan430071China
- Department of Biological RepositoriesHuman Genetic Resource Preservation Center of Hubei ProvinceZhongnan Hospital of Wuhan UniversityWuhan430071China
- Medical Research InstituteFrontier Science Center of Immunology and MetabolismWuhan UniversityWuhan430071China
| | - Tiangang Liu
- Key Laboratory of Combinatorial Biosynthesis and Drug DiscoveryMinistry of Education and School of Pharmaceutical SciencesWuhan UniversityWuhan430071China
- Wuhan Hesheng Technology Co., LtdWuhan430074China
- State Key Laboratory of Microbial MetabolismSchool of Life Sciences and BiotechnologyShanghai Jiao Tong UniversityShanghai200240China
- Department of UrologyZhongnan Hospital of Wuhan UniversitySchool of Pharmaceutical SciencesWuhan UniversityWuhan430071China
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2
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Wang Q, Liu N, Deng Y, Guan Y, Xiao H, Nitka TA, Yang H, Yadav A, Vukovic L, Mathews II, Chen X, Kim CY. Triepoxide formation by a flavin-dependent monooxygenase in monensin biosynthesis. Nat Commun 2023; 14:6273. [PMID: 37805629 PMCID: PMC10560226 DOI: 10.1038/s41467-023-41889-0] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2021] [Accepted: 09/18/2023] [Indexed: 10/09/2023] Open
Abstract
Monensin A is a prototypical natural polyether polyketide antibiotic. It acts by binding a metal cation and facilitating its transport across the cell membrane. Biosynthesis of monensin A involves construction of a polyene polyketide backbone, subsequent epoxidation of the alkenes, and, lastly, formation of cyclic ethers via epoxide-opening cyclization. MonCI, a flavin-dependent monooxygenase, is thought to transform all three alkenes in the intermediate polyketide premonensin A into epoxides. Our crystallographic study has revealed that MonCI's exquisite stereocontrol is due to the preorganization of the active site residues which allows only one specific face of the alkene to approach the reactive C(4a)-hydroperoxyflavin moiety. Furthermore, MonCI has an unusually large substrate-binding cavity that can accommodate premonensin A in an extended or folded conformation which allows any of the three alkenes to be placed next to C(4a)-hydroperoxyflavin. MonCI, with its ability to perform multiple epoxidations on the same substrate in a stereospecific manner, demonstrates the extraordinary versatility of the flavin-dependent monooxygenase family of enzymes.
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Affiliation(s)
- Qian Wang
- Department of Chemistry and Biochemistry, The University of Texas at El Paso, 500 West University Avenue, El Paso, TX, 79968, USA
| | - Ning Liu
- Key Laboratory of Synthetic and Natural Functional Molecular Chemistry of Ministry of Education, College of Chemistry and Materials Science, Northwest University, 710127, Xi'an, China
| | - Yaming Deng
- Key Laboratory of Synthetic and Natural Functional Molecular Chemistry of Ministry of Education, College of Chemistry and Materials Science, Northwest University, 710127, Xi'an, China
| | - Yuze Guan
- Key Laboratory of Synthetic and Natural Functional Molecular Chemistry of Ministry of Education, College of Chemistry and Materials Science, Northwest University, 710127, Xi'an, China
| | - Hongli Xiao
- Key Laboratory of Synthetic and Natural Functional Molecular Chemistry of Ministry of Education, College of Chemistry and Materials Science, Northwest University, 710127, Xi'an, China
| | - Tara A Nitka
- Department of Chemistry and Biochemistry, The University of Texas at El Paso, 500 West University Avenue, El Paso, TX, 79968, USA
| | - Hui Yang
- Key Laboratory of Synthetic and Natural Functional Molecular Chemistry of Ministry of Education, College of Chemistry and Materials Science, Northwest University, 710127, Xi'an, China
| | - Anju Yadav
- Department of Chemistry and Biochemistry, The University of Texas at El Paso, 500 West University Avenue, El Paso, TX, 79968, USA
| | - Lela Vukovic
- Department of Chemistry and Biochemistry, The University of Texas at El Paso, 500 West University Avenue, El Paso, TX, 79968, USA
| | - Irimpan I Mathews
- Stanford Synchrotron Radiation Lightsource, SLAC National Accelerator Laboratory, 2575 Sand Hill Road, Menlo Park, CA, 95124, USA
| | - Xi Chen
- Key Laboratory of Synthetic and Natural Functional Molecular Chemistry of Ministry of Education, College of Chemistry and Materials Science, Northwest University, 710127, Xi'an, China.
| | - Chu-Young Kim
- Department of Chemistry and Biochemistry, The University of Texas at El Paso, 500 West University Avenue, El Paso, TX, 79968, USA.
- Department of Biochemistry, University of Illinois Urbana-Champaign, Urbana, IL, 61801, USA.
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3
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Wen Y, Zhang G, Bahadur A, Xu Y, Liu Y, Tian M, Ding W, Chen T, Zhang W, Liu G. Genomic Investigation of Desert Streptomyces huasconensis D23 Reveals Its Environmental Adaptability and Antimicrobial Activity. Microorganisms 2022; 10:2408. [PMID: 36557661 PMCID: PMC9784485 DOI: 10.3390/microorganisms10122408] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2022] [Revised: 11/29/2022] [Accepted: 12/02/2022] [Indexed: 12/12/2022] Open
Abstract
The harsh climatic conditions of deserts may lead to unique adaptations of microbes, which could serve as potential sources of new metabolites to cope with environmental stresses. However, the mechanisms governing the environmental adaptability and antimicrobial activity of desert Streptomyces remain inadequate, especially in extreme temperature differences, drought conditions, and strong radiation. Here, we isolated a Streptomyces strain from rocks in the Kumtagh Desert in Northwest China and tested its antibacterial activity, resistance to UV-C irradiation, and tolerance to hydrogen peroxide (H2O2). The whole-genome sequencing was carried out to study the mechanisms underlying physiological characteristics and ecological adaptation from a genomic perspective. This strain has a growth inhibitory effect against a variety of indicator bacteria, and the highest antibacterial activity recorded was against Bacillus cereus. Moreover, strain D23 can withstand UV-C irradiation up to 100 J/m2 (D10 = 80 J/m2) and tolerate stress up to 70 mM H2O2. The genome prediction of strain D23 revealed the mechanisms associated with its adaptation to extreme environmental and stressful conditions. In total, 33 biosynthetic gene clusters (BGCs) were predicted based on anti-SMASH. Gene annotation found that S. huasconensis D23 contains several genes and proteins associated with the biosynthesis of factors required to cope with environmental stress of temperature, UV radiation, and osmotic pressure. The results of this study provide information about the genome and BGCs of the strain S. huasconensis D23. The experimental results combined with the genome sequencing data show that antimicrobial activity and stress resistance of S. huasconensis D23 was due to the rich and diverse secondary metabolite production capacity and the induction of stress-responsive genes. The environmental adaptability and antimicrobial activity information presented here will be valuable for subsequent work regarding the isolation of bioactive compounds and provide insight into the ecological adaptation mechanism of microbes to extreme desert environments.
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Affiliation(s)
- Ying Wen
- Key Laboratory of Desert and Desertification, Northwest Institute of Eco-Environment and Resources, Chinese Academy of Sciences, Lanzhou 100864, Gansu, China
- Key Laboratory of Extreme Environmental Microbial Resources and Engineering, Lanzhou 100864, Gansu, China
- University of Chinese Academy of Sciences, No.19A Yuquan Road, Beijing 100049, China
| | - Gaosen Zhang
- Key Laboratory of Desert and Desertification, Northwest Institute of Eco-Environment and Resources, Chinese Academy of Sciences, Lanzhou 100864, Gansu, China
- Key Laboratory of Extreme Environmental Microbial Resources and Engineering, Lanzhou 100864, Gansu, China
| | - Ali Bahadur
- Key Laboratory of Extreme Environmental Microbial Resources and Engineering, Lanzhou 100864, Gansu, China
- State Key Laboratory of Cryospheric Sciences, Northwest Institute of Eco-Environment and Resources, Chinese Academy of Sciences, Lanzhou 100864, Gansu, China
| | - Yeteng Xu
- Key Laboratory of Extreme Environmental Microbial Resources and Engineering, Lanzhou 100864, Gansu, China
- University of Chinese Academy of Sciences, No.19A Yuquan Road, Beijing 100049, China
- State Key Laboratory of Cryospheric Sciences, Northwest Institute of Eco-Environment and Resources, Chinese Academy of Sciences, Lanzhou 100864, Gansu, China
| | - Yang Liu
- Key Laboratory of Extreme Environmental Microbial Resources and Engineering, Lanzhou 100864, Gansu, China
- University of Chinese Academy of Sciences, No.19A Yuquan Road, Beijing 100049, China
- State Key Laboratory of Cryospheric Sciences, Northwest Institute of Eco-Environment and Resources, Chinese Academy of Sciences, Lanzhou 100864, Gansu, China
| | - Mao Tian
- Key Laboratory of Extreme Environmental Microbial Resources and Engineering, Lanzhou 100864, Gansu, China
- University of Chinese Academy of Sciences, No.19A Yuquan Road, Beijing 100049, China
- State Key Laboratory of Cryospheric Sciences, Northwest Institute of Eco-Environment and Resources, Chinese Academy of Sciences, Lanzhou 100864, Gansu, China
| | - Wei Ding
- State Key Laboratory of Microbial Metabolism, School of Life Sciences & Biotechnology, Shanghai Jiao Tong University, Shanghai 200030, China
| | - Tuo Chen
- Key Laboratory of Extreme Environmental Microbial Resources and Engineering, Lanzhou 100864, Gansu, China
- State Key Laboratory of Cryospheric Sciences, Northwest Institute of Eco-Environment and Resources, Chinese Academy of Sciences, Lanzhou 100864, Gansu, China
| | - Wei Zhang
- Key Laboratory of Desert and Desertification, Northwest Institute of Eco-Environment and Resources, Chinese Academy of Sciences, Lanzhou 100864, Gansu, China
- Key Laboratory of Extreme Environmental Microbial Resources and Engineering, Lanzhou 100864, Gansu, China
| | - Guangxiu Liu
- Key Laboratory of Desert and Desertification, Northwest Institute of Eco-Environment and Resources, Chinese Academy of Sciences, Lanzhou 100864, Gansu, China
- Key Laboratory of Extreme Environmental Microbial Resources and Engineering, Lanzhou 100864, Gansu, China
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4
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Xu Y, Han H, Jie Liu Q, Zhao Y, Zhang M, Jiao RH, Zhang B, Ge HM. Salinopyridins A and B, two novel polyethers with a unique pyridine moiety from Streptomyces sp. NA4227. Tetrahedron Lett 2022. [DOI: 10.1016/j.tetlet.2022.154177] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022]
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5
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Bowen JI, Wang L, Crump MP, Willis CL. Synthetic and biosynthetic methods for selective cyclisations of 4,5-epoxy alcohols to tetrahydropyrans. Org Biomol Chem 2022; 20:1150-1175. [PMID: 35029626 PMCID: PMC8827043 DOI: 10.1039/d1ob01905h] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2021] [Accepted: 12/21/2021] [Indexed: 12/20/2022]
Abstract
Tetrahydropyrans (THPs) are common structural motifs found in natural products and synthetic therapeutic molecules. In Nature these 6-membered oxygen heterocycles are often assembled via intramolecular reactions involving either oxy-Michael additions or ring opening of epoxy-alcohols. Indeed, the polyether natural products have been particularly widely studied due to their fascinating structures and important biological properties; these are commonly formed via endo-selective epoxide-opening cascades. In this review we outline synthetic approaches for endo-selective intramolecular epoxide ring opening (IERO) of 4,5-epoxy-alcohols and their applications in natural product synthesis. In addition, the biosynthesis of THP-containing natural products which utilise IERO reactions are reviewed.
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Affiliation(s)
- James I Bowen
- School of Chemistry, University of Bristol, Cantock's Close, Bristol, BS8 1TS, UK.
| | - Luoyi Wang
- CAS Key Laboratory of Microbial Physiological and Metabolic Engineering, State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Beijing, China
| | - Matthew P Crump
- School of Chemistry, University of Bristol, Cantock's Close, Bristol, BS8 1TS, UK.
| | - Christine L Willis
- School of Chemistry, University of Bristol, Cantock's Close, Bristol, BS8 1TS, UK.
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6
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Ren CY, Liu Y, Wei WP, Dai J, Ye BC. Reconstruction of Secondary Metabolic Pathway to Synthesize Novel Metabolite in Saccharopolyspora erythraea. Front Bioeng Biotechnol 2021; 9:628569. [PMID: 34277577 PMCID: PMC8283810 DOI: 10.3389/fbioe.2021.628569] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2020] [Accepted: 04/16/2021] [Indexed: 12/31/2022] Open
Abstract
Natural polyketides play important roles in clinical treatment, agriculture, and animal husbandry. Compared to natural hosts, heterologous chassis (especially Actinomycetes) have many advantages in production of polyketide compounds. As a widely studied model Actinomycete, Saccharopolyspora erythraea is an excellent host to produce valuable heterologous polyketide compounds. However, many host factors affect the expression efficiency of heterologous genes, and it is necessary to modify the host to adapt heterologous production. In this study, the CRISPR-Cas9 system was used to knock out the erythromycin biosynthesis gene cluster of Ab (erythromycin high producing stain). A fragment of 49491 bp in genome (from SACE_0715 to SACE_0733) was deleted, generating the recombinant strain AbΔery in which erythromycin synthesis was blocked and synthetic substrates methylmalonyl-CoA and propionyl-CoA accumulated enormously. Based on AbΔery as heterologous host, three genes, AsCHS, RgTAL, and Sc4CL, driven by strong promoters Pj23119, PermE, and PkasO, respectively, were introduced to produce novel polyketide by L-tyrosine and methylmalonyl-CoA. The product (E)-4-hydroxy-6-(4-hydroxystyryl)-3,5-dimethyl-2H-pyrone was identified in fermentation by LC-MS. High performance liquid chromatography analysis showed that knocking out ery BGC resulted in an increase of methylmalonyl-CoA by 142% and propionyl-CoA by 57.9% in AbΔery compared to WT, and the yield of heterologous product in AbΔery:AsCHS-RgTAL-Sc4CL was higher than WT:AsCHS-RgTAL-Sc4CL. In summary, this study showed that AbΔery could potentially serve as a precious heterologous host to boost the synthesis of other valuable polyketone compounds using methylmalonyl-CoA and propionyl-CoA in the future.
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Affiliation(s)
- Chong-Yang Ren
- Institute of Engineering Biology and Health, Collaborative Innovation Center of Yangtze River Delta Region Green Pharmaceuticals, College of Pharmaceutical Sciences, Zhejiang University of Technology, Hangzhou, China
| | - Yong Liu
- Laboratory of Biosystems and Microanalysis, State Key Laboratory of Bioreactor Engineering, East China University of Science and Technology, Shanghai, China.,Guangdong Provincial Key Laboratory of Synthetic Genomics, Shenzhen Key Laboratory of Synthetic Genomics and Center for Synthetic Genomics, Shenzhen Institute of Synthetic Biology, Shenzhen Institutes of Advanced Technology, Chinese Academy of Sciences, Shenzhen, China
| | - Wen-Ping Wei
- Laboratory of Biosystems and Microanalysis, State Key Laboratory of Bioreactor Engineering, East China University of Science and Technology, Shanghai, China
| | - Junbiao Dai
- Guangdong Provincial Key Laboratory of Synthetic Genomics, Shenzhen Key Laboratory of Synthetic Genomics and Center for Synthetic Genomics, Shenzhen Institute of Synthetic Biology, Shenzhen Institutes of Advanced Technology, Chinese Academy of Sciences, Shenzhen, China
| | - Bang-Ce Ye
- Institute of Engineering Biology and Health, Collaborative Innovation Center of Yangtze River Delta Region Green Pharmaceuticals, College of Pharmaceutical Sciences, Zhejiang University of Technology, Hangzhou, China.,Laboratory of Biosystems and Microanalysis, State Key Laboratory of Bioreactor Engineering, East China University of Science and Technology, Shanghai, China
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7
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Wang Y, Correa Marrero M, Medema MH, van Dijk ADJ. Coevolution-based prediction of protein-protein interactions in polyketide biosynthetic assembly lines. Bioinformatics 2021; 36:4846-4853. [PMID: 32592463 DOI: 10.1093/bioinformatics/btaa595] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2019] [Revised: 05/20/2020] [Accepted: 06/19/2020] [Indexed: 11/13/2022] Open
Abstract
MOTIVATION Polyketide synthases (PKSs) are enzymes that generate diverse molecules of great pharmaceutical importance, including a range of clinically used antimicrobials and antitumor agents. Many polyketides are synthesized by cis-AT modular PKSs, which are organized in assembly lines, in which multiple enzymes line up in a specific order. This order is defined by specific protein-protein interactions (PPIs). The unique modular structure and catalyzing mechanism of these assembly lines makes their products predictable and also spurred combinatorial biosynthesis studies to produce novel polyketides using synthetic biology. However, predicting the interactions of PKSs, and thereby inferring the order of their assembly line, is still challenging, especially for cases in which this order is not reflected by the ordering of the PKS-encoding genes in the genome. RESULTS Here, we introduce PKSpop, which uses a coevolution-based PPI algorithm to infer protein order in PKS assembly lines. Our method accurately predicts protein orders (93% accuracy). Additionally, we identify new residue pairs that are key in determining interaction specificity, and show that coevolution of N- and C-terminal docking domains of PKSs is significantly more predictive for PPIs than coevolution between ketosynthase and acyl carrier protein domains. AVAILABILITY AND IMPLEMENTATION The code is available on http://www.bif.wur.nl/ (under 'Software'). SUPPLEMENTARY INFORMATION Supplementary data are available at Bioinformatics online.
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Affiliation(s)
| | | | | | - Aalt D J van Dijk
- Bioinformatics Group.,Department of Plant Sciences Biometris, Wageningen University & Research, 6708 PB Wageningen, The Netherlands
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8
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Kim MC, Winter JM, Cullum R, Li Z, Fenical W. Complementary Genomic, Bioinformatics, and Chemical Approaches Facilitate the Absolute Structure Assignment of Ionostatin, a Linear Polyketide from a Rare Marine-Derived Actinomycete. ACS Chem Biol 2020; 15:2507-2515. [PMID: 32852937 DOI: 10.1021/acschembio.0c00526] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
A new linear type-1 polyketide, ionostatin (1), has been fully defined using a combined genomic and bioinformatics approach coupled with confirmatory chemical analyses. The 41 carbon-containing polyether is the product of the 101 kbp ion biosynthetic cluster containing seven modular type-1 polyketide synthases. Ionostatin is composed of 15 chiral centers that were proposed using the stereospecificities installed by the different classes of ketoreductases and enoylreductases and confirmed by rigorous NMR analyses. Incorporated into the structure are two tetrahydrofuran rings that appear to be the product of stereospecific epoxidation, followed by stereospecific ring opening and cyclization. These transformations are proposed to be catalyzed by conserved enzymes analogous to those found in other bacterial-derived polyether biosynthetic clusters. Ionostatin shows moderate cancer cell cytotoxicity against U87 glioblastoma and SKOV3 ovarian carcinoma at 7.4 μg/mL.
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Affiliation(s)
- Min Cheol Kim
- Center for Marine Biotechnology and Biomedicine, Scripps Institution of Oceanography, University of California, San Diego, La Jolla, California 92093, United States
| | - Jaclyn M. Winter
- Department of Medicinal Chemistry, University of Utah, Salt Lake City, Utah 84112, United States
| | - Reiko Cullum
- Center for Marine Biotechnology and Biomedicine, Scripps Institution of Oceanography, University of California, San Diego, La Jolla, California 92093, United States
| | - Zhifei Li
- Center for Marine Biotechnology and Biomedicine, Scripps Institution of Oceanography, University of California, San Diego, La Jolla, California 92093, United States
| | - William Fenical
- Center for Marine Biotechnology and Biomedicine, Scripps Institution of Oceanography, University of California, San Diego, La Jolla, California 92093, United States
- Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California, San Diego, La Jolla, California 92093, United States
- Moores Comprehensive Cancer Center, University of California, San Diego, La Jolla, California 92093, United States
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9
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Li Y, Zhang J, Zheng J, Guan H, Liu W, Tan H. Co-expression of a SARP Family Activator ChlF2 and a Type II Thioesterase ChlK Led to High Production of Chlorothricin in Streptomyces antibioticus DSM 40725. Front Bioeng Biotechnol 2020; 8:1013. [PMID: 32974326 PMCID: PMC7471628 DOI: 10.3389/fbioe.2020.01013] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2020] [Accepted: 08/03/2020] [Indexed: 11/20/2022] Open
Abstract
Chlorothricin (CHL), produced by Streptomyces antibioticus DSM 40725 (wild-type strain, WT), belongs to a growing family of spirotetronate antibiotics that have biological activities inhibiting pyruvate carboxylase and malate dehydrogenase. ChlF2, a cluster-situated SARP regulator, can activate the transcription of chlJ, chlC3, chlC6, chlE1, chlM, and chlL to control CHL biosynthesis. Co-expression of chlF2 and chlK encoding type II thioesterase in WT strain under the control of Pkan led to high production of chlorothricin by 840% in comparison with that of WT. Since the inhibitory activity of CHL against several Gram-positive bacteria is higher than des-CHL, combinatorial strategies were applied to promote the conversion of des-CHL to CHL. Over-expression of chlB4, encoding a halogenase, combining with the supplementation of sodium chloride led to further 41% increase of CHL production compared to that of F2OE, a chlF2 over-expression strain. These findings provide new insights into the fine-tuned regulation of spirotetronate family of antibiotics and the construction of high-yield engineered strains.
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Affiliation(s)
- Yue Li
- State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Beijing, China
| | - Jihui Zhang
- State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Beijing, China
| | - Jiazhen Zheng
- State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Beijing, China.,University of Chinese Academy of Sciences, Beijing, China
| | - Hanye Guan
- State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Beijing, China.,University of Chinese Academy of Sciences, Beijing, China
| | - Wen Liu
- State Key Laboratory of Bioorganic and Natural Products Chemistry, Shanghai Institute of Organic Chemistry, Chinese Academy of Sciences, Shanghai, China
| | - Huarong Tan
- State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Beijing, China.,University of Chinese Academy of Sciences, Beijing, China
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10
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Booth TJ, Kalaitzis JA, Vuong D, Crombie A, Lacey E, Piggott AM, Wilkinson B. Production of novel pladienolide analogues through native expression of a pathway-specific activator. Chem Sci 2020; 11:8249-8255. [PMID: 34094178 PMCID: PMC8163091 DOI: 10.1039/d0sc01928c] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022] Open
Abstract
Aberrant splicing of pre-mRNA is implicated in many human genetic disorders. Small molecules that target the spliceosome are important leads as therapeutics and research tools, and one compound of significant interest is the polyketide natural product pladienolide B. Here, we describe the reactivation of quiescent pladienolide B production in the domesticated lab strain Streptomyces platensis AS6200 by overexpression of the pathway-specific activator PldR. The resulting dysregulation of the biosynthetic genes led to the accumulation and isolation of five additional intermediate or shunt metabolites of pladienolide B biosynthesis, including three previously unreported congeners. These compounds likely comprise the entire pladienolide biosynthetic pathway and demonstrate the link between polyketide tailoring reactions and bioactivity, particularly the importance of the 18,19-epoxide. Each congener demonstrated specific inhibitory activity against mammalian cell lines, with successive modifications leading to increased activity (IC50: 8 mM to 5 μM). Reactivation of quiescent polyketide production in a domesticated lab strain.![]()
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Affiliation(s)
- Thomas J Booth
- Department of Molecular Microbiology, John Innes Centre Norwich Research Park Norwich NR4 7UH UK
| | - John A Kalaitzis
- Department of Molecular Sciences, Macquarie University NSW 2109 Australia
| | - Daniel Vuong
- Microbial Screening Technologies Smithfield NSW 2164 Australia
| | - Andrew Crombie
- Microbial Screening Technologies Smithfield NSW 2164 Australia
| | - Ernest Lacey
- Microbial Screening Technologies Smithfield NSW 2164 Australia
| | - Andrew M Piggott
- Department of Molecular Sciences, Macquarie University NSW 2109 Australia
| | - Barrie Wilkinson
- Department of Molecular Microbiology, John Innes Centre Norwich Research Park Norwich NR4 7UH UK
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11
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Chen J, Gui C, Wei Q, Liu J, Ye L, Tian X, Gu YC, Li Q, Ju J. Characterization of Tailoring Methyltransferases Involved in K-41A Biosynthesis: Modulating Methylation to Improve K-41A Anti-infective Activity. Org Lett 2020; 22:4627-4632. [PMID: 32511927 DOI: 10.1021/acs.orglett.0c01347] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/13/2023]
Abstract
The biosynthetic gene cluster (BGC) for polyether antibiotic K-41A was identified from marine-derived Streptomyces sp. SCSIO 01680 and subjected to combinatorial biosynthetic study. Bioinformatics analyses, gene disruption, and metabolomics analyses afforded eight new derivatives and one known polyether, showcasing five region-specific methyltransferases Pak13, Pak15, Pak20, Pak31, and Pak38 and their respective modification loci. Moreover, bioassays revealed that two disaccharide-bearing polyethers, K-41B and K-41Bm, display enhanced anti-HIV and potent antibacterial activities.
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Affiliation(s)
- Jiang Chen
- CAS Key Laboratory of Tropical Marine Bio-resources and Ecology, Guangdong Key Laboratory of Marine Materia Medica, RNAM Center for Marine Microbiology, South China Sea Institute of Oceanology, Chinese Academy of Sciences, 164 West Xingang Road, Guangzhou, 510301, China.,College of Oceanology, University of Chinese Academy of Sciences, 19 Yuquan Road, Beijing, 100049, China
| | - Chun Gui
- CAS Key Laboratory of Tropical Marine Bio-resources and Ecology, Guangdong Key Laboratory of Marine Materia Medica, RNAM Center for Marine Microbiology, South China Sea Institute of Oceanology, Chinese Academy of Sciences, 164 West Xingang Road, Guangzhou, 510301, China.,College of Oceanology, University of Chinese Academy of Sciences, 19 Yuquan Road, Beijing, 100049, China
| | - Qiuyu Wei
- Guangxi Collaborative Innovation Center for Biomedicine, Life Sciences Institute, Guangxi Medical University, Nanning, 530021, Guangxi, China
| | - Jie Liu
- Guangxi Collaborative Innovation Center for Biomedicine, Life Sciences Institute, Guangxi Medical University, Nanning, 530021, Guangxi, China
| | - Li Ye
- Guangxi Collaborative Innovation Center for Biomedicine, Life Sciences Institute, Guangxi Medical University, Nanning, 530021, Guangxi, China
| | - Xinpeng Tian
- CAS Key Laboratory of Tropical Marine Bio-resources and Ecology, Guangdong Key Laboratory of Marine Materia Medica, RNAM Center for Marine Microbiology, South China Sea Institute of Oceanology, Chinese Academy of Sciences, 164 West Xingang Road, Guangzhou, 510301, China
| | - Yu-Cheng Gu
- Syngenta Jealott's Hill International Research Centre, Bracknell, Berkshire RG42 6EY, U.K
| | - Qinglian Li
- CAS Key Laboratory of Tropical Marine Bio-resources and Ecology, Guangdong Key Laboratory of Marine Materia Medica, RNAM Center for Marine Microbiology, South China Sea Institute of Oceanology, Chinese Academy of Sciences, 164 West Xingang Road, Guangzhou, 510301, China
| | - Jianhua Ju
- CAS Key Laboratory of Tropical Marine Bio-resources and Ecology, Guangdong Key Laboratory of Marine Materia Medica, RNAM Center for Marine Microbiology, South China Sea Institute of Oceanology, Chinese Academy of Sciences, 164 West Xingang Road, Guangzhou, 510301, China.,College of Oceanology, University of Chinese Academy of Sciences, 19 Yuquan Road, Beijing, 100049, China
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12
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Komaki H, Harunari E, Ichikawa N, Hosoyama A, Hamada M, Duangmal K, Thamchaipenet A, Igarashi Y. Draft genome sequence of Actinomadura sp. K4S16 and elucidation of the nonthmicin biosynthetic pathway. J Genomics 2020; 8:53-61. [PMID: 32494308 PMCID: PMC7256010 DOI: 10.7150/jgen.44650] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2020] [Accepted: 04/21/2020] [Indexed: 11/28/2022] Open
Abstract
Actinomadura sp. K4S16 (=NBRC 110471) is a producer of a novel tetronate polyether compound nonthmicin. Here, we report the draft genome sequence of this strain together with features of the organism and assembly, annotation and analysis of the genome sequence. The 9.6 Mb genome of Actinomadura sp. K4S16 encoded 9,004 putative ORFs, of which 7,701 were assigned with COG categories. The genome contained four type-I polyketide synthase (PKS) gene clusters, two type-II PKS gene clusters, and three nonribosomal peptide synthetase (NRPS) gene clusters. Among the type-I PKS gene (t1pks) clusters, a large t1pks cluster was annotated to be responsible for nonthmicin synthesis based on bioinformatic analyses. We also performed feeding experiments using labeled precursors and propose the biosynthetic pathway of nonthmicin.
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Affiliation(s)
- Hisayuki Komaki
- Biological Resource Center, National Institute of Technology and Evaluation (NBRC), Kisarazu, Chiba 292-0818, Japan
| | - Enjuro Harunari
- Biotechnology Research Center and Department of Biotechnology, Toyama Prefectural University, Imizu, Toyama 939-0398, Japan
| | | | | | - Moriyuki Hamada
- Biological Resource Center, National Institute of Technology and Evaluation (NBRC), Kisarazu, Chiba 292-0818, Japan
| | | | | | - Yasuhiro Igarashi
- Biotechnology Research Center and Department of Biotechnology, Toyama Prefectural University, Imizu, Toyama 939-0398, Japan
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13
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Antimicrobial biosynthetic potential and diversity of culturable soil actinobacteria from forest ecosystems of Northeast India. Sci Rep 2020; 10:4104. [PMID: 32139731 PMCID: PMC7057963 DOI: 10.1038/s41598-020-60968-6] [Citation(s) in RCA: 32] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2019] [Accepted: 02/06/2020] [Indexed: 02/07/2023] Open
Abstract
Actinobacteria is a goldmine for the discovery of abundant secondary metabolites with diverse biological activities. This study explores antimicrobial biosynthetic potential and diversity of actinobacteria from Pobitora Wildlife Sanctuary and Kaziranga National Park of Assam, India, lying in the Indo-Burma mega-biodiversity hotspot. A total of 107 actinobacteria were isolated, of which 77 exhibited significant antagonistic activity. 24 isolates tested positive for at least one of the polyketide synthase type I, polyketide synthase type II or non-ribosomal peptide synthase genes within their genome. Their secondary metabolite pathway products were predicted to be involved in the production of ansamycin, benzoisochromanequinone, streptogramin using DoBISCUIT database. Molecular identification indicated that these actinobacteria predominantly belonged to genus Streptomyces, followed by Nocardia and Kribbella. 4 strains, viz. Streptomyces sp. PB-79 (GenBank accession no. KU901725; 1313 bp), Streptomyces sp. Kz-28 (GenBank accession no. KY000534; 1378 bp), Streptomyces sp. Kz-32 (GenBank accession no. KY000536; 1377 bp) and Streptomyces sp. Kz-67 (GenBank accession no. KY000540; 1383 bp) showed ~89.5% similarity to the nearest type strain in EzTaxon database and may be considered novel. Streptomyces sp. Kz-24 (GenBank accession no. KY000533; 1367 bp) showed only 96.2% sequence similarity to S. malaysiensis and exhibited minimum inhibitory concentration of 0.024 µg/mL against methicilin resistant Staphylococcus aureus ATCC 43300 and Candida albicans MTCC 227. This study establishes that actinobacteria isolated from the poorly explored Indo-Burma mega-biodiversity hotspot may be an extremely rich reservoir for production of biologically active compounds for human welfare.
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14
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Genomics-driven discovery of the biosynthetic gene cluster of maduramicin and its overproduction in Actinomadura sp. J1-007. ACTA ACUST UNITED AC 2020; 47:275-285. [DOI: 10.1007/s10295-019-02256-5] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2019] [Accepted: 12/09/2019] [Indexed: 02/07/2023]
Abstract
Abstract
Maduramicin is the most efficient and possesses the largest market share of all anti-coccidiosis polyether antibiotics (ionophore); however, its biosynthetic gene cluster (BGC) has yet to been identified, and the associated strains have not been genetically engineered. Herein, we performed whole-genome sequencing of a maduramicin-producing industrial strain of Actinomadura sp. J1-007 and identified its BGC. Additionally, we analyzed the identified BGCs in silico to predict the biosynthetic pathway of maduramicin. We then developed a conjugation method for the non-spore-forming Actinomadura sp. J1-007, consisting of a site-specific integration method for gene overexpression. The maduramicin titer increased by 30% to 7.16 g/L in shake-flask fermentation following overexpression of type II thioesterase MadTE that is the highest titer at present. Our findings provide insights into the biosynthetic mechanism of polyethers and provide a platform for the metabolic engineering of maduramicin-producing microorganisms for overproduction and development of maduramicin analogs in the future.
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15
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Low ZJ, Xiong J, Xie Y, Ma GL, Saw H, Thi Tran H, Wong SL, Pang LM, Fong J, Lu P, Hu JF, Yang L, Miao Y, Liang ZX. Discovery, biosynthesis and antifungal mechanism of the polyene-polyol meijiemycin. Chem Commun (Camb) 2019; 56:822-825. [PMID: 31848534 DOI: 10.1039/c9cc08908j] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023]
Abstract
Produced by a newly isolated Streptomycetes strain, meijiemycin is a gigantic linear polyene-polyol that exhibits structural features not seen in other members of the polyene-polyol family. We propose a biosynthetic mechanism and demonstrate that meijiemycin inhibits hyphal growth by inducing the aggregation of ergosterol and restructuring of the fungal plasma membrane.
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Affiliation(s)
- Zhen Jie Low
- School of Biological Sciences, Nanyang Technological University, 637551, Singapore.
| | - Juan Xiong
- School of Biological Sciences, Nanyang Technological University, 637551, Singapore. and School of Pharmacy, Fudan University, Shanghai, China
| | - Ying Xie
- School of Biological Sciences, Nanyang Technological University, 637551, Singapore.
| | - Guang-Lei Ma
- School of Biological Sciences, Nanyang Technological University, 637551, Singapore.
| | - Howard Saw
- School of Biological Sciences, Nanyang Technological University, 637551, Singapore.
| | - Hoa Thi Tran
- School of Biological Sciences, Nanyang Technological University, 637551, Singapore.
| | - Soo Lin Wong
- School of Biological Sciences, Nanyang Technological University, 637551, Singapore.
| | - Li Mei Pang
- School of Biological Sciences, Nanyang Technological University, 637551, Singapore.
| | - July Fong
- The Singapore Centre for Environmental Life Sciences Engineering (SCELSE), Nanyang Technological University, 637551, Singapore
| | - Peng Lu
- School of Biological Sciences, Nanyang Technological University, 637551, Singapore.
| | - Jin-Feng Hu
- School of Pharmacy, Fudan University, Shanghai, China
| | - Liang Yang
- School of Medicine, Southern University of Science and Technology, Shenzhen, Guangdong, China
| | - Yansong Miao
- School of Biological Sciences, Nanyang Technological University, 637551, Singapore.
| | - Zhao-Xun Liang
- School of Biological Sciences, Nanyang Technological University, 637551, Singapore. and The Singapore Centre for Environmental Life Sciences Engineering (SCELSE), Nanyang Technological University, 637551, Singapore
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16
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Wan X, Yao G, Liu Y, Chen J, Jiang H. Research Progress in the Biosynthetic Mechanisms of Marine Polyether Toxins. Mar Drugs 2019; 17:E594. [PMID: 31652489 PMCID: PMC6835853 DOI: 10.3390/md17100594] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2019] [Revised: 10/17/2019] [Accepted: 10/18/2019] [Indexed: 12/28/2022] Open
Abstract
Marine polyether toxins, mainly produced by marine dinoflagellates, are novel, complex, and diverse natural products with extensive toxicological and pharmacological effects. Owing to their harmful effects during outbreaks of marine red tides, as well as their potential value for the development of new drugs, marine polyether toxins have been extensively studied, in terms of toxicology, pharmacology, detection, and analysis, structural identification, as well as their biosynthetic mechanisms. Although the biosynthetic mechanisms of marine polyether toxins are still unclear, certain progress has been made. In this review, research progress and current knowledge on the biosynthetic mechanisms of polyether toxins are summarized, including the mechanisms of carbon skeleton deletion, pendant alkylation, and polyether ring formation, along with providing a summary of mined biosynthesis-related genes. Finally, future research directions and applications of marine polyether toxins are discussed.
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Affiliation(s)
- Xiukun Wan
- State Key Laboratory of NBC Protection for Civilian, Beijing 102205, China.
| | - Ge Yao
- State Key Laboratory of NBC Protection for Civilian, Beijing 102205, China.
| | - Yanli Liu
- State Key Laboratory of NBC Protection for Civilian, Beijing 102205, China.
| | - Jisheng Chen
- State Key Laboratory of NBC Protection for Civilian, Beijing 102205, China.
| | - Hui Jiang
- State Key Laboratory of NBC Protection for Civilian, Beijing 102205, China.
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17
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Cytochrome P450 Monooxygenase CYP139 Family Involved in the Synthesis of Secondary Metabolites in 824 Mycobacterial Species. Int J Mol Sci 2019; 20:ijms20112690. [PMID: 31159249 PMCID: PMC6600245 DOI: 10.3390/ijms20112690] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2019] [Revised: 05/10/2019] [Accepted: 05/11/2019] [Indexed: 12/15/2022] Open
Abstract
Tuberculosis (TB) is one of the top infectious diseases causing numerous human deaths in the world. Despite enormous efforts, the physiology of the causative agent, Mycobacterium tuberculosis, is poorly understood. To contribute to better understanding the physiological capacity of these microbes, we have carried out extensive in silico analyses of the 1111 mycobacterial species genomes focusing on revealing the role of the orphan cytochrome P450 monooxygenase (CYP) CYP139 family. We have found that CYP139 members are present in 894 species belonging to three mycobacterial groups: M. tuberculosis complex (850-species), Mycobacterium avium complex (34-species), and non-tuberculosis mycobacteria (10-species), with all CYP139 members belonging to the subfamily “A”. CYP139 members have unique amino acid patterns at the CXG motif. Amino acid conservation analysis placed this family in the 8th among CYP families belonging to different biological domains and kingdoms. Biosynthetic gene cluster analyses have revealed that 92% of CYP139As might be associated with producing different secondary metabolites. Such enhanced secondary metabolic potentials with the involvement of CYP139A members might have provided mycobacterial species with advantageous traits in diverse niches competing with other microbial or viral agents, and might help these microbes infect hosts by interfering with the hosts’ metabolism and immune system.
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18
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Liu R, Deng Z, Liu T. Streptomyces species: Ideal chassis for natural product discovery and overproduction. Metab Eng 2018; 50:74-84. [DOI: 10.1016/j.ymben.2018.05.015] [Citation(s) in RCA: 69] [Impact Index Per Article: 11.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2018] [Revised: 05/24/2018] [Accepted: 05/25/2018] [Indexed: 11/26/2022]
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19
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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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20
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Synthetic biology of polyketide synthases. ACTA ACUST UNITED AC 2018; 45:621-633. [DOI: 10.1007/s10295-018-2021-9] [Citation(s) in RCA: 25] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2017] [Accepted: 02/03/2018] [Indexed: 12/31/2022]
Abstract
Abstract
Complex reduced polyketides represent the largest class of natural products that have applications in medicine, agriculture, and animal health. This structurally diverse class of compounds shares a common methodology of biosynthesis employing modular enzyme systems called polyketide synthases (PKSs). The modules are composed of enzymatic domains that share sequence and functional similarity across all known PKSs. We have used the nomenclature of synthetic biology to classify the enzymatic domains and modules as parts and devices, respectively, and have generated detailed lists of both. In addition, we describe the chassis (hosts) that are used to assemble, express, and engineer the parts and devices to produce polyketides. We describe a recently developed software tool to design PKS system and provide an example of its use. Finally, we provide perspectives of what needs to be accomplished to fully realize the potential that synthetic biology approaches bring to this class of molecules.
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21
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Leulmi N, Sighel D, Defant A, Khenaka K, Boulahrouf A, Mancini I. Nigericin and grisorixin methyl ester from the Algerian soil-living Streptomyces youssoufiensis SF10 strain: a computational study on their epimeric structures and evaluation of glioblastoma stem cells growth inhibition. Nat Prod Res 2018. [DOI: 10.1080/14786419.2018.1446014] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/13/2023]
Affiliation(s)
- Nassima Leulmi
- Bioorganic Chemistry Laboratory, Department of Physics, University of Trento, Trento, Italy
- Microbiological Laboratory Engineering and Application, Department of Microbiology, Mentouri Brothers University, Constantine, Algeria
- Department of Cellular and Molecular Biology, University Abbes Laghrour Khenchela, Khenchela, Algeria
| | - Denise Sighel
- Bioorganic Chemistry Laboratory, Department of Physics, University of Trento, Trento, Italy
- Centre for Integrative Biology (CIBIO), University of Trento, Trento, Italy
| | - Andrea Defant
- Bioorganic Chemistry Laboratory, Department of Physics, University of Trento, Trento, Italy
| | - Karima Khenaka
- Microbiological Laboratory Engineering and Application, Department of Microbiology, Mentouri Brothers University, Constantine, Algeria
| | - Abderrahmane Boulahrouf
- Microbiological Laboratory Engineering and Application, Department of Microbiology, Mentouri Brothers University, Constantine, Algeria
| | - Ines Mancini
- Bioorganic Chemistry Laboratory, Department of Physics, University of Trento, Trento, Italy
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22
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Barajas JF, Blake-Hedges JM, Bailey CB, Curran S, Keasling JD. Engineered polyketides: Synergy between protein and host level engineering. Synth Syst Biotechnol 2017; 2:147-166. [PMID: 29318196 PMCID: PMC5655351 DOI: 10.1016/j.synbio.2017.08.005] [Citation(s) in RCA: 60] [Impact Index Per Article: 8.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2017] [Revised: 08/26/2017] [Accepted: 08/26/2017] [Indexed: 01/01/2023] Open
Abstract
Metabolic engineering efforts toward rewiring metabolism of cells to produce new compounds often require the utilization of non-native enzymatic machinery that is capable of producing a broad range of chemical functionalities. Polyketides encompass one of the largest classes of chemically diverse natural products. With thousands of known polyketides, modular polyketide synthases (PKSs) share a particularly attractive biosynthetic logic for generating chemical diversity. The engineering of modular PKSs could open access to the deliberate production of both existing and novel compounds. In this review, we discuss PKS engineering efforts applied at both the protein and cellular level for the generation of a diverse range of chemical structures, and we examine future applications of PKSs in the production of medicines, fuels and other industrially relevant chemicals.
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Key Words
- ACP, Acyl carrier protein
- AT, Acyltransferase
- CoL, CoA-Ligase
- Commodity chemical
- DE, Dimerization element
- DEBS, 6-deoxyerythronolide B synthase
- DH, Dehydratase
- ER, Enoylreductase
- FAS, Fatty acid synthases
- KR, Ketoreductase
- KS, Ketosynthase
- LM, Loading module
- LTTR, LysR-type transcriptional regulator
- Metabolic engineering
- Natural products
- PCC, Propionyl-CoA carboxylase
- PDB, Precursor directed biosynthesis
- PK, Polyketide
- PKS, Polyketide synthase
- Polyketide
- Polyketide synthase
- R, Reductase domain
- SARP, Streptomyces antibiotic regulatory protein
- SNAC, N-acetylcysteamine
- Synthetic biology
- TE, Thioesterase
- TKL, Triketide lactone
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Affiliation(s)
| | | | - Constance B. Bailey
- Joint BioEnergy Institute, Emeryville, CA 94608, USA
- Physical Biosciences Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA
| | - Samuel Curran
- Physical Biosciences Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA
- Comparative Biochemistry Graduate Group, University of California, Berkeley, Berkeley, CA 94720, USA
| | - Jay. D. Keasling
- Joint BioEnergy Institute, Emeryville, CA 94608, USA
- Physical Biosciences Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA
- QB3 Institute, University of California, Berkeley, Emeryville, CA 94608, USA
- Department of Chemical & Biomolecular Engineering, Department of Bioengineering, University of California, Berkeley, Berkeley, CA 94720, USA
- Novo Nordisk Foundation Center for Biosustainability, Technical University Denmark, DK2970 Horsholm, Denmark
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23
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Xie X, Garg A, Khosla C, Cane DE. Elucidation of the Cryptic Methyl Group Epimerase Activity of Dehydratase Domains from Modular Polyketide Synthases Using a Tandem Modules Epimerase Assay. J Am Chem Soc 2017; 139:9507-9510. [PMID: 28682630 DOI: 10.1021/jacs.7b05502] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Dehydratase (DH) domains of cryptic function are often found in polyketide synthase (PKS) modules that produce epimerized (2S)-2-methyl-3-ketoacyl-ACP (acyl carrier protein) intermediates. A combination of tandem equilibrium isotope exchange (EIX) and a newly developed Tandem Modules Epimerase assay revealed the intrinsic epimerase activity of NanDH1 and NanDH5, from modules 1 and 5, respectively, of the nanchangmycin (1) PKS as well of NigDH1, from module 1 of the nigericin (3) PKS. Unexpectedly, all three epimerase-active DH domains were also found to possess intrinsic dehydratase activity, whereas the conventional DH domains, EryDH4, from module 4 of the erythromycin synthase, and NanDH2 from module 2 of the nanchangmycin synthase, were shown to have cryptic epimerase activity.
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Affiliation(s)
- Xinqiang Xie
- Department of Chemistry, Brown University , Box H, Providence, Rhode Island 02912-9108, United States
| | - Ashish Garg
- Department of Chemistry, Brown University , Box H, Providence, Rhode Island 02912-9108, United States
| | - Chaitan Khosla
- Departments of Chemical Engineering, Chemistry, and Biochemistry, Stanford University , Stanford, California 94305, United States
| | - David E Cane
- Department of Chemistry, Brown University , Box H, Providence, Rhode Island 02912-9108, United States
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24
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Abstract
Oxidative cyclizations are important transformations that occur widely during natural product biosynthesis. The transformations from acyclic precursors to cyclized products can afford morphed scaffolds, structural rigidity, and biological activities. Some of the most dramatic structural alterations in natural product biosynthesis occur through oxidative cyclization. In this Review, we examine the different strategies used by nature to create new intra(inter)molecular bonds via redox chemistry. This Review will cover both oxidation- and reduction-enabled cyclization mechanisms, with an emphasis on the former. Radical cyclizations catalyzed by P450, nonheme iron, α-KG-dependent oxygenases, and radical SAM enzymes are discussed to illustrate the use of molecular oxygen and S-adenosylmethionine to forge new bonds at unactivated sites via one-electron manifolds. Nonradical cyclizations catalyzed by flavin-dependent monooxygenases and NAD(P)H-dependent reductases are covered to show the use of two-electron manifolds in initiating cyclization reactions. The oxidative installations of epoxides and halogens into acyclic scaffolds to drive subsequent cyclizations are separately discussed as examples of "disappearing" reactive handles. Last, oxidative rearrangement of rings systems, including contractions and expansions, will be covered.
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Affiliation(s)
- Man-Cheng Tang
- Department of Chemical and Biomolecular Engineering, Department of Chemistry and Biochemistry, University of California, Los Angeles, 420 Westwood Plaza, Los Angeles, CA 90095, USA
| | - Yi Zou
- Department of Chemical and Biomolecular Engineering, Department of Chemistry and Biochemistry, University of California, Los Angeles, 420 Westwood Plaza, Los Angeles, CA 90095, USA
| | - Kenji Watanabe
- Department of Pharmaceutical Sciences, University of Shizuoka, Shizuoka 422-8526, Japan
| | - Christopher T. Walsh
- Stanford University Chemistry, Engineering, and Medicine for Human Health (ChEM-H), Stanford University, 443 Via Ortega, Stanford, CA 94305
| | - Yi Tang
- Department of Chemical and Biomolecular Engineering, Department of Chemistry and Biochemistry, University of California, Los Angeles, 420 Westwood Plaza, Los Angeles, CA 90095, USA
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25
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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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26
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Kohli GS, Campbell K, John U, Smith KF, Fraga S, Rhodes LL, Murray SA. Role of Modular Polyketide Synthases in the Production of Polyether Ladder Compounds in Ciguatoxin-Producing Gambierdiscus polynesiensis and G. excentricus (Dinophyceae). J Eukaryot Microbiol 2017; 64:691-706. [PMID: 28211202 DOI: 10.1111/jeu.12405] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2016] [Revised: 01/31/2017] [Accepted: 02/03/2017] [Indexed: 11/28/2022]
Abstract
Gambierdiscus, a benthic dinoflagellate, produces ciguatoxins that cause the human illness Ciguatera. Ciguatoxins are polyether ladder compounds that have a polyketide origin, indicating that polyketide synthases (PKS) are involved in their production. We sequenced transcriptomes of Gambierdiscus excentricus and Gambierdiscus polynesiensis and found 264 contigs encoding single domain ketoacyl synthases (KS; G. excentricus: 106, G. polynesiensis: 143) and ketoreductases (KR; G. excentricus: 7, G. polynesiensis: 8) with sequence similarity to type I PKSs, as reported in other dinoflagellates. In addition, 24 contigs (G. excentricus: 3, G. polynesiensis: 21) encoding multiple PKS domains (forming typical type I PKSs modules) were found. The proposed structure produced by one of these megasynthases resembles a partial carbon backbone of a polyether ladder compound. Seventeen contigs encoding single domain KS, KR, s-malonyltransacylase, dehydratase and enoyl reductase with sequence similarity to type II fatty acid synthases (FAS) in plants were found. Type I PKS and type II FAS genes were distinguished based on the arrangement of domains on the contigs and their sequence similarity and phylogenetic clustering with known PKS/FAS genes in other organisms. This differentiation of PKS and FAS pathways in Gambierdiscus is important, as it will facilitate approaches to investigating toxin biosynthesis pathways in dinoflagellates.
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Affiliation(s)
- Gurjeet S Kohli
- Climate Change Cluster, University of Technology Sydney, Ultimo, NSW, 2007, Australia.,Singapore Centre for Environmental Life Sciences Engineering, Nanyang Technological University, Singapore, 689528, Singapore
| | - Katrina Campbell
- Institute for Global Food Security, School of Biological Sciences, Queen's University Belfast, David Keir Building, Stranmillis Road, Belfast, BT9 5AG, United Kingdom
| | - Uwe John
- Alfred-Wegener-Institute Helmholtz-Zentrum für Polar- und Meeresforschung, Bremerhaven, 27515, Germany.,Helmholtz Institute for Functional Marine Biodiversity, University of Oldenburg, Oldenburg, 26111, Germany
| | - Kirsty F Smith
- Cawthron Institute, 98 Halifax Street East, Nelson, 7010, New Zealand
| | - Santiago Fraga
- Instituto Español de Oceanografía, Centro Oceanográfico de Vigo, Subida a Radio Faro 50, Vigo, 36390, Spain
| | - Lesley L Rhodes
- Cawthron Institute, 98 Halifax Street East, Nelson, 7010, New Zealand
| | - Shauna A Murray
- Climate Change Cluster, University of Technology Sydney, Ultimo, NSW, 2007, Australia
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Xie X, Garg A, Khosla C, Cane DE. Mechanism and Stereochemistry of Polyketide Chain Elongation and Methyl Group Epimerization in Polyether Biosynthesis. J Am Chem Soc 2017; 139:3283-3292. [PMID: 28157306 DOI: 10.1021/jacs.7b00278] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
The polyketide synthases responsible for the biosynthesis of the polyether antibiotics nanchangmycin (1) and salinomycin (4) harbor a number of redox-inactive ketoreductase (KR0) domains that are implicated in the generation of C2-epimerized (2S)-2-methyl-3-ketoacyl-ACP intermediates. Evidence that the natural substrate for the polyether KR0 domains is, as predicted, a (2R)-2-methyl-3-ketoacyl-ACP intermediate, came from a newly developed coupled ketosynthase (KS)-ketoreductase (KR) assay that established that the decarboxylative condensation of methylmalonyl-CoA with S-propionyl-N-acetylcysteamine catalyzed by the Nan[KS1][AT1] didomain from module 1 of the nanchangmycin synthase generates exclusively the corresponding (2R)-2-methyl-3-ketopentanoyl-ACP (7a) product. In tandem equilibrium isotope exchange experiments, incubation of [2-2H]-(2R,3S)-2-methyl-3-hydroxypentanoyl-ACP (6a) with redox-active, epimerase-inactive EryKR6 from module 6 of the 6-deoxyerythronolide B synthase and catalytic quantities of NADP+ in the presence of redox-inactive, recombinant NanKR10 or NanKR50, from modules 1 and 5 of the nanchangmycin synthase, or recombinant SalKR70 from module 7 of the salinomycin synthase, resulted in first-order, time-dependent washout of deuterium from 6a. Control experiments confirmed that this washout was due to KR0-catalyzed isotope exchange of the reversibly generated, transiently formed oxidation product [2-2H]-(2R)-2-methyl-3-ketopentanoyl-ACP (7a), consistent with the proposed epimerase activity of each of the KR0 domains. Although they belong to the superfamily of short chain dehydrogenase-reductases, the epimerase-active KR0 domains from polyether synthases lack one or both residues of the conserved Tyr-Ser dyad that has previously been implicated in KR-catalyzed epimerizations.
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Affiliation(s)
- Xinqiang Xie
- Department of Chemistry, Brown University , Box H, Providence, Rhode Island 02912-9108, United States
| | - Ashish Garg
- Department of Chemistry, Brown University , Box H, Providence, Rhode Island 02912-9108, United States
| | - Chaitan Khosla
- Departments of Chemical Engineering, Chemistry, and Biochemistry, Stanford University , Stanford, California 94305, United States
| | - David E Cane
- Department of Chemistry, Brown University , Box H, Providence, Rhode Island 02912-9108, United States
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28
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Sun P, Leeson C, Zhi X, Leng F, Pierce RH, Henry MS, Rein KS. Characterization of an epoxide hydrolase from the Florida red tide dinoflagellate, Karenia brevis. PHYTOCHEMISTRY 2016; 122:11-21. [PMID: 26626160 PMCID: PMC4724521 DOI: 10.1016/j.phytochem.2015.11.002] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/20/2015] [Revised: 10/19/2015] [Accepted: 11/05/2015] [Indexed: 05/11/2023]
Abstract
Epoxide hydrolases (EH, EC 3.3.2.3) have been proposed to be key enzymes in the biosynthesis of polyether (PE) ladder compounds such as the brevetoxins which are produced by the dinoflagellate Karenia brevis. These enzymes have the potential to catalyze kinetically disfavored endo-tet cyclization reactions. Data mining of K. brevis transcriptome libraries revealed two classes of epoxide hydrolases: microsomal and leukotriene A4 (LTA4) hydrolases. A microsomal EH was cloned and expressed for characterization. The enzyme is a monomeric protein with molecular weight 44kDa. Kinetic parameters were evaluated using a variety of epoxide substrates to assess substrate selectivity and enantioselectivity, as well as its potential to catalyze the critical endo-tet cyclization of epoxy alcohols. Monitoring of EH activity in high and low toxin producing cultures of K. brevis over a three week period showed consistently higher activity in the high toxin producing culture implicating the involvement of one or more EH in brevetoxin biosynthesis.
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Affiliation(s)
- Pengfei Sun
- Department of Chemistry and Biochemistry, Florida International University, Miami, FL 33199, USA.
| | - Cristian Leeson
- Department of Chemistry and Biochemistry, Florida International University, Miami, FL 33199, USA
| | - Xiaoduo Zhi
- Department of Chemistry and Biochemistry, Florida International University, Miami, FL 33199, USA
| | - Fenfei Leng
- Department of Chemistry and Biochemistry, Florida International University, Miami, FL 33199, USA.
| | - Richard H Pierce
- Mote Marine Laboratory, 1600 Ken Thompson Parkway, Sarasota, FL 34236, USA.
| | - Michael S Henry
- Mote Marine Laboratory, 1600 Ken Thompson Parkway, Sarasota, FL 34236, USA.
| | - Kathleen S Rein
- Department of Chemistry and Biochemistry, Florida International University, Miami, FL 33199, USA.
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29
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Elshahawi SI, Shaaban KA, Kharel MK, Thorson JS. A comprehensive review of glycosylated bacterial natural products. Chem Soc Rev 2015; 44:7591-697. [PMID: 25735878 PMCID: PMC4560691 DOI: 10.1039/c4cs00426d] [Citation(s) in RCA: 299] [Impact Index Per Article: 33.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
A systematic analysis of all naturally-occurring glycosylated bacterial secondary metabolites reported in the scientific literature up through early 2013 is presented. This comprehensive analysis of 15 940 bacterial natural products revealed 3426 glycosides containing 344 distinct appended carbohydrates and highlights a range of unique opportunities for future biosynthetic study and glycodiversification efforts.
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Affiliation(s)
- Sherif I Elshahawi
- Department of Pharmaceutical Sciences, College of Pharmacy, University of Kentucky, Lexington, KY, USA. and Center for Pharmaceutical Research and Innovation, College of Pharmacy, University of Kentucky, Lexington, KY, USA
| | - Khaled A Shaaban
- Department of Pharmaceutical Sciences, College of Pharmacy, University of Kentucky, Lexington, KY, USA. and Center for Pharmaceutical Research and Innovation, College of Pharmacy, University of Kentucky, Lexington, KY, USA
| | - Madan K Kharel
- School of Pharmacy, University of Maryland Eastern Shore, Princess Anne, Maryland, USA
| | - Jon S Thorson
- Department of Pharmaceutical Sciences, College of Pharmacy, University of Kentucky, Lexington, KY, USA. and Center for Pharmaceutical Research and Innovation, College of Pharmacy, University of Kentucky, Lexington, KY, USA
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30
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Polyketide synthesis genes associated with toxin production in two species of Gambierdiscus (Dinophyceae). BMC Genomics 2015; 16:410. [PMID: 26016672 PMCID: PMC4445524 DOI: 10.1186/s12864-015-1625-y] [Citation(s) in RCA: 48] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2014] [Accepted: 05/07/2015] [Indexed: 11/10/2022] Open
Abstract
Background Marine microbial protists, in particular, dinoflagellates, produce polyketide toxins with ecosystem-wide and human health impacts. Species of Gambierdiscus produce the polyether ladder compounds ciguatoxins and maitotoxins, which can lead to ciguatera fish poisoning, a serious human illness associated with reef fish consumption. Genes associated with the biosynthesis of polyether ladder compounds are yet to be elucidated, however, stable isotope feeding studies of such compounds consistently support their polyketide origin indicating that polyketide synthases are involved in their biosynthesis. Results Here, we report the toxicity, genome size, gene content and transcriptome of Gambierdiscus australes and G. belizeanus. G. australes produced maitotoxin-1 and maitotoxin-3, while G. belizeanus produced maitotoxin-3, for which cell extracts were toxic to mice by IP injection (LD50 = 3.8 mg kg-1). The gene catalogues comprised 83,353 and 84,870 unique contigs, with genome sizes of 32.5 ± 3.7 Gbp and 35 ± 0.88 Gbp, respectively, and are amongst the most comprehensive yet reported from a dinoflagellate. We found three hundred and six genes involved in polyketide biosynthesis, including one hundred and ninty-two ketoacyl synthase transcripts, which formed five unique phylogenetic clusters. Conclusions Two clusters were unique to these maitotoxin-producing dinoflagellate species, suggesting that they may be associated with maitotoxin biosynthesis. This work represents a significant step forward in our understanding of the genetic basis of polyketide production in dinoflagellates, in particular, species responsible for ciguatera fish poisoning. Electronic supplementary material The online version of this article (doi:10.1186/s12864-015-1625-y) contains supplementary material, which is available to authorized users.
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31
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Wong FT, Hotta K, Chen X, Fang M, Watanabe K, Kim CY. Epoxide Hydrolase–Lasalocid A Structure Provides Mechanistic Insight into Polyether Natural Product Biosynthesis. J Am Chem Soc 2014; 137:86-9. [DOI: 10.1021/ja511374k] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Fong T. Wong
- Molecular
Engineering Lab, Biomedical Sciences Institutes, 138673 Singapore
| | - Kinya Hotta
- Department
of Biological Sciences, National University of Singapore, 117543 Singapore
| | - Xi Chen
- Department
of Biological Sciences, National University of Singapore, 117543 Singapore
| | - Minyi Fang
- Department
of Biological Sciences, National University of Singapore, 117543 Singapore
| | - Kenji Watanabe
- Division
of Pharmaceutical Sciences, University of Shizuoka, Shizuoka 422-8526, Japan
| | - Chu-Young Kim
- Department
of Biological Sciences, National University of Singapore, 117543 Singapore
- Synthetic
Biology Research Consortium, National University of Singapore, 117456 Singapore
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32
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Suzuki G, Minami A, Shimaya M, Kodama T, Morimoto Y, Oguri H, Oikawa H. Analysis of Enantiofacial Selective Epoxidation Catalyzed by Flavin-containing Monooxygenase Lsd18 Involved in Ionophore Polyether Lasalocid Biosynthesis. CHEM LETT 2014. [DOI: 10.1246/cl.140721] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022]
Affiliation(s)
- Gaku Suzuki
- Division of Chemistry, Graduate School of Science, Hokkaido University
| | - Atsushi Minami
- Division of Chemistry, Graduate School of Science, Hokkaido University
| | - Mayu Shimaya
- Division of Chemistry, Graduate School of Science, Hokkaido University
| | - Takeshi Kodama
- Department of Chemistry, Graduate School of Science, Osaka City University
| | - Yoshiki Morimoto
- Department of Chemistry, Graduate School of Science, Osaka City University
| | - Hiroki Oguri
- Division of Chemistry, Graduate School of Science, Hokkaido University
| | - Hideaki Oikawa
- Division of Chemistry, Graduate School of Science, Hokkaido University
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Wang XJ, Zhang B, Yan YJ, An J, Zhang J, Liu CX, Xiang WS. Characterization and analysis of an industrial strain of Streptomyces bingchenggensis by genome sequencing and gene microarray. Genome 2014; 56:677-89. [PMID: 24299107 DOI: 10.1139/gen-2013-0098] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/14/2023]
Abstract
Streptomyces bingchenggensis is a soil bacterium that produces milbemycins, a family of macrolide antibiotics that are commercially important in crop protection and veterinary medicine. In addition, S. bingchenggensis produces many other natural products including the polyether nanchangmycin and novel cyclic pentapeptides. To identify the gene clusters involved in the biosynthesis of these compounds, and better clarify the biochemical pathways of these gene clusters, the whole genome of S. bingchenggensis was sequenced, and the transcriptome profile was subsequently investigated by microarray. In comparison with other sequenced genomes in Streptomyces, S. bingchenggensis has the largest linear chromosome consisting of 11 936 683 base pairs (bp), with an average GC content of 70.8%. The 10 023 predicted protein-coding sequences include at least 47 gene clusters correlated with the biosynthesis of known or predicted secondary metabolites. Transcriptional analysis demonstrated an extremely high expression level of the milbemycin gene cluster during the entire growth period and a moderately high expression level of the nanchangmycin gene cluster during the initial hours that subsequently decreased. However, other gene clusters appear to be silent. The genome-wide analysis of the secondary metabolite gene clusters in S. bingchenggensis, coupled with transcriptional analysis, will facilitate the rational development of high milbemycins-producing strains as well as the discovery of new natural products.
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Affiliation(s)
- Xiang-Jing Wang
- a School of Life Science, Northeast Agricultural University, Harbin 150030, China
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34
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Van Wagoner RM, Satake M, Wright JLC. Polyketide biosynthesis in dinoflagellates: what makes it different? Nat Prod Rep 2014; 31:1101-37. [DOI: 10.1039/c4np00016a] [Citation(s) in RCA: 56] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/12/2023]
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35
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Minami A, Ose T, Sato K, Oikawa A, Kuroki K, Maenaka K, Oguri H, Oikawa H. Allosteric regulation of epoxide opening cascades by a pair of epoxide hydrolases in monensin biosynthesis. ACS Chem Biol 2014; 9:562-9. [PMID: 24320215 DOI: 10.1021/cb4006485] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Multistep catalysis of epoxide hydrolase/cyclase in the epoxide opening cascade is an intriguing issue in polyether biosynthesis. A pair of structurally homologous epoxide hydrolases was found in gene clusters of ionophore polyethers. In the epoxide opening reactions with MonBI and MonBII involved in monensin biosynthesis, we found that MonBII and catalytically inactive MonBI mutant catalyzed two-step reactions of bisepoxide substrate analogue to afford bicyclic product although MonBII alone catalyzed only the first cyclization. The X-ray crystal structure of MonBI dimers suggested the importance of the KSD motif in MonBI/MonBI interaction, which was further supported by gel filtration chromatography of wild-type MonBI and mutant MonBI. The involvement of the KSD motif in heterodimer formation was confirmed by in vitro assay. Direct evidence of MonBI/MonBII interaction was obtained by native mass spectrometry. Its dissociation constant was determined as 2.21 × 10(-5) M by surface plasmon resonance. Our results suggested the involvement of an allosteric regulation mechanism by MonBI/MonBII interaction in monensin skeletal construction.
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Affiliation(s)
- Atsushi Minami
- Division of Chemistry, Graduate School of Science and ‡Faculty of Pharmaceutical Sciences, Hokkaido University, Sapporo 060-0810, Japan
| | - Toyoyuki Ose
- Division of Chemistry, Graduate School of Science and ‡Faculty of Pharmaceutical Sciences, Hokkaido University, Sapporo 060-0810, Japan
| | - Kyohei Sato
- Division of Chemistry, Graduate School of Science and ‡Faculty of Pharmaceutical Sciences, Hokkaido University, Sapporo 060-0810, Japan
| | - Azusa Oikawa
- Division of Chemistry, Graduate School of Science and ‡Faculty of Pharmaceutical Sciences, Hokkaido University, Sapporo 060-0810, Japan
| | - Kimiko Kuroki
- Division of Chemistry, Graduate School of Science and ‡Faculty of Pharmaceutical Sciences, Hokkaido University, Sapporo 060-0810, Japan
| | - Katsumi Maenaka
- Division of Chemistry, Graduate School of Science and ‡Faculty of Pharmaceutical Sciences, Hokkaido University, Sapporo 060-0810, Japan
| | - Hiroki Oguri
- Division of Chemistry, Graduate School of Science and ‡Faculty of Pharmaceutical Sciences, Hokkaido University, Sapporo 060-0810, Japan
| | - Hideaki Oikawa
- Division of Chemistry, Graduate School of Science and ‡Faculty of Pharmaceutical Sciences, Hokkaido University, Sapporo 060-0810, Japan
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36
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Pöplau P, Frank S, Morinaka BI, Piel J. Eine enzymatische Domäne für die Erzeugung cyclischer Ether in komplexen Polyketiden. Angew Chem Int Ed Engl 2013. [DOI: 10.1002/ange.201307406] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
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37
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Pöplau P, Frank S, Morinaka BI, Piel J. An Enzymatic Domain for the Formation of Cyclic Ethers in Complex Polyketides. Angew Chem Int Ed Engl 2013; 52:13215-8. [DOI: 10.1002/anie.201307406] [Citation(s) in RCA: 72] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2013] [Indexed: 11/06/2022]
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38
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Minami A, Oguri H, Watanabe K, Oikawa H. Biosynthetic machinery of ionophore polyether lasalocid: enzymatic construction of polyether skeleton. Curr Opin Chem Biol 2013; 17:555-61. [DOI: 10.1016/j.cbpa.2013.06.004] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2013] [Revised: 05/29/2013] [Accepted: 06/01/2013] [Indexed: 02/02/2023]
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39
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Liu G, Chater KF, Chandra G, Niu G, Tan H. Molecular regulation of antibiotic biosynthesis in streptomyces. Microbiol Mol Biol Rev 2013; 77:112-43. [PMID: 23471619 PMCID: PMC3591988 DOI: 10.1128/mmbr.00054-12] [Citation(s) in RCA: 503] [Impact Index Per Article: 45.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023] Open
Abstract
Streptomycetes are the most abundant source of antibiotics. Typically, each species produces several antibiotics, with the profile being species specific. Streptomyces coelicolor, the model species, produces at least five different antibiotics. We review the regulation of antibiotic biosynthesis in S. coelicolor and other, nonmodel streptomycetes in the light of recent studies. The biosynthesis of each antibiotic is specified by a large gene cluster, usually including regulatory genes (cluster-situated regulators [CSRs]). These are the main point of connection with a plethora of generally conserved regulatory systems that monitor the organism's physiology, developmental state, population density, and environment to determine the onset and level of production of each antibiotic. Some CSRs may also be sensitive to the levels of different kinds of ligands, including products of the pathway itself, products of other antibiotic pathways in the same organism, and specialized regulatory small molecules such as gamma-butyrolactones. These interactions can result in self-reinforcing feed-forward circuitry and complex cross talk between pathways. The physiological signals and regulatory mechanisms may be of practical importance for the activation of the many cryptic secondary metabolic gene cluster pathways revealed by recent sequencing of numerous Streptomyces genomes.
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Affiliation(s)
- Gang Liu
- State Key Laboratory of Microbial Resources
- State Key Laboratory of Mycology, Institute of Microbiology, Chinese Academy of Sciences, Beijing, China
| | - Keith F. Chater
- Department of Molecular Microbiology, John Innes Centre, Norwich, United Kingdom
| | - Govind Chandra
- Department of Molecular Microbiology, John Innes Centre, Norwich, United Kingdom
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40
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Lei X, Kong L, Zhang C, Liu Q, Yao F, Zhang W, Deng Z, You D. In vivo investigation of the substrate recognition capability and activity affecting amino acid residues of glycosyltransferase FscMI in the biosynthesis of candicidin. MOLECULAR BIOSYSTEMS 2013; 9:422-30. [PMID: 23324745 DOI: 10.1039/c2mb25464f] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Alteration of sugar moieties of natural products often leads to novel antibiotics with different chemical and physical properties. fscMI is a putative glycosyltransferase (GT) in a gene cluster for the production of candicidin, a polyene macrolide antibiotic, produced by Streptomyces sp. FR-008. In this report, we established an in vivo biochemical detection system by inactivating fscMI and the DH11 domain of polyketide synthase (PKS) through double homologous recombination to unveil the interaction between polyene GTs and their substrates. We found that homologous GT genes including amphDI, nysDI and pimK can catalyze the conversion of candicidin aglycone into candicidin/FR-008-III in fscMI mutant, suggesting that homologous polyene GTs show some tolerance toward aglycones and that it is possible to create new polyene analogues with altered aglycones through genetic engineering. Inactivation of the DH11 domain of PKS led to novel polyene derivatives with mycosamine added to the altered polyketide backbones, further confirming the loose substrate specificity of polyene GTs. Furthermore, mutation of Ser346, Ser361, His362 or Cys387 of FscMI by site-directed mutagenesis significantly reduced its catalytic activity. Further analysis suggested that Ser361 and Cys387 are likely the critical donor interacting residues that could affect the activity of GT FscMI. To our knowledge, this is the first report of the critical residues in a polyene GT.
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Affiliation(s)
- Xuan Lei
- State Key Laboratory of Microbial Metabolism and School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, 1954 Huashan Road, Shanghai 200030, China
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41
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Thibodeaux CJ, Chang WC, Liu HW. Enzymatic chemistry of cyclopropane, epoxide, and aziridine biosynthesis. Chem Rev 2012; 112:1681-709. [PMID: 22017381 PMCID: PMC3288687 DOI: 10.1021/cr200073d] [Citation(s) in RCA: 204] [Impact Index Per Article: 17.0] [Reference Citation Analysis] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
| | - Wei-chen Chang
- College of Pharmacy and Department of Chemistry and Biochemistry, University of Texas at Austin, Austin, Texas 78712
| | - Hung-wen Liu
- Institute for Cellular and Molecular Biology, University of Texas at Austin, Austin, Texas 78712
- College of Pharmacy and Department of Chemistry and Biochemistry, University of Texas at Austin, Austin, Texas 78712
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42
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Hotta K, Chen X, Paton RS, Minami A, Li H, Swaminathan K, Mathews II, Watanabe K, Oikawa H, Houk KN, Kim CY. Enzymatic catalysis of anti-Baldwin ring closure in polyether biosynthesis. Nature 2012; 483:355-8. [PMID: 22388816 DOI: 10.1038/nature10865] [Citation(s) in RCA: 85] [Impact Index Per Article: 7.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2011] [Accepted: 01/13/2012] [Indexed: 11/09/2022]
Abstract
Polycyclic polyether natural products have fascinated chemists and biologists alike owing to their useful biological activity, highly complex structure and intriguing biosynthetic mechanisms. Following the original proposal for the polyepoxide origin of lasalocid and isolasalocid and the experimental determination of the origins of the oxygen and carbon atoms of both lasalocid and monensin, a unified stereochemical model for the biosynthesis of polyether ionophore antibiotics was proposed. The model was based on a cascade of nucleophilic ring closures of postulated polyepoxide substrates generated by stereospecific oxidation of all-trans polyene polyketide intermediates. Shortly thereafter, a related model was proposed for the biogenesis of marine ladder toxins, involving a series of nominally disfavoured anti-Baldwin, endo-tet epoxide-ring-opening reactions. Recently, we identified Lsd19 from the Streptomyces lasaliensis gene cluster as the epoxide hydrolase responsible for the epoxide-opening cyclization of bisepoxyprelasalocid A to form lasalocid A. Here we report the X-ray crystal structure of Lsd19 in complex with its substrate and product analogue to provide the first atomic structure-to our knowledge-of a natural enzyme capable of catalysing the disfavoured epoxide-opening cyclic ether formation. On the basis of our structural and computational studies, we propose a general mechanism for the enzymatic catalysis of polyether natural product biosynthesis.
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Affiliation(s)
- Kinya Hotta
- National University of Singapore, Department of Biological Sciences, 14 Science Drive 4, 117543 Singapore
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43
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Favouring the unfavoured. Nature 2012; 483:285-6. [DOI: 10.1038/483285a] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
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44
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Guo X, Liu T, Deng Z, Cane DE. Essential role of the donor acyl carrier protein in stereoselective chain translocation to a fully reducing module of the nanchangmycin polyketide synthase. Biochemistry 2012; 51:879-87. [PMID: 22229794 PMCID: PMC3273620 DOI: 10.1021/bi201768v] [Citation(s) in RCA: 12] [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
Incubation of recombinant module 2 of the polyether nanchangmycin synthase (NANS), carrying an appended thioesterase domain, with the ACP-bound substrate (2RS)-2-methyl-3-ketobutyryl-NANS_ACP1 (2-ACP1) and methylmalonyl-CoA in the presence of NADPH gave diastereomerically pure (2S,4R)-2,4-dimethyl-5-ketohexanoic acid (4a). These results contrast with the previously reported weak discrimination by NANS module 2+TE between the enantiomers of the corresponding N-acetylcysteamine-conjugated substrate analogue (±)-2-methyl-3-ketobutyryl-SNAC (2-SNAC), which resulted in formation of a 5:3 mixture of 4a and its (2S,4S)-diastereomer 4b. Incubation of NANS module 2+TE with 2-ACP1 in the absence of NADPH gave unreduced 3,5,6-trimethyl-4-hydroxypyrone (3) with a k(cat) of 4.4 ± 0.9 min⁻¹ and a k(cat)/K(m) of 67 min⁻¹ mM⁻¹, corresponding to a ∼2300-fold increase compared to the k(cat)/K(m) for the diffusive substrate 2-SNAC. Covalent tethering of the 2-methyl-3-ketobutyryl thioester substrate to the NANS ACP1 domain derived from the natural upstream PKS module of the nanchangmycin synthase significantly enhanced both the stereospecificity and the kinetic efficiency of the sequential polyketide chain translocation and condensation reactions catalyzed by the ketosynthase domain of NANS module 2.
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Affiliation(s)
- Xun Guo
- Department of Chemistry, Box H, Brown University, Providence, Rhode Island 02912-9108, USA
| | - Tiangang Liu
- Key Laboratory of Combinatorial Biosynthesis and Drug Discovery (Wuhan University), Ministry of Education, and Wuhan University School of Pharmaceutical Sciences, Wuhan 430071, P. R. China
| | - Zixin Deng
- Key Laboratory of Combinatorial Biosynthesis and Drug Discovery (Wuhan University), Ministry of Education, and Wuhan University School of Pharmaceutical Sciences, Wuhan 430071, P. R. China
- Key Laboratory of Microbial Metabolism and School of Life Sciences & Biotechnology, Shanghai Jiaotong University, Shanghai 200030, P. R. China
| | - David E. Cane
- Department of Chemistry, Box H, Brown University, Providence, Rhode Island 02912-9108, USA
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45
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Cloning and characterization of the polyether salinomycin biosynthesis gene cluster of Streptomyces albus XM211. Appl Environ Microbiol 2011; 78:994-1003. [PMID: 22156425 DOI: 10.1128/aem.06701-11] [Citation(s) in RCA: 56] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/04/2023] Open
Abstract
Salinomycin is widely used in animal husbandry as a food additive due to its antibacterial and anticoccidial activities. However, its biosynthesis had only been studied by feeding experiments with isotope-labeled precursors. A strategy with degenerate primers based on the polyether-specific epoxidase sequences was successfully developed to clone the salinomycin gene cluster. Using this strategy, a putative epoxidase gene, slnC, was cloned from the salinomycin producer Streptomyces albus XM211. The targeted replacement of slnC and subsequent trans-complementation proved its involvement in salinomycin biosynthesis. A 127-kb DNA region containing slnC was sequenced, including genes for polyketide assembly and release, oxidative cyclization, modification, export, and regulation. In order to gain insight into the salinomycin biosynthesis mechanism, 13 gene replacements and deletions were conducted. Including slnC, 7 genes were identified as essential for salinomycin biosynthesis and putatively responsible for polyketide chain release, oxidative cyclization, modification, and regulation. Moreover, 6 genes were found to be relevant to salinomycin biosynthesis and possibly involved in precursor supply, removal of aberrant extender units, and regulation. Sequence analysis and a series of gene replacements suggest a proposed pathway for the biosynthesis of salinomycin. The information presented here expands the understanding of polyether biosynthesis mechanisms and paves the way for targeted engineering of salinomycin activity and productivity.
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The biosynthesis of the polyether antibiotic nanchangmycin is controlled by two pathway-specific transcriptional activators. Arch Microbiol 2011; 194:415-26. [PMID: 22109812 DOI: 10.1007/s00203-011-0768-8] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/04/2011] [Revised: 09/28/2011] [Accepted: 10/24/2011] [Indexed: 10/15/2022]
Abstract
The nanchangmycin (NAN) produced by Streptomyces nanchangensis NS3226 is a polyether antibiotic resembling monensin in their gene clusters and the chemical structures. They can inhibit gram-positive bacteria and be a growth promoter for ruminants. Within the nanchangmycin gene cluster (nan), we identified that two SARP-family regulatory genes, nanR1 and nanR2, were both required to activate the transcription of all nan polyketide genes. Overexpression of NanR1 and NanR2 in wild-type increase NAN yields by at least three folds. Bioinformatic analysis of the immediate upstream DNA sequence of each nan gene and quantitative real-time RT-PCR analysis of the nan operons identified five putative SARP binding sites. Moreover, deletion of an AraC-family repressor gene nanR4 increased expression of NanR1 and R2 and led to a threefold increase in NAN production.
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Yurkovich ME, Tyrakis PA, Hong H, Sun Y, Samborskyy M, Kamiya K, Leadlay PF. A Late-Stage Intermediate in Salinomycin Biosynthesis Is Revealed by Specific Mutation in the Biosynthetic Gene Cluster. Chembiochem 2011; 13:66-71. [DOI: 10.1002/cbic.201100590] [Citation(s) in RCA: 54] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2011] [Indexed: 12/24/2022]
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Characterization of Streptomyces padanus JAU4234, a producer of actinomycin X₂, fungichromin, and a new polyene macrolide antibiotic. Appl Environ Microbiol 2011; 78:589-92. [PMID: 22057866 DOI: 10.1128/aem.06561-11] [Citation(s) in RCA: 42] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Strain JAU4234, identified as Streptomyces padanus, was isolated from soil collected in Jiangxi Province, China. It produced actinomycin X2, fungichromin, and a new polyene macrolide compound with antifungal activity, antifungalmycin 702. Antifungalmycin 702 had good general antifungal activity and may have potential future agricultural and/or clinical applications.
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Tosin M, Smith L, Leadlay PF. Insights into Lasalocid A Ring Formation by Chemical Chain Termination In Vivo. Angew Chem Int Ed Engl 2011. [DOI: 10.1002/ange.201106323] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/18/2023]
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Tosin M, Smith L, Leadlay PF. Insights into Lasalocid A Ring Formation by Chemical Chain Termination In Vivo. Angew Chem Int Ed Engl 2011; 50:11930-3. [DOI: 10.1002/anie.201106323] [Citation(s) in RCA: 39] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2011] [Indexed: 11/07/2022]
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