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Kostka M, Krug D, Herrmann J, Dickschat JS, Meyer J, Müller R, Schulz S. Identification by Synthesis: Imidacins, Urocanate-Derived Alkaloids from the Myxobacterium Stigmatella aurantiaca. Org Lett 2024; 26:6359-6363. [PMID: 39037587 DOI: 10.1021/acs.orglett.4c02036] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 07/23/2024]
Abstract
Innovative discovery approaches such as genome-mining and metabolomics-inspired methods have reshaped the natural product research field, complementing traditional bioactivity-based screens and allowing hitherto unseen compounds to be uncovered from previously investigated producers. In line with these trends, we report here imidacins, a novel class of secondary metabolites specific to the myxobacterial genus Stigmatella. A combination of secondary metabolome analysis, genome-mining techniques, spectroscopic analysis, and finally total synthesis was used to allow structure elucidation. Imidacins are urocanate-derived aliphatic acids with an adjacent cyclopropane moiety, structural features unprecedented in natural products to date.
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Affiliation(s)
- Michael Kostka
- Institute of Organic Chemistry, Technische Universität Braunschweig, Hagenring 30, 38106 Braunschweig, Germany
| | - Daniel Krug
- Helmholtz Institute for Pharmaceutical Research Saarland (HIPS), Department of Microbial Natural Products, Helmholtz Centre for Infection Research (HZI) and Department of Pharmaceutical Biotechnology, Universität des Saarlandes, Campus E8.1, 66123 Saarbrücken, Germany
- German Centre for Infection Research (DZIF), Partner Site Hannover-Braunschweig, 38124 Braunschweig, Germany
| | - Jennifer Herrmann
- Helmholtz Institute for Pharmaceutical Research Saarland (HIPS), Department of Microbial Natural Products, Helmholtz Centre for Infection Research (HZI) and Department of Pharmaceutical Biotechnology, Universität des Saarlandes, Campus E8.1, 66123 Saarbrücken, Germany
| | - Jeroen S Dickschat
- Helmholtz Institute for Pharmaceutical Research Saarland (HIPS), Department of Microbial Natural Products, Helmholtz Centre for Infection Research (HZI) and Department of Pharmaceutical Biotechnology, Universität des Saarlandes, Campus E8.1, 66123 Saarbrücken, Germany
- Kekulé Institute of Organic Chemistry and Biochemistry, University of Bonn, Gerhard-Domagk-Straße 1, 53121 Bonn, Germany
| | - Julia Meyer
- Institute of Organic Chemistry, Technische Universität Braunschweig, Hagenring 30, 38106 Braunschweig, Germany
| | - Rolf Müller
- Helmholtz Institute for Pharmaceutical Research Saarland (HIPS), Department of Microbial Natural Products, Helmholtz Centre for Infection Research (HZI) and Department of Pharmaceutical Biotechnology, Universität des Saarlandes, Campus E8.1, 66123 Saarbrücken, Germany
- German Centre for Infection Research (DZIF), Partner Site Hannover-Braunschweig, 38124 Braunschweig, Germany
| | - Stefan Schulz
- Institute of Organic Chemistry, Technische Universität Braunschweig, Hagenring 30, 38106 Braunschweig, Germany
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2
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Shende VV, Bauman KD, Moore BS. The shikimate pathway: gateway to metabolic diversity. Nat Prod Rep 2024; 41:604-648. [PMID: 38170905 PMCID: PMC11043010 DOI: 10.1039/d3np00037k] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2024]
Abstract
Covering: 1997 to 2023The shikimate pathway is the metabolic process responsible for the biosynthesis of the aromatic amino acids phenylalanine, tyrosine, and tryptophan. Seven metabolic steps convert phosphoenolpyruvate (PEP) and erythrose 4-phosphate (E4P) into shikimate and ultimately chorismate, which serves as the branch point for dedicated aromatic amino acid biosynthesis. Bacteria, fungi, algae, and plants (yet not animals) biosynthesize chorismate and exploit its intermediates in their specialized metabolism. This review highlights the metabolic diversity derived from intermediates of the shikimate pathway along the seven steps from PEP and E4P to chorismate, as well as additional sections on compounds derived from prephenate, anthranilate and the synonymous aminoshikimate pathway. We discuss the genomic basis and biochemical support leading to shikimate-derived antibiotics, lipids, pigments, cofactors, and other metabolites across the tree of life.
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Affiliation(s)
- Vikram V Shende
- Scripps Institution of Oceanography, University of California San Diego, La Jolla, CA, 92093, USA.
| | - Katherine D Bauman
- Department of Bioengineering, Stanford University, Stanford, CA, 94305, USA
| | - Bradley S Moore
- Scripps Institution of Oceanography, University of California San Diego, La Jolla, CA, 92093, USA.
- Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California San Diego, La Jolla, CA, 92093, USA
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3
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Kruth S, Nett M. Aurachins, Bacterial Antibiotics Interfering with Electron Transport Processes. Antibiotics (Basel) 2023; 12:1067. [PMID: 37370386 DOI: 10.3390/antibiotics12061067] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2023] [Revised: 06/12/2023] [Accepted: 06/15/2023] [Indexed: 06/29/2023] Open
Abstract
Aurachins are farnesylated quinolone alkaloids of bacterial origin and excellent inhibitors of the respiratory chain in pro- and eukaryotes. Therefore, they have become important tool compounds for the investigation of electron transport processes and they also serve as lead structures for the development of antibacterial and antiprotozoal drugs. Especially aurachin D proved to be a valuable starting point for structure-activity relationship studies. Aurachin D is a selective inhibitor of the cytochrome bd oxidase, which has received increasing attention as a target for the treatment of infectious diseases caused by mycobacteria. Moreover, aurachin D possesses remarkable activities against Leishmania donovani, the causative agent of leishmaniasis. Aurachins are naturally produced by myxobacteria of the genus Stigmatella as well as by some Streptomyces and Rhodococcus strains. The recombinant production of these antibiotics turned out to be challenging due to their complex biosynthesis and their inherent toxicity. Recently, the biotechnological production of aurachin D was established in E. coli with a titer which is higher than previously reported from natural producer organisms.
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Affiliation(s)
- Sebastian Kruth
- Laboratory of Technical Biology, Department of Biochemical and Chemical Engineering, TU Dortmund University, 44227 Dortmund, Germany
| | - Markus Nett
- Laboratory of Technical Biology, Department of Biochemical and Chemical Engineering, TU Dortmund University, 44227 Dortmund, Germany
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4
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Feng Z. O-methyltransferases selectively modify anthraquinone natural products. Structure 2023; 31:507-508. [PMID: 37146572 DOI: 10.1016/j.str.2023.04.006] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2023] [Revised: 04/04/2023] [Accepted: 04/06/2023] [Indexed: 05/07/2023]
Abstract
In this issue of Structure, Huber et al. identify five O-methyltransferases, and three of them catalyze the sequential methylation of the Gram-negative bacterium-derived aromatic polyketide anthraquinone AQ-256. They present co-crystal structures with bound AQ-256 and its methylated derivatives, which explains the specificities of these O-methyltransferases.
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Affiliation(s)
- Zhiyang Feng
- College of Food Science and Technology, Nanjing Agricultural University, Nanjing 210095, China.
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5
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Huber EM, Kreling L, Heinrich AK, Dünnebacke M, Pöthig A, Bode HB, Groll M. A set of closely related methyltransferases for site-specific tailoring of anthraquinone pigments. Structure 2023; 31:573-583.e5. [PMID: 36963398 DOI: 10.1016/j.str.2023.03.001] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2022] [Revised: 02/01/2023] [Accepted: 02/28/2023] [Indexed: 03/26/2023]
Abstract
Modification of the polyketide anthraquinone AQ-256 in the entomopathogenic Photorhabdus luminescens involves several O-methylations, but the biosynthetic gene cluster antA-I lacks corresponding tailoring enzymes. We here describe the identification of five putative, highly homologous O-methyltransferases encoded in the genome of P. luminescens. Activity assays in vitro and deletion experiments in vivo revealed that three of them account for anthraquinone tailoring by producing three monomethylated and two dimethylated species of AQ-256. X-ray structures of all five enzymes indicate high structural and mechanistic similarity. As confirmed by structure-based mutagenesis, a conserved histidine at the active site likely functions as a general base for substrate deprotonation and subsequent methyl transfer in all enzymes. Eight complex structures with AQ-256 as well as mono- and dimethylated derivatives confirm the substrate specificity patterns found in vitro and visualize how single amino acid differences in the active-site pockets impact substrate orientation and govern site-specific methylation.
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Affiliation(s)
- Eva M Huber
- Technical University of Munich, TUM School of Natural Sciences, Department of Bioscience, Center for Protein Assemblies, Chair of Biochemistry, Ernst-Otto-Fischer-Str. 8, 85748 Garching, Germany.
| | - Lukas Kreling
- Molecular Biotechnology, Department of Biosciences, Goethe University Frankfurt, 60438 Frankfurt am Main, Germany
| | - Antje K Heinrich
- Molecular Biotechnology, Department of Biosciences, Goethe University Frankfurt, 60438 Frankfurt am Main, Germany
| | - Maximilian Dünnebacke
- Technical University of Munich, TUM School of Natural Sciences, Department of Bioscience, Center for Protein Assemblies, Chair of Biochemistry, Ernst-Otto-Fischer-Str. 8, 85748 Garching, Germany
| | - Alexander Pöthig
- Technical University of Munich, TUM School of Natural Sciences, Department of Chemistry, Catalysis Research Center, Chair of Inorganic and Metal-Organic Chemistry, Ernst-Otto-Fischer-Str. 1, 85748 Garching, Germany
| | - Helge B Bode
- Molecular Biotechnology, Department of Biosciences, Goethe University Frankfurt, 60438 Frankfurt am Main, Germany; Department of Natural Products in Organismic Interactions, Max Planck Institute for Terrestrial Microbiology, 35043 Marburg, Germany; Chemical Biology, Department of Chemistry, Phillips University Marburg, 35043 Marburg, Germany; Center for Synthetic Microbiology (SYNMIKRO), Philipps University Marburg, 35043 Marburg, Germany; Senckenberg Gesellschaft für Naturforschung, 60325 Frankfurt am Main, Germany.
| | - Michael Groll
- Technical University of Munich, TUM School of Natural Sciences, Department of Bioscience, Center for Protein Assemblies, Chair of Biochemistry, Ernst-Otto-Fischer-Str. 8, 85748 Garching, Germany.
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6
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Kruth S, Schibajew L, Nett M. Biocatalytic production of the antibiotic aurachin D in Escherichia coli. AMB Express 2022; 12:138. [DOI: 10.1186/s13568-022-01478-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2022] [Accepted: 10/15/2022] [Indexed: 11/06/2022] Open
Abstract
Abstract
Aurachin D is a potent inhibitor of cytochrome bd oxidases, which are potential targets in the treatment of infectious diseases. In this study, our aim was to improve the biocatalytic production of aurachin D from a quinolone precursor molecule with recombinant Escherichia coli cells expressing the biosynthesis enzyme AuaA. In order to achieve a high-level production of this membrane-bound farnesyltransferase in E. coli, the expression of the auaA gene was translationally coupled to an upstream cistron in accordance with a bicistronic design (BCD) strategy. Screening of various BCD elements led to the identification of optimized auaA expression cassettes, which increased the aurachin D titer in E. coli up to 29-fold in comparison to T7-mediated expression. This titer could be further raised by codon optimization of auaA and by introducing the mevalonate pathway into the production strain. The latter measure was intended to improve the availability of farnesyl pyrophosphate, which is needed as a cosubstrate for the AuaA-catalyzed reaction. In sum, the described efforts resulted in a strain producing aurachin D with a titer that is 424 times higher than that obtained with the original, non-optimized expression host.
Graphical Abstract
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7
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Stief L, Speicher A. Setup of 4‐Prenylated Quinolines through Suzuki‐Miyaura Coupling for the Synthesis of Aurachins A and B. Adv Synth Catal 2022. [DOI: 10.1002/adsc.202100884] [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]
Affiliation(s)
- Laura Stief
- FB VI Environmental Toxicology Trier University D-54296 Trier Germany
| | - Andreas Speicher
- FR Chemistry – Organic Chemistry Saarland University D-66041 Saarbrücken Germany
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8
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Kim MC, Winter JM, Asolkar RN, Boonlarppradab C, Cullum R, Fenical W. Marinoterpins A-C: Rare Linear Merosesterterpenoids from Marine-Derived Actinomycete Bacteria of the Family Streptomycetaceae. J Org Chem 2021; 86:11140-11148. [PMID: 33844925 PMCID: PMC8383307 DOI: 10.1021/acs.joc.1c00262] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2021] [Indexed: 12/16/2022]
Abstract
The chemical examination of two undescribed marine actinobacteria has yielded three rare merosesterterpenoids, marinoterpins A-C (1-3, respectively). These compounds were isolated from the culture broth extracts of two marine-derived actinomycetes associated with the family Streptomycetaceae, (our strains were CNQ-253 and AJS-327). The structures of the new compounds were determined by extensive interpretation of 1D and 2D NMR, MS, and combined spectroscopic data. These compounds represent new chemical motifs, combining quinoline-N-oxides with a linear sesterterpenoid side chain. Additionally, consistent in all three metabolites is the rare occurrence of two five-ring ethers, which were derived from an apparent cyclization of methyl group carbons to adjacent hydroxy-bearing methylene groups in the sesterterpenoid side chain. Genome scanning of AJS-327 allowed for the identification of the marinoterpin (mrt) biosynthetic cluster, which consists of 16 open-reading frames that code for a sesterterpene pyrophosphate synthase, prenyltransferase, type II polyketide synthase, anthranilate:CoA-ligase, and several tailoring enzymes apparently responsible for installing the N-oxide and bis-tetrahydrofuran ring motifs.
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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
| | - Ratnakar N. Asolkar
- Center
for Marine Biotechnology and Biomedicine, Scripps Institution of Oceanography, University of California, San Diego, La Jolla, California 92093, United States
| | - Chollaratt Boonlarppradab
- Center
for Marine Biotechnology and Biomedicine, Scripps Institution of Oceanography, University of California, San Diego, La Jolla, California 92093, 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
| | - 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 Science, University of California, San Diego, La Jolla, California 92093, United States
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9
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Bhat MA, Mishra AK, Bhat MA, Banday MI, Bashir O, Rather IA, Rahman S, Shah AA, Jan AT. Myxobacteria as a Source of New Bioactive Compounds: A Perspective Study. Pharmaceutics 2021; 13:1265. [PMID: 34452226 PMCID: PMC8401837 DOI: 10.3390/pharmaceutics13081265] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2021] [Revised: 08/06/2021] [Accepted: 08/09/2021] [Indexed: 12/18/2022] Open
Abstract
Myxobacteria are unicellular, Gram-negative, soil-dwelling, gliding bacteria that belong to class δ-proteobacteria and order Myxococcales. They grow and proliferate by transverse fission under normal conditions, but form fruiting bodies which contain myxospores during unfavorable conditions. In view of the escalating problem of antibiotic resistance among disease-causing pathogens, it becomes mandatory to search for new antibiotics effective against such pathogens from natural sources. Among the different approaches, Myxobacteria, having a rich armor of secondary metabolites, preferably derivatives of polyketide synthases (PKSs) along with non-ribosomal peptide synthases (NRPSs) and their hybrids, are currently being explored as producers of new antibiotics. The Myxobacterial species are functionally characterized to assess their ability to produce antibacterial, antifungal, anticancer, antimalarial, immunosuppressive, cytotoxic and antioxidative bioactive compounds. In our study, we have found their compounds to be effective against a wide range of pathogens associated with the concurrence of different infectious diseases.
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Affiliation(s)
- Mudasir Ahmad Bhat
- Department of Biotechnology, Baba Ghulam Shah Badshah University, Rajouri 185234, Jammu and Kashmir, India;
| | | | - Mujtaba Aamir Bhat
- Department of Botany, Baba Ghulam Shah Badshah University, Rajouri 185234, Jammu and Kashmir, India;
| | - Mohammad Iqbal Banday
- Department of Microbiology, Baba Ghulam Shah Badshah University, Rajouri 185234, Jammu and Kashmir, India;
| | - Ommer Bashir
- Department of School Education, Jammu 181205, Jammu and Kashmir, India;
| | - Irfan A. Rather
- Department of Biological Sciences, Faculty of Science, King Abdulaziz University (KAU), Jeddah 21589, Saudi Arabia;
| | - Safikur Rahman
- Department of Botany, MS College, BR Ambedkar Bihar University, Muzaffarpur 845401, Bihar, India;
| | - Ali Asghar Shah
- Department of Biotechnology, Baba Ghulam Shah Badshah University, Rajouri 185234, Jammu and Kashmir, India;
| | - Arif Tasleem Jan
- Department of Botany, Baba Ghulam Shah Badshah University, Rajouri 185234, Jammu and Kashmir, India;
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10
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Abstract
Covering: up to mid-2020 Terpenoids, also called isoprenoids, are the largest and most structurally diverse family of natural products. Found in all domains of life, there are over 80 000 known compounds. The majority of characterized terpenoids, which include some of the most well known, pharmaceutically relevant, and commercially valuable natural products, are produced by plants and fungi. Comparatively, terpenoids of bacterial origin are rare. This is counter-intuitive to the fact that recent microbial genomics revealed that almost all bacteria have the biosynthetic potential to create the C5 building blocks necessary for terpenoid biosynthesis. In this review, we catalogue terpenoids produced by bacteria. We collected 1062 natural products, consisting of both primary and secondary metabolites, and classified them into two major families and 55 distinct subfamilies. To highlight the structural and chemical space of bacterial terpenoids, we discuss their structures, biosynthesis, and biological activities. Although the bacterial terpenome is relatively small, it presents a fascinating dichotomy for future research. Similarities between bacterial and non-bacterial terpenoids and their biosynthetic pathways provides alternative model systems for detailed characterization while the abundance of novel skeletons, biosynthetic pathways, and bioactivies presents new opportunities for drug discovery, genome mining, and enzymology.
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Affiliation(s)
- Jeffrey D Rudolf
- Department of Chemistry, University of Florida, Gainesville, Florida 32611, USA.
| | - Tyler A Alsup
- Department of Chemistry, University of Florida, Gainesville, Florida 32611, USA.
| | - Baofu Xu
- Department of Chemistry, University of Florida, Gainesville, Florida 32611, USA.
| | - Zining Li
- Department of Chemistry, University of Florida, Gainesville, Florida 32611, USA.
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11
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Zhang G, Yang K, Wang S, Feng Q, Song Q. N 2H 4-H 2O Enabled Umpolung Cyclization of o-Nitro Chalcones for the Construction of Quinoline N-Oxides. Org Lett 2021; 23:595-600. [PMID: 33378210 DOI: 10.1021/acs.orglett.0c04162] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Umpolung is a unique strategy which converts the property of an atom into the opposite one. An efficient and general method for the construction of quinoline N-oxides via umpolung of carbonyl groups was developed from ortho-nitro chalcones and hydrazine in basic conditions. The strategy is transition-metal free and has good functional group tolerance, environmental friendliness, as well as mild reaction conditions with nitrogen gas as the byproduct.
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Affiliation(s)
- Guan Zhang
- Institute of Next Generation Matter Transformation, College of Chemical Engineering, College of Material Sciences Engineering at Huaqiao University, 668 Jimei Boulevard, Xiamen, Fujian 361021, P. R. China
| | - Kai Yang
- College of Chemistry, Fuzhou University, Fuzhou 350116, P. R. China
| | - Shihui Wang
- Institute of Next Generation Matter Transformation, College of Chemical Engineering, College of Material Sciences Engineering at Huaqiao University, 668 Jimei Boulevard, Xiamen, Fujian 361021, P. R. China
| | - Qiang Feng
- Institute of Next Generation Matter Transformation, College of Chemical Engineering, College of Material Sciences Engineering at Huaqiao University, 668 Jimei Boulevard, Xiamen, Fujian 361021, P. R. China
| | - Qiuling Song
- Institute of Next Generation Matter Transformation, College of Chemical Engineering, College of Material Sciences Engineering at Huaqiao University, 668 Jimei Boulevard, Xiamen, Fujian 361021, P. R. China.,College of Chemistry, Fuzhou University, Fuzhou 350116, P. R. China
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12
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Shaker B, Ahmad S, Thai TD, Eyun SI, Na D. Rational Drug Design for Pseudomonas aeruginosa PqsA Enzyme: An in silico Guided Study to Block Biofilm Formation. Front Mol Biosci 2020; 7:577316. [PMID: 33195420 PMCID: PMC7593710 DOI: 10.3389/fmolb.2020.577316] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2020] [Accepted: 09/11/2020] [Indexed: 12/31/2022] Open
Abstract
Pseudomonas aeruginosa is an opportunistic gram-negative bacterium implicated in acute and chronic nosocomial infections and a leading cause of patient mortality. Such infections occur owing to biofilm formation that confers multidrug resistance and enhanced pathogenesis to the bacterium. In this study, we used a rational drug design strategy to inhibit the quorum signaling system of P. aeruginosa by designing potent inhibitory lead molecules against anthranilate-CoA ligase enzyme encoded by the pqsA gene. This enzyme produces autoinducers for cell-to-cell communication, which result in biofilm formation, and thus plays a pivotal role in the virulence of P. aeruginosa. A library of potential drug molecules was prepared by performing ligand-based screening using an available set of enzyme inhibitors. Subsequently, structure-based virtual screening was performed to identify compounds showing the best binding conformation with the target enzyme and forming a stable complex. The two hit compounds interact with the binding site of the enzyme through multiple short-range hydrophilic and hydrophobic interactions. Molecular dynamic simulation and MM-PBSA/GBSA results to calculate the affinity and stability of the hit compounds with the PqsA enzyme further confirmed their strong interactions. The hit compounds might be useful in tackling the resistant phenotypes of this pathogen.
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Affiliation(s)
- Bilal Shaker
- 84 Heukseok-ro, Dongjak-gu, Department of Biomedical Engineering, Chung-Ang University, Seoul, South Korea
| | - Sajjad Ahmad
- National Centre for Bioinformatics, Quaid-i-Azam University, Islamabad, Pakistan
| | - Thi Duc Thai
- 84 Heukseok-ro, Dongjak-gu, Department of Biomedical Engineering, Chung-Ang University, Seoul, South Korea
| | - Seong-il Eyun
- 84 Heukseok-ro, Dongjak-gu, Department of Life Science, Chung-Ang University, Seoul, South Korea
| | - Dokyun Na
- 84 Heukseok-ro, Dongjak-gu, Department of Biomedical Engineering, Chung-Ang University, Seoul, South Korea
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13
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Ishida K, Shabuer G, Schieferdecker S, Pidot SJ, Stinear TP, Knuepfer U, Cyrulies M, Hertweck C. Oak-Associated Negativicute Equipped with Ancestral Aromatic Polyketide Synthase Produces Antimycobacterial Dendrubins. Chemistry 2020; 26:13147-13151. [PMID: 32597507 PMCID: PMC7693217 DOI: 10.1002/chem.202001939] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2020] [Revised: 06/26/2020] [Indexed: 11/07/2022]
Abstract
Anaerobic bacteria have only recently been recognized as a source of antibiotics; yet, the metabolic potential of Negativicutes (Gram-negative staining Firmicutes) such as the oak-associated Dendrosporobacter quercicolus has remained unknown. Genome mining of D. quercicolus and phylogenetic analyses revealed a gene cluster for a type II polyketide synthase (PKS) complex that belongs to the most ancestral enzyme systems of this type. Metabolic profiling, NMR analyses, and stable-isotope labeling led to the discovery of a new family of anthraquinone-type polyphenols, the dendrubins, which are diversified by acylation, methylation, and dimerization. Dendrubin A and B were identified as strong antibiotics against a range of clinically relevant, human-pathogenic mycobacteria.
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Affiliation(s)
- Keishi Ishida
- Biomolecular Chemistry, Leibniz Institute for Natural Products Chemistry and Infection Biology, Beutenbergstr. 11a, 07745, Jena, Germany
| | - Gulimila Shabuer
- Biomolecular Chemistry, Leibniz Institute for Natural Products Chemistry and Infection Biology, Beutenbergstr. 11a, 07745, Jena, Germany
| | - Sebastian Schieferdecker
- Biomolecular Chemistry, Leibniz Institute for Natural Products Chemistry and Infection Biology, Beutenbergstr. 11a, 07745, Jena, Germany
| | - Sacha J Pidot
- Department of Microbiology and Immunology, University of Melbourne, 792 Elizabeth Street, 3000, Melbourne, Australia
| | - Timothy P Stinear
- Department of Microbiology and Immunology, University of Melbourne, 792 Elizabeth Street, 3000, Melbourne, Australia
| | - Uwe Knuepfer
- Biopilot Plant, Leibniz Institute for Natural Products Chemistry and Infection Biology, Beutenbergstr. 11a, 07745, Jena, Germany
| | - Michael Cyrulies
- Biopilot Plant, Leibniz Institute for Natural Products Chemistry and Infection Biology, Beutenbergstr. 11a, 07745, Jena, Germany
| | - Christian Hertweck
- Biomolecular Chemistry, Leibniz Institute for Natural Products Chemistry and Infection Biology, Beutenbergstr. 11a, 07745, Jena, Germany.,Institute for Microbiology, Faculty of Biological Sciences, Friedrich Schiller University Jena, 07743, Jena, Germany
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14
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Sester A, Stüer-Patowsky K, Hiller W, Kloss F, Lütz S, Nett M. Biosynthetic Plasticity Enables Production of Fluorinated Aurachins. Chembiochem 2020; 21:2268-2273. [PMID: 32216075 PMCID: PMC7496329 DOI: 10.1002/cbic.202000166] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2020] [Revised: 03/25/2020] [Indexed: 12/15/2022]
Abstract
Enzyme promiscuity has important implications in the field of biocatalysis. In some cases, structural analogues of simple metabolic building blocks can be processed through entire pathways to give natural product derivatives that are not readily accessible by chemical means. In this study, we explored the plasticity of the aurachin biosynthesis pathway with regard to using fluoro‐ and chloroanthranilic acids, which are not abundant in the bacterial producers of these quinolone antibiotics. The incorporation rates of the tested precursor molecules disclosed a regiopreference for halogen substitution as well as steric limitations of enzymatic substrate tolerance. Three previously undescribed fluorinated aurachin derivatives were produced in preparative amounts by fermentation and structurally characterized. Furthermore, their antibacterial activities were evaluated in comparison to their natural congener aurachin D.
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Affiliation(s)
- Angela Sester
- Department of Biochemical and Chemical Engineering Laboratory of Technical Biology, TU Dortmund, Emil-Figge-Strasse 66, 44227, Dortmund, Germany
| | - Katrin Stüer-Patowsky
- Department of Biochemical and Chemical Engineering Laboratory of Technical Biology, TU Dortmund, Emil-Figge-Strasse 66, 44227, Dortmund, Germany
| | - Wolf Hiller
- Department of Chemistry and Chemical Biology NMR Laboratory, TU Dortmund, Otto-Hahn-Strasse 4a, 44227, Dortmund, Germany
| | - Florian Kloss
- Transfer Group Antiinfectives, Leibniz Institute for Natural Product Research and Infection Biology, Beutenbergstrasse 11a, 07745, Jena, Germany
| | - Stephan Lütz
- Department of Biochemical and Chemical Engineering Chair for Bioprocess Engineering, TU Dortmund, Emil-Figge-Strase 66, 44227, Dortmund, Germany
| | - Markus Nett
- Department of Biochemical and Chemical Engineering Laboratory of Technical Biology, TU Dortmund, Emil-Figge-Strasse 66, 44227, Dortmund, Germany
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15
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Kilgour SL, Kilgour DPA, Prasongpholchai P, O'Connor PB, Tosin M. A Light-Activated Acyl Carrier Protein "Trap" for Intermediate Capture in Type II Iterative Polyketide Biocatalysis. Chemistry 2019; 25:16515-16518. [PMID: 31596972 PMCID: PMC6972679 DOI: 10.1002/chem.201903662] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2019] [Revised: 10/03/2019] [Indexed: 01/24/2023]
Abstract
A discrete acyl carrier protein (ACP) bearing a photolabile nonhydrolysable carba(dethia) malonyl pantetheine cofactor was chemoenzymatically prepared and utilised for the trapping of biosynthetic polyketide intermediates following light activation. From the in vitro assembly of the polyketides SEK4 and SEK4b, by the type II actinorhodin "minimal" polyketide synthase (PKS), a range of putative ACP-bound diketides, tetraketides, pentaketides and hexaketides were identified and characterised by FT-ICR-MS, providing direct insights on active site accessibility and substrate processing for this enzyme class.
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Affiliation(s)
| | - David P. A. Kilgour
- Department of Chemistry and ForensicsNottingham Trent UniversityNottinghamNG11 8NSUK
| | | | - Peter B. O'Connor
- Department of ChemistryUniversity of WarwickLibrary RoadCoventryCV4 7ALUK
| | - Manuela Tosin
- Department of ChemistryUniversity of WarwickLibrary RoadCoventryCV4 7ALUK
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16
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The ADEP Biosynthetic Gene Cluster in Streptomyces hawaiiensis NRRL 15010 Reveals an Accessory clpP Gene as a Novel Antibiotic Resistance Factor. Appl Environ Microbiol 2019; 85:AEM.01292-19. [PMID: 31399403 DOI: 10.1128/aem.01292-19] [Citation(s) in RCA: 22] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2019] [Accepted: 08/02/2019] [Indexed: 02/06/2023] Open
Abstract
The increasing threat posed by multiresistant bacterial pathogens necessitates the discovery of novel antibacterials with unprecedented modes of action. ADEP1, a natural compound produced by Streptomyces hawaiiensis NRRL 15010, is the prototype for a new class of acyldepsipeptide (ADEP) antibiotics. ADEP antibiotics deregulate the proteolytic core ClpP of the bacterial caseinolytic protease, thereby exhibiting potent antibacterial activity against Gram-positive bacteria, including multiresistant pathogens. ADEP1 and derivatives, here collectively called ADEP, have been previously investigated for their antibiotic potency against different species, structure-activity relationship, and mechanism of action; however, knowledge on the biosynthesis of the natural compound and producer self-resistance have remained elusive. In this study, we identified and analyzed the ADEP biosynthetic gene cluster in S. hawaiiensis NRRL 15010, which comprises two NRPSs, genes necessary for the biosynthesis of (4S,2R)-4-methylproline, and a type II polyketide synthase (PKS) for the assembly of highly reduced polyenes. While no resistance factor could be identified within the gene cluster itself, we discovered an additional clpP homologous gene (named clpP ADEP) located further downstream of the biosynthetic genes, separated from the biosynthetic gene cluster by several transposable elements. Heterologous expression of ClpPADEP in three ADEP-sensitive Streptomyces species proved its role in conferring ADEP resistance, thereby revealing a novel type of antibiotic resistance determinant.IMPORTANCE Antibiotic acyldepsipeptides (ADEPs) represent a promising new class of potent antibiotics and, at the same time, are valuable tools to study the molecular functioning of their target, ClpP, the proteolytic core of the bacterial caseinolytic protease. Here, we present a straightforward purification procedure for ADEP1 that yields substantial amounts of the pure compound in a time- and cost-efficient manner, which is a prerequisite to conveniently study the antimicrobial effects of ADEP and the operating mode of bacterial ClpP machineries in diverse bacteria. Identification and characterization of the ADEP biosynthetic gene cluster in Streptomyces hawaiiensis NRRL 15010 enables future bioinformatics screenings for similar gene clusters and/or subclusters to find novel natural compounds with specific substructures. Most strikingly, we identified a cluster-associated clpP homolog (named clpP ADEP) as an ADEP resistance gene. ClpPADEP constitutes a novel bacterial resistance factor that alone is necessary and sufficient to confer high-level ADEP resistance to Streptomyces across species.
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17
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Greule A, Stok JE, De Voss JJ, Cryle MJ. Unrivalled diversity: the many roles and reactions of bacterial cytochromes P450 in secondary metabolism. Nat Prod Rep 2019; 35:757-791. [PMID: 29667657 DOI: 10.1039/c7np00063d] [Citation(s) in RCA: 140] [Impact Index Per Article: 28.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
Covering: 2000 up to 2018 The cytochromes P450 (P450s) are a superfamily of heme-containing monooxygenases that perform diverse catalytic roles in many species, including bacteria. The P450 superfamily is widely known for the hydroxylation of unactivated C-H bonds, but the diversity of reactions that P450s can perform vastly exceeds this undoubtedly impressive chemical transformation. Within bacteria, P450s play important roles in many biosynthetic and biodegradative processes that span a wide range of secondary metabolite pathways and present diverse chemical transformations. In this review, we aim to provide an overview of the range of chemical transformations that P450 enzymes can catalyse within bacterial secondary metabolism, with the intention to provide an important resource to aid in understanding of the potential roles of P450 enzymes within newly identified bacterial biosynthetic pathways.
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Affiliation(s)
- Anja Greule
- The Monash Biomedicine Discovery Institute, Department of Biochemistry and Molecular Biology, ARC Centre of Excellence in Advanced Molecular Imaging, Monash University, Clayton, Victoria 3800, Australia. and EMBL Australia, Monash University, Clayton, Victoria 3800, Australia
| | - Jeanette E Stok
- School of Chemistry and Molecular Biosciences, University of Queensland, Brisbane 4072, Australia.
| | - James J De Voss
- School of Chemistry and Molecular Biosciences, University of Queensland, Brisbane 4072, Australia.
| | - Max J Cryle
- The Monash Biomedicine Discovery Institute, Department of Biochemistry and Molecular Biology, ARC Centre of Excellence in Advanced Molecular Imaging, Monash University, Clayton, Victoria 3800, Australia. and EMBL Australia, Monash University, Clayton, Victoria 3800, Australia and Department of Biomolecular Mechanisms, Max Planck Institute for Medical Research, Jahnstrasse 29, 69120 Heidelberg, Germany.
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18
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Cummings M, Peters AD, Whitehead GFS, Menon BRK, Micklefield J, Webb SJ, Takano E. Assembling a plug-and-play production line for combinatorial biosynthesis of aromatic polyketides in Escherichia coli. PLoS Biol 2019; 17:e3000347. [PMID: 31318855 PMCID: PMC6638757 DOI: 10.1371/journal.pbio.3000347] [Citation(s) in RCA: 25] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2019] [Accepted: 06/14/2019] [Indexed: 11/19/2022] Open
Abstract
Polyketides are a class of specialised metabolites synthesised by both eukaryotes and prokaryotes. These chemically and structurally diverse molecules are heavily used in the clinic and include frontline antimicrobial and anticancer drugs such as erythromycin and doxorubicin. To replenish the clinicians' diminishing arsenal of bioactive molecules, a promising strategy aims at transferring polyketide biosynthetic pathways from their native producers into the biotechnologically desirable host Escherichia coli. This approach has been successful for type I modular polyketide synthases (PKSs); however, despite more than 3 decades of research, the large and important group of type II PKSs has until now been elusive in E. coli. Here, we report on a versatile polyketide biosynthesis pipeline, based on identification of E. coli-compatible type II PKSs. We successfully express 5 ketosynthase (KS) and chain length factor (CLF) pairs-e.g., from Photorhabdus luminescens TT01, Streptomyces resistomycificus, Streptoccocus sp. GMD2S, Pseudoalteromonas luteoviolacea, and Ktedonobacter racemifer-as soluble heterodimeric recombinant proteins in E. coli for the first time. We define the anthraquinone minimal PKS components and utilise this biosynthetic system to synthesise anthraquinones, dianthrones, and benzoisochromanequinones (BIQs). Furthermore, we demonstrate the tolerance and promiscuity of the anthraquinone heterologous biosynthetic pathway in E. coli to act as genetically applicable plug-and-play scaffold, showing it to function successfully when combined with enzymes from phylogenetically distant species, endophytic fungi and plants, which resulted in 2 new-to-nature compounds, neomedicamycin and neochaetomycin. This work enables plug-and-play combinatorial biosynthesis of aromatic polyketides using bacterial type II PKSs in E. coli, providing full access to its many advantages in terms of easy and fast genetic manipulation, accessibility for high-throughput robotics, and convenient biotechnological scale-up. Using the synthetic and systems biology toolbox, this plug-and-play biosynthetic platform can serve as an engine for the production of new and diversified bioactive polyketides in an automated, rapid, and versatile fashion.
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Affiliation(s)
- Matthew Cummings
- Manchester Synthetic Biology Research Centre SYNBIOCHEM, Manchester Institute of Biotechnology, School of Chemistry, The University of Manchester, Manchester, United Kingdom
| | - Anna D. Peters
- Manchester Synthetic Biology Research Centre SYNBIOCHEM, Manchester Institute of Biotechnology, School of Chemistry, The University of Manchester, Manchester, United Kingdom
| | - George F. S. Whitehead
- Manchester Synthetic Biology Research Centre SYNBIOCHEM, Manchester Institute of Biotechnology, School of Chemistry, The University of Manchester, Manchester, United Kingdom
| | - Binuraj R. K. Menon
- Manchester Synthetic Biology Research Centre SYNBIOCHEM, Manchester Institute of Biotechnology, School of Chemistry, The University of Manchester, Manchester, United Kingdom
- Warwick Integrative Synthetic Biology Centre, WISB, School of Life Sciences, The University of Warwick, Coventry, United Kingdom
| | - Jason Micklefield
- Manchester Synthetic Biology Research Centre SYNBIOCHEM, Manchester Institute of Biotechnology, School of Chemistry, The University of Manchester, Manchester, United Kingdom
| | - Simon J. Webb
- Manchester Synthetic Biology Research Centre SYNBIOCHEM, Manchester Institute of Biotechnology, School of Chemistry, The University of Manchester, Manchester, United Kingdom
| | - Eriko Takano
- Manchester Synthetic Biology Research Centre SYNBIOCHEM, Manchester Institute of Biotechnology, School of Chemistry, The University of Manchester, Manchester, United Kingdom
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19
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Zhou Q, Bräuer A, Adihou H, Schmalhofer M, Saura P, Grammbitter GLC, Kaila VRI, Groll M, Bode HB. Molecular mechanism of polyketide shortening in anthraquinone biosynthesis of Photorhabdus luminescens. Chem Sci 2019; 10:6341-6349. [PMID: 31341589 PMCID: PMC6601290 DOI: 10.1039/c9sc00749k] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2019] [Accepted: 05/08/2019] [Indexed: 12/31/2022] Open
Abstract
Anthraquinones, produced by a type II polyketide synthase in Photorhabdus luminescens, are derived from polyketide chain shortening.
Anthraquinones, a widely distributed class of aromatic natural products, are produced by a type II polyketide synthase system in the Gram-negative bacterium Photorhabdus luminescens. Heterologous expression of the antABCDEFGHI anthraquinone biosynthetic gene cluster in Escherichia coli identified AntI as an unusual lyase, catalysing terminal polyketide shortening prior to formation of the third aromatic ring. Functional in vitro and in vivo analysis of AntI using X-ray crystallography, structure-based mutagenesis, and molecular simulations revealed that AntI converts a defined octaketide to the tricyclic anthraquinone ring via retro-Claisen and Dieckmann reactions. Thus, AntI catalyses a so far unobserved multistep reaction in this PKS system.
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Affiliation(s)
- Qiuqin Zhou
- Molekulare Biotechnologie , Fachbereich Biowissenschaften , Buchmann Institute for Molecular Life Sciences (BMLS) , Goethe Universität Frankfurt , Max-von-Laue-Str. 15, Max-von-Laue-Str. 9 , 60438 Frankfurt am Main , Germany .
| | - Alois Bräuer
- Center for Integrated Protein Science Munich (CIPSM) , Department of Chemistry , Technische Universität München , Lichtenbergstraße 4 , 85748 Garching , Germany .
| | - Hélène Adihou
- Molekulare Biotechnologie , Fachbereich Biowissenschaften , Buchmann Institute for Molecular Life Sciences (BMLS) , Goethe Universität Frankfurt , Max-von-Laue-Str. 15, Max-von-Laue-Str. 9 , 60438 Frankfurt am Main , Germany .
| | - Maximilian Schmalhofer
- Center for Integrated Protein Science Munich (CIPSM) , Department of Chemistry , Technische Universität München , Lichtenbergstraße 4 , 85748 Garching , Germany .
| | - Patricia Saura
- Center for Integrated Protein Science Munich (CIPSM) , Department of Chemistry , Technische Universität München , Lichtenbergstraße 4 , 85748 Garching , Germany .
| | - Gina L C Grammbitter
- Molekulare Biotechnologie , Fachbereich Biowissenschaften , Buchmann Institute for Molecular Life Sciences (BMLS) , Goethe Universität Frankfurt , Max-von-Laue-Str. 15, Max-von-Laue-Str. 9 , 60438 Frankfurt am Main , Germany .
| | - Ville R I Kaila
- Center for Integrated Protein Science Munich (CIPSM) , Department of Chemistry , Technische Universität München , Lichtenbergstraße 4 , 85748 Garching , Germany .
| | - Michael Groll
- Center for Integrated Protein Science Munich (CIPSM) , Department of Chemistry , Technische Universität München , Lichtenbergstraße 4 , 85748 Garching , Germany .
| | - Helge B Bode
- Molekulare Biotechnologie , Fachbereich Biowissenschaften , Buchmann Institute for Molecular Life Sciences (BMLS) , Goethe Universität Frankfurt , Max-von-Laue-Str. 15, Max-von-Laue-Str. 9 , 60438 Frankfurt am Main , Germany .
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20
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Shen C, Wang A, Xu J, An Z, Loh KY, Zhang P, Liu X. Recent Advances in the Catalytic Synthesis of 4-Quinolones. Chem 2019. [DOI: 10.1016/j.chempr.2019.01.006] [Citation(s) in RCA: 34] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
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21
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Grammbitter GLC, Schmalhofer M, Karimi K, Shi YM, Schöner TA, Tobias NJ, Morgner N, Groll M, Bode HB. An Uncommon Type II PKS Catalyzes Biosynthesis of Aryl Polyene Pigments. J Am Chem Soc 2019; 141:16615-16623. [DOI: 10.1021/jacs.8b10776] [Citation(s) in RCA: 38] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/15/2023]
Affiliation(s)
- Gina L. C. Grammbitter
- Molekulare Biotechnologie, Fachbereich Biowissenschaften, Goethe-Universität Frankfurt am Main and Buchmann Institute for Molecular Life Sciences (BMLS), Goethe-Universität Frankfurt, Max-von-Laue-Straße 9 and 15, 60438 Frankfurt am Main, Germany
| | - Maximilian Schmalhofer
- Center for Integrated Protein Science at the Department Chemie, Lehrstuhl für Biochemie, Technische Universität München, Lichtenbergstraße 4, 85748 Garching, Germany
| | - Kudratullah Karimi
- Institut für Physikalische und Theoretische Chemie, Goethe-Universität Frankfurt, Max-von-Laue-Straße 7, 60438 Frankfurt am Main, Germany
| | - Yi-Ming Shi
- Molekulare Biotechnologie, Fachbereich Biowissenschaften, Goethe-Universität Frankfurt am Main and Buchmann Institute for Molecular Life Sciences (BMLS), Goethe-Universität Frankfurt, Max-von-Laue-Straße 9 and 15, 60438 Frankfurt am Main, Germany
| | - Tim A. Schöner
- Molekulare Biotechnologie, Fachbereich Biowissenschaften, Goethe-Universität Frankfurt am Main and Buchmann Institute for Molecular Life Sciences (BMLS), Goethe-Universität Frankfurt, Max-von-Laue-Straße 9 and 15, 60438 Frankfurt am Main, Germany
| | - Nicholas J. Tobias
- Molekulare Biotechnologie, Fachbereich Biowissenschaften, Goethe-Universität Frankfurt am Main and Buchmann Institute for Molecular Life Sciences (BMLS), Goethe-Universität Frankfurt, Max-von-Laue-Straße 9 and 15, 60438 Frankfurt am Main, Germany
| | - Nina Morgner
- Institut für Physikalische und Theoretische Chemie, Goethe-Universität Frankfurt, Max-von-Laue-Straße 7, 60438 Frankfurt am Main, Germany
| | - Michael Groll
- Center for Integrated Protein Science at the Department Chemie, Lehrstuhl für Biochemie, Technische Universität München, Lichtenbergstraße 4, 85748 Garching, Germany
| | - Helge B. Bode
- Molekulare Biotechnologie, Fachbereich Biowissenschaften, Goethe-Universität Frankfurt am Main and Buchmann Institute for Molecular Life Sciences (BMLS), Goethe-Universität Frankfurt, Max-von-Laue-Straße 9 and 15, 60438 Frankfurt am Main, Germany
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22
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Villebro R, Shaw S, Blin K, Weber T. Sequence-based classification of type II polyketide synthase biosynthetic gene clusters for antiSMASH. J Ind Microbiol Biotechnol 2019; 46:469-475. [PMID: 30610412 DOI: 10.1007/s10295-018-02131-9] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2018] [Accepted: 12/24/2018] [Indexed: 02/01/2023]
Abstract
The software antiSMASH examines microbial genome data to identify and analyze biosynthetic gene clusters for a wide range of natural products. So far, type II polyketide synthase (PKS) gene clusters could only be identified, but no detailed predictions for type II PKS gene clusters could be provided. In this study, an antiSMASH module for analyzing type II PKS gene clusters has been developed. The module detects genes/proteins in the type II PKS gene cluster involved with polyketide biosynthesis and is able to make predictions about the aromatic polyketide product. Predictions include the putative starter unit, the number of malonyl elongations during polyketide biosynthesis, the putative class and the molecular weight of the product. Furthermore, putative cyclization patterns are predicted. The accuracy of the predictions generated with the new PKSII antiSMASH module was evaluated using a leave-one-out cross validation. The prediction module is available in antiSMASH version 5 at https://antismash.secondarymetabolites.org .
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Affiliation(s)
- Rasmus Villebro
- The Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Kemitorvet, Bygning 220, 2800, Kongens Lyngby, Denmark
| | - Simon Shaw
- The Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Kemitorvet, Bygning 220, 2800, Kongens Lyngby, Denmark
| | - Kai Blin
- The Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Kemitorvet, Bygning 220, 2800, Kongens Lyngby, Denmark.
| | - Tilmann Weber
- The Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Kemitorvet, Bygning 220, 2800, Kongens Lyngby, Denmark.
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23
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Witzgall F, Ewert W, Blankenfeldt W. Structures of the N-Terminal Domain of PqsA in Complex with Anthraniloyl- and 6-Fluoroanthraniloyl-AMP: Substrate Activation in Pseudomonas Quinolone Signal (PQS) Biosynthesis. Chembiochem 2017; 18:2045-2055. [PMID: 28834007 DOI: 10.1002/cbic.201700374] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2017] [Indexed: 12/16/2022]
Abstract
Pseudomonas aeruginosa, a prevalent pathogen in nosocomial infections and a major burden in cystic fibrosis, uses three interconnected quorum-sensing systems to coordinate virulence processes. At variance with other Gram-negative bacteria, one of these systems relies on 2-alkyl-4(1H)-quinolones (Pseudomonas quinolone signal, PQS) and might hence be an attractive target for new anti-infective agents. Here we report crystal structures of the N-terminal domain of anthranilate-CoA ligase PqsA, the first enzyme of PQS biosynthesis, in complex with anthraniloyl-AMP and with 6-fluoroanthraniloyl-AMP (6FABA-AMP) at 1.4 and 1.7 Å resolution. We find that PqsA belongs to an unrecognized subfamily of anthranilate-CoA ligases that recognize the amino group of anthranilate through a water-mediated hydrogen bond. The complex with 6FABA-AMP explains why 6FABA, an inhibitor of PQS biosynthesis, is a good substrate of PqsA. Together, our data might pave a way to new pathoblockers in P. aeruginosa infections.
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Affiliation(s)
- Florian Witzgall
- Structure and Function of Proteins, Helmholtz Centre for Infection Research, Inhoffenstrasse 7, 38124, Braunschweig, Germany
| | - Wiebke Ewert
- Structure and Function of Proteins, Helmholtz Centre for Infection Research, Inhoffenstrasse 7, 38124, Braunschweig, Germany.,Institut für Biophysikalische Chemie, Medizinische Hochschule Hannover, Carl-Neuberg-Strasse 1, 30625, Hannover, Germany
| | - Wulf Blankenfeldt
- Structure and Function of Proteins, Helmholtz Centre for Infection Research, Inhoffenstrasse 7, 38124, Braunschweig, Germany.,Institut für Biochemie, Biotechnologie und Bioinformatik, Technische Universität Braunschweig, Spielmannstrasse 7, 38106, Braunschweig, Germany
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24
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Hattori H, Yokoshima S, Fukuyama T. Total Syntheses of Aurachins A and B. Angew Chem Int Ed Engl 2017; 56:6980-6983. [DOI: 10.1002/anie.201702204] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2017] [Indexed: 11/12/2022]
Affiliation(s)
- Haruhiko Hattori
- Graduate School of Pharmaceutical Sciences; Nagoya University, Furo-cho, Chikusa-ku; Nagoya 464-8601 Japan
| | - Satoshi Yokoshima
- Graduate School of Pharmaceutical Sciences; Nagoya University, Furo-cho, Chikusa-ku; Nagoya 464-8601 Japan
| | - Tohru Fukuyama
- Graduate School of Pharmaceutical Sciences; Nagoya University, Furo-cho, Chikusa-ku; Nagoya 464-8601 Japan
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25
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Affiliation(s)
- Haruhiko Hattori
- Graduate School of Pharmaceutical Sciences; Nagoya University, Furo-cho, Chikusa-ku; Nagoya 464-8601 Japan
| | - Satoshi Yokoshima
- Graduate School of Pharmaceutical Sciences; Nagoya University, Furo-cho, Chikusa-ku; Nagoya 464-8601 Japan
| | - Tohru Fukuyama
- Graduate School of Pharmaceutical Sciences; Nagoya University, Furo-cho, Chikusa-ku; Nagoya 464-8601 Japan
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26
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Zhang M, Yang CL, Xiao YS, Zhang B, Deng XZ, Yang L, Shi J, Wang YS, Li W, Jiao RH, Tan RX, Ge HM. Aurachin SS, a new antibiotic from Streptomyces sp. NA04227. J Antibiot (Tokyo) 2017; 70:853-855. [DOI: 10.1038/ja.2017.50] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2017] [Revised: 03/20/2017] [Accepted: 03/23/2017] [Indexed: 11/09/2022]
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27
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Lin CI, McCarty RM, Liu HW. The Enzymology of Organic Transformations: A Survey of Name Reactions in Biological Systems. Angew Chem Int Ed Engl 2017; 56:3446-3489. [PMID: 27505692 PMCID: PMC5477795 DOI: 10.1002/anie.201603291] [Citation(s) in RCA: 46] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2016] [Indexed: 01/05/2023]
Abstract
Chemical reactions that are named in honor of their true, or at least perceived, discoverers are known as "name reactions". This Review is a collection of biological representatives of named chemical reactions. Emphasis is placed on reaction types and catalytic mechanisms that showcase both the chemical diversity in natural product biosynthesis as well as the parallels with synthetic organic chemistry. An attempt has been made, whenever possible, to describe the enzymatic mechanisms of catalysis within the context of their synthetic counterparts and to discuss the mechanistic hypotheses for those reactions that are currently active areas of investigation. This Review has been categorized by reaction type, for example condensation, nucleophilic addition, reduction and oxidation, substitution, carboxylation, radical-mediated, and rearrangements, which are subdivided by name reactions.
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Affiliation(s)
- Chia-I Lin
- Division of Chemical Biology and Medicinal Chemistry, College of Pharmacy, and Department of Chemistry, University of Texas at Austin, Austin, TX, 78731, USA
| | - Reid M McCarty
- Division of Chemical Biology and Medicinal Chemistry, College of Pharmacy, and Department of Chemistry, University of Texas at Austin, Austin, TX, 78731, USA
| | - Hung-Wen Liu
- Division of Chemical Biology and Medicinal Chemistry, College of Pharmacy, and Department of Chemistry, University of Texas at Austin, Austin, TX, 78731, USA
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28
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Lin C, McCarty RM, Liu H. Die Enzymologie organischer Umwandlungen: Namensreaktionen in biologischen Systemen. Angew Chem Int Ed Engl 2017. [DOI: 10.1002/ange.201603291] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/20/2023]
Affiliation(s)
- Chia‐I. Lin
- Division of Chemical Biology and Medicinal Chemistry College of Pharmacy, and Department of Chemistry University of Texas at Austin Austin TX 78731 USA
| | - Reid M. McCarty
- Division of Chemical Biology and Medicinal Chemistry College of Pharmacy, and Department of Chemistry University of Texas at Austin Austin TX 78731 USA
| | - Hung‐wen Liu
- Division of Chemical Biology and Medicinal Chemistry College of Pharmacy, and Department of Chemistry University of Texas at Austin Austin TX 78731 USA
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29
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Du D, Katsuyama Y, Onaka H, Fujie M, Satoh N, Shin-ya K, Ohnishi Y. Production of a Novel Amide-Containing Polyene by Activating a Cryptic Biosynthetic Gene Cluster inStreptomycessp. MSC090213JE08. Chembiochem 2016; 17:1464-71. [DOI: 10.1002/cbic.201600167] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2016] [Indexed: 12/18/2022]
Affiliation(s)
- Danyao Du
- Department of Biotechnology; Graduate School of Agricultural and Life Sciences; The University of Tokyo; 1-1-1 Yayoi Bunkyo-ku Tokyo 113-8657 Japan
| | - Yohei Katsuyama
- Department of Biotechnology; Graduate School of Agricultural and Life Sciences; The University of Tokyo; 1-1-1 Yayoi Bunkyo-ku Tokyo 113-8657 Japan
| | - Hiroyasu Onaka
- Department of Biotechnology; Graduate School of Agricultural and Life Sciences; The University of Tokyo; 1-1-1 Yayoi Bunkyo-ku Tokyo 113-8657 Japan
| | - Manabu Fujie
- Okinawa Institute of Science and Technology Graduate University; 1919-1 Tancha, Onna-son Kunigami-gun Okinawa 904-0495 Japan
| | - Noriyuki Satoh
- Okinawa Institute of Science and Technology Graduate University; 1919-1 Tancha, Onna-son Kunigami-gun Okinawa 904-0495 Japan
| | - Kazuo Shin-ya
- National Institute of Advanced Industrial Science and Technology (AIST); 2-4-7 Aomi Koto-ku Tokyo 135-0064 Japan
| | - Yasuo Ohnishi
- Department of Biotechnology; Graduate School of Agricultural and Life Sciences; The University of Tokyo; 1-1-1 Yayoi Bunkyo-ku Tokyo 113-8657 Japan
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30
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Jackson DR, Tu SS, Nguyen M, Barajas JF, Schaub AJ, Krug D, Pistorius D, Luo R, Müller R, Tsai SC. Structural Insights into Anthranilate Priming during Type II Polyketide Biosynthesis. ACS Chem Biol 2016; 11:95-103. [PMID: 26473393 DOI: 10.1021/acschembio.5b00500] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
The incorporation of nonacetate starter units during type II polyketide biosynthesis helps diversify natural products. Currently, there are few enzymatic strategies for the incorporation of nonacetate starter units in type II polyketide synthase (PKS) pathways. Here we report the crystal structure of AuaEII, the anthranilate:CoA ligase responsible for the generation of anthraniloyl-CoA, which is used as a starter unit by a type II PKS in aurachin biosynthesis. We present structural and protein sequence comparisons to other aryl:CoA ligases. We also compare the AuaEII crystal structure to a model of a CoA ligase homologue, AuaE, which is present in the same gene cluster. AuaE is predicted to have the same fold as AuaEII, but instead of CoA ligation, AuaE catalyzes acyl transfer of anthranilate from anthraniloyl-CoA to the acyl carrier protein (ACP). Together, this work provides insight into the molecular basis for starter unit selection of anthranilate in type II PKS biosynthesis.
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Affiliation(s)
| | | | | | | | | | - Daniel Krug
- Department
of Microbial Natural Products, Helmholtz-Institute for Pharmaceutical
Research Saarland (HIPS), Helmholtz Centre for Infection Research
(HZI) and Pharmaceutical Biotechnology, Saarland University, Campus C2 3, 66123 Saarbrücken, Germany
| | - Dominik Pistorius
- Department
of Microbial Natural Products, Helmholtz-Institute for Pharmaceutical
Research Saarland (HIPS), Helmholtz Centre for Infection Research
(HZI) and Pharmaceutical Biotechnology, Saarland University, Campus C2 3, 66123 Saarbrücken, Germany
| | | | - Rolf Müller
- Department
of Microbial Natural Products, Helmholtz-Institute for Pharmaceutical
Research Saarland (HIPS), Helmholtz Centre for Infection Research
(HZI) and Pharmaceutical Biotechnology, Saarland University, Campus C2 3, 66123 Saarbrücken, Germany
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Shabuer G, Ishida K, Pidot SJ, Roth M, Dahse HM, Hertweck C. Plant pathogenic anaerobic bacteria use aromatic polyketides to access aerobic territory. Science 2015; 350:670-4. [PMID: 26542569 DOI: 10.1126/science.aac9990] [Citation(s) in RCA: 46] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
Around 25% of vegetable food is lost worldwide because of infectious plant diseases, including microbe-induced decay of harvested crops. In wet seasons and under humid storage conditions, potato tubers are readily infected and decomposed by anaerobic bacteria (Clostridium puniceum). We found that these anaerobic plant pathogens harbor a gene locus (type II polyketide synthase) to produce unusual polyketide metabolites (clostrubins) with dual functions. The clostrubins, which act as antibiotics against other microbial plant pathogens, enable the anaerobic bacteria to survive an oxygen-rich plant environment.
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Affiliation(s)
- Gulimila Shabuer
- Department of Biomolecular Chemistry, Leibniz Institute for Natural Product Research and Infection Biology (HKI), Jena, Germany
| | - Keishi Ishida
- Department of Biomolecular Chemistry, Leibniz Institute for Natural Product Research and Infection Biology (HKI), Jena, Germany
| | - Sacha J Pidot
- Department of Biomolecular Chemistry, Leibniz Institute for Natural Product Research and Infection Biology (HKI), Jena, Germany. Department of Microbiology and Immunology, University of Melbourne at the Peter Doherty Institute for Infection and Immunity, VIC 3010, Australia
| | - Martin Roth
- Bio Pilot Plant, Leibniz Institute for Natural Product Research and Infection Biology (HKI), Jena, Germany
| | - Hans-Martin Dahse
- Department of Infection Biology, Leibniz Institute for Natural Product Research and Infection Biology (HKI), Jena, Germany
| | - Christian Hertweck
- Department of Biomolecular Chemistry, Leibniz Institute for Natural Product Research and Infection Biology (HKI), Jena, Germany. Department of Natural Product Chemistry, Friedrich Schiller University, Jena, Germany.
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Katsuyama Y, Li XW, Müller R, Nay B. Chemically unprecedented biocatalytic (AuaG) retro-[2,3]-Wittig rearrangement: a new insight into aurachin B biosynthesis. Chembiochem 2014; 15:2349-52. [PMID: 25209961 DOI: 10.1002/cbic.201402373] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2014] [Indexed: 11/07/2022]
Abstract
AuaG is flavin-dependent monooxygenase responsible for the conversion of aurachin C to aurachin B, a reaction thought to resemble semipinacol migration of the farnesyl substituent. A study of the substrate tolerance of AuaG reveals that it has the peculiar ability to oxidise short-chain analogues of aurachin D. Unexpectedly, a novel retro-[2,3]-Wittig rearrangement was observed with an isoprenyl substrate analogue, thus leading to the 1,1-dimethylallyl ether. Additionally, we found that saturated-chain analogues of N-oxidised aurachin C were not transformed by the C3→C4 semipinacol reaction, as might have been expected for such substrates. Based on this and the unique retro-[2,3]-Wittig rearrangement, we discuss an alternative biosynthetic route for the conversion of aurachin C to aurachin B.
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Affiliation(s)
- Yohei Katsuyama
- Department of Biotechnology, Graduate School of Agricultural and Life Sciences, University of Tokyo, Tokyo (Japan)
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Yang Y, Fu L, Zhang J, Hu L, Xu M, Xu J. Characterization of the xiamenmycin biosynthesis gene cluster in Streptomyces xiamenensis 318. PLoS One 2014; 9:e99537. [PMID: 24919072 PMCID: PMC4053376 DOI: 10.1371/journal.pone.0099537] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2014] [Accepted: 05/15/2014] [Indexed: 11/19/2022] Open
Abstract
Xiamenmycin (1) is a prenylated benzopyran derivative with anti-fibrotic activity. To investigate the genetic basis of xiamenmycin biosynthesis, we performed genome mining in the xiamenmycin-producing Streptomyces xiamenensis wild-type strain 318 to identify a candidate gene cluster. The complete gene cluster, consisting of five genes, was confirmed by a series of gene inactivations and heterologous expression. Based on bioinformatics analyses of each gene and feeding experiments, we found that the structure of an intermediate xiamenmycin B (3) accumulated in a ximA inactivation mutant, allowing us to propose a biosynthetic pathway. All five of the genes in the pathway were genetically and biochemically characterized. XimA was biochemically characterized as an ATP-dependent amide synthetase, catalyzing an amide bond formation in the presence of ATP as the final step in Xiamenmycin biosynthesis. The Km value of XimA was determined to be 474.38 µM for the substrate xiamenmycin B. These studies provide opportunities to use genetic and chemo-enzymatic methods to create new benzopyran derivatives as potential therapeutic agents.
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Affiliation(s)
- Yong Yang
- State Key Laboratory of Microbial Metabolism and School of Life Sciences. & Biotechnology, State Key Laboratory of Ocean Engineering, Shanghai Jiao Tong University, Shanghai, China
| | - Ling Fu
- State Key Laboratory of Microbial Metabolism and School of Life Sciences. & Biotechnology, State Key Laboratory of Ocean Engineering, Shanghai Jiao Tong University, Shanghai, China
| | - Jinlong Zhang
- State Key Laboratory of Microbial Metabolism and School of Life Sciences. & Biotechnology, State Key Laboratory of Ocean Engineering, Shanghai Jiao Tong University, Shanghai, China
| | - Linghan Hu
- State Key Laboratory of Microbial Metabolism and School of Life Sciences. & Biotechnology, State Key Laboratory of Ocean Engineering, Shanghai Jiao Tong University, Shanghai, China
| | - Minjuan Xu
- Key Laboratory of Systems Biomedicine, Shanghai Center for Systems Biomedicine, Shanghai Jiao Tong University, Shanghai, China
- * E-mail: (JX); (MX)
| | - Jun Xu
- State Key Laboratory of Microbial Metabolism and School of Life Sciences. & Biotechnology, State Key Laboratory of Ocean Engineering, Shanghai Jiao Tong University, Shanghai, China
- Institute of oceanology, Shanghai Jiao Tong University, Shanghai, China
- * E-mail: (JX); (MX)
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Abstract
Covering: up to the end of 2013. Myxobacteria produce a vast range of structurally diverse natural products with prominent biological activities. Here, we provide a detailed description and judge the potential of all antibiotically active myxobacterial compounds as lead structures, pointing out their particularities and, if known, their mode of action. Thus, the review provides an overview of the potential of specific compounds, suitable for future investigations and possible clinical applications.
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Affiliation(s)
- Till F Schäberle
- Institute for Pharmaceutical Biology, University of Bonn, Nussallee 6, 53115 Bonn, Germany.
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35
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Pidot S, Ishida K, Cyrulies M, Hertweck C. Discovery of Clostrubin, an Exceptional Polyphenolic Polyketide Antibiotic from a Strictly Anaerobic Bacterium. Angew Chem Int Ed Engl 2014; 53:7856-9. [DOI: 10.1002/anie.201402632] [Citation(s) in RCA: 50] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2014] [Indexed: 01/09/2023]
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36
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Pidot S, Ishida K, Cyrulies M, Hertweck C. Discovery of Clostrubin, an Exceptional Polyphenolic Polyketide Antibiotic from a Strictly Anaerobic Bacterium. Angew Chem Int Ed Engl 2014. [DOI: 10.1002/ange.201402632] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
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Wang M, Zhao H. Characterization and Engineering of the Adenylation Domain of a NRPS-Like Protein: A Potential Biocatalyst for Aldehyde Generation. ACS Catal 2014; 4:1219-1225. [PMID: 24804152 PMCID: PMC3985451 DOI: 10.1021/cs500039v] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2014] [Revised: 02/17/2014] [Indexed: 01/24/2023]
Abstract
The adenylation (A) domain acts as the first "gate-keeper" to ensure the activation and thioesterification of the correct monomer to nonribosomal peptide synthetases (NRPSs). Our understanding of the specificity-conferring code and our ability to engineer A domains are critical for increasing the chemical diversity of nonribosomal peptides (NRPs). We recently discovered a novel NRPS-like protein (ATEG_03630) that can activate 5-methyl orsellinic acid (5-MOA) and reduce it to 2,4-dihydroxy-5,6-dimethyl benzaldehyde. A NRPS-like protein is much smaller than multidomain NRPSs, but it still represents the thioesterification half-reaction, which is otherwise missed from a stand-alone A domain. Therefore, a NRPS-like protein may serve as a better model system for A domain engineering. Here, we characterize the substrate specificity of ATEG_03630 and conclude that the hydrogen-bond donor at the 4-position is crucial for substrate recognition. Next, we show that the substrate specificity of ATEG_03630 can be engineered toward our target substrate anthranilate via bioinformatics analysis and mutagenesis. The resultant mutant H358A increased its activity toward anthranilate by 10.9-fold, which led to a 26-fold improvement in specificity. Finally, we demonstrate one-pot chemoenzymatic synthesis of 4-hydroxybenzaldoxime from 4-hydroxybenzoic acid with high yield.
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Affiliation(s)
- Meng Wang
- Department of Chemical and Biomolecular Engineering, Institute for
Genomic Biology, Departments of Chemistry, Biochemistry, and Bioengineering, University of Illinois at Urbana−Champaign, Urbana, Illinois 61801, United States
| | - Huimin Zhao
- Department of Chemical and Biomolecular Engineering, Institute for
Genomic Biology, Departments of Chemistry, Biochemistry, and Bioengineering, University of Illinois at Urbana−Champaign, Urbana, Illinois 61801, United States
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38
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Synthesis of aurachin D and isoprenoid analogues from the myxobacterium Stigmatella aurantiaca. Tetrahedron Lett 2013. [DOI: 10.1016/j.tetlet.2013.09.085] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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39
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Yasutake Y, Kitagawa W, Hata M, Nishioka T, Ozaki T, Nishiyama M, Kuzuyama T, Tamura T. Structure of the quinoline N-hydroxylating cytochrome P450 RauA, an essential enzyme that confers antibiotic activity on aurachin alkaloids. FEBS Lett 2013; 588:105-10. [PMID: 24269679 DOI: 10.1016/j.febslet.2013.11.016] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2013] [Revised: 11/06/2013] [Accepted: 11/06/2013] [Indexed: 01/08/2023]
Abstract
The cytochrome P450 RauA from Rhodococcus erythropolis JCM 6824 catalyzes the hydroxylation of a nitrogen atom in the quinolone ring of aurachin, thereby conferring strong antibiotic activity on the aurachin alkaloid. Here, we report the crystal structure of RauA in complex with its substrate, a biosynthetic intermediate of aurachin RE. Clear electron density showed that the quinolone ring is oriented parallel to the porphyrin plane of the heme cofactor, while the farnesyl chain curls into a U-shape topology and is buried inside the solvent-inaccessible hydrophobic interior of RauA. The nearest atom from the heme iron is the quinolone nitrogen (4.3Å), which is consistent with RauA catalyzing the N-hydroxylation of the quinolone ring to produce mature aurachin RE.
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Affiliation(s)
- Yoshiaki Yasutake
- Bioproduction Research Institute, National Institute of Advanced Industrial Science and Technology (AIST), 2-17-2-1 Tsukisamu-Higashi, Toyohira-ku, Sapporo 062-8517, Japan.
| | - Wataru Kitagawa
- Bioproduction Research Institute, National Institute of Advanced Industrial Science and Technology (AIST), 2-17-2-1 Tsukisamu-Higashi, Toyohira-ku, Sapporo 062-8517, Japan; Graduate School of Agriculture, Hokkaido University, Kita-9, Nishi-9, Kita-ku, Sapporo 060-8589, Japan
| | - Miyako Hata
- Bioproduction Research Institute, National Institute of Advanced Industrial Science and Technology (AIST), 2-17-2-1 Tsukisamu-Higashi, Toyohira-ku, Sapporo 062-8517, Japan
| | - Taiki Nishioka
- Graduate School of Agriculture, Hokkaido University, Kita-9, Nishi-9, Kita-ku, Sapporo 060-8589, Japan
| | - Taro Ozaki
- Biotechnology Research Center, The University of Tokyo, 1-1-1 Yayoi, Bunkyo-ku, Tokyo 113-8657, Japan
| | - Makoto Nishiyama
- Biotechnology Research Center, The University of Tokyo, 1-1-1 Yayoi, Bunkyo-ku, Tokyo 113-8657, Japan
| | - Tomohisa Kuzuyama
- Biotechnology Research Center, The University of Tokyo, 1-1-1 Yayoi, Bunkyo-ku, Tokyo 113-8657, Japan
| | - Tomohiro Tamura
- Bioproduction Research Institute, National Institute of Advanced Industrial Science and Technology (AIST), 2-17-2-1 Tsukisamu-Higashi, Toyohira-ku, Sapporo 062-8517, Japan; Graduate School of Agriculture, Hokkaido University, Kita-9, Nishi-9, Kita-ku, Sapporo 060-8589, Japan
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40
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Li XW, Herrmann J, Zang Y, Grellier P, Prado S, Müller R, Nay B. Synthesis and biological activities of the respiratory chain inhibitor aurachin D and new ring versus chain analogues. Beilstein J Org Chem 2013; 9:1551-8. [PMID: 23946854 PMCID: PMC3740496 DOI: 10.3762/bjoc.9.176] [Citation(s) in RCA: 35] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2013] [Accepted: 07/10/2013] [Indexed: 01/25/2023] Open
Abstract
Aurachins are myxobacterial 3-farnesyl-4(1H)-quinolone derived compounds initially described as respiratory chain inhibitors, more specifically as inhibitors of various cytochrome complexes. They are also known as potent antibiotic compounds. We describe herein the first synthesis of aurachin D through a key Conrad–Limpach reaction. The same strategy was used to reach some ring as opposed to chain analogues, allowing for the description of structure–activity relationships. Biological screening of the analogues showed antiparasitic, cytotoxic, antibacterial and antifungal activities, and depletion of the mitochondrial membrane potential. The strongest activity was found on Plasmodium falciparum with a selectivity index of 345, compared to Vero cells, for the natural product and its geranyl analogue. The loss of mitochondrial membrane potential induced by aurachins in human U-2 OS osteosarcoma cells was studied, showing the best activity for aurachin D and a naphthalene analogue, yet without totally explaining the observed cytotoxic activity of the compounds. Finally, a synthetic entry is given to the complete carboheterocyclic core of aurachin H through the N-oxidation/epoxidation of aurachin D and a shorter chain analogue, followed by subsequent biomimetic cyclization.
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Affiliation(s)
- Xu-Wen Li
- Muséum National d'Histoire Naturelle, Unité Molécules de Communication et Adaptation des Micro-organismes (UMR 7245 CNRS-MNHN), 57 rue Cuvier (CP 54), 75005 Paris, France
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41
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Kitagawa W, Ozaki T, Nishioka T, Yasutake Y, Hata M, Nishiyama M, Kuzuyama T, Tamura T. Cloning and Heterologous Expression of the Aurachin RE Biosynthesis Gene Cluster Afford a New Cytochrome P450 for Quinoline N-Hydroxylation. Chembiochem 2013; 14:1085-93. [DOI: 10.1002/cbic.201300167] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2013] [Indexed: 11/10/2022]
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42
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Katsuyama Y, Harmrolfs K, Pistorius D, Li Y, Müller R. Eine Semipinakol-Umlagerung - katalysiert durch ein Enzymsystem mit difunktioneller FAD-abhängiger Monooxygenase. Angew Chem Int Ed Engl 2012. [DOI: 10.1002/ange.201204138] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/03/2023]
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43
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Katsuyama Y, Harmrolfs K, Pistorius D, Li Y, Müller R. A Semipinacol Rearrangement Directed by an Enzymatic System Featuring Dual-Function FAD-Dependent Monooxygenase. Angew Chem Int Ed Engl 2012; 51:9437-40. [DOI: 10.1002/anie.201204138] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2012] [Indexed: 11/08/2022]
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44
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Nguyen QT, Merlo ME, Medema MH, Jankevics A, Breitling R, Takano E. Metabolomics methods for the synthetic biology of secondary metabolism. FEBS Lett 2012; 586:2177-83. [PMID: 22710183 DOI: 10.1016/j.febslet.2012.02.008] [Citation(s) in RCA: 57] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2011] [Accepted: 02/07/2012] [Indexed: 11/26/2022]
Abstract
Many microbial secondary metabolites are of high biotechnological value for medicine, agriculture, and the food industry. Bacterial genome mining has revealed numerous novel secondary metabolite biosynthetic gene clusters, which encode the potential to synthesize a large diversity of compounds that have never been observed before. The stimulation or "awakening" of this cryptic microbial secondary metabolism has naturally attracted the attention of synthetic microbiologists, who exploit recent advances in DNA sequencing and synthesis to achieve unprecedented control over metabolic pathways. One of the indispensable tools in the synthetic biology toolbox is metabolomics, the global quantification of small biomolecules. This review illustrates the pivotal role of metabolomics for the synthetic microbiology of secondary metabolism, including its crucial role in novel compound discovery in microbes, the examination of side products of engineered metabolic pathways, as well as the identification of major bottlenecks for the overproduction of compounds of interest, especially in combination with metabolic modeling. We conclude by highlighting remaining challenges and recent technological advances that will drive metabolomics towards fulfilling its potential as a cornerstone technology of synthetic microbiology.
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Affiliation(s)
- Quoc-Thai Nguyen
- Department of Microbial Physiology, Groningen Biomolecular Sciences and Biotechnology Institute, University of Groningen, Nijenborgh 7, 9747 AG Groningen, The Netherlands
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45
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Lengyel L, Nagy TZ, Sipos G, Jones R, Dormán G, Ürge L, Darvas F. Highly efficient thermal cyclization reactions of alkylidene esters in continuous flow to give aromatic/heteroaromatic derivatives. Tetrahedron Lett 2012. [DOI: 10.1016/j.tetlet.2011.11.125] [Citation(s) in RCA: 37] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
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46
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Pistorius D, Li Y, Mann S, Müller R. Unprecedented Anthranilate Priming Involving Two Enzymes of the Acyl Adenylating Superfamily in Aurachin Biosynthesis. J Am Chem Soc 2011; 133:12362-5. [DOI: 10.1021/ja203653w] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Dominik Pistorius
- Helmholtz-Institut für Pharmazeutische Forschung Saarland, Helmholtz Zentrum für Infektionsforschung Braunschweig and Pharmazeutische Biotechnologie, Universität des Saarlandes, Postfach 151150, 66041 Saarbrücken, Germany
| | - Yanyan Li
- Helmholtz-Institut für Pharmazeutische Forschung Saarland, Helmholtz Zentrum für Infektionsforschung Braunschweig and Pharmazeutische Biotechnologie, Universität des Saarlandes, Postfach 151150, 66041 Saarbrücken, Germany
| | - Stéphane Mann
- Chimie ParisTech, ENSCP, Laboratoire Charles Friedel, UMR 7223-CNRS, 75005 Paris, France
| | - Rolf Müller
- Helmholtz-Institut für Pharmazeutische Forschung Saarland, Helmholtz Zentrum für Infektionsforschung Braunschweig and Pharmazeutische Biotechnologie, Universität des Saarlandes, Postfach 151150, 66041 Saarbrücken, Germany
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47
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Stec E, Pistorius D, Müller R, Li SM. AuaA, a Membrane-Bound Farnesyltransferase from Stigmatella aurantiaca, Catalyzes the Prenylation of 2-Methyl-4-hydroxyquinoline in the Biosynthesis of Aurachins. Chembiochem 2011; 12:1724-30. [DOI: 10.1002/cbic.201100188] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2011] [Indexed: 01/05/2023]
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48
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Pohle S, Appelt C, Roux M, Fiedler HP, Süssmuth RD. Biosynthetic gene cluster of the non-ribosomally synthesized cyclodepsipeptide skyllamycin: deciphering unprecedented ways of unusual hydroxylation reactions. J Am Chem Soc 2011; 133:6194-205. [PMID: 21456593 DOI: 10.1021/ja108971p] [Citation(s) in RCA: 96] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
The cyclic depsipeptide skyllamycin A is a potent inhibitor of the platelet-derived growth factor (PDGF) signaling pathway by inhibiting binding of homodimeric PDGF BB to the PDGF β-receptor. Its structure contains a cinnamoyl side chain and shows a high amount of β-hydroxylated amino acids as well as an unusual α-hydroxyglycine moiety as a rare structural modification. The skyllamycin biosynthetic gene cluster was cloned and sequenced from Streptomyces sp. Acta 2897. Its analysis revealed the presence of open reading frames encoding proteins for fatty acid precursor biosynthesis, non-ribosomal peptide synthetases, regulators, and transporters along with other modifying enzymes. Specific in-frame mutagenesis of these tailoring enzymes resulted in the production of novel skyllamycin derivatives revealing that β-hydroxy groups in skyllamycin A are introduced by a promiscuous cytochrome P450 monooxygenase, whereas a two-component flavin-dependent monooxygenase is involved in α-hydroxylation.
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Affiliation(s)
- Stefan Pohle
- Technische Universität Berlin, Institut für Chemie, Strasse des 17. Juni 124, 10623 Berlin, Germany
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49
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Pistorius D, Li Y, Sandmann A, Müller R. Completing the puzzle of aurachin biosynthesis in Stigmatella aurantiaca Sg a15. MOLECULAR BIOSYSTEMS 2011; 7:3308-15. [DOI: 10.1039/c1mb05328k] [Citation(s) in RCA: 37] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/22/2023]
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50
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Li Y, Müller R. Non-modular polyketide synthases in myxobacteria. PHYTOCHEMISTRY 2009; 70:1850-1857. [PMID: 19586645 DOI: 10.1016/j.phytochem.2009.05.003] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/28/2009] [Revised: 04/14/2009] [Accepted: 05/12/2009] [Indexed: 05/28/2023]
Abstract
Myxobacteria are prolific producers of a wide variety of secondary metabolites. The vast majority of these compounds are complex polyketides which are biosynthesised by multimodular polyketide synthases (PKSs). In contrast, few myxobacterial metabolites isolated to date are derived from non-modular PKSs, in particular type III PKSs. This review reports our progress on the characterisation of type III PKSs in myxobacteria. We also summarize current knowledge on bacterial type III PKSs, with a special focus on the evolutionary relationship between plant and bacterial enzymes. The biosynthesis of a quinoline alkaloid in Stigmatella aurantiaca by a non-modular PKS is also discussed.
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Affiliation(s)
- Yanyan Li
- Department of Pharmaceutical Biotechnology, Saarland University, Saarbrücken, Germany
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