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Cochrane RVK, Sanichar R, Lambkin GR, Reiz B, Xu W, Tang Y, Vederas JC. Production of New Cladosporin Analogues by Reconstitution of the Polyketide Synthases Responsible for the Biosynthesis of this Antimalarial Agent. Angew Chem Int Ed Engl 2015. [DOI: 10.1002/ange.201509345] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
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52
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Luhavaya H, Dias MVB, Williams SR, Hong H, de Oliveira LG, Leadlay PF. Enzymology of Pyran Ring A Formation in Salinomycin Biosynthesis. ACTA ACUST UNITED AC 2015; 127:13826-13829. [PMID: 27587902 PMCID: PMC4988243 DOI: 10.1002/ange.201507090] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2015] [Indexed: 01/25/2023]
Abstract
Tetrahydropyran rings are a common feature of complex polyketide natural products, but much remains to be learned about the enzymology of their formation. The enzyme SalBIII from the salinomycin biosynthetic pathway resembles other polyether epoxide hydrolases/cyclases of the MonB family, but SalBIII plays no role in the conventional cascade of ring opening/closing. Mutation in the salBIII gene gave a metabolite in which ring A is not formed. Using this metabolite in vitro as a substrate analogue, SalBIII has been shown to form pyran ring A. We have determined the X-ray crystal structure of SalBIII, and structure-guided mutagenesis of putative active-site residues has identified Asp38 and Asp104 as an essential catalytic dyad. The demonstrated pyran synthase activity of SalBIII further extends the impressive catalytic versatility of α+β barrel fold proteins.
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Affiliation(s)
- Hanna Luhavaya
- Department of Biochemistry, University of Cambridge, 80 Tennis Court Road, Cambridge CB2 1GA (UK)
| | - Marcio V B Dias
- Department of Microbiology, Institute of Biomedical Science, University of São Paulo, Av. Prof. Lineu Prestes, 1374, 05508-000, São Paulo-SP (Brazil)
| | - Simon R Williams
- University Chemical Laboratory, University of Cambridge, Lensfield Road, Cambridge CB2 1EW (UK)
| | - Hui Hong
- Department of Biochemistry, University of Cambridge, 80 Tennis Court Road, Cambridge CB2 1GA (UK)
| | - Luciana G de Oliveira
- Department of Organic Chemistry, University of Campinas UNICAMP, Cidade Universitária Zeferino Vaz s/n, P.O. Box 6154, 13083-970, Campinas-SP (Brazil)
| | - Peter F Leadlay
- Department of Biochemistry, University of Cambridge, 80 Tennis Court Road, Cambridge CB2 1GA (UK)
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53
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Luhavaya H, Dias MVB, Williams SR, Hong H, de Oliveira LG, Leadlay PF. Enzymology of Pyran Ring A Formation in Salinomycin Biosynthesis. Angew Chem Int Ed Engl 2015; 54:13622-5. [PMID: 26377145 PMCID: PMC4648038 DOI: 10.1002/anie.201507090] [Citation(s) in RCA: 35] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2015] [Indexed: 02/06/2023]
Abstract
Tetrahydropyran rings are a common feature of complex polyketide natural products, but much remains to be learned about the enzymology of their formation. The enzyme SalBIII from the salinomycin biosynthetic pathway resembles other polyether epoxide hydrolases/cyclases of the MonB family, but SalBIII plays no role in the conventional cascade of ring opening/closing. Mutation in the salBIII gene gave a metabolite in which ring A is not formed. Using this metabolite in vitro as a substrate analogue, SalBIII has been shown to form pyran ring A. We have determined the X-ray crystal structure of SalBIII, and structure-guided mutagenesis of putative active-site residues has identified Asp38 and Asp104 as an essential catalytic dyad. The demonstrated pyran synthase activity of SalBIII further extends the impressive catalytic versatility of α+β barrel fold proteins.
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Affiliation(s)
- Hanna Luhavaya
- Department of Biochemistry, University of Cambridge, 80 Tennis Court Road, Cambridge CB2 1GA (UK)
| | - Marcio V B Dias
- Department of Microbiology, Institute of Biomedical Science, University of São Paulo, Av. Prof. Lineu Prestes, 1374, 05508-000, São Paulo-SP (Brazil)
| | - Simon R Williams
- University Chemical Laboratory, University of Cambridge, Lensfield Road, Cambridge CB2 1EW (UK)
| | - Hui Hong
- Department of Biochemistry, University of Cambridge, 80 Tennis Court Road, Cambridge CB2 1GA (UK)
| | - Luciana G de Oliveira
- Department of Organic Chemistry, University of Campinas UNICAMP, Cidade Universitária Zeferino Vaz s/n, P.O. Box 6154, 13083-970, Campinas-SP (Brazil)
| | - Peter F Leadlay
- Department of Biochemistry, University of Cambridge, 80 Tennis Court Road, Cambridge CB2 1GA (UK).
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54
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Ueoka R, Uria AR, Reiter S, Mori T, Karbaum P, Peters EE, Helfrich EJN, Morinaka BI, Gugger M, Takeyama H, Matsunaga S, Piel J. Metabolic and evolutionary origin of actin-binding polyketides from diverse organisms. Nat Chem Biol 2015; 11:705-12. [PMID: 26236936 DOI: 10.1038/nchembio.1870] [Citation(s) in RCA: 98] [Impact Index Per Article: 10.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2014] [Accepted: 06/05/2015] [Indexed: 11/09/2022]
Abstract
Actin-targeting macrolides comprise a large, structurally diverse group of cytotoxins isolated from remarkably dissimilar micro- and macroorganisms. In spite of their disparate origins and structures, many of these compounds bind actin at the same site and exhibit structural relationships reminiscent of modular, combinatorial drug libraries. Here we investigate biosynthesis and evolution of three compound groups: misakinolides, scytophycin-type compounds and luminaolides. For misakinolides from the sponge Theonella swinhoei WA, our data suggest production by an uncultivated 'Entotheonella' symbiont, further supporting the relevance of these bacteria as sources of bioactive polyketides and peptides in sponges. Insights into misakinolide biosynthesis permitted targeted genome mining for other members, providing a cyanobacterial luminaolide producer as the first cultivated source for this dimeric compound family. The data indicate that this polyketide family is bacteria-derived and that the unusual macrolide diversity is the result of combinatorial pathway modularity for some compounds and of convergent evolution for others.
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Affiliation(s)
- Reiko Ueoka
- Institute of Microbiology, Eigenössische Technische Hochschule (ETH) Zurich, Zurich, Switzerland
| | - Agustinus R Uria
- Institute of Microbiology, Eigenössische Technische Hochschule (ETH) Zurich, Zurich, Switzerland
| | - Silke Reiter
- Institute of Microbiology, Eigenössische Technische Hochschule (ETH) Zurich, Zurich, Switzerland
| | - Tetsushi Mori
- Faculty of Science and Engineering, Waseda University Center for Advanced Biomedical Sciences, Tokyo, Japan
| | - Petra Karbaum
- 1] Institute of Microbiology, Eigenössische Technische Hochschule (ETH) Zurich, Zurich, Switzerland. [2] Kekulé Institute of Organic Chemistry and Biochemistry, Bonn, Germany
| | - Eike E Peters
- Institute of Microbiology, Eigenössische Technische Hochschule (ETH) Zurich, Zurich, Switzerland
| | - Eric J N Helfrich
- Institute of Microbiology, Eigenössische Technische Hochschule (ETH) Zurich, Zurich, Switzerland
| | - Brandon I Morinaka
- Institute of Microbiology, Eigenössische Technische Hochschule (ETH) Zurich, Zurich, Switzerland
| | - Muriel Gugger
- Institut Pasteur, Collection des Cyanobactéries, Paris, France
| | - Haruko Takeyama
- Faculty of Science and Engineering, Waseda University Center for Advanced Biomedical Sciences, Tokyo, Japan
| | - Shigeki Matsunaga
- Laboratory of Aquatic Natural Products Chemistry, Graduate School of Agricultural and Life Sciences, The University of Tokyo, Tokyo, Japan
| | - Jörn Piel
- Institute of Microbiology, Eigenössische Technische Hochschule (ETH) Zurich, Zurich, Switzerland
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Li Y, Dodge GJ, Fiers WD, Fecik RA, Smith JL, Aldrich CC. Functional Characterization of a Dehydratase Domain from the Pikromycin Polyketide Synthase. J Am Chem Soc 2015; 137:7003-6. [PMID: 26027428 DOI: 10.1021/jacs.5b02325] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
Metabolic engineering of polyketide synthase (PKS) pathways represents a promising approach to natural products discovery. The dehydratase (DH) domains of PKSs, which generate an α,β-unsaturated bond through a dehydration reaction, have been poorly studied compared with other domains, likely because of the simple nature of the chemical reaction they catalyze and the lack of a convenient assay to measure substrate turnover. Herein we report the first steady-state kinetic analysis of a PKS DH domain employing LC-MS/MS analysis for product quantitation. PikDH2 was selected as a model DH domain. Its substrate specificity and mechanism were interrogated with a systematic series of synthetic triketide substrates containing a nonhydrolyzable thioether linkage as well as by site-directed mutagenesis, evaluation of the pH dependence of the catalytic efficiency (V(max)/K(M)), and kinetic characterization of a mechanism-based inhibitor. These studies revealed that PikDH2 converts d-alcohol substrates to trans-olefin products. The reaction is reversible with equilibrium constants ranging from 1.2 to 2. Moreover, the enzyme activity is robust, and PikDH2 was used on a preparative scale for the chemoenzymatic synthesis of unsaturated triketide products. PikDH2 was shown to possess remarkably strict substrate specificity and is unable to turn over substrates that are epimeric at the β-, γ-, or δ-position. We also demonstrated that PikDH2 has a key ionizable group with a pK(a) of 7.0 and can be irreversibly inactivated through covalent modification by a mechanism-based inhibitor, which provides a foundation for future structural studies to elucidate substrate-protein interactions.
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Affiliation(s)
- Yang Li
- †Department of Medicinal Chemistry, College of Pharmacy, University of Minnesota, Minneapolis, Minnesota 55455, United States
| | - Greg J Dodge
- ‡Department of Biological Chemistry and Life Sciences Institute, University of Michigan, Ann Arbor, Michigan 48109, United States
| | - William D Fiers
- †Department of Medicinal Chemistry, College of Pharmacy, University of Minnesota, Minneapolis, Minnesota 55455, United States
| | - Robert A Fecik
- †Department of Medicinal Chemistry, College of Pharmacy, University of Minnesota, Minneapolis, Minnesota 55455, United States
| | - Janet L Smith
- ‡Department of Biological Chemistry and Life Sciences Institute, University of Michigan, Ann Arbor, Michigan 48109, United States
| | - Courtney C Aldrich
- †Department of Medicinal Chemistry, College of Pharmacy, University of Minnesota, Minneapolis, Minnesota 55455, United States
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Hertweck C. Decoding and reprogramming complex polyketide assembly lines: prospects for synthetic biology. Trends Biochem Sci 2015; 40:189-99. [PMID: 25757401 DOI: 10.1016/j.tibs.2015.02.001] [Citation(s) in RCA: 65] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/06/2015] [Revised: 02/11/2015] [Accepted: 02/11/2015] [Indexed: 12/12/2022]
Abstract
Bacterial modular type I polyketide synthases (PKSs) represent giant megasynthases that produce a vast number of complex polyketides, many of which are pharmaceutically relevant. This review highlights recent advances in elucidating the mechanism of bacterial type I PKSs and associated enzymes, and outlines the ramifications of this knowledge for synthetic biology approaches to expand structural diversity. New insights into biosynthetic codes and structures of thiotemplate systems pave the way to rational bioengineering strategies. Through advances in genome mining, DNA recombination technologies, and biochemical analyses, the toolbox of non-canonical polyketide-modifying enzymes has been greatly enlarged. In addition to various chain-branching and chain-fusing enzymes, an increasing set of scaffold modifying biocatalysts is now available for synthetically hard-to-emulate reactions.
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Affiliation(s)
- Christian Hertweck
- Department of Biomolecular Chemistry, Leibniz Institute for Natural Product Research and Infection Biology (HKI), Beutenbergstr. 11a, 07745 Jena, Germany; Chair of Natural Product Chemistry, Friedrich Schiller University, Jena, Germany.
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Bis DM, Ban YH, James ED, Alqahtani N, Viswanathan R, Lane AL. Characterization of the nocardiopsin biosynthetic gene cluster reveals similarities to and differences from the rapamycin and FK-506 pathways. Chembiochem 2015; 16:990-7. [PMID: 25755076 DOI: 10.1002/cbic.201500007] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2015] [Indexed: 01/19/2023]
Abstract
Macrolide-pipecolate natural products, such as rapamycin (1) and FK-506 (2), are renowned modulators of FK506-binding proteins (FKBPs). The nocardiopsins, from Nocardiopsis sp. CMB-M0232, are the newest members of this structural class. Here, the biosynthetic pathway for nocardiopsins A-D (4-7) is revealed by cloning, sequencing, and bioinformatic analyses of the nsn gene cluster. In vitro evaluation of recombinant NsnL revealed that this lysine cyclodeaminase catalyzes the conversion of L-lysine into the L-pipecolic acid incorporated into 4 and 5. Bioinformatic analyses supported the conjecture that a linear nocardiopsin precursor is equipped with the hydroxy group required for macrolide closure in a previously unobserved manner by employing a P450 epoxidase (NsnF) and limonene epoxide hydrolase homologue (NsnG). The nsn cluster also encodes candidates for tetrahydrofuran group biosynthesis. The nocardiopsin pathway provides opportunities for engineering of FKBP-binding metabolites and for probing new enzymology in nature's polyketide tailoring arsenal.
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Affiliation(s)
- Dana M Bis
- Chemistry Department, University of North Florida, 1 UNF Drive, Jacksonville, FL 32224 (USA)
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