1
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Mabesoone MFJ, Leopold-Messer S, Minas HA, Chepkirui C, Chawengrum P, Reiter S, Meoded RA, Wolf S, Genz F, Magnus N, Piechulla B, Walker AS, Piel J. Evolution-guided engineering of trans-acyltransferase polyketide synthases. Science 2024; 383:1312-1317. [PMID: 38513027 DOI: 10.1126/science.adj7621] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2023] [Accepted: 02/13/2024] [Indexed: 03/23/2024]
Abstract
Bacterial multimodular polyketide synthases (PKSs) are giant enzymes that generate a wide range of therapeutically important but synthetically challenging natural products. Diversification of polyketide structures can be achieved by engineering these enzymes. However, notwithstanding successes made with textbook cis-acyltransferase (cis-AT) PKSs, tailoring such large assembly lines remains challenging. Unlike textbook PKSs, trans-AT PKSs feature an extraordinary diversity of PKS modules and commonly evolve to form hybrid PKSs. In this study, we analyzed amino acid coevolution to identify a common module site that yields functional PKSs. We used this site to insert and delete diverse PKS parts and create 22 engineered trans-AT PKSs from various pathways and in two bacterial producers. The high success rates of our engineering approach highlight the broader applicability to generate complex designer polyketides.
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Affiliation(s)
- Mathijs F J Mabesoone
- Institute of Microbiology, Eidgenössische Technische Hochschule (ETH) Zürich, Vladimir-Prelog-Weg 4, 8093 Zürich, Switzerland
| | - Stefan Leopold-Messer
- Institute of Microbiology, Eidgenössische Technische Hochschule (ETH) Zürich, Vladimir-Prelog-Weg 4, 8093 Zürich, Switzerland
| | - Hannah A Minas
- Institute of Microbiology, Eidgenössische Technische Hochschule (ETH) Zürich, Vladimir-Prelog-Weg 4, 8093 Zürich, Switzerland
| | - Clara Chepkirui
- Institute of Microbiology, Eidgenössische Technische Hochschule (ETH) Zürich, Vladimir-Prelog-Weg 4, 8093 Zürich, Switzerland
| | - Pornsuda Chawengrum
- Institute of Microbiology, Eidgenössische Technische Hochschule (ETH) Zürich, Vladimir-Prelog-Weg 4, 8093 Zürich, Switzerland
- Chemical Biology Program, Chulabhorn Graduate Institute, Chulabhorn Royal Academy, Bangkok 10210, Thailand
| | - Silke Reiter
- Institute of Microbiology, Eidgenössische Technische Hochschule (ETH) Zürich, Vladimir-Prelog-Weg 4, 8093 Zürich, Switzerland
| | - Roy A Meoded
- Institute of Microbiology, Eidgenössische Technische Hochschule (ETH) Zürich, Vladimir-Prelog-Weg 4, 8093 Zürich, Switzerland
| | - Sarah Wolf
- Institute of Microbiology, Eidgenössische Technische Hochschule (ETH) Zürich, Vladimir-Prelog-Weg 4, 8093 Zürich, Switzerland
| | - Ferdinand Genz
- Institute of Microbiology, Eidgenössische Technische Hochschule (ETH) Zürich, Vladimir-Prelog-Weg 4, 8093 Zürich, Switzerland
| | - Nancy Magnus
- Institute for Biological Sciences, University of Rostock, Albert-Einstein-Straße 3, 18059 Rostock, Germany
| | - Birgit Piechulla
- Institute for Biological Sciences, University of Rostock, Albert-Einstein-Straße 3, 18059 Rostock, Germany
| | - Allison S Walker
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, 240 Longwood Avenue, Boston, MA 02115, USA
- Department of Chemistry, Vanderbilt University, 1234 Stevenson Center Lane, Nashville, TN 37240, USA
- Department of Biological Sciences, Vanderbilt University, 465 21st Avenue S, Nashville, TN 37232, USA
| | - Jörn Piel
- Institute of Microbiology, Eidgenössische Technische Hochschule (ETH) Zürich, Vladimir-Prelog-Weg 4, 8093 Zürich, Switzerland
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2
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Ogonkov A, Dieterich CL, Meoded RA, Piel J, Fraley AE, Sasso S. Characterization of an Unusual α-Oxoamine Synthase Off-Loading Domain from a Cyanobacterial Type I Fatty Acid Synthase. Chembiochem 2023; 24:e202300209. [PMID: 37144248 DOI: 10.1002/cbic.202300209] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2023] [Revised: 05/03/2023] [Accepted: 05/04/2023] [Indexed: 05/06/2023]
Abstract
Type I fatty acid synthases (FASs) are known from higher eukaryotes and fungi. We report the discovery of FasT, a rare type I FAS from the cyanobacterium Chlorogloea sp. CCALA695. FasT possesses an unusual off-loading domain, which was heterologously expressed in E. coli and found to act as an α-oxoamine synthase (AOS) in vitro. Similar to serine palmitoyltransferases from sphingolipid biosynthesis, the AOS off-loading domain catalyzes a decarboxylative Claisen condensation between l-serine and a fatty acyl thioester. While the AOS domain was strictly specific for l-serine, thioesters with saturated fatty acyl chains of six carbon atoms and longer were tolerated, with the highest activity observed for stearoyl-coenzyme A (C18 ). Our findings suggest a novel route to α-amino ketones via the direct condensation of iteratively produced long-chain fatty acids with l-serine by a FAS with a cis-acting AOS off-loading domain.
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Affiliation(s)
- Andrei Ogonkov
- Department of Biology, Institute of Microbiology, ETH Zurich, Vladimir-Prelog-Weg 4, 8093, Zurich, Switzerland
- Institute of Biology, Leipzig University, Johannisallee 23, 04107, Leipzig, Germany
| | - Cora L Dieterich
- Department of Biology, Institute of Microbiology, ETH Zurich, Vladimir-Prelog-Weg 4, 8093, Zurich, Switzerland
| | - Roy A Meoded
- Department of Biology, Institute of Microbiology, ETH Zurich, Vladimir-Prelog-Weg 4, 8093, Zurich, Switzerland
| | - Jörn Piel
- Department of Biology, Institute of Microbiology, ETH Zurich, Vladimir-Prelog-Weg 4, 8093, Zurich, Switzerland
| | - Amy E Fraley
- Department of Biology, Institute of Microbiology, ETH Zurich, Vladimir-Prelog-Weg 4, 8093, Zurich, Switzerland
| | - Severin Sasso
- Institute of Biology, Leipzig University, Johannisallee 23, 04107, Leipzig, Germany
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3
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Minas HA, François RMM, Hemmerling F, Fraley AE, Dieterich CL, Rüdisser SH, Meoded RA, Collin S, Weissman KJ, Gruez A, Piel J. Modular Oxime Formation by a trans-AT Polyketide Synthase. Angew Chem Int Ed Engl 2023; 62:e202304481. [PMID: 37216334 DOI: 10.1002/anie.202304481] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2023] [Revised: 05/16/2023] [Accepted: 05/22/2023] [Indexed: 05/24/2023]
Abstract
Modular trans-acyltransferase polyketide synthases (trans-AT PKSs) are enzymatic assembly lines that biosynthesize complex polyketide natural products. Relative to their better studied cis-AT counterparts, the trans-AT PKSs introduce remarkable chemical diversity into their polyketide products. A notable example is the lobatamide A PKS, which incorporates a methylated oxime. Here we demonstrate biochemically that this functionality is installed on-line by an unusual oxygenase-containing bimodule. Furthermore, analysis of the oxygenase crystal structure coupled with site-directed mutagenesis allows us to propose a model for catalysis, as well as identifying key protein-protein interactions that support this chemistry. Overall, our work adds oxime-forming machinery to the biomolecular toolbox available for trans-AT PKS engineering, opening the way to introducing such masked aldehyde functionalities into diverse polyketides.
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Affiliation(s)
- Hannah A Minas
- Institute of Microbiology, Eidgenössische Technische Hochschule (ETH) Zürich, Vladimir-Prelog-Weg 4, 8093, Zürich, Switzerland
| | - Romain M M François
- Institute of Microbiology, Eidgenössische Technische Hochschule (ETH) Zürich, Vladimir-Prelog-Weg 4, 8093, Zürich, Switzerland
- Université de Lorraine, CNRS, IMoPA, 54000, Nancy, France
| | - Franziska Hemmerling
- Institute of Microbiology, Eidgenössische Technische Hochschule (ETH) Zürich, Vladimir-Prelog-Weg 4, 8093, Zürich, Switzerland
| | - Amy E Fraley
- Institute of Microbiology, Eidgenössische Technische Hochschule (ETH) Zürich, Vladimir-Prelog-Weg 4, 8093, Zürich, Switzerland
| | - Cora L Dieterich
- Institute of Microbiology, Eidgenössische Technische Hochschule (ETH) Zürich, Vladimir-Prelog-Weg 4, 8093, Zürich, Switzerland
| | - Simon H Rüdisser
- Institute of Molecular Biology and Biophysics, Biomolecular NMR Spectroscopy Platform, Eidgenössische Technische Hochschule (ETH) Zürich, Hönggerbergring 64, 8093, Zürich, Switzerland
| | - Roy A Meoded
- Institute of Microbiology, Eidgenössische Technische Hochschule (ETH) Zürich, Vladimir-Prelog-Weg 4, 8093, Zürich, Switzerland
| | - Sabrina Collin
- Université de Lorraine, CNRS, IMoPA, 54000, Nancy, France
| | | | - Arnaud Gruez
- Université de Lorraine, CNRS, IMoPA, 54000, Nancy, France
| | - Jörn Piel
- Institute of Microbiology, Eidgenössische Technische Hochschule (ETH) Zürich, Vladimir-Prelog-Weg 4, 8093, Zürich, Switzerland
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4
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Fraley AE, Dell M, Schmalhofer M, Meoded RA, Bergande C, Groll M, Piel J. Heterocomplex structure of a polyketide synthase component involved in modular backbone halogenation. Structure 2023; 31:565-572.e4. [PMID: 36917986 DOI: 10.1016/j.str.2023.02.010] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2022] [Revised: 12/14/2022] [Accepted: 02/15/2023] [Indexed: 03/14/2023]
Abstract
Bacterial modular polyketide synthases (PKSs) generate diverse, complex and bioactive natural products that are constructed mainly based on principles of fatty acid biosynthesis. The cytotoxic oocydin-type polyketides contain a vinyl chloride moiety introduced during polyketide chain elongation. Required for modular polyketide backbone halogenation are a non-heme iron and ɑ-ketoglutarate-dependent halogenase OocP and OocQ lacking characterized homologs. This work provides structural insights into these unusual PKS components and their interactions via a high-resolution X-ray crystallography structure of the heterocomplex. By mapping the protein-protein interactions and comparison with structures of similar halogenases, we illustrate the potential of this heterodimer complex as a replacement for the conserved homodimeric structure of homologous enzymes. The OocPQ protein pair has thus evolved as a means of stabilizing the halogenase and facilitating chemical transformations with great synthetic utility.
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Affiliation(s)
- Amy E Fraley
- Institute of Microbiology, Eidgenössische Technische Hochschule (ETH) Zurich, Zurich, Switzerland
| | - Maria Dell
- Institute of Microbiology, Eidgenössische Technische Hochschule (ETH) Zurich, Zurich, Switzerland
| | - Maximilian Schmalhofer
- Chair of Biochemistry, Center for Protein Assemblies, Technical University of Munich, Ernst-Otto-Fischer-Strasse 8, 85748 Garching, Germany
| | - Roy A Meoded
- Institute of Microbiology, Eidgenössische Technische Hochschule (ETH) Zurich, Zurich, Switzerland
| | - Cedric Bergande
- Institute of Microbiology, Eidgenössische Technische Hochschule (ETH) Zurich, Zurich, Switzerland
| | - Michael Groll
- Chair of Biochemistry, Center for Protein Assemblies, Technical University of Munich, Ernst-Otto-Fischer-Strasse 8, 85748 Garching, Germany
| | - Jörn Piel
- Institute of Microbiology, Eidgenössische Technische Hochschule (ETH) Zurich, Zurich, Switzerland.
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5
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Fraley AE, Dieterich CL, Mabesoone MFJ, Minas HA, Meoded RA, Hemmerling F, Piel J. Structure of a Promiscuous Thioesterase Domain Responsible for Branching Acylation in Polyketide Biosynthesis. Angew Chem Int Ed Engl 2022; 61:e202206385. [DOI: 10.1002/anie.202206385] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2022] [Indexed: 11/08/2022]
Affiliation(s)
- Amy E. Fraley
- Department of Biology, Institute of Microbiology Eidgenössische Technische Hochschule (ETH) Zurich Vladimir-Prelog-Weg 4 8093 Zurich Switzerland
| | - Cora L. Dieterich
- Department of Biology, Institute of Microbiology Eidgenössische Technische Hochschule (ETH) Zurich Vladimir-Prelog-Weg 4 8093 Zurich Switzerland
| | - Mathijs F. J. Mabesoone
- Department of Biology, Institute of Microbiology Eidgenössische Technische Hochschule (ETH) Zurich Vladimir-Prelog-Weg 4 8093 Zurich Switzerland
| | - Hannah A. Minas
- Department of Biology, Institute of Microbiology Eidgenössische Technische Hochschule (ETH) Zurich Vladimir-Prelog-Weg 4 8093 Zurich Switzerland
| | - Roy A Meoded
- Department of Biology, Institute of Microbiology Eidgenössische Technische Hochschule (ETH) Zurich Vladimir-Prelog-Weg 4 8093 Zurich Switzerland
| | - Franziska Hemmerling
- Department of Biology, Institute of Microbiology Eidgenössische Technische Hochschule (ETH) Zurich Vladimir-Prelog-Weg 4 8093 Zurich Switzerland
| | - Jörn Piel
- Department of Biology, Institute of Microbiology Eidgenössische Technische Hochschule (ETH) Zurich Vladimir-Prelog-Weg 4 8093 Zurich Switzerland
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6
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Fraley AE, Dieterich C, Mabesoone M, Minas HA, Meoded RA, Hemmerling F, Piel J. Structure of a promiscuous thioesterase domain responsible for branching acylation in polyketide biosynthesis. Angew Chem Int Ed Engl 2022. [DOI: 10.1002/ange.202206385] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Affiliation(s)
- Amy E. Fraley
- Eidgenossische Technische Hochschule Zurich Institute of Microbiology SWITZERLAND
| | - Cora Dieterich
- Eidgenossische Technische Hochschule Zurich Institute of Microbiology SWITZERLAND
| | - Mathijs Mabesoone
- Eidgenossische Technische Hochschule Zurich Institute of Microbiology SWITZERLAND
| | - Hannah A. Minas
- Eidgenossische Technische Hochschule Zurich Institute of Microbiology SWITZERLAND
| | - Roy A. Meoded
- Eidgenossische Technische Hochschule Zurich Institute of Microbiology SWITZERLAND
| | - Franziska Hemmerling
- Eidgenossische Technische Hochschule Zurich Institute of Microbiology SWITZERLAND
| | - Jörn Piel
- ETH Zürich Department of Biology Vladimir-Prelog-Weg 4 8093 Zürich SWITZERLAND
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7
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Hemmerling F, Meoded RA, Fraley AE, Minas HA, Dieterich CL, Rust M, Ueoka R, Jensen K, Helfrich EJN, Bergande C, Biedermann M, Magnus N, Piechulla B, Piel J. Modular Halogenation, α-Hydroxylation, and Acylation by a Remarkably Versatile Polyketide Synthase. Angew Chem Int Ed Engl 2022; 61:e202116614. [PMID: 35020279 DOI: 10.1002/anie.202116614] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2021] [Indexed: 12/14/2022]
Abstract
Bacterial multimodular polyketide synthases (PKSs) are large enzymatic assembly lines that synthesize many bioactive natural products of therapeutic relevance. While PKS catalysis is mostly based on fatty acid biosynthetic principles, polyketides can be further diversified by post-PKS enzymes. Here, we characterized a remarkably versatile trans-acyltransferase (trans-AT) PKS from Serratia that builds structurally complex macrolides via more than ten functionally distinct PKS modules. In the oocydin PKS, we identified a new oxygenation module that α-hydroxylates polyketide intermediates, a halogenating module catalyzing backbone γ-chlorination, and modular O-acetylation by a thioesterase-like domain. These results from a single biosynthetic assembly line highlight the expansive biochemical repertoire of trans-AT PKSs and provide diverse modular tools for engineered biosynthesis from a close relative of E. coli.
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Affiliation(s)
- Franziska Hemmerling
- Institute of Microbiology, Eidgenössische Technische Hochschule (ETH) Zurich, Vladimir-Prelog-Weg 4, 8093, Zurich, Switzerland
| | - Roy A Meoded
- Institute of Microbiology, Eidgenössische Technische Hochschule (ETH) Zurich, Vladimir-Prelog-Weg 4, 8093, Zurich, Switzerland
| | - Amy E Fraley
- Institute of Microbiology, Eidgenössische Technische Hochschule (ETH) Zurich, Vladimir-Prelog-Weg 4, 8093, Zurich, Switzerland
| | - Hannah A Minas
- Institute of Microbiology, Eidgenössische Technische Hochschule (ETH) Zurich, Vladimir-Prelog-Weg 4, 8093, Zurich, Switzerland
| | - Cora L Dieterich
- Institute of Microbiology, Eidgenössische Technische Hochschule (ETH) Zurich, Vladimir-Prelog-Weg 4, 8093, Zurich, Switzerland
| | - Michael Rust
- Institute of Microbiology, Eidgenössische Technische Hochschule (ETH) Zurich, Vladimir-Prelog-Weg 4, 8093, Zurich, Switzerland
| | - Reiko Ueoka
- Institute of Microbiology, Eidgenössische Technische Hochschule (ETH) Zurich, Vladimir-Prelog-Weg 4, 8093, Zurich, Switzerland.,School of Marine Bioscience, Kitasato University, 1-15-1, Kitazato, Minami-ku, Sagamirhara-shi Kanagawa, 252-0373, Japan
| | - Katja Jensen
- Institute of Microbiology, Eidgenössische Technische Hochschule (ETH) Zurich, Vladimir-Prelog-Weg 4, 8093, Zurich, Switzerland
| | - Eric J N Helfrich
- Institute of Microbiology, Eidgenössische Technische Hochschule (ETH) Zurich, Vladimir-Prelog-Weg 4, 8093, Zurich, Switzerland.,Institute of Molecular Bio Science, Goethe University Frankfurt, Max-von-Laue-Str. 9, 60438, Frankfurt am Main, Germany.,LOEWE Center for Translational Biodiversity Genomics (TBG), Senckenberganlage 25, 60325, Frankfurt am Main, Germany
| | - Cedric Bergande
- Institute of Microbiology, Eidgenössische Technische Hochschule (ETH) Zurich, Vladimir-Prelog-Weg 4, 8093, Zurich, Switzerland
| | - Maurice Biedermann
- Institute of Microbiology, Eidgenössische Technische Hochschule (ETH) Zurich, Vladimir-Prelog-Weg 4, 8093, Zurich, Switzerland
| | - Nancy Magnus
- Institute for Biological Sciences, University of Rostock, Albert-Einstein-Straße 3, 18059, Rostock, Germany
| | - Birgit Piechulla
- Institute for Biological Sciences, University of Rostock, Albert-Einstein-Straße 3, 18059, Rostock, Germany
| | - Jörn Piel
- Institute of Microbiology, Eidgenössische Technische Hochschule (ETH) Zurich, Vladimir-Prelog-Weg 4, 8093, Zurich, Switzerland
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8
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Ueoka R, Meoded RA, Gran‐Scheuch A, Bhushan A, Fraaije MW, Piel J. Corrigendum: Genome Mining of Oxidation Modules in
trans
‐Acyltransferase Polyketide Synthases Reveals a Culturable Source for Lobatamides. Angew Chem Int Ed Engl 2020; 59:11698. [DOI: 10.1002/anie.202007393] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
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9
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Ueoka R, Meoded RA, Gran‐Scheuch A, Bhushan A, Fraaije MW, Piel J. Berichtigung: Genome Mining of Oxidation Modules in
trans
‐Acyltransferase Polyketide Synthases Reveals a Culturable Source for Lobatamides. Angew Chem Int Ed Engl 2020. [DOI: 10.1002/ange.202007393] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
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10
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Ueoka R, Meoded RA, Gran‐Scheuch A, Bhushan A, Fraaije MW, Piel J. Genome Mining of Oxidation Modules in
trans
‐Acyltransferase Polyketide Synthases Reveals a Culturable Source for Lobatamides. Angew Chem Int Ed Engl 2020. [DOI: 10.1002/ange.201916005] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
Affiliation(s)
- Reiko Ueoka
- Institute of Microbiology ETH Zurich Vladimir-Prelog-Weg 4 8093 Zurich Switzerland
| | - Roy A. Meoded
- Institute of Microbiology ETH Zurich Vladimir-Prelog-Weg 4 8093 Zurich Switzerland
| | - Alejandro Gran‐Scheuch
- Molecular Enzymology Group University of Groningen Nijenborgh 4 9747AG Groningen The Netherlands
- Department of Chemical and Bioprocesses Engineering Pontificia Universidad Católica de Chile Avenida Vicuña Mackenna 4860 7820436 Santiago Chile
| | - Agneya Bhushan
- Institute of Microbiology ETH Zurich Vladimir-Prelog-Weg 4 8093 Zurich Switzerland
| | - Marco W. Fraaije
- Molecular Enzymology Group University of Groningen Nijenborgh 4 9747AG Groningen The Netherlands
| | - Jörn Piel
- Institute of Microbiology ETH Zurich Vladimir-Prelog-Weg 4 8093 Zurich Switzerland
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11
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Ueoka R, Meoded RA, Gran‐Scheuch A, Bhushan A, Fraaije MW, Piel J. Genome Mining of Oxidation Modules in trans-Acyltransferase Polyketide Synthases Reveals a Culturable Source for Lobatamides. Angew Chem Int Ed Engl 2020; 59:7761-7765. [PMID: 32040255 PMCID: PMC7586987 DOI: 10.1002/anie.201916005] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2019] [Indexed: 11/22/2022]
Abstract
Bacterial trans-acyltransferase polyketide synthases (trans-AT PKSs) are multimodular megaenzymes that biosynthesize many bioactive natural products. They contain a remarkable range of domains and module types that introduce different substituents into growing polyketide chains. As one such modification, we recently reported Baeyer-Villiger-type oxygen insertion into nascent polyketide backbones, thereby generating malonyl thioester intermediates. In this work, genome mining focusing on architecturally diverse oxidation modules in trans-AT PKSs led us to the culturable plant symbiont Gynuella sunshinyii, which harbors two distinct modules in one orphan PKS. The PKS product was revealed to be lobatamide A, a potent cytotoxin previously only known from a marine tunicate. Biochemical studies show that one module generates glycolyl thioester intermediates, while the other is proposed to be involved in oxime formation. The data suggest varied roles of oxygenation modules in the biosynthesis of polyketide scaffolds and support the importance of trans-AT PKSs in the specialized metabolism of symbiotic bacteria.
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Affiliation(s)
- Reiko Ueoka
- Institute of MicrobiologyETH ZurichVladimir-Prelog-Weg 48093ZurichSwitzerland
| | - Roy A. Meoded
- Institute of MicrobiologyETH ZurichVladimir-Prelog-Weg 48093ZurichSwitzerland
| | - Alejandro Gran‐Scheuch
- Molecular Enzymology GroupUniversity of GroningenNijenborgh 49747AGGroningenThe Netherlands
- Department of Chemical and Bioprocesses EngineeringPontificia Universidad Católica de ChileAvenida Vicuña Mackenna 48607820436SantiagoChile
| | - Agneya Bhushan
- Institute of MicrobiologyETH ZurichVladimir-Prelog-Weg 48093ZurichSwitzerland
| | - Marco W. Fraaije
- Molecular Enzymology GroupUniversity of GroningenNijenborgh 49747AGGroningenThe Netherlands
| | - Jörn Piel
- Institute of MicrobiologyETH ZurichVladimir-Prelog-Weg 48093ZurichSwitzerland
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12
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Helfrich EJN, Ueoka R, Dolev A, Rust M, Meoded RA, Bhushan A, Califano G, Costa R, Gugger M, Steinbeck C, Moreno P, Piel J. Automated structure prediction of trans-acyltransferase polyketide synthase products. Nat Chem Biol 2019; 15:813-821. [PMID: 31308532 PMCID: PMC6642696 DOI: 10.1038/s41589-019-0313-7] [Citation(s) in RCA: 79] [Impact Index Per Article: 15.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2018] [Accepted: 05/23/2019] [Indexed: 12/01/2022]
Abstract
Bacterial trans-acyltransferase polyketide synthases (trans-AT PKSs) are among the most complex known enzymes from secondary metabolism and are responsible for the biosynthesis of highly diverse bioactive polyketides. However, most of these metabolites remain uncharacterized, since trans-AT PKSs frequently occur in poorly studied microbes and feature a remarkable array of non-canonical biosynthetic components with poorly understood functions. As a consequence, genome-guided natural product identification has been challenging. To enable de novo structural predictions for trans-AT PKS-derived polyketides, we developed the trans-AT PKS polyketide predictor (TransATor). TransATor is a versatile bio- and chemoinformatics web application that suggests informative chemical structures for even highly aberrant trans-AT PKS biosynthetic gene clusters, thus permitting hypothesis-based, targeted biotechnological discovery and biosynthetic studies. We demonstrate the applicative scope in several examples, including the characterization of new variants of bioactive natural products as well as structurally new polyketides from unusual bacterial sources.
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Affiliation(s)
- Eric J N Helfrich
- Institute of Microbiology, Eidgenössische Technische Hochschule Zürich, Zurich, Switzerland
| | - Reiko Ueoka
- Institute of Microbiology, Eidgenössische Technische Hochschule Zürich, Zurich, Switzerland
| | - Alon Dolev
- Institute of Microbiology, Eidgenössische Technische Hochschule Zürich, Zurich, Switzerland
| | - Michael Rust
- Institute of Microbiology, Eidgenössische Technische Hochschule Zürich, Zurich, Switzerland
| | - Roy A Meoded
- Institute of Microbiology, Eidgenössische Technische Hochschule Zürich, Zurich, Switzerland
| | - Agneya Bhushan
- Institute of Microbiology, Eidgenössische Technische Hochschule Zürich, Zurich, Switzerland
| | - Gianmaria Califano
- Centre of Marine Sciences, University of Algarve, Faro, Portugal
- Institute for Inorganic and Analytical Chemistry, Friedrich-Schiller-Universität Jena, Jena, Germany
| | - Rodrigo Costa
- Centre of Marine Sciences, University of Algarve, Faro, Portugal
- Institute for Bioengineering and Biosciences, Instituto Superior Técnico, Universidade de Lisboa, Lisbon, Portugal
| | - Muriel Gugger
- Institut Pasteur, Collection des Cyanobactéries, Paris, France
| | - Christoph Steinbeck
- Institute for Inorganic and Analytical Chemistry, Friedrich-Schiller-Universität Jena, Jena, Germany
- European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton Cambridge, UK
| | - Pablo Moreno
- European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton Cambridge, UK.
| | - Jörn Piel
- Institute of Microbiology, Eidgenössische Technische Hochschule Zürich, Zurich, Switzerland.
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13
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Meoded RA, Ueoka R, Helfrich EJN, Jensen K, Magnus N, Piechulla B, Piel J. A Polyketide Synthase Component for Oxygen Insertion into Polyketide Backbones. Angew Chem Int Ed Engl 2018; 57:11644-11648. [PMID: 29898240 PMCID: PMC6174933 DOI: 10.1002/anie.201805363] [Citation(s) in RCA: 30] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2018] [Revised: 06/08/2018] [Indexed: 12/31/2022]
Abstract
Enzymatic core components from trans-acyltransferase polyketide synthases (trans-AT PKSs) catalyze exceptionally diverse biosynthetic transformations to generate structurally complex bioactive compounds. Here we focus on a group of oxygenases identified in various trans-AT PKS pathways, including those for pederin, oocydins, and toblerols. Using the oocydin pathway homologue (OocK) from Serratia plymuthica 4Rx13 and N-acetylcysteamine (SNAC) thioesters as test surrogates for acyl carrier protein (ACP)-tethered intermediates, we show that the enzyme inserts oxygen into β-ketoacyl moieties to yield malonyl ester SNAC products. Based on these data and the identification of a non-hydrolyzed oocydin congener with retained ester moiety, we propose a unified biosynthetic pathway of oocydins, haterumalides, and biselides. By providing access to internal ester, carboxylate pseudostarter, and terminal hydroxyl functions, oxygen insertion into polyketide backbones greatly expands the biosynthetic scope of PKSs.
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Affiliation(s)
- Roy A. Meoded
- Institute of MicrobiologyEigenössische Technische Hochschule (ETH) ZurichVladimir-Prelog-Weg 48093ZurichSwitzerland
| | - Reiko Ueoka
- Institute of MicrobiologyEigenössische Technische Hochschule (ETH) ZurichVladimir-Prelog-Weg 48093ZurichSwitzerland
| | - Eric J. N. Helfrich
- Institute of MicrobiologyEigenössische Technische Hochschule (ETH) ZurichVladimir-Prelog-Weg 48093ZurichSwitzerland
| | - Katja Jensen
- Institute of MicrobiologyEigenössische Technische Hochschule (ETH) ZurichVladimir-Prelog-Weg 48093ZurichSwitzerland
| | - Nancy Magnus
- Institute for Biological SciencesUniversity of RostockAlbert-Einstein-Straße 318059RostockGermany
| | - Birgit Piechulla
- Institute for Biological SciencesUniversity of RostockAlbert-Einstein-Straße 318059RostockGermany
| | - Jörn Piel
- Institute of MicrobiologyEigenössische Technische Hochschule (ETH) ZurichVladimir-Prelog-Weg 48093ZurichSwitzerland
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14
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Meoded RA, Ueoka R, Helfrich EJN, Jensen K, Magnus N, Piechulla B, Piel J. A Polyketide Synthase Component for Oxygen Insertion into Polyketide Backbones. Angew Chem Int Ed Engl 2018. [DOI: 10.1002/ange.201805363] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/23/2023]
Affiliation(s)
- Roy A. Meoded
- Institute of Microbiology; Eigenössische Technische Hochschule (ETH) Zurich; Vladimir-Prelog-Weg 4 8093 Zurich Switzerland
| | - Reiko Ueoka
- Institute of Microbiology; Eigenössische Technische Hochschule (ETH) Zurich; Vladimir-Prelog-Weg 4 8093 Zurich Switzerland
| | - Eric J. N. Helfrich
- Institute of Microbiology; Eigenössische Technische Hochschule (ETH) Zurich; Vladimir-Prelog-Weg 4 8093 Zurich Switzerland
| | - Katja Jensen
- Institute of Microbiology; Eigenössische Technische Hochschule (ETH) Zurich; Vladimir-Prelog-Weg 4 8093 Zurich Switzerland
| | - Nancy Magnus
- Institute for Biological Sciences; University of Rostock; Albert-Einstein-Straße 3 18059 Rostock Germany
| | - Birgit Piechulla
- Institute for Biological Sciences; University of Rostock; Albert-Einstein-Straße 3 18059 Rostock Germany
| | - Jörn Piel
- Institute of Microbiology; Eigenössische Technische Hochschule (ETH) Zurich; Vladimir-Prelog-Weg 4 8093 Zurich Switzerland
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15
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Wagner DT, Zhang Z, Meoded RA, Cepeda AJ, Piel J, Keatinge-Clay AT. Structural and Functional Studies of a Pyran Synthase Domain from a trans-Acyltransferase Assembly Line. ACS Chem Biol 2018; 13:975-983. [PMID: 29481043 DOI: 10.1021/acschembio.8b00049] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
trans-Acyltransferase assembly lines possess enzymatic domains often not observed in their better characterized cis-acyltransferase counterparts. Within this repertoire of largely unexplored biosynthetic machinery is a class of enzymes called the pyran synthases that catalyze the formation of five- and six-membered cyclic ethers from diverse polyketide chains. The 1.55 Å resolution crystal structure of a pyran synthase domain excised from the ninth module of the sorangicin assembly line highlights the similarity of this enzyme to the ubiquitous dehydratase domain and provides insight into the mechanism of ring formation. Functional assays of point mutants reveal the central importance of the active site histidine that is shared with the dehydratases as well as the supporting role of a neighboring semiconserved asparagine.
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Affiliation(s)
- Drew T. Wagner
- Department of Molecular Biosciences, The University of Texas at Austin, Austin, Texas 78712, United States
| | - Zhicheng Zhang
- Department of Chemistry, The University of Texas at Austin, Austin, Texas 78712, United States
| | - Roy A. Meoded
- Institut für Mikrobiologie, Eidgenössiche Technische Hochschule (ETH) Zürich, Vladimir-Prelog-Weg 4, 8093 Zürich, Switzerland
| | - Alexis J. Cepeda
- Department of Molecular Biosciences, The University of Texas at Austin, Austin, Texas 78712, United States
| | - Jörn Piel
- Institut für Mikrobiologie, Eidgenössiche Technische Hochschule (ETH) Zürich, Vladimir-Prelog-Weg 4, 8093 Zürich, Switzerland
| | - Adrian T. Keatinge-Clay
- Department of Molecular Biosciences, The University of Texas at Austin, Austin, Texas 78712, United States
- Department of Chemistry, The University of Texas at Austin, Austin, Texas 78712, United States
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16
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Abstract
Thiamin analogs were used to synthesize mono gold(i)-carbene derivatives in a single step under aqueous conditions. The resulting thiazolium gold(i)-carbenes catalyze 5-endo-dig carbocyclization of an acetylenic dicarbonyl compound in organic solvents and hydroalkoxylation of an allene in aqueous buffer.
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Affiliation(s)
- Clément C Dince
- Laboratory of Organic Chemistry, Department of Chemistry and Applied Biosciences, ETH Zürich, CH-8093, Switzerland.
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