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Su L, Souaibou Y, Hôtel L, Paris C, Weissman KJ, Aigle B. Biosynthesis of novel desferrioxamine derivatives requires unprecedented crosstalk between separate NRPS-independent siderophore pathways. Appl Environ Microbiol 2024; 90:e0211523. [PMID: 38323847 PMCID: PMC10952394 DOI: 10.1128/aem.02115-23] [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] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2023] [Accepted: 12/13/2023] [Indexed: 02/08/2024] Open
Abstract
Iron is essential to many biological processes but its poor solubility in aerobic environments restricts its bioavailability. To overcome this limitation, bacteria have evolved a variety of strategies, including the production and secretion of iron-chelating siderophores. Here, we describe the discovery of four series of siderophores from Streptomyces ambofaciens ATCC23877, three of which are unprecedented. MS/MS-based molecular networking revealed that one of these series corresponds to acylated desferrioxamines (acyl-DFOs) recently identified from S. coelicolor. The remaining sets include tetra- and penta-hydroxamate acyl-DFO derivatives, all of which incorporate a previously undescribed building block. Stable isotope labeling and gene deletion experiments provide evidence that biosynthesis of the acyl-DFO congeners requires unprecedented crosstalk between two separate non-ribosomal peptide synthetase (NRPS)-independent siderophore (NIS) pathways in the producing organism. Although the biological role(s) of these new derivatives remain to be elucidated, they may confer advantages in terms of metal chelation in the competitive soil environment due to the additional bidentate hydroxamic functional groups. The metabolites may also find application in various fields including biotechnology, bioremediation, and immuno-PET imaging.IMPORTANCEIron-chelating siderophores play important roles for their bacterial producers in the environment, but they have also found application in human medicine both in iron chelation therapy to prevent iron overload and in diagnostic imaging, as well as in biotechnology, including as agents for biocontrol of pathogens and bioremediation. In this study, we report the discovery of three novel series of related siderophores, whose biosynthesis depends on the interplay between two NRPS-independent (NIS) pathways in the producing organism S. ambofaciens-the first example to our knowledge of such functional cross-talk. We further reveal that two of these series correspond to acyl-desferrioxamines which incorporate four or five hydroxamate units. Although the biological importance of these novel derivatives is unknown, the increased chelating capacity of these metabolites may find utility in diagnostic imaging (for instance, 89Zr-based immuno-PET imaging) and other applications of metal chelators.
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Affiliation(s)
- Li Su
- Université de Lorraine, INRAE, DynAMic, Nancy, France
- Université de Lorraine, CNRS, IMoPA, Nancy, France
| | - Yaouba Souaibou
- Université de Lorraine, INRAE, DynAMic, Nancy, France
- Université de Lorraine, CNRS, IMoPA, Nancy, France
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2
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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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3
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Su L, Hôtel L, Paris C, Chepkirui C, Brachmann AO, Piel J, Jacob C, Aigle B, Weissman KJ. Author Correction: Engineering the stambomycin modular polyketide synthase yields 37-membered mini-stambomycins. Nat Commun 2022; 13:5896. [PMID: 36202861 PMCID: PMC9537511 DOI: 10.1038/s41467-022-33524-1] [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] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022] Open
Affiliation(s)
- Li Su
- Université de Lorraine, CNRS, IMoPA, F-54000, Nancy, France.,Université de Lorraine, INRAE, DynAMic, F-54000, Nancy, France.,Max-Planck-Institute for Terrestrial Microbiology, Department of Natural Products in Organismic Interactions, 35043, Marburg, Germany
| | - Laurence Hôtel
- Université de Lorraine, INRAE, DynAMic, F-54000, Nancy, France
| | - Cédric Paris
- Université de Lorraine, LIBio, F-54000, Nancy, France
| | - Clara Chepkirui
- Institute of Microbiology, Eidgenössische Technische Hochschule (ETH) Zurich, 8093, Zurich, Switzerland
| | - Alexander O Brachmann
- Institute of Microbiology, Eidgenössische Technische Hochschule (ETH) Zurich, 8093, Zurich, Switzerland
| | - Jörn Piel
- Institute of Microbiology, Eidgenössische Technische Hochschule (ETH) Zurich, 8093, Zurich, Switzerland
| | | | - Bertrand Aigle
- Université de Lorraine, INRAE, DynAMic, F-54000, Nancy, France.
| | - Kira J Weissman
- Université de Lorraine, CNRS, IMoPA, F-54000, Nancy, France.
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4
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Massicard JM, Su L, Jacob C, Weissman KJ. Engineering Modular Polyketide Biosynthesis in Streptomyces Using CRISPR/Cas: A Practical Guide. Methods Mol Biol 2022; 2489:173-200. [PMID: 35524051 DOI: 10.1007/978-1-0716-2273-5_10] [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] [Indexed: 06/14/2023]
Abstract
The CRISPR/Cas system, which has been widely applied to organisms ranging from microbes to animals, is currently being adapted for use in Streptomyces bacteria. In this case, it is notably applied to rationally modify the biosynthetic pathways giving rise to the polyketide natural products, which are heavily exploited in the medical and agricultural arenas. Our aim here is to provide the potential user with a practical guide to exploit this approach for manipulating polyketide biosynthesis, by treating key experimental aspects including vector choice, design of the basic engineering components, and trouble-shooting.
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Affiliation(s)
- Jean-Malo Massicard
- Molecular and Structural Enzymology Group, UMR 7365 CNRS-UL IMoPA, Lorraine University, Faculté de médecine, Batiment Biopôle, Vandœuvre-lès-Nancy Cedex, France
| | - Li Su
- Molecular and Structural Enzymology Group, UMR 7365 CNRS-UL IMoPA, Lorraine University, Faculté de médecine, Batiment Biopôle, Vandœuvre-lès-Nancy Cedex, France
| | - Christophe Jacob
- Molecular and Structural Enzymology Group, UMR 7365 CNRS-UL IMoPA, Lorraine University, Faculté de médecine, Batiment Biopôle, Vandœuvre-lès-Nancy Cedex, France.
| | - Kira J Weissman
- Molecular and Structural Enzymology Group, UMR 7365 CNRS-UL IMoPA, Lorraine University, Faculté de médecine, Batiment Biopôle, Vandœuvre-lès-Nancy Cedex, France.
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5
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Miethke M, Pieroni M, Weber T, Brönstrup M, Hammann P, Halby L, Arimondo PB, Glaser P, Aigle B, Bode HB, Moreira R, Li Y, Luzhetskyy A, Medema MH, Pernodet JL, Stadler M, Tormo JR, Genilloud O, Truman AW, Weissman KJ, Takano E, Sabatini S, Stegmann E, Brötz-Oesterhelt H, Wohlleben W, Seemann M, Empting M, Hirsch AKH, Loretz B, Lehr CM, Titz A, Herrmann J, Jaeger T, Alt S, Hesterkamp T, Winterhalter M, Schiefer A, Pfarr K, Hoerauf A, Graz H, Graz M, Lindvall M, Ramurthy S, Karlén A, van Dongen M, Petkovic H, Keller A, Peyrane F, Donadio S, Fraisse L, Piddock LJV, Gilbert IH, Moser HE, Müller R. Towards the sustainable discovery and development of new antibiotics. Nat Rev Chem 2021; 5:726-749. [PMID: 37118182 PMCID: PMC8374425 DOI: 10.1038/s41570-021-00313-1] [Citation(s) in RCA: 350] [Impact Index Per Article: 116.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 07/01/2021] [Indexed: 02/08/2023]
Abstract
An ever-increasing demand for novel antimicrobials to treat life-threatening infections caused by the global spread of multidrug-resistant bacterial pathogens stands in stark contrast to the current level of investment in their development, particularly in the fields of natural-product-derived and synthetic small molecules. New agents displaying innovative chemistry and modes of action are desperately needed worldwide to tackle the public health menace posed by antimicrobial resistance. Here, our consortium presents a strategic blueprint to substantially improve our ability to discover and develop new antibiotics. We propose both short-term and long-term solutions to overcome the most urgent limitations in the various sectors of research and funding, aiming to bridge the gap between academic, industrial and political stakeholders, and to unite interdisciplinary expertise in order to efficiently fuel the translational pipeline for the benefit of future generations. ![]()
Antimicrobial resistance is an increasing threat to public health and encouraging the development of new antimicrobials is one of the most important ways to address the problem. This Roadmap article aims to bring together industrial, academic and political partners, and proposes both short-term and long-term solutions to this challenge.
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Affiliation(s)
- Marcus Miethke
- Helmholtz Institute for Pharmaceutical Research Saarland (HIPS) - Helmholtz Centre for Infection Research (HZI), and Department of Pharmacy, Saarland University Campus E8.1, Saarbrücken, Germany.,German Center for Infection Research (DZIF), Braunschweig, Germany
| | - Marco Pieroni
- Food and Drug Department, University of Parma, Parma, Italy
| | - Tilmann Weber
- The Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Lyngby, Denmark
| | - Mark Brönstrup
- German Center for Infection Research (DZIF), Braunschweig, Germany.,Department of Chemical Biology (CBIO), Helmholtz Centre for Infection Research (HZI), Braunschweig, Germany
| | - Peter Hammann
- Infectious Diseases & Natural Product Research at EVOTEC, and Justus Liebig University Giessen, Giessen, Germany
| | - Ludovic Halby
- Epigenetic Chemical Biology, Department of Structural Biology and Chemistry, Institut Pasteur, UMR n°3523, CNRS, Paris, France
| | - Paola B Arimondo
- Epigenetic Chemical Biology, Department of Structural Biology and Chemistry, Institut Pasteur, UMR n°3523, CNRS, Paris, France
| | - Philippe Glaser
- Ecology and Evolution of Antibiotic Resistance Unit, Microbiology Department, Institut Pasteur, CNRS UMR3525, Paris, France
| | | | - Helge B Bode
- Department of Biosciences, Goethe University Frankfurt, Frankfurt, Germany.,Max Planck Institute for Terrestrial Microbiology, Department of Natural Products in Organismic Interactions, Marburg, Germany
| | - Rui Moreira
- Faculty of Pharmacy, University of Lisbon, Lisbon, Portugal
| | - Yanyan Li
- Unit MCAM, CNRS, National Museum of Natural History (MNHN), Paris, France
| | - Andriy Luzhetskyy
- Pharmaceutical Biotechnology, Saarland University, Saarbrücken, Germany
| | - Marnix H Medema
- Bioinformatics Group, Wageningen University and Research, Wageningen, Netherlands
| | - Jean-Luc Pernodet
- Institute for Integrative Biology of the Cell (I2BC) & Microbiology Department, University of Paris-Saclay, Gif-sur-Yvette, France
| | - Marc Stadler
- German Center for Infection Research (DZIF), Braunschweig, Germany.,Microbial Drugs (MWIS), Helmholtz Centre for Infection Research (HZI), Braunschweig, Germany
| | | | | | - Andrew W Truman
- Department of Molecular Microbiology, John Innes Centre, Norwich, United Kingdom
| | - Kira J Weissman
- Molecular and Structural Enzymology Group, Université de Lorraine, CNRS, IMoPA, Nancy, France
| | - Eriko Takano
- Manchester Institute of Biotechnology, Department of Chemistry, School of Natural Sciences, Faculty of Science and Engineering, University of Manchester, Manchester, United Kingdom
| | - Stefano Sabatini
- Department of Pharmaceutical Sciences, University of Perugia, Perugia, Italy
| | - Evi Stegmann
- German Center for Infection Research (DZIF), Braunschweig, Germany.,Department of Microbial Bioactive Compounds, Interfaculty Institute of Microbiology and Infection Medicine, University of Tübingen, Tübingen, Germany
| | - Heike Brötz-Oesterhelt
- German Center for Infection Research (DZIF), Braunschweig, Germany.,Department of Microbial Bioactive Compounds, Interfaculty Institute of Microbiology and Infection Medicine, University of Tübingen, Tübingen, Germany
| | - Wolfgang Wohlleben
- German Center for Infection Research (DZIF), Braunschweig, Germany.,Department of Microbiology/Biotechnology, Interfaculty Institute of Microbiology and Infection Medicine, University of Tübingen, Tübingen, Germany
| | - Myriam Seemann
- Institute for Chemistry UMR 7177, University of Strasbourg/CNRS, ITI InnoVec, Strasbourg, France
| | - Martin Empting
- Helmholtz Institute for Pharmaceutical Research Saarland (HIPS) - Helmholtz Centre for Infection Research (HZI), and Department of Pharmacy, Saarland University Campus E8.1, Saarbrücken, Germany.,German Center for Infection Research (DZIF), Braunschweig, Germany
| | - Anna K H Hirsch
- Helmholtz Institute for Pharmaceutical Research Saarland (HIPS) - Helmholtz Centre for Infection Research (HZI), and Department of Pharmacy, Saarland University Campus E8.1, Saarbrücken, Germany.,German Center for Infection Research (DZIF), Braunschweig, Germany
| | - Brigitta Loretz
- Helmholtz Institute for Pharmaceutical Research Saarland (HIPS) - Helmholtz Centre for Infection Research (HZI), and Department of Pharmacy, Saarland University Campus E8.1, Saarbrücken, Germany
| | - Claus-Michael Lehr
- Helmholtz Institute for Pharmaceutical Research Saarland (HIPS) - Helmholtz Centre for Infection Research (HZI), and Department of Pharmacy, Saarland University Campus E8.1, Saarbrücken, Germany
| | - Alexander Titz
- Helmholtz Institute for Pharmaceutical Research Saarland (HIPS) - Helmholtz Centre for Infection Research (HZI), and Department of Pharmacy, Saarland University Campus E8.1, Saarbrücken, Germany.,German Center for Infection Research (DZIF), Braunschweig, Germany
| | - Jennifer Herrmann
- Helmholtz Institute for Pharmaceutical Research Saarland (HIPS) - Helmholtz Centre for Infection Research (HZI), and Department of Pharmacy, Saarland University Campus E8.1, Saarbrücken, Germany.,German Center for Infection Research (DZIF), Braunschweig, Germany
| | - Timo Jaeger
- German Center for Infection Research (DZIF), Braunschweig, Germany
| | - Silke Alt
- German Center for Infection Research (DZIF), Braunschweig, Germany
| | | | | | - Andrea Schiefer
- German Center for Infection Research (DZIF), Braunschweig, Germany.,Institute of Medical Microbiology, Immunology and Parasitology (IMMIP), University Hospital Bonn, Bonn, Germany
| | - Kenneth Pfarr
- German Center for Infection Research (DZIF), Braunschweig, Germany.,Institute of Medical Microbiology, Immunology and Parasitology (IMMIP), University Hospital Bonn, Bonn, Germany
| | - Achim Hoerauf
- German Center for Infection Research (DZIF), Braunschweig, Germany.,Institute of Medical Microbiology, Immunology and Parasitology (IMMIP), University Hospital Bonn, Bonn, Germany
| | - Heather Graz
- Biophys Ltd., Usk, Monmouthshire, United Kingdom
| | - Michael Graz
- School of Law, University of Bristol, Bristol, United Kingdom
| | | | | | - Anders Karlén
- Department of Medicinal Chemistry, Uppsala University, Uppsala, Sweden
| | | | - Hrvoje Petkovic
- Department of Food Science and Technology, Biotechnical Faculty, University of Ljubljana, Ljubljana, Slovenia
| | - Andreas Keller
- Chair for Clinical Bioinformatics, Saarland University, University Hospital, Saarbrücken, Germany
| | | | | | - Laurent Fraisse
- Drugs for Neglected Diseases initiative (DNDi), Geneva, Switzerland
| | - Laura J V Piddock
- The Global Antibiotic Research and Development Partnership (GARDP), Geneva, Switzerland
| | - Ian H Gilbert
- Division of Biological Chemistry and Drug Discovery, University of Dundee, Dundee, United Kingdom
| | - Heinz E Moser
- Novartis Institutes for BioMedical Research (NIBR), Emeryville, CA USA
| | - Rolf Müller
- Helmholtz Institute for Pharmaceutical Research Saarland (HIPS) - Helmholtz Centre for Infection Research (HZI), and Department of Pharmacy, Saarland University Campus E8.1, Saarbrücken, Germany.,German Center for Infection Research (DZIF), Braunschweig, Germany
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6
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Dorival J, Risser F, Jacob C, Collin S, Dräger G, Paris C, Chagot B, Kirschning A, Gruez A, Weissman KJ. Author Correction: Insights into a dual function amide oxidase/macrocyclase from lankacidin biosynthesis. Nat Commun 2020; 11:683. [PMID: 31996686 PMCID: PMC6989693 DOI: 10.1038/s41467-020-14473-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/02/2022] Open
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7
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Risser F, Collin S, Dos Santos-Morais R, Gruez A, Chagot B, Weissman KJ. Towards improved understanding of intersubunit interactions in modular polyketide biosynthesis: Docking in the enacyloxin IIa polyketide synthase. J Struct Biol 2020; 212:107581. [DOI: 10.1016/j.jsb.2020.107581] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2020] [Revised: 07/14/2020] [Accepted: 07/16/2020] [Indexed: 12/26/2022]
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8
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Massicard JM, Soligot C, Weissman KJ, Jacob C. Manipulating polyketide stereochemistry by exchange of polyketide synthase modules. Chem Commun (Camb) 2020; 56:12749-12752. [DOI: 10.1039/d0cc05068g] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/27/2023]
Abstract
Exchange of polyketide synthase (PKS) modules by genetic engineering leads to efficient modification of polyketide stereochemistry.
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Affiliation(s)
| | - Claire Soligot
- Université de Lorraine
- UR AFPA
- USC 340 INRAE
- F-54000 Nancy
- France
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9
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Dorival J, Risser F, Jacob C, Collin S, Dräger G, Paris C, Chagot B, Kirschning A, Gruez A, Weissman KJ. Insights into a dual function amide oxidase/macrocyclase from lankacidin biosynthesis. Nat Commun 2018; 9:3998. [PMID: 30266997 PMCID: PMC6162330 DOI: 10.1038/s41467-018-06323-w] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2018] [Accepted: 08/20/2018] [Indexed: 11/21/2022] Open
Abstract
Acquisition of new catalytic activity is a relatively rare evolutionary event. A striking example appears in the pathway to the antibiotic lankacidin, as a monoamine oxidase (MAO) family member, LkcE, catalyzes both an unusual amide oxidation, and a subsequent intramolecular Mannich reaction to form the polyketide macrocycle. We report evidence here for the molecular basis for this dual activity. The reaction sequence involves several essential active site residues and a conformational change likely comprising an interdomain hinge movement. These features, which have not previously been described in the MAO family, both depend on a unique dimerization mode relative to all structurally characterized members. Taken together, these data add weight to the idea that designing new multifunctional enzymes may require changes in both architecture and catalytic machinery. Encouragingly, however, our data also show LkcE to bind alternative substrates, supporting its potential utility as a general cyclization catalyst in synthetic biology. The monoamine oxidase family member LkcE is an enzyme from the lankacidin polyketide biosynthetic pathway, where it catalyzes an amide oxidation followed by an intramolecular Mannich reaction, yielding the polyketide macrocycle. Here the authors characterize LkcE and present several of its crystal structures, which explains the unusual dual activity of LkcE.
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Affiliation(s)
- Jonathan Dorival
- UMR 7365, Ingénierie Moléculaire et Physiopathologie Articulaire (IMoPA), CNRS-Université de Lorraine, Biopôle de l'Université de Lorraine, Campus Biologie Santé, 9 Avenue de la Forêt de Haye, BP 20199, 54505, Vandœuvre-lès-Nancy Cedex, France.,Sorbonne Universités, UPMC Univ. Paris 06, CNRS, UMR 8227, Integrative Biology of Marine Models, Station Biologique de Roscoff, CS 90074, Roscoff, Bretagne, France
| | - Fanny Risser
- UMR 7365, Ingénierie Moléculaire et Physiopathologie Articulaire (IMoPA), CNRS-Université de Lorraine, Biopôle de l'Université de Lorraine, Campus Biologie Santé, 9 Avenue de la Forêt de Haye, BP 20199, 54505, Vandœuvre-lès-Nancy Cedex, France
| | - Christophe Jacob
- UMR 7365, Ingénierie Moléculaire et Physiopathologie Articulaire (IMoPA), CNRS-Université de Lorraine, Biopôle de l'Université de Lorraine, Campus Biologie Santé, 9 Avenue de la Forêt de Haye, BP 20199, 54505, Vandœuvre-lès-Nancy Cedex, France
| | - Sabrina Collin
- UMR 7365, Ingénierie Moléculaire et Physiopathologie Articulaire (IMoPA), CNRS-Université de Lorraine, Biopôle de l'Université de Lorraine, Campus Biologie Santé, 9 Avenue de la Forêt de Haye, BP 20199, 54505, Vandœuvre-lès-Nancy Cedex, France
| | - Gerald Dräger
- Institut für Organische Chemie, Leibniz Universität Hannover, Schneiderberg 1B, Hannover, 30167, Germany
| | - Cédric Paris
- Laboratoire d'Ingénierie des Biomolécules, Ecole Nationale Supérieure d'Agronomie et des Industries Alimentaires (ENSAIA), Université de Lorraine, 2 Avenue de la Fôret de Haye, BP 172, 54518, Vandœuvre-lès-Nancy Cedex, France
| | - Benjamin Chagot
- UMR 7365, Ingénierie Moléculaire et Physiopathologie Articulaire (IMoPA), CNRS-Université de Lorraine, Biopôle de l'Université de Lorraine, Campus Biologie Santé, 9 Avenue de la Forêt de Haye, BP 20199, 54505, Vandœuvre-lès-Nancy Cedex, France
| | - Andreas Kirschning
- Institut für Organische Chemie, Leibniz Universität Hannover, Schneiderberg 1B, Hannover, 30167, Germany
| | - Arnaud Gruez
- UMR 7365, Ingénierie Moléculaire et Physiopathologie Articulaire (IMoPA), CNRS-Université de Lorraine, Biopôle de l'Université de Lorraine, Campus Biologie Santé, 9 Avenue de la Forêt de Haye, BP 20199, 54505, Vandœuvre-lès-Nancy Cedex, France.
| | - Kira J Weissman
- UMR 7365, Ingénierie Moléculaire et Physiopathologie Articulaire (IMoPA), CNRS-Université de Lorraine, Biopôle de l'Université de Lorraine, Campus Biologie Santé, 9 Avenue de la Forêt de Haye, BP 20199, 54505, Vandœuvre-lès-Nancy Cedex, France.
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10
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Maier T, Weissman KJ. Editorial overview: Macromolecular assemblies: Assembly, dynamics and control of activity. Curr Opin Struct Biol 2018; 49:vi-vii. [DOI: 10.1016/j.sbi.2018.04.001] [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: 10/17/2022]
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Abstract
Streptomyces are the principle source of antibiotics in clinical use, but what the bacteria use these molecules for remains largely a mystery. In this issue of Cell Chemical Biology, Hoefler et al. (2017) demonstrate a direct link between biosynthesis of the polyketide linearmycins and extracellular membrane vesicles.
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Affiliation(s)
- Christophe Jacob
- UMR 7365, Ingénierie Moléculaire et Physiopathologie Articulaire (IMoPA), CNRS-Université de Lorraine, Biopôle de l'Université de Lorraine, Campus Biologie Santé, 9 Avenue de la Forêt de Haye, CS 50184, 54505 Vandœuvre-lès-Nancy Cedex, France.
| | - Kira J Weissman
- UMR 7365, Ingénierie Moléculaire et Physiopathologie Articulaire (IMoPA), CNRS-Université de Lorraine, Biopôle de l'Université de Lorraine, Campus Biologie Santé, 9 Avenue de la Forêt de Haye, CS 50184, 54505 Vandœuvre-lès-Nancy Cedex, France.
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Abstract
The biosynthesis of reduced polyketides in bacteria by modular polyketide synthases (PKSs) proceeds with exquisite stereocontrol. As the stereochemistry is intimately linked to the strong bioactivity of these molecules, the origins of stereochemical control are of significant interest in attempts to create derivatives of these compounds by genetic engineering. In this review, we discuss the current state of knowledge regarding this key aspect of the biosynthetic pathways. Given that much of this information has been obtained using chemical biology tools, work in this area serves as a showcase for the power of this approach to provide answers to fundamental biological questions.
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Affiliation(s)
- Kira J Weissman
- UMR 7365, Ingénierie Moléculaire et Physiopathologie Articulaire (IMoPA), CNRS-Université de Lorraine, Biopôle de l’Université de Lorraine, Campus Biologie Santé, Avenue de la Forêt de Haye, BP 50184, 54505 Vandœuvre-lès-Nancy Cedex, France
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13
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Abstract
Correction for 'Uncovering the structures of modular polyketide synthases' by Kira J. Weissman, Nat. Prod. Rep., 2015, 32, 436-453.
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Affiliation(s)
- Kira J Weissman
- Molecular and Structural Enzymology Group, Université de Lorraine, IMoPA, UMR 7365, Vandœuvre-lès-Nancy, F-54500, France
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14
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Dorival J, Annaval T, Risser F, Collin S, Roblin P, Jacob C, Gruez A, Chagot B, Weissman KJ. Characterization of Intersubunit Communication in the Virginiamycin trans-Acyl Transferase Polyketide Synthase. J Am Chem Soc 2016; 138:4155-67. [DOI: 10.1021/jacs.5b13372] [Citation(s) in RCA: 38] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/28/2023]
Affiliation(s)
- Jonathan Dorival
- UMR
7365, Ingénierie Moléculaire et Physiopathologie Articulaire
(IMoPA), CNRS-Université de Lorraine, Biopôle de l’Université de Lorraine, Campus Biologie Santé, 9
Avenue de la Forêt de Haye, CS 50184, 54505 Vandœuvre-lès-Nancy CEDEX, France
| | - Thibault Annaval
- UMR
7365, Ingénierie Moléculaire et Physiopathologie Articulaire
(IMoPA), CNRS-Université de Lorraine, Biopôle de l’Université de Lorraine, Campus Biologie Santé, 9
Avenue de la Forêt de Haye, CS 50184, 54505 Vandœuvre-lès-Nancy CEDEX, France
| | - Fanny Risser
- UMR
7365, Ingénierie Moléculaire et Physiopathologie Articulaire
(IMoPA), CNRS-Université de Lorraine, Biopôle de l’Université de Lorraine, Campus Biologie Santé, 9
Avenue de la Forêt de Haye, CS 50184, 54505 Vandœuvre-lès-Nancy CEDEX, France
| | - Sabrina Collin
- UMR
7365, Ingénierie Moléculaire et Physiopathologie Articulaire
(IMoPA), CNRS-Université de Lorraine, Biopôle de l’Université de Lorraine, Campus Biologie Santé, 9
Avenue de la Forêt de Haye, CS 50184, 54505 Vandœuvre-lès-Nancy CEDEX, France
| | - Pierre Roblin
- Synchrotron SOLEIL, L'Orme des Merisiers, Saint-Aubin BP 48, 91192 Gif-sur-Yvette CEDEX, France
- UR1268 Biopolymères, Interactions Assemblages (BIA), INRA, Rue de la Géraudière
BP 71627, 44316 Nantes CEDEX 3, France
| | - Christophe Jacob
- UMR
7365, Ingénierie Moléculaire et Physiopathologie Articulaire
(IMoPA), CNRS-Université de Lorraine, Biopôle de l’Université de Lorraine, Campus Biologie Santé, 9
Avenue de la Forêt de Haye, CS 50184, 54505 Vandœuvre-lès-Nancy CEDEX, France
| | - Arnaud Gruez
- UMR
7365, Ingénierie Moléculaire et Physiopathologie Articulaire
(IMoPA), CNRS-Université de Lorraine, Biopôle de l’Université de Lorraine, Campus Biologie Santé, 9
Avenue de la Forêt de Haye, CS 50184, 54505 Vandœuvre-lès-Nancy CEDEX, France
| | - Benjamin Chagot
- UMR
7365, Ingénierie Moléculaire et Physiopathologie Articulaire
(IMoPA), CNRS-Université de Lorraine, Biopôle de l’Université de Lorraine, Campus Biologie Santé, 9
Avenue de la Forêt de Haye, CS 50184, 54505 Vandœuvre-lès-Nancy CEDEX, France
| | - Kira J. Weissman
- UMR
7365, Ingénierie Moléculaire et Physiopathologie Articulaire
(IMoPA), CNRS-Université de Lorraine, Biopôle de l’Université de Lorraine, Campus Biologie Santé, 9
Avenue de la Forêt de Haye, CS 50184, 54505 Vandœuvre-lès-Nancy CEDEX, France
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15
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Abstract
This reviews covers on-going efforts at engineering the gigantic modular polyketide synthases (PKSs), highlighting both notable successes and failures.
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Affiliation(s)
- Kira J. Weissman
- UMR 7365
- Ingénierie Moléculaire et Physiopathologie Articulaire (IMoPA)
- CNRS-Université de Lorraine
- Biopôle de l'Université de Lorraine
- 54505 Vandœuvre-lès-Nancy Cedex
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16
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Annaval T, Paris C, Leadlay PF, Jacob C, Weissman KJ. Evaluating Ketoreductase Exchanges as a Means of Rationally Altering Polyketide Stereochemistry. Chembiochem 2015; 16:1357-64. [DOI: 10.1002/cbic.201500113] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2015] [Indexed: 12/22/2022]
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17
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Abstract
This review covers a breakthrough in the structural biology of the gigantic modular polyketide synthases (PKS): the structural characterization of intact modules by single-particle cryo-electron microscopy and small-angle X-ray scattering.
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Affiliation(s)
- Kira J. Weissman
- Molecular and Structural Enzymology Group
- Université de Lorraine
- IMoPA
- UMR 7365
- Vandœuvre-lès-Nancy
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18
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Weissman KJ. Probing interactions in fungal PKS. ACTA ACUST UNITED AC 2014; 20:1089-91. [PMID: 24054181 DOI: 10.1016/j.chembiol.2013.09.001] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/26/2022]
Abstract
Biosynthesis of polyketides can depend on interactions between the acyl carrier proteins (ACPs) which hold the growing chains and their enzymatic partners. In this issue of Chemistry & Biology, Bruegger and colleagues demonstrate that mechanism-based probes tethered to the ACPs of fungal nonreducing polyketide synthases can provide insights into these contacts.
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Affiliation(s)
- Kira J Weissman
- Molecular and Structural Enzymology Group, UMR 7365 CNRS-UL:IMoPA, Lorraine University, Faculté de Médecine, Batiment Biopôle, 9 Avenue de la Forêt de Haye, BP 184, 54506 Vandoeuvre-lès-Nancy, France.
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19
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Davison J, Dorival J, Rabeharindranto H, Mazon H, Chagot B, Gruez A, Weissman KJ. Insights into the function of trans-acyl transferase polyketide synthases from the SAXS structure of a complete module. Chem Sci 2014. [DOI: 10.1039/c3sc53511h] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/02/2023] Open
Abstract
Combined analysis by SAXS, NMR and homology modeling reveals the structure of an apo module from a trans-acyltransferase polyketide synthase.
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Affiliation(s)
- Jack Davison
- Molecular and Structural Enzymology Group
- Université de Lorraine
- Vandœuvre-Lès-Nancy, France
| | - Jonathan Dorival
- Molecular and Structural Enzymology Group
- Université de Lorraine
- Vandœuvre-Lès-Nancy, France
| | - Hery Rabeharindranto
- Molecular and Structural Enzymology Group
- Université de Lorraine
- Vandœuvre-Lès-Nancy, France
| | - Hortense Mazon
- Molecular and Structural Enzymology Group
- Université de Lorraine
- Vandœuvre-Lès-Nancy, France
| | - Benjamin Chagot
- Molecular and Structural Enzymology Group
- Université de Lorraine
- Vandœuvre-Lès-Nancy, France
| | - Arnaud Gruez
- Molecular and Structural Enzymology Group
- Université de Lorraine
- Vandœuvre-Lès-Nancy, France
| | - Kira J. Weissman
- Molecular and Structural Enzymology Group
- Université de Lorraine
- Vandœuvre-Lès-Nancy, France
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20
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21
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Kopp M, Irschik H, Gemperlein K, Buntin K, Meiser P, Weissman KJ, Bode HB, Müller R. Insights into the complex biosynthesis of the leupyrrins in Sorangium cellulosum So ce690. Mol Biosyst 2011; 7:1549-63. [PMID: 21365089 DOI: 10.1039/c0mb00240b] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/13/2023]
Abstract
The anti-fungal leupyrrins are secondary metabolites produced by several strains of the myxobacterium Sorangium cellulosum. These intriguing compounds incorporate an atypically substituted γ-butyrolactone ring, as well as pyrrole and oxazolinone functionalities, which are located within an unusual asymmetrical macrodiolide. Previous feeding studies revealed that this novel structure arises from the homologation of four distinct structural units, nonribosomally-derived peptide, polyketide, isoprenoid and a dicarboxylic acid, coupled with modification of the various building blocks. Here we have attempted to reconcile the biosynthetic pathway proposed on the basis of the feeding studies with the underlying enzymatic machinery in the S. cellulosum strain So ce690. Gene products can be assigned to many of the suggested steps, but inspection of the gene set provokes the reconsideration of several key transformations. We support our analysis by the reconstitution in vitro of the biosynthesis of the pyrrole carboxylic starter unit along with gene inactivation. In addition, this study reveals that a significant proportion of the genes for leupyrrin biosynthesis are located outside the core cluster, a 'split' organization which is increasingly characteristic of the myxobacteria. Finally, we report the generation of four novel deshydroxy leupyrrin analogues by genetic engineering of the pathway.
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Affiliation(s)
- Maren Kopp
- Helmholtz Institute for Pharmaceutical Research, Helmholtz Center for Infection Research and Department of Pharmaceutical Biotechnology, Saarland University, PO Box 151150, 66041 Saarbrücken, Germany
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22
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Irschik H, Kopp M, Weissman KJ, Buntin K, Piel J, Müller R. Analysis of the sorangicin gene cluster reinforces the utility of a combined phylogenetic/retrobiosynthetic analysis for deciphering natural product assembly by trans-AT PKS. Chembiochem 2011; 11:1840-9. [PMID: 20715267 DOI: 10.1002/cbic.201000313] [Citation(s) in RCA: 63] [Impact Index Per Article: 4.8] [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)
- Herbert Irschik
- Microbial Drugs, Helmholtz Center for Infection Research, Inhoffenstrasse 7, 38124 Braunschweig, Germany
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23
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Tran L, Broadhurst RW, Tosin M, Cavalli A, Weissman KJ. Insights into Protein-Protein and Enzyme-Substrate Interactions in Modular Polyketide Synthases. ACTA ACUST UNITED AC 2010; 17:705-16. [DOI: 10.1016/j.chembiol.2010.05.017] [Citation(s) in RCA: 37] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2010] [Revised: 04/26/2010] [Accepted: 05/03/2010] [Indexed: 11/29/2022]
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Affiliation(s)
- Kira J Weissman
- Department of Pharmaceutical Biotechnology, Saarland University, P. O. Box 151150, 66041 Saarbrücken, Germany.
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25
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Buntin K, Weissman KJ, Müller R. An Unusual Thioesterase Promotes Isochromanone Ring Formation in Ajudazol Biosynthesis. Chembiochem 2010; 11:1137-46. [DOI: 10.1002/cbic.200900712] [Citation(s) in RCA: 26] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
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26
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Li Y, Weissman KJ, Müller R. Insights into Multienzyme Docking in Hybrid PKS-NRPS Megasynthetases Revealed by Heterologous Expression and Genetic Engineering. Chembiochem 2010; 11:1069-75. [DOI: 10.1002/cbic.201000103] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.9] [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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27
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Buntin K, Irschik H, Weissman KJ, Luxenburger E, Blöcker H, Müller R. Biosynthesis of Thuggacins in Myxobacteria: Comparative Cluster Analysis Reveals Basis for Natural Product Structural Diversity. ACTA ACUST UNITED AC 2010; 17:342-56. [DOI: 10.1016/j.chembiol.2010.02.013] [Citation(s) in RCA: 46] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2009] [Revised: 01/22/2010] [Accepted: 02/18/2010] [Indexed: 10/19/2022]
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29
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Rachid S, Scharfe M, Blöcker H, Weissman KJ, Müller R. Unusual chemistry in the biosynthesis of the antibiotic chondrochlorens. ACTA ACUST UNITED AC 2009; 16:70-81. [PMID: 19171307 DOI: 10.1016/j.chembiol.2008.11.005] [Citation(s) in RCA: 45] [Impact Index Per Article: 3.0] [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: 07/21/2008] [Revised: 10/28/2008] [Accepted: 11/13/2008] [Indexed: 11/17/2022]
Abstract
The antibiotic chondrochlorens A and B from the myxobacterium Chondromyces crocatus Cm c5 incorporate several unusual structural features, notable among them a shared chloro-hydroxy-styryl functionality and the ethoxy group of chondrochloren B. Our analysis of the chondrochloren gene cluster by targeted gene inactivation coupled with assays in vitro has shed significant light on the biosynthesis of these metabolites. Chlorination of tyrosine occurs early in the pathway, likely on a peptidyl carrier protein-bound intermediate, whereas decarboxylation to the styryl moiety appears to be accomplished by an unprecedented oxidative decarboxylase. We also show that the chondrochloren B ethoxy group arises from initial incorporation by the polyketide synthase of hydroxy malonate as an extender unit, methylation in cis by an O-methyltransferase, followed by a second methylation. This report therefore constitutes a direct demonstration of the involvement of a radical S-adenosylmethionine methylase in bacterial secondary metabolism.
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Affiliation(s)
- Shwan Rachid
- Pharmaceutical Biotechnology, Saarland University, Saarbrücken, Germany
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30
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Betancor L, Fernández MJ, Weissman KJ, Leadlay PF. Improved catalytic activity of a purified multienzyme from a modular polyketide synthase after coexpression with Streptomyces chaperonins in Escherichia coli. Chembiochem 2009; 9:2962-6. [PMID: 19021139 DOI: 10.1002/cbic.200800475] [Citation(s) in RCA: 29] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Affiliation(s)
- Lorena Betancor
- Department of Biochemistry, University of Cambridge, Cambridge, UK
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31
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32
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Affiliation(s)
- Kira J Weissman
- Department of Pharmaceutical Biotechnology, Saarland University, P.O. Box 151150, 66041 Saarbrücken, Germany
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33
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34
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Tran L, Tosin M, Spencer JB, Leadlay PF, Weissman KJ. Covalent linkage mediates communication between ACP and TE domains in modular polyketide synthases. Chembiochem 2008; 9:905-15. [PMID: 18348128 DOI: 10.1002/cbic.200700738] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Abstract
Polyketide natural products such as erythromycin A and epothilone are assembled on multienzyme polyketide synthases (PKSs), which consist of modular sets of protein domains. Within these type I systems, the fidelity of biosynthesis depends on the programmed interaction among the multiple domains within each module, centered around the acyl carrier protein (ACP). A detailed understanding of interdomain communication will therefore be vital for attempts to reprogram these pathways by genetic engineering. We report here that the interaction between a representative ACP domain and its downstream thioesterase (TE) is mediated largely by covalent tethering through a short "linker" region, with only a minor energetic contribution from protein-protein molecular recognition. This finding helps explain in part the empirical observation that TE domains can function out of their normal context in engineered assembly lines, and supports the view that overall PKS architecture may dictate at least a subset of interdomain interactions.
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Affiliation(s)
- Lucky Tran
- Department of Biochemistry, University of Cambridge, 80 Tennis Court Road, Cambridge CB2 1GA, UK
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35
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Li Y, Weissman KJ, Müller R. Myxochelin Biosynthesis: Direct Evidence for Two- and Four-Electron Reduction of a Carrier Protein-Bound Thioester. J Am Chem Soc 2008; 130:7554-5. [DOI: 10.1021/ja8025278] [Citation(s) in RCA: 57] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Yanyan Li
- Pharmaceutical Biotechnology, Saarland University, P.O. Box 151150, 66041 Saarbrücken, Germany
| | - Kira J. Weissman
- Pharmaceutical Biotechnology, Saarland University, P.O. Box 151150, 66041 Saarbrücken, Germany
| | - Rolf Müller
- Pharmaceutical Biotechnology, Saarland University, P.O. Box 151150, 66041 Saarbrücken, Germany
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36
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37
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Affiliation(s)
- Kira J. Weissman
- Department of Pharmaceutical Biotechnology, Saarland University, 60041 Saarbrücken, Germany
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38
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Richter CD, Nietlispach D, Broadhurst RW, Weissman KJ. Multienzyme docking in hybrid megasynthetases. Nat Chem Biol 2007; 4:75-81. [DOI: 10.1038/nchembio.2007.61] [Citation(s) in RCA: 73] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2007] [Accepted: 10/30/2007] [Indexed: 11/09/2022]
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Schneiker S, Perlova O, Kaiser O, Gerth K, Alici A, Altmeyer MO, Bartels D, Bekel T, Beyer S, Bode E, Bode HB, Bolten CJ, Choudhuri JV, Doss S, Elnakady YA, Frank B, Gaigalat L, Goesmann A, Groeger C, Gross F, Jelsbak L, Jelsbak L, Kalinowski J, Kegler C, Knauber T, Konietzny S, Kopp M, Krause L, Krug D, Linke B, Mahmud T, Martinez-Arias R, McHardy AC, Merai M, Meyer F, Mormann S, Muñoz-Dorado J, Perez J, Pradella S, Rachid S, Raddatz G, Rosenau F, Rückert C, Sasse F, Scharfe M, Schuster SC, Suen G, Treuner-Lange A, Velicer GJ, Vorhölter FJ, Weissman KJ, Welch RD, Wenzel SC, Whitworth DE, Wilhelm S, Wittmann C, Blöcker H, Pühler A, Müller R. Complete genome sequence of the myxobacterium Sorangium cellulosum. Nat Biotechnol 2007; 25:1281-9. [PMID: 17965706 DOI: 10.1038/nbt1354] [Citation(s) in RCA: 267] [Impact Index Per Article: 15.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2007] [Accepted: 10/04/2007] [Indexed: 12/11/2022]
Abstract
The genus Sorangium synthesizes approximately half of the secondary metabolites isolated from myxobacteria, including the anti-cancer metabolite epothilone. We report the complete genome sequence of the model Sorangium strain S. cellulosum So ce56, which produces several natural products and has morphological and physiological properties typical of the genus. The circular genome, comprising 13,033,779 base pairs, is the largest bacterial genome sequenced to date. No global synteny with the genome of Myxococcus xanthus is apparent, revealing an unanticipated level of divergence between these myxobacteria. A large percentage of the genome is devoted to regulation, particularly post-translational phosphorylation, which probably supports the strain's complex, social lifestyle. This regulatory network includes the highest number of eukaryotic protein kinase-like kinases discovered in any organism. Seventeen secondary metabolite loci are encoded in the genome, as well as many enzymes with potential utility in industry.
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Affiliation(s)
- Susanne Schneiker
- Department of Genetics, Bielefeld University, PO Box 100131, D-33501 Bielefeld, Germany
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40
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Elnakady YA, Rohde M, Sasse F, Backes C, Keller A, Lenhof HP, Weissman KJ, Müller R. Evidence for the mode of action of the highly cytotoxic Streptomyces polyketide kendomycin. Chembiochem 2007; 8:1261-72. [PMID: 17592829 DOI: 10.1002/cbic.200700050] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022]
Abstract
The macrocyclic polyketide kendomycin exhibits antiosteoporotic and antibacterial activity, as well as strong cytotoxicity against multiple human tumor cell lines. Despite the promise of this compound in several therapeutic areas, the cellular target(s) of kendomycin have not been identified to date. We have used a number of approaches, including microscopy, proteomics, and bioinformatics, to investigate the mode of action of kendomycin in mammalian cell cultures. In response to kendomycin treatment, human U-937 tumor cells exhibit depolarization of the mitochondrial membrane, caspase 3 activation, and DNA laddering, consistent with induction of the intrinsic apoptotic pathway. To elucidate possible apoptotic triggers, DIGE and MALDI-TOF were used to identify proteins that are differently regulated in U-937 cells relative to controls. Statistical analysis of the proteomics data by the new web-based application GeneTrail highlighted several significant changes in protein expression, most notably among proteasomal regulatory subunits. Overall, the profile of altered expression closely matches that observed with other tumor cell lines in response to proteasome inhibition. Direct assay in vitro further shows that kendomycin inhibits the chymotrypsin-like activity of the rabbit reticulocyte proteasome, with comparable efficacy to the established inhibitor MG-132. We have also demonstrated that ubiquitinylated proteins accumulate in kendomycin-treated U-937 cells, while vacuolization of the endoplasmic reticulum and mitochondrial swelling are induced in a second cell line derived from kangaroo rat epithelial (PtK(2)) cells, phenotypes classically associated with inhibition of the proteasome. This study therefore provides evidence that kendomycin mediates its cytotoxic effects, at least in part, through proteasome inhibition.
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Affiliation(s)
- Yasser A Elnakady
- Department of Pharmaceutical Biotechnology, Saarland University, P.O. Box 151150, 66041 Saarbrücken, Germany
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41
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Harvey BM, Mironenko T, Sun Y, Hong H, Deng Z, Leadlay PF, Weissman KJ, Haydock SF. Insights into polyether biosynthesis from analysis of the nigericin biosynthetic gene cluster in Streptomyces sp. DSM4137. ACTA ACUST UNITED AC 2007; 14:703-14. [PMID: 17584617 DOI: 10.1016/j.chembiol.2007.05.011] [Citation(s) in RCA: 98] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2007] [Revised: 04/05/2007] [Accepted: 05/04/2007] [Indexed: 11/18/2022]
Abstract
Nigericin was among the first polyether ionophores to be discovered, but its biosynthesis remains obscure. The biosynthetic gene cluster for nigericin has been serendipitously cloned from Streptomyces sp. DSM4137, and deletion of this gene cluster abolished the production of both nigericin and the closely related metabolite abierixin. Detailed comparison of the nigericin biosynthetic genes with their counterparts in the biosynthetic clusters for other polyketides has prompted a significant revision of the proposed common pathway for polyether biosynthesis. In particular, we present evidence that in nigericin, nanchangmycin, and monensin, an unusual ketosynthase-like protein, KSX, transfers the initially formed linear polyketide chain to a discrete acyl carrier protein, ACPX, for oxidative cyclization. Consistent with this, deletion of either monACPX or monKSX from the monensin gene cluster effectively abolished monensin A biosynthesis.
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Affiliation(s)
- Barbara M Harvey
- Department of Biochemistry, University of Cambridge, Cambridge CB2 1GA, UK
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42
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Elnakady YA, Rohde M, Sasse F, Backes C, Keller A, Lenhof HP, Weissman KJ, Müller R. Cover Picture: Evidence for the Mode of Action of the Highly CytotoxicStreptomyces Polyketide Kendomycin (ChemBioChem 11/2007). Chembiochem 2007. [DOI: 10.1002/cbic.200790033] [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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Rachid S, Krug D, Weissman KJ, Müller R. Biosynthesis of (R)-beta-tyrosine and its incorporation into the highly cytotoxic chondramides produced by Chondromyces crocatus. J Biol Chem 2007; 282:21810-7. [PMID: 17545150 DOI: 10.1074/jbc.m703439200] [Citation(s) in RCA: 45] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
The chondramides are mixed non-ribosomal peptide/polyketide secondary metabolites produced by the myxobacterium Chondromyces crocatus Cm c5, which exhibit strong cytotoxic activity. On the basis of their striking structural similarity to the marine depsipeptides jaspamides, the chondramides have been assumed to incorporate a (R)-beta-tyrosine moiety, an expectation we confirm here. Thus, the recent sequencing of the chondramide biosynthetic gene cluster provided the opportunity to probe the shared origin of this unusual beta-amino acid. We demonstrate here that (R)-beta-tyrosine is produced directly from l-tyrosine by the aminomutase CmdF. Along with the tyrosine aminomutase SgcC4 from the C-1027 enediyne pathway, this enzyme belongs to a novel family of tyrosine aminomutases related to the ammonium lyase family of enzymes but exhibits opposite facial selectivity for the hydroxycinnamate intermediate. We also show that the adenylation (A) domain in the chondramide pathway, which activates the beta-tyrosine building block, exhibits the required preference for (R)-beta-tyrosine, further arguing against alternative origins for the moiety in the chondramides. Comparison to the (S)-beta-tyrosine specific A domain SgcC1 should enhance our understanding of the structural and stereochemical determinants guiding amino acid selection by non-ribosomal peptide synthetase multienzymes.
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Affiliation(s)
- Shwan Rachid
- Institute for Pharmaceutical Biotechnology, Saarland University, Saarbrücken, Germany
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Bali S, Weissman KJ. Ketoreduction in mycolactone biosynthesis: insight into substrate specificity and stereocontrol from studies of discrete ketoreductase domains in vitro. Chembiochem 2007; 7:1935-42. [PMID: 17031885 DOI: 10.1002/cbic.200600285] [Citation(s) in RCA: 34] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Abstract
Mycolactone, a polyketide toxin responsible for the extensive tissue destruction seen in Buruli ulcer, is assembled on a modular polyketide synthase (PKS). Despite operating on structurally different intermediates during synthesis, many of the ketoreductase (KR) domains of the mycolactone (MLS) PKS have identical sequences. This suggests that these enzymes might exhibit an unusually high level of substrate promiscuity. However, we show here that when recombinant mycolactone KR domains are tested with a range of surrogate substrates, their specificity closely matches that of KR domains derived from other PKS systems. In addition, our findings reinforce the role of substrate tethering for achieving stereochemical control in modular PKSs by affecting the delicate energetics of ketoreduction.
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Affiliation(s)
- Shilpa Bali
- Department of Biochemistry, University of Cambridge, 80 Tennis Court Road, Cambridge, CB2 1GA, UK
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Richter CD, Stanmore DA, Miguel RN, Moncrieffe MC, Tran L, Brewerton S, Meersman F, Broadhurst RW, Weissman KJ. Autonomous folding of interdomain regions of a modular polyketide synthase. FEBS J 2007; 274:2196-209. [PMID: 17419733 DOI: 10.1111/j.1742-4658.2007.05757.x] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
Abstract
Domains within the multienzyme polyketide synthases are linked by noncatalytic sequences of variable length and unknown function. Recently, the crystal structure was reported of a portion of the linker between the acyltransferase (AT) and ketoreductase (KR) domains from module 1 of the erythromycin synthase (6-deoxyerythronolide B synthase), as a pseudodimer with the adjacent ketoreductase (KR). On the basis of this structure, the homologous linker region between the dehydratase (DH) and enoyl reductase (ER) domains in fully reducing modules has been proposed to occupy a position on the periphery of the polyketide synthases complex, as in porcine fatty acid synthase. We report here the expression and characterization of the same region of the 6-deoxyerythronolide B synthase module 1 AT-KR linker, without the adjacent KR domain (termed DeltaN AT1-KR1), as well as the corresponding section of the DH-ER linker. The linkers fold autonomously and are well structured. However, analytical gel filtration and ultracentrifugation analysis independently show that DeltaN AT1-KR1 is homodimeric in solution; site-directed mutagenesis further demonstrates that linker self-association is compatible with the formation of a linker-KR pseudodimer. Our data also strongly indicate that the DH-ER linker associates with the upstream DH domain. Both of these findings are incompatible with the proposed model for polyketide synthase architecture, suggesting that it is premature to allocate the linker regions to a position in the multienzymes based on the solved structure of animal fatty acid synthase.
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Abstract
Mutasynthesis couples the power of chemical synthesis with molecular biology to generate derivatives of medicinally valuable, natural products. Recently, this technique has been exploited by Cambridge-based biotech company Biotica Technology Ltd, and their collaborators, to generate promising new variants of the polyketide anti-cancer compounds rapamycin and borrelidin.
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Affiliation(s)
- Kira J Weissman
- Department of Biochemistry, University of Cambridge, Cambridge CB2 1GA, UK.
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Weissman KJ, Hong H, Popovic B, Meersman F. Evidence for a protein-protein interaction motif on an acyl carrier protein domain from a modular polyketide synthase. ACTA ACUST UNITED AC 2006; 13:625-36. [PMID: 16793520 DOI: 10.1016/j.chembiol.2006.04.010] [Citation(s) in RCA: 30] [Impact Index Per Article: 1.7] [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: 12/13/2005] [Revised: 04/24/2006] [Accepted: 04/25/2006] [Indexed: 11/19/2022]
Abstract
During biosynthesis on modular polyketide synthases (PKSs), chain extension intermediates are tethered to acyl carrier protein (ACP) domains through phosphopantetheinyl prosthetic groups. Each ACP must therefore interact with every other domain within the module, and also with a downstream acceptor domain. The nature of these interactions is key to our understanding of the topology and operation of these multienzymes. Sequence analysis and homology modeling implicates a potential helical region (helix II) on the ACPs as a protein-protein interaction motif. Using site-directed mutagenesis, we show that residues along this putative helix lie at the interface between the ACP and the phosphopantetheinyl transferase that catalyzes its activation. Our results accord with previous studies of discrete ACP proteins from fatty acid and aromatic polyketide biosynthesis, suggesting that helix II may also serve as a universal interaction motif in modular PKSs.
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Affiliation(s)
- Kira J Weissman
- Department of Biochemistry, University of Cambridge, 80 Tennis Court Road, Cambridge CB2 1GA, United Kingdom.
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Affiliation(s)
- Kira J Weissman
- Department of Biochemistry, University of Cambridge, 80 Tennis Court Road, Cambridge CB2 1GA, UK.
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Abstract
Recombinant ketoreductase (KR) domains derived from antibiotic-producing modular polyketide synthases (PKSs) have been examined as potential catalysts for the enantioselective reduction of non-polyketide substrates. KR domains from two modular PKSs show significant activity toward alternative substrates, particularly those that incorporate cyclohexyl moieties. Through site-directed mutagenesis of the amino acid motifs previously implicated in stereocontrol by KRs, we have identified mutants with improved activity toward such compounds. These results suggest that PKS KRs could potentially be used as biotransformation catalysts for the production of chiral alcohols.
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Affiliation(s)
- Shilpa Bali
- Department of Biochemistry, University of Cambridge, 80 Tennis Court Road, Cambridge CB2 1GA, UK
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Abstract
Polyketide natural products such as erythromycin and rapamycin are assembled on polyketide synthases (PKSs), which consist of modular sets of catalytic activities distributed across multiple protein subunits. Correct protein-protein interactions among the PKS subunits which are critical to the fidelity of biosynthesis are mediated in part by "docking domains" at the termini of the proteins. The NMR solution structure of a representative docking domain complex from the erythromycin PKS (DEBS) was recently solved, and on this basis it has been proposed that PKS docking is mediated by the formation of an intermolecular four-alpha-helix bundle. Herein, we report the genetic engineering of such a docking domain complex by replacement of specific helical segments and analysis of triketide synthesis by mutant PKSs in vivo. The results of these helix swaps are fully consistent with the model and highlight residues in the docking domains that may be targeted to alter the efficiency or specificity of subunit-subunit docking in hybrid PKSs.
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Affiliation(s)
- Kira J Weissman
- Department of Biochemistry, University of Cambridge, 80 Tennis Court Road, Cambridge CB2 1GA, UK.
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