1
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Yin Z, Dickschat JS. Substrate specificity of a ketosynthase domain involved in bacillaene biosynthesis. Beilstein J Org Chem 2024; 20:734-740. [PMID: 38590531 PMCID: PMC10999986 DOI: 10.3762/bjoc.20.67] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2023] [Accepted: 03/27/2024] [Indexed: 04/10/2024] Open
Abstract
An isotopic labelling method was developed to investigate substrate binding by ketosynthases, exemplified by the second ketosynthase of the polyketide synthase BaeJ involved in bacillaene biosynthesis (BaeJ-KS2). For this purpose, both enantiomers of a 13C-labelled N-acetylcysteamine thioester (SNAC ester) surrogate of the proposed natural intermediate of BaeJ-KS2 were synthesised, including an enzymatic step with glutamate decarboxylase, and incubated with BaeJ-KS2. Substrate binding was demonstrated through 13C NMR analysis of the products against the background of various control experiments.
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Affiliation(s)
- Zhiyong Yin
- Kekulé-Institute of Organic Chemistry and Biochemistry, University of Bonn, Gerhard-Domagk-Straße 1, 53121 Bonn, Germany
| | - Jeroen S Dickschat
- Kekulé-Institute of Organic Chemistry and Biochemistry, University of Bonn, Gerhard-Domagk-Straße 1, 53121 Bonn, Germany
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2
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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] [Abstract] [MESH Headings] [Grants] [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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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] [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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Bonhomme S, Contreras-Martel C, Dessen A, Macheboeuf P. Architecture of a PKS-NRPS hybrid megaenzyme involved in the biosynthesis of the genotoxin colibactin. Structure 2023:S0969-2126(23)00095-3. [PMID: 37059096 DOI: 10.1016/j.str.2023.03.012] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2022] [Revised: 10/21/2022] [Accepted: 03/20/2023] [Indexed: 04/16/2023]
Abstract
The genotoxin colibactin produced by Escherichia coli is involved in the development of colorectal cancers. This secondary metabolite is synthesized by a multi-protein machinery, mainly composed of non-ribosomal peptide synthetase (NRPS)/polyketide synthase (PKS) enzymes. In order to decipher the function of a PKS-NRPS hybrid enzyme implicated in a key step of colibactin biosynthesis, we conducted an extensive structural characterization of the ClbK megaenzyme. Here we present the crystal structure of the complete trans-AT PKS module of ClbK showing structural specificities of hybrid enzymes. In addition, we report the SAXS solution structure of the full-length ClbK hybrid that reveals a dimeric organization as well as several catalytic chambers. These results provide a structural framework for the transfer of a colibactin precursor through a PKS-NRPS hybrid enzyme and can pave the way for re-engineering PKS-NRPS hybrid megaenzymes to generate diverse metabolites with many applications.
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Affiliation(s)
- Sarah Bonhomme
- University Grenoble Alpes, CNRS, CEA, Institut de Biologie Structurale (IBS), Bacterial Pathogenesis Group, 38000 Grenoble, France
| | - Carlos Contreras-Martel
- University Grenoble Alpes, CNRS, CEA, Institut de Biologie Structurale (IBS), Bacterial Pathogenesis Group, 38000 Grenoble, France
| | - Andréa Dessen
- University Grenoble Alpes, CNRS, CEA, Institut de Biologie Structurale (IBS), Bacterial Pathogenesis Group, 38000 Grenoble, France
| | - Pauline Macheboeuf
- University Grenoble Alpes, CNRS, CEA, Institut de Biologie Structurale (IBS), Bacterial Pathogenesis Group, 38000 Grenoble, France.
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5
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Yun CS, Nishimoto K, Motoyama T, Shimizu T, Hino T, Dohmae N, Nagano S, Osada H. Unique features of the ketosynthase domain in a nonribosomal peptide synthetase-polyketide synthase hybrid enzyme, tenuazonic acid synthetase 1. J Biol Chem 2020; 295:11602-11612. [PMID: 32565425 DOI: 10.1074/jbc.ra120.013105] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2020] [Revised: 06/18/2020] [Indexed: 11/06/2022] Open
Abstract
Many microbial secondary metabolites are produced by multienzyme complexes comprising nonribosomal peptide synthetases (NRPSs) and polyketide synthases (PKSs). The ketosynthase (KS) domains of polyketide synthase normally catalyze the decarboxylative Claisen condensation of acyl and malonyl blocks to extend the polyketide chain. However, the terminal KS domain in tenuazonic acid synthetase 1 (TAS1) from the fungus Pyricularia oryzae conducts substrate cyclization. Here, we report on the unique features of the KS domain in TAS1. We observed that this domain is monomeric, not dimeric as is typical for KSs. Analysis of a 1.68-Å resolution crystal structure suggests that the substrate cyclization is triggered via proton abstraction from the active methylene moiety in the substrate by a catalytic His-322 residue. Additionally, we show that TAS1 KS promiscuously accepts aminoacyl substrates and that this promiscuity can be increased by a single amino acid substitution in the substrate-binding pocket of the enzyme. These findings provide insight into a KS domain that accepts the amino acid-containing substrate in an NRPS-PKS hybrid enzyme and provide hints to the substrate cyclization mechanism performed by the KS domain in the biosynthesis of the mycotoxin tenuazonic acid.
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Affiliation(s)
- Choong-Soo Yun
- Chemical Biology Research Group, RIKEN Center for Sustainable Resource Science, Wako-shi, Saitama, Japan
| | - Kazuki Nishimoto
- Department of Chemistry and Biotechnology, Graduate School of Engineering, Tottori University, Tottori, Japan
| | - Takayuki Motoyama
- Chemical Biology Research Group, RIKEN Center for Sustainable Resource Science, Wako-shi, Saitama, Japan
| | - Takeshi Shimizu
- Chemical Biology Research Group, RIKEN Center for Sustainable Resource Science, Wako-shi, Saitama, Japan
| | - Tomoya Hino
- Department of Chemistry and Biotechnology, Graduate School of Engineering, Tottori University, Tottori, Japan
| | - Naoshi Dohmae
- Biomolecular Characterization Unit, RIKEN Center for Sustainable Resource Science, Wako-shi, Saitama, Japan
| | - Shingo Nagano
- Department of Chemistry and Biotechnology, Graduate School of Engineering, Tottori University, Tottori, Japan
| | - Hiroyuki Osada
- Chemical Biology Research Group, RIKEN Center for Sustainable Resource Science, Wako-shi, Saitama, Japan
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6
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Paulus C, Rebets Y, Zapp J, Rückert C, Kalinowski J, Luzhetskyy A. New Alpiniamides From Streptomyces sp. IB2014/011-12 Assembled by an Unusual Hybrid Non-ribosomal Peptide Synthetase Trans-AT Polyketide Synthase Enzyme. Front Microbiol 2018; 9:1959. [PMID: 30186270 PMCID: PMC6113372 DOI: 10.3389/fmicb.2018.01959] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2018] [Accepted: 08/02/2018] [Indexed: 11/13/2022] Open
Abstract
The environment of Lake Baikal is a well-known source of microbial diversity. The strain Streptomyces sp. IB2014/011-12, isolated from samples collected at Lake Baikal, was found to exhibit potent activity against Gram-positive bacteria. Here, we report isolation and characterization of linear polyketide alpiniamide A (1) and its new derivatives B-D (2-5). The structures of alpiniamides A-D were established and their relative configuration was determined by combination of partial Murata's method and ROESY experiment. The absolute configuration of alpiniamide A was established through Mosher's method. The gene cluster, responsible for the biosynthesis of alpiniamides (alp) has been identified by genome mining and gene deletion experiments. The successful expression of the cloned alp gene cluster in a heterologous host supports these findings. Analysis of the architecture of the alp gene cluster and the feeding of labeled precursors elucidated the alpiniamide biosynthetic pathway. The biosynthesis of alpiniamides is an example of a rather simple polyketide assembly line generating unusual chemical diversity through the combination of domain/module skipping and double bond migration events.
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Affiliation(s)
- Constanze Paulus
- Helmholtz-Institute for Pharmaceutical Research Saarland, Saarbrücken, Germany
- Department for Pharmaceutical Biotechnology, University of Saarland, Saarbrücken, Germany
| | - Yuriy Rebets
- Department for Pharmaceutical Biotechnology, University of Saarland, Saarbrücken, Germany
| | - Josef Zapp
- Department for Pharmaceutical Biotechnology, University of Saarland, Saarbrücken, Germany
| | - Christian Rückert
- Center for Biotechnology (CeBiTec), Bielefeld University, Bielefeld, Germany
| | - Jörn Kalinowski
- Center for Biotechnology (CeBiTec), Bielefeld University, Bielefeld, Germany
| | - Andriy Luzhetskyy
- Helmholtz-Institute for Pharmaceutical Research Saarland, Saarbrücken, Germany
- Department for Pharmaceutical Biotechnology, University of Saarland, Saarbrücken, Germany
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7
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Tao X, Zheng B, Bai T, Li MH, Ling J. Polymerization of N-Substituted Glycine N-Thiocarboxyanhydride through Regioselective Initiation of Cysteamine: A Direct Way toward Thiol-Capped Polypeptoids. Macromolecules 2018. [DOI: 10.1021/acs.macromol.8b00259] [Citation(s) in RCA: 31] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Affiliation(s)
- Xinfeng Tao
- MOE Key Laboratory of Macromolecular Synthesis and Functionalization, Department of Polymer Science and Engineering, Zhejiang University, Hangzhou 310027, China
- PSL Université Paris, CNRS, Institut de Recherche de Chimie Paris, UMR8247, Chimie ParisTech, 11 rue Pierre et Marie Curie, 75005 Paris, France
| | - Botuo Zheng
- MOE Key Laboratory of Macromolecular Synthesis and Functionalization, Department of Polymer Science and Engineering, Zhejiang University, Hangzhou 310027, China
| | - Tianwen Bai
- MOE Key Laboratory of Macromolecular Synthesis and Functionalization, Department of Polymer Science and Engineering, Zhejiang University, Hangzhou 310027, China
| | - Min-Hui Li
- MOE Key Laboratory of Macromolecular Synthesis and Functionalization, Department of Polymer Science and Engineering, Zhejiang University, Hangzhou 310027, China
- PSL Université Paris, CNRS, Institut de Recherche de Chimie Paris, UMR8247, Chimie ParisTech, 11 rue Pierre et Marie Curie, 75005 Paris, France
- Beijing Advanced Innovation Center for Soft Matter Science and Engineering, Beijing University of Chemical Technology, 15 North Third Ring Road, Chaoyang District, 100029 Beijing, China
| | - Jun Ling
- MOE Key Laboratory of Macromolecular Synthesis and Functionalization, Department of Polymer Science and Engineering, Zhejiang University, Hangzhou 310027, China
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8
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Uria AR, Piel J, Wakimoto T. Biosynthetic Insights of Calyculin- and Misakinolide-Type Compounds in "Candidatus Entotheonella sp.". Methods Enzymol 2018; 604:287-330. [PMID: 29779656 DOI: 10.1016/bs.mie.2018.02.017] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/09/2022]
Abstract
Microbial symbionts are recognized as the important sources of numerous sponge-derived metabolites with potent biological activities. The limitation to cultivate the majority of potential symbionts has hampered attempts to explore and exploit their natural products for further development toward medical applications. Metagenomics-guided approaches have enabled cloning of natural product biosynthesis genes from uncultured microbial symbionts. Subsequent activation of biosynthesis genes in easily culturable bacteria could lead to the sustainable production of rare sponge-derived compounds. In this chapter, we highlight metagenomic strategies to reveal natural product biosynthetic pathways in sponge metagenomes based on the calyculin and misakinolide polyketides. Techniques to identify the compound producer are briefly discussed. We further describe examples of functional studies of the biosynthetic pathways of these two compound types with a special emphasis on the general experimental protocols for the activity assays of key proteins involved in their biosynthesis.
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Affiliation(s)
- Agustinus R Uria
- Faculty of Pharmaceutical Sciences, Hokkaido University, Sapporo, Japan.
| | - Jörn Piel
- Institute of Microbiology, Eidgenössische Technische Hochschule (ETH) Zurich, Zurich, Switzerland.
| | - Toshiyuki Wakimoto
- Faculty of Pharmaceutical Sciences, Hokkaido University, Sapporo, Japan.
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9
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Increased Biosynthetic Gene Dosage in a Genome-Reduced Defensive Bacterial Symbiont. mSystems 2017; 2:mSystems00096-17. [PMID: 29181447 PMCID: PMC5698493 DOI: 10.1128/msystems.00096-17] [Citation(s) in RCA: 40] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2017] [Accepted: 10/18/2017] [Indexed: 12/31/2022] Open
Abstract
Secondary metabolites, which are small-molecule organic compounds produced by living organisms, provide or inspire drugs for many different diseases. These natural products have evolved over millions of years to provide a survival benefit to the producing organism and often display potent biological activity with important therapeutic applications. For instance, defensive compounds in the environment may be cytotoxic to eukaryotic cells, a property exploitable for cancer treatment. Here, we describe the genome of an uncultured symbiotic bacterium that makes such a cytotoxic metabolite. This symbiont is losing genes that do not endow a selective advantage in a hospitable host environment. Secondary metabolism genes, however, are repeated multiple times in the genome, directly demonstrating their selective advantage. This finding shows the strength of selective forces in symbiotic relationships and suggests that uncultured bacteria in such relationships should be targeted for drug discovery efforts. A symbiotic lifestyle frequently results in genome reduction in bacteria; the isolation of small populations promotes genetic drift and the fixation of deletions and deleterious mutations over time. Transitions in lifestyle, including host restriction or adaptation to an intracellular habitat, are thought to precipitate a wave of sequence degradation events and consequent proliferation of pseudogenes. We describe here a verrucomicrobial symbiont of the tunicate Lissoclinum sp. that appears to be undergoing such a transition, with low coding density and many identifiable pseudogenes. However, despite the overall drive toward genome reduction, this symbiont maintains seven copies of a large polyketide synthase (PKS) pathway for the mandelalides (mnd), cytotoxic compounds that likely constitute a chemical defense for the host. There is evidence of ongoing degradation in a small number of these repeats—including variable borders, internal deletions, and single nucleotide polymorphisms (SNPs). However, the gene dosage of most of the pathway is increased at least 5-fold. Correspondingly, this single pathway accounts for 19% of the genome by length and 25.8% of the coding capacity. This increased gene dosage in the face of generalized sequence degradation and genome reduction suggests that mnd genes are under strong purifying selection and are important to the symbiotic relationship. IMPORTANCE Secondary metabolites, which are small-molecule organic compounds produced by living organisms, provide or inspire drugs for many different diseases. These natural products have evolved over millions of years to provide a survival benefit to the producing organism and often display potent biological activity with important therapeutic applications. For instance, defensive compounds in the environment may be cytotoxic to eukaryotic cells, a property exploitable for cancer treatment. Here, we describe the genome of an uncultured symbiotic bacterium that makes such a cytotoxic metabolite. This symbiont is losing genes that do not endow a selective advantage in a hospitable host environment. Secondary metabolism genes, however, are repeated multiple times in the genome, directly demonstrating their selective advantage. This finding shows the strength of selective forces in symbiotic relationships and suggests that uncultured bacteria in such relationships should be targeted for drug discovery efforts. Author Video: An author video summary of this article is available.
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10
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Helfrich EJN, Piel J. Biosynthesis of polyketides by trans-AT polyketide synthases. Nat Prod Rep 2016; 33:231-316. [DOI: 10.1039/c5np00125k] [Citation(s) in RCA: 230] [Impact Index Per Article: 28.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
This review discusses the biosynthesis of natural products that are generated bytrans-AT polyketide synthases, a family of catalytically versatile enzymes that represents one of the major group of proteins involved in the production of bioactive polyketides.
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Affiliation(s)
- Eric J. N. Helfrich
- Institute of Microbiology
- Eidgenössische Technische Hochschule (ETH) Zurich
- 8093 Zurich
- Switzerland
| | - Jörn Piel
- Institute of Microbiology
- Eidgenössische Technische Hochschule (ETH) Zurich
- 8093 Zurich
- Switzerland
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11
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Murphy AC, Hong H, Vance S, Broadhurst RW, Leadlay PF. Broadening substrate specificity of a chain-extending ketosynthase through a single active-site mutation. Chem Commun (Camb) 2016; 52:8373-6. [DOI: 10.1039/c6cc03501a] [Citation(s) in RCA: 35] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
An in vitro model system based on a ketosynthase domain of the erythromycin polyketide synthase was used to probe the apparent substrate tolerance of ketosynthase domains of the mycolactone polyketide synthase.
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Affiliation(s)
- Annabel C. Murphy
- Department of Biochemistry
- University of Cambridge
- Cambridge CB2 1GA
- UK
| | - Hui Hong
- Department of Biochemistry
- University of Cambridge
- Cambridge CB2 1GA
- UK
| | - Steve Vance
- Department of Biochemistry
- University of Cambridge
- Cambridge CB2 1GA
- UK
- Crescendo Biologics Ltd
| | | | - Peter F. Leadlay
- Department of Biochemistry
- University of Cambridge
- Cambridge CB2 1GA
- UK
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12
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Uytterhoeven B, Appermans K, Song L, Masschelein J, Lathouwers T, Michiels CW, Lavigne R. Systematic analysis of the kalimantacin assembly line NRPS module using an adapted targeted mutagenesis approach. Microbiologyopen 2015; 5:279-86. [PMID: 26666990 PMCID: PMC4831472 DOI: 10.1002/mbo3.326] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2015] [Revised: 10/26/2015] [Accepted: 11/04/2015] [Indexed: 01/10/2023] Open
Abstract
Kalimantacin is an antimicrobial compound with strong antistaphylococcal activity that is produced by a hybrid trans‐acyltransferase polyketide synthase/nonribosomal peptide synthetase system in Pseudomonas fluorescens BCCM_ID9359. We here present a systematic analysis of the substrate specificity of the glycine‐incorporating adenylation domain from the kalimantacin biosynthetic assembly line by a targeted mutagenesis approach. The specificity‐conferring code was adapted for use in Pseudomonas and mutated adenylation domain active site sequences were introduced in the kalimantacin gene cluster, using a newly adapted ligation independent cloning method. Antimicrobial activity screens and LC‐MS analyses revealed that the production of the kalimantacin analogues in the mutated strains was abolished. These results support the idea that further insight in the specificity of downstream domains in nonribosomal peptide synthetases and polyketide synthases is required to efficiently engineer these strains in vivo.
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Affiliation(s)
- Birgit Uytterhoeven
- Laboratory of Gene Technology, KU Leuven, Kasteelpark Arenberg 21 box 2462, Heverlee, B-3001, Belgium
| | - Kenny Appermans
- Laboratory of Gene Technology, KU Leuven, Kasteelpark Arenberg 21 box 2462, Heverlee, B-3001, Belgium
| | - Lijiang Song
- Department of Chemistry, University of Warwick, Gibbet Hill, Coventry, CV4 7AL, United Kingdom
| | - Joleen Masschelein
- Laboratory of Gene Technology, KU Leuven, Kasteelpark Arenberg 21 box 2462, Heverlee, B-3001, Belgium.,Department of Chemistry, University of Warwick, Gibbet Hill, Coventry, CV4 7AL, United Kingdom
| | - Thomas Lathouwers
- Laboratory of Gene Technology, KU Leuven, Kasteelpark Arenberg 21 box 2462, Heverlee, B-3001, Belgium
| | - Chris W Michiels
- Centre for Food and Microbial Technology, KU Leuven, Kasteelpark Arenberg 23 box 2457, Heverlee, B-3001, Belgium
| | - Rob Lavigne
- Laboratory of Gene Technology, KU Leuven, Kasteelpark Arenberg 21 box 2462, Heverlee, B-3001, Belgium
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13
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Structural and evolutionary relationships of "AT-less" type I polyketide synthase ketosynthases. Proc Natl Acad Sci U S A 2015; 112:12693-8. [PMID: 26420866 DOI: 10.1073/pnas.1515460112] [Citation(s) in RCA: 42] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Acyltransferase (AT)-less type I polyketide synthases (PKSs) break the type I PKS paradigm. They lack the integrated AT domains within their modules and instead use a discrete AT that acts in trans, whereas a type I PKS module minimally contains AT, acyl carrier protein (ACP), and ketosynthase (KS) domains. Structures of canonical type I PKS KS-AT didomains reveal structured linkers that connect the two domains. AT-less type I PKS KSs have remnants of these linkers, which have been hypothesized to be AT docking domains. Natural products produced by AT-less type I PKSs are very complex because of an increased representation of unique modifying domains. AT-less type I PKS KSs possess substrate specificity and fall into phylogenetic clades that correlate with their substrates, whereas canonical type I PKS KSs are monophyletic. We have solved crystal structures of seven AT-less type I PKS KS domains that represent various sequence clusters, revealing insight into the large structural and subtle amino acid residue differences that lead to unique active site topologies and substrate specificities. One set of structures represents a larger group of KS domains from both canonical and AT-less type I PKSs that accept amino acid-containing substrates. One structure has a partial AT-domain, revealing the structural consequences of a type I PKS KS evolving into an AT-less type I PKS KS. These structures highlight the structural diversity within the AT-less type I PKS KS family, and most important, provide a unique opportunity to study the molecular evolution of substrate specificity within the type I PKSs.
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Ueoka R, Uria AR, Reiter S, Mori T, Karbaum P, Peters EE, Helfrich EJN, Morinaka BI, Gugger M, Takeyama H, Matsunaga S, Piel J. Metabolic and evolutionary origin of actin-binding polyketides from diverse organisms. Nat Chem Biol 2015; 11:705-12. [PMID: 26236936 DOI: 10.1038/nchembio.1870] [Citation(s) in RCA: 98] [Impact Index Per Article: 10.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2014] [Accepted: 06/05/2015] [Indexed: 11/09/2022]
Abstract
Actin-targeting macrolides comprise a large, structurally diverse group of cytotoxins isolated from remarkably dissimilar micro- and macroorganisms. In spite of their disparate origins and structures, many of these compounds bind actin at the same site and exhibit structural relationships reminiscent of modular, combinatorial drug libraries. Here we investigate biosynthesis and evolution of three compound groups: misakinolides, scytophycin-type compounds and luminaolides. For misakinolides from the sponge Theonella swinhoei WA, our data suggest production by an uncultivated 'Entotheonella' symbiont, further supporting the relevance of these bacteria as sources of bioactive polyketides and peptides in sponges. Insights into misakinolide biosynthesis permitted targeted genome mining for other members, providing a cyanobacterial luminaolide producer as the first cultivated source for this dimeric compound family. The data indicate that this polyketide family is bacteria-derived and that the unusual macrolide diversity is the result of combinatorial pathway modularity for some compounds and of convergent evolution for others.
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Affiliation(s)
- Reiko Ueoka
- Institute of Microbiology, Eigenössische Technische Hochschule (ETH) Zurich, Zurich, Switzerland
| | - Agustinus R Uria
- Institute of Microbiology, Eigenössische Technische Hochschule (ETH) Zurich, Zurich, Switzerland
| | - Silke Reiter
- Institute of Microbiology, Eigenössische Technische Hochschule (ETH) Zurich, Zurich, Switzerland
| | - Tetsushi Mori
- Faculty of Science and Engineering, Waseda University Center for Advanced Biomedical Sciences, Tokyo, Japan
| | - Petra Karbaum
- 1] Institute of Microbiology, Eigenössische Technische Hochschule (ETH) Zurich, Zurich, Switzerland. [2] Kekulé Institute of Organic Chemistry and Biochemistry, Bonn, Germany
| | - Eike E Peters
- Institute of Microbiology, Eigenössische Technische Hochschule (ETH) Zurich, Zurich, Switzerland
| | - Eric J N Helfrich
- Institute of Microbiology, Eigenössische Technische Hochschule (ETH) Zurich, Zurich, Switzerland
| | - Brandon I Morinaka
- Institute of Microbiology, Eigenössische Technische Hochschule (ETH) Zurich, Zurich, Switzerland
| | - Muriel Gugger
- Institut Pasteur, Collection des Cyanobactéries, Paris, France
| | - Haruko Takeyama
- Faculty of Science and Engineering, Waseda University Center for Advanced Biomedical Sciences, Tokyo, Japan
| | - Shigeki Matsunaga
- Laboratory of Aquatic Natural Products Chemistry, Graduate School of Agricultural and Life Sciences, The University of Tokyo, Tokyo, Japan
| | - Jörn Piel
- Institute of Microbiology, Eigenössische Technische Hochschule (ETH) Zurich, Zurich, Switzerland
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Jenner M, Afonso JP, Bailey HR, Frank S, Kampa A, Piel J, Oldham NJ. Acyl-Chain Elongation Drives Ketosynthase Substrate Selectivity intrans-Acyltransferase Polyketide Synthases. Angew Chem Int Ed Engl 2014. [DOI: 10.1002/ange.201410219] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
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Jenner M, Afonso JP, Bailey HR, Frank S, Kampa A, Piel J, Oldham NJ. Acyl-chain elongation drives ketosynthase substrate selectivity in trans-acyltransferase polyketide synthases. Angew Chem Int Ed Engl 2014; 54:1817-21. [PMID: 25529827 DOI: 10.1002/anie.201410219] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2014] [Revised: 11/10/2014] [Indexed: 11/09/2022]
Abstract
Type I modular polyketide synthases (PKSs), which are responsible for the biosynthesis of many biologically active agents, possess a ketosynthase (KS) domain within each module to catalyze chain elongation. Acylation of the KS active site Cys residue is followed by transfer to malonyl-ACP to yield an extended β-ketoacyl chain (ACP = acyl carrier protein). To date, the precise contribution of KS selectivity in controlling product fidelity has been unclear. Six KS domains from trans-acyltransferase (trans-AT) PKSs were subjected to a mass spectrometry based elongation assay, and higher substrate selectivity was identified for the elongating step than in preceding acylation. A close correspondence between the observed KS selectivity and that predicted by phylogenetic analysis was seen. These findings provide insights into the mechanism of KS selectivity in this important group of PKSs, can serve as guidance for engineering, and show that targeted mutagenesis can be used to expand the repertoire of acceptable substrates.
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Affiliation(s)
- Matthew Jenner
- School of Chemistry, University of Nottingham, University Park, Nottingham NG7 2RD (UK)
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Gay DC, Gay G, Axelrod AJ, Jenner M, Kohlhaas C, Kampa A, Oldham NJ, Piel J, Keatinge-Clay AT. A close look at a ketosynthase from a trans-acyltransferase modular polyketide synthase. Structure 2014; 22:444-51. [PMID: 24508341 DOI: 10.1016/j.str.2013.12.016] [Citation(s) in RCA: 49] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2013] [Revised: 12/15/2013] [Accepted: 12/16/2013] [Indexed: 10/25/2022]
Abstract
The recently discovered trans-acyltransferase modular polyketide synthases catalyze the biosynthesis of a wide range of bioactive natural products in bacteria. Here we report the structure of the second ketosynthase from the bacillaene trans-acyltransferase polyketide synthase. This 1.95 Å resolution structure provides the highest resolution view available of a modular polyketide synthase ketosynthase and reveals a flanking subdomain that is homologous to an ordered linker in cis-acyltransferase modular polyketide synthases. The structure of the cysteine-to-serine mutant of the ketosynthase acylated by its natural substrate provides high-resolution details of how a native polyketide intermediate is bound and helps explain the basis of ketosynthase substrate specificity. The substrate range of the ketosynthase was further investigated by mass spectrometry.
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Affiliation(s)
- Darren C Gay
- Department of Molecular Biosciences, The University of Texas at Austin, 1 University Station A5300, Austin, TX 78712, USA
| | - Glen Gay
- Department of Molecular Biosciences, The University of Texas at Austin, 1 University Station A5300, Austin, TX 78712, USA
| | - Abram J Axelrod
- Department of Chemistry, The University of Texas at Austin, 1 University Station A5300, Austin, TX 78712, USA
| | - Matthew Jenner
- School of Chemistry, University of Nottingham, University Park, Nottingham NG7 2RD, UK
| | - Christoph Kohlhaas
- Kekulé Institute of Organic Chemistry and Biochemistry, University of Bonn, Gerhard-Domagk-Straße 1, 53121 Bonn, Germany
| | - Annette Kampa
- Kekulé Institute of Organic Chemistry and Biochemistry, University of Bonn, Gerhard-Domagk-Straße 1, 53121 Bonn, Germany
| | - Neil J Oldham
- School of Chemistry, University of Nottingham, University Park, Nottingham NG7 2RD, UK
| | - Jörn Piel
- Kekulé Institute of Organic Chemistry and Biochemistry, University of Bonn, Gerhard-Domagk-Straße 1, 53121 Bonn, Germany; Institute of Microbiology, Eidgenössische Technische Hochschule (ETH) Zürich, Vladimir-Prelog-Weg 1-5/10, 8093 Zürich, Switzerland
| | - Adrian T Keatinge-Clay
- Department of Molecular Biosciences, The University of Texas at Austin, 1 University Station A5300, Austin, TX 78712, USA; Department of Chemistry, The University of Texas at Austin, 1 University Station A5300, Austin, TX 78712, USA.
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