1
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Wang S, Wu K, Tang YJ, Deng H. Dehydroamino acid residues in bioactive natural products. Nat Prod Rep 2024; 41:273-297. [PMID: 37942836 PMCID: PMC10880069 DOI: 10.1039/d3np00041a] [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: 09/08/2023] [Indexed: 11/10/2023]
Abstract
Covering: 2000 to up to 2023α,β-Dehydroamino acids (dhAAs) are unsaturated nonproteinogenic amino acids found in a wide array of naturally occurring peptidyl metabolites, predominantly those from bacteria. Other organisms, such as fungi, higher plants and marine invertebrates, have also been found to produce dhAA-containing peptides. The α,β-unsaturation in dhAAs has profound effects on the properties of these molecules. They display significant synthetic flexibility, readily undergoing reactions such as Michael additions, transition-metal-catalysed cross-couplings, and cycloadditions. These residues in peptides/proteins also exhibit great potential in bioorthogonal applications using click chemistry. Peptides containing contiguous dhAA residues have been extensively investigated in the field of foldamers, self-assembling supermolecules that mimic biomacromolecules such as proteins to fold into well-defined conformations. dhAA residues in these peptidyl materials tend to form a 2.05-helix. As a result, stretches of dhAA residues arrange in an extended conformation. In particular, peptidyl foldamers containing β-enamino acid units display interesting conformational, electronic, and supramolecular aggregation properties that can be modulated by light-dependent E-Z isomerization. Among approximately 40 dhAAs found in the natural product inventory, dehydroalanine (Dha) and dehydrobutyrine (Dhb) are the most abundant. Dha is the simplest dehydro-α-amino acid, or α-dhAA, without any geometrical isomers, while its re-arranged isomer, 3-aminoacrylic acid (Aaa or ΔβAla), is the simplest dehydro-β-amino acid, or β-enamino acid, and displays E/Z isomerism. Dhb is the simplest α-dhAA that exhibits E/Z isomerism. The Z-isomer of Dhb (Z-Dhb) is sterically favourable and is present in the majority of naturally occurring peptides containing Dhb residues. Dha and Z-Dhb motifs are commonly found in ribosomally synthesized and post-translationally modified peptides (RiPPs). In the last decade, the formation of Dha and Dhb motifs in RiPPs has been extensively investigated, which will be briefly discussed in this review. The formation of other dhAA residues in natural products (NPs) is, however, less understood. In this review, we will discuss recent advances in the biosynthesis of peptidyl NPs containing unusual dhAA residues and cryptic dhAA residues. The proposed biosynthetic pathways of these natural products will also be discussed.
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Affiliation(s)
- Shan Wang
- State Key Laboratory of Microbial Technology, Shandong University, Qingdao 266237, China.
| | - Kewen Wu
- Department of Chemistry, University of Aberdeen, Aberdeen AB24 3UE, UK.
| | - Ya-Jie Tang
- State Key Laboratory of Microbial Technology, Shandong University, Qingdao 266237, China.
| | - Hai Deng
- Department of Chemistry, University of Aberdeen, Aberdeen AB24 3UE, UK.
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2
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Fallon TR, Shende VV, Wierzbicki IH, Auber RP, Gonzalez DJ, Wisecaver JH, Moore BS. Giant polyketide synthase enzymes biosynthesize a giant marine polyether biotoxin. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.01.29.577497. [PMID: 38352448 PMCID: PMC10862718 DOI: 10.1101/2024.01.29.577497] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 02/22/2024]
Abstract
Prymnesium parvum are harmful haptophyte algae that cause massive environmental fish-kills. Their polyketide polyether toxins, the prymnesins, are amongst the largest nonpolymeric compounds in nature, alongside structurally-related health-impacting "red-tide" polyether toxins whose biosynthetic origins have been an enigma for over 40 years. Here we report the 'PKZILLAs', massive P. parvum polyketide synthase (PKS) genes, whose existence and challenging genomic structure evaded prior detection. PKZILLA-1 and -2 encode giant protein products of 4.7 and 3.2 MDa with 140 and 99 enzyme domains, exceeding the largest known protein titin and all other known PKS systems. Their predicted polyene product matches the proposed pre-prymnesin precursor of the 90-carbon-backbone A-type prymnesins. This discovery establishes a model system for microalgal polyether biosynthesis and expands expectations of genetic and enzymatic size limits in biology.
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Affiliation(s)
- Timothy R. Fallon
- Center for Marine Biotechnology and Biomedicine, Scripps Institution of Oceanography and University of California, San Diego; 9500 Gilman Dr #0204, La Jolla, CA 92093, USA
| | - Vikram V. Shende
- Center for Marine Biotechnology and Biomedicine, Scripps Institution of Oceanography and University of California, San Diego; 9500 Gilman Dr #0204, La Jolla, CA 92093, USA
| | - Igor H. Wierzbicki
- Department of Pharmacology, University of California, San Diego; 9500 Gilman Dr, La Jolla, CA 92093, USA
| | - Robert P. Auber
- Department of Biochemistry, Purdue University; 175 S University St, West Lafayette, IN 47907, USA
- Purdue Center for Plant Biology, Purdue University; 175 S University St, West Lafayette, IN 47907, USA
| | - David J. Gonzalez
- Department of Pharmacology, University of California, San Diego; 9500 Gilman Dr, La Jolla, CA 92093, USA
- Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California, San Diego; 9500 Gilman Dr, La Jolla, CA 92093, USA
| | - Jennifer H. Wisecaver
- Department of Biochemistry, Purdue University; 175 S University St, West Lafayette, IN 47907, USA
- Purdue Center for Plant Biology, Purdue University; 175 S University St, West Lafayette, IN 47907, USA
| | - Bradley S. Moore
- Center for Marine Biotechnology and Biomedicine, Scripps Institution of Oceanography and University of California, San Diego; 9500 Gilman Dr #0204, La Jolla, CA 92093, USA
- Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California, San Diego; 9500 Gilman Dr, La Jolla, CA 92093, USA
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3
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Vriens E, De Ruysscher D, Weir ANM, Dekimpe S, Steurs G, Shemy A, Persoons L, Santos AR, Williams C, Daelemans D, Crump MP, Voet A, De Borggraeve W, Lescrinier E, Masschelein J. Polyketide Synthase-Mediated O-Methyloxime Formation in the Biosynthesis of the Oximidine Anticancer Agents. Angew Chem Int Ed Engl 2023; 62:e202304476. [PMID: 37218580 DOI: 10.1002/anie.202304476] [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: 03/28/2023] [Revised: 05/18/2023] [Accepted: 05/22/2023] [Indexed: 05/24/2023]
Abstract
Bacterial trans-acyltransferase polyketide synthases (trans-AT PKSs) are modular megaenzymes that employ unusual catalytic domains to assemble diverse bioactive natural products. One such PKS is responsible for the biosynthesis of the oximidine anticancer agents, oxime-substituted benzolactone enamides that inhibit vacuolar H+ -ATPases. Here, we describe the identification of the oximidine gene cluster in Pseudomonas baetica and the characterization of four novel oximidine variants, including a structurally simpler intermediate that retains potent anticancer activity. Using a combination of in vivo, in vitro and computational approaches, we experimentally elucidate the oximidine biosynthetic pathway and reveal an unprecedented mechanism for O-methyloxime formation. We show that this process involves a specialized monooxygenase and methyltransferase domain and provide insight into their activity, mechanism and specificity. Our findings expand the catalytic capabilities of trans-AT PKSs and identify potential strategies for the production of novel oximidine analogues.
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Affiliation(s)
- Eveline Vriens
- Laboratory for Biomolecular Discovery and Engineering, Department of Biology, KU Leuven, 3001, Heverlee, Belgium
- VIB-KU Leuven Center for Microbiology, 3001, Heverlee, Belgium
| | - Dries De Ruysscher
- Laboratory for Biomolecular Discovery and Engineering, Department of Biology, KU Leuven, 3001, Heverlee, Belgium
- VIB-KU Leuven Center for Microbiology, 3001, Heverlee, Belgium
| | - Angus N M Weir
- Laboratory for Biomolecular Discovery and Engineering, Department of Biology, KU Leuven, 3001, Heverlee, Belgium
- VIB-KU Leuven Center for Microbiology, 3001, Heverlee, Belgium
| | - Sofie Dekimpe
- Laboratory for Biomolecular Discovery and Engineering, Department of Biology, KU Leuven, 3001, Heverlee, Belgium
- VIB-KU Leuven Center for Microbiology, 3001, Heverlee, Belgium
| | - Gert Steurs
- Department of Chemistry, KU Leuven, 3001, Heverlee, Belgium
| | - Ahmed Shemy
- Laboratory for Biomolecular Modelling and Design, Department of Chemistry, KU Leuven, 3001, Heverlee, Belgium
| | - Leentje Persoons
- Laboratory of Virology and Chemotherapy, Rega Institute for Medical Research, KU Leuven, 3000, Leuven, Belgium
| | | | | | - Dirk Daelemans
- Laboratory of Virology and Chemotherapy, Rega Institute for Medical Research, KU Leuven, 3000, Leuven, Belgium
| | - Matthew P Crump
- School of Chemistry, University of Bristol, Bristol, BS8 1TS, UK
| | - Arnout Voet
- Laboratory for Biomolecular Modelling and Design, Department of Chemistry, KU Leuven, 3001, Heverlee, Belgium
| | - Wim De Borggraeve
- Sustainable Chemistry for Metals and Molecules, Department of Chemistry, KU Leuven, 3001, Heverlee, Belgium
| | - Eveline Lescrinier
- Laboratory for Medicinal Chemistry, Rega Institute for Medical Research, KU Leuven, 3000, Leuven, Belgium
| | - Joleen Masschelein
- Laboratory for Biomolecular Discovery and Engineering, Department of Biology, KU Leuven, 3001, Heverlee, Belgium
- VIB-KU Leuven Center for Microbiology, 3001, Heverlee, Belgium
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4
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Hobson C, Jenner M, Jian X, Griffiths D, Roberts DM, Rey-Carrizo M, Challis GL. Diene incorporation by a dehydratase domain variant in modular polyketide synthases. Nat Chem Biol 2022; 18:1410-1416. [PMID: 36109649 PMCID: PMC7613849 DOI: 10.1038/s41589-022-01127-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2020] [Accepted: 07/27/2022] [Indexed: 11/09/2022]
Abstract
Modular polyketide synthases (PKSs) are biosynthetic assembly lines that construct structurally diverse natural products with wide-ranging applications in medicine and agriculture. Various mechanisms contribute to structural diversification during PKS-mediated chain assembly, including dehydratase (DH) domain-mediated elimination of water from R and S-configured 3-hydroxy-thioesters to introduce E- and Z-configured carbon-carbon double bonds, respectively. Here we report the discovery of a DH domain variant that catalyzes the sequential elimination of two molecules of water from a (3R, 5S)-3,5-dihydroxy thioester during polyketide chain assembly, introducing a conjugated E,Z-diene into various modular PKS products. We show that the reaction proceeds via a (2E, 5S)-2-enoyl-5-hydroxy-thioester intermediate and involves an additional universally conserved histidine residue that is absent from the active site of most conventional DH domains. These findings expand the diverse range of chemistries mediated by DH-like domains in modular PKSs, highlighting the catalytic versatility of the double hotdog fold.
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Affiliation(s)
- Christian Hobson
- Department of Chemistry, University of Warwick, Coventry, UK.,Willow Biosciences Inc., Vancouver, British Columbia, Canada
| | - Matthew Jenner
- Department of Chemistry, University of Warwick, Coventry, UK.,Warwick Integrative Synthetic Biology Centre, University of Warwick, Coventry, UK
| | - Xinyun Jian
- Department of Chemistry, University of Warwick, Coventry, UK.,Warwick Integrative Synthetic Biology Centre, University of Warwick, Coventry, UK.,Department of Biochemistry and Molecular Biology, Biomedicine Discovery Institute, Monash University, Clayton, Victoria, Australia
| | - Daniel Griffiths
- Department of Chemistry, University of Warwick, Coventry, UK.,Monash University Accident Research Centre, Clayton, Victoria, Australia
| | | | - Matias Rey-Carrizo
- Department of Chemistry, University of Warwick, Coventry, UK.,BCN Medical Writing, Sabadell, Spain
| | - Gregory L Challis
- Department of Chemistry, University of Warwick, Coventry, UK. .,Warwick Integrative Synthetic Biology Centre, University of Warwick, Coventry, UK. .,Department of Biochemistry and Molecular Biology, Biomedicine Discovery Institute, Monash University, Clayton, Victoria, Australia. .,ARC Centre of Excellence for Innovations in Peptide and Protein Science, Monash University, Clayton, Victoria, Australia.
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5
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Xu H, Wochele A, Luo M, Schnakenburg G, Sun Y, Brötz-Oesterhelt H, Dickschat JS. Synthesis of tryptophan-dehydrobutyrine diketopiperazine and biological activity of hangtaimycin and its co-metabolites. Beilstein J Org Chem 2022; 18:1159-1165. [PMID: 36128431 PMCID: PMC9475180 DOI: 10.3762/bjoc.18.120] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2022] [Accepted: 08/29/2022] [Indexed: 11/23/2022] Open
Abstract
An improved synthesis for tryptophan-dehydrobutyrine diketopiperazine (TDD), a co-metabolite of the hybrid polyketide/non-ribosomal peptide hangtaimycin, starting from ʟ-tryptophan is presented. Comparison to TDD isolated from the hangtaimycin producer Streptomyces spectabilis confirmed its S configuration. The X-ray structure of the racemate shows an interesting dimerisation through hydrogen bridges. The results from bioactivity testings of hangtaimycin, TDD and the hangtaimycin degradation product HTM222 are given.
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Affiliation(s)
- Houchao Xu
- Kekulé-Institute of Organic Chemistry and Biochemistry, University of Bonn, Gerhard-Domagk-Straße 1, 53121 Bonn, Germany
| | - Anne Wochele
- Interfaculty Institute of Microbiology and Infection Medicine, Department of Microbial Bioactive Compounds, University of Tübingen, Auf der Morgenstelle 28, 72076 Tübingen, Germany
| | - Minghe Luo
- Key Laboratory of Combinatorial Biosynthesis and Drug Discovery, Ministry of Education, and School of Pharmaceutical Sciences, Wuhan University, No. 185 East Lake Road, Wuhan, 430071, People's Republic of China
| | - Gregor Schnakenburg
- Institute of Inorganic Chemistry, University of Bonn, Gerhard-Domagk-Straße 1, 53121 Bonn, Germany
| | - Yuhui Sun
- Key Laboratory of Combinatorial Biosynthesis and Drug Discovery, Ministry of Education, and School of Pharmaceutical Sciences, Wuhan University, No. 185 East Lake Road, Wuhan, 430071, People's Republic of China
| | - Heike Brötz-Oesterhelt
- Interfaculty Institute of Microbiology and Infection Medicine, Department of Microbial Bioactive Compounds, University of Tübingen, Auf der Morgenstelle 28, 72076 Tübingen, 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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6
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Passmore M, Gallo A, Lewandowski JR, Jenner M. Molecular basis for acyl carrier protein-ketoreductase interaction in trans-acyltransferase polyketide synthases. Chem Sci 2021; 12:13676-13685. [PMID: 34760152 PMCID: PMC8549798 DOI: 10.1039/d1sc03478b] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2021] [Accepted: 09/29/2021] [Indexed: 12/29/2022] Open
Abstract
The biosynthesis of polyketides by type I modular polyketide synthases (PKS) relies on co-ordinated interactions between acyl carrier protein (ACP) domains and catalytic domains within the megasynthase. Despite the importance of these interactions, and their implications for biosynthetic engineering efforts, they remain poorly understood. Here, we report the molecular details of the interaction interface between an ACP domain and a ketoreductase (KR) domain from a trans-acyltransferase (trans-AT) PKS. Using a high-throughput mass spectrometry (MS)-based assay in combination with scanning alanine mutagenesis, residues contributing to the KR-binding epitope of the ACP domain were identified. Application of carbene footprinting revealed the ACP-binding site on the KR domain surface, and molecular docking simulations driven by experimental data allowed production of an accurate model of the complex. Interactions between ACP and KR domains from trans-AT PKSs were found to be specific for their cognate partner, indicating highly optimised interaction interfaces driven by evolutionary processes. Using detailed knowledge of the ACP:KR interaction epitope, an ACP domain was engineered to interact with a non-cognate KR domain partner. The results provide novel, high resolution insights into the ACP:KR interface and offer valuable rules for future engineering efforts of biosynthetic assembly lines. The interaction epitope between a cognate KR–ACP domain pairing from a trans-AT polyketide synthase is elucidated in molecular detail, providing unique insights into recognition and specificity of the interface.![]()
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Affiliation(s)
- Munro Passmore
- Department of Chemistry, University of Warwick Coventry CV4 7AL UK
| | - Angelo Gallo
- Department of Chemistry, University of Warwick Coventry CV4 7AL UK
| | | | - Matthew Jenner
- Department of Chemistry, University of Warwick Coventry CV4 7AL UK .,Warwick Integrative Synthetic Biology Centre (WISB), University of Warwick Coventry CV4 7AL UK
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7
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Luo M, Xu H, Dong Y, Shen K, Lu J, Yin Z, Qi M, Sun G, Tang L, Xiang J, Deng Z, Dickschat JS, Sun Y. Der Mechanismus von dehydatisierenden Bimodulen in der
trans
‐Acyltransferase‐Polketidbiosynthese: Eine Modellstudie am hepatoprotektiven Hangtaimycin. Angew Chem Int Ed Engl 2021. [DOI: 10.1002/ange.202106250] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Affiliation(s)
- Minghe Luo
- Key Laboratory of Combinatorial Biosynthesis und Drug Discovery Ministry of Education, und School of Pharmaceutical Sciences Wuhan University No. 185 East Lake Road Wuhan 430071 People's Republic of China
| | - Houchao Xu
- Kekulé-Institut für Organische Chemie und Biochemie Universität Bonn Gerhard-Domagk-Straße 1 53121 Bonn Deutschland
| | - Yulu Dong
- Key Laboratory of Combinatorial Biosynthesis und Drug Discovery Ministry of Education, und School of Pharmaceutical Sciences Wuhan University No. 185 East Lake Road Wuhan 430071 People's Republic of China
| | - Kun Shen
- Key Laboratory of Combinatorial Biosynthesis und Drug Discovery Ministry of Education, und School of Pharmaceutical Sciences Wuhan University No. 185 East Lake Road Wuhan 430071 People's Republic of China
| | - Junlei Lu
- Key Laboratory of Combinatorial Biosynthesis und Drug Discovery Ministry of Education, und School of Pharmaceutical Sciences Wuhan University No. 185 East Lake Road Wuhan 430071 People's Republic of China
| | - Zhiyong Yin
- Kekulé-Institut für Organische Chemie und Biochemie Universität Bonn Gerhard-Domagk-Straße 1 53121 Bonn Deutschland
| | - Miaomiao Qi
- Key Laboratory of Combinatorial Biosynthesis und Drug Discovery Ministry of Education, und School of Pharmaceutical Sciences Wuhan University No. 185 East Lake Road Wuhan 430071 People's Republic of China
| | - Guo Sun
- Key Laboratory of Combinatorial Biosynthesis und Drug Discovery Ministry of Education, und School of Pharmaceutical Sciences Wuhan University No. 185 East Lake Road Wuhan 430071 People's Republic of China
| | - Lingjie Tang
- Key Laboratory of Combinatorial Biosynthesis und Drug Discovery Ministry of Education, und School of Pharmaceutical Sciences Wuhan University No. 185 East Lake Road Wuhan 430071 People's Republic of China
| | - Jin Xiang
- Key Laboratory of Combinatorial Biosynthesis und Drug Discovery Ministry of Education, und School of Pharmaceutical Sciences Wuhan University No. 185 East Lake Road Wuhan 430071 People's Republic of China
| | - Zixin Deng
- Key Laboratory of Combinatorial Biosynthesis und Drug Discovery Ministry of Education, und School of Pharmaceutical Sciences Wuhan University No. 185 East Lake Road Wuhan 430071 People's Republic of China
| | - Jeroen S. Dickschat
- Kekulé-Institut für Organische Chemie und Biochemie Universität Bonn Gerhard-Domagk-Straße 1 53121 Bonn Deutschland
| | - Yuhui Sun
- Key Laboratory of Combinatorial Biosynthesis und Drug Discovery Ministry of Education, und School of Pharmaceutical Sciences Wuhan University No. 185 East Lake Road Wuhan 430071 People's Republic of China
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8
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Luo M, Xu H, Dong Y, Shen K, Lu J, Yin Z, Qi M, Sun G, Tang L, Xiang J, Deng Z, Dickschat JS, Sun Y. The Mechanism of Dehydrating Bimodules in trans-Acyltransferase Polyketide Biosynthesis: A Showcase Study on Hepatoprotective Hangtaimycin. Angew Chem Int Ed Engl 2021; 60:19139-19143. [PMID: 34219345 PMCID: PMC8456789 DOI: 10.1002/anie.202106250] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2021] [Revised: 06/30/2021] [Indexed: 11/29/2022]
Abstract
A bioassay‐guided fractionation led to the isolation of hangtaimycin (HTM) from Streptomyces spectabilis CCTCC M2017417 and the discovery of its hepatoprotective properties. Structure elucidation by NMR suggested the need for a structural revision. A putative HTM degradation product was also isolated and its structure was confirmed by total synthesis. The biosynthetic gene cluster was identified and resembles a hybrid trans‐AT PKS/NRPS biosynthetic machinery whose first PKS enzyme contains an internal dehydrating bimodule, which is usually found split in other trans‐AT PKSs. The mechanisms of such dehydrating bimodules have often been proposed, but have never been deeply investigated. Here we present in vivo mutations and in vitro enzymatic experiments that give first and detailed mechanistic insights into catalysis by dehydrating bimodules.
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Affiliation(s)
- Minghe Luo
- Key Laboratory of Combinatorial Biosynthesis and Drug Discovery, Ministry of Education, and School of Pharmaceutical Sciences, Wuhan University, No. 185 East Lake Road, Wuhan, 430071, People's Republic of China
| | - Houchao Xu
- Kekulé-Institute for Organic Chemistry and Biochemistry, University of Bonn, Gerhard-Domagk-Straße 1, 53121, Bonn, Germany
| | - Yulu Dong
- Key Laboratory of Combinatorial Biosynthesis and Drug Discovery, Ministry of Education, and School of Pharmaceutical Sciences, Wuhan University, No. 185 East Lake Road, Wuhan, 430071, People's Republic of China
| | - Kun Shen
- Key Laboratory of Combinatorial Biosynthesis and Drug Discovery, Ministry of Education, and School of Pharmaceutical Sciences, Wuhan University, No. 185 East Lake Road, Wuhan, 430071, People's Republic of China
| | - Junlei Lu
- Key Laboratory of Combinatorial Biosynthesis and Drug Discovery, Ministry of Education, and School of Pharmaceutical Sciences, Wuhan University, No. 185 East Lake Road, Wuhan, 430071, People's Republic of China
| | - Zhiyong Yin
- Kekulé-Institute for Organic Chemistry and Biochemistry, University of Bonn, Gerhard-Domagk-Straße 1, 53121, Bonn, Germany
| | - Miaomiao Qi
- Key Laboratory of Combinatorial Biosynthesis and Drug Discovery, Ministry of Education, and School of Pharmaceutical Sciences, Wuhan University, No. 185 East Lake Road, Wuhan, 430071, People's Republic of China
| | - Guo Sun
- Key Laboratory of Combinatorial Biosynthesis and Drug Discovery, Ministry of Education, and School of Pharmaceutical Sciences, Wuhan University, No. 185 East Lake Road, Wuhan, 430071, People's Republic of China
| | - Lingjie Tang
- Key Laboratory of Combinatorial Biosynthesis and Drug Discovery, Ministry of Education, and School of Pharmaceutical Sciences, Wuhan University, No. 185 East Lake Road, Wuhan, 430071, People's Republic of China
| | - Jin Xiang
- Key Laboratory of Combinatorial Biosynthesis and Drug Discovery, Ministry of Education, and School of Pharmaceutical Sciences, Wuhan University, No. 185 East Lake Road, Wuhan, 430071, People's Republic of China
| | - Zixin Deng
- Key Laboratory of Combinatorial Biosynthesis and Drug Discovery, Ministry of Education, and School of Pharmaceutical Sciences, Wuhan University, No. 185 East Lake Road, Wuhan, 430071, People's Republic of China
| | - Jeroen S Dickschat
- Kekulé-Institute for Organic Chemistry and Biochemistry, University of Bonn, Gerhard-Domagk-Straße 1, 53121, Bonn, Germany
| | - Yuhui Sun
- Key Laboratory of Combinatorial Biosynthesis and Drug Discovery, Ministry of Education, and School of Pharmaceutical Sciences, Wuhan University, No. 185 East Lake Road, Wuhan, 430071, People's Republic of China
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9
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Yin Z, Dickschat JS. Cis double bond formation in polyketide biosynthesis. Nat Prod Rep 2021; 38:1445-1468. [PMID: 33475122 DOI: 10.1039/d0np00091d] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
Covering: up to 2020Polyketides form a large group of bioactive secondary metabolites that usually contain one or more double bonds. Although most of the double bonds found in polyketides are trans or E-configured, several cases are known in which cis or Z-configurations are observed. Double bond formation by polyketide synthases (PKSs) is widely recognised to be catalysed by ketoreduction and subsequent dehydration of the acyl carrier protein (ACP)-tethered 3-ketoacyl intermediate in the PKS biosynthetic assembly line with a specific stereochemical course in which the ketoreduction step determines the usual trans or more rare cis double bond configuration. Occasionally, other mechanisms for the installation of cis double bonds such as double bond formation during chain release or post-PKS modifications including, amongst others, isomerisations or double bond installations by oxidation are observed. This review discusses the peculiar mechanisms of cis double bond formation in polyketide biosynthesis.
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Affiliation(s)
- Zhiyong Yin
- Kekulé-Institute for Organic Chemistry and Biochemistry, University of Bonn, Gerhard-Domagk-Straße 1, 53121 Bonn, Germany.
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10
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Drufva EE, Spengler NR, Hix EG, Bailey CB. Site-Directed Mutagenesis of Modular Polyketide Synthase Ketoreductase Domains for Altered Stereochemical Control. Chembiochem 2020; 22:1122-1150. [PMID: 33185924 DOI: 10.1002/cbic.202000613] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2020] [Revised: 11/12/2020] [Indexed: 12/18/2022]
Abstract
Bacterial modular type I polyketide synthases (PKSs) are complex multidomain assembly line proteins that produce a range of pharmaceutically relevant molecules with a high degree of stereochemical control. Due to their colinear properties, they have been considerable targets for rational biosynthetic pathway engineering. Among the domains harbored within these complex assembly lines, ketoreductase (KR) domains have been extensively studied with the goal of altering their stereoselectivity by site-directed mutagenesis, as they confer much of the stereochemical complexity present in pharmaceutically active reduced polyketide scaffolds. Here we review all efforts to date to perform site-directed mutagenesis on PKS KRs, most of which have been done in the context of excised KR domains on model diffusible substrates such as β-keto N-acetyl cysteamine thioesters. We also discuss the challenges around translating the findings of these studies to alter stereocontrol in the context of a complex multidomain enzymatic assembly line.
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Affiliation(s)
- Erin E Drufva
- Department of Chemistry, University of Tennessee, Knoxville, Knoxville, TN 37996, USA
| | - Nolan R Spengler
- Department of Chemistry, University of Tennessee, Knoxville, Knoxville, TN 37996, USA
| | - Elijah G Hix
- Department of Chemistry, University of Tennessee, Knoxville, Knoxville, TN 37996, USA
| | - Constance B Bailey
- Department of Chemistry, University of Tennessee, Knoxville, Knoxville, TN 37996, USA
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11
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Hjerrild P, Tørring T, Poulsen TB. Dehydration reactions in polyfunctional natural products. Nat Prod Rep 2020; 37:1043-1064. [DOI: 10.1039/d0np00009d] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
Abstract
Here, we review methods for chemical dehydration of alcohols to alkenes and discuss the potential of late-stage functionalization by direct, site- and chemo-selective dehydration of complex molecular substrates.
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Affiliation(s)
- Per Hjerrild
- Department of Chemistry
- Aarhus University
- DK-8000 Aarhus C
- Denmark
| | - Thomas Tørring
- Department of Engineering – Microbial Biosynthesis
- Aarhus University
- Aarhus C
- Denmark
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12
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Kosol S, Jenner M, Lewandowski JR, Challis GL. Protein-protein interactions in trans-AT polyketide synthases. Nat Prod Rep 2019; 35:1097-1109. [PMID: 30280735 DOI: 10.1039/c8np00066b] [Citation(s) in RCA: 23] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Covering: up to 2018 The construction of polyketide natural products by type I modular polyketide synthases (PKSs) requires the coordinated action of several protein subunits to ensure biosynthetic fidelity. This is particularly the case for trans-AT PKSs, which in contrast to most cis-AT PKSs, contain split modules and employ several trans-acting catalytic domains. This article summarises recent advances in understanding the protein-protein interactions underpinning subunit assembly and intra-subunit communication in such systems and highlights potential avenues and approaches for future research.
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Affiliation(s)
- Simone Kosol
- Department of Chemistry, University of Warwick, Coventry, CV4 7AL, UK.
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13
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Xie X, Cane DE. pH-Rate profiles establish that polyketide synthase dehydratase domains utilize a single-base mechanism. Org Biomol Chem 2019; 16:9165-9170. [PMID: 30457629 DOI: 10.1039/c8ob02637h] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
FosDH1 from module 1 of the fostriecin polyketide synthase (PKS) catalyzes the dehydration of a 3-hydroxybutyryl-SACP to the (E)-3-butenoyl-SACP. The steady-state kinetic parameters, kcat and kcat/Km, were determined over the pH range 3.0 to 9.2 for the FosDH1-catalyzed dehydration of the N-acetycsteamine thioester, 3-hydroxybutyryl-SNAC (3), to (E)-3-butenoyl-SNAC (4). The pH rate profiles for both log(kcat) and log(kcat/Km) each corresponded to a single pH-dependent ionization to give an active site general base, with a calculated pKa 6.1 ± 0.2 for kcat and pKa 5.7 ± 0.1 for kcat/Km. These results are inconsistent with the commonly suggested "two-base" (base-acid) mechanism for the dehydratases of PKS and fatty acid biosynthesis and support a simple one-base mechanism in which the universally conserved active site His residue acts as the base to deprotonate C-2 of the substrate, then redonates the proton to the C-3 hydroxyl group to promote C-O bond-cleavage and elimination of water. The carboxylate of the paired Asp or Glu residue is thought to bind and orient the hydroxyl group of the substrate in the stereoelectonically favored conformation.
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Affiliation(s)
- Xinqiang Xie
- Department of Chemistry, Box H, Brown University, Providence, Rhode Island 02912-9108, USA.
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14
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Al-Dhelaan R, Russo PS, Padden SE, Amaya A, Dong DW, You YO. Condensation-Incompetent Ketosynthase Inhibits trans-Acyltransferase Activity. ACS Chem Biol 2019; 14:304-312. [PMID: 30642162 DOI: 10.1021/acschembio.8b01043] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Nonelongating modules with condensation-incompetent ketosynthase (KS0) are frequently found in many trans-acyltransferase polyketide synthases ( trans-AT PKS). KS0 catalyzes translocation of carbon chain without decarboxylative condensation. Unlike typical elongating modules where malonylation of acyl carrier protein (ACP) precedes elongation, the malonylation of ACP downstream of KS0 is assumed to be prevented. In this study, the regulation mechanism(s) of ACP malonylation in a non-elongating module of difficidin biosynthase was investigated. In vitro reconstitution, protein mass spectrometry, and enzyme kinetics demonstrated that KS0 controls the pathway by inhibiting the trans-AT activity. Protein-protein interactions of the surrounding domains also contribute to the regulation. Enzyme kinetics further identified the DfnKS05 as an allosteric inhibitor of trans-AT. The principle and knowledge discovered from this study will enhance the understanding of this unusual PKS system.
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Affiliation(s)
- Reham Al-Dhelaan
- Department of Chemistry and Biochemistry , George Mason University , Fairfax , Virginia 22030 , United States
| | | | - Sean E Padden
- Department of Chemistry and Biochemistry , George Mason University , Fairfax , Virginia 22030 , United States
| | - Anthony Amaya
- Department of Chemistry and Biochemistry , George Mason University , Fairfax , Virginia 22030 , United States
| | | | - Young-Ok You
- Department of Chemistry and Biochemistry , George Mason University , Fairfax , Virginia 22030 , United States
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15
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Wang B, Guo F, Dong SH, Zhao H. Activation of silent biosynthetic gene clusters using transcription factor decoys. Nat Chem Biol 2019; 15:111-114. [PMID: 30598544 PMCID: PMC6339570 DOI: 10.1038/s41589-018-0187-0] [Citation(s) in RCA: 65] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2018] [Accepted: 11/07/2018] [Indexed: 11/09/2022]
Abstract
Here we report a transcription factor decoy strategy for targeted activation of eight large silent polyketide synthase and non-ribosomal peptide synthetase gene clusters, ranging from 50 to 134 kilobases (kb) in multiple streptomycetes, and characterization of a novel oxazole family compound produced by a 98-kb biosynthetic gene cluster. Owing to its simplicity and ease of use, this strategy can be scaled up readily for discovery of natural products in streptomycetes.
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Affiliation(s)
- Bin Wang
- Carl R. Woese Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, IL, USA
| | - Fang Guo
- Department of Chemical and Biomolecular Engineering, University of Illinois at Urbana-Champaign, Urbana, IL, USA
| | - Shi-Hui Dong
- Carl R. Woese Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, IL, USA
- Department of Biochemistry, University of Illinois at Urbana-Champaign, Urbana, IL, USA
| | - Huimin Zhao
- Carl R. Woese Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, IL, USA.
- Department of Chemical and Biomolecular Engineering, University of Illinois at Urbana-Champaign, Urbana, IL, USA.
- Department of Biochemistry, University of Illinois at Urbana-Champaign, Urbana, IL, USA.
- Department of Chemistry, University of Illinois at Urbana-Champaign, Urbana, IL, USA.
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16
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Meinke JL, Mehaffey MR, Wagner DT, Sun N, Zhang Z, Brodbelt JS, Keatinge-Clay AT. Structural and Functional Studies of a gem-Dimethylating Methyltransferase from a trans-Acyltransferase Assembly Line. ACS Chem Biol 2018; 13:3306-3314. [PMID: 30371052 DOI: 10.1021/acschembio.8b00733] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Abstract
The methyl substituents in products of trans-acyltransferase assembly lines are usually incorporated by S-adenosyl-methionine (SAM)-dependent methyltransferase (MT) domains. The gem-dimethyl moieties within the polyketide disorazol are installed through the iterative action of an MT in the third module of its assembly line. The 1.75-Å-resolution crystal structure of this MT helps elucidate how it catalyzes the addition of two methyl groups. Activity assays of point mutants on β-ketoacyl chains linked to an acyl carrier protein and N-acetylcysteamine provide additional insights into the roles of active site residues. The replacement of an alanine with a phenylalanine at an apparent gatekeeping position resulted in more monomethylation than dimethylation. MTs may form an interface with ketoreductases (KRs) and even mediate the docking of trans-acyltransferase assembly line polypeptides through this association.
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Affiliation(s)
- Jessica L. Meinke
- Department of Molecular Biosciences, The University of Texas at Austin, Austin, Texas 78712, United States
| | - M. Rachel Mehaffey
- Department of Chemistry, The University of Texas at Austin, Austin, Texas 78712, United States
| | - Drew T. Wagner
- Department of Molecular Biosciences, The University of Texas at Austin, Austin, Texas 78712, United States
| | - Ningze Sun
- Department of Molecular Biosciences, The University of Texas at Austin, Austin, Texas 78712, United States
| | - Zhicheng Zhang
- Department of Chemistry, The University of Texas at Austin, Austin, Texas 78712, United States
| | - Jennifer S. Brodbelt
- Department of Chemistry, The University of Texas at Austin, Austin, Texas 78712, United States
| | - Adrian T. Keatinge-Clay
- Department of Molecular Biosciences, The University of Texas at Austin, Austin, Texas 78712, United States
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17
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Wagner DT, Zhang Z, Meoded RA, Cepeda AJ, Piel J, Keatinge-Clay AT. Structural and Functional Studies of a Pyran Synthase Domain from a trans-Acyltransferase Assembly Line. ACS Chem Biol 2018; 13:975-983. [PMID: 29481043 DOI: 10.1021/acschembio.8b00049] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
trans-Acyltransferase assembly lines possess enzymatic domains often not observed in their better characterized cis-acyltransferase counterparts. Within this repertoire of largely unexplored biosynthetic machinery is a class of enzymes called the pyran synthases that catalyze the formation of five- and six-membered cyclic ethers from diverse polyketide chains. The 1.55 Å resolution crystal structure of a pyran synthase domain excised from the ninth module of the sorangicin assembly line highlights the similarity of this enzyme to the ubiquitous dehydratase domain and provides insight into the mechanism of ring formation. Functional assays of point mutants reveal the central importance of the active site histidine that is shared with the dehydratases as well as the supporting role of a neighboring semiconserved asparagine.
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Affiliation(s)
- Drew T. Wagner
- Department of Molecular Biosciences, The University of Texas at Austin, Austin, Texas 78712, United States
| | - Zhicheng Zhang
- Department of Chemistry, The University of Texas at Austin, Austin, Texas 78712, United States
| | - Roy A. Meoded
- Institut für Mikrobiologie, Eidgenössiche Technische Hochschule (ETH) Zürich, Vladimir-Prelog-Weg 4, 8093 Zürich, Switzerland
| | - Alexis J. Cepeda
- Department of Molecular Biosciences, The University of Texas at Austin, Austin, Texas 78712, United States
| | - Jörn Piel
- Institut für Mikrobiologie, Eidgenössiche Technische Hochschule (ETH) Zürich, Vladimir-Prelog-Weg 4, 8093 Zürich, Switzerland
| | - Adrian T. Keatinge-Clay
- Department of Molecular Biosciences, The University of Texas at Austin, Austin, Texas 78712, United States
- Department of Chemistry, The University of Texas at Austin, Austin, Texas 78712, United States
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18
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Vander Wood DA, Keatinge-Clay AT. The modules of trans-acyltransferase assembly lines redefined with a central acyl carrier protein. Proteins 2018. [PMID: 29524261 DOI: 10.1002/prot.25493] [Citation(s) in RCA: 33] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
Abstract
Here, the term "module" is redefined for trans-acyltransferase (trans-AT) assembly lines to agree with how its domains cooperate and evolutionarily co-migrate. The key domain in both the polyketide synthase (PKS) and nonribosomal peptide synthetase (NRPS) modules of assembly lines is the acyl carrier protein (ACP). ACPs not only relay growing acyl chains through the assembly line but also collaborate with enzymes in modules, both in cis and in trans, to add a specific chemical moiety. A ketosynthase (KS) downstream of ACP often plays the role of gatekeeper, ensuring that only a single intermediate generated by the enzymes of a module is passed downstream. Bioinformatic analysis of 526 ACPs from 33 characterized trans-AT assembly lines reveals ACPs from the same module type generally clade together, reflective of the co-evolution of these domains with their cognate enzymes. While KSs downstream of ACPs from the same module type generally also clade together, KSs upstream of ACPs do not-in disagreement with the traditional definition of a module. Beyond nomenclature, the presented analysis impacts our understanding of module function, the evolution of assembly lines, pathway prediction, and assembly line engineering.
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Affiliation(s)
- Drew A Vander Wood
- Department of Molecular Biosciences, The University of Texas at Austin, Austin, TX, 78712, USA
| | - Adrian T Keatinge-Clay
- Department of Molecular Biosciences, The University of Texas at Austin, Austin, TX, 78712, USA
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19
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Jenner M, Kosol S, Griffiths D, Prasongpholchai P, Manzi L, Barrow AS, Moses JE, Oldham NJ, Lewandowski JR, Challis GL. Mechanism of intersubunit ketosynthase-dehydratase interaction in polyketide synthases. Nat Chem Biol 2018; 14:270-275. [PMID: 29309054 PMCID: PMC5846730 DOI: 10.1038/nchembio.2549] [Citation(s) in RCA: 27] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2017] [Accepted: 11/15/2017] [Indexed: 12/16/2022]
Abstract
Modular polyketide synthases (PKSs) produce numerous structurally complex natural products that have diverse applications in medicine and agriculture. PKSs typically consist of several multienzyme subunits that utilize structurally defined docking domains (DDs) at their N and C termini to ensure correct assembly into functional multiprotein complexes. Here we report a fundamentally different mechanism for subunit assembly in trans-acyltransferase (trans-AT) modular PKSs at the junction between ketosynthase (KS) and dehydratase (DH) domains. This mechanism involves direct interaction of a largely unstructured docking domain (DD) at the C terminus of the KS with the surface of the downstream DH. Acyl transfer assays and mechanism-based crosslinking established that the DD is required for the KS to communicate with the acyl carrier protein appended to the DH. Two distinct regions for binding of the DD to the DH were identified using NMR spectroscopy, carbene footprinting, and mutagenesis, providing a foundation for future elucidation of the molecular basis for interaction specificity.
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Affiliation(s)
- Matthew Jenner
- Department of Chemistry and Warwick Integrative Synthetic Biology Centre, University of Warwick, Coventry CV4 7AL, UK
| | - Simone Kosol
- Department of Chemistry and Warwick Integrative Synthetic Biology Centre, University of Warwick, Coventry CV4 7AL, UK
| | - Daniel Griffiths
- Department of Chemistry and Warwick Integrative Synthetic Biology Centre, University of Warwick, Coventry CV4 7AL, UK
| | - Panward Prasongpholchai
- Department of Chemistry and Warwick Integrative Synthetic Biology Centre, University of Warwick, Coventry CV4 7AL, UK
| | - Lucio Manzi
- School of Chemistry, University of Nottingham, Nottingham NG7 2RD, UK
| | - Andrew S. Barrow
- School of Chemistry, University of Nottingham, Nottingham NG7 2RD, UK
| | - John E. Moses
- School of Chemistry, University of Nottingham, Nottingham NG7 2RD, UK
| | - Neil J. Oldham
- School of Chemistry, University of Nottingham, Nottingham NG7 2RD, UK
| | - Józef R. Lewandowski
- Department of Chemistry and Warwick Integrative Synthetic Biology Centre, University of Warwick, Coventry CV4 7AL, UK
| | - Gregory L. Challis
- Department of Chemistry and Warwick Integrative Synthetic Biology Centre, University of Warwick, Coventry CV4 7AL, UK
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20
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Characterization of the biosynthetic gene cluster for cryptic phthoxazolin A in Streptomyces avermitilis. PLoS One 2018; 13:e0190973. [PMID: 29324854 PMCID: PMC5764310 DOI: 10.1371/journal.pone.0190973] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/02/2017] [Accepted: 12/23/2017] [Indexed: 11/19/2022] Open
Abstract
Phthoxazolin A, an oxazole-containing polyketide, has a broad spectrum of anti-oomycete activity and herbicidal activity. We recently identified phthoxazolin A as a cryptic metabolite of Streptomyces avermitilis that produces the important anthelmintic agent avermectin. Even though genome data of S. avermitilis is publicly available, no plausible biosynthetic gene cluster for phthoxazolin A is apparent in the sequence data. Here, we identified and characterized the phthoxazolin A (ptx) biosynthetic gene cluster through genome sequencing, comparative genomic analysis, and gene disruption. Sequence analysis uncovered that the putative ptx biosynthetic genes are laid on an extra genomic region that is not found in the public database, and 8 open reading frames in the extra genomic region could be assigned roles in the biosynthesis of the oxazole ring, triene polyketide and carbamoyl moieties. Disruption of the ptxA gene encoding a discrete acyltransferase resulted in a complete loss of phthoxazolin A production, confirming that the trans-AT type I PKS system is responsible for the phthoxazolin A biosynthesis. Based on the predicted functional domains in the ptx assembly line, we propose the biosynthetic pathway of phthoxazolin A.
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