1
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Fallon TR, Shende VV, Wierzbicki IH, Pendleton AL, Watervoort NF, Auber RP, Gonzalez DJ, Wisecaver JH, Moore BS. Giant polyketide synthase enzymes in the biosynthesis of giant marine polyether toxins. Science 2024; 385:671-678. [PMID: 39116217 DOI: 10.1126/science.ado3290] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2024] [Accepted: 07/10/2024] [Indexed: 08/10/2024]
Abstract
Prymnesium parvum are harmful haptophyte algae that cause massive environmental fish kills. Their polyketide polyether toxins, the prymnesins, are among the largest nonpolymeric compounds in nature and have biosynthetic origins that have remained enigmatic for more than 40 years. In this work, we report the "PKZILLAs," massive P. parvum polyketide synthase (PKS) genes that have evaded previous detection. PKZILLA-1 and -2 encode giant protein products of 4.7 and 3.2 megadaltons that have 140 and 99 enzyme domains. Their predicted polyene product matches the proposed pre-prymnesin precursor of the 90-carbon-backbone A-type prymnesins. We further characterize the variant PKZILLA-B1, which is responsible for the shorter B-type analog prymnesin-B1, from P. parvum RCC3426 and thus establish a general model of haptophyte polyether biosynthetic logic. This work 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, La Jolla, CA 92093, USA
| | - Vikram V Shende
- Center for Marine Biotechnology and Biomedicine, Scripps Institution of Oceanography and University of California, San Diego, La Jolla, CA 92093, USA
| | - Igor H Wierzbicki
- Department of Pharmacology, University of California, San Diego, La Jolla, CA 92093, USA
| | - Amanda L Pendleton
- Department of Biochemistry, Purdue University, West Lafayette, IN 47907, USA
- Purdue Center for Plant Biology, Purdue University, West Lafayette, IN 47907, USA
| | - Nathan F Watervoort
- Department of Biochemistry, Purdue University, West Lafayette, IN 47907, USA
- Purdue Center for Plant Biology, Purdue University, West Lafayette, IN 47907, USA
| | - Robert P Auber
- Department of Biochemistry, Purdue University, West Lafayette, IN 47907, USA
- Purdue Center for Plant Biology, Purdue University, West Lafayette, IN 47907, USA
| | - David J Gonzalez
- Department of Pharmacology, University of California, San Diego, La Jolla, CA 92093, USA
- Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California, San Diego, La Jolla, CA 92093, USA
| | - Jennifer H Wisecaver
- Department of Biochemistry, Purdue University, West Lafayette, IN 47907, USA
- Purdue Center for Plant Biology, Purdue University, West Lafayette, IN 47907, USA
| | - Bradley S Moore
- Center for Marine Biotechnology and Biomedicine, Scripps Institution of Oceanography and University of California, San Diego, La Jolla, CA 92093, USA
- Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California, San Diego, La Jolla, CA 92093, USA
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2
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Skala LE, Philmus B, Mahmud T. Modifications of Protein-Bound Substrates by Trans-Acting Enzymes in Natural Products Biosynthesis. Chembiochem 2024; 25:e202400056. [PMID: 38386898 PMCID: PMC11021167 DOI: 10.1002/cbic.202400056] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2024] [Revised: 02/21/2024] [Accepted: 02/22/2024] [Indexed: 02/24/2024]
Abstract
Enzymatic modifications of small molecules are a common phenomenon in natural product biosynthesis, leading to the production of diverse bioactive compounds. In polyketide biosynthesis, modifications commonly take place after the completion of the polyketide backbone assembly by the polyketide synthases and the mature products are released from the acyl-carrier protein (ACP). However, exceptions to this rule appear to be widespread, as on-line hydroxylation, methyl transfer, and cyclization during polyketide assembly process are common, particularly in trans-AT PKS systems. Many of these modifications are catalyzed by specific domains within the modular PKS systems. However, several of the on-line modifications are catalyzed by stand-alone proteins. Those include the on-line Baeyer-Villiger oxidation, α-hydroxylation, halogenation, epoxidation, and methyl esterification during polyketide assembly, dehydrogenation of ACP-bound short fatty acids by acyl-CoA dehydrogenase-like enzymes, and glycosylation of ACP-bound intermediates by discrete glycosyltransferase enzymes. This review article highlights some of these trans-acting proteins that catalyze enzymatic modifications of ACP-bound small molecules in natural product biosynthesis.
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Affiliation(s)
- Leigh E Skala
- Department of Pharmaceutical Sciences, Oregon State University, 203 Pharmacy Building, Corvallis, Oregon, 97331, U.S.A
| | - Benjamin Philmus
- Department of Pharmaceutical Sciences, Oregon State University, 203 Pharmacy Building, Corvallis, Oregon, 97331, U.S.A
| | - Taifo Mahmud
- Department of Pharmaceutical Sciences, Oregon State University, 203 Pharmacy Building, Corvallis, Oregon, 97331, U.S.A
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3
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Mabesoone MF, 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 PMCID: PMC11260071 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, Massachusetts 02115, United States
- Department of Chemistry, Vanderbilt University, 1234 Stevenson Center Lane, Nashville, Tennessee 37240, United States
- Department of Biological Sciences, Vanderbilt University, 465 21st Avenue S, Nashville, Tennesee 37232, United States
| | - Jörn Piel
- Institute of Microbiology, Eidgenössische Technische Hochschule (ETH) Zürich, Vladimir-Prelog-Weg 4, 8093 Zürich, Switzerland
- Lead contact
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4
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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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5
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Winter AJ, Khanizeman RN, Barker‐Mountford AMC, Devine AJ, Wang L, Song Z, Davies JA, Race PR, Williams C, Simpson TJ, Willis CL, Crump MP. Structure and Function of the α-Hydroxylation Bimodule of the Mupirocin Polyketide Synthase. Angew Chem Int Ed Engl 2023; 62:e202312514. [PMID: 37768840 PMCID: PMC10953402 DOI: 10.1002/anie.202312514] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2023] [Revised: 09/27/2023] [Accepted: 09/28/2023] [Indexed: 09/30/2023]
Abstract
Mupirocin is a clinically important antibiotic produced by a trans-AT Type I polyketide synthase (PKS) in Pseudomonas fluorescens. The major bioactive metabolite, pseudomonic acid A (PA-A), is assembled on a tetrasubstituted tetrahydropyran (THP) core incorporating a 6-hydroxy group proposed to be introduced by α-hydroxylation of the thioester of the acyl carrier protein (ACP) bound polyketide chain. Herein, we describe an in vitro approach combining purified enzyme components, chemical synthesis, isotopic labelling, mass spectrometry and NMR in conjunction with in vivo studies leading to the first characterisation of the α-hydroxylation bimodule of the mupirocin biosynthetic pathway. These studies reveal the precise timing of hydroxylation by MupA, substrate specificity and the ACP dependency of the enzyme components that comprise this α-hydroxylation bimodule. Furthermore, using purified enzyme, it is shown that the MmpA KS0 shows relaxed substrate specificity, suggesting precise spatiotemporal control of in trans MupA recruitment in the context of the PKS. Finally, the detection of multiple intermodular MupA/ACP interactions suggests these bimodules may integrate MupA into their assembly.
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Affiliation(s)
| | | | | | | | - Luoyi Wang
- Institute of MicrobiologyChinese Academy of SciencesBeijing100101China
| | - Zhongshu Song
- School of ChemistryUniversity of BristolBristolBS8 1TSUK
| | | | - Paul R. Race
- School of BiochemistryUniversity of BristolBristolBS8 1TDUK
- current addressSchool of Natural and Environmental SciencesNewcastle UniversityNewcastle upon TyneNE1 7RUUK
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6
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Winter AJ, Khanizeman RN, Barker‐Mountford AMC, Devine AJ, Wang L, Song Z, Davies JA, Race PR, Williams C, Simpson TJ, Willis CL, Crump MP. Structure and Function of the α-Hydroxylation Bimodule of the Mupirocin Polyketide Synthase. ANGEWANDTE CHEMIE (WEINHEIM AN DER BERGSTRASSE, GERMANY) 2023; 135:e202312514. [PMID: 38515435 PMCID: PMC10952193 DOI: 10.1002/ange.202312514] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 08/25/2023] [Indexed: 03/23/2024]
Abstract
Mupirocin is a clinically important antibiotic produced by a trans-AT Type I polyketide synthase (PKS) in Pseudomonas fluorescens. The major bioactive metabolite, pseudomonic acid A (PA-A), is assembled on a tetrasubstituted tetrahydropyran (THP) core incorporating a 6-hydroxy group proposed to be introduced by α-hydroxylation of the thioester of the acyl carrier protein (ACP) bound polyketide chain. Herein, we describe an in vitro approach combining purified enzyme components, chemical synthesis, isotopic labelling, mass spectrometry and NMR in conjunction with in vivo studies leading to the first characterisation of the α-hydroxylation bimodule of the mupirocin biosynthetic pathway. These studies reveal the precise timing of hydroxylation by MupA, substrate specificity and the ACP dependency of the enzyme components that comprise this α-hydroxylation bimodule. Furthermore, using purified enzyme, it is shown that the MmpA KS0 shows relaxed substrate specificity, suggesting precise spatiotemporal control of in trans MupA recruitment in the context of the PKS. Finally, the detection of multiple intermodular MupA/ACP interactions suggests these bimodules may integrate MupA into their assembly.
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Affiliation(s)
| | | | | | | | - Luoyi Wang
- Institute of MicrobiologyChinese Academy of SciencesBeijing100101China
| | - Zhongshu Song
- School of ChemistryUniversity of BristolBristolBS8 1TSUK
| | | | - Paul R. Race
- School of BiochemistryUniversity of BristolBristolBS8 1TDUK
- current addressSchool of Natural and Environmental SciencesNewcastle UniversityNewcastle upon TyneNE1 7RUUK
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7
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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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8
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Murphy A, Corney M, Monson RE, Matilla MA, Salmond GPC, Leeper FJ. Biosynthesis of Antifungal Solanimycin May Involve an Iterative Nonribosomal Peptide Synthetase Module. ACS Chem Biol 2023; 18:1148-1157. [PMID: 37068480 PMCID: PMC10204066 DOI: 10.1021/acschembio.2c00947] [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: 12/24/2022] [Accepted: 04/05/2023] [Indexed: 04/19/2023]
Abstract
Dickeya solani, a plant-pathogenic bacterium, produces solanimycin, a potent hybrid polyketide/nonribosomal peptide (PKS/NRPS) anti-fungal compound. The biosynthetic gene cluster responsible for synthesis of this compound has been identified. Because of instability, the complete structure of the compound has not yet been elucidated, but LC-MS2 identified that the cluster produces two main compounds, solanimycin A and B, differing by a single hydroxyl group. The fragmentation pattern revealed that the central part of solanimycin A is a hexapeptide, Gly-Dha-Dha-Dha-Dha-Dha (where Dha is dehydroalanine). This is supported by isotopic labeling studies using labeled serine and glycine. The N-terminal group is a polyketide-derived C16 acyl group containing a conjugated hexaene, a hydroxyl, and an amino group. The additional hydroxyl group in solanimycin B is on the α-carbon of the glycine residue. The incorporation of five sequential Dha residues is unprecedented because there is only one NRPS module in the cluster that is predicted to activate and attach serine (which is subsequently dehydrated to Dha), meaning that this NRPS module must act iteratively. While a few other iterative NRPS modules are known, they all involve iteration of two or three modules. We believe that the repetitive use of a single module makes the solanimycin biosynthetic pathway unique among NRPSs so far reported.
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Affiliation(s)
- Annabel
C. Murphy
- Yusuf
Hamied Department of Chemistry, University
of Cambridge, Lensfield Road, Cambridge CB2 1EW, U.K.
| | - Matthew Corney
- Yusuf
Hamied Department of Chemistry, University
of Cambridge, Lensfield Road, Cambridge CB2 1EW, U.K.
| | - Rita E. Monson
- Department
of Biochemistry, University of Cambridge, Tennis Court Road, Cambridge CB2 1QW, U.K.
| | - Miguel A. Matilla
- Department
of Biochemistry, University of Cambridge, Tennis Court Road, Cambridge CB2 1QW, U.K.
| | - George P. C. Salmond
- Department
of Biochemistry, University of Cambridge, Tennis Court Road, Cambridge CB2 1QW, U.K.
| | - Finian J. Leeper
- Yusuf
Hamied Department of Chemistry, University
of Cambridge, Lensfield Road, Cambridge CB2 1EW, U.K.
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9
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Fraley AE, Dell M, Schmalhofer M, Meoded RA, Bergande C, Groll M, Piel J. Heterocomplex structure of a polyketide synthase component involved in modular backbone halogenation. Structure 2023; 31:565-572.e4. [PMID: 36917986 DOI: 10.1016/j.str.2023.02.010] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2022] [Revised: 12/14/2022] [Accepted: 02/15/2023] [Indexed: 03/14/2023]
Abstract
Bacterial modular polyketide synthases (PKSs) generate diverse, complex and bioactive natural products that are constructed mainly based on principles of fatty acid biosynthesis. The cytotoxic oocydin-type polyketides contain a vinyl chloride moiety introduced during polyketide chain elongation. Required for modular polyketide backbone halogenation are a non-heme iron and ɑ-ketoglutarate-dependent halogenase OocP and OocQ lacking characterized homologs. This work provides structural insights into these unusual PKS components and their interactions via a high-resolution X-ray crystallography structure of the heterocomplex. By mapping the protein-protein interactions and comparison with structures of similar halogenases, we illustrate the potential of this heterodimer complex as a replacement for the conserved homodimeric structure of homologous enzymes. The OocPQ protein pair has thus evolved as a means of stabilizing the halogenase and facilitating chemical transformations with great synthetic utility.
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Affiliation(s)
- Amy E Fraley
- Institute of Microbiology, Eidgenössische Technische Hochschule (ETH) Zurich, Zurich, Switzerland
| | - Maria Dell
- Institute of Microbiology, Eidgenössische Technische Hochschule (ETH) Zurich, Zurich, Switzerland
| | - Maximilian Schmalhofer
- Chair of Biochemistry, Center for Protein Assemblies, Technical University of Munich, Ernst-Otto-Fischer-Strasse 8, 85748 Garching, Germany
| | - Roy A Meoded
- Institute of Microbiology, Eidgenössische Technische Hochschule (ETH) Zurich, Zurich, Switzerland
| | - Cedric Bergande
- Institute of Microbiology, Eidgenössische Technische Hochschule (ETH) Zurich, Zurich, Switzerland
| | - Michael Groll
- Chair of Biochemistry, Center for Protein Assemblies, Technical University of Munich, Ernst-Otto-Fischer-Strasse 8, 85748 Garching, Germany
| | - Jörn Piel
- Institute of Microbiology, Eidgenössische Technische Hochschule (ETH) Zurich, Zurich, Switzerland.
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10
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Abstract
Invertebrates, particularly sponges, have been a dominant source of new marine natural products. For example, lasonolide A (LSA) is a potential anticancer molecule isolated from the marine sponge Forcepia sp., with nanomolar growth inhibitory activity and a unique cytotoxicity profile against the National Cancer Institute 60-cell-line screen. Here, we identified the putative biosynthetic pathway for LSA. Genomic binning of the Forcepia sponge metagenome revealed a Gram-negative bacterium belonging to the phylum Verrucomicrobia as the candidate producer of LSA. Phylogenetic analysis showed that this bacterium, here named "Candidatus Thermopylae lasonolidus," only has 88.78% 16S rRNA identity with the closest relative, Pedosphaera parvula Ellin514, indicating that it represents a new genus. The lasonolide A (las) biosynthetic gene cluster (BGC) was identified as a trans-acyltransferase (AT) polyketide synthase (PKS) pathway. Compared with its host genome, the las BGC exhibits a significantly different GC content and pentanucleotide frequency, suggesting a potential horizontal acquisition of the gene cluster. Furthermore, three copies of the putative las pathway were identified in the candidate producer genome. Differences between the three las repeats were observed, including the presence of three insertions, two single-nucleotide polymorphisms, and the absence of a stand-alone acyl carrier protein in one of the repeats. Even though the verrucomicrobial producer shows signs of genome reduction, its genome size is still fairly large (about 5 Mbp), and, compared to its closest free-living relative, it contains most of the primary metabolic pathways, suggesting that it is in the early stages of reduction. IMPORTANCE While sponges are valuable sources of bioactive natural products, a majority of these compounds are produced in small quantities by uncultured symbionts, hampering the study and clinical development of these unique compounds. Lasonolide A (LSA), isolated from marine sponge Forcepia sp., is a cytotoxic molecule active at nanomolar concentrations, which causes premature chromosome condensation, blebbing, cell contraction, and loss of cell adhesion, indicating a novel mechanism of action and making it a potential anticancer drug lead. However, its limited supply hampers progression to clinical trials. We investigated the microbiome of Forcepia sp. using culture-independent DNA sequencing, identified genes likely responsible for LSA synthesis in an uncultured bacterium, and assembled the symbiont's genome. These insights provide future opportunities for heterologous expression and cultivation efforts that may minimize LSA's supply problem.
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11
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Welch SD, Cossin J, Paulsel TQ, Williams GJ. Targeted Enzyme Modifications Enable Regioselective Biosynthesis of Fluorinated Polyketides. CHEM CATALYSIS 2022; 2:2440-2443. [PMID: 38213411 PMCID: PMC10783197 DOI: 10.1016/j.checat.2022.09.042] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/13/2024]
Abstract
In attempts to enhance natural products as therapeutic agents, fluorination has emerged as a new tool for synthetic biologists and chemists. In recent articles published in Nature Chem. and Nature Chem. Bio., Grininger, Chang, and co-workers leveraged their expertise in engineering polyketide biosynthesis to incorporate fluorine into polyketide scaffolds.
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Affiliation(s)
- Sydney D. Welch
- Department of Chemistry, North Carolina State University, Raleigh, NC, United States
| | - Jared Cossin
- Department of Chemistry, North Carolina State University, Raleigh, NC, United States
| | - Thaddeus Q. Paulsel
- Department of Chemistry, North Carolina State University, Raleigh, NC, United States
| | - Gavin J. Williams
- Department of Chemistry, North Carolina State University, Raleigh, NC, United States
- Comparative Medicine Institute, North Carolina State University, Raleigh, NC, United States
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12
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Fraley AE, Dieterich CL, Mabesoone MFJ, Minas HA, Meoded RA, Hemmerling F, Piel J. Structure of a Promiscuous Thioesterase Domain Responsible for Branching Acylation in Polyketide Biosynthesis. Angew Chem Int Ed Engl 2022; 61:e202206385. [DOI: 10.1002/anie.202206385] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2022] [Indexed: 11/08/2022]
Affiliation(s)
- Amy E. Fraley
- Department of Biology, Institute of Microbiology Eidgenössische Technische Hochschule (ETH) Zurich Vladimir-Prelog-Weg 4 8093 Zurich Switzerland
| | - Cora L. Dieterich
- Department of Biology, Institute of Microbiology Eidgenössische Technische Hochschule (ETH) Zurich Vladimir-Prelog-Weg 4 8093 Zurich Switzerland
| | - Mathijs F. J. Mabesoone
- Department of Biology, Institute of Microbiology Eidgenössische Technische Hochschule (ETH) Zurich Vladimir-Prelog-Weg 4 8093 Zurich Switzerland
| | - Hannah A. Minas
- Department of Biology, Institute of Microbiology Eidgenössische Technische Hochschule (ETH) Zurich Vladimir-Prelog-Weg 4 8093 Zurich Switzerland
| | - Roy A Meoded
- Department of Biology, Institute of Microbiology Eidgenössische Technische Hochschule (ETH) Zurich Vladimir-Prelog-Weg 4 8093 Zurich Switzerland
| | - Franziska Hemmerling
- Department of Biology, Institute of Microbiology Eidgenössische Technische Hochschule (ETH) Zurich Vladimir-Prelog-Weg 4 8093 Zurich Switzerland
| | - Jörn Piel
- Department of Biology, Institute of Microbiology Eidgenössische Technische Hochschule (ETH) Zurich Vladimir-Prelog-Weg 4 8093 Zurich Switzerland
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13
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Fraley AE, Dieterich C, Mabesoone M, Minas HA, Meoded RA, Hemmerling F, Piel J. Structure of a promiscuous thioesterase domain responsible for branching acylation in polyketide biosynthesis. Angew Chem Int Ed Engl 2022. [DOI: 10.1002/ange.202206385] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Affiliation(s)
- Amy E. Fraley
- Eidgenossische Technische Hochschule Zurich Institute of Microbiology SWITZERLAND
| | - Cora Dieterich
- Eidgenossische Technische Hochschule Zurich Institute of Microbiology SWITZERLAND
| | - Mathijs Mabesoone
- Eidgenossische Technische Hochschule Zurich Institute of Microbiology SWITZERLAND
| | - Hannah A. Minas
- Eidgenossische Technische Hochschule Zurich Institute of Microbiology SWITZERLAND
| | - Roy A. Meoded
- Eidgenossische Technische Hochschule Zurich Institute of Microbiology SWITZERLAND
| | - Franziska Hemmerling
- Eidgenossische Technische Hochschule Zurich Institute of Microbiology SWITZERLAND
| | - Jörn Piel
- ETH Zürich Department of Biology Vladimir-Prelog-Weg 4 8093 Zürich SWITZERLAND
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14
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Shi YM, Hirschmann M, Shi YN, Bode HB. Cleavage Off-Loading and Post-assembly-Line Conversions Yield Products with Unusual Termini during Biosynthesis. ACS Chem Biol 2022; 17:2221-2228. [PMID: 35860925 PMCID: PMC9396620 DOI: 10.1021/acschembio.2c00367] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
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Piscibactins and photoxenobactins are metallophores and
virulence
factors, whose biosynthetic gene cluster, termed pxb, is the most prevalent polyketide synthase/non-ribosomal peptide
synthetase hybrid cluster across entomopathogenic bacteria. They are
structurally similar to yersiniabactin, which contributes to the virulence
of the human pathogen Yersinia pestis. However, the pxb-derived products feature various
chain lengths and unusual carboxamide, thiocarboxylic acid, and dithioperoxoate
termini, which are rarely found in thiotemplated biosyntheses. Here,
we characterize the pxb biosynthetic logic by gene
deletions, site-directed mutagenesis, and isotope labeling experiments.
Notably, we propose that it involves (1) heterocyclization domains
with various catalytic efficiencies catalyzing thiazoline and amide/thioester
bond formation and (2) putative C–N and C–S bond cleavage
off-loading manners, which lead to products with different chain lengths
and usual termini. Additionally, the post-assembly-line spontaneous
conversions of the biosynthetic end product contribute to production
titers of the other products in the culture medium. This study broadens
our knowledge of thiotemplated biosynthesis and how bacterial host
generate a chemical arsenal.
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Affiliation(s)
- Yi-Ming Shi
- Department of Natural Products in Organismic Interactions, Max Planck Institute for Terrestrial Microbiology, 35043 Marburg, Germany.,Molecular Biotechnology, Department of Biosciences, Goethe University Frankfurt, 60438 Frankfurt am Main, Germany
| | - Merle Hirschmann
- Molecular Biotechnology, Department of Biosciences, Goethe University Frankfurt, 60438 Frankfurt am Main, Germany
| | - Yan-Ni Shi
- Department of Natural Products in Organismic Interactions, Max Planck Institute for Terrestrial Microbiology, 35043 Marburg, Germany.,Molecular Biotechnology, Department of Biosciences, Goethe University Frankfurt, 60438 Frankfurt am Main, Germany
| | - Helge B Bode
- Department of Natural Products in Organismic Interactions, Max Planck Institute for Terrestrial Microbiology, 35043 Marburg, Germany.,Molecular Biotechnology, Department of Biosciences, Goethe University Frankfurt, 60438 Frankfurt am Main, Germany.,Chemical Biology, Department of Chemistry, Philipps University Marburg, 35043 Marburg, Germany.,Senckenberg Gesellschaft für Naturforschung, 60325 Frankfurt am Main, Germany
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15
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Abstract
A personal selection of 32 recent papers is presented, covering various aspects of current developments in bioorganic chemistry and novel natural products, such as daphnepapytone A from Daphne papyracea.
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Affiliation(s)
- Robert A Hill
- School of Chemistry, Glasgow University, Glasgow, G12 8QQ, UK.
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