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Fergusson CH, Saulog J, Paulo BS, Wilson DM, Liu DY, Morehouse NJ, Waterworth S, Barkei J, Gray CA, Kwan JC, Eustaquio AS, Linington RG. Discovery of a lagriamide polyketide by integrated genome mining, isotopic labeling, and untargeted metabolomics. Chem Sci 2024; 15:8089-8096. [PMID: 38817573 PMCID: PMC11134395 DOI: 10.1039/d4sc00825a] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2024] [Accepted: 04/18/2024] [Indexed: 06/01/2024] Open
Abstract
Microorganisms from the order Burkholderiales have been the source of a number of important classes of natural products in recent years. For example, study of the beetle-associated symbiont Burkholderia gladioli led to the discovery of the antifungal polyketide lagriamide; an important molecule from the perspectives of both biotechnology and chemical ecology. As part of a wider project to sequence Burkholderiales genomes from our in-house Burkholderiales library we identified a strain containing a biosynthetic gene cluster (BGC) similar to the original lagriamide BGC. Structure prediction failed to identify any candidate masses for the products of this BGC from untargeted metabolomics mass spectrometry data. However, genome mining from publicly available databases identified fragments of this BGC from a culture collection strain of Paraburkholderia. Whole genome sequencing of this strain revealed the presence of a homologue of this BGC with very high sequence identity. Stable isotope feeding of the two strains in parallel using our newly developed IsoAnalyst platform identified the product of this lagriamide-like BGC directly from the crude fermentation extracts, affording a culturable supply of this interesting compound class. Using a combination of bioinformatic, computational and spectroscopic methods we defined the absolute configurations for all 11 chiral centers in this new metabolite, which we named lagriamide B. Biological testing of lagriamide B against a panel of 21 bacterial and fungal pathogens revealed antifungal activity against the opportunistic human pathogen Aspergillus niger, while image-based Cell Painting analysis indicated that lagriamide B also causes actin filament disruption in U2-OS osteosarcoma cells.
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Affiliation(s)
- Claire H Fergusson
- Department of Chemistry, Simon Fraser University 8888 University Drive Burnaby BC V5A 1S6 Canada
| | - Julia Saulog
- Department of Chemistry, Simon Fraser University 8888 University Drive Burnaby BC V5A 1S6 Canada
| | - Bruno S Paulo
- Department of Pharmaceutical Sciences and Center for Biomolecular Sciences, College of Pharmacy, University of Illinois at Chicago Chicago IL 60607 USA
| | - Darryl M Wilson
- Department of Chemistry, Simon Fraser University 8888 University Drive Burnaby BC V5A 1S6 Canada
| | - Dennis Y Liu
- Department of Chemistry, Simon Fraser University 8888 University Drive Burnaby BC V5A 1S6 Canada
| | - Nicholas J Morehouse
- Department of Biological Sciences, University of New Brunswick Saint John NB Canada
| | - Samantha Waterworth
- Division of Pharmaceutical Sciences, School of Pharmacy, University of Wisconsin Madison WI 53705 USA
| | - John Barkei
- Division of Pharmaceutical Sciences, School of Pharmacy, University of Wisconsin Madison WI 53705 USA
| | - Christopher A Gray
- Department of Biological Sciences, University of New Brunswick Saint John NB Canada
| | - Jason C Kwan
- Division of Pharmaceutical Sciences, School of Pharmacy, University of Wisconsin Madison WI 53705 USA
| | - Alessandra S Eustaquio
- Department of Pharmaceutical Sciences and Center for Biomolecular Sciences, College of Pharmacy, University of Illinois at Chicago Chicago IL 60607 USA
| | - Roger G Linington
- Department of Chemistry, Simon Fraser University 8888 University Drive Burnaby BC V5A 1S6 Canada
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Kishore S, Del Rio Flores A, Lynch SR, Yuet KP, Khosla C. Discovery and Characterization of the Fully Decorated Nocardiosis-Associated Polyketide Natural Product. J Am Chem Soc 2024; 146:4212-4220. [PMID: 38295028 PMCID: PMC11009873 DOI: 10.1021/jacs.3c13670] [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] [Indexed: 02/02/2024]
Abstract
The genomes of 40 strains of Nocardia, most of which were associated with life-threatening human infections, encode a highly conserved assembly line polyketide synthase designated as the NOCAP (NOCardiosis-Associated Polyketide) synthase, whose product structure has been previously described. Here we report the structure and inferred biosynthetic pathway of the fully decorated glycolipid natural product. Its structure reveals a fully substituted benzaldehyde headgroup harboring an unusual polyfunctional tail and an O-linked disaccharide comprising a 3-α-epimycarose and 2-O-methyl-α-rhamnose whose installation requires flavin monooxygenase-dependent hydroxylation of the polyketide product. Production of the fully decorated glycolipid was verified in cultures of two patient-derived Nocardia species. In both E. coli and Nocardia spp., the glycolipid was only detected in culture supernatants, consistent with data from genetic knockout experiments implicating roles for two dedicated proteins in installing the second sugar substituent only after the monoglycosyl intermediate is exported across the bacterial cell membrane. With the NOCAP product in hand, the stage is set for investigating the evolutionary benefit of this polyketide biosynthetic pathway for Nocardia strains capable of infecting human hosts.
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Affiliation(s)
- Shreya Kishore
- Department of Chemistry, Stanford University, Stanford, California 94305, United States
| | | | - Stephen R Lynch
- Department of Chemistry, Stanford University, Stanford, California 94305, United States
| | - Kai P Yuet
- Department of Chemistry, Stanford University, Stanford, California 94305, United States
| | - Chaitan Khosla
- Department of Chemistry, Stanford University, Stanford, California 94305, United States
- Department of Chemical Engineering, Stanford University, Stanford, California 94305, United States
- Sarafan ChEM-H, Stanford University, Stanford, California 94305, United States
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Herisse M, Ishida K, Staiger-Creed J, Judd L, Williams SJ, Howden BP, Stinear TP, Dahse HM, Voigt K, Hertweck C, Pidot SJ. Discovery and Biosynthesis of the Cytotoxic Polyene Terpenomycin in Human Pathogenic Nocardia. ACS Chem Biol 2023; 18:1872-1879. [PMID: 37498707 DOI: 10.1021/acschembio.3c00311] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 07/29/2023]
Abstract
Nocardia are opportunistic human pathogens that can cause a range of debilitating and difficult to treat infections of the lungs, brain, skin, and soft tissues. Despite their close relationship to the well-known secondary metabolite-producing genus, Streptomyces, comparatively few natural products are known from the Nocardia, and even less is known about their involvement in the pathogenesis. Here, we combine chemistry, genomics, and molecular microbiology to reveal the production of terpenomycin, a new cytotoxic and antifungal polyene from a human pathogenic Nocardia terpenica isolate. We unveil the polyketide synthase (PKS) responsible for terpenomycin biosynthesis and show that it combines several unusual features, including "split", skipped, and iteratively used modules, and the use of the unusual extender unit methoxymalonate as a starter unit. To link genes to molecules, we constructed a transposon mutant library in N. terpenica, identifying a terpenomycin-null mutant with an inactivated terpenomycin PKS. Our findings show that the neglected actinomycetes have an unappreciated capacity for the production of bioactive molecules with unique biosynthetic pathways waiting to be uncovered and highlights these organisms as producers of diverse natural products.
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Affiliation(s)
- Marion Herisse
- Department of Microbiology and Immunology, Doherty Institute for Infection and Immunity, University of Melbourne, Melbourne, Victoria 3000, Australia
| | - Keishi Ishida
- Department of Biomolecular Chemistry, Leibniz Institute, for Natural Product Chemistry and Infection Biology (HKI), Beutenbergstrasse 11a, Jena 07745, Germany
| | - Jordan Staiger-Creed
- Department of Microbiology and Immunology, Doherty Institute for Infection and Immunity, University of Melbourne, Melbourne, Victoria 3000, Australia
| | - Louise Judd
- Department of Microbiology and Immunology, Doherty Institute for Infection and Immunity, University of Melbourne, Melbourne, Victoria 3000, Australia
| | - Spencer J Williams
- School of Chemistry, University of Melbourne, Melbourne, Victoria 3000, Australia
- Bio21 Molecular Science and Biotechnology Institute, University of Melbourne, Melbourne, Victoria 3000, Australia
| | - Benjamin P Howden
- Department of Microbiology and Immunology, Doherty Institute for Infection and Immunity, University of Melbourne, Melbourne, Victoria 3000, Australia
- Microbiological Diagnostic Unit Public Health Laboratory, Department of Microbiology and Immunology, Doherty Institute for Infection and Immunity, University of Melbourne, Melbourne, Victoria3000, Australia
| | - Timothy P Stinear
- Department of Microbiology and Immunology, Doherty Institute for Infection and Immunity, University of Melbourne, Melbourne, Victoria 3000, Australia
| | - Hans-Martin Dahse
- Department of Infection Biology, Leibniz Institute, for Natural Product Chemistry and Infection Biology (HKI), Beutenbergstrasse 11a, Jena 07745, Germany
| | - Kerstin Voigt
- Jena Microbial Resource Collection, Leibniz Institute for Natural Product Research and Infection Biology (HKI), Beutenbergstrasse 11a, Jena 07745, Germany
- Institute of Microbiology, Friedrich Schiller University Jena, 07743 Jena, Germany
| | - Christian Hertweck
- Department of Biomolecular Chemistry, Leibniz Institute, for Natural Product Chemistry and Infection Biology (HKI), Beutenbergstrasse 11a, Jena 07745, Germany
- Natural Product Chemistry, Faculty of Biological Sciences, Friedrich Schiller University Jena, Jena 07743, Germany
| | - Sacha J Pidot
- Department of Microbiology and Immunology, Doherty Institute for Infection and Immunity, University of Melbourne, Melbourne, Victoria 3000, Australia
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Winter AJ, Rowe MT, Weir ANM, Akter N, Mbatha SZ, Walker PD, Williams C, Song Z, Race PR, Willis CL, Crump MP. Programmed Iteration Controls the Assembly of the Nonanoic Acid Side Chain of the Antibiotic Mupirocin. ANGEWANDTE CHEMIE (WEINHEIM AN DER BERGSTRASSE, GERMANY) 2022; 134:e202212393. [PMID: 38505625 PMCID: PMC10947060 DOI: 10.1002/ange.202212393] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/22/2022] [Indexed: 11/11/2022]
Abstract
Mupirocin is a clinically important antibiotic produced by Pseudomonas fluorescens NCIMB 10586 that is assembled by a complex trans-AT polyketide synthase. The polyketide fragment, monic acid, is esterified by a 9-hydroxynonanoic acid (9HN) side chain which is essential for biological activity. The ester side chain assembly is initialised from a 3-hydroxypropionate (3HP) starter unit attached to the acyl carrier protein (ACP) MacpD, but the fate of this species is unknown. Herein we report the application of NMR spectroscopy, mass spectrometry, chemical probes and in vitro assays to establish the remaining steps of 9HN biosynthesis. These investigations reveal a complex interplay between a novel iterative or "stuttering" KS-AT didomain (MmpF), the multidomain module MmpB and multiple ACPs. This work has important implications for understanding the late-stage biosynthetic steps of mupirocin and will be important for future engineering of related trans-AT biosynthetic pathways (e.g. thiomarinol).
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Affiliation(s)
| | | | | | - Nahida Akter
- School of ChemistryUniversity of BristolBristolBS8 1TSUK
| | | | - Paul D. Walker
- School of ChemistryUniversity of BristolBristolBS8 1TSUK
| | | | - Zhongshu Song
- School of ChemistryUniversity of BristolBristolBS8 1TSUK
| | - Paul R. Race
- School of BiochemistryUniversity of BristolBristolBS8 1TDUK
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Winter AJ, Rowe MT, Weir ANM, Akter N, Mbatha SZ, Walker PD, Williams C, Song Z, Race PR, Willis CL, Crump MP. Programmed Iteration Controls the Assembly of the Nonanoic Acid Side Chain of the Antibiotic Mupirocin. Angew Chem Int Ed Engl 2022; 61:e202212393. [PMID: 36227272 PMCID: PMC10098928 DOI: 10.1002/anie.202212393] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2022] [Indexed: 11/12/2022]
Abstract
Mupirocin is a clinically important antibiotic produced by Pseudomonas fluorescens NCIMB 10586 that is assembled by a complex trans-AT polyketide synthase. The polyketide fragment, monic acid, is esterified by a 9-hydroxynonanoic acid (9HN) side chain which is essential for biological activity. The ester side chain assembly is initialised from a 3-hydroxypropionate (3HP) starter unit attached to the acyl carrier protein (ACP) MacpD, but the fate of this species is unknown. Herein we report the application of NMR spectroscopy, mass spectrometry, chemical probes and in vitro assays to establish the remaining steps of 9HN biosynthesis. These investigations reveal a complex interplay between a novel iterative or "stuttering" KS-AT didomain (MmpF), the multidomain module MmpB and multiple ACPs. This work has important implications for understanding the late-stage biosynthetic steps of mupirocin and will be important for future engineering of related trans-AT biosynthetic pathways (e.g. thiomarinol).
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Affiliation(s)
| | - Matthew T. Rowe
- School of Chemistry University of Bristol Bristol BS8 1TS UK
| | | | - Nahida Akter
- School of Chemistry University of Bristol Bristol BS8 1TS UK
| | | | - Paul D. Walker
- School of Chemistry University of Bristol Bristol BS8 1TS UK
| | | | - Zhongshu Song
- School of Chemistry University of Bristol Bristol BS8 1TS UK
| | - Paul R. Race
- School of Biochemistry University of Bristol Bristol BS8 1TD UK
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