1
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Ray KA, Lutgens JD, Bista R, Zhang J, Desai RR, Hirsch M, Miyazawa T, Cordova A, Keatinge-Clay AT. Assessing and harnessing updated polyketide synthase modules through combinatorial engineering. Nat Commun 2024; 15:6485. [PMID: 39090122 PMCID: PMC11294587 DOI: 10.1038/s41467-024-50844-6] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2023] [Accepted: 07/23/2024] [Indexed: 08/04/2024] Open
Abstract
The modular nature of polyketide assembly lines and the significance of their products make them prime targets for combinatorial engineering. The recently updated module boundary has been successful for engineering short synthases, yet larger synthases constructed using the updated boundary have not been investigated. Here we describe our design and implementation of a BioBricks-like platform to rapidly construct 5 triketide, 25 tetraketide, and 125 pentaketide synthases to test every module combination of the pikromycin synthase. Anticipated products are detected from 60% of the triketide synthases, 32% of the tetraketide synthases, and 6.4% of the pentaketide synthases. We determine ketosynthase gatekeeping and module-skipping are the principal impediments to obtaining functional synthases. The platform is also employed to construct active hybrid synthases by incorporating modules from the erythromycin, spinosyn, and rapamycin assembly lines. The relaxed gatekeeping of a ketosynthase in the rapamycin synthase is especially encouraging in the quest to produce designer polyketides.
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Affiliation(s)
- Katherine A Ray
- Department of Molecular Biosciences, The University of Texas at Austin, Austin, TX, USA
| | - Joshua D Lutgens
- Department of Molecular Biosciences, The University of Texas at Austin, Austin, TX, USA
| | - Ramesh Bista
- Department of Molecular Biosciences, The University of Texas at Austin, Austin, TX, USA
| | - Jie Zhang
- Department of Molecular Biosciences, The University of Texas at Austin, Austin, TX, USA
| | - Ronak R Desai
- Department of Molecular Biosciences, The University of Texas at Austin, Austin, TX, USA
| | - Melissa Hirsch
- Department of Chemistry, The University of Texas at Austin, Austin, TX, USA
| | - Takeshi Miyazawa
- Department of Molecular Biosciences, The University of Texas at Austin, Austin, TX, USA
| | - Antonio Cordova
- Department of Molecular Biosciences, The University of Texas at Austin, Austin, TX, USA
| | - Adrian T Keatinge-Clay
- Department of Molecular Biosciences, The University of Texas at Austin, Austin, TX, USA.
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2
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Zhao C, Slocum ST, Sherman DH, Ruotolo BT. Time-Resolved Ion Mobility-Mass Spectrometry Reveals Structural Transitions in the Disassembly of Modular Polyketide Syntheses. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2024. [PMID: 39038158 DOI: 10.1021/jasms.4c00181] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/24/2024]
Abstract
The type 1 polyketide synthase (PKS) assembly line uses its modular structure to produce polyketide natural products that form the basis of many pharmaceuticals. Currently, several cryoelectron microscopy (cryo-EM) structures of a multidomain PKS module have been constructed, but much remains to be learned. Here we utilize ion-mobility mass spectrometry (IM-MS) to record size and shape information and detect different conformational states of a 207 kDa didomain dimer comprised of ketosynthase (KS) and acyl transferase (AT), excised from full-length module. Furthermore, gas-phase stability differences between these different conformations are captured by collision induced unfolding (CIU) technology. Additionally, through tracking these forms as a function of time, we elucidate a detailed disassembly pathway for KS-AT dimers for the first time.
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Affiliation(s)
- Chunyi Zhao
- Department of Chemistry, University of Michigan, Ann Arbor, Michigan 48109, United States
| | - Samuel T Slocum
- Life Science Institute, Departments of Medicinal Chemistry, Chemistry and Microbiology & Immunology, University of Michigan, Ann Arbor, Michigan 48109, United States
| | - David H Sherman
- Life Science Institute, Departments of Medicinal Chemistry, Chemistry and Microbiology & Immunology, University of Michigan, Ann Arbor, Michigan 48109, United States
| | - Brandon T Ruotolo
- Department of Chemistry, University of Michigan, Ann Arbor, Michigan 48109, United States
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3
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Xiang C, Yao S, Wang R, Zhang L. Bioinformatic prediction of the stereoselectivity of modular polyketide synthase: an update of the sequence motifs in ketoreductase domain. Beilstein J Org Chem 2024; 20:1476-1485. [PMID: 38978744 PMCID: PMC11228615 DOI: 10.3762/bjoc.20.131] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2024] [Accepted: 06/21/2024] [Indexed: 07/10/2024] Open
Abstract
Polyketides are a major class of natural products, including bioactive medicines such as erythromycin and rapamycin. They are often rich in stereocenters biosynthesized by the ketoreductase (KR) domain within the polyketide synthase (PKS) assembly line. Previous studies have identified conserved motifs in KR sequences that enable the bioinformatic prediction of product stereochemistry. However, the reliability and applicability of these prediction methods have not been thoroughly assessed. In this study, we conducted a comprehensive bioinformatic analysis of 1,762 KR sequences from cis-AT PKSs to reevaluate the residues involved in conferring stereoselectivity. Our findings indicate that the previously identified fingerprint motifs remain valid for KRs in β-modules from actinobacteria, but their reliability diminishes for KRs from other module types or taxonomic origins. Additionally, we have identified several new motifs that exhibit a strong correlation with the stereochemical outcomes of KRs. These updated fingerprint motifs for stereochemical prediction not only enhance our understanding of the enzymatic mechanisms governing stereocontrol but also facilitate accurate stereochemical prediction and genome mining of polyketides derived from modular cis-AT PKSs.
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Affiliation(s)
- Changjun Xiang
- Department of Chemistry, Fudan University, Shanghai 200433, China
- Key Laboratory of Precise Synthesis of Functional Molecules of Zhejiang Province, Department of Chemistry, School of Science and Research Center for Industries of the Future, Westlake University, Hangzhou 310030, China
| | - Shunyu Yao
- Key Laboratory of Precise Synthesis of Functional Molecules of Zhejiang Province, Department of Chemistry, School of Science and Research Center for Industries of the Future, Westlake University, Hangzhou 310030, China
| | - Ruoyu Wang
- Key Laboratory of Precise Synthesis of Functional Molecules of Zhejiang Province, Department of Chemistry, School of Science and Research Center for Industries of the Future, Westlake University, Hangzhou 310030, China
| | - Lihan Zhang
- Key Laboratory of Precise Synthesis of Functional Molecules of Zhejiang Province, Department of Chemistry, School of Science and Research Center for Industries of the Future, Westlake University, Hangzhou 310030, China
- Institute of Natural Sciences, Westlake Institute for Advanced Study, Hangzhou 310024, China
- Westlake Laboratory of Life Sciences and Biomedicine, Hangzhou 310030, China
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4
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Mahmoud Mohamed MM, Yang Z, Lum KY, Peschel G, Rosenbaum MA, Weber T, Coriani S, Gotfredsen CH, Ding L. Genome-Driven Discovery of Hygrocins in Streptomyces rapamycinicus. JOURNAL OF NATURAL PRODUCTS 2024; 87:1321-1329. [PMID: 38647518 DOI: 10.1021/acs.jnatprod.3c00767] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/25/2024]
Abstract
Ansamycins, represented by the antituberculosis drug rifamycin, are an important family of natural products. To obtain new ansamycins, Streptomyces rapamycinicus IMET 43975 harboring an ansamycin biosynthetic gene cluster was fermented in a 50 L scale, and subsequent purification work led to the isolation of five known and four new analogues, where hygrocin W (2) belongs to benzoquinonoid ansamycins, and the other three hygrocins, hygrocins X-Z (6-8), are new seco-hygrocins. The structures of ansamycins (1-8) were determined by the analysis of spectroscopic (1D/2D NMR and ECD) and MS spectrometric data. The Baeyer-Villiger enzyme which catalyzed the ester formation in the ansa-ring was confirmed through in vivo CRISPR base editing. The discovery of these compounds further enriches the structural diversity of ansamycins.
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Affiliation(s)
- Manar Magdy Mahmoud Mohamed
- Department of Biotechnology and Biomedicine, Technical University of Denmark, Søltofts Plads 221, 2800 Kgs. Lyngby, Denmark
| | - Zhijie Yang
- Department of Biotechnology and Biomedicine, Technical University of Denmark, Søltofts Plads 221, 2800 Kgs. Lyngby, Denmark
| | - Kah Yean Lum
- Department of Biotechnology and Biomedicine, Technical University of Denmark, Søltofts Plads 221, 2800 Kgs. Lyngby, Denmark
| | - Gundela Peschel
- Leibniz Institute for Natural Product Research and Infection Biology - Hans-Knöll-Institute (HKI), Beutenbergstraße 11a, 07745 Jena, Germany
| | - Miriam A Rosenbaum
- Leibniz Institute for Natural Product Research and Infection Biology - Hans-Knöll-Institute (HKI), Beutenbergstraße 11a, 07745 Jena, Germany
| | - Tilmann Weber
- The Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Kemitorvet, Building 220, 2800 Kgs. Lyngby, Denmark
| | - Sonia Coriani
- Department of Chemistry, Technical University of Denmark, Kemitorvet Building 207, 2800 Kgs. Lyngby, Denmark
| | - Charlotte H Gotfredsen
- Department of Chemistry, Technical University of Denmark, Kemitorvet Building 207, 2800 Kgs. Lyngby, Denmark
| | - Ling Ding
- Department of Biotechnology and Biomedicine, Technical University of Denmark, Søltofts Plads 221, 2800 Kgs. Lyngby, Denmark
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5
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Chen L, Liu K, Hong J, Cui Z, He W, Wang Y, Deng Z, Tao M. The Discovery of Weddellamycin, a Tricyclic Polyene Macrolactam Antibiotic from an Antarctic Deep-Sea-Derived Streptomyces sp. DSS69, by Heterologous Expression. Mar Drugs 2024; 22:189. [PMID: 38667806 PMCID: PMC11051340 DOI: 10.3390/md22040189] [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: 01/19/2024] [Revised: 04/11/2024] [Accepted: 04/18/2024] [Indexed: 04/28/2024] Open
Abstract
Polyene macrolactams are a special group of natural products with great diversity, unique structural features, and a wide range of biological activities. Herein, a cryptic gene cluster for the biosynthesis of putative macrolactams was disclosed from a sponge-associated bacterium, Streptomyces sp. DSS69, by genome mining. Cloning and heterologous expression of the whole biosynthetic gene cluster led to the discovery of weddellamycin, a polyene macrolactam bearing a 23/5/6 ring skeleton. A negative regulator, WdlO, and two positive regulators, WdlA and WdlB, involved in the regulation of weddellamycin production were unraveled. The fermentation titer of weddellamycin was significantly improved by overexpression of wdlA and wdlB and deletion of wdlO. Notably, weddellamycin showed remarkable antibacterial activity against various Gram-positive bacteria including MRSA, with MIC values of 0.10-0.83 μg/mL, and antifungal activity against Candida albicans, with an MIC value of 3.33 μg/mL. Weddellamycin also displayed cytotoxicity against several cancer cell lines, with IC50 values ranging from 2.07 to 11.50 µM.
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Affiliation(s)
- Lu Chen
- State Key Laboratory of Microbial Metabolism, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai 200240, China; (L.C.); (K.L.); (J.H.); (Z.C.); (W.H.); (Y.W.); (Z.D.)
| | - Kai Liu
- State Key Laboratory of Microbial Metabolism, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai 200240, China; (L.C.); (K.L.); (J.H.); (Z.C.); (W.H.); (Y.W.); (Z.D.)
| | - Jiali Hong
- State Key Laboratory of Microbial Metabolism, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai 200240, China; (L.C.); (K.L.); (J.H.); (Z.C.); (W.H.); (Y.W.); (Z.D.)
| | - Zhanzhao Cui
- State Key Laboratory of Microbial Metabolism, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai 200240, China; (L.C.); (K.L.); (J.H.); (Z.C.); (W.H.); (Y.W.); (Z.D.)
| | - Weijun He
- State Key Laboratory of Microbial Metabolism, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai 200240, China; (L.C.); (K.L.); (J.H.); (Z.C.); (W.H.); (Y.W.); (Z.D.)
| | - Yemin Wang
- State Key Laboratory of Microbial Metabolism, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai 200240, China; (L.C.); (K.L.); (J.H.); (Z.C.); (W.H.); (Y.W.); (Z.D.)
| | - Zixin Deng
- State Key Laboratory of Microbial Metabolism, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai 200240, China; (L.C.); (K.L.); (J.H.); (Z.C.); (W.H.); (Y.W.); (Z.D.)
- Haihe Laboratory of Synthetic Biology, Tianjin 300308, China
- Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin 300308, China
| | - Meifeng Tao
- State Key Laboratory of Microbial Metabolism, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai 200240, China; (L.C.); (K.L.); (J.H.); (Z.C.); (W.H.); (Y.W.); (Z.D.)
- Haihe Laboratory of Synthetic Biology, Tianjin 300308, China
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6
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Schmidt K, Cox RJ. Investigation of chain-length selection by the tenellin iterative highly-reducing polyketide synthase. RSC Adv 2024; 14:8963-8970. [PMID: 38495992 PMCID: PMC10941261 DOI: 10.1039/d3ra08463a] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2023] [Accepted: 03/07/2024] [Indexed: 03/19/2024] Open
Abstract
The programming of widely distributed iterative fungal hr-PKS is mysterious, yet it is central for generating polyketide natural product diversity by controlling the chain length, β-processing level and methylation patterns of fungal polyketides. For the iterative hr-PKS TENS, responsible for producing the pentaketide-tyrosine hybrid pretenellin A 1, the chain length programming is known to be determined by the KR domain. Structure prediction of the KR domain enabled the identification of a relevant substrate binding helix, which was the focus of swap experiments with corresponding sequences from the related hr-PKS DMBS and MILS that produce similar hexa- and heptaketides (2, 3). The investigations of chimeric TENS variants expressed in vivo in the host Aspergillus oryzae NSAR1 revealed the substrate binding helix as a promising target for further investigations, evidenced by observed increase of the chain length during swap experiments. Building on these findings, rational engineering of TENS was applied based on structural analysis and sequence alignment. A minimal set of four simultaneous amino acid mutations achieved the re-programming of TENS by producing hexaketides in minor amounts. To refine our understanding and minimize the number of mutations impacting polyketide chain length, we conducted an alanine scan, pinpointing crucial amino acid positions. Our findings give indications on the intrinsic programming of hr-PKS domains by minimal changes in the amino acid sequence as one influence factor for programming.
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Affiliation(s)
- Katharina Schmidt
- OCI, BMWZ, Leibniz University of Hannover Schneiderberg 38 30167 Hannover Germany
| | - Russell J Cox
- OCI, BMWZ, Leibniz University of Hannover Schneiderberg 38 30167 Hannover Germany
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7
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Walesch S, Garcia R, Mahmoud AB, Panter F, Bollenbach S, Mäser P, Kaiser M, Krug D, Müller R. New myxobacteria of the Myxococcaceae clade produce angiolams with antiparasitic activities. Microbiol Spectr 2024; 12:e0368923. [PMID: 38298128 PMCID: PMC10913735 DOI: 10.1128/spectrum.03689-23] [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: 10/16/2023] [Accepted: 01/02/2024] [Indexed: 02/02/2024] Open
Abstract
In the past century, microbial natural products have proven themselves to be substantial and fruitful sources of anti-infectives. In addition to the well-studied Actinobacteria, understudied bacterial taxa like the Gram-negative myxobacteria have increasingly gained attention in the ongoing search for novel and biologically active natural products. In the course of a regional sampling campaign to source novel myxobacteria, we recently uncovered new myxobacterial strains MCy12716 and MCy12733 belonging to the Myxococcaceae clade. Early bioactivity screens of the bacterial extracts revealed the presence of bioactive natural products that were identified as angiolam A and several novel derivatives. Sequencing of the corresponding producer strains allowed the identification of the angiolam biosynthetic gene cluster, which was verified by targeted gene inactivation. Based on bioinformatic analysis of the biosynthetic gene cluster, a concise biosynthesis model was devised to explain angiolam biosynthesis. Importantly, novel angiolam derivatives uncovered in this study named angiolams B, C, and D were found to display promising antiparasitic activities against the malaria pathogen Plasmodium falciparum in the 0.3-0.8 µM range.IMPORTANCEThe COVID-19 pandemic and continuously emerging antimicrobial resistance (AMR) have recently raised awareness about limited treatment options against infectious diseases. However, the shortage of treatment options against protozoal parasitic infections, like malaria, is much more severe, especially for the treatment of so-called neglected tropical diseases. The detection of anti-parasitic bioactivities of angiolams produced by MCy12716 and MCy12733 displays the hidden potential of scarcely studied natural products to have promising biological activities in understudied indications. Furthermore, the improved biological activities of novel angiolam derivatives against Plasmodium falciparum and the evaluation of its biosynthesis display the opportunities of the angiolam scaffold on route to treat protozoal parasitic infections as well as possible ways to increase the production of derivatives with improved bioactivities.
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Affiliation(s)
- Sebastian Walesch
- Helmholtz Centre for Infection Research, Helmholtz Institute for Pharmaceutical Research Saarland (HIPS), Saarland University Campus, Saarbrücken, Germany
- Department of Pharmacy, Saarland University, Saarbrücken, Germany
- Helmholtz Centre for Infection Research (HZI), Braunschweig, Germany
- DZIF-German Center for Infection Research, partner site Hannover-Braunschweig, Braunschweig, Germany
| | - Ronald Garcia
- Helmholtz Centre for Infection Research, Helmholtz Institute for Pharmaceutical Research Saarland (HIPS), Saarland University Campus, Saarbrücken, Germany
- Department of Pharmacy, Saarland University, Saarbrücken, Germany
- Helmholtz Centre for Infection Research (HZI), Braunschweig, Germany
- DZIF-German Center for Infection Research, partner site Hannover-Braunschweig, Braunschweig, Germany
| | - Abdelhalim B. Mahmoud
- Helmholtz Centre for Infection Research, Helmholtz Institute for Pharmaceutical Research Saarland (HIPS), Saarland University Campus, Saarbrücken, Germany
- Department of Pharmacy, Saarland University, Saarbrücken, Germany
- Helmholtz Centre for Infection Research (HZI), Braunschweig, Germany
- DZIF-German Center for Infection Research, partner site Hannover-Braunschweig, Braunschweig, Germany
- Faculty of Pharmacy, University of Khartoum, Khartoum, Sudan
| | - Fabian Panter
- Helmholtz Centre for Infection Research, Helmholtz Institute for Pharmaceutical Research Saarland (HIPS), Saarland University Campus, Saarbrücken, Germany
- Department of Pharmacy, Saarland University, Saarbrücken, Germany
- Helmholtz Centre for Infection Research (HZI), Braunschweig, Germany
- DZIF-German Center for Infection Research, partner site Hannover-Braunschweig, Braunschweig, Germany
- Helmholtz International Lab for Anti-Infectives, Saarbrücken, Germany
| | - Sophie Bollenbach
- Helmholtz Centre for Infection Research, Helmholtz Institute for Pharmaceutical Research Saarland (HIPS), Saarland University Campus, Saarbrücken, Germany
- Department of Pharmacy, Saarland University, Saarbrücken, Germany
- Helmholtz Centre for Infection Research (HZI), Braunschweig, Germany
- DZIF-German Center for Infection Research, partner site Hannover-Braunschweig, Braunschweig, Germany
| | - Pascal Mäser
- Parasite Chemotherapy Unit, Swiss Tropical and Public Health Institute, Allschwil, Switzerland
- Faculty of Science, University of Basel, Basel, Switzerland
| | - Marcel Kaiser
- Parasite Chemotherapy Unit, Swiss Tropical and Public Health Institute, Allschwil, Switzerland
- Faculty of Science, University of Basel, Basel, Switzerland
| | - Daniel Krug
- Helmholtz Centre for Infection Research, Helmholtz Institute for Pharmaceutical Research Saarland (HIPS), Saarland University Campus, Saarbrücken, Germany
- Department of Pharmacy, Saarland University, Saarbrücken, Germany
- Helmholtz Centre for Infection Research (HZI), Braunschweig, Germany
- DZIF-German Center for Infection Research, partner site Hannover-Braunschweig, Braunschweig, Germany
| | - Rolf Müller
- Helmholtz Centre for Infection Research, Helmholtz Institute for Pharmaceutical Research Saarland (HIPS), Saarland University Campus, Saarbrücken, Germany
- Department of Pharmacy, Saarland University, Saarbrücken, Germany
- Helmholtz Centre for Infection Research (HZI), Braunschweig, Germany
- DZIF-German Center for Infection Research, partner site Hannover-Braunschweig, Braunschweig, Germany
- Helmholtz International Lab for Anti-Infectives, Saarbrücken, Germany
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8
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García-Gutiérrez C, Pérez-Victoria I, Montero I, Fernández-De la Hoz J, Malmierca MG, Martín J, Salas JA, Olano C, Reyes F, Méndez C. Unearthing a Cryptic Biosynthetic Gene Cluster for the Piperazic Acid-Bearing Depsipeptide Diperamycin in the Ant-Dweller Streptomyces sp. CS113. Int J Mol Sci 2024; 25:2347. [PMID: 38397022 PMCID: PMC10888640 DOI: 10.3390/ijms25042347] [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: 01/10/2024] [Revised: 02/05/2024] [Accepted: 02/07/2024] [Indexed: 02/25/2024] Open
Abstract
Piperazic acid is a cyclic nonproteinogenic amino acid that contains a hydrazine N-N bond formed by a piperazate synthase (KtzT-like). This amino acid, found in bioactive natural products synthesized by non-ribosomal peptide synthetases (NRPSs), confers conformational constraint to peptides, an important feature for their biological activities. Genome mining of Streptomyces strains has been revealed as a strategy to identify biosynthetic gene clusters (BGCs) for potentially active compounds. Moreover, the isolation of new strains from underexplored habitats or associated with other organisms has allowed to uncover new BGCs for unknown compounds. The in-house "Carlos Sialer (CS)" strain collection consists of seventy-one Streptomyces strains isolated from the cuticle of leaf-cutting ants of the tribe Attini. Genomes from twelve of these strains have been sequenced and mined using bioinformatics tools, highlighting their potential to encode secondary metabolites. In this work, we have screened in silico those genomes, using KtzT as a hook to identify BGCs encoding piperazic acid-containing compounds. This resulted in uncovering the new BGC dpn in Streptomyces sp. CS113, which encodes the biosynthesis of the hybrid polyketide-depsipeptide diperamycin. Analysis of the diperamycin polyketide synthase (PKS) and NRPS reveals their functional similarity to those from the aurantimycin A biosynthetic pathway. Experimental proof linking the dpn BGC to its encoded compound was achieved by determining the growth conditions for the expression of the cluster and by inactivating the NRPS encoding gene dpnS2 and the piperazate synthase gene dpnZ. The identity of diperamycin was confirmed by High-Resolution Mass Spectrometry (HRMS) and Nuclear Magnetic Resonance (NMR) and by analysis of the domain composition of modules from the DpnP PKS and DpnS NRPS. The identification of the dpn BGC expands the number of BGCs that have been confirmed to encode the relatively scarcely represented BGCs for depsipeptides of the azinothricin family of compounds and will facilitate the generation of new-to-nature analogues by combinatorial biosynthesis.
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Affiliation(s)
- Coral García-Gutiérrez
- Departamento de Biología Funcional e Instituto Universitario de Oncología del Principado de Asturias (I.U.O.P.A), Universidad de Oviedo, 33006 Oviedo, Spain; (C.G.-G.); (I.M.); (J.F.-D.l.H.); (M.G.M.); (J.A.S.); (C.O.)
- Instituto de Investigación Sanitaria de Asturias (ISPA), 33011 Oviedo, Spain
| | - Ignacio Pérez-Victoria
- Fundación MEDINA, Centro de Excelencia en Investigación de Medicamentos Innovadores en Andalucía, 18016 Granada, Spain; (I.P.-V.); (J.M.); (F.R.)
| | - Ignacio Montero
- Departamento de Biología Funcional e Instituto Universitario de Oncología del Principado de Asturias (I.U.O.P.A), Universidad de Oviedo, 33006 Oviedo, Spain; (C.G.-G.); (I.M.); (J.F.-D.l.H.); (M.G.M.); (J.A.S.); (C.O.)
- Instituto de Investigación Sanitaria de Asturias (ISPA), 33011 Oviedo, Spain
| | - Jorge Fernández-De la Hoz
- Departamento de Biología Funcional e Instituto Universitario de Oncología del Principado de Asturias (I.U.O.P.A), Universidad de Oviedo, 33006 Oviedo, Spain; (C.G.-G.); (I.M.); (J.F.-D.l.H.); (M.G.M.); (J.A.S.); (C.O.)
| | - Mónica G. Malmierca
- Departamento de Biología Funcional e Instituto Universitario de Oncología del Principado de Asturias (I.U.O.P.A), Universidad de Oviedo, 33006 Oviedo, Spain; (C.G.-G.); (I.M.); (J.F.-D.l.H.); (M.G.M.); (J.A.S.); (C.O.)
| | - Jesús Martín
- Fundación MEDINA, Centro de Excelencia en Investigación de Medicamentos Innovadores en Andalucía, 18016 Granada, Spain; (I.P.-V.); (J.M.); (F.R.)
| | - José A. Salas
- Departamento de Biología Funcional e Instituto Universitario de Oncología del Principado de Asturias (I.U.O.P.A), Universidad de Oviedo, 33006 Oviedo, Spain; (C.G.-G.); (I.M.); (J.F.-D.l.H.); (M.G.M.); (J.A.S.); (C.O.)
- Instituto de Investigación Sanitaria de Asturias (ISPA), 33011 Oviedo, Spain
| | - Carlos Olano
- Departamento de Biología Funcional e Instituto Universitario de Oncología del Principado de Asturias (I.U.O.P.A), Universidad de Oviedo, 33006 Oviedo, Spain; (C.G.-G.); (I.M.); (J.F.-D.l.H.); (M.G.M.); (J.A.S.); (C.O.)
- Instituto de Investigación Sanitaria de Asturias (ISPA), 33011 Oviedo, Spain
| | - Fernando Reyes
- Fundación MEDINA, Centro de Excelencia en Investigación de Medicamentos Innovadores en Andalucía, 18016 Granada, Spain; (I.P.-V.); (J.M.); (F.R.)
| | - Carmen Méndez
- Departamento de Biología Funcional e Instituto Universitario de Oncología del Principado de Asturias (I.U.O.P.A), Universidad de Oviedo, 33006 Oviedo, Spain; (C.G.-G.); (I.M.); (J.F.-D.l.H.); (M.G.M.); (J.A.S.); (C.O.)
- Instituto de Investigación Sanitaria de Asturias (ISPA), 33011 Oviedo, Spain
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9
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Liao Y, Wang XJ, Ma GL, Candra H, Qiu En SL, Khandelwal S, Liang ZX. Biosynthesis of Octacosamicin A: Uncommon Starter/extender Units and Product Releasing via Intermolecular Amidation. Chembiochem 2024; 25:e202300590. [PMID: 37908177 DOI: 10.1002/cbic.202300590] [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: 08/22/2023] [Revised: 10/28/2023] [Accepted: 10/31/2023] [Indexed: 11/02/2023]
Abstract
Octacosamicin A is an antifungal metabolite featuring a linear polyene-polyol chain flanked by N-hydroxyguanidine and glycine moieties. We report here that sub-inhibitory concentrations of streptomycin elicited the production of octacosamicin A in Amycolatopsis azurea DSM 43854T . We identified the biosynthetic gene cluster (oca BGC) that encodes a modular polyketide synthase (PKS) system for assembling the polyene-polyol chain of octacosamicin A. Our analysis suggested that the N-hydroxyguanidine unit originates from a 4-guanidinobutyryl-CoA starter unit, while the PKS incorporates an α-hydroxyketone moiety using a (2R)-hydroxymalonyl-CoA extender unit. The modular PKS system contains a non-canonical terminal module that lacks thioesterase (TE) and acyl carrier protein (ACP) domains, indicating the biosynthesis is likely to employ an unconventional and cryptic off-loading mechanism that attaches glycine to the polyene-polyol chain via an intermolecular amidation reaction.
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Affiliation(s)
- Yanghui Liao
- School of Biological Sciences, Nanyang Technological University, Singapore, 67551, Singapore
| | - Xue-Jiao Wang
- School of Biological Sciences, Nanyang Technological University, Singapore, 67551, Singapore
| | - Guang-Lei Ma
- Future Health Laboratory, Innovation Center of Yangtze River Delta, Zhejiang University, Jiaxing, 314102, China
| | - Hartono Candra
- School of Biological Sciences, Nanyang Technological University, Singapore, 67551, Singapore
| | - Sean Lee Qiu En
- School of Biological Sciences, Nanyang Technological University, Singapore, 67551, Singapore
| | - Srashti Khandelwal
- School of Biological Sciences, Nanyang Technological University, Singapore, 67551, Singapore
| | - Zhao-Xun Liang
- School of Biological Sciences, Nanyang Technological University, Singapore, 67551, Singapore
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10
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Wang J, Deng Z, Liang J, Wang Z. Structural enzymology of iterative type I polyketide synthases: various routes to catalytic programming. Nat Prod Rep 2023; 40:1498-1520. [PMID: 37581222 DOI: 10.1039/d3np00015j] [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: 08/16/2023]
Abstract
Time span of literature covered: up to mid-2023Iterative type I polyketide synthases (iPKSs) are outstanding natural chemists: megaenzymes that repeatedly utilize their catalytic domains to synthesize complex natural products with diverse bioactivities. Perhaps the most fascinating but least understood question about type I iPKSs is how they perform the iterative yet programmed reactions in which the usage of domain combinations varies during the synthetic cycle. The programmed patterns are fulfilled by multiple factors, and strongly influence the complexity of the resulting natural products. This article reviews selected reports on the structural enzymology of iPKSs, focusing on the individual domain structures followed by highlighting the representative programming activities that each domain may contribute.
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Affiliation(s)
- Jialiang Wang
- State Key Laboratory of Microbial Metabolism, Joint International Research Laboratory of Metabolic & Developmental Sciences, School of Life Science & Biotechnology, Shanghai Jiao Tong University, Shanghai, China.
| | - Zixin Deng
- State Key Laboratory of Microbial Metabolism, Joint International Research Laboratory of Metabolic & Developmental Sciences, School of Life Science & Biotechnology, Shanghai Jiao Tong University, Shanghai, China.
| | - Jingdan Liang
- State Key Laboratory of Microbial Metabolism, Joint International Research Laboratory of Metabolic & Developmental Sciences, School of Life Science & Biotechnology, Shanghai Jiao Tong University, Shanghai, China.
| | - Zhijun Wang
- State Key Laboratory of Microbial Metabolism, Joint International Research Laboratory of Metabolic & Developmental Sciences, School of Life Science & Biotechnology, Shanghai Jiao Tong University, Shanghai, China.
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11
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McCullough TM, Dhar A, Akey DL, Konwerski JR, Sherman DH, Smith JL. Structure of a modular polyketide synthase reducing region. Structure 2023; 31:1109-1120.e3. [PMID: 37348494 PMCID: PMC10527585 DOI: 10.1016/j.str.2023.05.019] [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: 02/21/2023] [Revised: 04/04/2023] [Accepted: 05/26/2023] [Indexed: 06/24/2023]
Abstract
The chemical scaffolds of numerous therapeutics are polyketide natural products, many formed by bacterial modular polyketide synthases (PKS). The large and flexible dimeric PKS modules have distinct extension and reducing regions. Structures are known for all individual enzyme domains and several extension regions. Here, we report the structure of the full reducing region from a modular PKS, the ketoreductase (KR), dehydratase (DH), and enoylreductase (ER) domains of module 5 of the juvenimicin PKS. The modular PKS-reducing region has a different architecture than the homologous fatty acid synthase (FAS) and iterative PKS systems in its arrangement of domains and dimer interface. The structure reveals a critical role for linker peptides in the domain interfaces, leading to discovery of key differences in KR domains dependent on module composition. Finally, our studies provide insight into the mechanism underlying modular PKS intermediate shuttling by carrier protein (ACP) domains.
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Affiliation(s)
- Tyler M McCullough
- Life Sciences Institute, University of Michigan, Ann Arbor MI 48109, USA; Department of Biological Chemistry, University of Michigan, Ann Arbor, MI 48109, USA
| | - Anya Dhar
- Life Sciences Institute, University of Michigan, Ann Arbor MI 48109, USA
| | - David L Akey
- Life Sciences Institute, University of Michigan, Ann Arbor MI 48109, USA; Department of Molecular, Cellular, and Developmental Biology, University of Michigan, Ann Arbor, MI 48109, USA
| | - Jamie R Konwerski
- Life Sciences Institute, University of Michigan, Ann Arbor MI 48109, USA
| | - David H Sherman
- Life Sciences Institute, University of Michigan, Ann Arbor MI 48109, USA; Department of Medicinal Chemistry, University of Michigan, Ann Arbor, MI 48109, USA; Department of Microbiology and Immunology, University of Michigan, Ann Arbor, MI 48109, USA; Department of Chemistry, University of Michigan, Ann Arbor, MI 48109, USA
| | - Janet L Smith
- Life Sciences Institute, University of Michigan, Ann Arbor MI 48109, USA; Department of Biological Chemistry, University of Michigan, Ann Arbor, MI 48109, USA.
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12
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Chen R, Minns SA, Kalaitzis JA, Butler MS, Rosin M, Vuong D, Lean SS, Chooi YH, Lacey E, Piggott AM. Turonicin A, an Antifungal Linear Polyene Polyketide from an Australian Streptomyces sp. JOURNAL OF NATURAL PRODUCTS 2023; 86:2054-2058. [PMID: 37526586 DOI: 10.1021/acs.jnatprod.3c00144] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 08/02/2023]
Abstract
Turonicin A (1) was isolated from Streptomyces sp. MST-123921, which was recovered from soil collected on the banks of the Turon River in New South Wales, Australia. Turonicin A (1) is an amphoteric linear polyene polyketide featuring independent pentaene and tetraenone chromophores and is structurally related to linearmycins A-C (2-4). The structure of 1 was determined by detailed spectroscopic analysis and comparison to literature data. Bioinformatic analysis of the linearmycin biosynthetic gene cluster also allowed the previously unresolved absolute stereostructures of 2-4 to be elucidated. Turonicin A (1) exhibited very potent activity against the fungi Candida albicans (MIC 0.0031 μg/mL, 2.7 nM) and Saccharomyces cerevisiae (MIC 0.0008 μg/mL, 0.7 nM), moderate activity against the bacteria Bacillus subtilis (MIC 0.097 μg/mL, 85 nM) and Staphylococcus aureus (MIC 0.39 μg/mL, 340 nM), and no cytotoxicity against human fibroblasts, making it an attractive candidate for further development as a potential next-generation antibiotic scaffold.
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Affiliation(s)
- Rachel Chen
- Microbial Screening Technologies Pty. Ltd., Smithfield, NSW 2164, Australia
| | - Scott A Minns
- Microbial Screening Technologies Pty. Ltd., Smithfield, NSW 2164, Australia
| | - John A Kalaitzis
- School of Natural Sciences, Macquarie University, Sydney, NSW 2109, Australia
| | | | - Maira Rosin
- Department of Molecular and Applied Microbiology, Jena Leibniz Institute for Natural Product Research and Infection Biology, Hans Knöll Institute, Jena D-07745, Germany
| | - Daniel Vuong
- School of Natural Sciences, Macquarie University, Sydney, NSW 2109, Australia
| | - Soo Sum Lean
- School of Molecular Sciences, The University of Western Australia, Perth, WA 6009, Australia
| | - Yit-Heng Chooi
- School of Molecular Sciences, The University of Western Australia, Perth, WA 6009, Australia
| | - Ernest Lacey
- Microbial Screening Technologies Pty. Ltd., Smithfield, NSW 2164, Australia
- School of Natural Sciences, Macquarie University, Sydney, NSW 2109, Australia
| | - Andrew M Piggott
- School of Natural Sciences, Macquarie University, Sydney, NSW 2109, Australia
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13
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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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14
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Kim MC, Winter JM, Cullum R, Smith AJ, Fenical W. Expanding the Utility of Bioinformatic Data for the Full Stereostructural Assignments of Marinolides A and B, 24- and 26-Membered Macrolactones Produced by a Chemically Exceptional Marine-Derived Bacterium. Mar Drugs 2023; 21:367. [PMID: 37367692 DOI: 10.3390/md21060367] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2023] [Revised: 06/15/2023] [Accepted: 06/16/2023] [Indexed: 06/28/2023] Open
Abstract
Marinolides A and B, two new 24- and 26-membered bacterial macrolactones, were isolated from the marine-derived actinobacterium AJS-327 and their stereostructures initially assigned by bioinformatic data analysis. Macrolactones typically possess complex stereochemistry, the assignments of which have been one of the most difficult undertakings in natural products chemistry, and in most cases, the use of X-ray diffraction methods and total synthesis have been the major methods of assigning their absolute configurations. More recently, however, it has become apparent that the integration of bioinformatic data is growing in utility to assign absolute configurations. Genome mining and bioinformatic analysis identified the 97 kb mld biosynthetic cluster harboring seven type I polyketide synthases. A detailed bioinformatic investigation of the ketoreductase and enoylreductase domains within the multimodular polyketide synthases, coupled with NMR and X-ray diffraction data, allowed for the absolute configurations of marinolides A and B to be determined. While using bioinformatics to assign the relative and absolute configurations of natural products has high potential, this method must be coupled with full NMR-based analysis to both confirm bioinformatic assignments as well as any additional modifications that occur during biosynthesis.
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Affiliation(s)
- Min Cheol Kim
- Center for Marine Biotechnology and Biomedicine, Scripps Institution of Oceanography, Skaggs School of Pharmacy and Pharmaceutical Sciences, Moores Comprehensive Cancer Center, University of California, La Jolla, San Diego, CA 92093, USA
| | - Jaclyn M Winter
- Department of Pharmacology and Toxicology, University of Utah, Salt Lake City, UT 84112, USA
| | - Reiko Cullum
- Center for Marine Biotechnology and Biomedicine, Scripps Institution of Oceanography, Skaggs School of Pharmacy and Pharmaceutical Sciences, Moores Comprehensive Cancer Center, University of California, La Jolla, San Diego, CA 92093, USA
| | - Alexander J Smith
- Center for Marine Biotechnology and Biomedicine, Scripps Institution of Oceanography, Skaggs School of Pharmacy and Pharmaceutical Sciences, Moores Comprehensive Cancer Center, University of California, La Jolla, San Diego, CA 92093, USA
| | - William Fenical
- Center for Marine Biotechnology and Biomedicine, Scripps Institution of Oceanography, Skaggs School of Pharmacy and Pharmaceutical Sciences, Moores Comprehensive Cancer Center, University of California, La Jolla, San Diego, CA 92093, USA
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15
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Guzman KM, Cogan DP, Brodsky KL, Soohoo AM, Li X, Sevillano N, Mathews II, Nguyen KP, Craik CS, Khosla C. Discovery and Characterization of Antibody Probes of Module 2 of the 6-Deoxyerythronolide B Synthase. Biochemistry 2023. [PMID: 37184546 DOI: 10.1021/acs.biochem.3c00156] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/16/2023]
Abstract
Fragment antigen-binding domains of antibodies (Fabs) are powerful probes of structure-function relationships of assembly line polyketide synthases (PKSs). We report the discovery and characterization of Fabs interrogating the structure and function of the ketosynthase-acyltransferase (KS-AT) core of Module 2 of the 6-deoxyerythronolide B synthase (DEBS). Two Fabs (AC2 and BB1) were identified to potently inhibit the catalytic activity of Module 2. Both AC2 and BB1 were found to modulate ACP-mediated reactions catalyzed by this module, albeit by distinct mechanisms. AC2 primarily affects the rate (kcat), whereas BB1 increases the KM of an ACP-mediated reaction. A third Fab, AA5, binds to the KS-AT fragment of DEBS Module 2 without altering either parameter; it is phenotypically reminiscent of a previously characterized Fab, 1B2, shown to principally recognize the N-terminal helical docking domain of DEBS Module 3. Crystal structures of AA5 and 1B2 bound to the KS-AT fragment of Module 2 were solved to 2.70 and 2.65 Å resolution, respectively, and revealed entirely distinct recognition features of the two antibodies. The new tools and insights reported here pave the way toward advancing our understanding of the structure-function relationships of DEBS Module 2, arguably the most well-studied module of an assembly line PKS.
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Affiliation(s)
- Katarina M Guzman
- Department of Chemical Engineering, Stanford University, Stanford, California 94305, United States
| | - Dillon P Cogan
- Department of Chemistry, Stanford University, Stanford, California 94305, United States
| | - Krystal L Brodsky
- Department of Chemistry, Stanford University, Stanford, California 94305, United States
| | - Alexander M Soohoo
- Department of Chemical Engineering, Stanford University, Stanford, California 94305, United States
| | - Xiuyuan Li
- Department of Chemistry, Stanford University, Stanford, California 94305, United States
| | - Natalia Sevillano
- Department of Pharmaceutical Chemistry, University of California San Francisco, San Francisco, California 94158, United States
| | - Irimpan I Mathews
- Stanford Synchrotron Radiation Lightsource, SLAC National Accelerator Laboratory, Stanford University, Menlo Park, California 94025, United States
| | - Khanh P Nguyen
- Department of Chemistry, Stanford University, Stanford, California 94305, United States
| | - Charles S Craik
- Department of Pharmaceutical Chemistry, University of California San Francisco, San Francisco, California 94158, United States
| | - Chaitan Khosla
- Department of Chemical Engineering, Stanford University, Stanford, California 94305, United States
- Department of Chemistry, Stanford University, Stanford, California 94305, United States
- Sarafan ChEM-H, Stanford University, Stanford, California 94305, United States
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16
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Lacey HJ, Chen R, Vuong D, Lacey E, Rutledge PJ, Chooi YH, Piggott AM, Booth TJ. Resorculins: hybrid polyketide macrolides from Streptomyces sp. MST-91080. Org Biomol Chem 2023; 21:2531-2538. [PMID: 36876905 DOI: 10.1039/d2ob02332f] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/06/2023]
Abstract
Fourteen-membered macrolides are a class of compounds with significant clinical value as antibacterial agents. As part of our ongoing investigation into the metabolites of Streptomyces sp. MST-91080, we report the discovery of resorculins A and B, unprecedented 3,5-dihydroxybenzoic acid (α-resorcylic acid)-containing 14-membered macrolides. We sequenced the genome of MST-91080 and identified the putative resorculin biosynthetic gene cluster (rsn BGC). The rsn BGC is hybrid of type I and type III polyketide synthases. Bioinformatic analysis revealed that the resorculins are relatives of known hybrid polyketides: kendomycin and venemycin. Resorculin A exhibited antibacterial activity against Bacillus subtilis (MIC 19.8 μg mL-1), while resorculin B showed cytotoxic activity against the NS-1 mouse myeloma cell line (IC50 3.6 μg mL-1).
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Affiliation(s)
- Heather J Lacey
- Microbial Screening Technologies, Smithfield, NSW 2164, Australia
- School of Chemistry, The University of Sydney, NSW 2006, Australia
| | - Rachel Chen
- Microbial Screening Technologies, Smithfield, NSW 2164, Australia
| | - Daniel Vuong
- Microbial Screening Technologies, Smithfield, NSW 2164, Australia
| | - Ernest Lacey
- Microbial Screening Technologies, Smithfield, NSW 2164, Australia
- School of Natural Sciences, Macquarie University, NSW 2109, Australia
| | - Peter J Rutledge
- School of Chemistry, The University of Sydney, NSW 2006, Australia
| | - Yit-Heng Chooi
- School of Molecular Sciences, The University of Western Australia, Perth, WA 6009, Australia.
| | - Andrew M Piggott
- School of Natural Sciences, Macquarie University, NSW 2109, Australia
| | - Thomas J Booth
- School of Molecular Sciences, The University of Western Australia, Perth, WA 6009, Australia.
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17
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Kudo F, Kishikawa K, Tsuboi K, Kido T, Usui T, Hashimoto J, Shin-Ya K, Miyanaga A, Eguchi T. Acyltransferase Domain Exchange between Two Independent Type I Polyketide Synthases in the Same Producer Strain of Macrolide Antibiotics. Chembiochem 2023; 24:e202200670. [PMID: 36602093 DOI: 10.1002/cbic.202200670] [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: 11/16/2022] [Revised: 01/04/2023] [Accepted: 01/05/2023] [Indexed: 01/06/2023]
Abstract
Streptomyces graminofaciens A-8890 produces two macrolide antibiotics, FD-891 and virustomycin A, both of which show significant biological activity. In this study, we identified the virustomycin A biosynthetic gene cluster, which encodes type I polyketide synthases (PKSs), ethylmalonyl-CoA biosynthetic enzymes, methoxymalony-acyl carrier protein biosynthetic enzymes, and post-PKS modification enzymes. Next, we demonstrated that the acyltransferase domain can be exchanged between the Vsm PKSs and the PKSs involved in FD-891 biosynthesis (Gfs PKSs), without any supply problems of the unique extender units. We exchanged the malonyltransferase domain in the loading module of Gfs PKS with the ethylmalonyltransferase domain and the methoxymalonyltransferase domain of Vsm PKSs. Consequently, the expected two-carbon-elongated analog 26-ethyl-FD-891 was successfully produced with a titer comparable to FD-891 production by the wild type; however, exchange with the methoxymalonyltransferase domain did not produce any FD-891 analogs. Furthermore, 26-ethyl-FD-891 showed potent cytotoxic activity against HeLa cells, like natural FD-891.
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Affiliation(s)
- Fumitaka Kudo
- Department of Chemistry, Tokyo Institute of Technology, 2-12-1 Meguro-ku, O-okayama, Tokyo, 152-8551, Japan
| | - Kosuke Kishikawa
- Department of Chemistry, Tokyo Institute of Technology, 2-12-1 Meguro-ku, O-okayama, Tokyo, 152-8551, Japan
| | - Kazuma Tsuboi
- Department of Chemistry, Tokyo Institute of Technology, 2-12-1 Meguro-ku, O-okayama, Tokyo, 152-8551, Japan
| | - Takafusa Kido
- Department of Chemistry, Tokyo Institute of Technology, 2-12-1 Meguro-ku, O-okayama, Tokyo, 152-8551, Japan
| | - Takeo Usui
- Graduate School of Life and Environmental Sciences, University of Tsukuba, 1-1-1 Tennodai, Tsukuba, 305-8572, Ibaraki, Japan
| | - Junko Hashimoto
- Japan Biological Informatics Consortium (JBIC), 2-4-7 Aomi, Koto-ku, Tokyo, 135-0064, Japan
| | - Kazuo Shin-Ya
- National Institute of Advanced Industrial Science and Technology, 2-4-7 Aomi, Koto-ku, Tokyo, 135-0064, Japan
| | - Akimasa Miyanaga
- Department of Chemistry, Tokyo Institute of Technology, 2-12-1 Meguro-ku, O-okayama, Tokyo, 152-8551, Japan
| | - Tadashi Eguchi
- Department of Chemistry, Tokyo Institute of Technology, 2-12-1 Meguro-ku, O-okayama, Tokyo, 152-8551, Japan
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18
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Wang J, Wang X, Li X, Kong L, Du Z, Li D, Gou L, Wu H, Cao W, Wang X, Lin S, Shi T, Deng Z, Wang Z, Liang J. C-N bond formation by a polyketide synthase. Nat Commun 2023; 14:1319. [PMID: 36899013 PMCID: PMC10006239 DOI: 10.1038/s41467-023-36989-w] [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: 06/15/2022] [Accepted: 02/28/2023] [Indexed: 03/12/2023] Open
Abstract
Assembly-line polyketide synthases (PKSs) are molecular factories that produce diverse metabolites with wide-ranging biological activities. PKSs usually work by constructing and modifying the polyketide backbone successively. Here, we present the cryo-EM structure of CalA3, a chain release PKS module without an ACP domain, and its structures with amidation or hydrolysis products. The domain organization reveals a unique "∞"-shaped dimeric architecture with five connected domains. The catalytic region tightly contacts the structural region, resulting in two stabilized chambers with nearly perfect symmetry while the N-terminal docking domain is flexible. The structures of the ketosynthase (KS) domain illustrate how the conserved key residues that canonically catalyze C-C bond formation can be tweaked to mediate C-N bond formation, revealing the engineering adaptability of assembly-line polyketide synthases for the production of novel pharmaceutical agents.
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Affiliation(s)
- Jialiang Wang
- State Key Laboratory of Microbial Metabolism, Joint International Research Laboratory of Metabolic & Developmental Sciences, and School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, China
| | - Xiaojie Wang
- State Key Laboratory of Microbial Metabolism, Joint International Research Laboratory of Metabolic & Developmental Sciences, and School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, China.,Department of Molecular Biology, Shanghai Jikaixing Biotech Inc., Shanghai, 200131, China
| | - Xixi Li
- State Key Laboratory of Microbial Metabolism, Joint International Research Laboratory of Metabolic & Developmental Sciences, and School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, China
| | - LiangLiang Kong
- National Facility for Protein Science in Shanghai, Chinese Academy of Sciences, Shanghai, 201204, China
| | - Zeqian Du
- State Key Laboratory of Microbial Metabolism, Joint International Research Laboratory of Metabolic & Developmental Sciences, and School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, China
| | - Dandan Li
- State Key Laboratory of Microbial Metabolism, Joint International Research Laboratory of Metabolic & Developmental Sciences, and School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, China
| | - Lixia Gou
- School of Life Science, North China University of Science and Technology, Tangshan, Hebei, China
| | - Hao Wu
- State Key Laboratory of Microbial Metabolism, Joint International Research Laboratory of Metabolic & Developmental Sciences, and School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, China
| | - Wei Cao
- State Key Laboratory of Microbial Metabolism, Joint International Research Laboratory of Metabolic & Developmental Sciences, and School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, China
| | - Xiaozheng Wang
- State Key Laboratory of Microbial Metabolism, Joint International Research Laboratory of Metabolic & Developmental Sciences, and School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, China
| | - Shuangjun Lin
- State Key Laboratory of Microbial Metabolism, Joint International Research Laboratory of Metabolic & Developmental Sciences, and School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, China.
| | - Ting Shi
- State Key Laboratory of Microbial Metabolism, Joint International Research Laboratory of Metabolic & Developmental Sciences, and School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, China.
| | - Zixin Deng
- State Key Laboratory of Microbial Metabolism, Joint International Research Laboratory of Metabolic & Developmental Sciences, and School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, China.
| | - Zhijun Wang
- State Key Laboratory of Microbial Metabolism, Joint International Research Laboratory of Metabolic & Developmental Sciences, and School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, China.
| | - Jingdan Liang
- State Key Laboratory of Microbial Metabolism, Joint International Research Laboratory of Metabolic & Developmental Sciences, and School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, China.
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19
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Oves-Costales D, Gren T, Sterndorff EB, Martín J, Ortiz-López FJ, Jørgensen TS, Jiang X, Román-Hurtado F, Reyes F, Genilloud O, Weber T. Identification and heterologous expression of the globomycin biosynthetic gene cluster. Synth Syst Biotechnol 2023; 8:206-212. [PMID: 36844473 PMCID: PMC9943842 DOI: 10.1016/j.synbio.2023.02.001] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2022] [Revised: 01/30/2023] [Accepted: 02/02/2023] [Indexed: 02/10/2023] Open
Abstract
Globomycin is a cyclic lipodepsipeptide originally isolated from several Streptomyces species which displays strong and selective antibacterial activity against Gram-negative pathogens. Its mode of action is based on the competitive inhibition of the lipoprotein signal peptidase II (LspA), which is absent in eukaryotes and considered an attractive target for the development of new antibiotics. Despite its interesting biological properties, the gene cluster encoding its biosynthesis has not yet been identified. In this study we employed a genome-mining approach in the globomycin-producing Streptomyces sp. CA-278952 to identify a candidate gene cluster responsible for its biosynthesis. A null mutant was constructed using CRISPR base editing where production was abolished, strongly suggesting its involvement in the biosynthesis. The putative gene cluster was then cloned and heterologously expressed in Streptomyces albus J1074 and Streptomyces coelicolor M1146, therefore unambiguously linking globomycin and its biosynthetic gene cluster. Our work paves the way for the biosynthesis of new globomycin derivatives with improved pharmacological properties.
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Affiliation(s)
- Daniel Oves-Costales
- Fundacion MEDINA, Centro de Excelencia en Investigación de Medicamentos Innovadores en Andalucía, Avda del Conocimiento 34, 18016, Armilla, Granada, Spain,Corresponding author.
| | - Tetiana Gren
- The Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Kemitorvet, building 220, 2800 Kgs. Lyngby, Denmark
| | - Eva Baggesgaard Sterndorff
- The Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Kemitorvet, building 220, 2800 Kgs. Lyngby, Denmark
| | - Jesús Martín
- Fundacion MEDINA, Centro de Excelencia en Investigación de Medicamentos Innovadores en Andalucía, Avda del Conocimiento 34, 18016, Armilla, Granada, Spain
| | - Francisco Javier Ortiz-López
- Fundacion MEDINA, Centro de Excelencia en Investigación de Medicamentos Innovadores en Andalucía, Avda del Conocimiento 34, 18016, Armilla, Granada, Spain
| | - Tue S. Jørgensen
- The Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Kemitorvet, building 220, 2800 Kgs. Lyngby, Denmark
| | - Xinglin Jiang
- The Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Kemitorvet, building 220, 2800 Kgs. Lyngby, Denmark
| | - Fernando Román-Hurtado
- Fundacion MEDINA, Centro de Excelencia en Investigación de Medicamentos Innovadores en Andalucía, Avda del Conocimiento 34, 18016, Armilla, Granada, Spain
| | - Fernando Reyes
- Fundacion MEDINA, Centro de Excelencia en Investigación de Medicamentos Innovadores en Andalucía, Avda del Conocimiento 34, 18016, Armilla, Granada, Spain
| | - Olga Genilloud
- Fundacion MEDINA, Centro de Excelencia en Investigación de Medicamentos Innovadores en Andalucía, Avda del Conocimiento 34, 18016, Armilla, Granada, Spain,Corresponding author.
| | - Tilmann Weber
- The Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Kemitorvet, building 220, 2800 Kgs. Lyngby, Denmark,Corresponding author.
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20
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Liu Z, Yashiroda Y, Sun P, Ma H, Wang Y, Li L, Yan F, Sun Y. Argenteolides A and B, Glycosylated Polyketide-Peptide Hybrid Macrolides from an Actinomycete Streptomyces argenteolus. Org Lett 2023; 25:571-575. [PMID: 36469481 DOI: 10.1021/acs.orglett.2c03290] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
Two novel glycosylated polyketide-peptide hybrid macrolides, argenteolides A (1) and B (2), were isolated from an actinomycete Streptomyces argenteolus. Argenteolide A (1) contains a unique 5/5/5 tricyclic system in a 20-membered macrocycle. Their structures were elucidated by extensive spectroscopic analysis, and their stereochemical configurations were established through the application of chemical derivatization, J-based configuration analysis, DP4+ calculation, and electronic circular dichroism calculation. The analysis of the genome sequence revealed a plausible biosynthesis mechanism, and isotope-labeled feeding studies suggested their biogenetic origins. Argenteolides A and B exhibited moderate cytotoxicities against A549, p388, and Hela human carcinoma cell lines as well as antibacterial activities against Staphylococcus aureus and Escherichia coli ATCC25922.
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Affiliation(s)
- Zhiguo Liu
- Institute of Chinese Materia Medica, China Academy of Chinese Medical Sciences, Beijing100700, China
| | - Yoko Yashiroda
- RIKEN Center for Sustainable Resource Science, 2-1 Hirosawa, Wako, Saitama351-0198, Japan
| | - Peng Sun
- Institute of Chinese Materia Medica, China Academy of Chinese Medical Sciences, Beijing100700, China
| | - Hai Ma
- Institute of Chinese Materia Medica, China Academy of Chinese Medical Sciences, Beijing100700, China
| | - Yanan Wang
- Institute of Materia Medica, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing100050, China
| | - Li Li
- Institute of Materia Medica, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing100050, China
| | - Fu Yan
- Helmholtz International Lab for Antiinfectives, Shandong University-Helmholtz Institute of Biotechnology, State Key Laboratory of Microbial Technology, Shandong University, Qingdao, Shandong266237, China
| | - Yi Sun
- Institute of Chinese Materia Medica, China Academy of Chinese Medical Sciences, Beijing100700, China
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21
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Tan B, Zhang Q, Li J, Zhu Y, Zhang L, Zhang W, Zhang H, Chen Y, Zhang C. Totopotensamide Congeners from a Halogenase-Inactivated Mutant. JOURNAL OF NATURAL PRODUCTS 2023; 86:76-84. [PMID: 36606742 DOI: 10.1021/acs.jnatprod.2c00772] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/17/2023]
Abstract
The installation of halogen atoms into aromatic and less activated polyketide substrates by halogenases is a powerful strategy to tune the bioactivity, bioavailability, and reactivity of compounds. In the biosynthetic pathway of totopotensamide A (1), the halogenase TotH was confirmed in vivo to catalyze the C-4 chlorination to form the nonproteinogenic amino acid ClMeDPG. Herein, we report the isolation, structure elucidation, and bioactivity evaluation of six new deschloro totopotensamide (TPM) congeners TPMs H2-H7 (5-10) from the totH-inactivated strain and the proposed absolute configuration of the polyketide chain in TPMs using 4 as a model compound by a combination of the JBCA and bioinformatic analysis. Compounds 5, 6, 8, and 9 displayed cytotoxicity against the A549, PANC-1, Calu3, and BXPC3 cell lines with IC50 values ranging from 2.3 to 9.7 μM.
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Affiliation(s)
- Bin Tan
- Key Laboratory of Tropical Marine Bio-resources and Ecology, Guangdong Key Laboratory of Marine Materia Medica, South China Sea Institute of Oceanology, Chinese Academy of Sciences, Guangzhou 510301, China
- University of Chinese Academy of Sciences, Beijing 100049, China
- Southern Marine Science and Engineering Guangdong Laboratory (Guangzhou), 1119 Haibin Road, Nansha District, Guangzhou 511458, China
- Sanya Institute of Ocean Eco-Environmental Engineering, Yazhou Scientific Bay, Sanya 572000, China
| | - Qingbo Zhang
- Key Laboratory of Tropical Marine Bio-resources and Ecology, Guangdong Key Laboratory of Marine Materia Medica, South China Sea Institute of Oceanology, Chinese Academy of Sciences, Guangzhou 510301, China
- University of Chinese Academy of Sciences, Beijing 100049, China
- Southern Marine Science and Engineering Guangdong Laboratory (Guangzhou), 1119 Haibin Road, Nansha District, Guangzhou 511458, China
- Sanya Institute of Ocean Eco-Environmental Engineering, Yazhou Scientific Bay, Sanya 572000, China
| | - Jieyi Li
- School of Pharmaceutical, Guangzhou University of Chinese Medicine, Guangzhou 510006, China
| | - Yiguang Zhu
- Key Laboratory of Tropical Marine Bio-resources and Ecology, Guangdong Key Laboratory of Marine Materia Medica, South China Sea Institute of Oceanology, Chinese Academy of Sciences, Guangzhou 510301, China
- University of Chinese Academy of Sciences, Beijing 100049, China
- Southern Marine Science and Engineering Guangdong Laboratory (Guangzhou), 1119 Haibin Road, Nansha District, Guangzhou 511458, China
- Sanya Institute of Ocean Eco-Environmental Engineering, Yazhou Scientific Bay, Sanya 572000, China
| | - Liping Zhang
- Key Laboratory of Tropical Marine Bio-resources and Ecology, Guangdong Key Laboratory of Marine Materia Medica, South China Sea Institute of Oceanology, Chinese Academy of Sciences, Guangzhou 510301, China
- Southern Marine Science and Engineering Guangdong Laboratory (Guangzhou), 1119 Haibin Road, Nansha District, Guangzhou 511458, China
- Sanya Institute of Ocean Eco-Environmental Engineering, Yazhou Scientific Bay, Sanya 572000, China
| | - Wenjun Zhang
- Key Laboratory of Tropical Marine Bio-resources and Ecology, Guangdong Key Laboratory of Marine Materia Medica, South China Sea Institute of Oceanology, Chinese Academy of Sciences, Guangzhou 510301, China
- University of Chinese Academy of Sciences, Beijing 100049, China
- Southern Marine Science and Engineering Guangdong Laboratory (Guangzhou), 1119 Haibin Road, Nansha District, Guangzhou 511458, China
- Sanya Institute of Ocean Eco-Environmental Engineering, Yazhou Scientific Bay, Sanya 572000, China
| | - Haibo Zhang
- Key Laboratory of Tropical Marine Bio-resources and Ecology, Guangdong Key Laboratory of Marine Materia Medica, South China Sea Institute of Oceanology, Chinese Academy of Sciences, Guangzhou 510301, China
- University of Chinese Academy of Sciences, Beijing 100049, China
- Southern Marine Science and Engineering Guangdong Laboratory (Guangzhou), 1119 Haibin Road, Nansha District, Guangzhou 511458, China
- Sanya Institute of Ocean Eco-Environmental Engineering, Yazhou Scientific Bay, Sanya 572000, China
| | - Yang Chen
- School of Pharmaceutical, Guangzhou University of Chinese Medicine, Guangzhou 510006, China
| | - Changsheng Zhang
- Key Laboratory of Tropical Marine Bio-resources and Ecology, Guangdong Key Laboratory of Marine Materia Medica, South China Sea Institute of Oceanology, Chinese Academy of Sciences, Guangzhou 510301, China
- University of Chinese Academy of Sciences, Beijing 100049, China
- Southern Marine Science and Engineering Guangdong Laboratory (Guangzhou), 1119 Haibin Road, Nansha District, Guangzhou 511458, China
- Sanya Institute of Ocean Eco-Environmental Engineering, Yazhou Scientific Bay, Sanya 572000, China
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22
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Shin YH, Im JH, Kang I, Kim E, Jang SC, Cho E, Shin D, Hwang S, Du YE, Huynh TH, Ko K, Ko YJ, Nam SJ, Awakawa T, Lee J, Hong S, Abe I, Moore BS, Fenical W, Yoon YJ, Cho JC, Lee SK, Oh KB, Oh DC. Genomic and Spectroscopic Signature-Based Discovery of Natural Macrolactams. J Am Chem Soc 2023; 145:1886-1896. [PMID: 36634356 DOI: 10.1021/jacs.2c11527] [Citation(s) in RCA: 8] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/14/2023]
Abstract
The logical and effective discovery of macrolactams, structurally unique natural molecules with diverse biological activities, has been limited by a lack of targeted search methods. Herein, a targeted discovery method for natural macrolactams was devised by coupling genomic signature-based PCR screening of a bacterial DNA library with spectroscopic signature-based early identification of macrolactams. DNA library screening facilitated the efficient selection of 43 potential macrolactam-producing strains (3.6% of 1,188 strains screened). The PCR amplicons of the amine-deprotecting enzyme-coding genes were analyzed to predict the macrolactam type (α-methyl, α-alkyl, or β-methyl) produced by the hit strains. 1H-15N HSQC-TOCSY NMR analysis of 15N-labeled culture extracts enabled macrolactam detection and structural type assignment without any purification steps. This method identified a high-titer Micromonospora strain producing salinilactam (1), a previously reported α-methyl macrolactam, and two Streptomyces strains producing new α-alkyl and β-methyl macrolactams. Subsequent purification and spectroscopic analysis led to the structural revision of 1 and the discovery of muanlactam (2), an α-alkyl macrolactam with diene amide and tetraene chromophores, and concolactam (3), a β-methyl macrolactam with a [16,6,6]-tricyclic skeleton. Detailed genomic analysis of the strains producing 1-3 identified putative biosynthetic gene clusters and pathways. Compound 2 displayed significant cytotoxicity against various cancer cell lines (IC50 = 1.58 μM against HCT116), whereas 3 showed inhibitory activity against Staphylococcus aureus sortase A. This genomic and spectroscopic signature-based method provides an efficient search strategy for new natural macrolactams and will be generally applicable for the discovery of nitrogen-bearing natural products.
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Affiliation(s)
- Yern-Hyerk Shin
- Natural Products Research Institute, College of Pharmacy, Seoul National University, Seoul 08826, Republic of Korea
| | - Ji Hyeon Im
- Natural Products Research Institute, College of Pharmacy, Seoul National University, Seoul 08826, Republic of Korea
| | - Ilnam Kang
- Department of Biological Sciences, Inha University, Incheon 22212, Republic of Korea
| | - Eunji Kim
- Natural Products Research Institute, College of Pharmacy, Seoul National University, Seoul 08826, Republic of Korea
| | - Sung Chul Jang
- Natural Products Research Institute, College of Pharmacy, Seoul National University, Seoul 08826, Republic of Korea
| | - Eunji Cho
- Department of Agricultural Biotechnology, College of Agriculture & Life Sciences, Seoul National University, Seoul 08826, Republic of Korea
| | - Daniel Shin
- Natural Products Research Institute, College of Pharmacy, Seoul National University, Seoul 08826, Republic of Korea
| | - Sunghoon Hwang
- Natural Products Research Institute, College of Pharmacy, Seoul National University, Seoul 08826, Republic of Korea
| | - Young Eun Du
- Natural Products Research Institute, College of Pharmacy, Seoul National University, Seoul 08826, Republic of Korea
| | - Thanh-Hau Huynh
- Natural Products Research Institute, College of Pharmacy, Seoul National University, Seoul 08826, Republic of Korea
| | - Keebeom Ko
- Natural Products Research Institute, College of Pharmacy, Seoul National University, Seoul 08826, Republic of Korea
| | - Yoon-Joo Ko
- Laboratory of Nuclear Magnetic Resonance, National Center of Inter-University Research Facilities (NCIRF), Seoul National University, Seoul 08826, Republic of Korea
| | - Sang-Jip Nam
- Department of Chemistry and Nanoscience, Ewha Womans University, Seoul 03760, Republic of Korea
| | - Takayoshi Awakawa
- Graduate School of Pharmaceutical Sciences, The University of Tokyo, Tokyo 113-0033, Japan.,RIKEN Center for Sustainable Resource Science, Wako, Saitama 351-0198, Japan
| | - Jeeyeon Lee
- Research Institute of Pharmaceutical Sciences, College of Pharmacy, Seoul National University, Seoul 08826, Republic of Korea
| | - Suckchang Hong
- Research Institute of Pharmaceutical Sciences, College of Pharmacy, Seoul National University, Seoul 08826, Republic of Korea
| | - Ikuro Abe
- Graduate School of Pharmaceutical Sciences, The University of Tokyo, Tokyo 113-0033, Japan
| | - Bradley S Moore
- Center for Marine Biotechnology and Biomedicine, Scripps Institution of Oceanography and Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California, San Diego, La Jolla, California 92093, United States
| | - William Fenical
- Center for Marine Biotechnology and Biomedicine, Scripps Institution of Oceanography and Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California, San Diego, La Jolla, California 92093, United States
| | - Yeo Joon Yoon
- Natural Products Research Institute, College of Pharmacy, Seoul National University, Seoul 08826, Republic of Korea.,MolGenBio Co., Ltd., Seoul 08826, Republic of Korea
| | - Jang-Cheon Cho
- Department of Biological Sciences, Inha University, Incheon 22212, Republic of Korea
| | - Sang Kook Lee
- Natural Products Research Institute, College of Pharmacy, Seoul National University, Seoul 08826, Republic of Korea
| | - Ki-Bong Oh
- Department of Agricultural Biotechnology, College of Agriculture & Life Sciences, Seoul National University, Seoul 08826, Republic of Korea
| | - Dong-Chan Oh
- Natural Products Research Institute, College of Pharmacy, Seoul National University, Seoul 08826, Republic of Korea
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23
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Fang C, Zhang Q, Zhang W, Zhang C, Zhu Y. Discovery of Efrotomycin Congeners and Heterologous Expression-Based Insights into the Self-Resistance Mechanism. JOURNAL OF NATURAL PRODUCTS 2022; 85:2865-2872. [PMID: 36445346 DOI: 10.1021/acs.jnatprod.2c00986] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/16/2023]
Abstract
Four new efrotomycins, A1-A4 (1-4), were isolated from the salt mine-derived Amycolatopsis cihanbeyliensis DSM 45679 and structurally determined. Efrotomycins A3 (3) and A4 (4) feature a tetrahydrofuran ring configured distinctly from known elfamycins. Heterologous expression of the efrotomycin gene cluster (efr BGC) in Streptomyces lividans SBT18 led to efrotomycin B1 (5), the yield of which was improved several fold upon introduction of the transporter gene efrT, a putative self-resistance determinant outside of the efr BGC.
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Affiliation(s)
- Chunyan Fang
- Key Laboratory of Tropical Marine Bio-resources and Ecology, Guangdong Key Laboratory of Marine Materia Medica, RNAM Center for Marine Microbiology, South China Sea Institute of Oceanology, Chinese Academy of Sciences, 164 West Xingang Road, Guangzhou 510301, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Qingbo Zhang
- Key Laboratory of Tropical Marine Bio-resources and Ecology, Guangdong Key Laboratory of Marine Materia Medica, RNAM Center for Marine Microbiology, South China Sea Institute of Oceanology, Chinese Academy of Sciences, 164 West Xingang Road, Guangzhou 510301, China
- University of Chinese Academy of Sciences, Beijing 100049, China
- Southern Marine Science and Engineering Guangdong Laboratory (Guangzhou), Guangzhou 511458, China
- Sanya Institute of Ocean Eco-Environmental Engineering, Yazhou Scientific Bay, Sanya 572000, China
| | - Wenjun Zhang
- Key Laboratory of Tropical Marine Bio-resources and Ecology, Guangdong Key Laboratory of Marine Materia Medica, RNAM Center for Marine Microbiology, South China Sea Institute of Oceanology, Chinese Academy of Sciences, 164 West Xingang Road, Guangzhou 510301, China
- University of Chinese Academy of Sciences, Beijing 100049, China
- Southern Marine Science and Engineering Guangdong Laboratory (Guangzhou), Guangzhou 511458, China
- Sanya Institute of Ocean Eco-Environmental Engineering, Yazhou Scientific Bay, Sanya 572000, China
| | - Changsheng Zhang
- Key Laboratory of Tropical Marine Bio-resources and Ecology, Guangdong Key Laboratory of Marine Materia Medica, RNAM Center for Marine Microbiology, South China Sea Institute of Oceanology, Chinese Academy of Sciences, 164 West Xingang Road, Guangzhou 510301, China
- University of Chinese Academy of Sciences, Beijing 100049, China
- Southern Marine Science and Engineering Guangdong Laboratory (Guangzhou), Guangzhou 511458, China
- Sanya Institute of Ocean Eco-Environmental Engineering, Yazhou Scientific Bay, Sanya 572000, China
| | - Yiguang Zhu
- Key Laboratory of Tropical Marine Bio-resources and Ecology, Guangdong Key Laboratory of Marine Materia Medica, RNAM Center for Marine Microbiology, South China Sea Institute of Oceanology, Chinese Academy of Sciences, 164 West Xingang Road, Guangzhou 510301, China
- University of Chinese Academy of Sciences, Beijing 100049, China
- Southern Marine Science and Engineering Guangdong Laboratory (Guangzhou), Guangzhou 511458, China
- Sanya Institute of Ocean Eco-Environmental Engineering, Yazhou Scientific Bay, Sanya 572000, China
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24
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Caradec T, Trivelli X, Desmecht E, Peucelle V, Khalife J, Hartkoorn RC. Dactylosporolides: Glycosylated Macrolides from Dactylosporangium fulvum. JOURNAL OF NATURAL PRODUCTS 2022; 85:2714-2722. [PMID: 36512509 PMCID: PMC9791991 DOI: 10.1021/acs.jnatprod.2c00484] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/25/2022] [Indexed: 05/30/2023]
Abstract
A series of novel macrolides were discovered from the culture supernatant of the rare soil actinobacteria Dactylosporangium fulvum and named dactylosporolides A-C. The structure and absolute configuration of these dactylosporolides were defined using a combination of NMR structural elucidation and analysis of the dactylosporolide biosynthetic gene cluster. Together these data revealed dactylosporolides to be composed of a central 22-membered macrolactone with an internal hemiketal ring and a protruding ketide tail that were (poly)glycosylated at two distal parts. While bearing no antibiotic activity, these dactylosporolides displayed activity against Plasmodium falciparum 3D7.
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Affiliation(s)
- Thibault Caradec
- Univ.
Lille, CNRS, Inserm, CHU Lille, Institut Pasteur Lille, U1019—UMR
9017—CIIL—Center for Infection and Immunity of Lille, F-59000 Lille, France
| | - Xavier Trivelli
- Univ.
Lille, CNRS, INRAE, Centrale Lille, Univ. Artois, FR 2638—IMEC—Institut
Michel-Eugène Chevreul, Lille 59000, France
| | - Eva Desmecht
- Univ.
Lille, CNRS, Inserm, CHU Lille, Institut Pasteur Lille, U1019—UMR
9017—CIIL—Center for Infection and Immunity of Lille, F-59000 Lille, France
| | - Veronique Peucelle
- Univ.
Lille, CNRS, Inserm, CHU Lille, Institut Pasteur Lille, U1019—UMR
9017—CIIL—Center for Infection and Immunity of Lille, F-59000 Lille, France
| | - Jamal Khalife
- Univ.
Lille, CNRS, Inserm, CHU Lille, Institut Pasteur Lille, U1019—UMR
9017—CIIL—Center for Infection and Immunity of Lille, F-59000 Lille, France
| | - Ruben C. Hartkoorn
- Univ.
Lille, CNRS, Inserm, CHU Lille, Institut Pasteur Lille, U1019—UMR
9017—CIIL—Center for Infection and Immunity of Lille, F-59000 Lille, France
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25
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Oh SH, Park J, Moon DH, Hyun GH, Jang YJ, Hwang S, An JS, Du YE, Kwon Y, Kang YP, Lee SK, Oh DC. Apoptolidin I: A new glycosylated macrocyclic lactone from wasp gut bacterium, Amycolatopsis sp. Tetrahedron 2022. [DOI: 10.1016/j.tet.2022.133091] [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]
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26
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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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27
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Freitas S, Castelo-Branco R, Wenzel-Storjohann A, Vasconcelos VM, Tasdemir D, Leão PN. Structure and Biosynthesis of Desmamides A-C, Lipoglycopeptides from the Endophytic Cyanobacterium Desmonostoc muscorum LEGE 12446. JOURNAL OF NATURAL PRODUCTS 2022; 85:1704-1714. [PMID: 35793792 PMCID: PMC9315949 DOI: 10.1021/acs.jnatprod.2c00162] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 06/15/2023]
Abstract
Certain cyanobacteria of the secondary metabolite-rich order Nostocales can establish permanent symbioses with a large number of cycads, by accumulating in their coralloid roots and shifting their metabolism to dinitrogen fixation. Here, we report the discovery of two new lipoglycopeptides, desmamides A (1) and B (2), together with their aglycone desmamide C (3), from the nostocalean cyanobacterium Desmonostoc muscorum LEGE 12446 isolated from a cycad (Cycas revoluta) coralloid root. The chemical structures of the compounds were elucidated using a combination of 1D and 2D NMR spectroscopy and mass spectrometry. The desmamides are decapeptides featuring O-glycosylation of tyrosine (in 1 and 2) and an unusual 3,5-dihydroxy-2-methyldecanoic acid residue. The biosynthesis of the desmamides was studied by substrate incubation experiments and bioinformatics. We describe herein the dsm biosynthetic gene cluster and propose it to be associated with desmamide production. The discovery of this class of very abundant (>1.5% d.w.) bacterial lipoglycopeptides paves the way for exploration of their potential role in root endosymbiosis.
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Affiliation(s)
- Sara Freitas
- Interdisciplinary
Centre of Marine and Environmental Research (CIIMAR/CIMAR), University of Porto, Avenida General Norton de Matos, s/n, 4450-208 Matosinhos, Portugal
- Department
of Biology, Faculty of Sciences, University
of Porto Rua do Campo Alegre, 4169-007 Porto, Portugal
| | - Raquel Castelo-Branco
- Interdisciplinary
Centre of Marine and Environmental Research (CIIMAR/CIMAR), University of Porto, Avenida General Norton de Matos, s/n, 4450-208 Matosinhos, Portugal
| | - Arlette Wenzel-Storjohann
- GEOMAR
Centre for Marine Biotechnology (GEOMAR-Biotech), Research Unit Marine Natural Product Chemistry, GEOMAR Helmholtz
Centre for Ocean Research Kiel, Am Kiel Kanal 44, 24106 Kiel, Germany
| | - Vitor M. Vasconcelos
- Interdisciplinary
Centre of Marine and Environmental Research (CIIMAR/CIMAR), University of Porto, Avenida General Norton de Matos, s/n, 4450-208 Matosinhos, Portugal
- Department
of Biology, Faculty of Sciences, University
of Porto Rua do Campo Alegre, 4169-007 Porto, Portugal
| | - Deniz Tasdemir
- GEOMAR
Centre for Marine Biotechnology (GEOMAR-Biotech), Research Unit Marine Natural Product Chemistry, GEOMAR Helmholtz
Centre for Ocean Research Kiel, Am Kiel Kanal 44, 24106 Kiel, Germany
- Kiel
University, Christian-Albrechts-Platz
4, 24118 Kiel, Germany
| | - Pedro N. Leão
- Interdisciplinary
Centre of Marine and Environmental Research (CIIMAR/CIMAR), University of Porto, Avenida General Norton de Matos, s/n, 4450-208 Matosinhos, Portugal
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Three New Stigmatellin Derivatives Reveal Biosynthetic Insights of Its Side Chain Decoration. Molecules 2022; 27:molecules27144656. [PMID: 35889529 PMCID: PMC9317276 DOI: 10.3390/molecules27144656] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2022] [Revised: 07/19/2022] [Accepted: 07/19/2022] [Indexed: 11/23/2022] Open
Abstract
Myxobacteria generate natural products with unique chemical structures, which not only feature remarkable biological functions, but also demonstrate unprecedented biosynthetic assembly strategies. The stigmatellins have been previously described as potent inhibitors of the mitochondrial and photosynthetic respiratory chain and originate from an unusual polyketide synthase assembly line. While previous biosynthetic investigations were focused on the formation of the 5,7-dimethoxy-8-hydroxychromone ring, side chain decoration of the hydrophobic alkenyl chain in position 2 was investigated less thoroughly. We report here the full structure elucidation, as well as cytotoxic and antimicrobial activities of three new stigmatellins isolated from the myxobacterium Vitiosangium cumulatum MCy10943T with side chain decorations distinct from previously characterized members of this compound family. The hydrophobic alkenyl chain in position 2 of the herein described stigmatellins feature a terminal carboxylic acid group (1), a methoxy group at C-12′ (2) or a vicinal diol (3). These findings provide further implications considering the side chain decoration of these aromatic myxobacterial polyketides and their underlying biosynthesis.
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29
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An JS, Lim HJ, Lee JY, Jang YJ, Nam SJ, Lee SK, Oh DC. Hamuramicin C, a Cytotoxic Bicyclic Macrolide Isolated from a Wasp Gut Bacterium. JOURNAL OF NATURAL PRODUCTS 2022; 85:936-942. [PMID: 35362983 DOI: 10.1021/acs.jnatprod.1c01075] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/14/2023]
Abstract
A new bicyclic macrolide, hamuramicin C (1), was isolated from Streptomyces sp. MBP16, a gut bacterial strain of the wasp Vespa crabro flavofasciata. Its 22-membered macrocyclic lactone structure was determined by NMR and mass spectrometry. The relative configurations of hamuramicin C (1) were assigned by J-based configuration analysis utilizing 1H rotating frame Overhauser effect spectroscopy and heteronuclear long-range coupling NMR spectroscopy. Genomic and bioinformatic analyses of the bacterial strain enabled identification of the type-I polyketide synthase pathway, which employs a trans-acyltransferase system. The absolute configurations of 1 were proposed based on the analysis of the sequences of ketoreductases in the modular gene cluster. Moreover, hamuramicin C (1) demonstrated significant inhibitory activity against diverse human cancer cell lines (HCT116, A549, SNU-638, SK-HEP-1, and MDA-MB-231).
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Affiliation(s)
- Joon Soo An
- Natural Products Research Institute, College of Pharmacy, Seoul National University, Seoul 08826, Republic of Korea
| | - Hyung-Ju Lim
- Natural Products Research Institute, College of Pharmacy, Seoul National University, Seoul 08826, Republic of Korea
| | - Ji Yun Lee
- Natural Products Research Institute, College of Pharmacy, Seoul National University, Seoul 08826, Republic of Korea
| | - Yong-Joon Jang
- Natura Center of Life and Environment, Seoul 08826, Republic of Korea
| | - Sang-Jip Nam
- Department of Chemistry and Nanoscience, Ewha Womans University, Seoul 03760, Republic of Korea
| | - Sang Kook Lee
- Natural Products Research Institute, College of Pharmacy, Seoul National University, Seoul 08826, Republic of Korea
| | - Dong-Chan Oh
- Natural Products Research Institute, College of Pharmacy, Seoul National University, Seoul 08826, Republic of Korea
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Zhang H, Zhang X, Huang Y, Yuan J, Wei X, Ju J. Discovery, Structure Correction, and Biosynthesis of Actinopyrones, Cytotoxic Polyketides from the Deep-Sea Hydrothermal-Vent-Derived Streptomyces sp. SCSIO ZS0520. JOURNAL OF NATURAL PRODUCTS 2022; 85:625-633. [PMID: 34852194 DOI: 10.1021/acs.jnatprod.1c00901] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/13/2023]
Abstract
Three new actinopyrone derivatives, actinopyrones E-G (1, 3, and 4), together with three known analogues, PM050463 (2), actinopyrone D (5), and PM050511 (6), were isolated from Streptomyces sp. SCSIO ZS0520 derived from a deep-sea hydrothermal vent. Their structures, complete with absolute configurations, were elucidated using extensive spectroscopic analyses combined with Mosher's method, ECD calculations, and bioinformatics analyses. These findings corrected the absolute configurations of previously reported actinopyrone analogues 2, 5, and 6 at C-3, C-9, and C-10. Notably, compound 6 displayed notable cytotoxicity against six human cell lines with IC50 values of 0.26-2.22 μM. A likely biosynthetic pathway and annotations of protein function are proposed on the basis of bioinformatics analyses. Genes coding for methyltransferase and glycosyltransferase tailoring chemistries needed to generate final structures were notably absent from the biosynthetic gene cluster. Taken together, these results enable further bioengineering of the actinopyrones and related congeners as potential antitumor agents.
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Affiliation(s)
- Huaran Zhang
- CAS Key Laboratory of Tropical Marine Bio-Resources and Ecology, Guangdong Key Laboratory of Marine Materia Medica, RNAM Center for Marine Microbiology, South China Sea Institute of Oceanology, Chinese Academy of Sciences, 164 West Xingang Road, Guangzhou 510301, China
- College of Oceanology, University of Chinese Academy of Sciences, Qingdao 266400, China
- Southern Marine Science and Engineering Guangdong Laboratory (Guangzhou), No. 1119, Haibin Road, Nansha District, Guangzhou 511458, China
| | - Xuejia Zhang
- CAS Key Laboratory of Tropical Marine Bio-Resources and Ecology, Guangdong Key Laboratory of Marine Materia Medica, RNAM Center for Marine Microbiology, South China Sea Institute of Oceanology, Chinese Academy of Sciences, 164 West Xingang Road, Guangzhou 510301, China
| | - Yun Huang
- School of Basic Medical Sciences, Southern Medical University, Guangzhou 510515, China
| | - Jie Yuan
- Key Laboratory of Tropical Disease Control, Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou 510080, China
| | - Xiaoyi Wei
- Key Laboratory of Plant Resources Conservation and Sustainable Utilization, Guangdong Provincial Key Laboratory of Applied Botany, South China Botanical Garden, Chinese Academy of Sciences, Xingke Road 723, Tianhe District, Guangzhou 510650, China
| | - Jianhua Ju
- CAS Key Laboratory of Tropical Marine Bio-Resources and Ecology, Guangdong Key Laboratory of Marine Materia Medica, RNAM Center for Marine Microbiology, South China Sea Institute of Oceanology, Chinese Academy of Sciences, 164 West Xingang Road, Guangzhou 510301, China
- College of Oceanology, University of Chinese Academy of Sciences, Qingdao 266400, China
- Southern Marine Science and Engineering Guangdong Laboratory (Guangzhou), No. 1119, Haibin Road, Nansha District, Guangzhou 511458, China
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31
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Caffrey P, Hogan M, Song Y. New Glycosylated Polyene Macrolides: Refining the Ore from Genome Mining. Antibiotics (Basel) 2022; 11:antibiotics11030334. [PMID: 35326797 PMCID: PMC8944477 DOI: 10.3390/antibiotics11030334] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2022] [Revised: 02/25/2022] [Accepted: 03/02/2022] [Indexed: 01/26/2023] Open
Abstract
Glycosylated polyene macrolides include effective antifungal agents, such as pimaricin, nystatin, candicidin, and amphotericin B. For the treatment of systemic mycoses, amphotericin B has been described as a gold-standard antibiotic because of its potent activity against a broad spectrum of fungal pathogens, which do not readily become resistant. However, amphotericin B has severe toxic side effects, and the development of safer alternatives remains an important objective. One approach towards obtaining such compounds is to discover new related natural products. Advances in next-generation sequencing have delivered a wealth of microbial genome sequences containing polyene biosynthetic gene clusters. These typically encode a modular polyketide synthase that catalyzes the assembly of the aglycone core, a cytochrome P450 that oxidizes a methyl branch to a carboxyl group, and additional enzymes for synthesis and attachment of a single mycosamine sugar residue. In some cases, further P450s catalyze epoxide formation or hydroxylation within the macrolactone. Bioinformatic analyses have identified over 250 of these clusters. Some are predicted to encode potentially valuable new polyenes that have not been uncovered by traditional screening methods. Recent experimental studies have characterized polyenes with new polyketide backbones, previously unknown late oxygenations, and additional sugar residues that increase water-solubility and reduce hemolytic activity. Here we review these studies and assess how this new knowledge can help to prioritize silent polyene clusters for further investigation. This approach should improve the chances of discovering better antifungal antibiotics.
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32
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Guzman KM, Khosla C. Fragment antigen binding domains (F abs) as tools to study assembly-line polyketide synthases. Synth Syst Biotechnol 2022; 7:506-512. [PMID: 34977395 PMCID: PMC8683866 DOI: 10.1016/j.synbio.2021.12.003] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2021] [Revised: 12/02/2021] [Accepted: 12/03/2021] [Indexed: 12/17/2022] Open
Abstract
The crystallization of proteins remains a bottleneck in our fundamental understanding of their functions. Therefore, discovering tools that aid crystallization is crucial. In this review, the versatility of fragment-antigen binding domains (Fabs) as protein crystallization chaperones is discussed. Fabs have aided the crystallization of membrane-bound and soluble proteins as well as RNA. The ability to bind three Fabs onto a single protein target has demonstrated their potential for crystallization of challenging proteins. We describe a high-throughput workflow for identifying Fabs to aid the crystallization of a protein of interest (POI) by leveraging phage display technologies and differential scanning fluorimetry (DSF). This workflow has proven to be especially effective in our structural studies of assembly-line polyketide synthases (PKSs), which harbor flexible domains and assume transient conformations. PKSs are of interest to us due to their ability to synthesize an unusually broad range of medicinally relevant compounds. Despite years of research studying these megasynthases, their overall topology has remained elusive. One Fab in particular, 1B2, has successfully enabled X-ray crystallographic and single particle cryo-electron microscopic (cryoEM) analyses of multiple modules from distinct assembly-line PKSs. Its use has not only facilitated multidomain protein crystallization but has also enhanced particle quality via cryoEM, thereby enabling the visualization of intact PKS modules at near-atomic (3-5 Å) resolution. The identification of PKS-binding Fabs can be expected to continue playing a key role in furthering our knowledge of polyketide biosynthesis on assembly-line PKSs.
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Affiliation(s)
- Katarina M. Guzman
- Department of Chemical Engineering, Stanford University, Stanford, CA, 94305, USA
| | - Chaitan Khosla
- Department of Chemical Engineering, Stanford University, Stanford, CA, 94305, USA
- Department of Chemistry, Stanford ChEM-H, Stanford University, Stanford, CA, 94305, USA
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33
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Engineering the stambomycin modular polyketide synthase yields 37-membered mini-stambomycins. Nat Commun 2022; 13:515. [PMID: 35082289 PMCID: PMC8792006 DOI: 10.1038/s41467-022-27955-z] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2021] [Accepted: 12/21/2021] [Indexed: 12/14/2022] Open
Abstract
The modular organization of the type I polyketide synthases (PKSs) would seem propitious for rational engineering of desirable analogous. However, despite decades of efforts, such experiments remain largely inefficient. Here, we combine multiple, state-of-the-art approaches to reprogram the stambomycin PKS by deleting seven internal modules. One system produces the target 37-membered mini-stambomycin metabolites − a reduction in chain length of 14 carbons relative to the 51-membered parental compounds − but also substantial quantities of shunt metabolites. Our data also support an unprecedented off-loading mechanism of such stalled intermediates involving the C-terminal thioesterase domain of the PKS. The mini-stambomycin yields are reduced relative to wild type, likely reflecting the poor tolerance of the modules downstream of the modified interfaces to the non-native substrates. Overall, we identify factors contributing to the productivity of engineered whole assembly lines, but our findings also highlight the need for further research to increase production titers. Genetic engineering of the type I polyketide synthases (PKSs) to produce desirable analogous remains largely inefficient. Here, the authors leverage multiple approaches to delete seven internal modules from the stambomycin PKS and generate 37-membered mini-stambomycin macrolactones.
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34
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Carretero-Molina D, Ortiz-López FJ, Gren T, Oves-Costales D, Martín J, Román-Hurtado F, Sparholt Jørgensen T, de la Cruz M, Díaz C, Vicente F, Blin K, Reyes F, Weber T, Genilloud O. Discovery of gargantulides B and C, new 52-membered macrolactones from Amycolatopsis sp. Complete absolute stereochemistry of the gargantulide family. Org Chem Front 2022. [DOI: 10.1039/d1qo01480c] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
Gargantulides B and C are among the most complex bacterial polyketides discovered so far. A combination of NMR and genome-based bioinformatics analyses allowed us to complete and revise the absolute stereochemistry of the entire gargantulide family.
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Affiliation(s)
- Daniel Carretero-Molina
- Fundación MEDINA, Centro de Excelencia en Investigación de Medicamentos Innovadores en Andalucía, Avda. del Conocimiento 34, 18016 Armilla, Granada, Spain
| | - Francisco Javier Ortiz-López
- Fundación MEDINA, Centro de Excelencia en Investigación de Medicamentos Innovadores en Andalucía, Avda. del Conocimiento 34, 18016 Armilla, Granada, Spain
| | - Tetiana Gren
- The Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Kemitorvet, building 220, 2800 Kgs. Lyngby, Denmark
| | - Daniel Oves-Costales
- Fundación MEDINA, Centro de Excelencia en Investigación de Medicamentos Innovadores en Andalucía, Avda. del Conocimiento 34, 18016 Armilla, Granada, Spain
| | - Jesús Martín
- Fundación MEDINA, Centro de Excelencia en Investigación de Medicamentos Innovadores en Andalucía, Avda. del Conocimiento 34, 18016 Armilla, Granada, Spain
| | - Fernando Román-Hurtado
- Fundación MEDINA, Centro de Excelencia en Investigación de Medicamentos Innovadores en Andalucía, Avda. del Conocimiento 34, 18016 Armilla, Granada, Spain
| | - Tue Sparholt Jørgensen
- The Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Kemitorvet, building 220, 2800 Kgs. Lyngby, Denmark
| | - Mercedes de la Cruz
- Fundación MEDINA, Centro de Excelencia en Investigación de Medicamentos Innovadores en Andalucía, Avda. del Conocimiento 34, 18016 Armilla, Granada, Spain
| | - Caridad Díaz
- Fundación MEDINA, Centro de Excelencia en Investigación de Medicamentos Innovadores en Andalucía, Avda. del Conocimiento 34, 18016 Armilla, Granada, Spain
| | - Francisca Vicente
- Fundación MEDINA, Centro de Excelencia en Investigación de Medicamentos Innovadores en Andalucía, Avda. del Conocimiento 34, 18016 Armilla, Granada, Spain
| | - Kai Blin
- The Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Kemitorvet, building 220, 2800 Kgs. Lyngby, Denmark
| | - Fernando Reyes
- Fundación MEDINA, Centro de Excelencia en Investigación de Medicamentos Innovadores en Andalucía, Avda. del Conocimiento 34, 18016 Armilla, Granada, Spain
| | - Tilmann Weber
- The Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Kemitorvet, building 220, 2800 Kgs. Lyngby, Denmark
| | - Olga Genilloud
- Fundación MEDINA, Centro de Excelencia en Investigación de Medicamentos Innovadores en Andalucía, Avda. del Conocimiento 34, 18016 Armilla, Granada, Spain
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35
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Wang Y, Chintalapudi V, Gudmundsson HG, Challis GL, Anderson EA. Synthesis of the C50 diastereomers of the C33–C51 fragment of stambomycin D. Org Chem Front 2022. [DOI: 10.1039/d1qo01635k] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
The preparation of two C50 diastereomers of the C33–C51 region of stambomycin D is described. In addition to excellent correlation with the natural product, this synthesis establishes conditions for eventual global deprotection.
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Affiliation(s)
- Yongchen Wang
- Chemistry Research Laboratory, University of Oxford, 12 Mansfield Road, Oxford, OX1 3TA, UK
| | - Venkaiah Chintalapudi
- Chemistry Research Laboratory, University of Oxford, 12 Mansfield Road, Oxford, OX1 3TA, UK
| | | | - Gregory L. Challis
- Department of Chemistry and Warwick Integrative Synthetic Biology Centre, University of Warwick, Coventry, CV4 7AL, UK
- Department of Biochemistry and Molecular Biology and ARC Centre of Excellence for Innovations in Peptide and Protein Science, Biomedicine Discovery Institute, Monash University, Clayton, Victoria 3800, Australia
| | - Edward A. Anderson
- Chemistry Research Laboratory, University of Oxford, 12 Mansfield Road, Oxford, OX1 3TA, UK
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36
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Wang D, Li P, Yan JL, Mao H, Liu L, Wang M, Chen M, Ye T, Chen Y. Assigning the stereochemical structures of aurantinin A and B with the assistance of biosynthetic investigations. Org Chem Front 2022. [DOI: 10.1039/d2qo01251k] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
The stereochemistry of aurantinin was determined by spectroscopic and computational analysis with the assistance of biosynthetic studies. The latter method provided critical evidence for the assignment of the configuration of the 3-ketosugar moiety.
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Affiliation(s)
- Dacheng Wang
- State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, China
| | - Pengwei Li
- State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, China
| | - Jia-Lei Yan
- Innovation Center of Marine Biotechnology and Pharmaceuticals, School of Biotechnology and Health Sciences, Wuyi University, Jiangmen 529020, Guangdong, China
| | - Huijin Mao
- State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Lilu Liu
- State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Min Wang
- State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, China
- Innovation Center of Marine Biotechnology and Pharmaceuticals, School of Biotechnology and Health Sciences, Wuyi University, Jiangmen 529020, Guangdong, China
| | - Meng Chen
- State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Tao Ye
- Innovation Center of Marine Biotechnology and Pharmaceuticals, School of Biotechnology and Health Sciences, Wuyi University, Jiangmen 529020, Guangdong, China
- State Key Laboratory of Chemical Oncogenomics, Peking University Shenzhen Graduate School, Xili, Nanshan District, Shenzhen 518055, China
| | - Yihua Chen
- State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, China
- University of Chinese Academy of Sciences, Beijing 100049, China
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37
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Identification and Heterologous Expression of the Kendomycin B Biosynthetic Gene Cluster from Verrucosispora sp. SCSIO 07399. Mar Drugs 2021; 19:md19120673. [PMID: 34940672 PMCID: PMC8708025 DOI: 10.3390/md19120673] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2021] [Revised: 11/16/2021] [Accepted: 11/22/2021] [Indexed: 11/17/2022] Open
Abstract
Verrucosispora sp. SCSIO 07399, a rare marine-derived actinomycete, produces a set of ansamycin-like polyketides kendomycin B–D (1–3) which possess potent antibacterial activities and moderate tumor cytotoxicity. Structurally, kendomycin B–D contain a unique aliphatic macrocyclic ansa scaffold in which the highly substituted pyran ring is connected to the quinone moiety. In this work, a type I/type III polyketide synthase (PKS) hybrid biosynthetic gene cluster coding for assembly of kendomycin B (kmy), and covering 33 open reading frames, was identified from Verrucosispora sp. SCSIO 07399. The kmy cluster was found to be essential for kendomycin B biosynthesis as verified by gene disruption and heterologous expression. Correspondingly, a biosynthetic pathway was proposed based on bioinformatics, cluster alignments, and previous research. Additionally, the role of type III PKS for generating the precursor unit 3,5-dihydroxybenzoic acid (3,5-DHBA) was demonstrated by chemical complementation, and type I PKS executed the polyketide chain elongation. The kmy cluster was found to contain a positive regulatory gene kmy4 whose regulatory effect was identified using real-time quantitative PCR (RT-qPCR). These advances shed important new insights into kendomycin B biosynthesis and help to set the foundation for further research aimed at understanding and exploiting the carbacylic ansa scaffold.
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38
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The Discovery of Actinospene, a New Polyene Macrolide with Broad Activity against Plant Fungal Pathogens and Pathogenic Yeasts. Molecules 2021; 26:molecules26227020. [PMID: 34834113 PMCID: PMC8621364 DOI: 10.3390/molecules26227020] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2021] [Revised: 11/17/2021] [Accepted: 11/17/2021] [Indexed: 02/07/2023] Open
Abstract
Phytopathogenic fungi infect crops, presenting a worldwide threat to agriculture. Polyene macrolides are one of the most effective antifungal agents applied in human therapy and crop protection. In this study, we found a cryptic polyene biosynthetic gene cluster in Actinokineospora spheciospongiae by genome mining. Then, this gene cluster was activated via varying fermentation conditions, leading to the discovery of new polyene actinospene (1), which was subsequently isolated and its structure determined through spectroscopic techniques including UV, HR-MS, and NMR. The absolute configuration was confirmed by comparing the calculated and experimental electronic circular dichroism (ECD) spectra. Unlike known polyene macrolides, actinospene (1) demonstrated more versatile post-assembling decorations including two epoxide groups and an unusual isobutenyl side chain. In bioassays, actinospene (1) showed a broad spectrum of antifungal activity against several plant fungal pathogens as well as pathogenic yeasts with minimum inhibitory concentrations ranging between 2 and 10 μg/mL.
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39
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Tsutsumi H, Katsuyama Y, Tezuka T, Miyano R, Inahashi Y, Takahashi Y, Nakashima T, Ohnishi Y. Identification and Analysis of the Biosynthetic Gene Cluster for the Indolizidine Alkaloid Iminimycin in Streptomyces griseus. Chembiochem 2021; 23:e202100517. [PMID: 34767291 DOI: 10.1002/cbic.202100517] [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: 09/27/2021] [Revised: 10/27/2021] [Indexed: 11/06/2022]
Abstract
Indolizidine alkaloids, which have versatile bioactivities, are produced by various organisms. Although the biosynthesis of some indolizidine alkaloids has been studied, the enzymatic machinery for their biosynthesis in Streptomyces remains elusive. Here, we report the identification and analysis of the biosynthetic gene cluster for iminimycin, an indolizidine alkaloid with a 6-5-3 tricyclic system containing an iminium cation from Streptomyces griseus. The gene cluster has 22 genes, including four genes encoding polyketide synthases (PKSs), which consist of eight modules in total. In vitro analysis of the first module revealed that its acyltransferase domain selects malonyl-CoA, although predicted to select methylmalonyl-CoA. Inactivation of seven tailoring enzyme-encoding genes and structural elucidation of four compounds accumulated in mutants provided important insights into iminimycin biosynthesis, although some of these compounds appeared to be shunt products. This study expands our knowledge of the biosynthetic machinery of indolizidine alkaloids and the enzymatic chemistry of PKS.
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Affiliation(s)
- Hayama Tsutsumi
- Department of Biotechnology, Graduate School of Agricultural and Life Sciences, The University of Tokyo, 1-1-1 Yayoi, Bunkyo-ku, Tokyo, 113-8657, Japan
| | - Yohei Katsuyama
- Department of Biotechnology, Graduate School of Agricultural and Life Sciences, The University of Tokyo, 1-1-1 Yayoi, Bunkyo-ku, Tokyo, 113-8657, Japan.,Collaborative Research Institute for Innovative Microbiology, The University of Tokyo, 1-1-1 Yayoi, Bunkyo-ku, Tokyo, 113-8657, Japan
| | - Takeaki Tezuka
- Department of Biotechnology, Graduate School of Agricultural and Life Sciences, The University of Tokyo, 1-1-1 Yayoi, Bunkyo-ku, Tokyo, 113-8657, Japan.,Collaborative Research Institute for Innovative Microbiology, The University of Tokyo, 1-1-1 Yayoi, Bunkyo-ku, Tokyo, 113-8657, Japan
| | - Rei Miyano
- Graduate School of Infection Control Sciences, Kitasato University, 5-9-1, Minato-ku, Tokyo, 108-8641, Japan
| | - Yuki Inahashi
- Graduate School of Infection Control Sciences, Kitasato University, 5-9-1, Minato-ku, Tokyo, 108-8641, Japan.,Kitasato Institute for Life Sciences, Present: Ōmura Satoshi Memorial Institute), Kitasato University, 5-9-1, Minato-ku, Tokyo, 108-8641, Japan
| | - Yoko Takahashi
- Kitasato Institute for Life Sciences, Present: Ōmura Satoshi Memorial Institute), Kitasato University, 5-9-1, Minato-ku, Tokyo, 108-8641, Japan
| | - Takuji Nakashima
- Graduate School of Infection Control Sciences, Kitasato University, 5-9-1, Minato-ku, Tokyo, 108-8641, Japan.,Kitasato Institute for Life Sciences, Present: Ōmura Satoshi Memorial Institute), Kitasato University, 5-9-1, Minato-ku, Tokyo, 108-8641, Japan
| | - Yasuo Ohnishi
- Department of Biotechnology, Graduate School of Agricultural and Life Sciences, The University of Tokyo, 1-1-1 Yayoi, Bunkyo-ku, Tokyo, 113-8657, Japan.,Collaborative Research Institute for Innovative Microbiology, The University of Tokyo, 1-1-1 Yayoi, Bunkyo-ku, Tokyo, 113-8657, Japan
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40
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Roux I, Bowles S, Kalaitzis JA, Vuong D, Lacey E, Chooi YH, Piggott AM. Characterisation and heterologous biosynthesis of burnettiene A, a new polyene-decalin polyketide from Aspergillus burnettii. Org Biomol Chem 2021; 19:9506-9513. [PMID: 34714309 DOI: 10.1039/d1ob01766g] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/14/2023]
Abstract
Chemical exploration of the recently described Australian fungus, Aspergillus burnettii, uncovered a new metabolite, burnettiene A. Here, we characterise the structure of burnettiene A as a polyene-decalin polyketide. Bioinformatic analysis of the genome of A. burnettii identified a putative biosynthetic gene cluster for burnettiene A (bue), consisting of eight genes and sharing similarity to the fusarielin gene cluster. Introduction of the reassembled bue gene cluster into Aspergillus nidulans for heterologous expression resulted in the production of burnettiene A under native promoters. Omission of bueE encoding a cytochrome P450 led to the production of preburnettiene A, confirming that BueE is responsible for catalysing the regiospecific multi-oxidation of terminal methyl groups to carboxylic acids. Similarly, bueF was shown to encode an ester-forming methyltransferase, with its omission resulting in the production of the tricarboxylic acid, preburnettiene B. Introduction of an additional copy of the transcription factor bueR under the regulation of the gpdA promoter significantly improved the heterologous production of the burnettienes. Burnettiene A displayed strong in vitro cytotoxicity against mouse myeloma NS-1 cells (MIC 0.8 μg mL-1).
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Affiliation(s)
- Indra Roux
- School of Molecular Sciences, The University of Western Australia, Perth, WA 6009, Australia.
| | - Simon Bowles
- Microbial Screening Technologies Pty. Ltd, Smithfield, NSW 2164, Australia
| | - John A Kalaitzis
- Microbial Screening Technologies Pty. Ltd, Smithfield, NSW 2164, Australia
- Department of Molecular Sciences, Macquarie University, Sydney, NSW 2109, Australia.
| | - Daniel Vuong
- Microbial Screening Technologies Pty. Ltd, Smithfield, NSW 2164, Australia
| | - Ernest Lacey
- Microbial Screening Technologies Pty. Ltd, Smithfield, NSW 2164, Australia
- Department of Molecular Sciences, Macquarie University, Sydney, NSW 2109, Australia.
| | - Yit-Heng Chooi
- School of Molecular Sciences, The University of Western Australia, Perth, WA 6009, Australia.
| | - Andrew M Piggott
- Department of Molecular Sciences, Macquarie University, Sydney, NSW 2109, Australia.
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41
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Lim J, Chintalapudi V, Gudmundsson HG, Tran M, Bernasconi A, Blanco A, Song L, Challis GL, Anderson EA. Synthesis of the C1-C27 Fragment of Stambomycin D Validates Modular Polyketide Synthase-Based Stereochemical Assignments. Org Lett 2021; 23:7439-7444. [PMID: 34494848 PMCID: PMC8491158 DOI: 10.1021/acs.orglett.1c02650] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/04/2023]
Abstract
![]()
The
stambomycins
are a family of bioactive macrolides isolated
from Streptomyces ambofaciens. Aside from two stereocenters
installed through cytochrome P450 oxidations, their stereochemistry
has been predicted by sequence analysis of the polyketide synthase.
We report a synthesis of the C1–C27 fragment of stambomycin
D, the spectroscopic data of which correlates well with that of the
natural product, further validating predictive sequence analysis as
a powerful tool for stereochemical assignment of complex polyketide
natural products.
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Affiliation(s)
- Jieyan Lim
- Chemistry Research Laboratory, University of Oxford, 12 Mansfield Road, Oxford, OX1 3TA, U.K
| | - Venkaiah Chintalapudi
- Chemistry Research Laboratory, University of Oxford, 12 Mansfield Road, Oxford, OX1 3TA, U.K
| | - Haraldur G Gudmundsson
- Chemistry Research Laboratory, University of Oxford, 12 Mansfield Road, Oxford, OX1 3TA, U.K
| | - Minh Tran
- Chemistry Research Laboratory, University of Oxford, 12 Mansfield Road, Oxford, OX1 3TA, U.K
| | - Alice Bernasconi
- Sezione Chimica Generale e Organica "A. Marchesini", Università degli Studi di Milano, Via G. Venezian 21, 20133 Milano, Italy
| | - Araceli Blanco
- Departamento de Química Orgánica, Facultad de Ciencias Químicas, Universidad de Salamanca, 37008 Salamanca, Spain
| | - Lijiang Song
- Department of Chemistry and Warwick Integrative Synthetic Biology Centre, University of Warwick, Coventry, CV4 7AL, U.K
| | - Gregory L Challis
- Department of Chemistry and Warwick Integrative Synthetic Biology Centre, University of Warwick, Coventry, CV4 7AL, U.K.,Department of Biochemistry and Molecular Biology and ARC Centre of Excellence for Innovations in Peptide and Protein Science, Biomedicine Discovery Institute, Monash University, Clayton, Victoria 3800, Australia
| | - Edward A Anderson
- Chemistry Research Laboratory, University of Oxford, 12 Mansfield Road, Oxford, OX1 3TA, U.K
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42
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Li N, Chen S, Yan Z, Han J, Ta Y, Pu T, Wang Y. Antimicrobial Activity and Identification of the Biosynthetic Gene Cluster of X-14952B From Streptomyces sp. 135. Front Microbiol 2021; 12:703093. [PMID: 34408734 PMCID: PMC8365161 DOI: 10.3389/fmicb.2021.703093] [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: 04/30/2021] [Accepted: 07/12/2021] [Indexed: 12/03/2022] Open
Abstract
The bacterial genus Streptomyces is an important source of antibiotics, and genome mining is a valuable tool to explore the potential of microbial biosynthesis in members of this genus. This study reports an actinomycete strain 135, which was isolated from Qinghai-Tibet Plateau in China and displayed broad antimicrobial activity. The fermentation broth of strain 135 displayed strong antifungal activity (>70%) against Sclerotinia sclerotiorum, Botrytis cinerea, Valsa mali, Phytophthora capsici, Glomerella cingulata, Magnaporthe grisea, Bipolaris maydis, Exserohilum turcicum in vitro, meanwhile possessed significant preventive and curative efficacy against S. sclerotiorum, Gaeumannomyces graminis, and P. capsici on rape leaves (54.04 and 74.18%), wheat (90.66 and 67.99%), and pepper plants (79.33 and 66.67%). X-14952B showed the greatest antifungal activity against S. sclerotiorum and Fusarium graminearum which the 50% inhibition concentration (EC50) were up to 0.049 and 0.04 μg/mL, respectively. Characterization of strain 135 using a polyphasic approach revealed that the strain displayed typical features of the genus Streptomyces. 16S rRNA gene sequencing and phylogenetic analysis demonstrated that the isolate was most closely related to and formed a clade with Streptomyces huasconensis HST28T (98.96% 16S rRNA gene sequence similarity). Average nucleotide identity (ANI) and DNA-DNA hybridization (DDH) values in strain 135 and related type strains were both below the threshold of species determination (91.39 and 56.5%, respectively). OrthoANI values between strain 135 and related type strains are under the cutoff of determining species (<95%). The biosynthetic gene cluster (BGC) designated to X-14952B biosynthesis was identified through genome mining and the possible biosynthesis process was deduced.
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Affiliation(s)
- Na Li
- Research and Development Center of Biorational Pesticides, Key Laboratory of Plant Protection Resources and Pest Management of Ministry of Education, Northwest A&F University, Xianyang, China.,Institute Vegetable, Zhangye Academy of Agricultural Sciences, Zhangye, China
| | - Simin Chen
- College of Plant Protection, Northwest A&F University, Xianyang, China
| | - Zhiqiang Yan
- Research and Development Center of Biorational Pesticides, Key Laboratory of Plant Protection Resources and Pest Management of Ministry of Education, Northwest A&F University, Xianyang, China
| | - Jinhua Han
- Research and Development Center of Biorational Pesticides, Key Laboratory of Plant Protection Resources and Pest Management of Ministry of Education, Northwest A&F University, Xianyang, China
| | - Yongquan Ta
- Research and Development Center of Biorational Pesticides, Key Laboratory of Plant Protection Resources and Pest Management of Ministry of Education, Northwest A&F University, Xianyang, China
| | - Taixun Pu
- Research and Development Center of Biorational Pesticides, Key Laboratory of Plant Protection Resources and Pest Management of Ministry of Education, Northwest A&F University, Xianyang, China
| | - Yonghong Wang
- Research and Development Center of Biorational Pesticides, Key Laboratory of Plant Protection Resources and Pest Management of Ministry of Education, Northwest A&F University, Xianyang, China
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43
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Kontou EE, Gren T, Ortiz-López FJ, Thomsen E, Oves-Costales D, Díaz C, de la Cruz M, Jiang X, Jørgensen TS, Blin K, Charusanti P, Reyes F, Genilloud O, Weber T. Discovery and Characterization of Epemicins A and B, New 30-Membered Macrolides from Kutzneria sp. CA-103260. ACS Chem Biol 2021; 16:1456-1468. [PMID: 34279911 DOI: 10.1021/acschembio.1c00318] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Actinobacteria have been a rich source of novel, structurally complex natural products for many decades. Although the largest genus is Streptomyces, from which the majority of antibiotics in current and past clinical use were originally isolated, other less common genera also have the potential to produce a wealth of novel secondary metabolites. One example is the Kutzneria genus, which currently contains only five reported species. One of these species is Kutzneria albida DSM 43870T, which has 46 predicted biosynthetic gene clusters and is known to produce the macrolide antibiotic aculeximycin. Here, we report the isolation and structural characterization of two novel 30-membered glycosylated macrolides, epemicins A and B, that are structurally related to aculeximycin, from a rare Kutzneria sp. The absolute configuration for all chiral centers in the two compounds is proposed based on extensive 1D and 2D NMR studies and bioinformatics analysis of the gene cluster. Through heterologous expression and genetic inactivation, we have confirmed the link between the biosynthetic gene cluster and the new molecules. These findings show the potential of rare Actinobacteria to produce new, structurally diverse metabolites. Furthermore, the gene inactivation represents the first published report to genetically manipulate a representative of the Kutzneria genus.
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Affiliation(s)
- Eftychia Eva Kontou
- The Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Kemitorvet bygning 220, 2800 Kgs. Lyngby, Denmark
| | - Tetiana Gren
- The Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Kemitorvet bygning 220, 2800 Kgs. Lyngby, Denmark
| | - Francisco Javier Ortiz-López
- Fundación MEDINA, Centro de Excelencia en Investigación de Medicamentos Innovadores en Andalucía, Avenida del Conocimiento, 34 Parque Tecnológico de Ciencias de la Salud, 18016 Armilla, Granada, Spain
| | - Emil Thomsen
- The Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Kemitorvet bygning 220, 2800 Kgs. Lyngby, Denmark
| | - Daniel Oves-Costales
- Fundación MEDINA, Centro de Excelencia en Investigación de Medicamentos Innovadores en Andalucía, Avenida del Conocimiento, 34 Parque Tecnológico de Ciencias de la Salud, 18016 Armilla, Granada, Spain
| | - Caridad Díaz
- Fundación MEDINA, Centro de Excelencia en Investigación de Medicamentos Innovadores en Andalucía, Avenida del Conocimiento, 34 Parque Tecnológico de Ciencias de la Salud, 18016 Armilla, Granada, Spain
| | - Mercedes de la Cruz
- Fundación MEDINA, Centro de Excelencia en Investigación de Medicamentos Innovadores en Andalucía, Avenida del Conocimiento, 34 Parque Tecnológico de Ciencias de la Salud, 18016 Armilla, Granada, Spain
| | - Xinglin Jiang
- The Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Kemitorvet bygning 220, 2800 Kgs. Lyngby, Denmark
| | - Tue Sparholt Jørgensen
- The Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Kemitorvet bygning 220, 2800 Kgs. Lyngby, Denmark
| | - Kai Blin
- The Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Kemitorvet bygning 220, 2800 Kgs. Lyngby, Denmark
| | - Pep Charusanti
- The Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Kemitorvet bygning 220, 2800 Kgs. Lyngby, Denmark
| | - Fernando Reyes
- Fundación MEDINA, Centro de Excelencia en Investigación de Medicamentos Innovadores en Andalucía, Avenida del Conocimiento, 34 Parque Tecnológico de Ciencias de la Salud, 18016 Armilla, Granada, Spain
| | - Olga Genilloud
- Fundación MEDINA, Centro de Excelencia en Investigación de Medicamentos Innovadores en Andalucía, Avenida del Conocimiento, 34 Parque Tecnológico de Ciencias de la Salud, 18016 Armilla, Granada, Spain
| | - Tilmann Weber
- The Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Kemitorvet bygning 220, 2800 Kgs. Lyngby, Denmark
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44
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Shi P, Li Y, Zhu J, Shen Y, Wang H. Targeted Discovery of the Polyene Macrolide Hexacosalactone A from Streptomyces by Reporter-Guided Selection of Fermentation Media. JOURNAL OF NATURAL PRODUCTS 2021; 84:1924-1929. [PMID: 34170140 DOI: 10.1021/acs.jnatprod.1c00144] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/13/2023]
Abstract
New approaches are still needed to fully explore the biosynthetic potential of microbes. We recently devised a melC reporter-guided fermentation media screening approach for targeted activation of cryptic gene clusters. Using this approach, we successfully activated the expression of the hcl gene cluster in Streptomyces sp. LZ35 and discovered a novel polyene macrolide hexacosalactone A (1).
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Affiliation(s)
- Peng Shi
- State Key Laboratory of Microbial Technology, Shandong University, Qingdao 266237, People's Republic of China
| | - Yaoyao Li
- Key Laboratory of Chemical Biology of Ministry of Education, School of Pharmaceutical Sciences, Cheeloo College of Medicine, Shandong University, Jinan 250012, People's Republic of China
| | - Jing Zhu
- State Key Laboratory of Microbial Technology, Shandong University, Qingdao 266237, People's Republic of China
| | - Yuemao Shen
- Key Laboratory of Chemical Biology of Ministry of Education, School of Pharmaceutical Sciences, Cheeloo College of Medicine, Shandong University, Jinan 250012, People's Republic of China
| | - Haoxin Wang
- State Key Laboratory of Microbial Technology, Shandong University, Qingdao 266237, People's Republic of China
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45
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Dong H, Chang MCY. Structural Basis for Branched Substrate Selectivity in a Ketoreductase from Ascaris suum. ACS Catal 2021. [DOI: 10.1021/acscatal.1c01642] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
Affiliation(s)
- Hongjun Dong
- Department of Chemistry, University of California, Berkeley, Berkeley, California 94720-1460, United States
| | - Michelle C. Y. Chang
- Department of Chemistry, University of California, Berkeley, Berkeley, California 94720-1460, United States
- Department of Molecular & Cell Biology, University of California, Berkeley, California 94720-3200, United States
- Department of Chemical & Biomolecular Engineering, University of California, Berkeley, California 94720-1462, United States
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46
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Atanasoff-Kardjalieff AK, Lünne F, Kalinina S, Strauss J, Humpf HU, Studt L. Biosynthesis of Fusapyrone Depends on the H3K9 Methyltransferase, FmKmt1, in Fusarium mangiferae. FRONTIERS IN FUNGAL BIOLOGY 2021; 2:671796. [PMID: 37744112 PMCID: PMC10512364 DOI: 10.3389/ffunb.2021.671796] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 02/24/2021] [Accepted: 06/09/2021] [Indexed: 09/26/2023]
Abstract
The phytopathogenic fungus Fusarium mangiferae belongs to the Fusarium fujikuroi species complex (FFSC). Members of this group cause a wide spectrum of devastating diseases on diverse agricultural crops. F. mangiferae is the causal agent of the mango malformation disease (MMD) and as such detrimental for agriculture in the southern hemisphere. During plant infection, the fungus produces a plethora of bioactive secondary metabolites (SMs), which most often lead to severe adverse defects on plants health. Changes in chromatin structure achieved by posttranslational modifications (PTM) of histones play a key role in regulation of fungal SM biosynthesis. Posttranslational tri-methylation of histone 3 lysine 9 (H3K9me3) is considered a hallmark of heterochromatin and established by the SET-domain protein Kmt1. Here, we show that FmKmt1 is involved in H3K9me3 in F. mangiferae. Loss of FmKmt1 only slightly though significantly affected fungal hyphal growth and stress response and is required for wild type-like conidiation. While FmKmt1 is largely dispensable for the biosynthesis of most known SMs, removal of FmKMT1 resulted in an almost complete loss of fusapyrone and deoxyfusapyrone, γ-pyrones previously only known from Fusarium semitectum. Here, we identified the polyketide synthase (PKS) FmPKS40 to be involved in fusapyrone biosynthesis, delineate putative cluster borders by co-expression studies and provide insights into its regulation.
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Affiliation(s)
- Anna K. Atanasoff-Kardjalieff
- Department of Applied Genetics and Cell Biology, Institute of Microbial Genetics, University of Natural Resources and Life Sciences, Vienna (BOKU), Tulln an der Donau, Austria
| | - Friederike Lünne
- Institute of Food Chemistry, Westfälische Wilhelms-Universität, Münster, Germany
| | - Svetlana Kalinina
- Institute of Food Chemistry, Westfälische Wilhelms-Universität, Münster, Germany
| | - Joseph Strauss
- Department of Applied Genetics and Cell Biology, Institute of Microbial Genetics, University of Natural Resources and Life Sciences, Vienna (BOKU), Tulln an der Donau, Austria
| | - Hans-Ulrich Humpf
- Institute of Food Chemistry, Westfälische Wilhelms-Universität, Münster, Germany
| | - Lena Studt
- Department of Applied Genetics and Cell Biology, Institute of Microbial Genetics, University of Natural Resources and Life Sciences, Vienna (BOKU), Tulln an der Donau, Austria
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47
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Paiva P, Medina FE, Viegas M, Ferreira P, Neves RPP, Sousa JPM, Ramos MJ, Fernandes PA. Animal Fatty Acid Synthase: A Chemical Nanofactory. Chem Rev 2021; 121:9502-9553. [PMID: 34156235 DOI: 10.1021/acs.chemrev.1c00147] [Citation(s) in RCA: 24] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
Fatty acids are crucial molecules for most living beings, very well spread and conserved across species. These molecules play a role in energy storage, cell membrane architecture, and cell signaling, the latter through their derivative metabolites. De novo synthesis of fatty acids is a complex chemical process that can be achieved either by a metabolic pathway built by a sequence of individual enzymes, such as in most bacteria, or by a single, large multi-enzyme, which incorporates all the chemical capabilities of the metabolic pathway, such as in animals and fungi, and in some bacteria. Here we focus on the multi-enzymes, specifically in the animal fatty acid synthase (FAS). We start by providing a historical overview of this vast field of research. We follow by describing the extraordinary architecture of animal FAS, a homodimeric multi-enzyme with seven different active sites per dimer, including a carrier protein that carries the intermediates from one active site to the next. We then delve into this multi-enzyme's detailed chemistry and critically discuss the current knowledge on the chemical mechanism of each of the steps necessary to synthesize a single fatty acid molecule with atomic detail. In line with this, we discuss the potential and achieved FAS applications in biotechnology, as biosynthetic machines, and compare them with their homologous polyketide synthases, which are also finding wide applications in the same field. Finally, we discuss some open questions on the architecture of FAS, such as their peculiar substrate-shuttling arm, and describe possible reasons for the emergence of large megasynthases during evolution, questions that have fascinated biochemists from long ago but are still far from answered and understood.
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Affiliation(s)
- Pedro Paiva
- LAQV, REQUIMTE, Departamento de Química e Bioquímica, Faculdade de Ciências, Universidade do Porto, Rua do Campo Alegre s/n, 4169-007 Porto, Portugal
| | - Fabiola E Medina
- Departamento de Ciencias Químicas, Facultad de Ciencias Exactas, Universidad Andres Bello, Autopista Concepción-Talcahuano, 7100 Talcahuano, Chile
| | - Matilde Viegas
- LAQV, REQUIMTE, Departamento de Química e Bioquímica, Faculdade de Ciências, Universidade do Porto, Rua do Campo Alegre s/n, 4169-007 Porto, Portugal
| | - Pedro Ferreira
- LAQV, REQUIMTE, Departamento de Química e Bioquímica, Faculdade de Ciências, Universidade do Porto, Rua do Campo Alegre s/n, 4169-007 Porto, Portugal
| | - Rui P P Neves
- LAQV, REQUIMTE, Departamento de Química e Bioquímica, Faculdade de Ciências, Universidade do Porto, Rua do Campo Alegre s/n, 4169-007 Porto, Portugal
| | - João P M Sousa
- LAQV, REQUIMTE, Departamento de Química e Bioquímica, Faculdade de Ciências, Universidade do Porto, Rua do Campo Alegre s/n, 4169-007 Porto, Portugal
| | - Maria J Ramos
- LAQV, REQUIMTE, Departamento de Química e Bioquímica, Faculdade de Ciências, Universidade do Porto, Rua do Campo Alegre s/n, 4169-007 Porto, Portugal
| | - Pedro A Fernandes
- LAQV, REQUIMTE, Departamento de Química e Bioquímica, Faculdade de Ciências, Universidade do Porto, Rua do Campo Alegre s/n, 4169-007 Porto, Portugal
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48
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Kahlert L, Villanueva M, Cox RJ, Skellam EJ. Biosynthesis of 6-Hydroxymellein Requires a Collaborating Polyketide Synthase-like Enzyme. Angew Chem Int Ed Engl 2021; 60:11423-11429. [PMID: 33661567 PMCID: PMC8251887 DOI: 10.1002/anie.202100969] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2021] [Revised: 02/22/2021] [Indexed: 12/12/2022]
Abstract
The polyketide synthase (PKS)-like protein TerB, consisting of inactive dehydratase, inactive C-methyltransferase, and functional ketoreductase domains collaborates with the iterative non reducing PKS TerA to produce 6-hydroxymellein, a key pathway intermediate during the biosynthesis of various fungal natural products. The catalytically inactive dehydratase domain of TerB appears to mediate productive interactions with TerA, demonstrating a new mode of trans-interaction between iterative PKS components.
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Affiliation(s)
- Lukas Kahlert
- Institute for Organic Chemistry and BMWZLeibniz Universität HannoverSchneiderberg 3830167HannoverGermany
| | - Miranda Villanueva
- Institute for Organic Chemistry and BMWZLeibniz Universität HannoverSchneiderberg 3830167HannoverGermany
- Current address: The Molecular Biology InstituteUCLALos AngelesCA90095-1570USA
| | - Russell J. Cox
- Institute for Organic Chemistry and BMWZLeibniz Universität HannoverSchneiderberg 3830167HannoverGermany
| | - Elizabeth J. Skellam
- Institute for Organic Chemistry and BMWZLeibniz Universität HannoverSchneiderberg 3830167HannoverGermany
- Current address: Department of Chemistry & BioDiscovery InstituteUniversity of North Texas1155 Union Circle 305220DentonTX76203USA
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49
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Kahlert L, Villanueva M, Cox RJ, Skellam EJ. Biosynthesis of 6‐Hydroxymellein Requires a Collaborating Polyketide Synthase‐like Enzyme. Angew Chem Int Ed Engl 2021. [DOI: 10.1002/ange.202100969] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
Affiliation(s)
- Lukas Kahlert
- Institute for Organic Chemistry and BMWZ Leibniz Universität Hannover Schneiderberg 38 30167 Hannover Germany
| | - Miranda Villanueva
- Institute for Organic Chemistry and BMWZ Leibniz Universität Hannover Schneiderberg 38 30167 Hannover Germany
- Current address: The Molecular Biology Institute UCLA Los Angeles CA 90095-1570 USA
| | - Russell J. Cox
- Institute for Organic Chemistry and BMWZ Leibniz Universität Hannover Schneiderberg 38 30167 Hannover Germany
| | - Elizabeth J. Skellam
- Institute for Organic Chemistry and BMWZ Leibniz Universität Hannover Schneiderberg 38 30167 Hannover Germany
- Current address: Department of Chemistry & BioDiscovery Institute University of North Texas 1155 Union Circle 305220 Denton TX 76203 USA
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50
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Zhang S, Zhang L, Zhu J, Chen H, Chen Z, Si T, Liu T. Genomic and Metabolomic Investigation of a Rhizosphere Isolate Streptomyces netropsis WLXQSS-4 Associated with a Traditional Chinese Medicine. Molecules 2021; 26:molecules26082147. [PMID: 33917975 PMCID: PMC8068340 DOI: 10.3390/molecules26082147] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2021] [Revised: 04/01/2021] [Accepted: 04/04/2021] [Indexed: 11/21/2022] Open
Abstract
Rhizosphere microorganisms play important ecological roles in promoting herb growth and producing abundant secondary metabolites. Studies on the rhizosphere microbes of traditional Chinese medicines (TCMs) are limited, especially on the genomic and metabolic levels. In this study, we reported the isolation and characterization of a Steptomyces netropsis WLXQSS-4 strain from the rhizospheric soil of Clematis manshurica Rupr. Genomic sequencing revealed an impressive total of 40 predicted biosynthetic gene clusters (BGCs), whereas metabolomic profiling revealed 13 secondary metabolites under current laboratory conditions. Particularly, medium screening activated the production of alloaureothin, whereas brominated and chlorinated pimprinine derivatives were identified through precursor-directed feeding. Moreover, antiproliferative activities against Hela and A549 cancer cell lines were observed for five compounds, of which two also elicited potent growth inhibition in Enterococcus faecalis and Staphylococcus aureus, respectively. Our results demonstrated the robust secondary metabolism of S. netropsis WLXQSS-4, which may serve as a biocontrol agent upon further investigation.
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Affiliation(s)
- Songya Zhang
- Shenzhen Institute of Synthetic Biology, Shenzhen Institutes of Advanced Technology, Chinese Academy of Sciences, Shenzhen 518055, China; (S.Z.); (J.Z.); (Z.C.)
| | - Lingxiao Zhang
- Department of Natural Products Chemistry, School of Pharmacy, China Medical University, Shenyang 110122, China; (L.Z.); (H.C.)
| | - Jing Zhu
- Shenzhen Institute of Synthetic Biology, Shenzhen Institutes of Advanced Technology, Chinese Academy of Sciences, Shenzhen 518055, China; (S.Z.); (J.Z.); (Z.C.)
| | - Hong Chen
- Department of Natural Products Chemistry, School of Pharmacy, China Medical University, Shenyang 110122, China; (L.Z.); (H.C.)
| | - Zhicong Chen
- Shenzhen Institute of Synthetic Biology, Shenzhen Institutes of Advanced Technology, Chinese Academy of Sciences, Shenzhen 518055, China; (S.Z.); (J.Z.); (Z.C.)
| | - Tong Si
- Shenzhen Institute of Synthetic Biology, Shenzhen Institutes of Advanced Technology, Chinese Academy of Sciences, Shenzhen 518055, China; (S.Z.); (J.Z.); (Z.C.)
- Correspondence: (T.S.); (T.L.)
| | - Tao Liu
- Department of Natural Products Chemistry, School of Pharmacy, China Medical University, Shenyang 110122, China; (L.Z.); (H.C.)
- Correspondence: (T.S.); (T.L.)
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