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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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2
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Löhr NA, Rakhmanov M, Wurlitzer JM, Lackner G, Gressler M, Hoffmeister D. Basidiomycete non-reducing polyketide synthases function independently of SAT domains. Fungal Biol Biotechnol 2023; 10:17. [PMID: 37542286 PMCID: PMC10401856 DOI: 10.1186/s40694-023-00164-z] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2023] [Accepted: 07/16/2023] [Indexed: 08/06/2023] Open
Abstract
BACKGROUND Non-reducing polyketide synthases (NR-PKSs) account for a major share of natural product diversity produced by both Asco- and Basidiomycota. The present evolutionary diversification into eleven clades further underscores the relevance of these multi-domain enzymes. Following current knowledge, NR-PKSs initiate polyketide assembly by an N-terminal starter unit:acyl transferase (SAT) domain that catalyzes the transfer of an acetyl starter from the acetyl-CoA thioester onto the acyl carrier protein (ACP). RESULTS A comprehensive phylogenetic analysis of NR-PKSs established a twelfth clade from which three representatives, enzymes CrPKS1-3 of the webcap mushroom Cortinarius rufoolivaceus, were biochemically characterized. These basidiomycete synthases lack a SAT domain yet are fully functional hepta- and octaketide synthases in vivo. Three members of the other clade of basidiomycete NR-PKSs (clade VIII) were produced as SAT-domainless versions and analyzed in vivo and in vitro. They retained full activity, thus corroborating the notion that the SAT domain is dispensable for many basidiomycete NR-PKSs. For comparison, the ascomycete octaketide synthase atrochrysone carboxylic acid synthase (ACAS) was produced as a SAT-domainless enzyme as well, but turned out completely inactive. However, a literature survey revealed that some NR-PKSs of ascomycetes carry mutations within the catalytic motif of the SAT domain. In these cases, the role of the domain and the origin of the formal acetate unit remains open. CONCLUSIONS The role of SAT domains differs between asco- and basidiomycete NR-PKSs. For the latter, it is not part of the minimal set of NR-PKS domains and not required for function. This knowledge may help engineer compact NR-PKSs for more resource-efficient routes. From the genomic standpoint, seemingly incomplete or corrupted genes encoding SAT-domainless NR-PKSs should not automatically be dismissed as non-functional pseudogenes, but considered during genome analysis to decipher the potential arsenal of natural products of a given fungus.
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Affiliation(s)
- Nikolai A Löhr
- Institute of Pharmacy, Department Pharmaceutical Microbiology, Friedrich Schiller University Jena, Winzerlaer Strasse 2, 07745, Jena, Germany
- Department Pharmaceutical Microbiology, Leibniz Institute for Natural Product Research and Infection Biology - Hans Knöll Institute, Winzerlaer Strasse 2, 07745, Jena, Germany
| | - Malik Rakhmanov
- Institute of Pharmacy, Department Pharmaceutical Microbiology, Friedrich Schiller University Jena, Winzerlaer Strasse 2, 07745, Jena, Germany
- Department Pharmaceutical Microbiology, Leibniz Institute for Natural Product Research and Infection Biology - Hans Knöll Institute, Winzerlaer Strasse 2, 07745, Jena, Germany
| | - Jacob M Wurlitzer
- Institute of Pharmacy, Department Pharmaceutical Microbiology, Friedrich Schiller University Jena, Winzerlaer Strasse 2, 07745, Jena, Germany
- Department Pharmaceutical Microbiology, Leibniz Institute for Natural Product Research and Infection Biology - Hans Knöll Institute, Winzerlaer Strasse 2, 07745, Jena, Germany
| | - Gerald Lackner
- Synthetic Microbiology, Leibniz Institute for Natural Product Research and Infection Biology - Hans Knöll Institute, Winzerlaer Strasse 2, 07745, Jena, Germany
| | - Markus Gressler
- Institute of Pharmacy, Department Pharmaceutical Microbiology, Friedrich Schiller University Jena, Winzerlaer Strasse 2, 07745, Jena, Germany
- Department Pharmaceutical Microbiology, Leibniz Institute for Natural Product Research and Infection Biology - Hans Knöll Institute, Winzerlaer Strasse 2, 07745, Jena, Germany
| | - Dirk Hoffmeister
- Institute of Pharmacy, Department Pharmaceutical Microbiology, Friedrich Schiller University Jena, Winzerlaer Strasse 2, 07745, Jena, Germany.
- Department Pharmaceutical Microbiology, Leibniz Institute for Natural Product Research and Infection Biology - Hans Knöll Institute, Winzerlaer Strasse 2, 07745, Jena, Germany.
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Xu Z, Tian P. Rethinking Biosynthesis of Aclacinomycin A. Molecules 2023; 28:molecules28062761. [PMID: 36985733 PMCID: PMC10054333 DOI: 10.3390/molecules28062761] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2023] [Revised: 03/01/2023] [Accepted: 03/06/2023] [Indexed: 03/22/2023] Open
Abstract
Aclacinomycin A (ACM-A) is an anthracycline antitumor agent widely used in clinical practice. The current industrial production of ACM-A relies primarily on chemical synthesis and microbial fermentation. However, chemical synthesis involves multiple reactions which give rise to high production costs and environmental pollution. Microbial fermentation is a sustainable strategy, yet the current fermentation yield is too low to satisfy market demand. Hence, strain improvement is highly desirable, and tremendous endeavors have been made to decipher biosynthesis pathways and modify key enzymes. In this review, we comprehensively describe the reported biosynthesis pathways, key enzymes, and, especially, catalytic mechanisms. In addition, we come up with strategies to uncover unknown enzymes and improve the activities of rate-limiting enzymes. Overall, this review aims to provide valuable insights for complete biosynthesis of ACM-A.
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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: 0] [Impact Index Per Article: 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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Cox RJ. Curiouser and curiouser: progress in understanding the programming of iterative highly-reducing polyketide synthases. Nat Prod Rep 2023; 40:9-27. [PMID: 35543313 DOI: 10.1039/d2np00007e] [Citation(s) in RCA: 19] [Impact Index Per Article: 19.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/04/2023]
Abstract
Covering: 1996-2022Investigations over the last 2 decades have begun to reveal how fungal iterative highly-reducing polyketide synthases are programmed. Both in vitro and in vivo experiments have revealed the interplay of intrinsic and extrinsic selectivity of the component catalytic domains of these systems. Structural biology has begun to provide high resolution structures of hr-PKS that can be used as the basis for their engineering and reprogramming, but progress to-date remains rudimentary. However, significant opportunities exist for translating the current level of understanding into the ability to rationally re-engineer these highly efficient systems for the production of important biologically active compounds through biotechnology.
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Affiliation(s)
- Russell J Cox
- Institute for Organic Chemistry and BMWZ, Leibniz University of Hannover, Schneiderberg 38, 30167, Hannover, Germany.
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6
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Geyer K, Hartmann S, Singh RR, Erb TJ. Multiple Functions of the Type II Thioesterase Associated with the Phoslactomycin Polyketide Synthase. Biochemistry 2022; 61:2662-2671. [DOI: 10.1021/acs.biochem.2c00234] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Affiliation(s)
- Kyra Geyer
- Department of Biochemistry and Synthetic Metabolism, Max Planck Institute for Terrestrial Microbiology, Karl-von-Frisch-Street 10, D-35043 Marburg, Germany
| | - Steffen Hartmann
- Department of Biochemistry and Synthetic Metabolism, Max Planck Institute for Terrestrial Microbiology, Karl-von-Frisch-Street 10, D-35043 Marburg, Germany
| | - Randolph R. Singh
- Luxembourg Centre for Systems Biomedicine (LCSB), University of Luxembourg, Avenue du Swing 6, L-4367 Belvaux, Luxembourg
| | - Tobias J. Erb
- Department of Biochemistry and Synthetic Metabolism, Max Planck Institute for Terrestrial Microbiology, Karl-von-Frisch-Street 10, D-35043 Marburg, Germany
- SYNMIKRO Center for Synthetic Microbiology, Karl-von-Frisch-Street 16, D-35043 Marburg, Germany
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7
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Dickinson MS, Miyazawa T, McCool RS, Keatinge-Clay AT. Priming enzymes from the pikromycin synthase reveal how assembly-line ketosynthases catalyze carbon-carbon chemistry. Structure 2022; 30:1331-1339.e3. [PMID: 35738283 PMCID: PMC9444953 DOI: 10.1016/j.str.2022.05.021] [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: 01/29/2022] [Revised: 04/28/2022] [Accepted: 05/27/2022] [Indexed: 10/17/2022]
Abstract
The first domain of modular polyketide synthases (PKSs) is most commonly a ketosynthase (KS)-like enzyme, KSQ, that primes polyketide synthesis. Unlike downstream KSs that fuse α-carboxyacyl groups to growing polyketide chains, it performs an extension-decoupled decarboxylation of these groups to generate primer units. When Pik127, a model triketide synthase constructed from modules of the pikromycin synthase, was studied by cryoelectron microscopy (cryo-EM), the dimeric didomain comprised of KSQ and the neighboring methylmalonyl-selective acyltransferase (AT) dominated the class averages and yielded structures at 2.5- and 2.8-Å resolution, respectively. Comparisons with ketosynthases complexed with their substrates revealed the conformation of the (2S)-methylmalonyl-S-phosphopantetheinyl portion of KSQ and KS substrates prior to decarboxylation. Point mutants of Pik127 probed the roles of residues in the KSQ active site, while an AT-swapped version of Pik127 demonstrated that KSQ can also decarboxylate malonyl groups. Mechanisms for how KSQ and KS domains catalyze carbon-carbon chemistry are proposed.
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Affiliation(s)
- Miles S Dickinson
- Sauer Structural Biology Lab, The University of Texas at Austin, 102 E. 24th Street, Austin, TX 78712, USA
| | - Takeshi Miyazawa
- Department of Molecular Biosciences, The University of Texas at Austin, 100 E. 24th Street, Austin, TX 78712, USA
| | - Ryan S McCool
- Department of Molecular Biosciences, The University of Texas at Austin, 100 E. 24th Street, Austin, TX 78712, USA
| | - Adrian T Keatinge-Clay
- Department of Molecular Biosciences, The University of Texas at Austin, 100 E. 24th Street, Austin, TX 78712, USA.
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8
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D’Ambrosio HK, Ganley JG, Keeler AM, Derbyshire ER. A single amino acid residue controls acyltransferase activity in a polyketide synthase from Toxoplasma gondii. iScience 2022; 25:104443. [PMID: 35874921 PMCID: PMC9301873 DOI: 10.1016/j.isci.2022.104443] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2021] [Revised: 04/12/2022] [Accepted: 05/16/2022] [Indexed: 11/17/2022] Open
Abstract
Type I polyketide synthases (PKSs) are multidomain, multimodule enzymes capable of producing complex polyketide metabolites. These modules contain an acyltransferase (AT) domain, which selects acyl-CoA substrates to be incorporated into the metabolite scaffold. Herein, we reveal the sequences of three AT domains from a polyketide synthase (TgPKS2) from the apicomplexan parasite Toxoplasma gondii. Phylogenic analysis indicates these ATs (AT1, AT2, and AT3) are distinct from domains in well-characterized microbial biosynthetic gene clusters. Biochemical investigations revealed that AT1 and AT2 hydrolyze malonyl-CoA but the terminal AT3 domain is non-functional. We further identify an "on-off switch" residue that controls activity such that a single amino acid change in AT3 confers hydrolysis activity while the analogous mutation in AT2 eliminates activity. This biochemical analysis of AT domains from an apicomplexan PKS lays the foundation for further molecular and structural studies on PKSs from T. gondii and other protists.
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Affiliation(s)
- Hannah K. D’Ambrosio
- Department of Chemistry, Duke University, 124 Science Drive, Durham, NC 27708, USA
| | - Jack G. Ganley
- Department of Chemistry, Duke University, 124 Science Drive, Durham, NC 27708, USA
| | - Aaron M. Keeler
- Department of Chemistry, Duke University, 124 Science Drive, Durham, NC 27708, USA
| | - Emily R. Derbyshire
- Department of Chemistry, Duke University, 124 Science Drive, Durham, NC 27708, USA
- Department of Molecular Genetics and Microbiology, Duke University Medical Center, 213 Research Drive, Durham, NC 27710, USA
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9
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Löhr NA, Eisen F, Thiele W, Platz L, Motter J, Hüttel W, Gressler M, Müller M, Hoffmeister D. Unprecedented Mushroom Polyketide Synthases Produce the Universal Anthraquinone Precursor. Angew Chem Int Ed Engl 2022; 61:e202116142. [PMID: 35218274 PMCID: PMC9325552 DOI: 10.1002/anie.202116142] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/26/2021] [Indexed: 11/11/2022]
Abstract
(Pre-)anthraquinones are widely distributed natural compounds and occur in plants, fungi, microorganisms, and animals, with atrochrysone (1) as the key biosynthetic precursor. Chemical analyses established mushrooms of the genus Cortinarius-the webcaps-as producers of atrochrysone-derived octaketide pigments. However, more recent genomic data did not provide any evidence for known atrochrysone carboxylic acid (4) synthases nor any other polyketide synthase (PKS) producing oligocyclic metabolites. Here, we describe an unprecedented class of non-reducing (NR-)PKS. In vitro assays with recombinant enzyme in combination with in vivo product formation in the heterologous host Aspergillus niger established CoPKS1 and CoPKS4 of C. odorifer as members of a new class of atrochrysone carboxylic acid synthases. CoPKS4 catalyzed both hepta- and octaketide synthesis and yielded 6-hydroxymusizin (6), along with 4. These first mushroom PKSs for oligocyclic products illustrate how the biosynthesis of bioactive natural metabolites evolved independently in various groups of life.
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Affiliation(s)
- Nikolai A Löhr
- Department Pharmaceutical Microbiology at the Hans-Knöll-Institute, Friedrich-Schiller-Universität, Beutenbergstrasse 11a, 07745, Jena, Germany
| | - Frederic Eisen
- Institute of Pharmaceutical Sciences, Albert-Ludwigs-Universität Freiburg, Albertstrasse 25, 79104, Freiburg, Germany
| | - Wiebke Thiele
- Institute of Pharmaceutical Sciences, Albert-Ludwigs-Universität Freiburg, Albertstrasse 25, 79104, Freiburg, Germany
| | - Lukas Platz
- Institute of Pharmaceutical Sciences, Albert-Ludwigs-Universität Freiburg, Albertstrasse 25, 79104, Freiburg, Germany
| | - Jonas Motter
- Department Pharmaceutical Microbiology at the Hans-Knöll-Institute, Friedrich-Schiller-Universität, Beutenbergstrasse 11a, 07745, Jena, Germany
| | - Wolfgang Hüttel
- Institute of Pharmaceutical Sciences, Albert-Ludwigs-Universität Freiburg, Albertstrasse 25, 79104, Freiburg, Germany
| | - Markus Gressler
- Department Pharmaceutical Microbiology at the Hans-Knöll-Institute, Friedrich-Schiller-Universität, Beutenbergstrasse 11a, 07745, Jena, Germany
| | - Michael Müller
- Institute of Pharmaceutical Sciences, Albert-Ludwigs-Universität Freiburg, Albertstrasse 25, 79104, Freiburg, Germany
| | - Dirk Hoffmeister
- Department Pharmaceutical Microbiology at the Hans-Knöll-Institute, Friedrich-Schiller-Universität, Beutenbergstrasse 11a, 07745, Jena, Germany
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10
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Wang Z, Yang FX, Liu C, Wang L, Qi Y, Cao M, Guo X, Li J, Huang X, Yang J, Huang SX. Isolation and Biosynthesis of Phenazine-Polyketide Hybrids from Streptomyces sp. KIB-H483. JOURNAL OF NATURAL PRODUCTS 2022; 85:1324-1331. [PMID: 35574837 DOI: 10.1021/acs.jnatprod.2c00067] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/15/2023]
Abstract
A phenazine-polyketide hybrid compound, nexphenazine A (1), was isolated from Streptomyces sp. KIB-H483. The bioinformatic analysis of the draft genome of the producing strain and gene inactivation experiments revealed that the biosynthesis of 1 involves a phenazine-polyketide hybrid gene cluster. The abolished production of 1 as well as the accumulation of shunt metabolites 4-7 in mutant strain ΔnpzI revealed the key role of the npzI gene, which encodes an NAD(P)H-dependent ketoreductase, in nexphenazine biosynthesis. The structures and absolute configurations of the isolated intermediates were established on the basis of spectroscopic data analysis, single-crystal X-ray diffraction, chiral chromatography, and chemical conversion experiments. NpzI exhibited stereochemical selectivity in reducing the carbonyl group of 4. Nexphenazine biosynthesis is proposed to involve a condensation of the carboxyl group of phenazine with one molecule of methylmalonyl-CoA by a type I PKS, followed by a ketone reduction by NpzI and an unknown methylation reaction.
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Affiliation(s)
- Zhiyan Wang
- State Key Laboratory of Phytochemistry and Plant Resources in West China and CAS Center for Excellence in Molecular Plant Sciences, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming 650201, People's Republic of China
- University of the Chinese Academy of Sciences, Beijing 100049, People's Republic of China
| | - Feng-Xian Yang
- State Key Laboratory of Phytochemistry and Plant Resources in West China and CAS Center for Excellence in Molecular Plant Sciences, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming 650201, People's Republic of China
| | - Chongxi Liu
- State Key Laboratory of Phytochemistry and Plant Resources in West China and CAS Center for Excellence in Molecular Plant Sciences, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming 650201, People's Republic of China
| | - Li Wang
- State Key Laboratory of Phytochemistry and Plant Resources in West China and CAS Center for Excellence in Molecular Plant Sciences, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming 650201, People's Republic of China
| | - Yuxin Qi
- State Key Laboratory of Phytochemistry and Plant Resources in West China and CAS Center for Excellence in Molecular Plant Sciences, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming 650201, People's Republic of China
- Hunan Provincial Key Laboratory for Synthetic Biology of Traditional Chinese Medicine, Hunan University of Medicine, Huaihua 418000, People's Republic of China
| | - Minghang Cao
- State Key Laboratory of Phytochemistry and Plant Resources in West China and CAS Center for Excellence in Molecular Plant Sciences, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming 650201, People's Republic of China
| | - Xiaowei Guo
- State Key Laboratory of Phytochemistry and Plant Resources in West China and CAS Center for Excellence in Molecular Plant Sciences, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming 650201, People's Republic of China
| | - Jie Li
- State Key Laboratory of Phytochemistry and Plant Resources in West China and CAS Center for Excellence in Molecular Plant Sciences, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming 650201, People's Republic of China
- University of the Chinese Academy of Sciences, Beijing 100049, People's Republic of China
| | - Xueshuang Huang
- Hunan Provincial Key Laboratory for Synthetic Biology of Traditional Chinese Medicine, Hunan University of Medicine, Huaihua 418000, People's Republic of China
| | - Jing Yang
- State Key Laboratory of Phytochemistry and Plant Resources in West China and CAS Center for Excellence in Molecular Plant Sciences, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming 650201, People's Republic of China
| | - Sheng-Xiong Huang
- State Key Laboratory of Phytochemistry and Plant Resources in West China and CAS Center for Excellence in Molecular Plant Sciences, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming 650201, People's Republic of China
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11
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Löhr NA, Eisen F, Thiele W, Platz L, Motter J, Hüttel W, Gressler M, Müller M, Hoffmeister D. Unprecedented Mushroom Polyketide Synthases Produce the Universal Anthraquinone Precursor. Angew Chem Int Ed Engl 2022. [DOI: 10.1002/ange.202116142] [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)
- Nikolai A Löhr
- Friedrich-Schiller-Universitat Jena Pharmaceutical Microbiology GERMANY
| | - Frederic Eisen
- Albert-Ludwigs-Universitat Freiburg Pharmaceutical and Medicinal Chemistry GERMANY
| | - Wiebke Thiele
- Albert-Ludwigs-Universitat Freiburg Pharmaceutical and Medicinal Chemistry GERMANY
| | - Lukas Platz
- Albert-Ludwigs-Universitat Freiburg Pharmaceutical and Medicinal Chemistry GERMANY
| | - Jonas Motter
- Friedrich-Schiller-Universitat Jena Pharmaceutical Microbiology GERMANY
| | - Wolfgang Hüttel
- Albert-Ludwigs-Universitat Freiburg Pharmaceutical and Medicinal Chemistry GERMANY
| | - Markus Gressler
- Friedrich-Schiller-Universitat Jena Pharmaceutical Microbiology GERMANY
| | - Michael Müller
- Albert-Ludwigs-Universitat Freiburg Pharmaceutical and Medicinal Chemistry GERMANY
| | - Dirk Hoffmeister
- Leibniz-Institut fur Naturstoff-Forschung und Infektionsbiologie eV Hans-Knoll-Institut Pharmaceutical Microbiology at the Hans-Kn�ll-Institute Beutenbergstrasse 11a 07745 Jena GERMANY
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12
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Chisuga T, Nagai A, Miyanaga A, Goto E, Kishikawa K, Kudo F, Eguchi T. Structural Insight into the Reaction Mechanism of Ketosynthase-Like Decarboxylase in a Loading Module of Modular Polyketide Synthases. ACS Chem Biol 2022; 17:198-206. [PMID: 34985877 DOI: 10.1021/acschembio.1c00856] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
Ketosynthase-like decarboxylase (KSQ) domains are widely distributed in the loading modules of modular polyketide synthases (PKSs) and are proposed to catalyze the decarboxylation of a malonyl or methylmalonyl unit for the construction of the PKS starter unit. KSQ domains have high sequence similarity to ketosynthase (KS) domains, which catalyze transacylation and decarboxylative condensation in polyketide and fatty acid biosynthesis, except that the catalytic Cys residue of KS domains is replaced by Gln in KSQ domains. Here, we present biochemical analyses of GfsA KSQ and CmiP4 KSQ, which are involved in the biosynthesis of FD-891 and cremimycin, respectively. In vitro analysis showed that these KSQ domains catalyze the decarboxylation of malonyl and methylmalonyl units. Furthermore, we determined the crystal structure of GfsA KSQ in complex with a malonyl thioester substrate analogue, which enabled identification of key amino acid residues involved in the decarboxylation reaction. The importance of these residues was confirmed by mutational analysis. On the basis of these findings, we propose a mechanism of the decarboxylation reaction catalyzed by GfsA KSQ. GfsA KSQ initiates decarboxylation by fixing the substrate in a suitable conformation for decarboxylation. The formation of enolate upon decarboxylation is assisted by two conserved threonine residues. Comparison of the structure of GfsA KSQ with those of KS domains suggests that the Gln residue in the active site of the KSQ domain mimics the acylated Cys residue in the active site of KS domains.
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Affiliation(s)
- Taichi Chisuga
- Department of Chemistry, Tokyo Institute of Technology, 2-12-1 O̅okayama, Meguro-ku, Tokyo 152-8851, Japan
| | - Akira Nagai
- Department of Chemistry, Tokyo Institute of Technology, 2-12-1 O̅okayama, Meguro-ku, Tokyo 152-8851, Japan
| | - Akimasa Miyanaga
- Department of Chemistry, Tokyo Institute of Technology, 2-12-1 O̅okayama, Meguro-ku, Tokyo 152-8851, Japan
| | - Ena Goto
- Department of Chemistry, Tokyo Institute of Technology, 2-12-1 O̅okayama, Meguro-ku, Tokyo 152-8851, Japan
| | - Kosuke Kishikawa
- Department of Chemistry, Tokyo Institute of Technology, 2-12-1 O̅okayama, Meguro-ku, Tokyo 152-8851, Japan
| | - Fumitaka Kudo
- Department of Chemistry, Tokyo Institute of Technology, 2-12-1 O̅okayama, Meguro-ku, Tokyo 152-8851, Japan
| | - Tadashi Eguchi
- Department of Chemistry, Tokyo Institute of Technology, 2-12-1 O̅okayama, Meguro-ku, Tokyo 152-8851, Japan
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13
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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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14
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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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15
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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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16
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Li P, Chen M, Tang W, Guo Z, Zhang Y, Wang M, Horsman GP, Zhong J, Lu Z, Chen Y. Initiating polyketide biosynthesis by on-line methyl esterification. Nat Commun 2021; 12:4499. [PMID: 34301953 PMCID: PMC8302727 DOI: 10.1038/s41467-021-24846-7] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2020] [Accepted: 07/09/2021] [Indexed: 12/04/2022] Open
Abstract
Aurantinins (ARTs) are antibacterial polyketides featuring a unique 6/7/8/5-fused tetracyclic ring system and a triene side chain with a carboxyl terminus. Here we identify the art gene cluster and dissect ART’s C-methyl incorporation patterns to study its biosynthesis. During this process, an apparently redundant methyltransferase Art28 was characterized as a malonyl-acyl carrier protein O-methyltransferase, which represents an unusual on-line methyl esterification initiation strategy for polyketide biosynthesis. The methyl ester bond introduced by Art28 is kept until the last step of ART biosynthesis, in which it is hydrolyzed by Art9 to convert inactive ART 9B to active ART B. The cryptic reactions catalyzed by Art28 and Art9 represent a protecting group biosynthetic logic to render the ART carboxyl terminus inert to unwanted side reactions and to protect producing organisms from toxic ART intermediates. Further analyses revealed a wide distribution of this initiation strategy for polyketide biosynthesis in various bacteria. Aurantinins are polyketides with unusual connectivities and broad antibacterial activity. Here the authors show the biosynthesis of aurantinins, which proceeds via an on-line methyl esterification at the terminus that enables the iterative chain elongations prior to condensation and cyclization.
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Affiliation(s)
- Pengwei Li
- State Key Laboratory of Microbial Resources & CAS Key Laboratory of Microbial Physiological and Metabolic Engineering, Institute of Microbiology, Chinese Academy of Sciences, Beijing, China
| | - Meng Chen
- State Key Laboratory of Microbial Resources & CAS Key Laboratory of Microbial Physiological and Metabolic Engineering, Institute of Microbiology, Chinese Academy of Sciences, Beijing, China.,University of Chinese Academy of Sciences, Beijing, China
| | - Wei Tang
- State Key Laboratory of Microbial Resources & CAS Key Laboratory of Microbial Physiological and Metabolic Engineering, Institute of Microbiology, Chinese Academy of Sciences, Beijing, China.,University of Chinese Academy of Sciences, Beijing, China
| | - Zhengyan Guo
- State Key Laboratory of Microbial Resources & CAS Key Laboratory of Microbial Physiological and Metabolic Engineering, Institute of Microbiology, Chinese Academy of Sciences, Beijing, China
| | - Yuwei Zhang
- State Key Laboratory of Microbial Resources & CAS Key Laboratory of Microbial Physiological and Metabolic Engineering, Institute of Microbiology, Chinese Academy of Sciences, Beijing, China.,University of Chinese Academy of Sciences, Beijing, China
| | - Min Wang
- State Key Laboratory of Microbial Resources & CAS Key Laboratory of Microbial Physiological and Metabolic Engineering, Institute of Microbiology, Chinese Academy of Sciences, Beijing, China.,University of Chinese Academy of Sciences, Beijing, China.,School of Biotechnology and Health Sciences, Wuyi University, Jiangmen, Guangdong, China
| | - Geoff P Horsman
- Department of Chemistry and Biochemistry, Wilfrid Laurier University, Waterloo, ON, Canada
| | - Jin Zhong
- State Key Laboratory of Microbial Resources & CAS Key Laboratory of Microbial Physiological and Metabolic Engineering, Institute of Microbiology, Chinese Academy of Sciences, Beijing, China
| | - Zhaoxin Lu
- College of Food Science and Technology, Nanjing Agriculture University, Nanjing, China
| | - Yihua Chen
- State Key Laboratory of Microbial Resources & CAS Key Laboratory of Microbial Physiological and Metabolic Engineering, Institute of Microbiology, Chinese Academy of Sciences, Beijing, China. .,University of Chinese Academy of Sciences, Beijing, China.
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17
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Xu J, Zhang X, Huang F, Li G, Leadlay PF. Efophylins A and B, Two C2-Asymmetric Macrodiolide Immunosuppressants from Streptomyces malaysiensis. JOURNAL OF NATURAL PRODUCTS 2021; 84:1579-1586. [PMID: 33973788 DOI: 10.1021/acs.jnatprod.1c00118] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/12/2023]
Abstract
Genomics-inspired isolation led to the identification of two new natural congeneric C2-asymmetric macrodiolide immunosuppressants, named efophylins A (1) and B (2), from Streptomyces malaysiensis DSM 4137. Their structures were elucidated by spectroscopic and computational methods and were in agreement with biosynthetic predictions from the efophylin gene cluster. Compound 2 exhibited potent immunosuppressive activity and demonstrated to inhibit the activation of the NFAT and block NFAT dephosphorylation in vitro. The immunosuppressive activity of compound 2 is possibly at least in part via the CaN/NFAT signaling pathway.
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Affiliation(s)
- Jing Xu
- School of Chemical Engineering and Technology, Hainan University, Haikou 570228, People's Republic of China
- Department of Biochemistry, University of Cambridge, 80 Tennis Court Road, Cambridge CB2 1GA, United Kingdom
| | - Xuexia Zhang
- School of Chemical Engineering and Technology, Hainan University, Haikou 570228, People's Republic of China
| | - Fanglu Huang
- Department of Biochemistry, University of Cambridge, 80 Tennis Court Road, Cambridge CB2 1GA, United Kingdom
| | - Gang Li
- School of Chemical Engineering and Technology, Hainan University, Haikou 570228, People's Republic of China
| | - Peter F Leadlay
- Department of Biochemistry, University of Cambridge, 80 Tennis Court Road, Cambridge CB2 1GA, United Kingdom
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18
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Santín O, Yuet K, Khosla C, Moncalián G. Structure and Mechanism of the Ketosynthase-Chain Length Factor Didomain from a Prototypical Polyunsaturated Fatty Acid Synthase. Biochemistry 2020; 59:4735-4743. [PMID: 33283513 DOI: 10.1021/acs.biochem.0c00785] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Long-chain polyunsaturated fatty acids (LC-PUFAs) are essential ingredients of the human diet. They are synthesized by LC-PUFA synthases (PFASs) expressed in marine bacteria and other organisms. PFASs are large enzyme complexes that are homologous to mammalian fatty acid synthases and microbial polyketide synthases. One subunit of each PFAS harbors consecutive ketosynthase (KSc) and chain length factor (CLF) domains that collectively catalyze the elongation of a nascent fatty acyl chain via iterative carbon-carbon bond formation. We report the X-ray crystal structure of the KS-CLF didomain from a well-studied PFAS in Moritella marina. Our structure, in combination with biochemical analysis, provides a foundation for understanding the mechanism of substrate recognition and chain length control by the KS-CLF didomain as well as its interaction with a cognate acyl carrier protein partner.
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Affiliation(s)
- Omar Santín
- Departamento de Biología Molecular, Universidad de Cantabria and Instituto de Biomedicina y Biotecnología de Cantabria (IBBTEC), CSIC-Universidad de Cantabria, E-39011 Santander, Spain
| | - Kai Yuet
- Department of Chemistry, Stanford University, Stanford, California 94305, United States.,Department of Chemical Engineering, Stanford University, Stanford, California 94305, United States.,Stanford ChEM-H, Stanford University, Stanford, California 94305, United States
| | - Chaitan Khosla
- Department of Chemistry, Stanford University, Stanford, California 94305, United States.,Department of Chemical Engineering, Stanford University, Stanford, California 94305, United States.,Stanford ChEM-H, Stanford University, Stanford, California 94305, United States
| | - Gabriel Moncalián
- Departamento de Biología Molecular, Universidad de Cantabria and Instituto de Biomedicina y Biotecnología de Cantabria (IBBTEC), CSIC-Universidad de Cantabria, E-39011 Santander, Spain
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19
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Deng Z, Liu J, Li T, Li H, Liu Z, Dong Y, Li W. An Unusual Type II Polyketide Synthase System Involved in Cinnamoyl Lipid Biosynthesis. Angew Chem Int Ed Engl 2020; 60:153-158. [PMID: 32860295 DOI: 10.1002/anie.202007777] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2020] [Revised: 08/13/2020] [Indexed: 12/13/2022]
Abstract
As a unique structural moiety in natural products, cinnamoyl lipids (CLs), are proposed to be assembled by unusual type II polyketide synthases (PKSs). Herein, we demonstrate that the assembly of the CL compounds youssoufenes is accomplished by a PKS system that uniquely harbors three phylogenetically different ketosynthase/chain length factor (KS/CLF) complexes (YsfB/C, YsfD/E, and YsfJ/K). Through in vivo gene inactivation and in vitro reconstitution, as well as an intracellular tagged carrier-protein tracking (ITCT) strategy developed in this study, we successfully elucidated the isomerase-dependent ACP-tethered polyunsaturated chain elongation process. The three KS/CLFs were revealed to modularly assemble different parts of the youssoufene skeleton, during which benzene ring closure happens right after the formation of an ACP-tethered C18 polyene. Of note, the ITCT strategy could significantly contribute to the elucidation of other carrier-protein-dependent biosynthetic machineries.
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Affiliation(s)
- Zirong Deng
- Key Laboratory of Marine Drugs, Ministry of Education, School of Medicine and Pharmacy, Ocean University of China, Qingdao, 266003, China
| | - Jing Liu
- Key Laboratory of Marine Drugs, Ministry of Education, School of Medicine and Pharmacy, Ocean University of China, Qingdao, 266003, China
| | - Tong Li
- Key Laboratory of Marine Drugs, Ministry of Education, School of Medicine and Pharmacy, Ocean University of China, Qingdao, 266003, China
| | - Huayue Li
- Key Laboratory of Marine Drugs, Ministry of Education, School of Medicine and Pharmacy, Ocean University of China, Qingdao, 266003, China.,Laboratory for Marine Drugs and Bioproducts of Qingdao National Laboratory for Marine Science and Technology, Qingdao, 266237, China
| | - Zengzhi Liu
- Key Laboratory of Marine Drugs, Ministry of Education, School of Medicine and Pharmacy, Ocean University of China, Qingdao, 266003, China
| | - Yujing Dong
- Key Laboratory of Marine Drugs, Ministry of Education, School of Medicine and Pharmacy, Ocean University of China, Qingdao, 266003, China
| | - Wenli Li
- Key Laboratory of Marine Drugs, Ministry of Education, School of Medicine and Pharmacy, Ocean University of China, Qingdao, 266003, China.,Laboratory for Marine Drugs and Bioproducts of Qingdao National Laboratory for Marine Science and Technology, Qingdao, 266237, China
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20
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Deng Z, Liu J, Li T, Li H, Liu Z, Dong Y, Li W. An Unusual Type II Polyketide Synthase System Involved in Cinnamoyl Lipid Biosynthesis. Angew Chem Int Ed Engl 2020. [DOI: 10.1002/ange.202007777] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/25/2023]
Affiliation(s)
- Zirong Deng
- Key Laboratory of Marine Drugs Ministry of Education School of Medicine and Pharmacy Ocean University of China Qingdao 266003 China
| | - Jing Liu
- Key Laboratory of Marine Drugs Ministry of Education School of Medicine and Pharmacy Ocean University of China Qingdao 266003 China
| | - Tong Li
- Key Laboratory of Marine Drugs Ministry of Education School of Medicine and Pharmacy Ocean University of China Qingdao 266003 China
| | - Huayue Li
- Key Laboratory of Marine Drugs Ministry of Education School of Medicine and Pharmacy Ocean University of China Qingdao 266003 China
- Laboratory for Marine Drugs and Bioproducts of Qingdao National Laboratory for Marine Science and Technology Qingdao 266237 China
| | - Zengzhi Liu
- Key Laboratory of Marine Drugs Ministry of Education School of Medicine and Pharmacy Ocean University of China Qingdao 266003 China
| | - Yujing Dong
- Key Laboratory of Marine Drugs Ministry of Education School of Medicine and Pharmacy Ocean University of China Qingdao 266003 China
| | - Wenli Li
- Key Laboratory of Marine Drugs Ministry of Education School of Medicine and Pharmacy Ocean University of China Qingdao 266003 China
- Laboratory for Marine Drugs and Bioproducts of Qingdao National Laboratory for Marine Science and Technology Qingdao 266237 China
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21
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Komaki H, Oguchi A, Tamura T, Hamada M, Ichikawa N. Diversity of nonribosomal peptide synthetase and polyketide synthase gene clusters in the genus Acrocarpospora. J GEN APPL MICROBIOL 2020; 66:315-322. [PMID: 32801283 DOI: 10.2323/jgam.2020.01.001] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/03/2022]
Abstract
Acrocarpospora is a rare, recently established actinomycete genus of the family Streptosporangiaceae. In the present study, we sequenced whole genomes of the type strains of Acrocarpospora corrugate, Acrocarpospora macrocephala, and Acrocarpospora pleiomorpha to assess their potency as secondary metabolite producers; we then surveyed their nonribosomal peptide synthetase (NRPS) and polyketide synthase (PKS) gene clusters. The genome sizes of A. corrugate NBRC 13972T, A. macrocephala NBRC 16266T, and A. pleiomorpha NBRC 16267T were 9.3 Mb, 12.1 Mb, and 11.8 Mb, respectively. Each genome contained 12-17 modular NRPS and PKS gene clusters. Among the 23 kinds of NRPS and PKS gene clusters identified from the three strains, eight clusters were conserved in all the strains, six were shared between A. macrocephala and A. pleiomorpha, and the remaining nine were strain-specific. We predicted the chemical structures of the products synthesized by these gene clusters based on bioinformatic analyses. Since the chemical structures are diverse, Acrocarpospora strains are considered an attractive source of diverse nonribosomal peptide and polyketide compounds.
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Affiliation(s)
- Hisayuki Komaki
- Biological Resource Center, National Institute of Technology and Evaluation (NBRC)
| | | | - Tomohiko Tamura
- Biological Resource Center, National Institute of Technology and Evaluation (NBRC)
| | - Moriyuki Hamada
- Biological Resource Center, National Institute of Technology and Evaluation (NBRC)
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Chen J, Gui C, Wei Q, Liu J, Ye L, Tian X, Gu YC, Li Q, Ju J. Characterization of Tailoring Methyltransferases Involved in K-41A Biosynthesis: Modulating Methylation to Improve K-41A Anti-infective Activity. Org Lett 2020; 22:4627-4632. [PMID: 32511927 DOI: 10.1021/acs.orglett.0c01347] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/13/2023]
Abstract
The biosynthetic gene cluster (BGC) for polyether antibiotic K-41A was identified from marine-derived Streptomyces sp. SCSIO 01680 and subjected to combinatorial biosynthetic study. Bioinformatics analyses, gene disruption, and metabolomics analyses afforded eight new derivatives and one known polyether, showcasing five region-specific methyltransferases Pak13, Pak15, Pak20, Pak31, and Pak38 and their respective modification loci. Moreover, bioassays revealed that two disaccharide-bearing polyethers, K-41B and K-41Bm, display enhanced anti-HIV and potent antibacterial activities.
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Affiliation(s)
- Jiang Chen
- 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, 19 Yuquan Road, Beijing, 100049, China
| | - Chun Gui
- 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, 19 Yuquan Road, Beijing, 100049, China
| | - Qiuyu Wei
- Guangxi Collaborative Innovation Center for Biomedicine, Life Sciences Institute, Guangxi Medical University, Nanning, 530021, Guangxi, China
| | - Jie Liu
- Guangxi Collaborative Innovation Center for Biomedicine, Life Sciences Institute, Guangxi Medical University, Nanning, 530021, Guangxi, China
| | - Li Ye
- Guangxi Collaborative Innovation Center for Biomedicine, Life Sciences Institute, Guangxi Medical University, Nanning, 530021, Guangxi, China
| | - Xinpeng Tian
- 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
| | - Yu-Cheng Gu
- Syngenta Jealott's Hill International Research Centre, Bracknell, Berkshire RG42 6EY, U.K
| | - Qinglian Li
- 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
| | - 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, 19 Yuquan Road, Beijing, 100049, China
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Yuet KP, Liu CW, Lynch SR, Kuo J, Michaels W, Lee RB, McShane AE, Zhong BL, Fischer CR, Khosla C. Complete Reconstitution and Deorphanization of the 3 MDa Nocardiosis-Associated Polyketide Synthase. J Am Chem Soc 2020; 142:5952-5957. [PMID: 32182063 DOI: 10.1021/jacs.0c00904] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Several Nocardia strains associated with nocardiosis, a potentially life-threatening disease, house a nonamodular assembly line polyketide synthase (PKS) that presumably synthesizes an unknown polyketide. Here, we report the discovery and structure elucidation of the NOCAP (nocardiosis-associated polyketide) aglycone by first fully reconstituting the NOCAP synthase in vitro from purified protein components followed by heterologous expression in E. coli and spectroscopic analysis of the purified products. The NOCAP aglycone has an unprecedented structure comprised of a substituted resorcylaldehyde headgroup linked to a 15-carbon tail that harbors two conjugated all-trans trienes separated by a stereogenic hydroxyl group. This report is the first example of reconstituting a trans-acyltransferase assembly line PKS in vitro and of using these approaches to "deorphanize" a complete assembly line PKS identified via genomic sequencing. With the NOCAP aglycone in hand, the stage is set for understanding how this PKS and associated tailoring enzymes confer an advantage to their native hosts during human Nocardia infections.
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24
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Kornfuehrer T, Eustáquio AS. Diversification of polyketide structures via synthase engineering. MEDCHEMCOMM 2019; 10:1256-1272. [PMID: 32180918 PMCID: PMC7053703 DOI: 10.1039/c9md00141g] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/08/2019] [Accepted: 05/09/2019] [Indexed: 12/16/2022]
Abstract
Polyketide natural products possess diverse biological activities including antibiotic, anticancer, and immunosuppressive. Their equally varied and complex structures arise from head-to-tail condensation of simple carboxyacyl monomers. Since the seminal discovery that biosynthesis of polyketides such as the macrolide erythromycin is catalyzed by uncharacteristically large, multifunctional enzymes, termed modular type I polyketide synthases, chemists and biologists alike have been inspired to harness the apparent modularity of the synthases to further diversify polyketide structures. Yet, initial attempts to perform "combinatorial biosynthesis" failed due to challenges associated with maintaining the structural and catalytic integrity of large, chimeric synthases. Fast forward nearly 30 years, and advancements in our understanding of polyketide synthase structure and function have allowed the field to make significant progress toward effecting desired modifications to polyketide scaffolds in addition to engineering small, chiral fragments. This review highlights selected examples of polyketide diversification via control of monomer selection, oxidation state, stereochemistry, and cyclization. We conclude with a perspective on the present and future of polyketide structure diversification and hope that the examples presented here will encourage medicinal chemists to embrace polyketide synthetic biology as a means to revitalize polyketide drug discovery.
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Affiliation(s)
- Taylor Kornfuehrer
- Department of Medicinal Chemistry and Pharmacognosy and Center for Biomolecular Sciences , College of Pharmacy , University of Illinois at Chicago , Chicago , Illinois 60607 , USA . ; Tel: +1 3124137082
| | - Alessandra S Eustáquio
- Department of Medicinal Chemistry and Pharmacognosy and Center for Biomolecular Sciences , College of Pharmacy , University of Illinois at Chicago , Chicago , Illinois 60607 , USA . ; Tel: +1 3124137082
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Abstract
Burkholderia bacteria are multifaceted organisms that are ecologically and metabolically diverse. The Burkholderia genus has gained prominence because it includes human pathogens; however, many strains are nonpathogenic and have desirable characteristics such as beneficial plant associations and degradation of pollutants. The diversity of the Burkholderia genus is reflected within the large genomes that feature multiple replicons. Burkholderia genomes encode a plethora of natural products with potential therapeutic relevance and biotechnological applications. This review highlights Burkholderia as an emerging source of natural products. An overview of the taxonomy of the Burkholderia genus, which is currently being revised, is provided. We then present a curated compilation of natural products isolated from Burkholderia sensu lato and analyze their characteristics in terms of biosynthetic class, discovery method, and bioactivity. Finally, we describe and discuss genome characteristics and highlight the biosynthesis of a select number of natural products that are encoded in unusual biosynthetic gene clusters. The availability of >1000 Burkholderia genomes in public databases provides an opportunity to realize the genetic potential of this underexplored taxon for natural product discovery.
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Affiliation(s)
- Sylvia Kunakom
- Department of Medicinal Chemistry and Pharmacognosy and Center for Biomolecular Sciences, College of Pharmacy, University of Illinois at Chicago, Chicago, IL 60607, USA
| | - Alessandra S. Eustáquio
- Department of Medicinal Chemistry and Pharmacognosy and Center for Biomolecular Sciences, College of Pharmacy, University of Illinois at Chicago, Chicago, IL 60607, USA
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Bilyk O, Samborskyy M, Leadlay PF. The biosynthetic pathway to ossamycin, a macrocyclic polyketide bearing a spiroacetal moiety. PLoS One 2019; 14:e0215958. [PMID: 31039188 PMCID: PMC6490886 DOI: 10.1371/journal.pone.0215958] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2019] [Accepted: 04/11/2019] [Indexed: 01/08/2023] Open
Abstract
Ossamycin from Streptomyces hygroscopicus var. ossamyceticus is an antifungal and cytotoxic polyketide and a potent inhibitor of the mitochondrial ATPase. Analysis of a near-complete genome sequence of the ossamycin producer has allowed the identification of the 127-kbp ossamycin biosynthetic gene cluster. The presence in the cluster of a specific crotonyl-CoA carboxylase/reductase homologue suggests that the 5-methylhexanoate extension unit used in construction of the macrocyclic core is incorporated intact from the unusual precursor isobutyrylmalonyl-CoA. Surprisingly, the modular polyketide synthase uses only 14 extension modules to accomplish 15 cycles of polyketide chain extension, a rare example of programmed iteration on a modular polyketide synthase. Specific deletion of genes encoding cytochrome P450 enzymes has given insight into the late-stage tailoring of the ossamycin macrocycle required for the attachment of the unusual 2,3,4,6-deoxyaminohexose sugar l-ossamine to C-8 of the ossamycin macrocycle. The ossamycin cluster also encodes a putative spirocyclase enzyme, OssO, which may play a role in establishing the characteristic spiroketal moiety of the natural product.
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Affiliation(s)
- Oksana Bilyk
- Department of Biochemistry, University of Cambridge, Cambridge, United Kingdom
- * E-mail:
| | - Markiyan Samborskyy
- Department of Biochemistry, University of Cambridge, Cambridge, United Kingdom
| | - Peter F. Leadlay
- Department of Biochemistry, University of Cambridge, Cambridge, United Kingdom
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27
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Hong SH, Ban YH, Byun WS, Kim D, Jang YJ, An JS, Shin B, Lee SK, Shin J, Yoon YJ, Oh DC. Camporidines A and B: Antimetastatic and Anti-inflammatory Polyketide Alkaloids from a Gut Bacterium of Camponotus kiusiuensis. JOURNAL OF NATURAL PRODUCTS 2019; 82:903-910. [PMID: 30912943 DOI: 10.1021/acs.jnatprod.8b01000] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/09/2023]
Abstract
Chemical studies of gut bacteria of the carpenter ant Camponotus kiusiuensis led to the discovery of two new alkaloids, camporidines A and B (1 and 2), from Streptomyces sp. STA1. The structures of 1 and 2 were established as new polyketide alkaloids bearing a piperidine-cyclopentene-epoxide 6/5/3 tricyclic system based on NMR spectroscopic and mass spectrometric analysis. The relative configurations of the camporidines were determined by their 1H-1H NOESY/ROESY and 1D NOE NMR correlations. The experimental ECD spectra of 1 and 2 were compared with their calculated ECD spectra to assign their absolute configurations. Camporidine A (1) displayed antimetastatic activity by suppression of cell invasion against the metastatic breast cancer cell line MDA-MB-231 and showed an anti-inflammatory effect by suppressing nitric oxide production induced by lipopolysaccharide. In addition, the putative biosynthetic gene cluster of the camporidines was identified, and the biosynthetic pathway of the camporidines was proposed based on bioinformatic analysis of the full genome of Streptomyces sp. STA1. Camporidines A and B (1 and 2) could be biosynthesized by a modular type I PKS containing an acyl transferase domain that accepts an unusual extender unit, which becomes the (C1'-C6') hexyl side chain. The post-PKS modification enzymes were predicted to perform an amination and an oxidation along with spontaneous Schiff base formation and generate the unique piperidine-cyclopentene-epoxide 6/5/3 tricyclic framework.
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Affiliation(s)
- Seong-Heon Hong
- Natural Products Research Institute, College of Pharmacy , Seoul National University , Seoul 08826 , Republic of Korea
| | - Yeon Hee Ban
- Department of Chemistry and Nanoscience , Ewha Womans University , Seoul 03760 , Republic of Korea
| | - Woong Sub Byun
- Natural Products Research Institute, College of Pharmacy , Seoul National University , Seoul 08826 , Republic of Korea
| | - Donghwa Kim
- Natural Products Research Institute, College of Pharmacy , Seoul National University , Seoul 08826 , Republic of Korea
| | - Yong-Joon Jang
- Natura Academia Research Center , Seoul 08826 , Republic of Korea
| | - Joon Soo An
- Natural Products Research Institute, College of Pharmacy , Seoul National University , Seoul 08826 , Republic of Korea
| | - Bora Shin
- Natural Products Research Institute, College of Pharmacy , Seoul National University , Seoul 08826 , Republic of Korea
| | - Sang Kook Lee
- Natural Products Research Institute, College of Pharmacy , Seoul National University , Seoul 08826 , Republic of Korea
| | - Jongheon Shin
- Natural Products Research Institute, College of Pharmacy , Seoul National University , Seoul 08826 , Republic of Korea
| | - Yeo Joon Yoon
- Department of Chemistry and Nanoscience , Ewha Womans University , Seoul 03760 , 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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Pérez-Victoria I, Oves-Costales D, Lacret R, Martín J, Sánchez-Hidalgo M, Díaz C, Cautain B, Vicente F, Genilloud O, Reyes F. Structure elucidation and biosynthetic gene cluster analysis of caniferolides A–D, new bioactive 36-membered macrolides from the marine-derived Streptomyces caniferus CA-271066. Org Biomol Chem 2019; 17:2954-2971. [DOI: 10.1039/c8ob03115k] [Citation(s) in RCA: 27] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Abstract
The structures of caniferolides A–D have been determined combining NMR and bioinformatics prediction of the absolute configuration.
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29
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Li Z, Chen X, Li J, Meng T, Wang L, Chen Z, Shi Y, Ling X, Luo W, Liang D, Lu Y, Li Q, He N. Functions of PKS Genes in Lipid Synthesis of Schizochytrium sp. by Gene Disruption and Metabolomics Analysis. MARINE BIOTECHNOLOGY (NEW YORK, N.Y.) 2018; 20:792-802. [PMID: 30136198 DOI: 10.1007/s10126-018-9849-x] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/16/2018] [Accepted: 08/03/2018] [Indexed: 05/26/2023]
Abstract
Schizochytrium sp. is a kind of marine microalgae with great potential as promising sustainable source of polyunsaturated fatty acids (PUFAs). Polyketide synthase-like (PKS synthase) is supposed to be one of the main ways to synthesize PUFAs in Schizochytrium sp. In order to study the exact relationship between PKS and PUFA biosynthesis, chain length factor (CLF) and dehydrogenase (DH) were cloned from the PKS gene cluster in Schizochytrium sp., then disrupted by homologous recombination. The results showed that DH- and CLF-disrupted strains had significant decreases (65.85 and 84.24%) in PUFA yield, while the saturated fatty acid (SFA) proportion in lipids was slightly increased. Meanwhile, the disruption of CLF decreased the C-22 PUFA proportion by 57.51% without effect on C-20 PUFA accumulation while DH-disrupted mutant decreased the production of each PUFA. Combined with analysis of protein prediction, it indicated that CLF gene exerted an enormous function on the carbon chain elongation in PUFA synthesis, especially for the final elongation from C-20 to C-22 PUFAs. Metabolomics analysis also suggested that the disruption of both genes resulted in the decrease of PUFAs but increase of SFAs, thus weakening glycolysis and tricarboxylic acid (TCA) cycle pathways. This study offers a broad new vision to research the mechanism of PUFA synthesis in Schizochytrium sp.
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Affiliation(s)
- Zhipeng Li
- Department of Chemical and Biochemical Engineering, College of Chemistry and Chemical Engineering, Xiamen University, Xiamen, 361005, People's Republic of China
- The Key Lab for Synthetic Biotechnology of Xiamen City, Xiamen University, Xiamen, 361005, People's Republic of China
| | - Xi Chen
- Department of Chemical and Biochemical Engineering, College of Chemistry and Chemical Engineering, Xiamen University, Xiamen, 361005, People's Republic of China
- The Key Lab for Synthetic Biotechnology of Xiamen City, Xiamen University, Xiamen, 361005, People's Republic of China
| | - Jun Li
- Department of Chemical and Biochemical Engineering, College of Chemistry and Chemical Engineering, Xiamen University, Xiamen, 361005, People's Republic of China
- The Key Lab for Synthetic Biotechnology of Xiamen City, Xiamen University, Xiamen, 361005, People's Republic of China
| | - Tong Meng
- Department of Chemical and Biochemical Engineering, College of Chemistry and Chemical Engineering, Xiamen University, Xiamen, 361005, People's Republic of China
- The Key Lab for Synthetic Biotechnology of Xiamen City, Xiamen University, Xiamen, 361005, People's Republic of China
| | - Lingwei Wang
- Department of Chemical and Biochemical Engineering, College of Chemistry and Chemical Engineering, Xiamen University, Xiamen, 361005, People's Republic of China
- The Key Lab for Synthetic Biotechnology of Xiamen City, Xiamen University, Xiamen, 361005, People's Republic of China
| | - Zhen Chen
- Department of Chemical and Biochemical Engineering, College of Chemistry and Chemical Engineering, Xiamen University, Xiamen, 361005, People's Republic of China
- The Key Lab for Synthetic Biotechnology of Xiamen City, Xiamen University, Xiamen, 361005, People's Republic of China
| | - Yanyan Shi
- Department of Chemical and Biochemical Engineering, College of Chemistry and Chemical Engineering, Xiamen University, Xiamen, 361005, People's Republic of China
- The Key Lab for Synthetic Biotechnology of Xiamen City, Xiamen University, Xiamen, 361005, People's Republic of China
| | - Xueping Ling
- Department of Chemical and Biochemical Engineering, College of Chemistry and Chemical Engineering, Xiamen University, Xiamen, 361005, People's Republic of China.
- The Key Lab for Synthetic Biotechnology of Xiamen City, Xiamen University, Xiamen, 361005, People's Republic of China.
| | - Weiang Luo
- Fujian Provincial Key Laboratory of Fire Retardant Materials, College of Materials, Xiamen University, Xiamen, 361005, People's Republic of China
| | - Dafeng Liang
- Guangxi State Farms Sugar Industrial Group Company Limited, Guangxi Sugarcane Industry R&D center, Guangxi, Nanning, 530002, People's Republic of China
- Guangdong Key Lab of Sugarcane Improvement and Biorefinery, Guangzhou Sugarcane Industry Research Institute, Guangzhou, 510316, Guangdong, People's Republic of China
| | - Yinghua Lu
- Department of Chemical and Biochemical Engineering, College of Chemistry and Chemical Engineering, Xiamen University, Xiamen, 361005, People's Republic of China
- The Key Lab for Synthetic Biotechnology of Xiamen City, Xiamen University, Xiamen, 361005, People's Republic of China
| | - Qingbiao Li
- Department of Chemical and Biochemical Engineering, College of Chemistry and Chemical Engineering, Xiamen University, Xiamen, 361005, People's Republic of China
- The Key Lab for Synthetic Biotechnology of Xiamen City, Xiamen University, Xiamen, 361005, People's Republic of China
| | - Ning He
- Department of Chemical and Biochemical Engineering, College of Chemistry and Chemical Engineering, Xiamen University, Xiamen, 361005, People's Republic of China.
- The Key Lab for Synthetic Biotechnology of Xiamen City, Xiamen University, Xiamen, 361005, People's Republic of China.
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Chen A, Re RN, Burkart MD. Type II fatty acid and polyketide synthases: deciphering protein-protein and protein-substrate interactions. Nat Prod Rep 2018; 35:1029-1045. [PMID: 30046786 PMCID: PMC6233901 DOI: 10.1039/c8np00040a] [Citation(s) in RCA: 55] [Impact Index Per Article: 9.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
Covering: up to April 5, 2018 Metabolites from type II fatty acid synthase (FAS) and polyketide synthase (PKS) pathways differ broadly in their identities and functional roles. The former are considered primary metabolites that are linear hydrocarbon acids, while the latter are complex aromatic or polyunsaturated secondary metabolites. Though the study of bacterial FAS has benefitted from decades of biochemical and structural investigations, type II PKSs have remained less understood. Here we review the recent approaches to understanding the protein-protein and protein-substrate interactions in these pathways, with an emphasis on recent chemical biology and structural applications. New approaches to the study of FAS have highlighted the critical role of the acyl carrier protein (ACP) with regard to how it stabilizes intermediates through sequestration and selectively delivers cargo to successive enzymes within these iterative pathways, utilizing protein-protein interactions to guide and organize enzymatic timing and specificity. Recent tools that have shown promise in FAS elucidation should find new approaches to studying type II PKS systems in the coming years.
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Affiliation(s)
- Aochiu Chen
- Department of Chemistry and Biochemistry, University of California-San Diego, 9500 Gilman Drive, La Jolla, CA 92093-0358, USA.
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31
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Mrak P, Krastel P, Pivk Lukančič P, Tao J, Pistorius D, Moore CM. Discovery of the actinoplanic acid pathway in Streptomyces rapamycinicus reveals a genetically conserved synergism with rapamycin. J Biol Chem 2018; 293:19982-19995. [PMID: 30327433 DOI: 10.1074/jbc.ra118.005314] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2018] [Revised: 10/11/2018] [Indexed: 01/11/2023] Open
Abstract
Actinobacteria possess a great wealth of pathways for production of bioactive compounds. Following advances in genome mining, dozens of natural product (NP) gene clusters are routinely found in each actinobacterial genome; however, the modus operandi of this large arsenal is poorly understood. During investigations of the secondary metabolome of Streptomyces rapamycinicus, the producer of rapamycin, we observed accumulation of two compounds never before reported from this organism. Structural elucidation revealed actinoplanic acid A and its demethyl analogue. Actinoplanic acids (APLs) are potent inhibitors of Ras farnesyltransferase and therefore represent bioactive compounds of medicinal interest. Supported with the unique structure of these polyketides and using genome mining, we identified a gene cluster responsible for their biosynthesis in S. rapamycinicus Based on experimental evidence and genetic organization of the cluster, we propose a stepwise biosynthesis of APL, the first bacterial example of a pathway incorporating the rare tricarballylic moiety into an NP. Although phylogenetically distant, the pathway shares some of the biosynthetic principles with the mycotoxins fumonisins. Namely, the core polyketide is acylated with the tricarballylate by an atypical nonribosomal peptide synthetase-catalyzed ester formation. Finally, motivated by the conserved colocalization of the rapamycin and APL pathway clusters in S. rapamycinicus and all other rapamycin-producing actinobacteria, we confirmed a strong synergism of these compounds in antifungal assays. Mining for such evolutionarily conserved coharboring of pathways would likely reveal further examples of NP sets, attacking multiple targets on the same foe. These could then serve as a guide for development of new combination therapies.
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Affiliation(s)
- Peter Mrak
- From the Novartis Technical Operations, Antiinfectives, SI-1234 Mengeš, Slovenia,; University of Ljubljana, 1000 Ljubljana, Slovenia.
| | - Philipp Krastel
- Novartis Institutes for BioMedical Research, Novartis Campus, 4056 Basel, Switzerland
| | - Petra Pivk Lukančič
- From the Novartis Technical Operations, Antiinfectives, SI-1234 Mengeš, Slovenia
| | - Jianshi Tao
- Genomics Institute of the Novartis Research Foundation, San Diego, California 92121, and
| | - Dominik Pistorius
- Novartis Institutes for BioMedical Research, Novartis Campus, 4056 Basel, Switzerland
| | - Charles M Moore
- Novartis Institutes for BioMedical Research, Novartis Campus, 4056 Basel, Switzerland,.
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32
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Cao XQ, Wang JY, Zhou L, Chen B, Jin Y, He YW. Biosynthesis of the yellow xanthomonadin pigments involves an ATP-dependent 3-hydroxybenzoic acid: acyl carrier protein ligase and an unusual type II polyketide synthase pathway. Mol Microbiol 2018; 110:16-32. [PMID: 29995983 DOI: 10.1111/mmi.14064] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 06/25/2018] [Indexed: 11/30/2022]
Abstract
Xanthomonadins are yellow pigments that are produced by the phytopathogen Xanthomonas campestris pv. campestris (Xcc). A pig cluster is responsible for xanthomonadin biosynthesis. Previously, Xcc4014 of the cluster was characterized as a bifunctional chorismatase that produces 3-hydroxybenzoic acid (3-HBA) and 4-HBA. In this study, genetic analysis identified 11 genes within the pig cluster to be essential for xanthomonadin biosynthesis. Biochemical and bioinformatics analysis suggest that xanthomonadins are synthesized via an unusual type II polyketide synthase pathway. Heterologous expression of the pig cluster in non-xanthomonadin-producing Pseudomonas aeruginosa strain resulted in the synthesis of chlorinated xanthomonadin-like pigments. Further analysis showed that xanC encodes an acyl carrier protein (ACP) while xanA2 encodes a ATP-dependent 3-HBA:ACP ligase. Both of them act together to catalyse the formation of 3-HBA-S-ACP from 3-HBA to initiate xanthomonadin biosynthesis. Finally, we showed that xanH encodes a FabG-like enzyme and xanK encodes a novel glycosyltransferase. Both xanH and xanK are not only required for xanthomonadin biosynthesis, but also required for the balanced biosynthesis of extracellular polysaccharides and DSF-family quorum sensing signals. These findings provide us with a better understanding of xanthomonadin biosynthetic mechanisms and directly demonstrate the presence of extensive cross-talk among xanthomonadin biosynthetic pathways and other metabolic pathways.
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Affiliation(s)
- Xue-Qiang Cao
- State Key Laboratory of Microbial Metabolism, Joint International Research Laboratory of Metabolic and Developmental Sciences, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, 200240, China
| | - Jia-Yuan Wang
- State Key Laboratory of Microbial Metabolism, Joint International Research Laboratory of Metabolic and Developmental Sciences, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, 200240, China
| | - Lian Zhou
- Zhiyuan Innovation Research Centre, Student Innovation Institute, Zhiyuan College, Shanghai Jiao Tong University, Shanghai, China
| | - Bo Chen
- State Key Laboratory of Microbial Metabolism, Joint International Research Laboratory of Metabolic and Developmental Sciences, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, 200240, China
| | - Yu Jin
- School of Biotechnology, East China Science and Technology University, Shanghai, China
| | - Ya-Wen He
- State Key Laboratory of Microbial Metabolism, Joint International Research Laboratory of Metabolic and Developmental Sciences, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, 200240, China
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Abdel-Hameed ME, Bertrand RL, Donald LJ, Sorensen JL. Lichen ketosynthase domains are not responsible for inoperative polyketide synthases in Ascomycota hosts. Biochem Biophys Res Commun 2018; 503:1228-1234. [DOI: 10.1016/j.bbrc.2018.07.029] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/04/2018] [Accepted: 07/06/2018] [Indexed: 02/06/2023]
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Akiyama H, Indananda C, Thamchaipenet A, Motojima A, Oikawa T, Komaki H, Hosoyama A, Kimura A, Oku N, Igarashi Y. Linfuranones B and C, Furanone-Containing Polyketides from a Plant-Associated Sphaerimonospora mesophila. JOURNAL OF NATURAL PRODUCTS 2018; 81:1561-1569. [PMID: 29939741 DOI: 10.1021/acs.jnatprod.8b00071] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/28/2023]
Abstract
Two new furanone-containing polyketides, linfuranones B and C, were isolated from a plant-associated actinomycete of the genus Sphaerimonospora. Their structures were determined by NMR and MS spectroscopic analyses, and the absolute configurations were established by anisotropic methods and chemical degradation approaches. In silico analysis of biosynthetic genes suggested that linfuranone B is generated from linfuranone C by oxidative cleavage of the polyketide chain. Linfuranones B and C induced preadipocyte differentiation into matured adipocytes at 20-40 μM without showing cytotoxicity.
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Affiliation(s)
- Hirofumi Akiyama
- Biotechnology Research Center , Toyama Prefectural University , Imizu , Toyama 939-0398 , Japan
| | - Chantra Indananda
- Department of Biology, Faculty of Science , Burapha University , Chonburi 20131 , Thailand
| | - Arinthip Thamchaipenet
- Actinobacteria Research Unit, Department of Genetics, Faculty of Science , Kasetsart University , Bangkok 10900 , Thailand
| | - Atsuko Motojima
- Department of Nutritional Biochemistry, School of Nutrition and Dietetics , Kanagawa University of Human Services , Yokosuka , Kanagawa 238-8522 , Japan
| | - Tsutomu Oikawa
- Department of Nutritional Biochemistry, School of Nutrition and Dietetics , Kanagawa University of Human Services , Yokosuka , Kanagawa 238-8522 , Japan
| | - Hisayuki Komaki
- Biological Resource Center , National Institute of Technology and Evaluation (NBRC) , Kisarazu , Chiba 292-0818 , Japan
| | | | | | - Naoya Oku
- Biotechnology Research Center , Toyama Prefectural University , Imizu , Toyama 939-0398 , Japan
| | - Yasuhiro Igarashi
- Biotechnology Research Center , Toyama Prefectural University , Imizu , Toyama 939-0398 , Japan
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Tsai SC(S. The Structural Enzymology of Iterative Aromatic Polyketide Synthases: A Critical Comparison with Fatty Acid Synthases. Annu Rev Biochem 2018; 87:503-531. [DOI: 10.1146/annurev-biochem-063011-164509] [Citation(s) in RCA: 20] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
Polyketides are a large family of structurally complex natural products including compounds with important bioactivities. Polyketides are biosynthesized by polyketide synthases (PKSs), multienzyme complexes derived evolutionarily from fatty acid synthases (FASs). The focus of this review is to critically compare the properties of FASs with iterative aromatic PKSs, including type II PKSs and fungal type I nonreducing PKSs whose chemical logic is distinct from that of modular PKSs. This review focuses on structural and enzymological studies that reveal both similarities and striking differences between FASs and aromatic PKSs. The potential application of FAS and aromatic PKS structures for bioengineering future drugs and biofuels is highlighted.
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Affiliation(s)
- Shiou-Chuan (Sheryl) Tsai
- Departments of Molecular Biology and Biochemistry, Chemistry, and Pharmaceutical Sciences, University of California, Irvine, California 92697, USA
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Du D, Katsuyama Y, Shin-ya K, Ohnishi Y. Reconstitution of a Type II Polyketide Synthase that Catalyzes Polyene Formation. Angew Chem Int Ed Engl 2018. [DOI: 10.1002/ange.201709636] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Affiliation(s)
- Danyao Du
- 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
| | - Kazuo Shin-ya
- National Institute of Advanced Industrial Science and Technology (AIST); 2-4-7, Aomi Koto-ku Tokyo 135-0064 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
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Du D, Katsuyama Y, Shin-ya K, Ohnishi Y. Reconstitution of a Type II Polyketide Synthase that Catalyzes Polyene Formation. Angew Chem Int Ed Engl 2018; 57:1954-1957. [DOI: 10.1002/anie.201709636] [Citation(s) in RCA: 30] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2017] [Revised: 12/11/2017] [Indexed: 12/20/2022]
Affiliation(s)
- Danyao Du
- 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
| | - Kazuo Shin-ya
- National Institute of Advanced Industrial Science and Technology (AIST); 2-4-7, Aomi Koto-ku Tokyo 135-0064 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
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Ma J, Huang H, Xie Y, Liu Z, Zhao J, Zhang C, Jia Y, Zhang Y, Zhang H, Zhang T, Ju J. Biosynthesis of ilamycins featuring unusual building blocks and engineered production of enhanced anti-tuberculosis agents. Nat Commun 2017; 8:391. [PMID: 28855504 PMCID: PMC5577134 DOI: 10.1038/s41467-017-00419-5] [Citation(s) in RCA: 76] [Impact Index Per Article: 10.9] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2017] [Accepted: 06/28/2017] [Indexed: 11/13/2022] Open
Abstract
Tuberculosis remains one of the world’s deadliest communicable diseases, novel anti-tuberculosis agents are urgently needed due to severe drug resistance and the co-epidemic of tuberculosis/human immunodeficiency virus. Here, we show the isolation of six anti-mycobacterial ilamycin congeners (1–6) bearing rare L-3-nitro-tyrosine and L-2-amino-4-hexenoic acid structural units from the deep sea-derived Streptomyces atratus SCSIO ZH16. The biosynthesis of the rare L-3-nitrotyrosine and L-2-amino-4-hexenoic acid units as well as three pre-tailoring and two post-tailoring steps are probed in the ilamycin biosynthetic machinery through a series of gene inactivation, precursor chemical complementation, isotope-labeled precursor feeding experiments, as well as structural elucidation of three intermediates (6–8) from the respective mutants. Most impressively, ilamycins E1/E2, which are produced in high titers by a genetically engineered mutant strain, show very potent anti-tuberculosis activity with an minimum inhibitory concentration value ≈9.8 nM to Mycobacterium tuberculosis H37Rv constituting extremely potent and exciting anti-tuberculosis drug leads. Tuberculosis (TB) remains one of the world’s deadliest communicable diseases, novel anti-TB agents are urgently needed due to severe drug resistance and the co-epidemic of TB/HIV. Here, the authors show that anti-mycobacterial ilamycin congeners bearing unusual structural units possess extremely potent anti-tuberculosis activities.
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Affiliation(s)
- Junying Ma
- 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, Guangzhou, 510301, China.
| | - Hongbo Huang
- 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, Guangzhou, 510301, China
| | - Yunchang Xie
- 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, Guangzhou, 510301, China
| | - Zhiyong Liu
- Tuberculosis Research Laboratory, State Key Laboratory of Respiratory Disease, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou, 510530, China
| | - Jin Zhao
- Guangdong Provincial Key Laboratory of Medical Molecular Diagnostics, Institute of Laboratory Medicine, Guangdong Medical University, Dongguan, 523808, China
| | - Chunyan 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, Guangzhou, 510301, China.,University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Yanxi Jia
- 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, Guangzhou, 510301, China.,University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Yun 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, Guangzhou, 510301, China
| | - Hua Zhang
- Guangdong Provincial Key Laboratory of Medical Molecular Diagnostics, Institute of Laboratory Medicine, Guangdong Medical University, Dongguan, 523808, China
| | - Tianyu Zhang
- Tuberculosis Research Laboratory, State Key Laboratory of Respiratory Disease, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou, 510530, 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, Guangzhou, 510301, China. .,University of Chinese Academy of Sciences, Beijing, 100049, China.
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39
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Tomita H, Katsuyama Y, Minami H, Ohnishi Y. Identification and characterization of a bacterial cytochrome P450 monooxygenase catalyzing the 3-nitration of tyrosine in rufomycin biosynthesis. J Biol Chem 2017; 292:15859-15869. [PMID: 28774961 DOI: 10.1074/jbc.m117.791269] [Citation(s) in RCA: 33] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2017] [Revised: 08/02/2017] [Indexed: 12/22/2022] Open
Abstract
Rufomycin is a circular heptapeptide with anti-mycobacterial activity and is produced by Streptomyces atratus ATCC 14046. Its structure contains three non-proteinogenic amino acids, N-dimethylallyltryptophan, trans-2-crotylglycine, and 3-nitrotyrosine (3NTyr). Although the rufomycin structure was already reported in the 1960s, its biosynthesis, including 3NTyr generation, remains unclear. To elucidate the rufomycin biosynthetic pathway, we assembled a draft genome sequence of S. atratus and identified the rufomycin biosynthetic gene cluster (ruf cluster), consisting of 20 ORFs (rufA-rufT). We found a putative heptamodular nonribosomal peptide synthetase encoded by rufT, a putative tryptophan N-dimethylallyltransferase encoded by rufP, and a putative trimodular type I polyketide synthase encoded by rufEF Moreover, the ruf cluster contains an apparent operon harboring putative cytochrome P450 (rufO) and nitric oxide synthase (rufN) genes. A similar operon, txtDE, is responsible for the formation of 4-nitrotryptophan in thaxtomin biosynthesis; the cytochrome P450 TxtE catalyzes the 4-nitration of Trp. Therefore, we hypothesized that RufO should catalyze the Tyr 3-nitration. Disruption of rufO abolished rufomycin production by S. atratus, which was restored when 3NTyr was added to the culture medium of the disruptant. Recombinant RufO protein exhibited Tyr 3-nitration activity both in vitro and in vivo Spectroscopic analysis further revealed that RufO recognizes Tyr as the substrate with a dissociation constant of ∼0.1 μm These results indicate that RufO is an unprecedented cytochrome P450 that catalyzes Tyr nitration. Taken together with the results of an in silico analysis of the ruf cluster, we propose a rufomycin biosynthetic pathway in S. atratus.
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Affiliation(s)
- Hiroya Tomita
- From the Department of Biotechnology, Graduate School of Agricultural and Life Sciences, The University of Tokyo, Bunkyo-ku, Tokyo 113-8657.,the Japan Science and Technology Agency (JST), CREST, 7, Gobancho, Chiyoda-ku, Tokyo 102-0076, and
| | - Yohei Katsuyama
- From the Department of Biotechnology, Graduate School of Agricultural and Life Sciences, The University of Tokyo, Bunkyo-ku, Tokyo 113-8657, .,the Japan Science and Technology Agency (JST), CREST, 7, Gobancho, Chiyoda-ku, Tokyo 102-0076, and
| | - Hiromichi Minami
- the Research Institute for Bioresources and Biotechnology, Ishikawa Prefectural University, 1-308, Suematsu, Nonoichi, Ishikawa 921-8836, Japan
| | - Yasuo Ohnishi
- From the Department of Biotechnology, Graduate School of Agricultural and Life Sciences, The University of Tokyo, Bunkyo-ku, Tokyo 113-8657, .,the Japan Science and Technology Agency (JST), CREST, 7, Gobancho, Chiyoda-ku, Tokyo 102-0076, and
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40
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Gao G, Liu X, Xu M, Wang Y, Zhang F, Xu L, Lv J, Long Q, Kang Q, Ou HY, Wang Y, Rohr J, Deng Z, Jiang M, Lin S, Tao M. Formation of an Angular Aromatic Polyketide from a Linear Anthrene Precursor via Oxidative Rearrangement. Cell Chem Biol 2017; 24:881-891.e4. [PMID: 28712746 DOI: 10.1016/j.chembiol.2017.06.008] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2017] [Revised: 04/28/2017] [Accepted: 06/16/2017] [Indexed: 12/24/2022]
Abstract
Bacterial aromatic polyketides are a group of natural products synthesized by polyketide synthases (PKSs) that show diverse structures and biological activities. They are structurally subclassified into linear, angular, and discoid aromatic polyketides, the formation of which is commonly determined by the shaping and folding of the poly-β-keto intermediates under the concerted actions of the minimal PKSs, cyclases and ketoreductases. Murayaquinone, found in several streptomycetes, possesses an unusual tricyclic angular aromatic polyketide core containing a 9,10-phenanthraquinone. In this study, genes essential for murayaquinone biosynthesis were identified, and a linear anthraoxirene intermediate was discovered. A unique biosynthetic model for the angular aromatic polyketide formation was discovered and confirmed through in vivo and in vitro studies. Three oxidoreductases, MrqO3, MrqO6, and MrqO7, were identified to catalyze the conversion of the linear aromatic polyketide intermediate into the final angularly arranged framework, which exemplifies a novel strategy for the biosynthesis of angular aromatic polyketides.
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Affiliation(s)
- Guixi Gao
- 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 200030, P. R. China
| | - Xiangyang Liu
- 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 200030, P. R. China
| | - Min Xu
- 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 200030, P. R. China
| | - Yemin 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 200030, P. R. China
| | - Fei Zhang
- 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 200030, P. R. China
| | - Lijun Xu
- 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 200030, P. R. China
| | - Jin Lv
- 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 200030, P. R. China
| | - Qingshan Long
- 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 200030, P. R. China
| | - Qianjin Kang
- 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 200030, P. R. China
| | - Hong-Yu Ou
- 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 200030, P. R. China
| | - Ying Wang
- Guangdong Province Key Laboratory of Pharmacodynamic Constituents of TCM and New Drugs Research, JNU-HKUST Joint Laboratory for Neuroscience and Innovative Drug Research, Jinan University, Guangzhou 510632, P. R. China
| | - Jürgen Rohr
- Department of Pharmaceutical Sciences, College of Pharmacy, University of Kentucky, Lexington, KY 40536, USA
| | - 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 200030, P. R. China
| | - Ming Jiang
- 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 200030, P. R. 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 200030, P. R. China.
| | - Meifeng Tao
- 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 200030, P. R. China.
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Ye S, Molloy B, Braña AF, Zabala D, Olano C, Cortés J, Morís F, Salas JA, Méndez C. Identification by Genome Mining of a Type I Polyketide Gene Cluster from Streptomyces argillaceus Involved in the Biosynthesis of Pyridine and Piperidine Alkaloids Argimycins P. Front Microbiol 2017; 8:194. [PMID: 28239372 PMCID: PMC5300972 DOI: 10.3389/fmicb.2017.00194] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2016] [Accepted: 01/26/2017] [Indexed: 12/21/2022] Open
Abstract
Genome mining of the mithramycin producer Streptomyces argillaceus ATCC 12956 revealed 31 gene clusters for the biosynthesis of secondary metabolites, and allowed to predict the encoded products for 11 of these clusters. Cluster 18 (renamed cluster arp) corresponded to a type I polyketide gene cluster related to the previously described coelimycin P1 and streptazone gene clusters. The arp cluster consists of fourteen genes, including genes coding for putative regulatory proteins (a SARP-like transcriptional activator and a TetR-like transcriptional repressor), genes coding for structural proteins (three PKSs, one aminotransferase, two dehydrogenases, two cyclases, one imine reductase, a type II thioesterase, and a flavin reductase), and one gene coding for a hypothetical protein. Identification of encoded compounds by this cluster was achieved by combining several strategies: (i) inactivation of the type I PKS gene arpPIII; (ii) inactivation of the putative TetR-transcriptional repressor arpRII; (iii) cultivation of strains in different production media; and (iv) using engineered strains with higher intracellular concentration of malonyl-CoA. This has allowed identifying six new alkaloid compounds named argimycins P, which were purified and structurally characterized by mass spectrometry and nuclear magnetic resonance spectroscopy. Some argimycins P showed a piperidine ring with a polyene side chain (argimycin PIX); others contain also a fused five-membered ring (argimycins PIV-PVI). Argimycins PI-PII showed a pyridine ring instead, and an additional N-acetylcysteinyl moiety. These compounds seem to play a negative role in growth and colony differentiation in S. argillaceus, and some of them show weak antibiotic activity. A pathway for the biosynthesis of argimycins P is proposed, based on the analysis of proposed enzyme functions and on the structure of compounds encoded by the arp cluster.
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Affiliation(s)
- Suhui Ye
- Departamento de Biología Funcional e Instituto Universitario de Oncología del Principado de Asturias, Universidad de Oviedo Oviedo, Spain
| | - Brian Molloy
- Departamento de Biología Funcional e Instituto Universitario de Oncología del Principado de Asturias, Universidad de Oviedo Oviedo, Spain
| | - Alfredo F Braña
- Departamento de Biología Funcional e Instituto Universitario de Oncología del Principado de Asturias, Universidad de Oviedo Oviedo, Spain
| | - Daniel Zabala
- Departamento de Biología Funcional e Instituto Universitario de Oncología del Principado de Asturias, Universidad de Oviedo Oviedo, Spain
| | - Carlos Olano
- Departamento de Biología Funcional e Instituto Universitario de Oncología del Principado de Asturias, Universidad de Oviedo Oviedo, Spain
| | | | | | - José A Salas
- Departamento de Biología Funcional e Instituto Universitario de Oncología del Principado de Asturias, Universidad de Oviedo Oviedo, Spain
| | - Carmen Méndez
- Departamento de Biología Funcional e Instituto Universitario de Oncología del Principado de Asturias, Universidad de Oviedo Oviedo, Spain
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Yurkovich ME, Jenkins R, Sun Y, Tosin M, Leadlay PF. The polyketide backbone of thiolactomycin is assembled by an unusual iterative polyketide synthase. Chem Commun (Camb) 2017; 53:2182-2185. [DOI: 10.1039/c6cc09934c] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Thiotetronate polyketide assembly by an unusual iterative synthase is reconstructed via in vitro enzymology and chemical probes.
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Affiliation(s)
| | | | - Yuhui Sun
- Key Laboratory of Combinatorial Biosynthesis and Drug Discovery (Wuhan University)
- Ministry of Education
- Wuhan University School of Pharmaceutical Sciences
- Wuhan 430071
- People's Republic of China
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Walther E, Boldt S, Kage H, Lauterbach T, Martin K, Roth M, Hertweck C, Sauerbrei A, Schmidtke M, Nett M. Zincophorin - biosynthesis in Streptomyces griseus and antibiotic properties. GMS INFECTIOUS DISEASES 2016; 4:Doc08. [PMID: 30671322 PMCID: PMC6301713 DOI: 10.3205/id000026] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Abstract
Zincophorin is a polyketide antibiotic that possesses potent activity against Gram-positive bacteria, including human pathogens. While a number of total syntheses of this highly functionalized natural product were reported since its initial discovery, the genetic basis for the biosynthesis of zincophorin has remained unclear. In this study, the co-linearity inherent to polyketide pathways was used to identify the zincophorin biosynthesis gene cluster in the genome of the natural producer Streptomyces griseus HKI 0741. Interestingly, the same locus is fully conserved in the streptomycin-producing actinomycete S. griseus IFO 13350, suggesting that the latter bacterium is also capable of zincophorin biosynthesis. Biological profiling of zincophorin revealed a dose-dependent inhibition of the Gram-positive bacterium Streptococcus pneumoniae. The antibacterial effect, however, is accompanied by cytotoxicity. Antibiotic and cytotoxic activities were completely abolished upon esterification of the carboxylic acid group in zincophorin.
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Affiliation(s)
- Elisabeth Walther
- Jena University Hospital, Department of Virology and Antiviral Therapy, Jena, Germany
| | - Sabrina Boldt
- Department of Biomolecular Chemistry, Leibniz Institute for Natural Product Research and Infection Biology, Hans Knöll Institute, Jena, Germany
| | - Hirokazu Kage
- Technical University Dortmund, Department of Biochemical and Chemical Engineering, Dortmund, Germany
| | - Tom Lauterbach
- Department of Biomolecular Chemistry, Leibniz Institute for Natural Product Research and Infection Biology, Hans Knöll Institute, Jena, Germany
| | - Karin Martin
- Bio Pilot Plant, Leibniz Institute for Natural Product Research and Infection Biology, Hans Knöll Institute, Jena, Germany
| | - Martin Roth
- Bio Pilot Plant, Leibniz Institute for Natural Product Research and Infection Biology, Hans Knöll Institute, Jena, Germany
| | - Christian Hertweck
- Department of Biomolecular Chemistry, Leibniz Institute for Natural Product Research and Infection Biology, Hans Knöll Institute, Jena, Germany
| | - Andreas Sauerbrei
- Jena University Hospital, Department of Virology and Antiviral Therapy, Jena, Germany
| | - Michaela Schmidtke
- Jena University Hospital, Department of Virology and Antiviral Therapy, Jena, Germany
| | - Markus Nett
- Technical University Dortmund, Department of Biochemical and Chemical Engineering, Dortmund, Germany
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The Draft Genome Sequence of Actinokineospora bangkokensis 44EHW T Reveals the Biosynthetic Pathway of the Antifungal Thailandin Compounds with Unusual Butylmalonyl-CoA Extender Units. Molecules 2016; 21:molecules21111607. [PMID: 27886115 PMCID: PMC6273641 DOI: 10.3390/molecules21111607] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2016] [Revised: 11/17/2016] [Accepted: 11/19/2016] [Indexed: 11/16/2022] Open
Abstract
We report the draft genome sequence of Actinokineospora bangkokensis 44EHWT, the producer of the antifungal polyene compounds, thailandins A and B. The sequence contains 7.45 Mb, 74.1% GC content and 35 putative gene clusters for the biosynthesis of secondary metabolites. There are three gene clusters encoding large polyketide synthases of type I. Annotation of the ORF functions and targeted gene disruption enabled us to identify the cluster for thailandin biosynthesis. We propose a plausible biosynthetic pathway for thailandin, where the unusual butylmalonyl-CoA extender unit is incorporated and results in an untypical side chain.
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Hong H, Sun Y, Zhou Y, Stephens E, Samborskyy M, Leadlay PF. Evidence for an iterative module in chain elongation on the azalomycin polyketide synthase. Beilstein J Org Chem 2016; 12:2164-2172. [PMID: 27829923 PMCID: PMC5082578 DOI: 10.3762/bjoc.12.206] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2016] [Accepted: 09/23/2016] [Indexed: 11/28/2022] Open
Abstract
The assembly-line synthases that produce bacterial polyketide natural products follow a modular paradigm in which each round of chain extension is catalysed by a different set or module of enzymes. Examples of deviation from this paradigm, in which a module catalyses either multiple extensions or none are of interest from both a mechanistic and an evolutionary viewpoint. We present evidence that in the biosynthesis of the 36-membered macrocyclic aminopolyol lactones (marginolactones) azalomycin and kanchanamycin, isolated respectively from Streptomyces malaysiensis DSM4137 and Streptomyces olivaceus Tü4018, the first extension module catalyses both the first and second cycles of polyketide chain extension. To confirm the integrity of the azl gene cluster, it was cloned intact on a bacterial artificial chromosome and transplanted into the heterologous host strain Streptomyces lividans, which does not possess the genes for marginolactone production. When furnished with 4-guanidinobutyramide, a specific precursor of the azalomycin starter unit, the recombinant S. lividans produced azalomycin, showing that the polyketide synthase genes in the sequenced cluster are sufficient to accomplish formation of the full-length polyketide chain. This provides strong support for module iteration in the azalomycin and kanchanamycin biosynthetic pathways. In contrast, re-sequencing of the gene cluster for biosynthesis of the polyketide β-lactone ebelactone in Streptomyces aburaviensis has shown that, contrary to a recently-published proposal, the ebelactone polyketide synthase faithfully follows the colinear modular paradigm.
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Affiliation(s)
- Hui Hong
- Department of Biochemistry, University of Cambridge, 80 Tennis Court Road, Cambridge, CB2 1GA, United Kingdom
| | - Yuhui Sun
- Key Laboratory of Combinatorial Biosynthesis and Drug Discovery, Wuhan University, Ministry of Education, and Wuhan University School of Pharmaceutical Sciences, Wuhan 430071, People’s Republic of China
| | - Yongjun Zhou
- Department of Biochemistry, University of Cambridge, 80 Tennis Court Road, Cambridge, CB2 1GA, United Kingdom
| | - Emily Stephens
- Department of Biochemistry, University of Cambridge, 80 Tennis Court Road, Cambridge, CB2 1GA, United Kingdom
| | - Markiyan Samborskyy
- Department of Biochemistry, University of Cambridge, 80 Tennis Court Road, Cambridge, CB2 1GA, United Kingdom
| | - Peter F Leadlay
- Department of Biochemistry, University of Cambridge, 80 Tennis Court Road, Cambridge, CB2 1GA, United Kingdom
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46
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Tautz T, Hoffmann J, Hoffmann T, Steinmetz H, Washausen P, Kunze B, Huch V, Kitsche A, Reichenbach H, Höfle G, Müller R, Kalesse M. Isolation, Structure Elucidation, Biosynthesis, and Synthesis of Antalid, a Secondary Metabolite from Polyangium species. Org Lett 2016; 18:2560-3. [DOI: 10.1021/acs.orglett.6b00810] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Thomas Tautz
- Institute
for Organic Chemistry, Leibniz Universität Hannover, Schneiderberg
1B, D-30167 Hannover, Germany
| | - Judith Hoffmann
- Helmholtz
Institute for Pharmaceutical Research Saarland, Helmholtz Centre for
Infection Research and Department of Pharmaceutical Biotechnology, Saarland University, Building E8.1, D-66123 Saarbrücken, Germany
| | - Thomas Hoffmann
- Helmholtz
Institute for Pharmaceutical Research Saarland, Helmholtz Centre for
Infection Research and Department of Pharmaceutical Biotechnology, Saarland University, Building E8.1, D-66123 Saarbrücken, Germany
| | - Heinrich Steinmetz
- Helmholtz Centre for Infection Research (HZI), Inhoffenstr. 7, D-38124 Braunschweig, Germany
| | - Peter Washausen
- Helmholtz Centre for Infection Research (HZI), Inhoffenstr. 7, D-38124 Braunschweig, Germany
| | - Brigitte Kunze
- Helmholtz Centre for Infection Research (HZI), Inhoffenstr. 7, D-38124 Braunschweig, Germany
| | - Volker Huch
- Institute
for Inorganic Chemistry, Saarland University, Building B2.2, D-66123 Saarbrücken, Germany
| | - Andreas Kitsche
- Institute
for Biostatistics, Leibniz Universität Hannover, Herrenhäuser
Straße 2, D-30419 Hannover, Germany
| | - Hans Reichenbach
- Helmholtz Centre for Infection Research (HZI), Inhoffenstr. 7, D-38124 Braunschweig, Germany
| | - Gerhard Höfle
- Helmholtz Centre for Infection Research (HZI), Inhoffenstr. 7, D-38124 Braunschweig, Germany
| | - Rolf Müller
- Helmholtz
Institute for Pharmaceutical Research Saarland, Helmholtz Centre for
Infection Research and Department of Pharmaceutical Biotechnology, Saarland University, Building E8.1, D-66123 Saarbrücken, Germany
| | - Markus Kalesse
- Institute
for Organic Chemistry, Leibniz Universität Hannover, Schneiderberg
1B, D-30167 Hannover, Germany
- Helmholtz Centre for Infection Research (HZI), Inhoffenstr. 7, D-38124 Braunschweig, Germany
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47
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Salcedo RG, Olano C, Gómez C, Fernández R, Braña AF, Méndez C, de la Calle F, Salas JA. Characterization and engineering of the biosynthesis gene cluster for antitumor macrolides PM100117 and PM100118 from a marine actinobacteria: generation of a novel improved derivative. Microb Cell Fact 2016; 15:44. [PMID: 26905289 PMCID: PMC4763440 DOI: 10.1186/s12934-016-0443-5] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2015] [Accepted: 02/11/2016] [Indexed: 12/28/2022] Open
Abstract
BACKGROUND PM100117 and PM100118 are glycosylated polyketides with remarkable antitumor activity, which derive from the marine symbiotic actinobacteria Streptomyces caniferus GUA-06-05-006A. Structurally, PM100117 and PM100118 are composed of a macrocyclic lactone, three deoxysugar units and a naphthoquinone (NQ) chromophore that shows a clear structural similarity to menaquinone. RESULTS Whole-genome sequencing of S. caniferus GUA-06-05-006A has enabled the identification of PM100117 and PM100118 biosynthesis gene cluster, which has been characterized on the basis of bioinformatics and genetic engineering data. The product of four genes shows high identity to proteins involved in the biosynthesis of menaquinone via futalosine. Deletion of one of these genes led to a decay in PM100117 and PM100118 production, and to the accumulation of several derivatives lacking NQ. Likewise, five additional genes have been genetically characterized to be involved in the biosynthesis of this moiety. Moreover, the generation of a mutant in a gene coding for a putative cytochrome P450 has led to the production of PM100117 and PM100118 structural analogues showing an enhanced in vitro cytotoxic activity relative to the parental products. CONCLUSIONS Although a number of compounds structurally related to PM100117 and PM100118 has been discovered, this is, to our knowledge, the first insight reported into their biosynthesis. The structural resemblance of the NQ moiety to menaquinone, and the presence in the cluster of four putative menaquinone biosynthetic genes, suggests a connection between the biosynthesis pathways of both compounds. The availability of the PM100117 and PM100118 biosynthetic gene cluster will surely pave a way to the combinatorial engineering of more derivatives.
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Affiliation(s)
- Raúl García Salcedo
- Departamento de Biología Funcional e Instituto Universitario de Oncología del Principado de Asturias (I.U.O.P.A), Universidad de Oviedo, 33006, Oviedo, Asturias, 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, Asturias, Spain.
| | - Cristina Gómez
- Departamento de Biología Funcional e Instituto Universitario de Oncología del Principado de Asturias (I.U.O.P.A), Universidad de Oviedo, 33006, Oviedo, Asturias, Spain.
| | - Rogelio Fernández
- Drug Discovery Area, PharmaMar SA, Avda. de los Reyes 1, Colmenar Viejo, 28770, Madrid, Spain.
| | - Alfredo F Braña
- Departamento de Biología Funcional e Instituto Universitario de Oncología del Principado de Asturias (I.U.O.P.A), Universidad de Oviedo, 33006, Oviedo, Asturias, Spain.
| | - 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, Asturias, Spain.
| | - Fernando de la Calle
- Drug Discovery Area, PharmaMar SA, Avda. de los Reyes 1, Colmenar Viejo, 28770, Madrid, Spain.
| | - 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, Asturias, Spain.
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48
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Chiu HT, Weng CP, Lin YC, Chen KH. Target-specific identification and characterization of the putative gene cluster for brasilinolide biosynthesis revealing the mechanistic insights and combinatorial synthetic utility of 2-deoxy-l-fucose biosynthetic enzymes. Org Biomol Chem 2016; 14:1988-2006. [DOI: 10.1039/c5ob02292d] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
From Nocardia was cloned and functionally characterized a giant gene cluster for biosyntheses of brasilinolides as potent immunosuppressive and anticancer agents.
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Affiliation(s)
- Hsien-Tai Chiu
- Department of Chemistry
- National Cheng Kung University
- Tainan 701
- Taiwan
| | - Chien-Pao Weng
- Department of Chemistry
- National Cheng Kung University
- Tainan 701
- Taiwan
| | - Yu-Chin Lin
- Department of Chemistry
- National Cheng Kung University
- Tainan 701
- Taiwan
- Department of Biological Science and Technology
| | - Kuan-Hung Chen
- Department of Biological Science and Technology
- National Chiao Tung University
- Hsinchu 300
- Taiwan
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49
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Tao W, Yurkovich ME, Wen S, Lebe KE, Samborskyy M, Liu Y, Yang A, Liu Y, Ju Y, Deng Z, Tosin M, Sun Y, Leadlay PF. A genomics-led approach to deciphering the mechanism of thiotetronate antibiotic biosynthesis. Chem Sci 2016; 7:376-385. [PMID: 28791099 PMCID: PMC5518548 DOI: 10.1039/c5sc03059e] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2015] [Accepted: 10/06/2015] [Indexed: 12/31/2022] Open
Abstract
Thiolactomycin (TLM) is a thiotetronate antibiotic that selectively targets bacterial fatty acid biosynthesis through inhibition of the β-ketoacyl-acyl carrier protein synthases (KASI/II) that catalyse chain elongation on the type II (dissociated) fatty acid synthase. It has proved effective in in vivo infection models of Mycobacterium tuberculosis and continues to attract interest as a template for drug discovery. We have used a comparative genomics approach to uncover the (hitherto elusive) biosynthetic pathway to TLM and related thiotetronates. Analysis of the whole-genome sequence of Streptomyces olivaceus Tü 3010 producing the more ramified thiotetronate Tü 3010 provided initial evidence that such thiotetronates are assembled by a novel iterative polyketide synthase-nonribosomal peptide synthetase, and revealed the identity of other pathway enzymes, encoded by adjacent genes. Subsequent genome sequencing of three other thiotetronate-producing actinomycetes, including the Lentzea sp. ATCC 31319 that produces TLM, confirmed that near-identical clusters were also present in these genomes. In-frame gene deletion within the cluster for Tü 3010 from Streptomyces thiolactonus NRRL 15439, or within the TLM cluster, led to loss of production of the respective thiotetronate, confirming their identity. Each cluster houses at least one gene encoding a KASI/II enzyme, suggesting plausible mechanisms for self-resistance. A separate genetic locus encodes a cysteine desulfurase and a (thiouridylase-like) sulfur transferase to supply the sulfur atom for thiotetronate ring formation. Transfer of the main Tü 3010 gene cluster (stu gene cluster) into Streptomyces avermitilis led to heterologous production of this thiotetronate, showing that an equivalent sulfur donor can be supplied by this host strain. Mutational analysis of the Tü 3010 and TLM clusters has revealed the unexpected role of a cytochrome P450 enzyme in thiotetronate ring formation. These insights have allowed us to propose a mechanism for sulfur insertion, and have opened the way to engineering of the biosynthesis of TLM and other thiotetronates to produce novel analogues.
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Affiliation(s)
- W Tao
- Key Laboratory of Combinatorial Biosynthesis and Drug Discovery (Wuhan University) , Ministry of Education , Wuhan University School of Pharmaceutical Sciences , Wuhan 430071 , People's Republic of China .
| | - M E Yurkovich
- Department of Biochemistry , University of Cambridge , Sanger Building, 80 Tennis Court Road , Cambridge CB2 1GA , UK .
| | - S Wen
- Key Laboratory of Combinatorial Biosynthesis and Drug Discovery (Wuhan University) , Ministry of Education , Wuhan University School of Pharmaceutical Sciences , Wuhan 430071 , People's Republic of China .
| | - K E Lebe
- Department of Biochemistry , University of Cambridge , Sanger Building, 80 Tennis Court Road , Cambridge CB2 1GA , UK .
| | - M Samborskyy
- Department of Biochemistry , University of Cambridge , Sanger Building, 80 Tennis Court Road , Cambridge CB2 1GA , UK .
| | - Y Liu
- Key Laboratory of Combinatorial Biosynthesis and Drug Discovery (Wuhan University) , Ministry of Education , Wuhan University School of Pharmaceutical Sciences , Wuhan 430071 , People's Republic of China .
| | - A Yang
- Key Laboratory of Combinatorial Biosynthesis and Drug Discovery (Wuhan University) , Ministry of Education , Wuhan University School of Pharmaceutical Sciences , Wuhan 430071 , People's Republic of China .
| | - Y Liu
- Key Laboratory of Combinatorial Biosynthesis and Drug Discovery (Wuhan University) , Ministry of Education , Wuhan University School of Pharmaceutical Sciences , Wuhan 430071 , People's Republic of China .
| | - Y Ju
- Key Laboratory of Combinatorial Biosynthesis and Drug Discovery (Wuhan University) , Ministry of Education , Wuhan University School of Pharmaceutical Sciences , Wuhan 430071 , People's Republic of China .
| | - Z Deng
- Key Laboratory of Combinatorial Biosynthesis and Drug Discovery (Wuhan University) , Ministry of Education , Wuhan University School of Pharmaceutical Sciences , Wuhan 430071 , People's Republic of China .
| | - M Tosin
- Department of Chemistry , University of Warwick , Library Road , Coventry CV4 7AL , UK
| | - Y Sun
- Key Laboratory of Combinatorial Biosynthesis and Drug Discovery (Wuhan University) , Ministry of Education , Wuhan University School of Pharmaceutical Sciences , Wuhan 430071 , People's Republic of China .
| | - P F Leadlay
- Department of Biochemistry , University of Cambridge , Sanger Building, 80 Tennis Court Road , Cambridge CB2 1GA , UK .
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50
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Sheng Y, Lam PW, Shahab S, Santosa DA, Proteau PJ, Zabriskie TM, Mahmud T. Identification of Elaiophylin Skeletal Variants from the Indonesian Streptomyces sp. ICBB 9297. JOURNAL OF NATURAL PRODUCTS 2015; 78:2768-2775. [PMID: 26510047 DOI: 10.1021/acs.jnatprod.5b00752] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/05/2023]
Abstract
Four new elaiophylin macrolides (1-4), together with five known elaiophylins (5-9), have been isolated from cultures of the Indonesian soil bacterium Streptomyces sp. ICBB 9297. The new compounds have macrocyclic skeletons distinct from those of the known dimeric elaiophylins in that one or both of the polyketide chains contain(s) an additional pendant methyl group. Further investigations revealed that 1 and 2 were derived from 3 and 4, respectively, during isolation processes. Compounds 1-3 showed comparable antibacterial activity to elaiophylin against Staphylococcus aureus. However, interestingly, only compounds 1 and 3, which contain a pendant methyl group at C-2, showed activity against Mycobacterium smegmatis, whereas compound 2, which has two pendant methyl groups at C-2 and C-2', and the known elaiophylin analogues (5-7), which lack pendant methyl groups at C-2 and/or C-2', showed no activity. The production of 3 and 4 in strain ICBB 9297 indicates that one of the acyltransferase (AT) domains in the elaiophylin polyketide synthases (PKSs) can recruit both malonyl-CoA and methylmalonyl-CoA as substrates. Bioinformatic analysis of the AT domains of the elaiophylin PKSs revealed that the ela_AT7 domain contains atypical active site amino acid residues, distinct from those conserved in malonyl-CoA- or methylmalonyl-CoA-specific ATs.
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Affiliation(s)
- Yan Sheng
- Department of Pharmaceutical Sciences, College of Pharmacy, Oregon State University , Corvallis, Oregon 97331-3507, United States
| | - Phillip W Lam
- Department of Pharmaceutical Sciences, College of Pharmacy, Oregon State University , Corvallis, Oregon 97331-3507, United States
| | - Salmah Shahab
- Indonesian Center for Biodiversity and Biotechnology , ICBB-Complex, JI. Cilubang Nagrak No. 62, Situgede, Bogor 16115, Indonesia
| | - Dwi Andreas Santosa
- Indonesian Center for Biodiversity and Biotechnology , ICBB-Complex, JI. Cilubang Nagrak No. 62, Situgede, Bogor 16115, Indonesia
- Department of Soil Science and Land Resources, Faculty of Agriculture, Bogor Agricultural University , Bogor, Indonesia
| | - Philip J Proteau
- Department of Pharmaceutical Sciences, College of Pharmacy, Oregon State University , Corvallis, Oregon 97331-3507, United States
| | - T Mark Zabriskie
- Department of Pharmaceutical Sciences, College of Pharmacy, Oregon State University , Corvallis, Oregon 97331-3507, United States
| | - Taifo Mahmud
- Department of Pharmaceutical Sciences, College of Pharmacy, Oregon State University , Corvallis, Oregon 97331-3507, United States
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