51
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Al-Dhelaan R, Russo PS, Padden SE, Amaya A, Dong DW, You YO. Condensation-Incompetent Ketosynthase Inhibits trans-Acyltransferase Activity. ACS Chem Biol 2019; 14:304-312. [PMID: 30642162 DOI: 10.1021/acschembio.8b01043] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Nonelongating modules with condensation-incompetent ketosynthase (KS0) are frequently found in many trans-acyltransferase polyketide synthases ( trans-AT PKS). KS0 catalyzes translocation of carbon chain without decarboxylative condensation. Unlike typical elongating modules where malonylation of acyl carrier protein (ACP) precedes elongation, the malonylation of ACP downstream of KS0 is assumed to be prevented. In this study, the regulation mechanism(s) of ACP malonylation in a non-elongating module of difficidin biosynthase was investigated. In vitro reconstitution, protein mass spectrometry, and enzyme kinetics demonstrated that KS0 controls the pathway by inhibiting the trans-AT activity. Protein-protein interactions of the surrounding domains also contribute to the regulation. Enzyme kinetics further identified the DfnKS05 as an allosteric inhibitor of trans-AT. The principle and knowledge discovered from this study will enhance the understanding of this unusual PKS system.
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Affiliation(s)
- Reham Al-Dhelaan
- Department of Chemistry and Biochemistry , George Mason University , Fairfax , Virginia 22030 , United States
| | | | - Sean E Padden
- Department of Chemistry and Biochemistry , George Mason University , Fairfax , Virginia 22030 , United States
| | - Anthony Amaya
- Department of Chemistry and Biochemistry , George Mason University , Fairfax , Virginia 22030 , United States
| | | | - Young-Ok You
- Department of Chemistry and Biochemistry , George Mason University , Fairfax , Virginia 22030 , United States
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52
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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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53
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Skiba MA, Bivins MM, Schultz JR, Bernard SM, Fiers WD, Dan Q, Kulkarni S, Wipf P, Gerwick WH, Sherman DH, Aldrich CC, Smitha JL. Structural Basis of Polyketide Synthase O-Methylation. ACS Chem Biol 2018; 13:3221-3228. [PMID: 30489068 PMCID: PMC6470024 DOI: 10.1021/acschembio.8b00687] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Abstract
Modular type I polyketide synthases (PKSs) produce some of the most chemically complex metabolites in nature through a series of multienzyme modules. Each module contains a variety of catalytic domains to selectively tailor the growing molecule. PKS O-methyltransferases ( O-MTs) are predicted to methylate β-hydroxyl or β-keto groups, but their activity and structure have not been reported. We determined the domain boundaries and characterized the catalytic activity and structure of the StiD and StiE O-MTs, which methylate opposite β-hydroxyl stereocenters in the myxobacterial stigmatellin biosynthetic pathway. Substrate stereospecificity was demonstrated for the StiD O-MT. Key catalytic residues were identified in the crystal structures and investigated in StiE O-MT via site-directed mutagenesis and further validated with the cyanobacterial CurL O-MT from the curacin biosynthetic pathway. Initial structural and biochemical analysis of PKS O-MTs supplies a new chemoenzymatic tool, with the unique ability to selectively modify hydroxyl groups during polyketide biosynthesis.
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Affiliation(s)
- Meredith A. Skiba
- Life Sciences Institute, University of Michigan, Ann Arbor, MI, 48109, United States
- Department of Biological Chemistry, University of Michigan, Ann Arbor, MI, 48109, United States
| | - Marissa M. Bivins
- Life Sciences Institute, University of Michigan, Ann Arbor, MI, 48109, United States
| | - John R. Schultz
- Department of Medicinal Chemistry, University of Minnesota, Minneapolis, MN, 55455, United States
| | - Steffen M. Bernard
- Life Sciences Institute, University of Michigan, Ann Arbor, MI, 48109, United States
- Chemical Biology Doctoral Program, University of Michigan, Ann Arbor, MI, 48109, United States
| | - William D. Fiers
- Department of Medicinal Chemistry, University of Minnesota, Minneapolis, MN, 55455, United States
| | - Qingyun Dan
- Life Sciences Institute, University of Michigan, Ann Arbor, MI, 48109, United States
| | - Sarang Kulkarni
- Department of Chemistry, University of Pittsburgh, Pittsburgh, PA, 15206, United States
| | - Peter Wipf
- Department of Chemistry, University of Pittsburgh, Pittsburgh, PA, 15206, United States
| | - William H. Gerwick
- Center for Marine Biotechnology and Biomedicine, Scripps Institution of Oceanography, University of California San Diego, La Jolla, CA, 92093, United States
- Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California San Diego, La Jolla, CA, 92093, United States
| | - David H. Sherman
- Life Sciences Institute, University of Michigan, Ann Arbor, MI, 48109, United States
- Department of Medicinal Chemistry, University of Michigan, Ann Arbor, MI, 48109, United States
- Department of Chemistry, University of Michigan, Ann Arbor, MI, 48109, United States
- Department of Microbiology and Immunology, University of Michigan, Ann Arbor, MI, 48109, United States
| | - Courtney C. Aldrich
- Department of Medicinal Chemistry, University of Minnesota, Minneapolis, MN, 55455, United States
| | - Janet L. Smitha
- Life Sciences Institute, University of Michigan, Ann Arbor, MI, 48109, United States
- Department of Biological Chemistry, University of Michigan, Ann Arbor, MI, 48109, United States
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54
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Moss NA, Leão T, Rankin MR, McCullough TM, Qu P, Korobeynikov A, Smith JL, Gerwick L, Gerwick WH. Ketoreductase Domain Dysfunction Expands Chemodiversity: Malyngamide Biosynthesis in the Cyanobacterium Okeania hirsuta. ACS Chem Biol 2018; 13:3385-3395. [PMID: 30444349 DOI: 10.1021/acschembio.8b00910] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
Dozens of type A malyngamides, principally identified by a decorated six-membered cyclohexanone headgroup and methoxylated lyngbic acid tail, have been isolated over several decades. Their environmental sources include macro- and microbiotic organisms, including sea hares, red alga, and cyanobacterial assemblages, but the true producing organism has remained enigmatic. Many type A analogues display potent bioactivity in human-health related assays, spurring an interest in this molecular class and its biosynthetic pathway. Here, we present the discovery of the type A malyngamide biosynthetic pathway in the first sequenced genome of the cyanobacterial genus Okeania. Bioinformatic analysis of two cultured Okeania genome assemblies identified 62 and 68 kb polyketide synthase/nonribosomal peptide synthetase (PKS/NRPS) pathways with unusual loading and termination genes. NMR data of malyngamide C acetate derived from 13C-substrate-fed cultures provided evidence that an intact octanoate moiety is transferred to the first KS module via a LipM homologue originally associated with lipoic acid metabolism and implicated an inactive ketoreductase (KR0) as critical for six-membered ring formation, a hallmark of the malyngamide family. Phylogenetic analysis and homology modeling of the penultimate KR0 domain inferred structural cofactor binding and active site alterations as contributory to domain dysfunction, which was confirmed by recombinant protein expression and NADPH binding assay. The carbonyl retained from this KR0 ultimately enables an intramolecular Knoevenagel condensation to form the characteristic cyclohexanone ring. Understanding this critical step allows assignment of a biosynthetic model for all type A malyngamides, whereby well-characterized tailoring modifications explain the surprising proliferation and diversity of analogues.
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Affiliation(s)
- Nathan A. Moss
- Center for Marine Biotechnology and Biomedicine, Scripps Institution of Oceanography, University of California, San Diego, 9500 Gilman Drive, La Jolla, California 92093, United States
| | - Tiago Leão
- Center for Marine Biotechnology and Biomedicine, Scripps Institution of Oceanography, University of California, San Diego, 9500 Gilman Drive, La Jolla, California 92093, United States
| | - Michael R. Rankin
- Department of Biological Chemistry, Life Sciences Institute, University of Michigan, 210 Washtenaw Avenue, Ann Arbor, Michigan 48109, United States
| | - Tyler M. McCullough
- Department of Biological Chemistry, Life Sciences Institute, University of Michigan, 210 Washtenaw Avenue, Ann Arbor, Michigan 48109, United States
| | - Pingping Qu
- Department of Biological Sciences, University of Southern California, 3616 Trousdale Parkway, Los Angeles, California 90089, United States
| | - Anton Korobeynikov
- Center for Algorithmic Biotechnology, St. Petersburg State University, Saint Petersburg 198504, Russia
| | - Janet L. Smith
- Department of Biological Chemistry, Life Sciences Institute, University of Michigan, 210 Washtenaw Avenue, Ann Arbor, Michigan 48109, United States
| | - Lena Gerwick
- Center for Marine Biotechnology and Biomedicine, Scripps Institution of Oceanography, University of California, San Diego, 9500 Gilman Drive, La Jolla, California 92093, United States
| | - William H. Gerwick
- Center for Marine Biotechnology and Biomedicine, Scripps Institution of Oceanography, University of California, San Diego, 9500 Gilman Drive, La Jolla, California 92093, United States
- Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California, San Diego, 9500 Gilman Drive, La Jolla, California 92093, United States
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55
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Hashimoto T, Hashimoto J, Kozone I, Amagai K, Kawahara T, Takahashi S, Ikeda H, Shin-ya K. Biosynthesis of Quinolidomicin, the Largest Known Macrolide of Terrestrial Origin: Identification and Heterologous Expression of a Biosynthetic Gene Cluster over 200 kb. Org Lett 2018; 20:7996-7999. [DOI: 10.1021/acs.orglett.8b03570] [Citation(s) in RCA: 25] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Affiliation(s)
- Takuya Hashimoto
- National Institute of Advanced Industrial Science and Technology, 2-4-7 Aomi, Koto-ku, Tokyo 135-0064, Japan
| | - Junko Hashimoto
- Japan Biological Informatics Consortium, 2-4-7 Aomi, Koto-ku, Tokyo 135-0064, Japan
| | - Ikuko Kozone
- Japan Biological Informatics Consortium, 2-4-7 Aomi, Koto-ku, Tokyo 135-0064, Japan
| | - Keita Amagai
- Technology Research Association for Next Generation Natural Products Chemistry, 2-4-7 Aomi, Koto-ku, Tokyo 135-0064, Japan
- RIKEN Center for Sustainable Resource Science, Natural Product Biosynthesis Research Unit, 2-1 Hirosawa, Wako, Saitama 351-0198, Japan
| | - Teppei Kawahara
- Japan Biological Informatics Consortium, 2-4-7 Aomi, Koto-ku, Tokyo 135-0064, Japan
| | - Shunji Takahashi
- RIKEN Center for Sustainable Resource Science, Natural Product Biosynthesis Research Unit, 2-1 Hirosawa, Wako, Saitama 351-0198, Japan
| | - Haruo Ikeda
- Kitasato Institute for Life Sciences, Kitasato University, 1-15-1 Kitasato, Minami-ku, Sagamihara, Kanagawa 252-0373, Japan
| | - Kazuo Shin-ya
- National Institute of Advanced Industrial Science and Technology, 2-4-7 Aomi, Koto-ku, Tokyo 135-0064, Japan
- The Biotechnology Research Center, The University of Tokyo, 1-1-1 Yayoi, Bunkyo-ku, Tokyo 113-8657, Japan
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56
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Son S, Hong YS, Futamura Y, Jang M, Lee JK, Heo KT, Ko SK, Lee JS, Takahashi S, Osada H, Jang JH, Ahn JS. Catenulisporolides, Glycosylated Triene Macrolides from the Chemically Underexploited Actinomycete Catenulispora Species. Org Lett 2018; 20:7234-7238. [DOI: 10.1021/acs.orglett.8b03160] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
Affiliation(s)
- Sangkeun Son
- Anticancer Agent Research Center, Korea Research Institute of Bioscience and Biotechnology, Cheongju 28116, Korea
| | - Young-Soo Hong
- Anticancer Agent Research Center, Korea Research Institute of Bioscience and Biotechnology, Cheongju 28116, Korea
- Department of Biomolecular Science, KRIBB School of Bioscience, Korea University of Science and Technology, Daejeon 34113, Korea
| | - Yushi Futamura
- Chemical Biology Research Group, RIKEN Center for Sustainable Research Science, Saitama 351-0198, Japan
| | - Mina Jang
- Anticancer Agent Research Center, Korea Research Institute of Bioscience and Biotechnology, Cheongju 28116, Korea
- Department of Biomolecular Science, KRIBB School of Bioscience, Korea University of Science and Technology, Daejeon 34113, Korea
| | - Jae Kyoung Lee
- Anticancer Agent Research Center, Korea Research Institute of Bioscience and Biotechnology, Cheongju 28116, Korea
| | - Kyung Taek Heo
- Anticancer Agent Research Center, Korea Research Institute of Bioscience and Biotechnology, Cheongju 28116, Korea
- Department of Biomolecular Science, KRIBB School of Bioscience, Korea University of Science and Technology, Daejeon 34113, Korea
| | - Sung-Kyun Ko
- Anticancer Agent Research Center, Korea Research Institute of Bioscience and Biotechnology, Cheongju 28116, Korea
- Department of Biomolecular Science, KRIBB School of Bioscience, Korea University of Science and Technology, Daejeon 34113, Korea
| | - Jung Sook Lee
- Korean Collection for Type Cultures, Korea Research Institute of Bioscience and Biotechnology, Jeongeup 56212, Korea
| | - Shunji Takahashi
- RIKEN-KRIBB Joint Research Unit, RIKEN Center for Sustainable Research Science, Saitama 351-0198, Japan
| | - Hiroyuki Osada
- Chemical Biology Research Group, RIKEN Center for Sustainable Research Science, Saitama 351-0198, Japan
| | - Jae-Hyuk Jang
- Anticancer Agent Research Center, Korea Research Institute of Bioscience and Biotechnology, Cheongju 28116, Korea
- Department of Biomolecular Science, KRIBB School of Bioscience, Korea University of Science and Technology, Daejeon 34113, Korea
| | - Jong Seog Ahn
- Anticancer Agent Research Center, Korea Research Institute of Bioscience and Biotechnology, Cheongju 28116, Korea
- Department of Biomolecular Science, KRIBB School of Bioscience, Korea University of Science and Technology, Daejeon 34113, Korea
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57
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Shin D, Byun WS, Moon K, Kwon Y, Bae M, Um S, Lee SK, Oh DC. Coculture of Marine Streptomyces sp. With Bacillus sp. Produces a New Piperazic Acid-Bearing Cyclic Peptide. Front Chem 2018; 6:498. [PMID: 30406080 PMCID: PMC6201156 DOI: 10.3389/fchem.2018.00498] [Citation(s) in RCA: 44] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2018] [Accepted: 10/01/2018] [Indexed: 11/30/2022] Open
Abstract
Microbial culture conditions in the laboratory, which conventionally involve the cultivation of one strain in one culture vessel, are vastly different from natural microbial environments. Even though perfectly mimicking natural microbial interactions is virtually impossible, the cocultivation of multiple microbial strains is a reasonable strategy to induce the production of secondary metabolites, which enables the discovery of new bioactive natural products. Our coculture of marine Streptomyces and Bacillus strains isolated together from an intertidal mudflat led to discover a new metabolite, dentigerumycin E (1). Dentigerumycin E was determined to be a new cyclic hexapeptide incorporating three piperazic acids, N-OH-Thr, N-OH-Gly, β-OH-Leu, and a pyran-bearing polyketide acyl chain mainly by analysis of its NMR and MS spectroscopic data. The putative PKS-NRPS biosynthetic gene cluster for dentigerumycin E was found in the Streptomyces strain, providing clear evidence that this cyclic peptide is produced by the Streptomyces strain. The absolute configuration of dentigerumycin E was established based on the advanced Marfey's method, ROESY NMR correlations, and analysis of the amino acid sequence of the ketoreductase domain in the biosynthetic gene cluster. In biological evaluation of dentigerumycin E (1) and its chemical derivatives [2-N,16-N-deoxydenteigerumycin E (2) and dentigerumycin methyl ester (3)], only dentigerumycin E exhibited antiproliferative and antimetastatic activities against human cancer cells, indicating that N-OH and carboxylic acid functional groups are essential for the biological activity.
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Affiliation(s)
- Daniel Shin
- Natural Products Research Institute, College of Pharmacy, Seoul National University, Seoul, South Korea
| | - Woong Sub Byun
- Natural Products Research Institute, College of Pharmacy, Seoul National University, Seoul, South Korea
| | - Kyuho Moon
- Natural Products Research Institute, College of Pharmacy, Seoul National University, Seoul, South Korea
| | - Yun Kwon
- Natural Products Research Institute, College of Pharmacy, Seoul National University, Seoul, South Korea
| | - Munhyung Bae
- Natural Products Research Institute, College of Pharmacy, Seoul National University, Seoul, South Korea
| | - Soohyun Um
- Natural Products Research Institute, College of Pharmacy, Seoul National University, Seoul, South Korea
| | - Sang Kook Lee
- Natural Products Research Institute, College of Pharmacy, Seoul National University, Seoul, South Korea
| | - Dong-Chan Oh
- Natural Products Research Institute, College of Pharmacy, Seoul National University, Seoul, South Korea
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58
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Dodge GJ, Ronnow D, Taylor RE, Smith JL. Molecular Basis for Olefin Rearrangement in the Gephyronic Acid Polyketide Synthase. ACS Chem Biol 2018; 13:2699-2707. [PMID: 30179448 PMCID: PMC6233718 DOI: 10.1021/acschembio.8b00645] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Polyketide synthases (PKS) are a rich source of natural products of varied chemical composition and biological significance. Here, we report the characterization of an atypical dehydratase (DH) domain from the PKS pathway for gephyronic acid, an inhibitor of eukaryotic protein synthesis. Using a library of synthetic substrate mimics, the reaction course, stereospecificity, and tolerance to non-native substrates of GphF DH1 are probed via LC-MS analysis. Taken together, the studies establish GphF DH1 as a dual-function dehydratase/isomerase that installs an odd-to-even double bond and yields a product consistent with the isobutenyl terminus of gephyronic acid. The studies also reveal an unexpected C2 epimerase function in catalytic turnover with the native substrate. A 1.55-Å crystal structure of GphF DH1 guided mutagenesis experiments to elucidate the roles of key amino acids in the multistep DH1 catalysis, identifying critical functions for leucine and tyrosine side chains. The mutagenesis results were applied to add a secondary isomerase functionality to a nonisomerizing DH in the first successful gain-of-function engineering of a PKS DH. Our studies of GphF DH1 catalysis highlight the versatility of the DH active site and adaptation for a specific catalytic outcome with a specific substrate.
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Affiliation(s)
- Greg J. Dodge
- Department of Biological Chemistry and Life Sciences Institute University of Michigan Ann Arbor, Michigan, 48109
| | - Danialle Ronnow
- Department of Chemistry and Biochemistry University of Notre Dame Notre Dame, Indiana 46556
| | - Richard E. Taylor
- Department of Chemistry and Biochemistry University of Notre Dame Notre Dame, Indiana 46556
| | - Janet L. Smith
- Department of Biological Chemistry and Life Sciences Institute University of Michigan Ann Arbor, Michigan, 48109
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59
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Moosmann P, Ueoka R, Gugger M, Piel J. Aranazoles: Extensively Chlorinated Nonribosomal Peptide-Polyketide Hybrids from the Cyanobacterium Fischerella sp. PCC 9339. Org Lett 2018; 20:5238-5241. [PMID: 30141631 DOI: 10.1021/acs.orglett.8b02193] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/10/2023]
Abstract
An analysis of cyanobacterial genomes revealed an architecturally unique biosynthetic gene cluster with an unusually high number of genes encoding predicted iron(II)/α-ketoglutarate-dependent halogenases. Mass spectrometry-guided identification of the corresponding metabolites yielded the aranazoles, extensively halogenated nonribosomal peptide-polyketide hybrids. Their chlorine-bearing fatty acyl-like moiety is reminiscent of the hyperhalogenated chlorosulfolipids, natural products of unknown enzymatic origin that were previously isolated from eukaryotic algae and mussels.
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Affiliation(s)
- Philipp Moosmann
- Institut für Mikrobiologie , ETH Zürich , Vladimir-Prelog-Weg 4 , 8093 Zürich , Switzerland
| | - Reiko Ueoka
- Institut für Mikrobiologie , ETH Zürich , Vladimir-Prelog-Weg 4 , 8093 Zürich , Switzerland
| | - Muriel Gugger
- Institut Pasteur, Collection des Cyanobactéries , Département de Microbiologie , 75015 Paris , France
| | - Jörn Piel
- Institut für Mikrobiologie , ETH Zürich , Vladimir-Prelog-Weg 4 , 8093 Zürich , Switzerland
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60
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Musiol-Kroll EM, Wohlleben W. Acyltransferases as Tools for Polyketide Synthase Engineering. Antibiotics (Basel) 2018; 7:antibiotics7030062. [PMID: 30022008 PMCID: PMC6164871 DOI: 10.3390/antibiotics7030062] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2018] [Revised: 07/14/2018] [Accepted: 07/16/2018] [Indexed: 12/16/2022] Open
Abstract
Polyketides belong to the most valuable natural products, including diverse bioactive compounds, such as antibiotics, anticancer drugs, antifungal agents, immunosuppressants and others. Their structures are assembled by polyketide synthases (PKSs). Modular PKSs are composed of modules, which involve sets of domains catalysing the stepwise polyketide biosynthesis. The acyltransferase (AT) domains and their “partners”, the acyl carrier proteins (ACPs), thereby play an essential role. The AT loads the building blocks onto the “substrate acceptor”, the ACP. Thus, the AT dictates which building blocks are incorporated into the polyketide structure. The precursor- and occasionally the ACP-specificity of the ATs differ across the polyketide pathways and therefore, the ATs contribute to the structural diversity within this group of complex natural products. Those features make the AT enzymes one of the most promising tools for manipulation of polyketide assembly lines and generation of new polyketide compounds. However, the AT-based PKS engineering is still not straightforward and thus, rational design of functional PKSs requires detailed understanding of the complex machineries. This review summarizes the attempts of PKS engineering by exploiting the AT attributes for the modification of polyketide structures. The article includes 253 references and covers the most relevant literature published until May 2018.
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Affiliation(s)
- Ewa Maria Musiol-Kroll
- Interfakultäres Institut für Mikrobiologie und Infektionsmedizin, Eberhard Karls Universität Tübingen, Auf der Morgenstelle 28, 72076 Tübingen, Germany.
| | - Wolfgang Wohlleben
- Interfakultäres Institut für Mikrobiologie und Infektionsmedizin, Eberhard Karls Universität Tübingen, Auf der Morgenstelle 28, 72076 Tübingen, Germany.
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61
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Flórez LV, Scherlach K, Miller IJ, Rodrigues A, Kwan JC, Hertweck C, Kaltenpoth M. An antifungal polyketide associated with horizontally acquired genes supports symbiont-mediated defense in Lagria villosa beetles. Nat Commun 2018; 9:2478. [PMID: 29946103 PMCID: PMC6018673 DOI: 10.1038/s41467-018-04955-6] [Citation(s) in RCA: 70] [Impact Index Per Article: 11.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2018] [Accepted: 06/05/2018] [Indexed: 12/13/2022] Open
Abstract
Microbial symbionts are often a source of chemical novelty and can contribute to host defense against antagonists. However, the ecological relevance of chemical mediators remains unclear for most systems. Lagria beetles live in symbiosis with multiple strains of Burkholderia bacteria that protect their offspring against pathogens. Here, we describe the antifungal polyketide lagriamide, and provide evidence supporting that it is produced by an uncultured symbiont, Burkholderia gladioli Lv-StB, which is dominant in field-collected Lagria villosa. Interestingly, lagriamide is structurally similar to bistramides, defensive compounds found in marine tunicates. We identify a gene cluster that is probably involved in lagriamide biosynthesis, provide evidence for horizontal acquisition of these genes, and show that the naturally occurring symbiont strains on the egg are protective in the soil environment. Our findings highlight the potential of microbial symbionts and horizontal gene transfer as influential sources of ecological innovation.
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Affiliation(s)
- Laura V Flórez
- Department for Evolutionary Ecology, Institute of Organismic and Molecular Evolution, Johannes Gutenberg University, Johann-Joachim-Becher-Weg 13, 55128, Mainz, Germany.
| | - Kirstin Scherlach
- Department of Biomolecular Chemistry, Leibniz Institute for Natural Products Research and Infection Biology, HKI, Beutenbergstr. 11a, 07745, Jena, Germany.
| | - Ian J Miller
- Pharmaceutical Sciences Division, School of Pharmacy, University of Wisconsin, 777 Highland Ave, Madison, WI, 53705-2222, USA
| | - Andre Rodrigues
- Department of Biochemistry and Microbiology, UNESP-São Paulo State University, Av. 24A, n. 1515-Bela Vista, Rio Claro, SP, 13506-900, Brazil
| | - Jason C Kwan
- Pharmaceutical Sciences Division, School of Pharmacy, University of Wisconsin, 777 Highland Ave, Madison, WI, 53705-2222, USA
| | - Christian Hertweck
- Department of Biomolecular Chemistry, Leibniz Institute for Natural Products Research and Infection Biology, HKI, Beutenbergstr. 11a, 07745, Jena, Germany
- Natural Product Chemistry, Friedrich Schiller University, 07743, Jena, Germany
| | - Martin Kaltenpoth
- Department for Evolutionary Ecology, Institute of Organismic and Molecular Evolution, Johannes Gutenberg University, Johann-Joachim-Becher-Weg 13, 55128, Mainz, Germany
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62
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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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63
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Xie X, Cane DE. Stereospecific Formation of Z-Trisubstituted Double Bonds by the Successive Action of Ketoreductase and Dehydratase Domains from trans-AT Polyketide Synthases. Biochemistry 2018; 57:3126-3129. [PMID: 29293329 PMCID: PMC5988919 DOI: 10.1021/acs.biochem.7b01253] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Incubation of (±)-2-methyl-3-ketobutyryl-SNAC (3) and (±)-2-methyl-3-ketopentanoyl-SNAC (4) with BonKR2 or OxaKR5, ketoreductase domains from the bongkrekic acid (1) and oxazolomycin (2) polyketide synthases, in the presence of NADPH gave in each case the corresponding (2 R,3 S)-2-methyl-3-hydroxybutyryl-SNAC (5) or (2 R,3 S)-2-methyl-3-hydroxypentanoyl-SNAC (6) products, as established by chiral gas chromatography-mass spectrometry analysis of the derived methyl esters. Identical results were obtained by BonKR2- and OxaKR5-catalyzed reduction of chemoenzymatically prepared (2 R)-2-methyl-3-ketopentanoyl-EryACP6, (2 R)-2-methyl-3-ketobutyryl-BonACP2 (12), and (2 R)-2-methyl-3-ketopentanoyl-BonACP2 (13). The paired dehydratase domains, BonDH2 and OxaDH5, were then shown to catalyze the reversible syn dehydration of (2 R,3 S)-2-methyl-3-hydroxybutyryl-BonACP2 (14) to give the corresponding trisubstituted ( Z)-2-methylbutenoyl-BonACP2 (16).
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Affiliation(s)
- Xinqiang Xie
- Department of Chemistry, Brown University, Box H, Providence, Rhode Island 02912-9108, United States
| | - David E. Cane
- Department of Chemistry, Brown University, Box H, Providence, Rhode Island 02912-9108, United States
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Kust A, Mareš J, Jokela J, Urajová P, Hájek J, Saurav K, Voráčová K, Fewer DP, Haapaniemi E, Permi P, Řeháková K, Sivonen K, Hrouzek P. Discovery of a Pederin Family Compound in a Nonsymbiotic Bloom-Forming Cyanobacterium. ACS Chem Biol 2018; 13:1123-1129. [PMID: 29570981 DOI: 10.1021/acschembio.7b01048] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
Abstract
The pederin family includes a number of bioactive compounds isolated from symbiotic organisms of diverse evolutionary origin. Pederin is linked to beetle-induced dermatitis in humans, and pederin family members possess potent antitumor activity caused by selective inhibition of the eukaryotic ribosome. Their biosynthesis is accomplished by a polyketide/nonribosomal peptide synthetase machinery employing an unusual trans-acyltransferase mechanism. Here, we report a novel pederin type compound, cusperin, from the free-living cyanobacterium Cuspidothrix issatschenkoi (earlier Aphanizomenon). The chemical structure of cusperin is similar to that of nosperin recently isolated from the lichen cyanobiont Nostoc sharing the tehrahydropyran moiety and major part of the linear backbone. However, the cusperin molecule is extended by a glycine residue and lacks one hydroxyl substituent. Pederins were previously thought to be exclusive to symbiotic relationships. However, C. issatschenkoi is a nonsymbiotic planktonic organism and a frequent component of toxic water blooms. Cusperin is devoid of the cytotoxic activity reported for other pederin family members. Hence, our findings raise questions about the role of pederin analogues in cyanobacteria and broaden the knowledge of ecological distribution of this group of polyketides.
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Affiliation(s)
- Andreja Kust
- Institute of Microbiology CAS, Center Algatech, Třeboň, Czech Republic
- The Czech Academy of Sciences, Biology Centre, Institute of Hydrobiology, České Budějovice, Czech Republic
- University of South Bohemia, Faculty of Science, České Budějovice, Czech Republic
| | - Jan Mareš
- Institute of Microbiology CAS, Center Algatech, Třeboň, Czech Republic
- The Czech Academy of Sciences, Biology Centre, Institute of Hydrobiology, České Budějovice, Czech Republic
- University of South Bohemia, Faculty of Science, České Budějovice, Czech Republic
| | - Jouni Jokela
- Department of Microbiology, University of Helsinki, FI-00014 Helsinki, Finland
| | - Petra Urajová
- Institute of Microbiology CAS, Center Algatech, Třeboň, Czech Republic
| | - Jan Hájek
- Institute of Microbiology CAS, Center Algatech, Třeboň, Czech Republic
- University of South Bohemia, Faculty of Science, České Budějovice, Czech Republic
| | - Kumar Saurav
- Institute of Microbiology CAS, Center Algatech, Třeboň, Czech Republic
| | - Kateřina Voráčová
- Institute of Microbiology CAS, Center Algatech, Třeboň, Czech Republic
| | - David P. Fewer
- Department of Microbiology, University of Helsinki, FI-00014 Helsinki, Finland
| | - Esa Haapaniemi
- Department of Chemistry, University of Jyväskylä, FI-40010 Jyväskylä, Finland
| | - Perttu Permi
- Department of Chemistry, University of Jyväskylä, FI-40010 Jyväskylä, Finland
- Department of Biology and Environmental Science, Nanoscience Center, University of Jyväskylä, FI-40010 Jyväskylä, Finland
| | - Klára Řeháková
- The Czech Academy of Sciences, Biology Centre, Institute of Hydrobiology, České Budějovice, Czech Republic
| | | | - Pavel Hrouzek
- Institute of Microbiology CAS, Center Algatech, Třeboň, Czech Republic
- University of South Bohemia, Faculty of Science, České Budějovice, Czech Republic
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65
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Uria AR, Piel J, Wakimoto T. Biosynthetic Insights of Calyculin- and Misakinolide-Type Compounds in "Candidatus Entotheonella sp.". Methods Enzymol 2018; 604:287-330. [PMID: 29779656 DOI: 10.1016/bs.mie.2018.02.017] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/09/2022]
Abstract
Microbial symbionts are recognized as the important sources of numerous sponge-derived metabolites with potent biological activities. The limitation to cultivate the majority of potential symbionts has hampered attempts to explore and exploit their natural products for further development toward medical applications. Metagenomics-guided approaches have enabled cloning of natural product biosynthesis genes from uncultured microbial symbionts. Subsequent activation of biosynthesis genes in easily culturable bacteria could lead to the sustainable production of rare sponge-derived compounds. In this chapter, we highlight metagenomic strategies to reveal natural product biosynthetic pathways in sponge metagenomes based on the calyculin and misakinolide polyketides. Techniques to identify the compound producer are briefly discussed. We further describe examples of functional studies of the biosynthetic pathways of these two compound types with a special emphasis on the general experimental protocols for the activity assays of key proteins involved in their biosynthesis.
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Affiliation(s)
- Agustinus R Uria
- Faculty of Pharmaceutical Sciences, Hokkaido University, Sapporo, Japan.
| | - Jörn Piel
- Institute of Microbiology, Eidgenössische Technische Hochschule (ETH) Zurich, Zurich, Switzerland.
| | - Toshiyuki Wakimoto
- Faculty of Pharmaceutical Sciences, Hokkaido University, Sapporo, Japan.
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66
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Zhang L, Ji J, Yuan M, Feng Y, Wang L, Deng Z, Bai L, Zheng J. Stereospecificity of Enoylreductase Domains from Modular Polyketide Synthases. ACS Chem Biol 2018; 13:871-875. [PMID: 29437374 DOI: 10.1021/acschembio.7b00982] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
An enoylreductase (ER) domain of a polyketide synthase module recruiting a methylmalonate extender unit sets the C2 methyl branch to either the S or R configuration during processing of a polyketide intermediate carried by an acyl carrier protein (ACP) domain. In the present study, pantetheine- and ACP-bound trans-2-methylcrotonyl substrate surrogates were used to scrutinize the stereospecificity of the ER domains. The pantetheine-bound thioester was reduced to mixtures of both 2 R and 2 S products, whereas the expected 2 S epimer was almost exclusively generated when the cognate ACP-bound substrate surrogate was utilized. The analogous incubation of an ER with the substrate surrogate carried by a noncognate ACP significantly increased the generation of the unexpected 2 R epimer, highlighting the dependence of stereospecificity on proper protein-protein interactions between ER and ACP domains. The ER mutant assays revealed the involvement of the conserved tyrosine and lysine in stereocontrol. Taken together, these results expand the current understanding of the ER stereochemistry and help in the engineering of modular PKSs.
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Affiliation(s)
- Luyun Zhang
- State Key Laboratory of Microbial Metabolism and School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai 200240, China
| | - Junjie Ji
- National Key Laboratory of Biochemical Engineering, Institute of Process Engineering, Chinese Academy of Sciences, Beijing, 100190, People’s Republic of China
| | - Meijuan Yuan
- State Key Laboratory of Microbial Metabolism and School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai 200240, China
| | - Yuanyuan Feng
- State Key Laboratory of Microbial Metabolism and School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai 200240, China
| | - Lei Wang
- State Key Laboratory of Microbial Metabolism and School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai 200240, China
| | - Zixin Deng
- State Key Laboratory of Microbial Metabolism and School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai 200240, China
| | - Linquan Bai
- State Key Laboratory of Microbial Metabolism and School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai 200240, China
| | - Jianting Zheng
- State Key Laboratory of Microbial Metabolism and School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai 200240, China
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67
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Liu C, Yuan M, Xu X, Wang L, Keatinge-Clay AT, Deng Z, Lin S, Zheng J. Substrate-bound structures of a ketoreductase from amphotericin modular polyketide synthase. J Struct Biol 2018; 203:135-141. [PMID: 29626512 DOI: 10.1016/j.jsb.2018.04.001] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2018] [Revised: 03/30/2018] [Accepted: 04/03/2018] [Indexed: 11/29/2022]
Abstract
Ketoreductase (KR) domains of modular polyketide synthases (PKSs) control the stereochemistry of C2 methyl and C3 hydroxyl substituents of polyketide intermediates. To understand the molecular basis of stereocontrol exerted by KRs, the crystal structure of a KR from the second module of the amphotericin PKS (AmpKR2) complexed with NADP+ and 2-methyl-3-oxopentanoyl-pantetheine was solved. This first ternary structure provides direct evidence to the hypothesis that a substrate enters into the active site of an A-type KR from the side opposite the coenzyme to generate an L-hydroxyl substituent. A comparison with the ternary complex of a G355T/Q364H mutant sheds light on the structural basis for stereospecificity toward the substrate C2 methyl substituent. Functional assays suggest the pantetheine handle shows obvious influence on the catalytic efficiency and the stereochemical outcome. Together, these findings extend our current understanding of the stereochemical control of PKS KR domains.
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Affiliation(s)
- Chenguang Liu
- State Key Laboratory of Microbial Metabolism, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai 200240, China
| | - Meijuan Yuan
- State Key Laboratory of Microbial Metabolism, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai 200240, China
| | - Xu Xu
- State Key Laboratory of Microbial Metabolism, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai 200240, China
| | - Lei Wang
- State Key Laboratory of Microbial Metabolism, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai 200240, China
| | - Adrian T Keatinge-Clay
- Department of Molecular Biosciences, University of Texas at Austin, Austin, TX 78712, USA
| | - Zixin Deng
- State Key Laboratory of Microbial Metabolism, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai 200240, China
| | - Shuangjun Lin
- State Key Laboratory of Microbial Metabolism, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai 200240, China
| | - Jianting Zheng
- State Key Laboratory of Microbial Metabolism, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai 200240, China.
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Hu Y, Wang M, Wu C, Tan Y, Li J, Hao X, Duan Y, Guan Y, Shang X, Wang Y, Xiao C, Gan M. Identification and Proposed Relative and Absolute Configurations of Niphimycins C-E from the Marine-Derived Streptomyces sp. IMB7-145 by Genomic Analysis. JOURNAL OF NATURAL PRODUCTS 2018; 81:178-187. [PMID: 29308897 DOI: 10.1021/acs.jnatprod.7b00859] [Citation(s) in RCA: 46] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/07/2023]
Abstract
Analysis of the whole genome sequence of Streptomyces sp. IMB7-145 revealed the presence of seven type I polyketide synthase biosynthetic gene clusters, one of which was highly homologous to the biosynthetic gene cluster of azalomycin F. Detailed bioinformatic analysis of the modular organization of the PKS gene suggested that this gene is responsible for niphimycin biosynthesis. Guided by genomic analysis, a large-scale cultivation ultimately led to the discovery and characterization of four new niphimycin congeners, namely, niphimycins C-E (1-3) and 17-O-methylniphimycin (4). The configurations of most stereocenters of niphimycins have not been determined to date. In the present study, the relative configurations were elucidated by spectroscopic analysis, including J-based analysis and the CNMR database method. Further, the full absolute configurations of niphimycins were completely proposed for the first time based on biosynthetic gene cluster analysis of the ketoreductase and enoylreductase domains for hydroxy- and methyl-bearing stereocenters. Compounds 1, 3, 4, and niphimycin Iα (5) showed antimicrobial activity against methicillin-resistant Staphylococcus aureus and vancomycin-resistant enterococci (MIC: 8-64 μg/mL), as well as cytotoxicity against the human HeLa cancer cell line (IC50: 3.0-9.0 μM). In addition, compounds 1 and 5 displayed significant activity against several Mycobacterium tuberculosis clinical isolates (MIC: 4-32 μg/mL).
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Affiliation(s)
- Yuanyuan Hu
- Institute of Medicinal Biotechnology, Chinese Academy of Medical Sciences and Peking Union Medical College , Beijing 100050, People's Republic of China
| | - Mian Wang
- Institute of Medicinal Biotechnology, Chinese Academy of Medical Sciences and Peking Union Medical College , Beijing 100050, People's Republic of China
| | - Chunyan Wu
- Institute of Medicinal Biotechnology, Chinese Academy of Medical Sciences and Peking Union Medical College , Beijing 100050, People's Republic of China
- Beijing Key Laboratory of Bioactive Substances and Functional Foods, Beijing Union University , Beijing 100191, People's Republic of China
| | - Yi Tan
- Institute of Medicinal Biotechnology, Chinese Academy of Medical Sciences and Peking Union Medical College , Beijing 100050, People's Republic of China
| | - Jiao Li
- Institute of Medicinal Biotechnology, Chinese Academy of Medical Sciences and Peking Union Medical College , Beijing 100050, People's Republic of China
| | - Xiaomeng Hao
- Institute of Medicinal Biotechnology, Chinese Academy of Medical Sciences and Peking Union Medical College , Beijing 100050, People's Republic of China
| | - Yanbo Duan
- Institute of Medicinal Biotechnology, Chinese Academy of Medical Sciences and Peking Union Medical College , Beijing 100050, People's Republic of China
| | - Yan Guan
- Institute of Medicinal Biotechnology, Chinese Academy of Medical Sciences and Peking Union Medical College , Beijing 100050, People's Republic of China
| | - Xiaoya Shang
- Beijing Key Laboratory of Bioactive Substances and Functional Foods, Beijing Union University , Beijing 100191, People's Republic of China
| | - Yiguang Wang
- Institute of Medicinal Biotechnology, Chinese Academy of Medical Sciences and Peking Union Medical College , Beijing 100050, People's Republic of China
| | - Chunling Xiao
- Institute of Medicinal Biotechnology, Chinese Academy of Medical Sciences and Peking Union Medical College , Beijing 100050, People's Republic of China
| | - Maoluo Gan
- Institute of Medicinal Biotechnology, Chinese Academy of Medical Sciences and Peking Union Medical College , Beijing 100050, People's Republic of China
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Characterization of the biosynthetic gene cluster for cryptic phthoxazolin A in Streptomyces avermitilis. PLoS One 2018; 13:e0190973. [PMID: 29324854 PMCID: PMC5764310 DOI: 10.1371/journal.pone.0190973] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/02/2017] [Accepted: 12/23/2017] [Indexed: 11/19/2022] Open
Abstract
Phthoxazolin A, an oxazole-containing polyketide, has a broad spectrum of anti-oomycete activity and herbicidal activity. We recently identified phthoxazolin A as a cryptic metabolite of Streptomyces avermitilis that produces the important anthelmintic agent avermectin. Even though genome data of S. avermitilis is publicly available, no plausible biosynthetic gene cluster for phthoxazolin A is apparent in the sequence data. Here, we identified and characterized the phthoxazolin A (ptx) biosynthetic gene cluster through genome sequencing, comparative genomic analysis, and gene disruption. Sequence analysis uncovered that the putative ptx biosynthetic genes are laid on an extra genomic region that is not found in the public database, and 8 open reading frames in the extra genomic region could be assigned roles in the biosynthesis of the oxazole ring, triene polyketide and carbamoyl moieties. Disruption of the ptxA gene encoding a discrete acyltransferase resulted in a complete loss of phthoxazolin A production, confirming that the trans-AT type I PKS system is responsible for the phthoxazolin A biosynthesis. Based on the predicted functional domains in the ptx assembly line, we propose the biosynthetic pathway of phthoxazolin A.
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70
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Moretto L, Vance S, Heames B, Broadhurst RW. Dissecting how modular polyketide synthase ketoreductases interact with acyl carrier protein-attached substrates. Chem Commun (Camb) 2017; 53:11457-11460. [PMID: 28980673 PMCID: PMC6038798 DOI: 10.1039/c7cc04625a] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2017] [Accepted: 06/29/2017] [Indexed: 11/21/2022]
Abstract
Interaction studies using fragments excised from the modular mycolactone polyketide synthase show that ketoreductase domains possess a generic binding site for acyl carrier protein domains and provide evidence that the pendant 5'-phosphopantetheine prosthetic group plays a key role in delivering acyl substrates to the active site in the correct orientation.
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Affiliation(s)
- Luisa Moretto
- Department of Molecular Biosciences
, The University of Texas at Austin
,
Austin
, TX 78712
, USA
| | - Steven Vance
- Crescendo Biologics Ltd
,
Meditrina Building 260
, Babraham Research Campus
, Cambridge CB22 3AT
, UK
| | - Brennan Heames
- Department of Biochemistry
, University of Cambridge
,
80 Tennis Court Road
, Cambridge CB2 1GA
, UK
.
| | - R. William Broadhurst
- Department of Biochemistry
, University of Cambridge
,
80 Tennis Court Road
, Cambridge CB2 1GA
, UK
.
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71
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Shah DD, You YO, Cane DE. Stereospecific Formation of E- and Z-Disubstituted Double Bonds by Dehydratase Domains from Modules 1 and 2 of the Fostriecin Polyketide Synthase. J Am Chem Soc 2017; 139:14322-14330. [PMID: 28902510 DOI: 10.1021/jacs.7b08896] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/17/2023]
Abstract
The dehydratase domain FosDH1 from module 1 of the fostriecin polyketide synthase (PKS) catalyzed the stereospecific interconversion of (3R)-3-hydroxybutyryl-FosACP1 (5) and (E)-2-butenoyl-FosACP1 (11), as established by a combination of direct LC-MS/MS and chiral GC-MS. FosDH1 did not act on either (3S)-3-hydroxybutyryl-FosACP1 (6) or (Z)-2-butenoyl-FosACP1 (12). FosKR2, the ketoreductase from module 2 of the fostriecin PKS that normally provides the natural substrate for FosDH2, was shown to catalyze the NADPH-dependent stereospecific reduction of 3-ketobutyryl-FosACP2 (23) to (3S)-3-hydroxybutyryl-FosACP2 (8). Consistent with this finding, FosDH2 catalyzed the interconversion of the corresponding triketide substrates (3R,4E)-3-hydroxy-4-hexenoyl-FosACP2 (18) and (2Z,4E)-2,4-hexadienoyl-FosACP2 (21). FosDH2 also catalyzed the stereospecific hydration of (Z)-2-butenoyl-FosACP2 (14) to (3S)-3-hydroxybutyryl-FosACP2 (8). Although incubation of FosDH2 with (3S)-3-hydroxybutyryl-FosACP2 (8) did not result in detectable accumulation of (Z)-2-butenoyl-FosACP2 (14), FosDH2 catalyzed the slow exchange of the 3-hydroxy group of 8 with [18O]-water. FosDH2 unexpectedly could also support the stereospecific interconversion of (3R)-3-hydroxybutyryl-FosACP2 (7) and (E)-2-butenoyl-FosACP2 (13).
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Affiliation(s)
- Dhara D Shah
- Department of Chemistry, Brown University , Box H, Providence, Rhode Island 02912-9108, United States
| | - Young-Ok You
- Department of Chemistry, Brown University , Box H, Providence, Rhode Island 02912-9108, United States
| | - David E Cane
- Department of Chemistry, Brown University , Box H, Providence, Rhode Island 02912-9108, United States
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72
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Structural and Functional Trends in Dehydrating Bimodules from trans-Acyltransferase Polyketide Synthases. Structure 2017; 25:1045-1055.e2. [PMID: 28625788 PMCID: PMC5553570 DOI: 10.1016/j.str.2017.05.011] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2017] [Revised: 05/04/2017] [Accepted: 05/15/2017] [Indexed: 01/07/2023]
Abstract
In an effort to uncover the structural motifs and biosynthetic logic of the relatively uncharacterized trans-acyltransferase polyketide synthases, we have begun the dissection of the enigmatic dehydrating bimodules common in these enzymatic assembly lines. We report the 1.98 Å resolution structure of a ketoreductase (KR) from the first half of a type A dehydrating bimodule and the 2.22 Å resolution structure of a dehydratase (DH) from the second half of a type B dehydrating bimodule. The KR, from the third module of the bacillaene synthase, and the DH, from the tenth module of the difficidin synthase, possess features not observed in structurally characterized homologs. The DH architecture provides clues for how it catalyzes a unique double dehydration. Correlations between the chemistries proposed for dehydrating bimodules and bioinformatic analysis indicate that type A dehydrating bimodules generally produce an α/β-cis alkene moiety, while type B dehydrating bimodules generally produce an α/β-trans, γ/δ-cis diene moiety.
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73
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Mo X, Shi C, Gui C, Zhang Y, Ju J, Wang Q. Identification of nocamycin biosynthetic gene cluster from Saccharothrix syringae NRRL B-16468 and generation of new nocamycin derivatives by manipulating gene cluster. Microb Cell Fact 2017; 16:100. [PMID: 28599654 PMCID: PMC5466765 DOI: 10.1186/s12934-017-0718-5] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2017] [Accepted: 06/05/2017] [Indexed: 11/20/2022] Open
Abstract
BACKGROUND Nocamycins I and II, produced by the rare actinomycete Saccharothrix syringae, belong to the tetramic acid family natural products. Nocamycins show potent antimicrobial activity and they hold great potential for antibacterial agent design. However, up to now, little is known about the exact biosynthetic mechanism of nocamycin. RESULTS In this report, we identified the gene cluster responsible for nocamycin biosynthesis from S. syringae and generated new nocamycin derivatives by manipulating its gene cluster. The biosynthetic gene cluster for nocamycin contains a 61 kb DNA locus, consisting of 21 open reading frames (ORFs). Five type I polyketide synthases (NcmAI, NcmAII, NcmAIII, NcmAIV, NcmAV) and a non-ribosomal peptide synthetase (NcmB) are proposed to be involved in synthesis of the backbone structure, a Dieckmann cyclase NcmC catalyze the releasing of linear chain and the formation of tetramic acid moiety, five enzymes (NcmEDGOP) are related to post-tailoring steps, and five enzymes (NcmNJKIM) function as regulators. Targeted inactivation of ncmB led to nocamycin production being completely abolished, which demonstrates that this gene cluster is involved in nocamycin biosynthesis. To generate new nocamycin derivatives, the gene ncmG, encoding for a cytochrome P450 oxidase, was inactivated. Two new nocamycin derivatives nocamycin III and nocamycin IV were isolated from the ncmG deletion mutant strain and their structures were elucidated by spectroscopic data analyses. Based on bioinformatics analysis and new derivatives isolated from gene inactivation mutant strains, a biosynthetic pathway of nocamycins was proposed. CONCLUSION These findings provide the basis for further understanding of nocamycin biosynthetic mechanism, and set the stage to rationally engineer new nocamycin derivatives via combinatorial biosynthesis strategy.
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Affiliation(s)
- Xuhua Mo
- Shandong Key Laboratory of Applied Mycology, School of Life Sciences, Qingdao Agricultural University, Qingdao, 266109 China
| | - Chunrong Shi
- Shandong Key Laboratory of Applied Mycology, School of Life Sciences, Qingdao Agricultural University, Qingdao, 266109 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 Rd., Guangzhou, 510301 China
| | - Yanjiao Zhang
- Shandong Key Laboratory of Applied Mycology, School of Life Sciences, Qingdao Agricultural University, Qingdao, 266109 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 Rd., Guangzhou, 510301 China
| | - Qingji Wang
- Shandong Key Laboratory of Applied Mycology, School of Life Sciences, Qingdao Agricultural University, Qingdao, 266109 China
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Abstract
The enzymology of 135 assembly lines containing primarily cis-acyltransferase modules is comprehensively analyzed, with greater attention paid to less common phenomena. Diverse online transformations, in which the substrate and/or product of the reaction is an acyl chain bound to an acyl carrier protein, are classified so that unusual reactions can be compared and underlying assembly-line logic can emerge. As a complement to the chemistry surrounding the loading, extension, and offloading of assembly lines that construct primarily polyketide products, structural aspects of the assembly-line machinery itself are considered. This review of assembly-line phenomena, covering the literature up to 2017, should thus be informative to the modular polyketide synthase novice and expert alike.
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Affiliation(s)
- Adrian T Keatinge-Clay
- Department of Molecular Biosciences, The University of Texas at Austin , Austin, Texas 78712, United States
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Faille A, Gavalda S, Slama N, Lherbet C, Maveyraud L, Guillet V, Laval F, Quémard A, Mourey L, Pedelacq JD. Insights into Substrate Modification by Dehydratases from Type I Polyketide Synthases. J Mol Biol 2017; 429:1554-1569. [PMID: 28377293 DOI: 10.1016/j.jmb.2017.03.026] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2017] [Revised: 03/21/2017] [Accepted: 03/27/2017] [Indexed: 02/04/2023]
Abstract
Dehydration reactions play a crucial role in the de novo biosynthesis of fatty acids and a wide range of pharmacologically active polyketide natural products with strong emphasis on human medicine. The type I polyketide synthase PpsC from Mycobacterium tuberculosis catalyzes key biosynthetic steps of lipid virulence factors phthiocerol dimycocerosates and phenolic glycolipids. Given the insolubility of the natural C28-C30 fatty acyl substrate of the PpsC dehydratase (DH) domain, we investigated its structure-function relationships in the presence of shorter surrogate substrates. Since most enzymes belonging to the (R)-specific enoyl hydratase/hydroxyacyl dehydratase family conduct the reverse hydration reaction in vitro, we have determined the X-ray structures of the PpsC DH domain, both unliganded (apo) and in complex with trans-but-2-enoyl-CoA or trans-dodec-2-enoyl-CoA derivatives. This study provides for the first time a snapshot of dehydratase-ligand interactions following a hydration reaction. Our structural analysis allowed us to identify residues essential for substrate binding and activity. The structural comparison of the two complexes also sheds light on the need for long acyl chains for this dehydratase to carry out its function, consistent with both its in vitro catalytic behavior and the physiological role of the PpsC enzyme.
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Affiliation(s)
- Alexandre Faille
- Institut de Pharmacologie et de Biologie Structurale, Université de Toulouse, CNRS, UPS, 31077 Toulouse Cedex 04, France
| | - Sabine Gavalda
- Institut de Pharmacologie et de Biologie Structurale, Université de Toulouse, CNRS, UPS, 31077 Toulouse Cedex 04, France
| | - Nawel Slama
- Institut de Pharmacologie et de Biologie Structurale, Université de Toulouse, CNRS, UPS, 31077 Toulouse Cedex 04, France
| | | | - Laurent Maveyraud
- Institut de Pharmacologie et de Biologie Structurale, Université de Toulouse, CNRS, UPS, 31077 Toulouse Cedex 04, France
| | - Valérie Guillet
- Institut de Pharmacologie et de Biologie Structurale, Université de Toulouse, CNRS, UPS, 31077 Toulouse Cedex 04, France
| | - Françoise Laval
- Institut de Pharmacologie et de Biologie Structurale, Université de Toulouse, CNRS, UPS, 31077 Toulouse Cedex 04, France
| | - Annaïk Quémard
- Institut de Pharmacologie et de Biologie Structurale, Université de Toulouse, CNRS, UPS, 31077 Toulouse Cedex 04, France
| | - Lionel Mourey
- Institut de Pharmacologie et de Biologie Structurale, Université de Toulouse, CNRS, UPS, 31077 Toulouse Cedex 04, France.
| | - Jean-Denis Pedelacq
- Institut de Pharmacologie et de Biologie Structurale, Université de Toulouse, CNRS, UPS, 31077 Toulouse Cedex 04, France.
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76
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Characterization of bafilomycin biosynthesis in Kitasatospora setae KM-6054 and comparative analysis of gene clusters in Actinomycetales microorganisms. J Antibiot (Tokyo) 2017; 70:616-624. [PMID: 28293034 DOI: 10.1038/ja.2017.33] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2016] [Revised: 01/04/2017] [Accepted: 02/01/2017] [Indexed: 11/08/2022]
Abstract
Bafilomycins A1, C1 and B1 (setamycin) produced by Kitasatospora setae KM-6054 belong to the plecomacrolide family, which exhibit antibacterial, antifungal, antineoplastic and immunosuppressive activities. An analysis of gene clusters from K. setae KM-6054 governing the biosynthesis of bafilomycins revealed that it contains five large open reading frames (ORFs) encoding the multifunctional polypeptides of bafilomycin polyketide synthases (PKSs). These clustered PKS genes, which are responsible for bafilomycin biosynthesis, together encode 11 homologous sets of enzyme activities, each catalyzing a specific round of polyketide chain elongation. The region contains an additional 13 ORFs spanning a distance of 73 287 bp, some of which encode polypeptides governing other key steps in bafilomycin biosynthesis. Five ORFs, BfmB, BfmC, BfmD, BfmE and BfmF, were involved in the formation of methoxymalonyl-acyl carrier protein (ACP). Two possible regulatory genes, bfmR and bfmH, were found downstream of the above genes. A gene-knockout analysis revealed that BfmR was only a transcriptional regulator for the transcription of bafilomycin biosynthetic genes. Two genes, bfmI and bfmJ, were found downstream of bfmH. An analysis of these gene-disruption mutants in addition to an enzymatic analysis of BfmI and BfmJ revealed that BfmJ activated fumarate and BfmI functioned as a catalyst to form a fumaryl ester at the C21 hydroxyl residue of bafilomycin A1. A comparative analysis of bafilomycin gene clusters in K. setae KM-6054, Streptomyces lohii JCM 14114 and Streptomyces griseus DSM 2608 revealed that each ORF of both gene clusters in two Streptomyces strains were quite similar to each other. However, each ORF of gene cluster in K. setae KM-6054 was of lower similarity to that of corresponding ORF in the two Streptomyces species.
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77
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Weissman KJ. Polyketide stereocontrol: a study in chemical biology. Beilstein J Org Chem 2017; 13:348-371. [PMID: 28326145 PMCID: PMC5331325 DOI: 10.3762/bjoc.13.39] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2016] [Accepted: 02/01/2017] [Indexed: 11/23/2022] Open
Abstract
The biosynthesis of reduced polyketides in bacteria by modular polyketide synthases (PKSs) proceeds with exquisite stereocontrol. As the stereochemistry is intimately linked to the strong bioactivity of these molecules, the origins of stereochemical control are of significant interest in attempts to create derivatives of these compounds by genetic engineering. In this review, we discuss the current state of knowledge regarding this key aspect of the biosynthetic pathways. Given that much of this information has been obtained using chemical biology tools, work in this area serves as a showcase for the power of this approach to provide answers to fundamental biological questions.
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Affiliation(s)
- Kira J Weissman
- UMR 7365, Ingénierie Moléculaire et Physiopathologie Articulaire (IMoPA), CNRS-Université de Lorraine, Biopôle de l’Université de Lorraine, Campus Biologie Santé, Avenue de la Forêt de Haye, BP 50184, 54505 Vandœuvre-lès-Nancy Cedex, France
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78
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Beemelmanns C, Ramadhar TR, Kim KH, Klassen JL, Cao S, Wyche TP, Hou Y, Poulsen M, Bugni TS, Currie CR, Clardy J. Macrotermycins A-D, Glycosylated Macrolactams from a Termite-Associated Amycolatopsis sp. M39. Org Lett 2017; 19:1000-1003. [PMID: 28207275 DOI: 10.1021/acs.orglett.6b03831] [Citation(s) in RCA: 93] [Impact Index Per Article: 13.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023]
Abstract
Bioassay-guided metabolomic analyses led to the characterization of four new 20-membered glycosylated polyketide macrolactams, macrotermycins A-D, from a termite-associated actinomycete, Amycolatopsis sp. M39. M39's sequenced genome revealed the macrotermycin's putative biosynthetic gene cluster. Macrotermycins A and C had antibacterial activity against human-pathogenic Staphylococcus aureus and, of greater ecological relevance, they also had selective antifungal activity against a fungal parasite of the termite fungal garden.
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Affiliation(s)
- Christine Beemelmanns
- Leibniz Institute for Natural Product Research and Infection Biology, Hans-Knöll-Institute , 07745 Jena, Germany
| | - Timothy R Ramadhar
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School , Boston, Massachusetts 02115, United States
| | - Ki Hyun Kim
- Natural Product Research Laboratory, School of Pharmacy, Sungkyunkwan University , Suwon 440-746, Republic of Korea
| | - Jonathan L Klassen
- Department of Molecular & Cell Biology, University of Connecticut , Storrs, Connecticut 06269, United States
| | - Shugeng Cao
- Daniel K. Inouye College of Pharmacy, University of Hawaii , Hilo, Hawaii 96720, United States
| | - Thomas P Wyche
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School , Boston, Massachusetts 02115, United States
| | | | - Michael Poulsen
- Centre for Social Evolution, Section for Ecology and Evolution, Department of Biology, University of Copenhagen , 2100 Copenhagen East, Denmark
| | | | | | - Jon Clardy
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School , Boston, Massachusetts 02115, United States
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79
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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: 27] [Impact Index Per Article: 3.9] [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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80
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Zhang L, Hashimoto T, Qin B, Hashimoto J, Kozone I, Kawahara T, Okada M, Awakawa T, Ito T, Asakawa Y, Ueki M, Takahashi S, Osada H, Wakimoto T, Ikeda H, Shin-ya K, Abe I. Characterization of Giant Modular PKSs Provides Insight into Genetic Mechanism for Structural Diversification of Aminopolyol Polyketides. Angew Chem Int Ed Engl 2017. [DOI: 10.1002/ange.201611371] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Affiliation(s)
- Lihan Zhang
- Graduate School of Pharmaceutical Sciences; The University of Tokyo; 7-3-1 Hongo, Bunkyo-ku Tokyo Japan
| | - Takuya Hashimoto
- National Institute of Advanced Industrial Science and Technology (AIST); 2-4-7 Aomi, Koto-ku Tokyo Japan
| | - Bin Qin
- Graduate School of Pharmaceutical Sciences; The University of Tokyo; 7-3-1 Hongo, Bunkyo-ku Tokyo Japan
| | - Junko Hashimoto
- Japan Biological Informatics Consortium; 2-4-7 Aomi, Koto-ku Tokyo Japan
| | - Ikuko Kozone
- Japan Biological Informatics Consortium; 2-4-7 Aomi, Koto-ku Tokyo Japan
| | - Teppei Kawahara
- Japan Biological Informatics Consortium; 2-4-7 Aomi, Koto-ku Tokyo Japan
| | - Masahiro Okada
- Graduate School of Pharmaceutical Sciences; The University of Tokyo; 7-3-1 Hongo, Bunkyo-ku Tokyo Japan
| | - Takayoshi Awakawa
- Graduate School of Pharmaceutical Sciences; The University of Tokyo; 7-3-1 Hongo, Bunkyo-ku Tokyo Japan
| | - Takuya Ito
- Faculty of Pharmaceutical Sciences; Tokushima Bunri University; 180 Nishihama, Yamashirocho Tokushima Japan
| | - Yoshinori Asakawa
- Faculty of Pharmaceutical Sciences; Tokushima Bunri University; 180 Nishihama, Yamashirocho Tokushima Japan
| | - Masashi Ueki
- Chemical Biology Research Group; RIKEN Center for Sustainable Resource Science; 2-1 Hirosawa, Wako Saitama Japan
| | - Shunji Takahashi
- Chemical Biology Research Group; RIKEN Center for Sustainable Resource Science; 2-1 Hirosawa, Wako Saitama Japan
| | - Hiroyuki Osada
- Chemical Biology Research Group; RIKEN Center for Sustainable Resource Science; 2-1 Hirosawa, Wako Saitama Japan
| | - Toshiyuki Wakimoto
- Graduate School of Pharmaceutical Sciences; The University of Tokyo; 7-3-1 Hongo, Bunkyo-ku Tokyo Japan
| | - Haruo Ikeda
- Laboratory of Microbial Engineering; Kitasato Institute for Life Sciences; Kitasato University; Kanagawa Japan
| | - Kazuo Shin-ya
- National Institute of Advanced Industrial Science and Technology (AIST); 2-4-7 Aomi, Koto-ku Tokyo Japan
| | - Ikuro Abe
- Graduate School of Pharmaceutical Sciences; The University of Tokyo; 7-3-1 Hongo, Bunkyo-ku Tokyo Japan
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81
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Zhang L, Hashimoto T, Qin B, Hashimoto J, Kozone I, Kawahara T, Okada M, Awakawa T, Ito T, Asakawa Y, Ueki M, Takahashi S, Osada H, Wakimoto T, Ikeda H, Shin-ya K, Abe I. Characterization of Giant Modular PKSs Provides Insight into Genetic Mechanism for Structural Diversification of Aminopolyol Polyketides. Angew Chem Int Ed Engl 2017; 56:1740-1745. [DOI: 10.1002/anie.201611371] [Citation(s) in RCA: 82] [Impact Index Per Article: 11.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2016] [Indexed: 11/10/2022]
Affiliation(s)
- Lihan Zhang
- Graduate School of Pharmaceutical Sciences; The University of Tokyo; 7-3-1 Hongo, Bunkyo-ku Tokyo Japan
| | - Takuya Hashimoto
- National Institute of Advanced Industrial Science and Technology (AIST); 2-4-7 Aomi, Koto-ku Tokyo Japan
| | - Bin Qin
- Graduate School of Pharmaceutical Sciences; The University of Tokyo; 7-3-1 Hongo, Bunkyo-ku Tokyo Japan
| | - Junko Hashimoto
- Japan Biological Informatics Consortium; 2-4-7 Aomi, Koto-ku Tokyo Japan
| | - Ikuko Kozone
- Japan Biological Informatics Consortium; 2-4-7 Aomi, Koto-ku Tokyo Japan
| | - Teppei Kawahara
- Japan Biological Informatics Consortium; 2-4-7 Aomi, Koto-ku Tokyo Japan
| | - Masahiro Okada
- Graduate School of Pharmaceutical Sciences; The University of Tokyo; 7-3-1 Hongo, Bunkyo-ku Tokyo Japan
| | - Takayoshi Awakawa
- Graduate School of Pharmaceutical Sciences; The University of Tokyo; 7-3-1 Hongo, Bunkyo-ku Tokyo Japan
| | - Takuya Ito
- Faculty of Pharmaceutical Sciences; Tokushima Bunri University; 180 Nishihama, Yamashirocho Tokushima Japan
| | - Yoshinori Asakawa
- Faculty of Pharmaceutical Sciences; Tokushima Bunri University; 180 Nishihama, Yamashirocho Tokushima Japan
| | - Masashi Ueki
- Chemical Biology Research Group; RIKEN Center for Sustainable Resource Science; 2-1 Hirosawa, Wako Saitama Japan
| | - Shunji Takahashi
- Chemical Biology Research Group; RIKEN Center for Sustainable Resource Science; 2-1 Hirosawa, Wako Saitama Japan
| | - Hiroyuki Osada
- Chemical Biology Research Group; RIKEN Center for Sustainable Resource Science; 2-1 Hirosawa, Wako Saitama Japan
| | - Toshiyuki Wakimoto
- Graduate School of Pharmaceutical Sciences; The University of Tokyo; 7-3-1 Hongo, Bunkyo-ku Tokyo Japan
| | - Haruo Ikeda
- Laboratory of Microbial Engineering; Kitasato Institute for Life Sciences; Kitasato University; Kanagawa Japan
| | - Kazuo Shin-ya
- National Institute of Advanced Industrial Science and Technology (AIST); 2-4-7 Aomi, Koto-ku Tokyo Japan
| | - Ikuro Abe
- Graduate School of Pharmaceutical Sciences; The University of Tokyo; 7-3-1 Hongo, Bunkyo-ku Tokyo Japan
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82
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Sheehan J, Murphy CD, Caffrey P. New insights into polyene macrolide biosynthesis in Couchioplanes caeruleus. MOLECULAR BIOSYSTEMS 2017; 13:866-873. [DOI: 10.1039/c7mb00112f] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Analysis of 67–121 biosynthesis reveals how aromatic heptaene producers impose double bond geometry and avoid interference with folate biosynthesis.
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Affiliation(s)
- J. Sheehan
- School of Biomolecular and Biomedical Science
- University College Dublin
- Belfield
- Ireland
| | - C. D. Murphy
- School of Biomolecular and Biomedical Science
- University College Dublin
- Belfield
- Ireland
| | - P. Caffrey
- School of Biomolecular and Biomedical Science
- University College Dublin
- Belfield
- Ireland
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83
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Zhang X, Li Z, Du L, Chlipala GE, Lopez PC, Zhang W, Sherman DH, Li S. Identification of an unexpected shunt pathway product provides new insights into tirandamycin biosynthesis. Tetrahedron Lett 2016; 57:5919-5923. [PMID: 28989201 PMCID: PMC5628624 DOI: 10.1016/j.tetlet.2016.11.080] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/20/2022]
Abstract
Tirandamycin K (7), the first linear 7,13;9,13-diseco-tirandamycin derivative, was isolated from the tamI (encoding the TamI P450 monooxygenase) disruption mutant strain (ΔtamI) of marine Streptomyces sp. 307-9. Its chemical structure with relative and absolute configurations was elucidated by a combination of extensive spectroscopic analyses and biosynthetic inferences. Structural elucidation of this unusual compound provides new insights into tirandamycin biosynthesis. Moreover, examination of the biological activity of 7 confirms the essential function of the bicyclic ketal ring for antibiotic activities of tirandamycins.
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Affiliation(s)
- Xingwang Zhang
- Shandong Provincial Key Laboratory of Synthetic Biology, and CAS Key Laboratory of Biofuels at Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, Qingdao, Shandong 266101, China
| | - Zhong Li
- Shandong Provincial Key Laboratory of Synthetic Biology, and CAS Key Laboratory of Biofuels at Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, Qingdao, Shandong 266101, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Lei Du
- Shandong Provincial Key Laboratory of Synthetic Biology, and CAS Key Laboratory of Biofuels at Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, Qingdao, Shandong 266101, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - George E. Chlipala
- Life Sciences Institute, Departments of Medicinal Chemistry, Chemistry, and Microbiology and Immunology, University of Michigan, Ann Arbor, MI 48109, USA
| | - Patricia C. Lopez
- Life Sciences Institute, Departments of Medicinal Chemistry, Chemistry, and Microbiology and Immunology, University of Michigan, Ann Arbor, MI 48109, USA
| | - Wei Zhang
- Shandong Provincial Key Laboratory of Synthetic Biology, and CAS Key Laboratory of Biofuels at Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, Qingdao, Shandong 266101, China
| | - David H. Sherman
- Life Sciences Institute, Departments of Medicinal Chemistry, Chemistry, and Microbiology and Immunology, University of Michigan, Ann Arbor, MI 48109, USA
| | - Shengying Li
- Shandong Provincial Key Laboratory of Synthetic Biology, and CAS Key Laboratory of Biofuels at Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, Qingdao, Shandong 266101, China
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84
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Molloy EM, Tietz JI, Blair PM, Mitchell DA. Biological characterization of the hygrobafilomycin antibiotic JBIR-100 and bioinformatic insights into the hygrolide family of natural products. Bioorg Med Chem 2016; 24:6276-6290. [PMID: 27234886 PMCID: PMC5108699 DOI: 10.1016/j.bmc.2016.05.021] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2016] [Revised: 05/08/2016] [Accepted: 05/13/2016] [Indexed: 01/04/2023]
Abstract
The hygrolides, a family of 16-member-ring-containing plecomacrolides produced by Actinobacteria, exhibit numerous reported bioactivities. Using HR-MS/MS, nucleophilic 1,4-addition-based labeling, NMR, and bioinformatic analysis, we identified Streptomyces varsoviensis as a novel producer of JBIR-100, a fumarate-containing hygrolide, and elucidated the previously unknown stereochemistry of the natural product. We investigated the antimicrobial activity of JBIR-100, with preliminary insight into mode of action indicating that it perturbs the membrane of Bacillus subtilis. S. varsoviensis is known to produce compounds from multiple hygrolide sub-families, namely hygrobafilomycins (JBIR-100 and hygrobafilomycin) and bafilomycins (bafilomycin C1 and D). In light of this, we identified the biosynthetic gene cluster for JBIR-100, which, to our knowledge, represents the first reported for a hygrobafilomycin. Finally, we performed a bioinformatic analysis of the hygrolide family, describing clusters from known and predicted producers. Our results indicate that potential remains for the Actinobacteria to yield novel hygrolide congeners, perhaps with differing biological activities.
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Affiliation(s)
- Evelyn M Molloy
- Carl R. Woese Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA.
| | - Jonathan I Tietz
- Department of Chemistry, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA.
| | - Patricia M Blair
- Department of Chemistry, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA.
| | - Douglas A Mitchell
- Carl R. Woese Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA; Department of Chemistry, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA; Department of Microbiology, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA.
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85
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Fiers WD, Dodge GJ, Sherman DH, Smith JL, Aldrich CC. Vinylogous Dehydration by a Polyketide Dehydratase Domain in Curacin Biosynthesis. J Am Chem Soc 2016; 138:16024-16036. [PMID: 27960309 DOI: 10.1021/jacs.6b09748] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]
Abstract
Polyketide synthase (PKS) enzymes continue to hold great promise as synthetic biology platforms for the production of novel therapeutic agents, biofuels, and commodity chemicals. Dehydratase (DH) catalytic domains play an important role during polyketide biosynthesis through the dehydration of the nascent polyketide intermediate to provide olefins. Our understanding of the detailed mechanistic and structural underpinning of DH domains that control substrate specificity and selectivity remains limited, thus hindering our efforts to rationally re-engineer PKSs. The curacin pathway houses a rare plurality of possible double bond permutations containing conjugated olefins as well as both cis- and trans-olefins, providing an unrivaled model system for polyketide dehydration. All four DH domains implicated in curacin biosynthesis were characterized in vitro using synthetic substrates, and activity was measured by LC-MS/MS analysis. These studies resulted in complete kinetic characterization of the all-trans-trienoate-forming CurK-DH, whose kcat of 72 s-1 is more than 3 orders of magnitude greater than that of any previously reported PKS DH domain. A novel stereospecific mechanism for diene formation involving a vinylogous enolate intermediate is proposed for the CurJ and CurH DHs on the basis of incubation studies with truncated substrates. A synthetic substrate was co-crystallized with a catalytically inactive Phe substitution in the His-Asp catalytic dyad of CurJ-DH to elucidate substrate-enzyme interactions. The resulting complex suggested the structural basis for dienoate formation and provided the first glimpse into the enzyme-substrate interactions essential for the formation of olefins in polyketide natural products. This examination of both canonical and non-canonical dehydration mechanisms reveals hidden catalytic activity inherent in some DH domains that may be leveraged for future applications in synthetic biology.
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Affiliation(s)
- William D Fiers
- Department of Medicinal Chemistry, College of Pharmacy, University of Minnesota , Minneapolis, Minnesota 55455, United States
| | - Greg J Dodge
- Department of Biological Chemistry and Life Sciences Institute, University of Michigan , Ann Arbor, Michigan 48109, United States
| | - David H Sherman
- Department of Medicinal Chemistry and Life Sciences Institute, University of Michigan , Ann Arbor, Michigan 48109, United States
| | - Janet L Smith
- Department of Biological Chemistry and Life Sciences Institute, University of Michigan , Ann Arbor, Michigan 48109, United States
| | - Courtney C Aldrich
- Department of Medicinal Chemistry, College of Pharmacy, University of Minnesota , Minneapolis, Minnesota 55455, United States
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86
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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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87
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Berkhan G, Merten C, Holec C, Hahn F. Das Zusammenspiel zwischen einer multifunktionalen Dehydratase-Domäne und einer C-Methyltransferase bewirkt die Doppelbindungsverschiebung in der Ambruticin-Biosynthese. Angew Chem Int Ed Engl 2016. [DOI: 10.1002/ange.201607827] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Affiliation(s)
- Gesche Berkhan
- Professur für Organische Chemie (Lebensmittelchemie), Fakultät für Biologie, Chemie und Geowissenschaften; Universität Bayreuth; Universitätsstraße 30 95447 Bayreuth Deutschland
- Zentrum für Biomolekulare Wirkstoffe; Leibniz Universität Hannover; Schneiderberg 38 30167 Hannover Deutschland
| | - Christian Merten
- Ruhr-Universität Bochum; Organische Chemie 2; Universitätsstraße 150 44801 Bochum Deutschland
| | - Claudia Holec
- Institut für Bioorganische Chemie; Heinrich-Heine-Universität, Düsseldorf im Forschungszentrum Jülich; Stetternicher Forst, Geb. 15.8 52426 Jülich Deutschland
| | - Frank Hahn
- Professur für Organische Chemie (Lebensmittelchemie), Fakultät für Biologie, Chemie und Geowissenschaften; Universität Bayreuth; Universitätsstraße 30 95447 Bayreuth Deutschland
- Zentrum für Biomolekulare Wirkstoffe; Leibniz Universität Hannover; Schneiderberg 38 30167 Hannover Deutschland
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88
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Berkhan G, Merten C, Holec C, Hahn F. The Interplay between a Multifunctional Dehydratase Domain and a C-Methyltransferase Effects Olefin Shift in Ambruticin Biosynthesis. Angew Chem Int Ed Engl 2016; 55:13589-13592. [DOI: 10.1002/anie.201607827] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2016] [Indexed: 01/27/2023]
Affiliation(s)
- Gesche Berkhan
- Professur für Organische Chemie (Lebensmittelchemie), Fakultät für Biologie, Chemie und Geowissenschaften; Universität Bayreuth; Universitätsstrasse 30 95447 Bayreuth Germany
- Zentrum für Biomolekulare Wirkstoffe; Leibniz Universität Hannover; Schneiderberg 38 30167 Hannover Germany
| | - Christian Merten
- Ruhr Universität Bochum; Organische Chemie 2; Universitätsstrasse 150 44801 Bochum Germany
| | - Claudia Holec
- Institut für Bioorganische Chemie; Heinrich-Heine-Universität Düsseldorf im Forschungszentrum Jülich; Stetternicher Forst, Geb. 15.8 52426 Jülich Germany
| | - Frank Hahn
- Professur für Organische Chemie (Lebensmittelchemie), Fakultät für Biologie, Chemie und Geowissenschaften; Universität Bayreuth; Universitätsstrasse 30 95447 Bayreuth Germany
- Zentrum für Biomolekulare Wirkstoffe; Leibniz Universität Hannover; Schneiderberg 38 30167 Hannover Germany
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89
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Steinmetz H, Li J, Fu C, Zaburannyi N, Kunze B, Harmrolfs K, Schmitt V, Herrmann J, Reichenbach H, Höfle G, Kalesse M, Müller R. Isolation, Structure Elucidation, and (Bio)Synthesis of Haprolid, a Cell-Type-Specific Myxobacterial Cytotoxin. Angew Chem Int Ed Engl 2016; 55:10113-7. [PMID: 27404448 DOI: 10.1002/anie.201603288] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2016] [Indexed: 11/09/2022]
Abstract
Myxobacteria are well-established sources for novel natural products exhibiting intriguing bioactivities. We here report on haprolid (1) isolated from Byssovorax cruenta Har1. The compound exhibits an unprecedented macrolactone comprising four modified amino acids and a polyketide fragment. As configurational assignment proved difficult, a bioinformatic analysis of the biosynthetic gene cluster was chosen to predict the configuration of each stereocenter. In-depth analysis of the corresponding biosynthetic proteins established a hybrid polyketide synthase/nonribosomal peptide synthetase origin of haprolid and allowed for stereochemical assignments. A subsequent total synthesis yielded haprolid and corroborated all predictions made. Intriguingly, haprolid showed cytotoxicity against several cell lines in the nanomolar range whereas other cells were almost unaffected by treatment with the compound.
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Affiliation(s)
- Heinrich Steinmetz
- Helmholtz Center for Infection Research (HZI), Department Microbial Drugs, Inhoffenstrasse 7, 38124, Braunschweig, Germany
| | - Jun Li
- Institute for Organic Chemistry, Gottfried Leibniz Universität Hannover.,Centre of Biomolecular Drug Research (BMWZ), Schneiderberg 1B, 30167, Hannover, Germany.,Helmholtz Center for Infection Research (HZI), Inhoffenstrasse 7, 38124, Braunschweig, Germany
| | - Chengzhang Fu
- Helmholtz Institute for Pharmaceutical Research Saarland (HIPS), Helmholtz Center for Infection Research and Pharmaceutical Biotechnology, Saarland University, Campus Building E8.1, 66123, Saarbrücken, Germany
| | - Nestor Zaburannyi
- Helmholtz Institute for Pharmaceutical Research Saarland (HIPS), Helmholtz Center for Infection Research and Pharmaceutical Biotechnology, Saarland University, Campus Building E8.1, 66123, Saarbrücken, Germany
| | - Birgitte Kunze
- Helmholtz Center for Infection Research (HZI), Department Microbial Drugs, Inhoffenstrasse 7, 38124, Braunschweig, Germany
| | - Kirsten Harmrolfs
- Helmholtz Institute for Pharmaceutical Research Saarland (HIPS), Helmholtz Center for Infection Research and Pharmaceutical Biotechnology, Saarland University, Campus Building E8.1, 66123, Saarbrücken, Germany
| | - Viktoria Schmitt
- Helmholtz Institute for Pharmaceutical Research Saarland (HIPS), Helmholtz Center for Infection Research and Pharmaceutical Biotechnology, Saarland University, Campus Building E8.1, 66123, Saarbrücken, Germany
| | - Jennifer Herrmann
- Helmholtz Institute for Pharmaceutical Research Saarland (HIPS), Helmholtz Center for Infection Research and Pharmaceutical Biotechnology, Saarland University, Campus Building E8.1, 66123, Saarbrücken, Germany
| | - Hans Reichenbach
- Helmholtz Center for Infection Research (HZI), Inhoffenstrasse 7, 38124, Braunschweig, Germany
| | - Gerhard Höfle
- Helmholtz Center for Infection Research (HZI), Inhoffenstrasse 7, 38124, Braunschweig, Germany
| | - Markus Kalesse
- Institute for Organic Chemistry, Gottfried Leibniz Universität Hannover. .,Centre of Biomolecular Drug Research (BMWZ), Schneiderberg 1B, 30167, Hannover, Germany. .,Helmholtz Center for Infection Research (HZI), Inhoffenstrasse 7, 38124, Braunschweig, Germany.
| | - Rolf Müller
- Helmholtz Institute for Pharmaceutical Research Saarland (HIPS), Helmholtz Center for Infection Research and Pharmaceutical Biotechnology, Saarland University, Campus Building E8.1, 66123, Saarbrücken, Germany.
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90
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Steinmetz H, Li J, Fu C, Zaburannyi N, Kunze B, Harmrolfs K, Schmitt V, Herrmann J, Reichenbach H, Höfle G, Kalesse M, Müller R. Isolierung, Strukturaufklärung und (Bio-)Synthese von Haprolid, einem zellspezifisch zytotoxischen myxobakteriellen Makrolidnaturstoff. Angew Chem Int Ed Engl 2016. [DOI: 10.1002/ange.201603288] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
Affiliation(s)
- Heinrich Steinmetz
- Helmholtz-Zentrum für Infektionsforschung (HZI); Forschungsgruppe Mikrobielle Wirkstoffe; Inhoffenstraße 7 38124 Braunschweig Deutschland
| | - Jun Li
- Institut für Organische Chemie; Gottfried Wilhelm Leibniz Universität Hannover
- Biomolekulares Wirkstoffzentrum (BMWZ); Schneiderberg 1B 30167 Hannover Deutschland
- Helmholtz-Zentrum für Infektionsforschung (HZI); Inhoffenstraße 7 38124 Braunschweig Deutschland
| | - Chengzhang Fu
- Helmholtz-Institut für Pharmazeutische Forschung Saarland (HIPS), Helmholtz-Zentrum für Infektionsforschung und Pharmazeutische Biotechnologie; Universitätscampus E8.1; 66123 Saarbrücken Deutschland
| | - Nestor Zaburannyi
- Helmholtz-Institut für Pharmazeutische Forschung Saarland (HIPS), Helmholtz-Zentrum für Infektionsforschung und Pharmazeutische Biotechnologie; Universitätscampus E8.1; 66123 Saarbrücken Deutschland
| | - Birgitte Kunze
- Helmholtz-Zentrum für Infektionsforschung (HZI); Forschungsgruppe Mikrobielle Wirkstoffe; Inhoffenstraße 7 38124 Braunschweig Deutschland
| | - Kirsten Harmrolfs
- Helmholtz-Institut für Pharmazeutische Forschung Saarland (HIPS), Helmholtz-Zentrum für Infektionsforschung und Pharmazeutische Biotechnologie; Universitätscampus E8.1; 66123 Saarbrücken Deutschland
| | - Viktoria Schmitt
- Helmholtz-Institut für Pharmazeutische Forschung Saarland (HIPS), Helmholtz-Zentrum für Infektionsforschung und Pharmazeutische Biotechnologie; Universitätscampus E8.1; 66123 Saarbrücken Deutschland
| | - Jennifer Herrmann
- Helmholtz-Institut für Pharmazeutische Forschung Saarland (HIPS), Helmholtz-Zentrum für Infektionsforschung und Pharmazeutische Biotechnologie; Universitätscampus E8.1; 66123 Saarbrücken Deutschland
| | - Hans Reichenbach
- Helmholtz-Zentrum für Infektionsforschung (HZI); Inhoffenstraße 7 38124 Braunschweig Deutschland
| | - Gerhard Höfle
- Helmholtz-Zentrum für Infektionsforschung (HZI); Inhoffenstraße 7 38124 Braunschweig Deutschland
| | - Markus Kalesse
- Institut für Organische Chemie; Gottfried Wilhelm Leibniz Universität Hannover
- Biomolekulares Wirkstoffzentrum (BMWZ); Schneiderberg 1B 30167 Hannover Deutschland
- Helmholtz-Zentrum für Infektionsforschung (HZI); Inhoffenstraße 7 38124 Braunschweig Deutschland
| | - Rolf Müller
- Helmholtz-Institut für Pharmazeutische Forschung Saarland (HIPS), Helmholtz-Zentrum für Infektionsforschung und Pharmazeutische Biotechnologie; Universitätscampus E8.1; 66123 Saarbrücken Deutschland
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91
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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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92
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Zhou Y, Murphy AC, Samborskyy M, Prediger P, Dias LC, Leadlay PF. Iterative Mechanism of Macrodiolide Formation in the Anticancer Compound Conglobatin. ACTA ACUST UNITED AC 2016; 22:745-54. [PMID: 26091168 PMCID: PMC4504003 DOI: 10.1016/j.chembiol.2015.05.010] [Citation(s) in RCA: 60] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2015] [Revised: 05/15/2015] [Accepted: 05/17/2015] [Indexed: 11/25/2022]
Abstract
Conglobatin is an unusual C2-symmetrical macrodiolide from the bacterium Streptomyces conglobatus with promising antitumor activity. Insights into the genes and enzymes that govern both the assembly-line production of the conglobatin polyketide and its dimerization are essential to allow rational alterations to be made to the conglobatin structure. We have used a rapid, direct in vitro cloning method to obtain the entire cluster on a 41-kbp fragment, encoding a modular polyketide synthase assembly line. The cloned cluster directs conglobatin biosynthesis in a heterologous host strain. Using a model substrate to mimic the conglobatin monomer, we also show that the conglobatin cyclase/thioesterase acts iteratively, ligating two monomers head-to-tail then re-binding the dimer product and cyclizing it. Incubation of two different monomers with the cyclase produces hybrid dimers and trimers, providing the first evidence that conglobatin analogs may in future become accessible through engineering of the polyketide synthase. The conglobatin cluster has been cloned using a single-step in vitro procedure The gene cluster in a heterologous strain confers the ability to produce conglobatin A model for ATP-dependent heterocyclization to the oxazole ring is proposed The conglobatin thioesterase catalyzes cyclodimerization by an iterative mechanism
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Affiliation(s)
- Yongjun Zhou
- Department of Biochemistry, University of Cambridge, Cambridge CB2 1GA, UK
| | - Annabel C Murphy
- Department of Biochemistry, University of Cambridge, Cambridge CB2 1GA, UK
| | | | - Patricia Prediger
- Faculty of Technology, State University of Campinas UNICAMP, CEP 134840332 Limeira, São Paulo, Brazil
| | - Luiz Carlos Dias
- Institute of Chemistry, State University of Campinas, UNICAMP, C.P. 6154, CEP 13084-971 Campinas, São Paulo, Brazil
| | - Peter F Leadlay
- Department of Biochemistry, University of Cambridge, Cambridge CB2 1GA, UK.
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93
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Caffrey P, De Poire E, Sheehan J, Sweeney P. Polyene macrolide biosynthesis in streptomycetes and related bacteria: recent advances from genome sequencing and experimental studies. Appl Microbiol Biotechnol 2016; 100:3893-908. [PMID: 27023916 DOI: 10.1007/s00253-016-7474-z] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2016] [Revised: 03/13/2016] [Accepted: 03/15/2016] [Indexed: 02/07/2023]
Abstract
The polyene macrolide group includes important antifungal drugs, to which resistance does not arise readily. Chemical and biological methods have been used in attempts to make polyene antibiotics with fewer toxic side effects. Genome sequencing of producer organisms is contributing to this endeavour, by providing access to new compounds and by enabling yield improvement for polyene analogues obtained by engineered biosynthesis. This recent work is also enhancing bioinformatic methods for deducing the structures of cryptic natural products from their biosynthetic enzymes. The stereostructure of candicidin D has recently been determined by NMR spectroscopy. Genes for the corresponding polyketide synthase have been uncovered in several different genomes. Analysis of this new information strengthens the view that protein sequence motifs can be used to predict double bond geometry in many polyketides.Chemical studies have shown that improved polyenes can be obtained by modifying the mycosamine sugar that is common to most of these compounds. Glycoengineered analogues might be produced by biosynthetic methods, but polyene glycosyltransferases show little tolerance for donors other than GDP-α-D-mycosamine. Genome sequencing has revealed extending glycosyltransferases that add a second sugar to the mycosamine of some polyenes. NppY of Pseudonocardia autotrophica uses UDP-N-acetyl-α-D-glucosamine as donor whereas PegA from Actinoplanes caeruleus uses GDP-α-D-mannose. These two enzymes show 51 % sequence identity and are also closely related to mycosaminyltransferases. These findings will assist attempts to construct glycosyltransferases that transfer alternative UDP- or (d)TDP-linked sugars to polyene macrolactones.
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Affiliation(s)
- Patrick Caffrey
- School of Biomolecular and Biomedical Science, University College Dublin, Belfield, Dublin 4, Ireland.
| | - Eimear De Poire
- School of Biomolecular and Biomedical Science, University College Dublin, Belfield, Dublin 4, Ireland
| | - James Sheehan
- School of Biomolecular and Biomedical Science, University College Dublin, Belfield, Dublin 4, Ireland
| | - Paul Sweeney
- School of Biomolecular and Biomedical Science, University College Dublin, Belfield, Dublin 4, Ireland
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94
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Eng CH, Yuzawa S, Wang G, Baidoo EEK, Katz L, Keasling JD. Alteration of Polyketide Stereochemistry from anti to syn by a Ketoreductase Domain Exchange in a Type I Modular Polyketide Synthase Subunit. Biochemistry 2016; 55:1677-80. [DOI: 10.1021/acs.biochem.6b00129] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Clara H. Eng
- Synthetic Biology Engineering Research Center, 5885 Hollis Street, Emeryville, California 94608, United States
| | | | - George Wang
- Joint BioEnergy Institute, 5885 Hollis Street, Emeryville, California 94608, United States
- Biological
Systems and Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, California 94270, United States
| | - Edward E. K. Baidoo
- Joint BioEnergy Institute, 5885 Hollis Street, Emeryville, California 94608, United States
- Biological
Systems and Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, California 94270, United States
| | - Leonard Katz
- Synthetic Biology Engineering Research Center, 5885 Hollis Street, Emeryville, California 94608, United States
| | - Jay D. Keasling
- Synthetic Biology Engineering Research Center, 5885 Hollis Street, Emeryville, California 94608, United States
- Joint BioEnergy Institute, 5885 Hollis Street, Emeryville, California 94608, United States
- Biological
Systems and Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, California 94270, United States
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95
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Essig S, Schmalzbauer B, Bretzke S, Scherer O, Koeberle A, Werz O, Müller R, Menche D. Predictive Bioinformatic Assignment of Methyl-Bearing Stereocenters, Total Synthesis, and an Additional Molecular Target of Ajudazol B. J Org Chem 2016; 81:1333-57. [DOI: 10.1021/acs.joc.5b02844] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/05/2023]
Affiliation(s)
- Sebastian Essig
- Institut
für Organische Chemie, Ruprecht-Karls Universität Heidelberg, Im Neuenheimer Feld 270, 69120 Heidelberg, Germany
| | - Björn Schmalzbauer
- Kekulé-Institut
für Organische Chemie und Biochemie, Universität Bonn, Gerhard-Domagk-Strasse 1, 53121 Bonn, Germany
| | - Sebastian Bretzke
- Institut
für Organische Chemie, Ruprecht-Karls Universität Heidelberg, Im Neuenheimer Feld 270, 69120 Heidelberg, Germany
| | - Olga Scherer
- Institute
of Pharmacy, Friedrich Schiller Universität Jena, Philosophenweg
14, 07743 Jena, Germany
| | - Andreas Koeberle
- Institute
of Pharmacy, Friedrich Schiller Universität Jena, Philosophenweg
14, 07743 Jena, Germany
| | - Oliver Werz
- Institute
of Pharmacy, Friedrich Schiller Universität Jena, Philosophenweg
14, 07743 Jena, Germany
| | - Rolf Müller
- Helmholtz
Institute for Pharmaceutical Research Saarland (HIPS) and Institut
for Pharmaceutical Biotechnology, Universität des Saarlandes, C 2.3, 66123 Saarbrücken, Germany
| | - Dirk Menche
- Kekulé-Institut
für Organische Chemie und Biochemie, Universität Bonn, Gerhard-Domagk-Strasse 1, 53121 Bonn, Germany
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96
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Hong H, Samborskyy M, Lindner F, Leadlay PF. An Amidinohydrolase Provides the Missing Link in the Biosynthesis of Amino Marginolactone Antibiotics. Angew Chem Int Ed Engl 2016; 55:1118-23. [PMID: 26630438 PMCID: PMC4737276 DOI: 10.1002/anie.201509300] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2015] [Indexed: 01/23/2023]
Abstract
Desertomycin A is an aminopolyol polyketide containing a macrolactone ring. We have proposed that desertomycin A and similar compounds (marginolactones) are formed by polyketide synthases primed not with γ-aminobutanoyl-CoA but with 4-guanidinylbutanoyl-CoA, to avoid facile cyclization of the starter unit. This hypothesis requires that there be a final-stage de-amidination of the corresponding guanidino-substituted natural product, but no enzyme for such a process has been described. We have now identified candidate amidinohydrolase genes within the desertomycin and primycin clusters. Deletion of the putative desertomycin amidinohydrolase gene dstH in Streptomyces macronensis led to the accumulation of desertomycin B, the guanidino form of the antibiotic. Also, purified DstH efficiently catalyzed the in vitro conversion of desertomycin B into the A form. Hence this amidinohydrolase furnishes the missing link in this proposed naturally evolved example of protective-group chemistry.
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Affiliation(s)
- Hui Hong
- Department of Biochemistry, University of Cambridge, 80 Tennis Court Road, Cambridge, CB2 1GA, UK
| | - Markiyan Samborskyy
- Department of Biochemistry, University of Cambridge, 80 Tennis Court Road, Cambridge, CB2 1GA, UK
| | - Frederick Lindner
- Department of Biochemistry, University of Cambridge, 80 Tennis Court Road, Cambridge, CB2 1GA, UK
- Institut für Organische Chemie, Leibniz Universität Hannover, Schneiderberg 1 B, 30167, Hannover, Germany
| | - Peter F Leadlay
- Department of Biochemistry, University of Cambridge, 80 Tennis Court Road, Cambridge, CB2 1GA, UK.
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97
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Bailey CB, Pasman ME, Keatinge-Clay AT. Substrate structure-activity relationships guide rational engineering of modular polyketide synthase ketoreductases. Chem Commun (Camb) 2016; 52:792-5. [PMID: 26568113 PMCID: PMC4690787 DOI: 10.1039/c5cc07315d] [Citation(s) in RCA: 29] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Modular polyketide synthase ketoreductases can set two chiral centers through a single reduction. To probe the basis of stereocontrol, a structure-activity relationship study was performed with three α-methyl, β-ketothioester substrates and four ketoreductases. Since interactions with the β-ketoacyl moiety were found to be most critical, residues implicated in contacting this moiety were mutated. Two mutations were sufficient to completely reverse the stereoselectivity of the model ketoreductase EryKR1, converting it from an enzyme that generates (2S,3R)-products into one that yields (2S,3S)-products.
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Affiliation(s)
- Constance B Bailey
- Department of Chemistry, University of Texas at Austin, 105 E. 24th St. Stop A5300, Austin, TX 78712, USA.
| | - Marjolein E Pasman
- Department of Chemistry, University of Texas at Austin, 105 E. 24th St. Stop A5300, Austin, TX 78712, USA.
| | - Adrian T Keatinge-Clay
- Department of Chemistry, University of Texas at Austin, 105 E. 24th St. Stop A5300, Austin, TX 78712, USA. and Department of Molecular Biosciences, University of Texas at Austin, 2506 Speedway Stop A5000, Austin, TX 78712, USA
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98
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Zarins-Tutt JS, Barberi TT, Gao H, Mearns-Spragg A, Zhang L, Newman DJ, Goss RJM. Prospecting for new bacterial metabolites: a glossary of approaches for inducing, activating and upregulating the biosynthesis of bacterial cryptic or silent natural products. Nat Prod Rep 2016; 33:54-72. [DOI: 10.1039/c5np00111k] [Citation(s) in RCA: 85] [Impact Index Per Article: 10.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023]
Abstract
Over the centuries, microbial secondary metabolites have played a central role in the treatment of human diseases and have revolutionised the pharmaceutical industry.
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Affiliation(s)
| | | | - Hong Gao
- School of Chemistry
- University of St Andrews
- St Andrews
- UK
| | | | - Lixin Zhang
- CAS Key Laboratory of Pathogenic Microbiology and Immunology
- Institute of Microbiology
- Chinese Academy of Sciences
- Beijing
- China
| | - David J. Newman
- Frederick National Laboratories for Cancer Research
- Natural Products Branch
- Frederick
- USA
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Booth TJ, Alt S, Capon RJ, Wilkinson B. Synchronous intramolecular cycloadditions of the polyene macrolactam polyketide heronamide C. Chem Commun (Camb) 2016; 52:6383-6. [DOI: 10.1039/c6cc01930g] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023]
Abstract
Two spontaneous intramolecular cycloadditions lead to the biosynthetic congeners heronamide A and B.
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Affiliation(s)
- Thomas J. Booth
- Department of Molecular Microbiology
- John Innes Centre
- Norwich Research Park
- Norwich NR4 7UH
- UK
| | - Silke Alt
- Department of Molecular Microbiology
- John Innes Centre
- Norwich Research Park
- Norwich NR4 7UH
- UK
| | - Robert J. Capon
- Institute for Molecular Bioscience
- The University of Queensland
- Australia 4072
| | - Barrie Wilkinson
- Department of Molecular Microbiology
- John Innes Centre
- Norwich Research Park
- Norwich NR4 7UH
- UK
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100
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Weissman KJ. Genetic engineering of modular PKSs: from combinatorial biosynthesis to synthetic biology. Nat Prod Rep 2016; 33:203-30. [DOI: 10.1039/c5np00109a] [Citation(s) in RCA: 115] [Impact Index Per Article: 14.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
This reviews covers on-going efforts at engineering the gigantic modular polyketide synthases (PKSs), highlighting both notable successes and failures.
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Affiliation(s)
- Kira J. Weissman
- UMR 7365
- Ingénierie Moléculaire et Physiopathologie Articulaire (IMoPA)
- CNRS-Université de Lorraine
- Biopôle de l'Université de Lorraine
- 54505 Vandœuvre-lès-Nancy Cedex
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