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Yin S, Liu Z, Shen J, Xia Y, Wang W, Gui P, Jia Q, Kachanuban K, Zhu W, Fu P. Chimeric natural products derived from medermycin and the nature-inspired construction of their polycyclic skeletons. Nat Commun 2022; 13:5169. [PMID: 36056035 PMCID: PMC9440243 DOI: 10.1038/s41467-022-32901-0] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2021] [Accepted: 08/23/2022] [Indexed: 12/02/2022] Open
Abstract
Medermycin, produced by Streptomyces species, represents a family of antibiotics with significant activity against Gram-positive pathogens. The biosynthesis of this family of natural products has been studied, and new skeletons related to medermycin have rarely been reported until recently. Herein, we report eight chimeric medermycin-type natural products with unusual polycyclic skeletons. The formation of these compounds features some key nonenzymatic steps, which inspired us to construct complex polycyclic skeletons via three efficient one-step reactions under mild conditions. This strategy was further developed to efficiently synthesize analogues for biological activity studies. The synthetic compounds, chimedermycins L and M, and sekgranaticin B, show potent antibacterial activity against Staphylococcus aureus, methicillin-resistant Staphylococcus aureus, and methicillin-resistant Staphylococcus epidermidis. This work paves the way for understanding the nonenzymatic formation of complex natural products and using it to synthesize natural product derivatives.
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Affiliation(s)
- Shupeng Yin
- Key Laboratory of Marine Drugs, Ministry of Education of China, School of Medicine and Pharmacy, Ocean University of China, Qingdao, 266003, China
| | - Zhi Liu
- Key Laboratory of Marine Drugs, Ministry of Education of China, School of Medicine and Pharmacy, Ocean University of China, Qingdao, 266003, China
- Laboratory for Marine Drugs and Bioproducts, Pilot National Laboratory for Marine Science and Technology (Qingdao), Qingdao, 266237, China
| | - Jingjing Shen
- Key Laboratory of Marine Drugs, Ministry of Education of China, School of Medicine and Pharmacy, Ocean University of China, Qingdao, 266003, China
- Laboratory for Marine Drugs and Bioproducts, Pilot National Laboratory for Marine Science and Technology (Qingdao), Qingdao, 266237, China
| | - Yuwei Xia
- Key Laboratory of Marine Drugs, Ministry of Education of China, School of Medicine and Pharmacy, Ocean University of China, Qingdao, 266003, China
- Laboratory for Marine Drugs and Bioproducts, Pilot National Laboratory for Marine Science and Technology (Qingdao), Qingdao, 266237, China
| | - Weihong Wang
- Key Laboratory of Marine Drugs, Ministry of Education of China, School of Medicine and Pharmacy, Ocean University of China, Qingdao, 266003, China
| | - Pengyan Gui
- Key Laboratory of Marine Drugs, Ministry of Education of China, School of Medicine and Pharmacy, Ocean University of China, Qingdao, 266003, China
| | - Qian Jia
- Key Laboratory of Marine Drugs, Ministry of Education of China, School of Medicine and Pharmacy, Ocean University of China, Qingdao, 266003, China
| | - Konthorn Kachanuban
- Key Laboratory of Marine Drugs, Ministry of Education of China, School of Medicine and Pharmacy, Ocean University of China, Qingdao, 266003, China
- Department of Fishery Products, Faculty of Fisheries, Kasetsart University, Bangkok, 10900, Thailand
| | - Weiming Zhu
- Key Laboratory of Marine Drugs, Ministry of Education of China, School of Medicine and Pharmacy, Ocean University of China, Qingdao, 266003, China.
- Laboratory for Marine Drugs and Bioproducts, Pilot National Laboratory for Marine Science and Technology (Qingdao), Qingdao, 266237, China.
| | - Peng Fu
- Key Laboratory of Marine Drugs, Ministry of Education of China, School of Medicine and Pharmacy, Ocean University of China, Qingdao, 266003, China.
- Laboratory for Marine Drugs and Bioproducts, Pilot National Laboratory for Marine Science and Technology (Qingdao), Qingdao, 266237, China.
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Ishikawa K, Hashimoto M, Komatsu K, Taguchi T, Okamoto S, Ichinose K. Characterization of stereospecific enoyl reductase ActVI-ORF2 for pyran ring formation in the actinorhodin biosynthesis of Streptomyces coelicolor A3(2). Bioorg Med Chem Lett 2022; 66:128727. [PMID: 35413414 DOI: 10.1016/j.bmcl.2022.128727] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2022] [Revised: 04/06/2022] [Accepted: 04/07/2022] [Indexed: 11/02/2022]
Abstract
Actinorhodin (ACT) is a benzoisochromanequinone antibiotic produced by Streptomyces coelicolor A3(2), which has served as a favored model organism for comprehensive studies of antibiotic biosynthesis and its regulation. (S)-DNPA undergoes various modifications as an intermediate in the ACT biosynthetic pathway, including enoyl reduction to DDHK. It has been suggested that actVI-ORF2 encodes an enoyl reductase (ER). However, its function has not been characterized in vitro. In this study, biochemical analysis of recombinant ActVI-ORF2 revealed that (S)-DNPA is converted to DDHK in a stereospecific manner with NADPH acting as a cofactor. (R)-DNPA was also reduced to 3-epi-DDHK with the comparable efficacy as (S)-DNPA, suggesting that the stereospecificity of ActVI-ORF2 was not affected by the stereochemistry at the C-3 of DNPA. ActVI-ORF2 is a new example of a discrete ER, which is distantly related to known ERs according to phylogenetic analysis.
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Affiliation(s)
- Kazuki Ishikawa
- Research Institute of Pharmaceutical Sciences, Musashino University 1-1-20, Shinmachi, Nishitokyo-shi, Tokyo 202-8585, Japan
| | - Makoto Hashimoto
- Research Institute of Pharmaceutical Sciences, Musashino University 1-1-20, Shinmachi, Nishitokyo-shi, Tokyo 202-8585, Japan
| | - Kunpei Komatsu
- Research Institute of Pharmaceutical Sciences, Musashino University 1-1-20, Shinmachi, Nishitokyo-shi, Tokyo 202-8585, Japan
| | - Takaaki Taguchi
- Research Institute of Pharmaceutical Sciences, Musashino University 1-1-20, Shinmachi, Nishitokyo-shi, Tokyo 202-8585, Japan; National Institute of Health Sciences 3-25-26, Tonomachi, Kawasaki-ku, Kawasaki-shi, Kanagawa 210-9501, Japan
| | - Susumu Okamoto
- National Agriculture and Food Research Organization 2-1-12 Kannondai, Tsukuba, Ibaraki 305-8642, Japan
| | - Koji Ichinose
- Research Institute of Pharmaceutical Sciences, Musashino University 1-1-20, Shinmachi, Nishitokyo-shi, Tokyo 202-8585, Japan.
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3
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Total Synthesis of 6-Deoxydihydrokalafungin, a Key Biosynthetic Precursor of Actinorhodin, and Its Epimer. Molecules 2021; 26:molecules26216397. [PMID: 34770806 PMCID: PMC8587838 DOI: 10.3390/molecules26216397] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2021] [Revised: 10/19/2021] [Accepted: 10/20/2021] [Indexed: 01/16/2023] Open
Abstract
In this article, we report the total synthesis of 6-deoxydihydrokalafungin (DDHK), a key biosynthetic intermediate of a dimeric benzoisochromanequinone antibiotic, actinorhodin (ACT), and its epimer, epi-DDHK. Tricyclic hemiacetal with 3-siloxyethyl group was subjected to Et3SiH reduction to establish the 1,3-cis stereochemistry in the benzoisochromane, and a subsequent oxidation/deprotection sequence then afforded epi-DDHK. A bicyclic acetal was subjected to AlH3 reduction to deliver the desired 1,3-trans isomer in an approximately 3:1 ratio, which was subjected to a similar sequence to that used for the 1,3-cis isomer that successfully afforded DDHK. A semisynthetic approach from (S)-DNPA, an isolable biosynthetic precursor of ACT, was also examined to afford DDHK and its epimer, which are identical to the synthetic products.
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4
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Zhu X, Siitonen V, Melançon III CE, Metsä-Ketelä M. Biosynthesis of Diverse Type II Polyketide Core Structures in Streptomyces coelicolor M1152. ACS Synth Biol 2021; 10:243-251. [PMID: 33471506 DOI: 10.1021/acssynbio.0c00482] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Synthetic biology-based approaches have been employed to generate advanced natural product (NP) pathway intermediates to overcome obstacles in NP drug discovery and production. Type II polyketides (PK-IIs) comprise a major subclass of NPs that provide attractive structures for antimicrobial and anticancer drug development. Herein, we have assembled five biosynthetic pathways using a generalized operon design strategy in Streptomyces coelicolor M1152 to allow comparative analysis of metabolite production in an improved heterologous host. The work resulted in production of four distinct PK-II core structures, namely benzoisochromanequinone, angucycline, tetracenomycin, and pentangular compounds, which serve as precursors to diverse pharmaceutically important NPs. Our bottom-up design strategy provided evidence that the biosynthetic pathway of BE-7585A proceeds via an angucycline core structure, instead of rearrangement of an anthracycline aglycone, and led to the discovery of a novel 26-carbon pentangular polyketide. The synthetic biology platform presented here provides an opportunity for further controlled production of diverse PK-IIs in a heterologous host.
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Affiliation(s)
- Xuechen Zhu
- Department of Chemistry and Chemical Biology, University of New Mexico, Albuquerque, New Mexico 87131-0001, United States
| | - Vilja Siitonen
- Department of Biochemistry, University of Turku, Turku, FIN-20014, Finland
| | - Charles E. Melançon III
- Department of Chemistry and Chemical Biology, University of New Mexico, Albuquerque, New Mexico 87131-0001, United States
| | - Mikko Metsä-Ketelä
- Department of Biochemistry, University of Turku, Turku, FIN-20014, Finland
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5
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Vuksanovic N, Zhu X, Serrano DA, Siitonen V, Metsä-Ketelä M, Melançon CE, Silvaggi NR. Structural characterization of three noncanonical NTF2-like superfamily proteins: implications for polyketide biosynthesis. Acta Crystallogr F Struct Biol Commun 2020; 76:372-383. [PMID: 32744249 PMCID: PMC7397469 DOI: 10.1107/s2053230x20009814] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2020] [Accepted: 07/17/2020] [Indexed: 12/12/2022] Open
Abstract
Proteins belonging to the NTF2-like superfamily are present in the biosynthetic pathways of numerous polyketide natural products, such as anthracyclins and benzoisochromanequinones. Some have been found to be bona fide polyketide cyclases, but many of them have roles that are currently unknown. Here, the X-ray crystal structures of three NTF2-like proteins of unknown function are reported: those of ActVI-ORFA from Streptomyces coelicolor A3(2) and its homologs Caci_6494, a protein from an uncharacterized biosynthetic cluster in Catenulispora acidiphila, and Aln2 from Streptomyces sp. CM020, a protein in the biosynthetic pathway of alnumycin. The presence of a solvent-accessible cavity and the conservation of the His/Asp dyad that is characteristic of many polyketide cyclases suggest a potential enzymatic role for these enzymes in polyketide biosynthesis.
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Affiliation(s)
- Nemanja Vuksanovic
- Department of Chemistry and Biochemistry, University of Wisconsin-Milwaukee, 3210 North Cramer Street, Milwaukee, WI 53211, USA
| | - Xuechen Zhu
- Department of Chemistry and Chemical Biology, University of New Mexico, Albuquerque, NM 87131-0001, USA
| | - Dante A. Serrano
- Department of Chemistry and Biochemistry, University of Wisconsin-Milwaukee, 3210 North Cramer Street, Milwaukee, WI 53211, USA
| | - Vilja Siitonen
- Department of Biochemistry, University of Turku, FIN-20014 Turku, Finland
| | - Mikko Metsä-Ketelä
- Department of Biochemistry, University of Turku, FIN-20014 Turku, Finland
| | - Charles E. Melançon
- Department of Chemistry and Chemical Biology, University of New Mexico, Albuquerque, NM 87131-0001, USA
| | - Nicholas R. Silvaggi
- Department of Chemistry and Biochemistry, University of Wisconsin-Milwaukee, 3210 North Cramer Street, Milwaukee, WI 53211, USA
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6
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Taguchi T, Awakawa T, Nishihara Y, Kawamura M, Ohnishi Y, Ichinose K. Bifunctionality of ActIV as a Cyclase-Thioesterase Revealed by in Vitro Reconstitution of Actinorhodin Biosynthesis in Streptomyces coelicolor A3(2). Chembiochem 2017; 18:316-323. [PMID: 27897367 DOI: 10.1002/cbic.201600589] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2016] [Indexed: 11/11/2022]
Abstract
Type II polyketide synthases iteratively generate a nascent polyketide thioester of the acyl carrier protein (ACP); this is structurally modified to produce an ACP-free intermediate towards the final metabolite. However, the timing of ACP off-loading is not well defined because of the lack of an apparent thioesterase (TE) among relevant biosynthetic enzymes. Here, ActIV, which had been assigned as a second ring cyclase (CYC) in actinorhodin (ACT) biosynthesis, was shown to possess TE activity in vitro with a model substrate, anthraquinone-2-carboxylic acid-N-acetylcysteamine. In order to investigate its function further, the ACT biosynthetic pathway in Streptomyces coelicolor A3(2) was reconstituted in vitro in a stepwise fashion up to (S)-DNPA, and the product of ActIV reaction was characterized as an ACP-free bicyclic intermediate. These findings indicate that ActIV is a bifunctional CYC-TE and provide clear evidence for the release timing of the intermediate from the ACP anchor.
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Affiliation(s)
- Takaaki Taguchi
- Research Institute of Pharmaceutical Sciences, Musashino University, Shinmachi, Nishitokyo-shi, Tokyo, 202-8585, Japan
| | - Takayoshi Awakawa
- Graduate School of Agricultural and Life Sciences, The University of Tokyo, Yayoi, Bunkyo-ku, Tokyo, 113-0032, Japan.,Present address: Graduate School of Pharmaceutical Sciences, The University of Tokyo, Hongo, Bunkyo-ku, Tokyo, 113-8657, Japan
| | - Yukitaka Nishihara
- Research Institute of Pharmaceutical Sciences, Musashino University, Shinmachi, Nishitokyo-shi, Tokyo, 202-8585, Japan
| | - Michiho Kawamura
- Research Institute of Pharmaceutical Sciences, Musashino University, Shinmachi, Nishitokyo-shi, Tokyo, 202-8585, Japan
| | - Yasuo Ohnishi
- Graduate School of Agricultural and Life Sciences, The University of Tokyo, Yayoi, Bunkyo-ku, Tokyo, 113-0032, Japan
| | - Koji Ichinose
- Research Institute of Pharmaceutical Sciences, Musashino University, Shinmachi, Nishitokyo-shi, Tokyo, 202-8585, Japan
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7
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Hemmerling F, Hahn F. Biosynthesis of oxygen and nitrogen-containing heterocycles in polyketides. Beilstein J Org Chem 2016; 12:1512-50. [PMID: 27559404 PMCID: PMC4979870 DOI: 10.3762/bjoc.12.148] [Citation(s) in RCA: 42] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2016] [Accepted: 06/22/2016] [Indexed: 01/01/2023] Open
Abstract
This review highlights the biosynthesis of heterocycles in polyketide natural products with a focus on oxygen and nitrogen-containing heterocycles with ring sizes between 3 and 6 atoms. Heterocycles are abundant structural elements of natural products from all classes and they often contribute significantly to their biological activity. Progress in recent years has led to a much better understanding of their biosynthesis. In this context, plenty of novel enzymology has been discovered, suggesting that these pathways are an attractive target for future studies.
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Affiliation(s)
- Franziska Hemmerling
- Institut für Organische Chemie and Zentrum für Biomolekulare Wirkstoffe, Gottfried Wilhelm Leibniz Universität Hannover, Schneiderberg 38, 30167 Hannover, Germany; Fakultät für Biologie, Chemie und Geowissenschaften, Universität Bayreuth, Universitätsstraße 30, 95440 Bayreuth, Germany
| | - Frank Hahn
- Institut für Organische Chemie and Zentrum für Biomolekulare Wirkstoffe, Gottfried Wilhelm Leibniz Universität Hannover, Schneiderberg 38, 30167 Hannover, Germany; Fakultät für Biologie, Chemie und Geowissenschaften, Universität Bayreuth, Universitätsstraße 30, 95440 Bayreuth, Germany
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8
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Metsä-Ketelä M, Oja T, Taguchi T, Okamoto S, Ichinose K. Biosynthesis of pyranonaphthoquinone polyketides reveals diverse strategies for enzymatic carbon–carbon bond formation. Curr Opin Chem Biol 2013; 17:562-70. [DOI: 10.1016/j.cbpa.2013.06.032] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2013] [Revised: 05/30/2013] [Accepted: 06/25/2013] [Indexed: 11/26/2022]
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9
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Taguchi T, Yabe M, Odaki H, Shinozaki M, Metsä-Ketelä M, Arai T, Okamoto S, Ichinose K. Biosynthetic Conclusions from the Functional Dissection of Oxygenases for Biosynthesis of Actinorhodin and Related Streptomyces Antibiotics. ACTA ACUST UNITED AC 2013; 20:510-20. [DOI: 10.1016/j.chembiol.2013.03.007] [Citation(s) in RCA: 38] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2012] [Revised: 02/25/2013] [Accepted: 03/06/2013] [Indexed: 11/28/2022]
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10
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Finefield JM, Sherman DH, Kreitman M, Williams RM. Enantiomeric natural products: occurrence and biogenesis. Angew Chem Int Ed Engl 2012; 51:4802-36. [PMID: 22555867 PMCID: PMC3498912 DOI: 10.1002/anie.201107204] [Citation(s) in RCA: 201] [Impact Index Per Article: 16.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2011] [Indexed: 01/07/2023]
Abstract
In nature, chiral natural products are usually produced in optically pure form-however, occasionally both enantiomers are formed. These enantiomeric natural products can arise from a single species or from different genera and/or species. Extensive research has been carried out over the years in an attempt to understand the biogenesis of naturally occurring enantiomers; however, many fascinating puzzles and stereochemical anomalies still remain.
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Finefield JM, Sherman DH, Kreitman M, Williams RM. Enantiomere Naturstoffe: Vorkommen und Biogenese. Angew Chem Int Ed Engl 2012. [DOI: 10.1002/ange.201107204] [Citation(s) in RCA: 38] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
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12
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Fitzgerald JT, Ridley CP, Khosla C. Engineered biosynthesis of the antiparasitic agent frenolicin B and rationally designed analogs in a heterologous host. J Antibiot (Tokyo) 2011; 64:759-62. [PMID: 21934692 PMCID: PMC3245331 DOI: 10.1038/ja.2011.86] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
The polyketide antibiotic frenolicin B harbors a biosynthetically intriguing benzoisochromanequinone core, and has been shown to exhibit promising antiparasitic activity against Eimeria tenella. To facilitate further exploration of its chemistry and biology, we constructed a biosynthetic route to frenolicin B in the heterologous host Streptomyces coelicolor CH999, despite the absence of key enzymes in the identified frenolicin gene cluster. Together with our understanding of the underlying polyketide biosynthetic pathway, this heterologous production system was exploited to produce analogs modified at the C15 position. Both the natural product and these analogs inhibited the growth of Toxoplasma gondii in a manner that reveals sensitivity to the length of the C15 substituent. The ability to construct a functional biosynthetic pathway, despite a lack of genetic information, illustrates the feasibility of a modular approach to engineering medicinally relevant polyketide products.
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Affiliation(s)
- Jay T Fitzgerald
- Department of Chemistry, Stanford University, Stanford, CA 94305, USA
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13
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Streptomyces vietnamensis GIMV4.0001: a granaticin-producing strain that can be readily genetically manipulated. J Antibiot (Tokyo) 2011; 64:345-7. [DOI: 10.1038/ja.2011.3] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
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Activation of the SoxR regulon in Streptomyces coelicolor by the extracellular form of the pigmented antibiotic actinorhodin. J Bacteriol 2010; 193:75-81. [PMID: 21037009 DOI: 10.1128/jb.00965-10] [Citation(s) in RCA: 54] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
The redox-sensitive transcription factor SoxR in enteric bacteria senses and regulates the cellular response to superoxide and nitric oxide. In other bacterial groups, however, it may respond to redox-active small molecules, as demonstrated for pyocyanin sensing in pseudomonads. The antibiotic-producing soil bacterium Streptomyces coelicolor contains a gene for an SoxR homologue (SCO1697) whose DNA recognition helix is identical to that of Escherichia coli SoxR. Using the E. coli SoxR binding sequence, we predicted five candidate genes of the SoxR regulon and demonstrated that SoxR binds to their promoter regions and activates their expression concurrently with the production of the blue antibiotic actinorhodin (a benzoisochromanequinone). These genes encode a probable NADPH-dependent flavin reductase (SCO2478), an NADPH-dependent quinone reductase (SCO4266), an ABC transporter (SCO7008), a monooxygenase (SCO1909), and a hypothetical protein (SCO1178). Addition of actinorhodin to exponentially growing cells activated the expression of SoxR target genes in an SoxR-dependent manner. The secreted γ-actinorhodin was over 10-fold more effective in activation than the intracellular form of actinorhodin, suggesting that SoxR is specified to respond more to exogenous signals than to intracellular metabolites. The ΔsoxR mutant was not compromised in resistance against oxidants but was slow in forming aerial mycelium on R2YE medium with reduced sporulation, and its production of actinorhodin and undecylprodigiosin was lowered by about 50% and 30%, respectively, compared to that of the wild type. These results support the proposal that SoxR senses redox-active molecules, such as actinorhodin in S. coelicolor, and induces a protective function against them. It also functions to ensure that cells undergo optimal differentiation and secondary metabolite production.
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15
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Zhou H, Li Y, Tang Y. Cyclization of aromatic polyketides from bacteria and fungi. Nat Prod Rep 2010; 27:839-68. [PMID: 20358042 DOI: 10.1039/b911518h] [Citation(s) in RCA: 102] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Affiliation(s)
- Hui Zhou
- Department of Chemical and Biomolecular Engineering, University of California, Los Angles, 420 Westwood Plaza, Los Angeles, CA 90095, USA
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16
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Oja T, Palmu K, Lehmussola H, Leppäranta O, Hännikäinen K, Niemi J, Mäntsälä P, Metsä-Ketelä M. Characterization of the alnumycin gene cluster reveals unusual gene products for pyran ring formation and dioxan biosynthesis. ACTA ACUST UNITED AC 2008; 15:1046-57. [PMID: 18940666 DOI: 10.1016/j.chembiol.2008.07.022] [Citation(s) in RCA: 45] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2007] [Revised: 07/23/2008] [Accepted: 07/28/2008] [Indexed: 11/28/2022]
Abstract
Alnumycin is closely related to the benzoisochromanequinone (BIQ) polyketides such as actinorhodin. Exceptional structural features include differences in aglycone tailoring that result in the unique alnumycin chromophore and the existence of an unusual 4-hydroxymethyl-5-hydroxy-1,3-dioxan moiety. Cloning and sequencing of the alnumycin gene cluster from Streptomyces sp. CM020 revealed expected biosynthesis genes for polyketide assembly, but several genes encoding subsequent tailoring enzymes were highly atypical. Heterologous expression studies confirmed that all of the genes required for alnumycin biosynthesis resided within the sequenced clone. Inactivation of genes aln4 and aln5 showed that the mechanism of pyran ring formation differs from actinorhodin and granaticin pathways. Further inactivation studies identified two genes, alnA and alnB, involved in the synthesis and attachment of the dioxan moiety, and resulted in the production of the polyketide prealnumycin.
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Affiliation(s)
- Terhi Oja
- Department of Biochemistry and Food Chemistry, University of Turku, FIN-20014 Turku, Finland
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17
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Willems AR, Tahlan K, Taguchi T, Zhang K, Lee ZZ, Ichinose K, Junop MS, Nodwell JR. Crystal structures of the Streptomyces coelicolor TetR-like protein ActR alone and in complex with actinorhodin or the actinorhodin biosynthetic precursor (S)-DNPA. J Mol Biol 2008; 376:1377-87. [PMID: 18207163 DOI: 10.1016/j.jmb.2007.12.061] [Citation(s) in RCA: 53] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2007] [Revised: 12/19/2007] [Accepted: 12/21/2007] [Indexed: 11/24/2022]
Abstract
Actinorhodin, an antibiotic produced by Streptomyces coelicolor, is exported from the cell by the ActA efflux pump. actA is divergently transcribed from actR, which encodes a TetR-like transcriptional repressor. We showed previously that ActR represses transcription by binding to an operator from the actA/actR intergenic region. Importantly, actinorhodin itself or various actinorhodin biosynthetic intermediates can cause ActR to dissociate from its operator, leading to derepression. This suggests that ActR may mediate timely self-resistance to an endogenously produced antibiotic by responding to one of its biosynthetic precursors. Here, we report the structural basis for this precursor-mediated derepression with crystal structures of homodimeric ActR by itself and in complex with either actinorhodin or the actinorhodin biosynthetic intermediate (S)-DNPA [4-dihydro-9-hydroxy-1-methyl-10-oxo-3-H-naphtho-[2,3-c]-pyran-3-(S)-acetic acid]. The ligand-binding tunnel in each ActR monomer has a striking hydrophilic/hydrophobic/hydrophilic arrangement of surface residues that accommodate either one hexacyclic actinorhodin molecule or two back-to-back tricyclic (S)-DNPA molecules. Moreover, our work also reveals the strongest structural evidence to date that TetR-mediated antibiotic resistance may have been acquired from an antibiotic-producer organism.
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Affiliation(s)
- A R Willems
- Department of Biochemistry and Biomedical Sciences, McMaster University, 1200 Main Street West, Hamilton, Ontario, Canada
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18
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He J, Roemer E, Lange C, Huang X, Maier A, Kelter G, Jiang Y, Xu LH, Menzel KD, Grabley S, Fiebig HH, Jiang CL, Sattler I. Structure, Derivatization, and Antitumor Activity of New Griseusins from Nocardiopsis sp. J Med Chem 2007; 50:5168-75. [PMID: 17877337 DOI: 10.1021/jm070170n] [Citation(s) in RCA: 32] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Four new griseusins, 4'-dehydro-deacetylgriseusin A (1) and 2a,8a-epoxy-epi-deacetylgriseusin B (2) as new constitutional derivatives and epi-deacetylgriseusin A (3) and epi-deacetylgriseusin B (4) as new stereoisomers, were isolated from Nocardiopsis sp. (YIM80133, DSM16644). 4'-Dehydro-deacetylgriseusin A (1) showed pronounced cytotoxic potency (mean IC50 = 0.430 microM) combined with a significant selectivity for mammary cancer, renal cancer, and melanoma in a panel consisting of 37 tumor cell lines. In a clonogenic assay with tumor cells from 51 solid tumors, 1 inhibited anchorage independent growth and in vitro colony formation of tumor cells in a concentration-dependent and tumor type selective manner. As 1 was only a minor product, a semisynthetic preparation from the major metabolite, epi-deacetylgriseusin A (3), was achieved. Our studies also yielded 9-hydroxy-epi-deacetylgriseusin B methylester (5), 4'-dehydro-9-hydroxy-deacetylgriseusin B methylester (6), and 4'-dehydro-2a,8a-epoxy-deacetylgriseusin B (7) as new synthetic isochromanequinone derivatives, which provided a basic structure-activity relationship study.
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Affiliation(s)
- Jian He
- Leibniz Institute for Natural Product Research and Infection Biology, Hans-Knöll-Institute, Beutenbergstr. 11a, D-07745 Jena, Germany
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Hertweck C, Luzhetskyy A, Rebets Y, Bechthold A. Type II polyketide synthases: gaining a deeper insight into enzymatic teamwork. Nat Prod Rep 2007; 24:162-90. [PMID: 17268612 DOI: 10.1039/b507395m] [Citation(s) in RCA: 386] [Impact Index Per Article: 22.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
This review covers advances in understanding of the biosynthesis of polyketides produced by type II PKS systems at the genetic, biochemical and structural levels.
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Affiliation(s)
- Christian Hertweck
- Leibniz Institute for Natural Product Research and Infection Biology, HKI, Beutenbergstrasse 11a, 07745 Jena, Germany
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20
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Li A, Itoh T, Taguchi T, Xiang T, Ebizuka Y, Ichinose K. Functional studies on a ketoreductase gene from Streptomyces sp. AM-7161 to control the stereochemistry in medermycin biosynthesis. Bioorg Med Chem 2005; 13:6856-63. [PMID: 16169737 DOI: 10.1016/j.bmc.2005.07.060] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2005] [Revised: 07/25/2005] [Accepted: 07/26/2005] [Indexed: 10/25/2022]
Abstract
Medermycin shows the same trans (3S,15R) configuration as actinorhodin in the pyran ring crucial for its bioactivity. One medermycin biosynthetic gene, med-ORF12, is assumed to be involved in the stereochemical control at C-3. Functional complementation suggested that it plays a similar role as actVI-ORF1 previously proved to determine the stereospecificity at C-3 in actinorhodin biosynthesis. Co-expression of med-ORF12 with actinorhodin early biosynthetic genes further demonstrated that med-ORF12 encodes a ketoreductase responsible for the enantioselective reduction at C-3 in the formation of the pyran ring.
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Affiliation(s)
- Aiying Li
- Graduate School of Pharmaceutical Sciences, The University of Tokyo, Hongo, Tokyo 113-0033, Japan
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Bililign T, Griffith BR, Thorson JS. Structure, activity, synthesis and biosynthesis of aryl-C-glycosides. Nat Prod Rep 2005; 22:742-60. [PMID: 16311633 DOI: 10.1039/b407364a] [Citation(s) in RCA: 220] [Impact Index Per Article: 11.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
The focus of this review is to highlight the structure, bioactivity and biosynthesis of naturally occurring aryl-C-glycosides. General synthetic methods and their relevance to proposed biochemical mechanisms for the aryl-C-glycoside bond formation are also presented.
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Affiliation(s)
- Tsion Bililign
- Chemistry Department, Johns Hopkins University, 3400 North Charles Street, Baltimore, MD 21218, USA.
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22
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Taguchi T, Kunieda K, Takeda-Shitaka M, Takaya D, Kawano N, Kimberley MR, Booker-Milburn KI, Stephenson GR, Umeyama H, Ebizuka Y, Ichinose K. Remarkably different structures and reaction mechanisms of ketoreductases for the opposite stereochemical control in the biosynthesis of BIQ antibiotics. Bioorg Med Chem 2004; 12:5917-27. [PMID: 15498668 DOI: 10.1016/j.bmc.2004.08.026] [Citation(s) in RCA: 15] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2004] [Revised: 08/16/2004] [Accepted: 08/17/2004] [Indexed: 10/26/2022]
Abstract
Two ketoreductases, RED1 and RED2, are involved in the biosynthesis of actinorhodin in Streptomyces coelicolor A3(2) and dihydrogranaticin in S. violaceoruber Tu22, respectively. They are responsible for the stereospecific reductions of the bicyclic intermediate to give (S)- or (R)-DNPA, although there is no similarity between their amino acid sequences. Biotransformation using synthetic analogous substrates revealed that the substrate specificities are quite different. Homology modelling studies and site directed mutagenesis showed remarkable differences in three-dimensional structures and catalytic mechanisms between RED1 and RED2.
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Affiliation(s)
- Takaaki Taguchi
- Graduate School of Pharmaceutical Sciences, The University of Tokyo, Hongo, Bunkyo-ku, Tokyo 113-0033, Japan
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Abstract
Combinatorial biosynthesis involves the genetic manipulation of natural product biosynthetic enzymes to produce potential new drug candidates that would otherwise be difficult to obtain. In either a theoretical or practical sense, the number of combinations possible from different types of natural product pathways ranges widely. Enzymes that have been the most amenable to this technology synthesize the polyketides, nonribosomal peptides, and hybrids of the two. The number of polyketide or peptide natural products theoretically possible is huge, but considerable work remains before these large numbers can be realized. Nevertheless, many analogs have been created by this technology, providing useful structure-activity relationship data and leading to a few compounds that may reach the clinic in the next few years. In this review the focus is on recent advances in our understanding of how different enzymes for natural product biosynthesis can be used successfully in this technology.
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Structure and biosynthetic implication of (S)-NHAB, a novel shunt product, from a disruptant of the actVI-ORFA gene for actinorhodin biosynthesis in Streptomyces coelicolor A3(2). Tetrahedron 2003. [DOI: 10.1016/j.tet.2003.09.036] [Citation(s) in RCA: 15] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022]
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Ichinose K, Ozawa M, Itou K, Kunieda K, Ebizuka Y. Cloning, sequencing and heterologous expression of the medermycin biosynthetic gene cluster of Streptomyces sp. AM-7161: towards comparative analysis of the benzoisochromanequinone gene clusters. MICROBIOLOGY (READING, ENGLAND) 2003; 149:1633-1645. [PMID: 12855716 DOI: 10.1099/mic.0.26310-0] [Citation(s) in RCA: 98] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
Abstract
Medermycin is a Streptomyces aromatic C-glycoside antibiotic classified in the benzoisochromanequinones (BIQs), which presents several interesting biosynthetic problems concerning polyketide synthase (PKS), post-PKS tailoring and deoxysugar pathways. The biosynthetic gene cluster for medermycin (the med cluster) was cloned from Streptomyces sp. AM-7161. Completeness of the clone was proved by the heterologous expression of a cosmid carrying the entire med cluster in Streptomyces coelicolor CH999 to produce medermycin. The DNA sequence of the cosmid (36 202 bp) revealed 34 complete ORFs, with an incomplete ORF at either end. Functional assignment of the deduced products was made for PKS and biosynthetically related enzymes, tailoring steps including strereochemical control, oxidation, angolosamine pathway, C-glycosylation, and regulation. The med cluster was estimated to be about 30 kb long, covering 29 ORFs. An unusual characteristic of the cluster is the disconnected organization of the minimal PKS genes: med-ORF23 encoding the acyl carrier protein is 20 kb apart from med-ORF1 and med-ORF2 for the two ketosynthase components. Secondly, the six genes (med-ORF14, 15, 16, 17, 18 and 20) for the biosynthesis of the deoxysugar, angolosamine, are all contiguous. Finally, the finding of a glycosyltransferase gene, med-ORF8, suggests a possible involvement of conventional C-glycosylation in medermycin biosynthesis. Comparison among the three complete BIQ gene clusters - med and those for actinorhodin (act) and granaticin (gra) - revealed some common genes whose deduced functions are unavailable from database searches (the 'unknowns'). An example is med-ORF5, a homologue of actVI-ORF3 and gra-ORF18, which was highlighted by a recent proteomic analysis of S. coelicolor A3(2).
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Affiliation(s)
- Koji Ichinose
- Graduate School of Pharmaceutical Sciences, The University of Tokyo, Hongo, Bunkyo-ku, Tokyo 113-0033, Japan
| | - Makoto Ozawa
- Graduate School of Pharmaceutical Sciences, The University of Tokyo, Hongo, Bunkyo-ku, Tokyo 113-0033, Japan
| | - Keiko Itou
- Graduate School of Pharmaceutical Sciences, The University of Tokyo, Hongo, Bunkyo-ku, Tokyo 113-0033, Japan
| | - Kanako Kunieda
- Graduate School of Pharmaceutical Sciences, The University of Tokyo, Hongo, Bunkyo-ku, Tokyo 113-0033, Japan
| | - Yutaka Ebizuka
- Graduate School of Pharmaceutical Sciences, The University of Tokyo, Hongo, Bunkyo-ku, Tokyo 113-0033, Japan
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