1
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Heo KT, Lee B, Hwang GJ, Park B, Jang JP, Hwang BY, Jang JH, Hong YS. A unique dual acyltransferase system shared in the polyketide chain initiation of kidamycinone and rubiflavinone biosynthesis. Front Microbiol 2023; 14:1274358. [PMID: 38029143 PMCID: PMC10646177 DOI: 10.3389/fmicb.2023.1274358] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2023] [Accepted: 10/04/2023] [Indexed: 12/01/2023] Open
Abstract
The pluramycin family of natural products has diverse substituents at the C2 position, which are closely related to their biological activity. Therefore, it is important to understand the biosynthesis of C2 substituents. In this study, we describe the biosynthesis of C2 moieties in Streptomyces sp. W2061, which produces kidamycin and rubiflavinone C-1, containing anthrapyran aglycones. Sequence analysis of the loading module (Kid13) of the PKS responsible for the synthesis of these anthrapyran aglycones is useful for confirming the incorporation of atypical primer units into the corresponding products. Kid13 is a ketosynthase-like decarboxylase (KSQ)-type loading module with unusual dual acyltransferase (AT) domains (AT1-1 and AT1-2). The AT1-2 domain primarily loads ethylmalonyl-CoA and malonyl-CoA for rubiflavinone and kidamycinone and rubiflavinone, respectively; however, the AT1-1 domain contributed to the functioning of the AT1-2 domain to efficiently load ethylmalonyl-CoA for rubiflavinone. We found that the dual AT system was involved in the production of kidamycinone, an aglycone of kidamycin, and rubiflavinone C-1 by other shared biosynthetic genes in Streptomyces sp. W2061. This study broadens our understanding of the incorporation of atypical primer units into polyketide products.
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Affiliation(s)
- Kyung Taek Heo
- Chemical Biology Research Center, Korea Research Institute of Bioscience and Biotechnology (KRIBB), Cheongju-si, Republic of Korea
| | - Byeongsan Lee
- Chemical Biology Research Center, Korea Research Institute of Bioscience and Biotechnology (KRIBB), Cheongju-si, Republic of Korea
- College of Pharmacy, Chungbuk National University, Cheongju-si, Republic of Korea
| | - Gwi Ja Hwang
- Chemical Biology Research Center, Korea Research Institute of Bioscience and Biotechnology (KRIBB), Cheongju-si, Republic of Korea
| | - Beomcheol Park
- Chemical Biology Research Center, Korea Research Institute of Bioscience and Biotechnology (KRIBB), Cheongju-si, Republic of Korea
- College of Pharmacy, Chungbuk National University, Cheongju-si, Republic of Korea
| | - Jun-Pil Jang
- Chemical Biology Research Center, Korea Research Institute of Bioscience and Biotechnology (KRIBB), Cheongju-si, Republic of Korea
| | - Bang Yeon Hwang
- College of Pharmacy, Chungbuk National University, Cheongju-si, Republic of Korea
| | - Jae-Hyuk Jang
- Chemical Biology Research Center, Korea Research Institute of Bioscience and Biotechnology (KRIBB), Cheongju-si, Republic of Korea
| | - Young-Soo Hong
- Chemical Biology Research Center, Korea Research Institute of Bioscience and Biotechnology (KRIBB), Cheongju-si, Republic of Korea
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2
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Vind K, Brunati C, Simone M, Sosio M, Donadio S, Iorio M. Megalochelin, a Tridecapeptide Siderophore from a Talented Streptomycete. ACS Chem Biol 2023; 18:861-874. [PMID: 36920304 PMCID: PMC10127220 DOI: 10.1021/acschembio.2c00958] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/29/2022] [Accepted: 03/06/2023] [Indexed: 03/16/2023]
Abstract
Streptomycetes are bacteria known for their extraordinary biosynthetic capabilities. Herein, we describe the genome and metabolome of a particularly talented strain, Streptomyces ID71268. Its 8.4-Mbp genome harbors 32 bioinformatically predicted biosynthetic gene clusters (BGCs), out of which 10 are expressed under a single experimental condition. In addition to five families of known metabolites with previously assigned BGCs (nigericin, azalomycin F, ectoine, SF2766, and piericidin), we were able to predict BGCs for three additional metabolites: streptochlorin, serpetene, and marinomycin. The strain also produced two families of presumably novel metabolites, one of which was associated with growth inhibitory activity against the human opportunistic pathogen Acinetobacter baumannii in an iron-dependent manner. Bioassay-guided fractionation, followed by extensive liquid chromatography-mass spectrometry (LC-MS) and NMR analyses, established that the molecule responsible for the observed antibacterial activity is an unusual tridecapeptide siderophore with a ring-and-tail structure: the heptapeptide ring is formed through a C-C bond between a 2,3-dihydroxybenzoate (DHB) cap on Gly1 and the imidazole moiety of His7, while the hexapeptide tail is sufficient for binding iron. This molecule, named megalochelin, is the largest known siderophore. The megalochelin BGC encodes a 13-module nonribosomal peptide synthetase for the synthesis of the tridecapeptide, and a copper-dependent oxidase, likely responsible for the DHB-imidazole cross-link, whereas the genes for synthesis of the DHB starter unit are apparently specified in trans by a different BGC. Our results suggest that prolific producers of specialized metabolites may conceal hidden treasures within a background of known compounds.
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Affiliation(s)
- Kristiina Vind
- NAICONS
Srl, 20139 Milan, Italy
- Host-Microbe
Interactomics Group, Wageningen University, 6708 WD Wageningen, The Netherlands
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3
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Salimimarand M, Rizzacasa MA. Synthesis of isochromanone containing natural products from myxobacteria. Org Biomol Chem 2023; 21:1341-1355. [PMID: 36655696 DOI: 10.1039/d2ob01926d] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/11/2023]
Abstract
This review details the biological activity, biosynthesis and synthesis of isochromanone metabolites isolated from myxobacteria. Strategies towards the synthesis of the isochomanone and oxazole fragments of these natural products are highlighted.
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Affiliation(s)
- Mina Salimimarand
- School of Chemistry, The Bio21 Molecular Science and Biotechnology Institute, The University of Melbourne, Parkville, Victoria, 3010, Australia.
| | - Mark A Rizzacasa
- School of Chemistry, The Bio21 Molecular Science and Biotechnology Institute, The University of Melbourne, Parkville, Victoria, 3010, Australia.
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4
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Yi D, Niroula D, Gutekunst WR, Loper JE, Yan Q, Agarwal V. A Nonfunctional Halogenase Masquerades as an Aromatizing Dehydratase in Biosynthesis of Pyrrolic Polyketides by Type I Polyketide Synthases. ACS Chem Biol 2022; 17:1351-1356. [PMID: 35675261 DOI: 10.1021/acschembio.2c00288] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
The bacterial modular type I polyketide synthases (PKSs) typically furnish nonaromatic lactone and lactam natural products. Here, by the complete in vitro enzymatic production of the polyketide antibiotic pyoluteorin, we describe the biosynthetic mechanism for the construction of an aromatic resorcylic ring by a type I PKS. We find that the pyoluteorin type I PKS does not produce an aromatic product, rather furnishing an alicyclic dihydrophloroglucinol that is later enzymatically dehydrated and aromatized. The aromatizing dehydratase is encoded in the pyoluteorin biosynthetic gene cluster (BGC), and its presence is conserved in other BGCs encoding production of pyrrolic polyketides. Sequence similarity and mutational analysis demonstrates that the overall structure and position of the active site for the aromatizing dehydratase is shared with flavin-dependent halogenases albeit with a loss in ability to perform redox catalysis. We demonstrate that the post-PKS dehydrative aromatization is critical for the antibiotic activity of pyoluteorin.
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Affiliation(s)
- Dongqi Yi
- School of Chemistry and Biochemistry, Georgia Institute of Technology, Atlanta, Georgia 30332, United States
| | - Dhirendra Niroula
- Department of Plant Sciences and Plant Pathology, Montana State University, Bozeman, Montana 59717, United States
| | - Will R Gutekunst
- School of Chemistry and Biochemistry, Georgia Institute of Technology, Atlanta, Georgia 30332, United States.,School of Materials Science and Engineering, Georgia Institute of Technology, Atlanta, Georgia 30332, United States
| | - Joyce E Loper
- Department of Botany and Plant Pathology, Oregon State University, Corvallis, Oregon 97331, United States.,USDA-Agricultural Research Service, Corvallis, Oregon 97330, United States
| | - Qing Yan
- Department of Plant Sciences and Plant Pathology, Montana State University, Bozeman, Montana 59717, United States.,Department of Botany and Plant Pathology, Oregon State University, Corvallis, Oregon 97331, United States
| | - Vinayak Agarwal
- School of Chemistry and Biochemistry, Georgia Institute of Technology, Atlanta, Georgia 30332, United States.,School of Biological Sciences, Georgia Institute of Technology, Atlanta, Georgia 30332, United States
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5
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Little R, Trottmann F, Preissler M, Hertweck C. An intramodular thioesterase domain catalyses chain release in the biosynthesis of a cytotoxic virulence factor. RSC Chem Biol 2022; 3:1121-1128. [PMID: 36128506 PMCID: PMC9428774 DOI: 10.1039/d2cb00121g] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2022] [Accepted: 07/15/2022] [Indexed: 11/21/2022] Open
Abstract
The bimodular PKS-NRPS BurA has two unusual non-C-terminal thioesterase domains. We show that the intramodular TE-B is responsible for the hydrolytic release of gonyol, an intermediate for the biosynthesis of the virulence factor malleicyprol.
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Affiliation(s)
- Rory Little
- Department of Biomolecular Chemistry, Leibniz Institute for Natural Product Research and Infection Biology HKI. Beutenbergstr. 11a, 07745 Jena, Germany
| | - Felix Trottmann
- Department of Biomolecular Chemistry, Leibniz Institute for Natural Product Research and Infection Biology HKI. Beutenbergstr. 11a, 07745 Jena, Germany
| | - Miriam Preissler
- Department of Biomolecular Chemistry, Leibniz Institute for Natural Product Research and Infection Biology HKI. Beutenbergstr. 11a, 07745 Jena, Germany
| | - Christian Hertweck
- Department of Biomolecular Chemistry, Leibniz Institute for Natural Product Research and Infection Biology HKI. Beutenbergstr. 11a, 07745 Jena, Germany
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6
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Little RF, Hertweck C. Chain release mechanisms in polyketide and non-ribosomal peptide biosynthesis. Nat Prod Rep 2021; 39:163-205. [PMID: 34622896 DOI: 10.1039/d1np00035g] [Citation(s) in RCA: 44] [Impact Index Per Article: 14.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
Review covering up to mid-2021The structure of polyketide and non-ribosomal peptide natural products is strongly influenced by how they are released from their biosynthetic enzymes. As such, Nature has evolved a diverse range of release mechanisms, leading to the formation of bioactive chemical scaffolds such as lactones, lactams, diketopiperazines, and tetronates. Here, we review the enzymes and mechanisms used for chain release in polyketide and non-ribosomal peptide biosynthesis, how these mechanisms affect natural product structure, and how they could be utilised to introduce structural diversity into the products of engineered biosynthetic pathways.
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Affiliation(s)
- Rory F Little
- Leibniz Institute for Natural Product Research and Infection Biology, HKI, Germany.
| | - Christian Hertweck
- Leibniz Institute for Natural Product Research and Infection Biology, HKI, Germany.
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7
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Gregory K, Salvador LA, Akbar S, Adaikpoh BI, Stevens DC. Survey of Biosynthetic Gene Clusters from Sequenced Myxobacteria Reveals Unexplored Biosynthetic Potential. Microorganisms 2019; 7:E181. [PMID: 31238501 PMCID: PMC6616573 DOI: 10.3390/microorganisms7060181] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2019] [Revised: 06/20/2019] [Accepted: 06/21/2019] [Indexed: 01/31/2023] Open
Abstract
Coinciding with the increase in sequenced bacteria, mining of bacterial genomes for biosynthetic gene clusters (BGCs) has become a critical component of natural product discovery. The order Myxococcales, a reputable source of biologically active secondary metabolites, spans three suborders which all include natural product producing representatives. Utilizing the BiG-SCAPE-CORASON platform to generate a sequence similarity network that contains 994 BGCs from 36 sequenced myxobacteria deposited in the antiSMASH database, a total of 843 BGCs with lower than 75% similarity scores to characterized clusters within the MIBiG database are presented. This survey provides the biosynthetic diversity of these BGCs and an assessment of the predicted chemical space yet to be discovered. Considering the mere snapshot of myxobacteria included in this analysis, these untapped BGCs exemplify the potential for natural product discovery from myxobacteria.
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Affiliation(s)
- Katherine Gregory
- Department of BioMolecular Sciences, School of Pharmacy, University of Mississippi, University, MS 38677, USA.
| | - Laura A Salvador
- Department of BioMolecular Sciences, School of Pharmacy, University of Mississippi, University, MS 38677, USA.
| | - Shukria Akbar
- Department of BioMolecular Sciences, School of Pharmacy, University of Mississippi, University, MS 38677, USA.
| | - Barbara I Adaikpoh
- Department of BioMolecular Sciences, School of Pharmacy, University of Mississippi, University, MS 38677, USA.
| | - D Cole Stevens
- Department of BioMolecular Sciences, School of Pharmacy, University of Mississippi, University, MS 38677, USA.
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8
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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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9
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Witte SNR, Hug JJ, Géraldy MNE, Müller R, Kalesse M. Biosynthesis and Total Synthesis of Pyrronazol B: a Secondary Metabolite fromNannocystis pusilla. Chemistry 2017; 23:15917-15921. [DOI: 10.1002/chem.201703782] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2017] [Indexed: 11/06/2022]
Affiliation(s)
- Swjatoslaw N. R. Witte
- Institute for Organic Chemistry; Leibniz University Hannover; Schneiderberg 1B 30167 Hannover Germany
- Centre of Biomolecular Drug Research (BMWZ); Schneiderberg 38 30167 Hannover Germany
- Germany and Helmholtz Centre for Infection Research GmbH (HZI); Inhoffenstraße 7 38124 Braunschweig Germany
| | - Joachim J. Hug
- Helmholtz-Institute for Pharmaceutical Research Saarland (HIPS); Helmholtz Centre for Infection Research (HZI) Saarland University Campus, Building E8.1; 66123 Saarbrücken Germany
| | - Magalie N. E. Géraldy
- Institute for Organic Chemistry; Leibniz University Hannover; Schneiderberg 1B 30167 Hannover Germany
- Centre of Biomolecular Drug Research (BMWZ); Schneiderberg 38 30167 Hannover Germany
- Germany and Helmholtz Centre for Infection Research GmbH (HZI); Inhoffenstraße 7 38124 Braunschweig Germany
- Deutsches Krebsforschungszentrum; Im Neuenheimer Feld 580 D-69120 Heidelberg Germany
| | - Rolf Müller
- Helmholtz-Institute for Pharmaceutical Research Saarland (HIPS); Helmholtz Centre for Infection Research (HZI) Saarland University Campus, Building E8.1; 66123 Saarbrücken Germany
| | - Markus Kalesse
- Institute for Organic Chemistry; Leibniz University Hannover; Schneiderberg 1B 30167 Hannover Germany
- Centre of Biomolecular Drug Research (BMWZ); Schneiderberg 38 30167 Hannover Germany
- Germany and Helmholtz Centre for Infection Research GmbH (HZI); Inhoffenstraße 7 38124 Braunschweig Germany
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10
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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: 19] [Impact Index Per Article: 2.7] [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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11
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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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12
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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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13
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Abstract
The α-pyrone moiety is a structural feature found in a huge variety of biologically active metabolites. In recent times new insights into additional biosynthetic mechanisms, yielding in such six-membered unsaturated ester ring residues have been obtained. The purpose of this mini-review is to give a brief overview of α-pyrones and the mechanisms forming the basis of their natural synthesis. Especially the chain interconnecting enzymes, showing homology to ketosynthases which catalyze Claisen-like condensation reactions, will be presented.
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Affiliation(s)
- Till F Schäberle
- Institute for Pharmaceutical Biology, University of Bonn, Nußallee 6, 53115 Bonn, Germany
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14
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Genome Analysis of the Fruiting Body-Forming Myxobacterium Chondromyces crocatus Reveals High Potential for Natural Product Biosynthesis. Appl Environ Microbiol 2016; 82:1945-1957. [PMID: 26773087 DOI: 10.1128/aem.03011-15] [Citation(s) in RCA: 28] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2015] [Accepted: 01/10/2016] [Indexed: 11/20/2022] Open
Abstract
Here, we report the complete genome sequence of the type strain of the myxobacterial genus Chondromyces, Chondromyces crocatus Cm c5. It presents one of the largest prokaryotic genomes featuring a single circular chromosome and no plasmids. Analysis revealed an enlarged set of tRNA genes, along with reduced pressure on preferred codon usage compared to that of other bacterial genomes. The large coding capacity and the plethora of encoded secondary metabolite biosynthetic gene clusters are in line with the capability of Cm c5 to produce an arsenal of antibacterial, antifungal, and cytotoxic compounds. Known pathways of the ajudazol, chondramide, chondrochloren, crocacin, crocapeptin, and thuggacin compound families are complemented by many more natural compound biosynthetic gene clusters in the chromosome. Whole-genome comparison of the fruiting-body-forming type strain (Cm c5, DSM 14714) to an accustomed laboratory strain which has lost this ability (nonfruiting phenotype, Cm c5 fr-) revealed genetic changes in three loci. In addition to the low synteny found with the closest sequenced representative of the same family, Sorangium cellulosum, extensive genetic information duplication and broad application of eukaryotic-type signal transduction systems are hallmarks of this 11.3-Mbp prokaryotic genome.
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15
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Helfrich EJN, Piel J. Biosynthesis of polyketides by trans-AT polyketide synthases. Nat Prod Rep 2016; 33:231-316. [DOI: 10.1039/c5np00125k] [Citation(s) in RCA: 230] [Impact Index Per Article: 28.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
This review discusses the biosynthesis of natural products that are generated bytrans-AT polyketide synthases, a family of catalytically versatile enzymes that represents one of the major group of proteins involved in the production of bioactive polyketides.
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Affiliation(s)
- Eric J. N. Helfrich
- Institute of Microbiology
- Eidgenössische Technische Hochschule (ETH) Zurich
- 8093 Zurich
- Switzerland
| | - Jörn Piel
- Institute of Microbiology
- Eidgenössische Technische Hochschule (ETH) Zurich
- 8093 Zurich
- Switzerland
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16
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Keller L, Plaza A, Dubiella C, Groll M, Kaiser M, Müller R. Macyranones: Structure, Biosynthesis, and Binding Mode of an Unprecedented Epoxyketone that Targets the 20S Proteasome. J Am Chem Soc 2015; 137:8121-30. [PMID: 26050527 DOI: 10.1021/jacs.5b03833] [Citation(s) in RCA: 33] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
In our screening efforts to identify unique scaffolds from myxobacteria for the drug discovery process, we used LC-SPE-NMR-MS techniques to isolate six linear peptides, termed macyranone A-F, from Cystobacter fuscus MCy9118. The macyranones are characterized by a rare 2-methylmalonamide moiety and an α-amino ketone fragment including an α',β'-epoxyketone in macyranone A. Gene disruption experiments confirmed the biosynthetic gene cluster of the macyranones as PKS/NRPS hybrid. Detailed in silico and phylogenetic analysis unraveled that the biosynthesis involves two conspicuous amide bond formations accomplished by an amidotransferase and a unique condensation domain. The gene cluster provides further insights into the formation of the powerful epoxyketone residue involving an acyl-CoA dehydrogenase and an unconventional free-standing thioesterase. Macyranone A was found to inhibit the chymotrypsin-like activity of the yeast 20S proteasome with an IC50 of 5.9 nM and the human constitutive proteasome and immunoproteasome with IC50 values of 21 and 15 nM, respectively. The β5 subunit of the 20S proteasome was characterized as target by X-ray crystallography revealing an irreversible binding mode similar to the natural product epoxomicin. The presence of the methylmalonamide residue facilitates the stabilization of macyranone A with the active β5 subunit of the proteasome. Macyranone A exhibits a potent inhibitory effect against the parasites Trypanosoma brucei rhodesiense and Leishmania donovani with IC50 values of 1.55 and 0.22 μM, respectively.
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Affiliation(s)
- Lena Keller
- †Department of Microbial Natural Products, Helmholtz-Institute for Pharmaceutical Research Saarland (HIPS), Helmholtz Centre for Infection Research (HZI) and Pharmaceutical Biotechnology, Saarland University, Campus C2 3, 66123 Saarbrücken, Germany.,∥German Center for Infection Research (DZIF), Partner site Hannover-Braunschweig 38124, Germany
| | - Alberto Plaza
- †Department of Microbial Natural Products, Helmholtz-Institute for Pharmaceutical Research Saarland (HIPS), Helmholtz Centre for Infection Research (HZI) and Pharmaceutical Biotechnology, Saarland University, Campus C2 3, 66123 Saarbrücken, Germany.,∥German Center for Infection Research (DZIF), Partner site Hannover-Braunschweig 38124, Germany
| | - Christian Dubiella
- ⊥Center for Integrated Protein Science Munich (CIPSM), Department für Chemie, Technische Universität München, Lichtenbergstraße 4, 85747 Garching, Germany
| | - Michael Groll
- ⊥Center for Integrated Protein Science Munich (CIPSM), Department für Chemie, Technische Universität München, Lichtenbergstraße 4, 85747 Garching, Germany
| | - Marcel Kaiser
- §Swiss Tropical and Public Health Institute (Swiss TPH), Socinstraße 57, CH-4002 Basel, Switzerland.,‡University of Basel, Petersplatz 1, CH-4003 Basel, Switzerland
| | - Rolf Müller
- †Department of Microbial Natural Products, Helmholtz-Institute for Pharmaceutical Research Saarland (HIPS), Helmholtz Centre for Infection Research (HZI) and Pharmaceutical Biotechnology, Saarland University, Campus C2 3, 66123 Saarbrücken, Germany.,∥German Center for Infection Research (DZIF), Partner site Hannover-Braunschweig 38124, Germany
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Nakamura H, Wang JX, Balskus EP. Assembly line termination in cylindrocyclophane biosynthesis: discovery of an editing type II thioesterase domain in a type I polyketide synthase. Chem Sci 2015; 6:3816-3822. [PMID: 29218151 PMCID: PMC5707447 DOI: 10.1039/c4sc03132f] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2014] [Accepted: 04/11/2015] [Indexed: 01/18/2023] Open
Abstract
Investigation of cylindrocyclophane biosynthesis reveals a C-terminal thioesterase domain involved in PKS assembly line editing, not termination.
The termination step is an important source of structural diversity in polyketide biosynthesis. Most type I polyketide synthase (PKS) assembly lines are terminated by a thioesterase (TE) domain located at the C-terminus of the final module, while other PKS assembly lines lack a terminal TE domain and are instead terminated by a separate enzyme in trans. In cylindrocyclophane biosynthesis, the type I modular PKS assembly line is terminated by a freestanding type III PKS (CylI). Unexpectedly, the final module of the type I PKS (CylH) also possesses a C-terminal TE domain. Unlike typical type I PKSs, the CylH TE domain does not influence assembly line termination by CylI in vitro. Instead, this domain phylogenetically resembles a type II TE and possesses activity consistent with an editing function. This finding may shed light on the evolution of unusual PKS termination logic. In addition, the presence of related type II TE domains in many cryptic type I PKS and nonribosomal peptide synthetase (NRPS) assembly lines has implications for pathway annotation, product prediction, and engineering.
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Affiliation(s)
- H Nakamura
- Department of Chemistry and Chemical Biology , Harvard University , Cambridge , Massachusetts 02138 , USA .
| | - J X Wang
- Small Molecule Mass Spectrometry Facility , FAS Division of Science , Cambridge , Massachusetts 02138 , USA
| | - E P Balskus
- Department of Chemistry and Chemical Biology , Harvard University , Cambridge , Massachusetts 02138 , USA .
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18
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Takesue T, Fujita M, Sugimura T, Akutsu H. A Series of Two Oxidation Reactions of ortho-Alkenylbenzamide with Hypervalent Iodine(III): A Concise Entry into (3R,4R)-4-Hydroxymellein and (3R,4R)-4-Hydroxy-6-methoxymellein. Org Lett 2014; 16:4634-7. [DOI: 10.1021/ol502225p] [Citation(s) in RCA: 39] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Affiliation(s)
- Takuya Takesue
- Graduate
School of Material
Science, University of Hyogo, Kohto, Kamigori, Hyogo 678-1297, Japan
| | - Morifumi Fujita
- Graduate
School of Material
Science, University of Hyogo, Kohto, Kamigori, Hyogo 678-1297, Japan
| | - Takashi Sugimura
- Graduate
School of Material
Science, University of Hyogo, Kohto, Kamigori, Hyogo 678-1297, Japan
| | - Hiroki Akutsu
- Graduate
School of Material
Science, University of Hyogo, Kohto, Kamigori, Hyogo 678-1297, Japan
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19
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Muliandi A, Katsuyama Y, Sone K, Izumikawa M, Moriya T, Hashimoto J, Kozone I, Takagi M, Shin-ya K, Ohnishi Y. Biosynthesis of the 4-methyloxazoline-containing nonribosomal peptides, JBIR-34 and -35, in Streptomyces sp. Sp080513GE-23. ACTA ACUST UNITED AC 2014; 21:923-34. [PMID: 25041948 DOI: 10.1016/j.chembiol.2014.06.004] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2014] [Revised: 06/03/2014] [Accepted: 06/04/2014] [Indexed: 01/19/2023]
Abstract
JBIR-34 and -35 produced by Streptomyces sp. Sp080513GE-23 are nonribosomal peptides that possess an unusual 4-methyloxazoline moiety. Through draft genome sequencing, cosmid cloning, and gene disruption, the JBIR-34 and -35 biosynthesis gene cluster (fmo cluster) was identified; it encodes 20 proteins including five nonribosomal peptide synthetases (NRPSs). Disruption of one of these NRPS genes (fmoA3) resulted in no JBIR-34 and -35 production and accumulation of 6-chloro-4-hydroxyindole-3-carboxylic acid. Stable isotope-feeding experiments indicated that the methyl group of the methyloxazoline ring is derived from alanine rather than methionine. A recombinant FmoH protein, a glycine/serine hydroxymethyltransferase homolog, catalyzed conversion of α-methyl-l-serine into d-alanine (the reverse reaction of α-methyl-l-serine synthesis catalyzed by FmoH in vivo). Taken together, we concluded that α-methyl-l-serine synthesized from d-alanine is incorporated into JBIR-34 and -35 to form the 4-methyloxazoline moiety. We also propose the biosynthesis pathway of JBIR-34 and -35.
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Affiliation(s)
- Adeline Muliandi
- Department of Biotechnology, Graduate School of Agricultural and Life Sciences, The University of Tokyo, 1-1-1 Yayoi, Bunkyo-ku, Tokyo 113-8657, Japan
| | - Yohei Katsuyama
- Department of Biotechnology, Graduate School of Agricultural and Life Sciences, The University of Tokyo, 1-1-1 Yayoi, Bunkyo-ku, Tokyo 113-8657, Japan
| | - Kaoru Sone
- Department of Biotechnology, Graduate School of Agricultural and Life Sciences, The University of Tokyo, 1-1-1 Yayoi, Bunkyo-ku, Tokyo 113-8657, Japan
| | - Miho Izumikawa
- Japan Biological Informatics Consortium (JBIC), 2-4-7 Aomi, Koto-ku, Tokyo 135-0064, Japan
| | - Tomohiro Moriya
- Department of Biotechnology, Graduate School of Agricultural and Life Sciences, The University of Tokyo, 1-1-1 Yayoi, Bunkyo-ku, Tokyo 113-8657, Japan
| | - Junko Hashimoto
- Japan Biological Informatics Consortium (JBIC), 2-4-7 Aomi, Koto-ku, Tokyo 135-0064, Japan
| | - Ikuko Kozone
- Japan Biological Informatics Consortium (JBIC), 2-4-7 Aomi, Koto-ku, Tokyo 135-0064, Japan
| | - Motoki Takagi
- Japan Biological Informatics Consortium (JBIC), 2-4-7 Aomi, Koto-ku, Tokyo 135-0064, Japan
| | - Kazuo Shin-ya
- National Institute of Advanced Industrial Science and Technology (AIST), 2-4-7 Aomi, Koto-ku, Tokyo 135-0064, Japan
| | - Yasuo Ohnishi
- Department of Biotechnology, Graduate School of Agricultural and Life Sciences, The University of Tokyo, 1-1-1 Yayoi, Bunkyo-ku, Tokyo 113-8657, Japan.
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Ahrendt T, Miltenberger M, Haneburger I, Kirchner F, Kronenwerth M, Brachmann AO, Hilbi H, Bode HB. Biosynthesis of the natural fluorophore legioliulin from legionella. Chembiochem 2013; 14:1415-8. [PMID: 23821465 DOI: 10.1002/cbic.201300373] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2013] [Indexed: 11/07/2022]
Abstract
Let it shine: The biosynthesis of the UV fluorophore legioliulin (1) from Legionella spp. was elucidated and the phenylalanine ammonium lyase LglD responsible for the formation of the starter unit cinnamic acid was biochemically characterized. Additionally, two novel derivatives differing in the starter unit have been identified by mutasynthesis experiments.
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Affiliation(s)
- Tilman Ahrendt
- Merck Stiftungsprofessur für Molekulare Biotechnologie, Fachbereich Biowissenschaften, Max-von-Laue-Str. 9, 60438 Frankfurt am Main, Germany
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21
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Birkett S, Ganame D, Hawkins BC, Meiries S, Quach T, Rizzacasa MA. Total Synthesis of the Proposed Structure of 8-Deshydroxyajudazol A: A Modified Approach to 2,4-Disubstituted Oxazoles. J Org Chem 2012; 78:116-23. [DOI: 10.1021/jo302055w] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/29/2023]
Affiliation(s)
- Stephen Birkett
- School of Chemistry, The Bio21 Institute, The University of Melbourne, Victoria 3010, Australia
| | - Danny Ganame
- School of Chemistry, The Bio21 Institute, The University of Melbourne, Victoria 3010, Australia
| | - Bill C. Hawkins
- School of Chemistry, The Bio21 Institute, The University of Melbourne, Victoria 3010, Australia
| | - Sébastien Meiries
- School of Chemistry, The Bio21 Institute, The University of Melbourne, Victoria 3010, Australia
| | - Tim Quach
- School of Chemistry, The Bio21 Institute, The University of Melbourne, Victoria 3010, Australia
| | - Mark A. Rizzacasa
- School of Chemistry, The Bio21 Institute, The University of Melbourne, Victoria 3010, Australia
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22
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Essig S, Bretzke S, Müller R, Menche D. Full Stereochemical Determination of Ajudazols A and B by Bioinformatics Gene Cluster Analysis and Total Synthesis of Ajudazol B by an Asymmetric Ortholithiation Strategy. J Am Chem Soc 2012; 134:19362-5. [DOI: 10.1021/ja309685n] [Citation(s) in RCA: 54] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/16/2023]
Affiliation(s)
- Sebastian Essig
- Institut für Organische
Chemie, Ruprecht-Karls Universität Heidelberg, Im Neuenheimer Feld 270, 69120 Heidelberg, Germany
| | - Sebastian Bretzke
- Institut für Organische
Chemie, Ruprecht-Karls Universität Heidelberg, Im Neuenheimer Feld 270, 69120 Heidelberg, Germany
| | - Rolf Müller
- Helmholtz-Institut für
Pharmazeutische Forschung Saarland (HIPS) and Institut für
Pharmazeutische Biotechnologie, Universität des Saarlandes, Gebäude C 2.3, 66123 Saarbrücken,
Germany
| | - Dirk Menche
- Kekulé-Institut
für
Organische Chemie und Biochemie, Universität Bonn, Gerhard-Domagk-Str. 1, 53121 Bonn, Germany
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23
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24
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25
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Mady ASA, Zolova OE, Millán MÁS, Villamizar G, de la Calle F, Lombó F, Garneau-Tsodikova S. Characterization of TioQ, a type II thioesterase from the thiocoraline biosynthetic cluster. MOLECULAR BIOSYSTEMS 2011; 7:1999-2011. [PMID: 21483938 DOI: 10.1039/c1mb05044c] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/12/2023]
Abstract
An antitumor agent thiocoraline is a thiodepsipeptide marine product derived from two Micromonospora sp. strains that inhibits protein synthesis by binding of its key 3-hydroxyquinaldic acid (3HQA) chromophores to duplex DNA. There are at least two potential pathways via which the 3HQA moiety could be biosynthesized from L-Trp. By biochemical characterization and by preparation of knockouts of an adenylation-thiolation enzyme, TioK, and of two type II thioesterases, TioP and TioQ, found in the thiocoraline biosynthetic gene cluster, we gained valuable insight into the pathway followed for the production of 3HQA.
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Affiliation(s)
- Ahmed S A Mady
- University of Michigan, Life Sciences Institute, 210 Washtenaw Ave, Ann Arbor, MI 48109, USA
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26
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Birkett S, Ganame D, Hawkins BC, Meiries S, Quach T, Rizzacasa MA. Total Synthesis of 8-Deshydroxyajudazol B. Org Lett 2011; 13:1964-7. [DOI: 10.1021/ol200331u] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/04/2023]
Affiliation(s)
- Stephen Birkett
- School of Chemistry, The Bio21 Institute, The University of Melbourne, Victoria 3010, Australia
| | - Danny Ganame
- School of Chemistry, The Bio21 Institute, The University of Melbourne, Victoria 3010, Australia
| | - Bill C. Hawkins
- School of Chemistry, The Bio21 Institute, The University of Melbourne, Victoria 3010, Australia
| | - Sébastien Meiries
- School of Chemistry, The Bio21 Institute, The University of Melbourne, Victoria 3010, Australia
| | - Tim Quach
- School of Chemistry, The Bio21 Institute, The University of Melbourne, Victoria 3010, Australia
| | - Mark A. Rizzacasa
- School of Chemistry, The Bio21 Institute, The University of Melbourne, Victoria 3010, Australia
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27
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Vickers CE, Blank LM, Krömer JO. Grand challenge commentary: Chassis cells for industrial biochemical production. Nat Chem Biol 2010; 6:875-7. [PMID: 21079595 DOI: 10.1038/nchembio.484] [Citation(s) in RCA: 54] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Abstract
Hyper-performing whole-cell catalysts are required for the renewable and sustainable production of petrochemical replacements. Chassis cells—self-replicating minimal machines that can be tailored for the production of specific chemicals—will provide the starting point for designing these hyper-performing 'turbo cells'.
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Affiliation(s)
- Claudia E Vickers
- Australian Institute for Bioengineering and Nanotechnology, The University of Queensland, St. Lucia, Australia.
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