1
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Fergusson CH, Saulog J, Paulo BS, Wilson DM, Liu DY, Morehouse NJ, Waterworth S, Barkei J, Gray CA, Kwan JC, Eustaquio AS, Linington RG. Discovery of a lagriamide polyketide by integrated genome mining, isotopic labeling, and untargeted metabolomics. Chem Sci 2024; 15:8089-8096. [PMID: 38817573 PMCID: PMC11134395 DOI: 10.1039/d4sc00825a] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2024] [Accepted: 04/18/2024] [Indexed: 06/01/2024] Open
Abstract
Microorganisms from the order Burkholderiales have been the source of a number of important classes of natural products in recent years. For example, study of the beetle-associated symbiont Burkholderia gladioli led to the discovery of the antifungal polyketide lagriamide; an important molecule from the perspectives of both biotechnology and chemical ecology. As part of a wider project to sequence Burkholderiales genomes from our in-house Burkholderiales library we identified a strain containing a biosynthetic gene cluster (BGC) similar to the original lagriamide BGC. Structure prediction failed to identify any candidate masses for the products of this BGC from untargeted metabolomics mass spectrometry data. However, genome mining from publicly available databases identified fragments of this BGC from a culture collection strain of Paraburkholderia. Whole genome sequencing of this strain revealed the presence of a homologue of this BGC with very high sequence identity. Stable isotope feeding of the two strains in parallel using our newly developed IsoAnalyst platform identified the product of this lagriamide-like BGC directly from the crude fermentation extracts, affording a culturable supply of this interesting compound class. Using a combination of bioinformatic, computational and spectroscopic methods we defined the absolute configurations for all 11 chiral centers in this new metabolite, which we named lagriamide B. Biological testing of lagriamide B against a panel of 21 bacterial and fungal pathogens revealed antifungal activity against the opportunistic human pathogen Aspergillus niger, while image-based Cell Painting analysis indicated that lagriamide B also causes actin filament disruption in U2-OS osteosarcoma cells.
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Affiliation(s)
- Claire H Fergusson
- Department of Chemistry, Simon Fraser University 8888 University Drive Burnaby BC V5A 1S6 Canada
| | - Julia Saulog
- Department of Chemistry, Simon Fraser University 8888 University Drive Burnaby BC V5A 1S6 Canada
| | - Bruno S Paulo
- Department of Pharmaceutical Sciences and Center for Biomolecular Sciences, College of Pharmacy, University of Illinois at Chicago Chicago IL 60607 USA
| | - Darryl M Wilson
- Department of Chemistry, Simon Fraser University 8888 University Drive Burnaby BC V5A 1S6 Canada
| | - Dennis Y Liu
- Department of Chemistry, Simon Fraser University 8888 University Drive Burnaby BC V5A 1S6 Canada
| | - Nicholas J Morehouse
- Department of Biological Sciences, University of New Brunswick Saint John NB Canada
| | - Samantha Waterworth
- Division of Pharmaceutical Sciences, School of Pharmacy, University of Wisconsin Madison WI 53705 USA
| | - John Barkei
- Division of Pharmaceutical Sciences, School of Pharmacy, University of Wisconsin Madison WI 53705 USA
| | - Christopher A Gray
- Department of Biological Sciences, University of New Brunswick Saint John NB Canada
| | - Jason C Kwan
- Division of Pharmaceutical Sciences, School of Pharmacy, University of Wisconsin Madison WI 53705 USA
| | - Alessandra S Eustaquio
- Department of Pharmaceutical Sciences and Center for Biomolecular Sciences, College of Pharmacy, University of Illinois at Chicago Chicago IL 60607 USA
| | - Roger G Linington
- Department of Chemistry, Simon Fraser University 8888 University Drive Burnaby BC V5A 1S6 Canada
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2
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Nogawa T, Kato N, Shimizu T, Okano A, Futamura Y, Takahashi S, Koshino H, Osada H. Wakodecaline C, new tetrahydrofuran-fused decalin metabolite isolated from fungus Pyrenochaetopsis sp. RK10-F058. J Antibiot (Tokyo) 2023; 76:346-350. [PMID: 37020042 DOI: 10.1038/s41429-023-00613-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2023] [Revised: 02/22/2023] [Accepted: 03/08/2023] [Indexed: 04/07/2023]
Abstract
A new decalin-containing secondary metabolite, wakodecaline C, was isolated from a fungus Pyrenochaetopsis sp. RK10-F058 by screening structurally interesting metabolites based on LC/MS profiling. The structure including the absolute configuration was determined by a combination of spectroscopic methods including NMR and mass spectrometry, chemical reaction, and calculation of ECD spectra. Wakodecaline C has unique structural features containing a tetrahydrofuran-fused decalin skeleton and tetramic acid moiety, which are connected through a double bond. The compound showed moderate cytotoxicity against HL-60 cells and antimalarial activity against the Plasmodium falciparum 3D7 strain.
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Affiliation(s)
- Toshihiko Nogawa
- Molecular Structure Characterization Unit, RIKEN Center for Sustainable Resource Science, 2-1 Hirosawa, Wako, Saitama, 351-0198, Japan
- Chemica Biology Research Group, RIKEN Center for Sustainable Resource Science, 2-1 Hirosawa, Wako, Saitama, 351-0198, Japan
| | - Naoki Kato
- Faculty of Agriculture, Setsunan University, 45-1 Nagaotoge-cho, Hirakata, Osaka, 573-0101, Japan.
- Natural Product Biosynthesis Research Unit, RIKEN Center for Sustainable Resource Science, 2-1 Hirosawa, Wako, Saitama, 351-0198, Japan.
| | - Takeshi Shimizu
- Chemica Biology Research Group, RIKEN Center for Sustainable Resource Science, 2-1 Hirosawa, Wako, Saitama, 351-0198, Japan
| | - Akiko Okano
- Chemica Biology Research Group, RIKEN Center for Sustainable Resource Science, 2-1 Hirosawa, Wako, Saitama, 351-0198, Japan
| | - Yushi Futamura
- Chemica Biology Research Group, RIKEN Center for Sustainable Resource Science, 2-1 Hirosawa, Wako, Saitama, 351-0198, Japan
- Waseda Research Institute for Science and Engineering, Waseda University, Tokyo, 169-8555, Japan
| | - Shunji Takahashi
- Natural Product Biosynthesis Research Unit, RIKEN Center for Sustainable Resource Science, 2-1 Hirosawa, Wako, Saitama, 351-0198, Japan
| | - Hiroyuki Koshino
- Molecular Structure Characterization Unit, RIKEN Center for Sustainable Resource Science, 2-1 Hirosawa, Wako, Saitama, 351-0198, Japan
| | - Hiroyuki Osada
- Chemica Biology Research Group, RIKEN Center for Sustainable Resource Science, 2-1 Hirosawa, Wako, Saitama, 351-0198, Japan
- Department of Pharmaceutical Sciences, University of Shizuoka, 52-1, Yada, Suruga-ku, Shizuoka, 422-8526, Japan
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3
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Magar RT, Pham VTT, Poudel PB, Nguyen HT, Bridget AF, Sohng JK. Biosynthetic pathway of peucemycin and identification of its derivative from Streptomyces peucetius. Appl Microbiol Biotechnol 2023; 107:1217-1231. [PMID: 36680588 DOI: 10.1007/s00253-023-12385-8] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2022] [Revised: 01/08/2023] [Accepted: 01/10/2023] [Indexed: 01/22/2023]
Abstract
Streptomyces peucetius ATCC 27952 is a well-known producer of important anticancer compounds, daunorubicin and doxorubicin. In this study, we successfully identified a new macrolide, 25-hydroxy peucemycin, that exhibited an antibacterial effect on some pathogens. Based on the structure of a newly identified compound and through the inactivation of a polyketide synthase gene, we successfully identified its biosynthetic gene cluster which was considered to be the cryptic biosynthetic gene cluster. The biosynthetic gene cluster spans 51 kb with 16 open reading frames. Five type I polyketide synthase (PKS) genes encode eight modules that synthesize the polyketide chain of peucemycin before undergoing post-PKS tailoring steps. In addition to the regular starter and extender units, some modules have specificity towards ethylmalonyl-CoA and unusual butylmalonyl-CoA. A credible explanation for the specificity of the unusual extender unit has been searched for. Moreover, the enzyme responsible for the final tailoring pathway was also identified. Based on all findings, a plausible biosynthetic pathway is here proposed. KEY POINTS: • Identification of a new macrolide, 25-hydroxy peucemycin. • An FMN-dependent monooxygenase is responsible for the hydroxylation of peucemycin. • The module encoded by peuC is unique to accept the butylmalonyl-CoA as an unusual extender unit.
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Affiliation(s)
- Rubin Thapa Magar
- Department of Life Science and Biochemical Engineering, Sun Moon University, 70 Sun Moon-Ro 221, Tangjeong-Myeon, Asan-Si, Chungnam, 31460, South Korea
| | - Van Thuy Thi Pham
- Department of Life Science and Biochemical Engineering, Sun Moon University, 70 Sun Moon-Ro 221, Tangjeong-Myeon, Asan-Si, Chungnam, 31460, South Korea
| | - Purna Bahadur Poudel
- Department of Life Science and Biochemical Engineering, Sun Moon University, 70 Sun Moon-Ro 221, Tangjeong-Myeon, Asan-Si, Chungnam, 31460, South Korea
| | - Hue Thi Nguyen
- Department of Life Science and Biochemical Engineering, Sun Moon University, 70 Sun Moon-Ro 221, Tangjeong-Myeon, Asan-Si, Chungnam, 31460, South Korea
| | - Adzemye Fovennso Bridget
- Department of Life Science and Biochemical Engineering, Sun Moon University, 70 Sun Moon-Ro 221, Tangjeong-Myeon, Asan-Si, Chungnam, 31460, South Korea
| | - Jae Kyung Sohng
- Department of Life Science and Biochemical Engineering, Sun Moon University, 70 Sun Moon-Ro 221, Tangjeong-Myeon, Asan-Si, Chungnam, 31460, South Korea.
- Department of Pharmaceutical Engineering and Biotechnology, Sun Moon University, 70 Sun Moon-Ro 221, Tangjeong-Myeon, Asan-Si, Chungnam, 31460, South Korea.
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4
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Yamamoto S, Matsuyama T, Ozaki T, Takino J, Sato H, Uchiyama M, Minami A, Oikawa H. Elucidation of Late-Stage Biosynthesis of Phomoidride: Proposal of Cyclization Mechanism Affording Characteristic Nine-Membered Ring of Fungal Dimeric Anhydride. J Am Chem Soc 2022; 144:20998-21004. [DOI: 10.1021/jacs.2c09308] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Affiliation(s)
- Shintaro Yamamoto
- Department of Chemistry, Faculty of Science, Hokkaido University, Sapporo 060-0810, Japan
| | - Taro Matsuyama
- Graduate School of Pharmaceutical Sciences, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-0033, Japan
| | - Taro Ozaki
- Graduate School of Pharmaceutical Sciences, Tohoku University, Sendai 980-8578, Japan
| | - Junya Takino
- Department of Chemistry, Faculty of Science, Hokkaido University, Sapporo 060-0810, Japan
| | - Hajime Sato
- Graduate School of Pharmaceutical Sciences, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-0033, Japan
- Interdisciplinary Graduate School of Medicine and Engineering, University of Yamanashi, Kofu, Yamanashi 400-8510, Japan
| | - Masanobu Uchiyama
- Graduate School of Pharmaceutical Sciences, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-0033, Japan
| | - Atsushi Minami
- Department of Chemistry, Faculty of Science, Hokkaido University, Sapporo 060-0810, Japan
| | - Hideaki Oikawa
- Department of Chemistry, Faculty of Science, Hokkaido University, Sapporo 060-0810, Japan
- Innovation Center of Marine Biotechnology and Pharmaceuticals, School of Biotechnology and Health Sciences, Wuyi University, Jiangmen, 529020, Guangdong, China
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5
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Bilyk O, Oliveira GS, de Angelo RM, Almeida MO, Honório KM, Leeper FJ, Dias MVB, Leadlay PF. Enzyme-Catalyzed Spiroacetal Formation in Polyketide Antibiotic Biosynthesis. J Am Chem Soc 2022; 144:14555-14563. [PMID: 35921248 DOI: 10.1021/jacs.2c03313] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
A key step in the biosynthesis of numerous polyketides is the stereospecific formation of a spiroacetal (spiroketal). We report here that spiroacetal formation in the biosynthesis of the macrocyclic polyketides ossamycin and oligomycin involves catalysis by a novel spiroacetal cyclase. OssO from the ossamycin biosynthetic gene cluster (BGC) is homologous to OlmO, the product of an unannotated gene from the oligomycin BGC. The deletion of olmO abolished oligomycin production and led to the isolation of oligomycin-like metabolites lacking the spiroacetal structure. Purified OlmO catalyzed complete conversion of the major metabolite into oligomycin C. Crystal structures of OssO and OlmO reveal an unusual 10-strand β-barrel. Three conserved polar residues are clustered together in the β-barrel cavity, and site-specific mutation of any of these residues either abolished or substantially diminished OlmO activity, supporting a role for general acid/general base catalysis in spiroacetal formation.
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Affiliation(s)
- Oksana Bilyk
- Department of Biochemistry, University of Cambridge, 80 Tennis Court Road, Cambridge CB2 1GA, United Kingdom
| | - Gabriel S Oliveira
- Department of Microbiology, Institute of Biomedical Science, University of Sao Paulo, Av. Prof. Lineu Prestes, 1374, São Paulo, SP 05508-000, Brazil
| | - Rafaela M de Angelo
- School of Arts, Sciences and Humanities (EACH), University of Sao Paulo, São Paulo, SP 03828-000, Brazil
| | - Michell O Almeida
- Institute of Chemistry of Sao Carlos (IQSC), University of Sao Paulo, Sao Carlos, SP 13566-590, Brazil
| | - Kathia Maria Honório
- School of Arts, Sciences and Humanities (EACH), University of Sao Paulo, São Paulo, SP 03828-000, Brazil
| | - Finian J Leeper
- Yusuf Hamied Department of Chemistry, University of Cambridge, Lensfield Road, Cambridge CB2 1EW, United Kingdom
| | - Marcio V B Dias
- Department of Microbiology, Institute of Biomedical Science, University of Sao Paulo, Av. Prof. Lineu Prestes, 1374, São Paulo, SP 05508-000, Brazil.,Department of Chemistry, University of Warwick, Coventry CV47 7AL, United Kingdom
| | - Peter F Leadlay
- Department of Biochemistry, University of Cambridge, 80 Tennis Court Road, Cambridge CB2 1GA, United Kingdom
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6
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Takahashi S. Studies on Streptomyces sp. SN-593: reveromycin biosynthesis, β-carboline biomediator activating LuxR family regulator, and construction of terpenoid biosynthetic platform. J Antibiot (Tokyo) 2022; 75:432-444. [PMID: 35778609 DOI: 10.1038/s41429-022-00539-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2022] [Revised: 06/08/2022] [Accepted: 06/09/2022] [Indexed: 11/09/2022]
Abstract
Streptomyces represents an important reservoir for biologically active natural products. Understanding the biosynthetic mechanism and the mode of gene expression is important for enhanced metabolite production and evaluation of biological activities. This review provides an overview of biosynthetic studies investigating reveromycin and β-carboline biomediators that enhanced the production of reveromycin in Streptomyces sp. SN-593 through activation of the LuxR family regulator. Furthermore, based on the optimal expression of a pathway specific regulator controlling the mevalonate pathway gene cluster, Streptomyces sp. SN-593 was developed as a platform for terpenoid compounds mass production.
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Affiliation(s)
- Shunji Takahashi
- Natural Product Biosynthesis Research Unit, RIKEN Centre for Sustainable Resource Science, 2-1 Hirosawa, Wako, Saitama, 351-0198, Japan.
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7
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Takao R, Sakai K, Koshino H, Osada H, Takahashi S. Identification of the kinanthraquinone biosynthetic gene cluster by expression of an atypical response regulator. Biosci Biotechnol Biochem 2021; 85:714-721. [DOI: 10.1093/bbb/zbaa082] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2020] [Accepted: 10/29/2020] [Indexed: 01/15/2023]
Abstract
ABSTRACT
Recent advances in genome sequencing have revealed a variety of secondary metabolite biosynthetic gene clusters in actinomycetes. Understanding the biosynthetic mechanism controlling secondary metabolite production is important for utilizing these gene clusters. In this study, we focused on the kinanthraquinone biosynthetic gene cluster, which has not been identified yet in Streptomyces sp. SN-593. Based on chemical structure, 5 type II polyketide synthase gene clusters were listed from the genome sequence of Streptomyces sp. SN-593. Among them, a candidate gene cluster was selected by comparing the gene organization with grincamycin, which is synthesized through an intermediate similar to kinanthraquinone. We initially utilized a BAC library for subcloning the kiq gene cluster, performed heterologous expression in Streptomyces lividans TK23, and identified the production of kinanthraquinone and kinanthraquinone B. We also found that heterologous expression of kiqA, which belongs to the DNA-binding response regulator OmpR family, dramatically enhanced the production of kinanthraquinones.
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Affiliation(s)
- Risa Takao
- Graduate School of Science and Engineering, Saitama University, Sakura-ku, Saitama-shi, Saitama, Japan
- Natural Product Biosynthesis Research Unit, RIKEN Centre for Sustainable Resource Science, Wako, Saitama, Japan
| | - Katsuyuki Sakai
- Natural Product Biosynthesis Research Unit, RIKEN Centre for Sustainable Resource Science, Wako, Saitama, Japan
| | - Hiroyuki Koshino
- Molecular Structure Characterization Unit, Technology Platform Division, RIKEN Center for Sustainable Resource Science, Wako, Saitama, Japan
| | - Hiroyuki Osada
- Chemical Biology Research Group, RIKEN Centre for Sustainable Resource Science, Wako, Saitama, Japan
| | - Shunji Takahashi
- Graduate School of Science and Engineering, Saitama University, Sakura-ku, Saitama-shi, Saitama, Japan
- Natural Product Biosynthesis Research Unit, RIKEN Centre for Sustainable Resource Science, Wako, Saitama, Japan
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8
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Panthee S, Kito N, Hayashi T, Shimizu T, Ishikawa J, Hamamoto H, Osada H, Takahashi S. β-carboline chemical signals induce reveromycin production through a LuxR family regulator in Streptomyces sp. SN-593. Sci Rep 2020; 10:10230. [PMID: 32576869 PMCID: PMC7311520 DOI: 10.1038/s41598-020-66974-y] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2019] [Accepted: 05/27/2020] [Indexed: 12/21/2022] Open
Abstract
Actinomycetes bacteria produce diverse bioactive molecules that are useful as drug seeds. To improve their yield, researchers often optimize the fermentation medium. However, exactly how the extracellular chemicals present in the medium activate secondary metabolite gene clusters remains unresolved. BR-1, a β-carboline compound, was recently identified as a chemical signal that enhanced reveromycin A production in Streptomyces sp. SN-593. Here we show that BR-1 specifically bound to the transcriptional regulator protein RevU in the reveromycin A biosynthetic gene cluster, and enhanced RevU binding to its promoter. RevU belongs to the LuxR family regulator that is widely found in bacteria. Interestingly, BR-1 and its derivatives also enhanced the production of secondary metabolites in other Streptomyces species. Although LuxR-N-acyl homoserine lactone systems have been characterized in Gram-negative bacteria, we revealed LuxR-β-carboline system in Streptomyces sp. SN-593 for the production of secondary metabolites. This study might aid in understanding hidden chemical communication by β-carbolines.
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Affiliation(s)
- Suresh Panthee
- RIKEN Center for Sustainable Resource Science, Natural Product Biosynthesis Research Unit, Wako, Hirosawa 2-1, 351-0198, Saitama, Japan.,Teikyo University Institute of Medical Mycology, Otsuka 359, Hachioji, Tokyo, Japan
| | - Naoko Kito
- RIKEN Center for Sustainable Resource Science, Natural Product Biosynthesis Research Unit, Wako, Hirosawa 2-1, 351-0198, Saitama, Japan
| | - Teruo Hayashi
- RIKEN Center for Sustainable Resource Science, Chemical Biology Research Group, Wako, Hirosawa 2-1, 351-0198, Saitama, Japan
| | - Takeshi Shimizu
- RIKEN Center for Sustainable Resource Science, Chemical Biology Research Group, Wako, Hirosawa 2-1, 351-0198, Saitama, Japan
| | - Jun Ishikawa
- Department of Bioactive Molecules, National Institute of Infectious Diseases, Toyama 1-23-1, Shinjuku, Tokyo, 162-8640, Japan
| | - Hiroshi Hamamoto
- Teikyo University Institute of Medical Mycology, Otsuka 359, Hachioji, Tokyo, Japan
| | - Hiroyuki Osada
- RIKEN Center for Sustainable Resource Science, Chemical Biology Research Group, Wako, Hirosawa 2-1, 351-0198, Saitama, Japan.
| | - Shunji Takahashi
- RIKEN Center for Sustainable Resource Science, Natural Product Biosynthesis Research Unit, Wako, Hirosawa 2-1, 351-0198, Saitama, Japan.
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9
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Kanoh N, Kawamata-Asano A, Suzuki K, Takahashi Y, Miyazawa T, Nakamura T, Moriya T, Hirano H, Osada H, Iwabuchi Y, Takahashi S. An integrated screening system for the selection of exemplary substrates for natural and engineered cytochrome P450s. Sci Rep 2019; 9:18023. [PMID: 31792277 PMCID: PMC6888865 DOI: 10.1038/s41598-019-54473-8] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2019] [Accepted: 11/14/2019] [Indexed: 11/26/2022] Open
Abstract
Information about substrate and product selectivity is critical for understanding the function of cytochrome P450 monooxygenases. In addition, comprehensive understanding of changes in substrate selectivity of P450 upon amino acid mutation would enable the design and creation of engineered P450s with desired selectivities. Therefore, systematic methods for obtaining such information are required. Herein, we developed an integrated P450 substrate screening system for the selection of “exemplary” substrates for a P450 of interest. The established screening system accurately selected the known exemplary substrates and also identified previously unknown exemplary substrates for microbial-derived P450s from a library containing sp3-rich synthetic small molecules. Synthetically potent transformations were also found by analyzing the reactions and oxidation products. The screening system was applied to analyze the substrate selectivity of the P450 BM3 mutants F87A and F87A/A330W, which acquired an ability to hydroxylate non-natural substrate steroids regio- and stereoselectively by two amino acid mutations. The distinct transition of exemplary substrates due to each single amino acid mutation was revealed, demonstrating the utility of the established system.
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Affiliation(s)
- Naoki Kanoh
- Graduate School of Pharmaceutical Sciences, Tohoku University, 6-3 Aza-Aoba, Aramaki, Aoba-ku, Sendai, 980-8578, Japan. .,Institute of Medicinal Chemistry, Hoshi University, 2-4-1 Ebara, Shinagawa-ku, Tokyo, 142-8501, Japan.
| | - Ayano Kawamata-Asano
- Graduate School of Pharmaceutical Sciences, Tohoku University, 6-3 Aza-Aoba, Aramaki, Aoba-ku, Sendai, 980-8578, Japan
| | - Kana Suzuki
- Graduate School of Pharmaceutical Sciences, Tohoku University, 6-3 Aza-Aoba, Aramaki, Aoba-ku, Sendai, 980-8578, Japan
| | - Yusuke Takahashi
- Graduate School of Pharmaceutical Sciences, Tohoku University, 6-3 Aza-Aoba, Aramaki, Aoba-ku, Sendai, 980-8578, Japan
| | - Takeshi Miyazawa
- Chemical Biology Research Group, RIKEN Center for Sustainable Resource Science, 2-1 Hirosawa, Wako, Saitama, 351-0198, Japan
| | - Takemichi Nakamura
- Molecular Structure Characterization Unit, Technology Platform Division, RIKEN Center for Sustainable Resource Science, 2-1 Hirosawa, Wako, Saitama, 351-0198, Japan
| | - Takashi Moriya
- Graduate School of Pharmaceutical Sciences, Tohoku University, 6-3 Aza-Aoba, Aramaki, Aoba-ku, Sendai, 980-8578, Japan
| | - Hiroyuki Hirano
- Chemical Resource Development Research Unit, Technology Platform Division, RIKEN Center for Sustainable Resource Science, 2-1 Hirosawa, Wako, Saitama, 351-0198, Japan
| | - Hiroyuki Osada
- Chemical Biology Research Group, RIKEN Center for Sustainable Resource Science, 2-1 Hirosawa, Wako, Saitama, 351-0198, Japan.,Chemical Resource Development Research Unit, Technology Platform Division, RIKEN Center for Sustainable Resource Science, 2-1 Hirosawa, Wako, Saitama, 351-0198, Japan
| | - Yoshiharu Iwabuchi
- Graduate School of Pharmaceutical Sciences, Tohoku University, 6-3 Aza-Aoba, Aramaki, Aoba-ku, Sendai, 980-8578, Japan
| | - Shunji Takahashi
- Natural Product Biosynthesis Research Unit, RIKEN Center for Sustainable Resource Science, 2-1 Hirosawa, Wako, Saitama, 351-0198, Japan
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10
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Repeated evolution of cytochrome P450-mediated spiroketal steroid biosynthesis in plants. Nat Commun 2019; 10:3206. [PMID: 31324795 PMCID: PMC6642093 DOI: 10.1038/s41467-019-11286-7] [Citation(s) in RCA: 97] [Impact Index Per Article: 19.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2019] [Accepted: 07/05/2019] [Indexed: 12/17/2022] Open
Abstract
Diosgenin is a spiroketal steroidal natural product extracted from plants and used as the single most important precursor for the world steroid hormone industry. The sporadic occurrences of diosgenin in distantly related plants imply possible independent biosynthetic origins. The characteristic 5,6-spiroketal moiety in diosgenin is reminiscent of the spiroketal moiety present in anthelmintic avermectins isolated from actinomycete bacteria. How plants gained the ability to biosynthesize spiroketal natural products is unknown. Here, we report the diosgenin-biosynthetic pathways in himalayan paris (Paris polyphylla), a monocot medicinal plant with hemostatic and antibacterial properties, and fenugreek (Trigonella foenum-graecum), an eudicot culinary herb plant commonly used as a galactagogue. Both plants have independently recruited pairs of cytochromes P450 that catalyze oxidative 5,6-spiroketalization of cholesterol to produce diosgenin, with evolutionary progenitors traced to conserved phytohormone metabolism. This study paves the way for engineering the production of diosgenin and derived analogs in heterologous hosts.
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11
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Wu ZZ, Zhang H, Qu MQ, Cui Y, Chen MS, Bin SY, Lin JT. Candidate genes involved in spiroacetal biosynthesis in the oriental fruit fly, Bactrocera dorsalis. COMPARATIVE BIOCHEMISTRY AND PHYSIOLOGY D-GENOMICS & PROTEOMICS 2019; 31:100601. [PMID: 31203141 DOI: 10.1016/j.cbd.2019.100601] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/24/2018] [Revised: 06/05/2019] [Accepted: 06/07/2019] [Indexed: 10/26/2022]
Abstract
Spiroacetals are widespread in nature as components of volatile semiochemical secretions from many insect species. The general pathway for spiroacetal biosynthesis in Bactrocera sp. is preliminarily established, but many genes involved in this pathway remain to be characterized. By analyzing transcriptomes of the rectal glands (RGs) from immature and mature females of the oriental fruit fly, Bactrocera dorsalis, a set of genes encoding two acetyl-CoA carboxylases (ACCs), two fatty acid synthases (FASs), eight desaturases (DESs), twelve fatty acyl-CoA reductases (FARs), seventy-two cytochrome P450 enzymes (CYPs), and twenty-three odorant binding proteins (OBPs) were identified. We investigated the expression of candidate genes in immature and mature stages based on the RNA-seq data and Real-time quantitative PCR. Expression profiling revealed that some of these genes were primarily expressed in female rectal glands among different tissues, and were up-regulated in mature females. Semi-quantitative RT-PCR assays were also adapted to examine tissue-specific expression of selected candidate genes. Additionally, their putative functions in spiroacetal synthesis and transportation are proposed. Our study provided large-scale sequence information for further functional studies on spiroacetal biosynthetic pathways.
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Affiliation(s)
- Zhong-Zhen Wu
- Guang Zhou City Key Laboratory of Subtropical Fruit Tree Outbreak Control, Zhongkai University of Agriculture and Engineering, Guangzhou 510225, People's Republic of China
| | - He Zhang
- Guang Zhou City Key Laboratory of Subtropical Fruit Tree Outbreak Control, Zhongkai University of Agriculture and Engineering, Guangzhou 510225, People's Republic of China
| | - Meng-Qiu Qu
- Guang Zhou City Key Laboratory of Subtropical Fruit Tree Outbreak Control, Zhongkai University of Agriculture and Engineering, Guangzhou 510225, People's Republic of China
| | - Yang Cui
- Guang Zhou City Key Laboratory of Subtropical Fruit Tree Outbreak Control, Zhongkai University of Agriculture and Engineering, Guangzhou 510225, People's Republic of China
| | - Ming-Shun Chen
- Department of Entomology, Kansas State University, Manhattan, KS 66506, USA
| | - Shu-Ying Bin
- Guang Zhou City Key Laboratory of Subtropical Fruit Tree Outbreak Control, Zhongkai University of Agriculture and Engineering, Guangzhou 510225, People's Republic of China
| | - Jin-Tian Lin
- Guang Zhou City Key Laboratory of Subtropical Fruit Tree Outbreak Control, Zhongkai University of Agriculture and Engineering, Guangzhou 510225, People's Republic of China.
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12
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β-carboline biomediators induce reveromycin production in Streptomyces sp. SN-593. Sci Rep 2019; 9:5802. [PMID: 30967594 PMCID: PMC6456619 DOI: 10.1038/s41598-019-42268-w] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2018] [Accepted: 03/22/2019] [Indexed: 12/22/2022] Open
Abstract
The biosynthetic potential of soil-dwelling actinomycetes to produce diverse bioactive molecules that are useful as drug seeds has been achieved in the laboratory by modifying culture conditions. Availability of a small molecule that can induce secondary metabolism in these microbes can greatly facilitate the exploration of bioactive natural products. In this manuscript, through the screening of natural products and chemical modification, we demonstrated that the presence of the β-carboline compound, BR-1, enhanced reveromycin A production in Streptomyces sp. SN-593. BR-1 induced reveromycins production at the wide range of concentrations without affecting cell growth. Our study indicates that BR-1 might serve as an alternative to activate specialized metabolite biosynthesis without genetic engineering.
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13
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Meng S, Tang GL, Pan HX. Enzymatic Formation of Oxygen-Containing Heterocycles in Natural Product Biosynthesis. Chembiochem 2018; 19:2002-2022. [PMID: 30039582 DOI: 10.1002/cbic.201800225] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2018] [Indexed: 01/12/2023]
Abstract
Oxygen-containing heterocycles are widely encountered in natural products that display diverse pharmacological properties and have potential benefits to human health. The formation of O-heterocycles catalyzed by different types of enzymes in the biosynthesis of natural products not only contributes to the structural diversity of these compounds, but also enriches our understanding of nature's ability to construct complex molecules. This minireview focuses on the various modes of enzymatic O-heterocyclization identified in natural product biosynthesis and summarizes the possible mechanisms involved in ring closure.
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Affiliation(s)
- Song Meng
- State Key Laboratory of Bio-organic and Natural Products Chemistry, Shanghai Institute of Organic Chemistry, University of the Chinese Academy of Sciences, 345 Lingling Road, Shanghai, 200032, China
| | - Gong-Li Tang
- State Key Laboratory of Bio-organic and Natural Products Chemistry, Shanghai Institute of Organic Chemistry, University of the Chinese Academy of Sciences, 345 Lingling Road, Shanghai, 200032, China
| | - Hai-Xue Pan
- State Key Laboratory of Bio-organic and Natural Products Chemistry, Shanghai Institute of Organic Chemistry, University of the Chinese Academy of Sciences, 345 Lingling Road, Shanghai, 200032, China
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14
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Zheng Q, Gong Y, Guo Y, Zhao Z, Wu Z, Zhou Z, Chen D, Pan L, Liu W. Structural Insights into a Flavin-Dependent [4 + 2] Cyclase that Catalyzes trans-Decalin Formation in Pyrroindomycin Biosynthesis. Cell Chem Biol 2018; 25:718-727.e3. [DOI: 10.1016/j.chembiol.2018.03.007] [Citation(s) in RCA: 26] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2017] [Revised: 01/28/2018] [Accepted: 03/12/2018] [Indexed: 12/13/2022]
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15
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Vögeli B, Geyer K, Gerlinger PD, Benkstein S, Cortina NS, Erb TJ. Combining Promiscuous Acyl-CoA Oxidase and Enoyl-CoA Carboxylase/Reductases for Atypical Polyketide Extender Unit Biosynthesis. Cell Chem Biol 2018; 25:833-839.e4. [PMID: 29731424 DOI: 10.1016/j.chembiol.2018.04.009] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2018] [Revised: 03/22/2018] [Accepted: 04/06/2018] [Indexed: 10/17/2022]
Abstract
The incorporation of different extender units generates structural diversity in polyketides. There is significant interest in engineering substrate specificity of polyketide synthases (PKSs) to change their chemical structure. Efforts to change extender unit selectivity are hindered by the lack of simple screening methods and easily available atypical extender units. Here, we present a chemo-biosynthetic strategy that employs biocatalytic proofreading and allows access to a large variety of extender units. First, saturated acids are chemically coupled to free coenzyme A (CoA). The corresponding acyl-CoAs are then converted to alkylmalonyl-CoAs in a "one-pot" reaction through the combined action of an acyl-CoA oxidase and enoyl-CoA carboxylase/reductase. We synthesized six different extender units and used them in in vitro competition screens to investigate active site residues conferring extender unit selectivity. Our results show the importance of an uncharacterized glutamine in extender unit selectivity and open the possibility for comprehensive studies on extender incorporation in PKSs.
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Affiliation(s)
- Bastian Vögeli
- Biochemistry and Synthetic Metabolism, Max-Planck-Institute for Terrestrial Microbiology, Karl-von-Frisch-Strasse 10, 35043 Marburg, Germany
| | - Kyra Geyer
- Biochemistry and Synthetic Metabolism, Max-Planck-Institute for Terrestrial Microbiology, Karl-von-Frisch-Strasse 10, 35043 Marburg, Germany
| | - Patrick D Gerlinger
- Biochemistry and Synthetic Metabolism, Max-Planck-Institute for Terrestrial Microbiology, Karl-von-Frisch-Strasse 10, 35043 Marburg, Germany
| | - Sarah Benkstein
- Biochemistry and Synthetic Metabolism, Max-Planck-Institute for Terrestrial Microbiology, Karl-von-Frisch-Strasse 10, 35043 Marburg, Germany
| | - Niña Socorro Cortina
- Biochemistry and Synthetic Metabolism, Max-Planck-Institute for Terrestrial Microbiology, Karl-von-Frisch-Strasse 10, 35043 Marburg, Germany
| | - Tobias J Erb
- Biochemistry and Synthetic Metabolism, Max-Planck-Institute for Terrestrial Microbiology, Karl-von-Frisch-Strasse 10, 35043 Marburg, Germany.
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16
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Li Y, Zhang W, Zhang H, Tian W, Wu L, Wang S, Zheng M, Zhang J, Sun C, Deng Z, Sun Y, Qu X, Zhou J. Structural Basis of a Broadly Selective Acyltransferase from the Polyketide Synthase of Splenocin. Angew Chem Int Ed Engl 2018. [PMID: 29536601 DOI: 10.1002/anie.201802805] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/12/2023]
Abstract
Polyketides are a large family of pharmaceutically important natural products, and the structural modification of their scaffolds is significant for drug development. Herein, we report high-resolution X-ray crystal structures of the broadly selective acyltransferase (AT) from the splenocin polyketide synthase (SpnD-AT) in the apo form and in complex with benzylmalonyl and pentynylmalonyl extender unit mimics. These structures revealed the molecular basis for the stereoselectivity and substrate specificity of SpnD-AT, and enabled the engineering of the industrially important Ery-AT6 to broaden its substrate scope to include three new types of extender units.
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Affiliation(s)
- Yuan Li
- Key Laboratory of Combinatorial Biosynthesis and Drug Discovery (Wuhan University), Ministry of Education, Wuhan University School of Pharmaceutical Sciences, 185 Donghu Road., Wuhan, 430071, China
| | - Wan Zhang
- Key Laboratory of Combinatorial Biosynthesis and Drug Discovery (Wuhan University), Ministry of Education, Wuhan University School of Pharmaceutical Sciences, 185 Donghu Road., Wuhan, 430071, China
| | - Hui Zhang
- Key Laboratory of Combinatorial Biosynthesis and Drug Discovery (Wuhan University), Ministry of Education, Wuhan University School of Pharmaceutical Sciences, 185 Donghu Road., Wuhan, 430071, China
| | - Wenya Tian
- Key Laboratory of Combinatorial Biosynthesis and Drug Discovery (Wuhan University), Ministry of Education, Wuhan University School of Pharmaceutical Sciences, 185 Donghu Road., Wuhan, 430071, China
| | - Lian Wu
- State Key Laboratory of Bioorganic and Natural Products Chemistry, Center for Excellence in Molecular Synthesis, Shanghai Institute of Organic Chemistry, Chinese Academy of Sciences, 345 Lingling Road, Shanghai, 200032, China
- Shaanxi Key Laboratory of Natural Products & Chemical Biology, College of Chemistry and Pharmacy, Northwest A&F University, 3 Taicheng Road, Yangling, 712100, Shaanxi, China
| | - Shuwen Wang
- Key Laboratory of Combinatorial Biosynthesis and Drug Discovery (Wuhan University), Ministry of Education, Wuhan University School of Pharmaceutical Sciences, 185 Donghu Road., Wuhan, 430071, China
| | - Mengmeng Zheng
- Key Laboratory of Combinatorial Biosynthesis and Drug Discovery (Wuhan University), Ministry of Education, Wuhan University School of Pharmaceutical Sciences, 185 Donghu Road., Wuhan, 430071, China
| | - Jinru Zhang
- State Key Laboratory of Bioorganic and Natural Products Chemistry, Center for Excellence in Molecular Synthesis, Shanghai Institute of Organic Chemistry, Chinese Academy of Sciences, 345 Lingling Road, Shanghai, 200032, China
- Shaanxi Key Laboratory of Natural Products & Chemical Biology, College of Chemistry and Pharmacy, Northwest A&F University, 3 Taicheng Road, Yangling, 712100, Shaanxi, China
| | - Chenghai Sun
- Key Laboratory of Combinatorial Biosynthesis and Drug Discovery (Wuhan University), Ministry of Education, Wuhan University School of Pharmaceutical Sciences, 185 Donghu Road., Wuhan, 430071, China
| | - Zixin Deng
- Key Laboratory of Combinatorial Biosynthesis and Drug Discovery (Wuhan University), Ministry of Education, Wuhan University School of Pharmaceutical Sciences, 185 Donghu Road., Wuhan, 430071, China
| | - Yuhui Sun
- Key Laboratory of Combinatorial Biosynthesis and Drug Discovery (Wuhan University), Ministry of Education, Wuhan University School of Pharmaceutical Sciences, 185 Donghu Road., Wuhan, 430071, China
| | - Xudong Qu
- Key Laboratory of Combinatorial Biosynthesis and Drug Discovery (Wuhan University), Ministry of Education, Wuhan University School of Pharmaceutical Sciences, 185 Donghu Road., Wuhan, 430071, China
| | - Jiahai Zhou
- State Key Laboratory of Bioorganic and Natural Products Chemistry, Center for Excellence in Molecular Synthesis, Shanghai Institute of Organic Chemistry, Chinese Academy of Sciences, 345 Lingling Road, Shanghai, 200032, China
- Shaanxi Key Laboratory of Natural Products & Chemical Biology, College of Chemistry and Pharmacy, Northwest A&F University, 3 Taicheng Road, Yangling, 712100, Shaanxi, China
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17
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Li Y, Zhang W, Zhang H, Tian W, Wu L, Wang S, Zheng M, Zhang J, Sun C, Deng Z, Sun Y, Qu X, Zhou J. Structural Basis of a Broadly Selective Acyltransferase from the Polyketide Synthase of Splenocin. Angew Chem Int Ed Engl 2018. [DOI: 10.1002/ange.201802805] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
Affiliation(s)
- Yuan Li
- Key Laboratory of Combinatorial Biosynthesis and Drug Discovery (Wuhan University); Ministry of Education; Wuhan University School of Pharmaceutical Sciences; 185 Donghu Road. Wuhan 430071 China
| | - Wan Zhang
- Key Laboratory of Combinatorial Biosynthesis and Drug Discovery (Wuhan University); Ministry of Education; Wuhan University School of Pharmaceutical Sciences; 185 Donghu Road. Wuhan 430071 China
| | - Hui Zhang
- Key Laboratory of Combinatorial Biosynthesis and Drug Discovery (Wuhan University); Ministry of Education; Wuhan University School of Pharmaceutical Sciences; 185 Donghu Road. Wuhan 430071 China
| | - Wenya Tian
- Key Laboratory of Combinatorial Biosynthesis and Drug Discovery (Wuhan University); Ministry of Education; Wuhan University School of Pharmaceutical Sciences; 185 Donghu Road. Wuhan 430071 China
| | - Lian Wu
- State Key Laboratory of Bioorganic and Natural Products Chemistry, Center for Excellence in Molecular Synthesis; Shanghai Institute of Organic Chemistry; Chinese Academy of Sciences; 345 Lingling Road Shanghai 200032 China
- Shaanxi Key Laboratory of Natural Products & Chemical Biology; College of Chemistry and Pharmacy; Northwest A&F University; 3 Taicheng Road, Yangling 712100 Shaanxi China
| | - Shuwen Wang
- Key Laboratory of Combinatorial Biosynthesis and Drug Discovery (Wuhan University); Ministry of Education; Wuhan University School of Pharmaceutical Sciences; 185 Donghu Road. Wuhan 430071 China
| | - Mengmeng Zheng
- Key Laboratory of Combinatorial Biosynthesis and Drug Discovery (Wuhan University); Ministry of Education; Wuhan University School of Pharmaceutical Sciences; 185 Donghu Road. Wuhan 430071 China
| | - Jinru Zhang
- State Key Laboratory of Bioorganic and Natural Products Chemistry, Center for Excellence in Molecular Synthesis; Shanghai Institute of Organic Chemistry; Chinese Academy of Sciences; 345 Lingling Road Shanghai 200032 China
- Shaanxi Key Laboratory of Natural Products & Chemical Biology; College of Chemistry and Pharmacy; Northwest A&F University; 3 Taicheng Road, Yangling 712100 Shaanxi China
| | - Chenghai Sun
- Key Laboratory of Combinatorial Biosynthesis and Drug Discovery (Wuhan University); Ministry of Education; Wuhan University School of Pharmaceutical Sciences; 185 Donghu Road. Wuhan 430071 China
| | - Zixin Deng
- Key Laboratory of Combinatorial Biosynthesis and Drug Discovery (Wuhan University); Ministry of Education; Wuhan University School of Pharmaceutical Sciences; 185 Donghu Road. Wuhan 430071 China
| | - Yuhui Sun
- Key Laboratory of Combinatorial Biosynthesis and Drug Discovery (Wuhan University); Ministry of Education; Wuhan University School of Pharmaceutical Sciences; 185 Donghu Road. Wuhan 430071 China
| | - Xudong Qu
- Key Laboratory of Combinatorial Biosynthesis and Drug Discovery (Wuhan University); Ministry of Education; Wuhan University School of Pharmaceutical Sciences; 185 Donghu Road. Wuhan 430071 China
| | - Jiahai Zhou
- State Key Laboratory of Bioorganic and Natural Products Chemistry, Center for Excellence in Molecular Synthesis; Shanghai Institute of Organic Chemistry; Chinese Academy of Sciences; 345 Lingling Road Shanghai 200032 China
- Shaanxi Key Laboratory of Natural Products & Chemical Biology; College of Chemistry and Pharmacy; Northwest A&F University; 3 Taicheng Road, Yangling 712100 Shaanxi China
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18
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Kinanthraquinone, a new anthraquinone carboxamide isolated from Streptomyces reveromyceticus SN-593-44. J Antibiot (Tokyo) 2018; 71:480-482. [DOI: 10.1038/s41429-017-0020-0] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2017] [Revised: 12/14/2017] [Accepted: 12/20/2017] [Indexed: 11/09/2022]
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19
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Zhang FM, Zhang SY, Tu YQ. Recent progress in the isolation, bioactivity, biosynthesis, and total synthesis of natural spiroketals. Nat Prod Rep 2018; 35:75-104. [DOI: 10.1039/c7np00043j] [Citation(s) in RCA: 57] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
The isolation, bioactivity, biosynthesis, and total synthesis of natural spiroketals from 2011 to July 2017 have been summarized in this review.
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Affiliation(s)
- Fu-Min Zhang
- State Key Laboratory of Applied Organic Chemistry and College of Chemistry and Chemical Engineering
- Lanzhou University
- Lanzhou 730000
- P. R. China
| | - Shu-Yu Zhang
- School of Chemistry and Chemical Engineering
- Shanghai Jiao Tong University
- Shanghai 200240
- P. R. China
| | - Yong-Qiang Tu
- State Key Laboratory of Applied Organic Chemistry and College of Chemistry and Chemical Engineering
- Lanzhou University
- Lanzhou 730000
- P. R. China
- School of Chemistry and Chemical Engineering
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20
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Khalid A, Takagi H, Panthee S, Muroi M, Chappell J, Osada H, Takahashi S. Development of a Terpenoid-Production Platform in Streptomyces reveromyceticus SN-593. ACS Synth Biol 2017; 6:2339-2349. [PMID: 29019653 DOI: 10.1021/acssynbio.7b00249] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Terpenoids represent the largest class of natural products, some of which are resources for pharmaceuticals, fragrances, and fuels. Generally, mass production of valuable terpenoid compounds is hampered by their low production levels in organisms and difficulty of chemical synthesis. Therefore, the development of microbial biosynthetic platforms represents an alternative approach. Although microbial terpenoid-production platforms have been established in Escherichia coli and yeast, an optimal platform has not been developed for Streptomyces species, despite the large capacity to produce secondary metabolites, such as polyketide compounds. To explore this potential, we constructed a terpenoid-biosynthetic platform in Streptomyces reveromyceticus SN-593. This strain is unique in that it harbors the mevalonate gene cluster enabling the production of furaquinocin, which can be controlled by the pathway specific regulator Fur22. We simultaneously expressed the mevalonate gene cluster and subsequent terpenoid-biosynthetic genes under the control of Fur22. To achieve improved fur22 gene expression, we screened promoters from S. reveromyceticus SN-593. Our results showed that the promoter associated with rvr2030 gene enabled production of 212 ± 20 mg/L botryococcene to levels comparable to those previously reported for other microbial hosts. Given that the rvr2030 gene encodes for an enzyme involved in the primary metabolism, these results suggest that optimized expression of terpenoid-biosynthetic genes with primary and secondary metabolism might be as important for high yields of terpenoid compounds as is the absolute expression level of a target gene(s).
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Affiliation(s)
- Ammara Khalid
- Chemical
Biology Research Group, RIKEN Centre for Sustainable Resource Science, Hirosawa, 2-1, Wako, Saitama 351-0198, Japan
- Graduate
School of Science and Engineering, Saitama University, Saitama 338-8570, Japan
| | - Hiroshi Takagi
- Natural
Product Biosynthesis Research Unit, RIKEN Centre for Sustainable Resource Science, Hirosawa 2-1, Wako, Saitama 351-0198, Japan
| | - Suresh Panthee
- Natural
Product Biosynthesis Research Unit, RIKEN Centre for Sustainable Resource Science, Hirosawa 2-1, Wako, Saitama 351-0198, Japan
| | - Makoto Muroi
- Chemical
Biology Research Group, RIKEN Centre for Sustainable Resource Science, Hirosawa, 2-1, Wako, Saitama 351-0198, Japan
| | - Joe Chappell
- Pharmaceutical
Sciences, University of Kentucky, 789 S Limestone Street, Lexington, Kentucky 40536-0596, United States
| | - Hiroyuki Osada
- Chemical
Biology Research Group, RIKEN Centre for Sustainable Resource Science, Hirosawa, 2-1, Wako, Saitama 351-0198, Japan
- Graduate
School of Science and Engineering, Saitama University, Saitama 338-8570, Japan
| | - Shunji Takahashi
- Natural
Product Biosynthesis Research Unit, RIKEN Centre for Sustainable Resource Science, Hirosawa 2-1, Wako, Saitama 351-0198, Japan
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21
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Metabolic Profile of the Cellulolytic Industrial Actinomycete Thermobifida fusca. Metabolites 2017; 7:metabo7040057. [PMID: 29137138 PMCID: PMC5746737 DOI: 10.3390/metabo7040057] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2017] [Revised: 11/03/2017] [Accepted: 11/08/2017] [Indexed: 11/17/2022] Open
Abstract
Actinomycetes have a long history of being the source of numerous valuable natural products and medicinals. To expedite product discovery and optimization of biochemical production, high-throughput technologies can now be used to screen the library of compounds present (or produced) at a given time in an organism. This not only facilitates chemical product screening, but also provides a comprehensive methodology to the study cellular metabolic networks to inform cellular engineering. Here, we present some of the first metabolomic data of the industrial cellulolytic actinomycete Thermobifida fusca generated using LC-MS/MS. The underlying objective of conducting global metabolite profiling was to gain better insight on the innate capabilities of T. fusca, with a long-term goal of facilitating T. fusca-based bioprocesses. The T. fusca metabolome was characterized for growth on two cellulose-relevant carbon sources, cellobiose and Avicel. Furthermore, the comprehensive list of measured metabolites was computationally integrated into a metabolic model of T. fusca, to study metabolic shifts in the network flux associated with carbohydrate and amino acid metabolism.
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22
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Ma J, Huang H, Xie Y, Liu Z, Zhao J, Zhang C, Jia Y, Zhang Y, Zhang H, Zhang T, Ju J. Biosynthesis of ilamycins featuring unusual building blocks and engineered production of enhanced anti-tuberculosis agents. Nat Commun 2017; 8:391. [PMID: 28855504 PMCID: PMC5577134 DOI: 10.1038/s41467-017-00419-5] [Citation(s) in RCA: 80] [Impact Index Per Article: 11.4] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2017] [Accepted: 06/28/2017] [Indexed: 11/13/2022] Open
Abstract
Tuberculosis remains one of the world’s deadliest communicable diseases, novel anti-tuberculosis agents are urgently needed due to severe drug resistance and the co-epidemic of tuberculosis/human immunodeficiency virus. Here, we show the isolation of six anti-mycobacterial ilamycin congeners (1–6) bearing rare L-3-nitro-tyrosine and L-2-amino-4-hexenoic acid structural units from the deep sea-derived Streptomyces atratus SCSIO ZH16. The biosynthesis of the rare L-3-nitrotyrosine and L-2-amino-4-hexenoic acid units as well as three pre-tailoring and two post-tailoring steps are probed in the ilamycin biosynthetic machinery through a series of gene inactivation, precursor chemical complementation, isotope-labeled precursor feeding experiments, as well as structural elucidation of three intermediates (6–8) from the respective mutants. Most impressively, ilamycins E1/E2, which are produced in high titers by a genetically engineered mutant strain, show very potent anti-tuberculosis activity with an minimum inhibitory concentration value ≈9.8 nM to Mycobacterium tuberculosis H37Rv constituting extremely potent and exciting anti-tuberculosis drug leads. Tuberculosis (TB) remains one of the world’s deadliest communicable diseases, novel anti-TB agents are urgently needed due to severe drug resistance and the co-epidemic of TB/HIV. Here, the authors show that anti-mycobacterial ilamycin congeners bearing unusual structural units possess extremely potent anti-tuberculosis activities.
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Affiliation(s)
- Junying Ma
- CAS Key Laboratory of Tropical Marine Bio-Resources and Ecology, Guangdong Key Laboratory of Marine Materia Medica, RNAM Center for Marine Microbiology, South China Sea Institute of Oceanology, Chinese Academy of Sciences, Guangzhou, 510301, China.
| | - Hongbo Huang
- CAS Key Laboratory of Tropical Marine Bio-Resources and Ecology, Guangdong Key Laboratory of Marine Materia Medica, RNAM Center for Marine Microbiology, South China Sea Institute of Oceanology, Chinese Academy of Sciences, Guangzhou, 510301, China
| | - Yunchang Xie
- CAS Key Laboratory of Tropical Marine Bio-Resources and Ecology, Guangdong Key Laboratory of Marine Materia Medica, RNAM Center for Marine Microbiology, South China Sea Institute of Oceanology, Chinese Academy of Sciences, Guangzhou, 510301, China
| | - Zhiyong Liu
- Tuberculosis Research Laboratory, State Key Laboratory of Respiratory Disease, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou, 510530, China
| | - Jin Zhao
- Guangdong Provincial Key Laboratory of Medical Molecular Diagnostics, Institute of Laboratory Medicine, Guangdong Medical University, Dongguan, 523808, China
| | - Chunyan Zhang
- CAS Key Laboratory of Tropical Marine Bio-Resources and Ecology, Guangdong Key Laboratory of Marine Materia Medica, RNAM Center for Marine Microbiology, South China Sea Institute of Oceanology, Chinese Academy of Sciences, Guangzhou, 510301, China.,University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Yanxi Jia
- CAS Key Laboratory of Tropical Marine Bio-Resources and Ecology, Guangdong Key Laboratory of Marine Materia Medica, RNAM Center for Marine Microbiology, South China Sea Institute of Oceanology, Chinese Academy of Sciences, Guangzhou, 510301, China.,University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Yun Zhang
- CAS Key Laboratory of Tropical Marine Bio-Resources and Ecology, Guangdong Key Laboratory of Marine Materia Medica, RNAM Center for Marine Microbiology, South China Sea Institute of Oceanology, Chinese Academy of Sciences, Guangzhou, 510301, China
| | - Hua Zhang
- Guangdong Provincial Key Laboratory of Medical Molecular Diagnostics, Institute of Laboratory Medicine, Guangdong Medical University, Dongguan, 523808, China
| | - Tianyu Zhang
- Tuberculosis Research Laboratory, State Key Laboratory of Respiratory Disease, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou, 510530, China
| | - Jianhua Ju
- CAS Key Laboratory of Tropical Marine Bio-Resources and Ecology, Guangdong Key Laboratory of Marine Materia Medica, RNAM Center for Marine Microbiology, South China Sea Institute of Oceanology, Chinese Academy of Sciences, Guangzhou, 510301, China. .,University of Chinese Academy of Sciences, Beijing, 100049, China.
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23
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Abstract
Oxidative cyclizations are important transformations that occur widely during natural product biosynthesis. The transformations from acyclic precursors to cyclized products can afford morphed scaffolds, structural rigidity, and biological activities. Some of the most dramatic structural alterations in natural product biosynthesis occur through oxidative cyclization. In this Review, we examine the different strategies used by nature to create new intra(inter)molecular bonds via redox chemistry. This Review will cover both oxidation- and reduction-enabled cyclization mechanisms, with an emphasis on the former. Radical cyclizations catalyzed by P450, nonheme iron, α-KG-dependent oxygenases, and radical SAM enzymes are discussed to illustrate the use of molecular oxygen and S-adenosylmethionine to forge new bonds at unactivated sites via one-electron manifolds. Nonradical cyclizations catalyzed by flavin-dependent monooxygenases and NAD(P)H-dependent reductases are covered to show the use of two-electron manifolds in initiating cyclization reactions. The oxidative installations of epoxides and halogens into acyclic scaffolds to drive subsequent cyclizations are separately discussed as examples of "disappearing" reactive handles. Last, oxidative rearrangement of rings systems, including contractions and expansions, will be covered.
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Affiliation(s)
- Man-Cheng Tang
- Department of Chemical and Biomolecular Engineering, Department of Chemistry and Biochemistry, University of California, Los Angeles, 420 Westwood Plaza, Los Angeles, CA 90095, USA
| | - Yi Zou
- Department of Chemical and Biomolecular Engineering, Department of Chemistry and Biochemistry, University of California, Los Angeles, 420 Westwood Plaza, Los Angeles, CA 90095, USA
| | - Kenji Watanabe
- Department of Pharmaceutical Sciences, University of Shizuoka, Shizuoka 422-8526, Japan
| | - Christopher T. Walsh
- Stanford University Chemistry, Engineering, and Medicine for Human Health (ChEM-H), Stanford University, 443 Via Ortega, Stanford, CA 94305
| | - Yi Tang
- Department of Chemical and Biomolecular Engineering, Department of Chemistry and Biochemistry, University of California, Los Angeles, 420 Westwood Plaza, Los Angeles, CA 90095, USA
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24
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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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25
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Competition and co-regulation of spirotoamide and tautomycetin biosynthesis in Streptomyces griseochromogenes, and isolation and structural elucidation of spirotoamide C and D. J Antibiot (Tokyo) 2017; 70:710-714. [PMID: 28196980 DOI: 10.1038/ja.2017.13] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2016] [Revised: 01/05/2017] [Accepted: 01/06/2017] [Indexed: 12/22/2022]
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26
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Ray L, Valentic TR, Miyazawa T, Withall DM, Song L, Milligan JC, Osada H, Takahashi S, Tsai SC, Challis GL. A crotonyl-CoA reductase-carboxylase independent pathway for assembly of unusual alkylmalonyl-CoA polyketide synthase extender units. Nat Commun 2016; 7:13609. [PMID: 28000660 PMCID: PMC5187497 DOI: 10.1038/ncomms13609] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2016] [Accepted: 10/19/2016] [Indexed: 11/12/2022] Open
Abstract
Type I modular polyketide synthases assemble diverse bioactive natural products. Such multienzymes typically use malonyl and methylmalonyl-CoA building blocks for polyketide chain assembly. However, in several cases more exotic alkylmalonyl-CoA extender units are also known to be incorporated. In all examples studied to date, such unusual extender units are biosynthesized via reductive carboxylation of α, β-unsaturated thioesters catalysed by crotonyl-CoA reductase/carboxylase (CCRC) homologues. Here we show using a chemically-synthesized deuterium-labelled mechanistic probe, and heterologous gene expression experiments that the unusual alkylmalonyl-CoA extender units incorporated into the stambomycin family of polyketide antibiotics are assembled by direct carboxylation of medium chain acyl-CoA thioesters. X-ray crystal structures of the unusual β-subunit of the acyl-CoA carboxylase (YCC) responsible for this reaction, alone and in complex with hexanoyl-CoA, reveal the molecular basis for substrate recognition, inspiring the development of methodology for polyketide bio-orthogonal tagging via incorporation of 6-azidohexanoic acid and 8-nonynoic acid into novel stambomycin analogues.
Polyketides are typically assembled from a starter unit and malonyl- and/or methylmalonyl-CoA-derived extender units, but the macrolide antibiotics stambomycins incorporate non-standard alkylmalonyl-CoA extender units. Here, the authors describe the biosynthetic pathway responsible for this unusual synthesis.
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Affiliation(s)
- Lauren Ray
- Department of Chemistry, University of Warwick, Coventry CV4 7AL, UK
| | - Timothy R Valentic
- Departments of Molecular Biology and Biochemistry, Chemistry, and Pharmaceutical Sciences, University of California, Irvine, California 92697, USA
| | - Takeshi Miyazawa
- Chemical Biology Research Group, RIKEN Center for Sustainable Resource Science, Saitama 351-0198, Japan.,Graduate School of Science and Engineering, Saitama University, Saitama 338-8570, Japan
| | - David M Withall
- Department of Chemistry, University of Warwick, Coventry CV4 7AL, UK
| | - Lijiang Song
- Department of Chemistry, University of Warwick, Coventry CV4 7AL, UK
| | - Jacob C Milligan
- Departments of Molecular Biology and Biochemistry, Chemistry, and Pharmaceutical Sciences, University of California, Irvine, California 92697, USA
| | - Hiroyuki Osada
- Chemical Biology Research Group, RIKEN Center for Sustainable Resource Science, Saitama 351-0198, Japan.,Graduate School of Science and Engineering, Saitama University, Saitama 338-8570, Japan
| | - Shunji Takahashi
- Chemical Biology Research Group, RIKEN Center for Sustainable Resource Science, Saitama 351-0198, Japan
| | - Shiou-Chuan Tsai
- Departments of Molecular Biology and Biochemistry, Chemistry, and Pharmaceutical Sciences, University of California, Irvine, California 92697, USA
| | - Gregory L Challis
- Department of Chemistry, University of Warwick, Coventry CV4 7AL, UK
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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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28
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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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29
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Chemical and biological studies of reveromycin A. J Antibiot (Tokyo) 2016; 69:723-730. [PMID: 27270304 DOI: 10.1038/ja.2016.57] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2016] [Revised: 03/21/2016] [Accepted: 03/22/2016] [Indexed: 12/12/2022]
Abstract
The research on antibiotics requires the integration of broad areas, such as microbiology, organic chemistry, biochemistry and pharmacology. It is similar to the field of chemical biology that is recently popular as an approach for drug discovery. When we isolate a new compound from a microorganism, we can pursue the interesting research on chemistry and biology. In this review, I would like to introduce our achievements in relation to reveromycin A.
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30
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In silico identification of lysocin biosynthetic gene cluster from Lysobacter sp. RH2180-5. J Antibiot (Tokyo) 2016; 70:204-207. [DOI: 10.1038/ja.2016.102] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2016] [Accepted: 07/09/2016] [Indexed: 11/08/2022]
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31
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Fujiwara R, Noda S, Tanaka T, Kondo A. Styrene production from a biomass-derived carbon source using a coculture system of phenylalanine ammonia lyase and phenylacrylic acid decarboxylase-expressing Streptomyces lividans transformants. J Biosci Bioeng 2016; 122:730-735. [PMID: 27405271 DOI: 10.1016/j.jbiosc.2016.05.005] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2016] [Revised: 05/16/2016] [Accepted: 05/18/2016] [Indexed: 10/21/2022]
Abstract
To produce styrene from a biomass-derived carbon source, Streptomyces lividans was adopted as a host strain. The gene encoding ferulic acid decarboxylase from Saccharomyces cerevisiae (FDC1) was introduced into S. lividans, and the resulting S. lividans transformant successfully expressed FDC1 and converted trans-cinnamic acid (CA) to styrene. A key factor in styrene production using microbes is the recovery of volatile styrene. In the present study, we selected polystyrene resin beads XRD-4 as the absorbent agent to recover styrene produced using S. lividans transformants, which enabled recovery of styrene from the culture broth. For styrene production from biomass-derived carbon sources, S. lividans/FDC1 was cultured together with S. lividans/p-encP, which we previously reported as a CA-producing S. lividans strain. This coculture system combined with the recovery of styrene using XAD-4 allowed the production of styrene from glucose, cellobiose, or xylo-oligosaccharide, respectively.
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Affiliation(s)
- Ryosuke Fujiwara
- Department of Chemical Science and Engineering, Graduate School of Engineering, Kobe University, 1-1 Rokkodai, Nada, Kobe 657-8501, Japan
| | - Shuhei Noda
- Center for Sustainable Resource Science, RIKEN, 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama, Kanagawa 230-0045, Japan
| | - Tsutomu Tanaka
- Department of Chemical Science and Engineering, Graduate School of Engineering, Kobe University, 1-1 Rokkodai, Nada, Kobe 657-8501, Japan
| | - Akihiko Kondo
- Department of Chemical Science and Engineering, Graduate School of Engineering, Kobe University, 1-1 Rokkodai, Nada, Kobe 657-8501, Japan; Center for Sustainable Resource Science, RIKEN, 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama, Kanagawa 230-0045, Japan.
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32
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Pang B, Wang M, Liu W. Cyclization of polyketides and non-ribosomal peptides on and off their assembly lines. Nat Prod Rep 2016; 33:162-73. [PMID: 26604034 DOI: 10.1039/c5np00095e] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Modular polyketide synthases (PKSs) and non-ribosomal peptide synthetases (NRPSs) are multifunctional megaenzymes that serve as templates to program the assembly of short carboxylic acids and amino acids in a primarily co-linear manner. The variation, combination, permutation and evolution of their functional units (e.g., modules, domains and proteins) along with their association with external enzymes have resulted in the generation of numerous versions of templates, the roles of which have not been fully recognized in the structural diversification of polyketides, non-ribosomal peptides and their hybrids present in nature. In this Highlight, we focus on the assembly-line enzymology and associated chemistry by providing examples of some newly characterized cyclization reactions that occur on and off the assembly lines during and after chain elongation for the purpose of elucidating the template effects of PKSs and NRPSs. A fundamental understanding of the underlying biosynthetic logic would facilitate the elucidation of chemical information contained within the PKS or NRPS templates and benefit the development of strategies for genome mining, biosynthesis-inspired chemical synthesis and combinatorial biosynthesis.
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Affiliation(s)
- Bo Pang
- State Key Laboratory of Bioorganic and Natural Products Chemistry, Shanghai Institute of Organic Chemistry, Chinese Academy of Sciences, 345 Lingling Road, Shanghai 200032, China.
| | - Min Wang
- State Key Laboratory of Bioorganic and Natural Products Chemistry, Shanghai Institute of Organic Chemistry, Chinese Academy of Sciences, 345 Lingling Road, Shanghai 200032, China.
| | - Wen Liu
- State Key Laboratory of Bioorganic and Natural Products Chemistry, Shanghai Institute of Organic Chemistry, Chinese Academy of Sciences, 345 Lingling Road, Shanghai 200032, China. and Huzhou Center of Bio-Synthetic Innovation, 1366 Hongfeng Road, Huzhou 313000, China
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33
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Zheng Q, Tian Z, Liu W. Recent advances in understanding the enzymatic reactions of [4+2] cycloaddition and spiroketalization. Curr Opin Chem Biol 2016; 31:95-102. [DOI: 10.1016/j.cbpa.2016.01.020] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2015] [Revised: 01/25/2016] [Accepted: 01/25/2016] [Indexed: 11/25/2022]
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34
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Pang B, Zhong G, Tang Z, Liu W. Enzymatic [4+2] Cycloadditions in the Biosynthesis of Spirotetramates and Spirotetronates. Methods Enzymol 2016; 575:39-63. [PMID: 27417924 DOI: 10.1016/bs.mie.2016.02.019] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
The Diels-Alder reaction is a quintessential type of [4+2] cycloaddition that remains one of the most intriguing transformations in synthetic chemistry. This reaction has long been envisaged to participate in the biosynthesis of a number of cyclohexene-containing natural products, although the question of whether a bona fide Diels-Alderase exists remains unsolved. In nature, there are remarkably few enzymes known to have the activity of [4+2] cycloaddition. These enzymes are phylogenetically distinct and are often classified according to the specific chemical structures. The variation of protein ancestors and in many cases the instability/complexity of the substrates and products pose a significant challenge in identification of the [4+2] cycloaddition catalysts using general homology-based mining approaches. We here provide the detailed description of the multiple comparison-based strategy and methods for the characterization of two distinct types of dedicated [4+2] cyclases (eg, PyrE3 and PyrI4) in the biosynthesis of spirotetramates and spirotetronates, where they act in tandem for coordinated cross-bridging of a linear polyene intermediate into a enantiomerically pure pentacyclic core. The search of new protein scaffolds with the [4+2] cycloaddition activity could enrich the pool of the candidates for mechanistic examination of a true enzymatic Diels-Alder reaction. The protocols presented in this study would also be applicable to the study of other functionally similar but phylogenetically different proteins, eg, the spiroketal cyclases.
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Affiliation(s)
- B Pang
- State Key Laboratory of Bioorganic and Natural Products Chemistry, Shanghai Institute of Organic Chemistry, Chinese Academy of Sciences, Shanghai, PR China
| | - G Zhong
- State Key Laboratory of Bioorganic and Natural Products Chemistry, Shanghai Institute of Organic Chemistry, Chinese Academy of Sciences, Shanghai, PR China
| | - Z Tang
- State Key Laboratory of Bioorganic and Natural Products Chemistry, Shanghai Institute of Organic Chemistry, Chinese Academy of Sciences, Shanghai, PR China
| | - W Liu
- State Key Laboratory of Bioorganic and Natural Products Chemistry, Shanghai Institute of Organic Chemistry, Chinese Academy of Sciences, Shanghai, PR China; Huzhou Center of Bio-Synthetic Innovation, Huzhou, PR China.
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35
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Vishwanath M, Vinayagam P, Gajulapalli VPR, Kesavan V. Asymmetric Organocatalytic Assembly of Oxindoles Fused with Spiro-3,4-dihydropyrans with Three Contiguous Stereocenters Consisting of Vicinal Quaternary Centers. ASIAN J ORG CHEM 2016. [DOI: 10.1002/ajoc.201600051] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/14/2023]
Affiliation(s)
- Manjunatha Vishwanath
- Chemical Biology Laboratory; Department of Biotechnology; Bhupat and Jyothi Mehta School of Biosciences; Indian Institute of Technology Madras; Chennai 600036 India
| | - Poopathy Vinayagam
- Chemical Biology Laboratory; Department of Biotechnology; Bhupat and Jyothi Mehta School of Biosciences; Indian Institute of Technology Madras; Chennai 600036 India
| | - V Pratap Reddy Gajulapalli
- Chemical Biology Laboratory; Department of Biotechnology; Bhupat and Jyothi Mehta School of Biosciences; Indian Institute of Technology Madras; Chennai 600036 India
| | - Venkitasamy Kesavan
- Chemical Biology Laboratory; Department of Biotechnology; Bhupat and Jyothi Mehta School of Biosciences; Indian Institute of Technology Madras; Chennai 600036 India
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36
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Khomutnyk YY, Argüelles AJ, Winschel GA, Sun Z, Zimmerman PM, Nagorny P. Studies of the Mechanism and Origins of Enantioselectivity for the Chiral Phosphoric Acid-Catalyzed Stereoselective Spiroketalization Reactions. J Am Chem Soc 2015; 138:444-56. [DOI: 10.1021/jacs.5b12528] [Citation(s) in RCA: 81] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Affiliation(s)
- Yaroslav Ya. Khomutnyk
- Department of Chemistry, University of Michigan, 930 North University
Avenue, Ann Arbor, Michigan 48109, United States
| | - Alonso J. Argüelles
- Department of Chemistry, University of Michigan, 930 North University
Avenue, Ann Arbor, Michigan 48109, United States
| | - Grace A. Winschel
- Department of Chemistry, University of Michigan, 930 North University
Avenue, Ann Arbor, Michigan 48109, United States
| | - Zhankui Sun
- Department of Chemistry, University of Michigan, 930 North University
Avenue, Ann Arbor, Michigan 48109, United States
| | - Paul M. Zimmerman
- Department of Chemistry, University of Michigan, 930 North University
Avenue, Ann Arbor, Michigan 48109, United States
| | - Pavel Nagorny
- Department of Chemistry, University of Michigan, 930 North University
Avenue, Ann Arbor, Michigan 48109, United States
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37
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Ma X, Lubin H, Ioja E, Kékesi O, Simon Á, Apáti Á, Orbán TI, Héja L, Kardos J, Markó IE. Straightforward and effective synthesis of γ-aminobutyric acid transporter subtype 2-selective acyl-substituted azaspiro[4.5]decanes. Bioorg Med Chem Lett 2015; 26:417-423. [PMID: 26706177 DOI: 10.1016/j.bmcl.2015.11.100] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/03/2015] [Revised: 11/26/2015] [Accepted: 11/27/2015] [Indexed: 10/22/2022]
Abstract
Supply of major metabolites such as γ-aminobutyric acid (GABA), β-alanine and taurine is an essential instrument that shapes signalling, proper cell functioning and survival in the brain and peripheral organs. This background motivates the synthesis of novel classes of compounds regulating their selective transport through various fluid-organ barriers via the low-affinity γ-aminobutyric acid (GABA) transporter subtype 2 (GAT2). Natural and synthetic spirocyclic compounds or therapeutics with a range of structures and biological activity are increasingly recognised in this regard. Based on pre-validated GABA transport activity, straightforward and efficient synthesis method was developed to provide an azaspiro[4.5]decane scaffold, holding a variety of charge, substituent and 3D constrain of spirocyclic amine. Investigation of the azaspiro[4.5]decane scaffold in cell lines expressing the four GABA transporter subtypes led to the discovery of a subclass of a GAT2-selective compounds with acyl-substituted azaspiro[4.5]decane core.
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Affiliation(s)
- Xiaofeng Ma
- Organic and Medicinal Chemistry Laboratories, Université catholique de Louvain, B-1348 Louvain-la-Neuve, Belgium
| | - Hodney Lubin
- Organic and Medicinal Chemistry Laboratories, Université catholique de Louvain, B-1348 Louvain-la-Neuve, Belgium
| | - Enikő Ioja
- Functional Pharmacology Research Group, Institute of Organic Chemistry, Research Centre for Natural Sciences, Hungarian Academy of Sciences, H-1117 Budapest, Hungary
| | - Orsolya Kékesi
- Functional Pharmacology Research Group, Institute of Organic Chemistry, Research Centre for Natural Sciences, Hungarian Academy of Sciences, H-1117 Budapest, Hungary
| | - Ágnes Simon
- Functional Pharmacology Research Group, Institute of Organic Chemistry, Research Centre for Natural Sciences, Hungarian Academy of Sciences, H-1117 Budapest, Hungary
| | - Ágota Apáti
- Laboratory of Molecular Cell Biology, Institute of Enzimology, Research Centre for Natural Sciences, Hungarian Academy of Sciences, H-1117 Budapest, Hungary
| | - Tamás I Orbán
- Biomembrane Research Group, Institute of Enzimology, Research Centre for Natural Sciences, Hungarian Academy of Sciences, H-1117 Budapest, Hungary
| | - László Héja
- Functional Pharmacology Research Group, Institute of Organic Chemistry, Research Centre for Natural Sciences, Hungarian Academy of Sciences, H-1117 Budapest, Hungary
| | - Julianna Kardos
- Functional Pharmacology Research Group, Institute of Organic Chemistry, Research Centre for Natural Sciences, Hungarian Academy of Sciences, H-1117 Budapest, Hungary.
| | - István E Markó
- Organic and Medicinal Chemistry Laboratories, Université catholique de Louvain, B-1348 Louvain-la-Neuve, Belgium.
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38
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Iterative polyketide biosynthesis by modular polyketide synthases in bacteria. Appl Microbiol Biotechnol 2015; 100:541-57. [PMID: 26549236 DOI: 10.1007/s00253-015-7093-0] [Citation(s) in RCA: 69] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2015] [Revised: 10/10/2015] [Accepted: 10/13/2015] [Indexed: 10/22/2022]
Abstract
Modular polyketide synthases (type I PKSs) in bacteria are responsible for synthesizing a significant percentage of bioactive natural products. This group of synthases has a characteristic modular organization, and each module within a PKS carries out one cycle of polyketide chain elongation; thus each module is non-iterative in function. It was possible to predict the basic structure of a polyketide product from the module organization of the PKSs, since there generally existed a co-linearity between the number of modules and the number of chain elongations. However, more and more bacterial modular PKSs fail to conform to the canonical rules, and a particularly noteworthy group of non-canonical PKSs is the bacterial iterative type I PKSs. This review covers recent examples of iteratively used modular PKSs in bacteria. These non-canonical PKSs give rise to a large array of natural products with impressive structural diversity. The molecular mechanism behind the iterations is often unclear, presenting a new challenge to the rational engineering of these PKSs with the goal of generating new natural products. Structural elucidation of these synthase complexes and better understanding of potential PKS-PKS interactions as well as PKS-substrate recognition may provide new prospects and inspirations for the discovery and engineering of new bioactive polyketides.
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39
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Yoneda N, Fukata Y, Asano K, Matsubara S. Asymmetric Synthesis of Spiroketals with Aminothiourea Catalysts. Angew Chem Int Ed Engl 2015. [DOI: 10.1002/ange.201508405] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
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40
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Yoneda N, Fukata Y, Asano K, Matsubara S. Asymmetric Synthesis of Spiroketals with Aminothiourea Catalysts. Angew Chem Int Ed Engl 2015; 54:15497-500. [DOI: 10.1002/anie.201508405] [Citation(s) in RCA: 51] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2015] [Indexed: 11/11/2022]
Affiliation(s)
- Naoki Yoneda
- Department of Material Chemistry, Graduate School of Engineering, Kyoto University, Kyotodaigaku‐Katsura, Nishikyo, Kyoto 615‐8510 (Japan)
| | - Yukihiro Fukata
- Department of Material Chemistry, Graduate School of Engineering, Kyoto University, Kyotodaigaku‐Katsura, Nishikyo, Kyoto 615‐8510 (Japan)
| | - Keisuke Asano
- Department of Material Chemistry, Graduate School of Engineering, Kyoto University, Kyotodaigaku‐Katsura, Nishikyo, Kyoto 615‐8510 (Japan)
| | - Seijiro Matsubara
- Department of Material Chemistry, Graduate School of Engineering, Kyoto University, Kyotodaigaku‐Katsura, Nishikyo, Kyoto 615‐8510 (Japan)
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41
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Peter DM, Schada von Borzyskowski L, Kiefer P, Christen P, Vorholt JA, Erb TJ. Screening and Engineering the Synthetic Potential of Carboxylating Reductases from Central Metabolism and Polyketide Biosynthesis. Angew Chem Int Ed Engl 2015; 54:13457-61. [PMID: 26383129 DOI: 10.1002/anie.201505282] [Citation(s) in RCA: 37] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2015] [Indexed: 11/06/2022]
Abstract
Carboxylating enoyl-thioester reductases (ECRs) are a recently discovered class of enzymes. They catalyze the highly efficient addition of CO2 to the double bond of α,β-unsaturated CoA-thioesters and serve two biological functions. In primary metabolism of many bacteria they produce ethylmalonyl-CoA during assimilation of the central metabolite acetyl-CoA. In secondary metabolism they provide distinct α-carboxyl-acyl-thioesters to vary the backbone of numerous polyketide natural products. Different ECRs were systematically assessed with a diverse library of potential substrates. We identified three active site residues that distinguish ECRs restricted to C4 and C5-enoyl-CoAs from highly promiscuous ECRs and successfully engineered a selected ECR as proof-of-principle. This study defines the molecular basis of ECR reactivity, allowing for predicting and manipulating a key reaction in natural product diversification.
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Affiliation(s)
- Dominik M Peter
- Biochemistry and Synthetic Biology of Microbial Metabolism Group, Max-Planck-Institute for terrestrial Microbiology, Karl-von-Frisch-Strasse 10, 35043 Marburg (Germany).,Institute of Microbiology, Eidgenössisch Technische Hochschule (ETH) Zürich, Vladimir-Prelog-Weg 4, 8050 Zürich (Switzerland)
| | - Lennart Schada von Borzyskowski
- Biochemistry and Synthetic Biology of Microbial Metabolism Group, Max-Planck-Institute for terrestrial Microbiology, Karl-von-Frisch-Strasse 10, 35043 Marburg (Germany).,Institute of Microbiology, Eidgenössisch Technische Hochschule (ETH) Zürich, Vladimir-Prelog-Weg 4, 8050 Zürich (Switzerland)
| | - Patrick Kiefer
- Institute of Microbiology, Eidgenössisch Technische Hochschule (ETH) Zürich, Vladimir-Prelog-Weg 4, 8050 Zürich (Switzerland)
| | - Philipp Christen
- Institute of Microbiology, Eidgenössisch Technische Hochschule (ETH) Zürich, Vladimir-Prelog-Weg 4, 8050 Zürich (Switzerland)
| | - Julia A Vorholt
- Institute of Microbiology, Eidgenössisch Technische Hochschule (ETH) Zürich, Vladimir-Prelog-Weg 4, 8050 Zürich (Switzerland)
| | - Tobias J Erb
- Biochemistry and Synthetic Biology of Microbial Metabolism Group, Max-Planck-Institute for terrestrial Microbiology, Karl-von-Frisch-Strasse 10, 35043 Marburg (Germany). .,Institute of Microbiology, Eidgenössisch Technische Hochschule (ETH) Zürich, Vladimir-Prelog-Weg 4, 8050 Zürich (Switzerland).
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42
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Peter DM, Schada von Borzyskowski L, Kiefer P, Christen P, Vorholt JA, Erb TJ. Klassifizierung und Manipulation des synthetischen Potenzials carboxylierender Reduktasen aus dem Zentralmetabolismus und der Polyketid‐Biosynthese. Angew Chem Int Ed Engl 2015. [DOI: 10.1002/ange.201505282] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/12/2023]
Affiliation(s)
- Dominik M. Peter
- Biochemie & Synthetische Biologie des Mikrobiellen Metabolismus, Max‐Planck‐Institut für Terrestrische Mikrobiologie, Karl‐von‐Frisch‐Straße 10, 35043 Marburg (Deutschland)
- Institut für Mikrobiologie, Eidgenössische Technische Hochschule (ETH) Zürich, Vladimir‐Prelog‐Weg 4, 8050 Zürich (Schweiz)
| | - Lennart Schada von Borzyskowski
- Biochemie & Synthetische Biologie des Mikrobiellen Metabolismus, Max‐Planck‐Institut für Terrestrische Mikrobiologie, Karl‐von‐Frisch‐Straße 10, 35043 Marburg (Deutschland)
- Institut für Mikrobiologie, Eidgenössische Technische Hochschule (ETH) Zürich, Vladimir‐Prelog‐Weg 4, 8050 Zürich (Schweiz)
| | - Patrick Kiefer
- Institut für Mikrobiologie, Eidgenössische Technische Hochschule (ETH) Zürich, Vladimir‐Prelog‐Weg 4, 8050 Zürich (Schweiz)
| | - Philipp Christen
- Institut für Mikrobiologie, Eidgenössische Technische Hochschule (ETH) Zürich, Vladimir‐Prelog‐Weg 4, 8050 Zürich (Schweiz)
| | - Julia A. Vorholt
- Institut für Mikrobiologie, Eidgenössische Technische Hochschule (ETH) Zürich, Vladimir‐Prelog‐Weg 4, 8050 Zürich (Schweiz)
| | - Tobias J. Erb
- Biochemie & Synthetische Biologie des Mikrobiellen Metabolismus, Max‐Planck‐Institut für Terrestrische Mikrobiologie, Karl‐von‐Frisch‐Straße 10, 35043 Marburg (Deutschland)
- Institut für Mikrobiologie, Eidgenössische Technische Hochschule (ETH) Zürich, Vladimir‐Prelog‐Weg 4, 8050 Zürich (Schweiz)
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43
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Miyazawa T, Takahashi S, Kawata A, Panthee S, Hayashi T, Shimizu T, Nogawa T, Osada H. Identification of Middle Chain Fatty Acyl-CoA Ligase Responsible for the Biosynthesis of 2-Alkylmalonyl-CoAs for Polyketide Extender Unit. J Biol Chem 2015; 290:26994-27011. [PMID: 26378232 DOI: 10.1074/jbc.m115.677195] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2015] [Indexed: 11/06/2022] Open
Abstract
Understanding the biosynthetic mechanism of the atypical polyketide extender unit is important for the development of bioactive natural products. Reveromycin (RM) derivatives produced by Streptomyces sp. SN-593 possess several aliphatic extender units. Here, we studied the molecular basis of 2-alkylmalonyl-CoA formation by analyzing the revR and revS genes, which form a transcriptional unit with the revT gene, a crotonyl-CoA carboxylase/reductase homolog. We mainly focused on the uncharacterized adenylate-forming enzyme (RevS). revS gene disruption resulted in the reduction of all RM derivatives, whereas reintroduction of the gene restored the yield of RMs. Although RevS was classified in the fatty acyl-AMP ligase clade based on phylogenetic analysis, biochemical characterization revealed that the enzyme catalyzed the middle chain fatty acyl-CoA ligase (FACL) but not the fatty acyl-AMP ligase activity, suggesting the molecular evolution for acyl-CoA biosynthesis. Moreover, we examined the in vitro conversion of fatty acid into 2-alkylmalonyl-CoA using purified RevS and RevT. The coupling reaction showed efficient conversion of hexenoic acid into butylmalonyl-CoA. RevS efficiently catalyzed C8-C10 middle chain FACL activity; therefore, we speculated that the acyl-CoA precursor was truncated via β-oxidation and converted into (E)-2-enoyl-CoA, a RevT substrate. To determine whether the β-oxidation process is involved between the RevS and RevT reaction, we performed the feeding experiment using [1,2,3,4-(13)C]octanoic acid. (13)C NMR analysis clearly demonstrated incorporation of the [3,4-(13)C]octanoic acid moiety into the structure of RM-A. Our results provide insight into the role of uncharacterized RevS homologs that may catalyze middle chain FACL to produce a unique polyketide extender unit.
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Affiliation(s)
- Takeshi Miyazawa
- RIKEN Center for Sustainable Resource Science, Chemical Biology Research Group, Saitama 351-0198 and; the Graduate School of Science and Engineering, Saitama University, Saitama 338-8570, Japan
| | - Shunji Takahashi
- RIKEN Center for Sustainable Resource Science, Chemical Biology Research Group, Saitama 351-0198 and
| | - Akihiro Kawata
- the Graduate School of Science and Engineering, Saitama University, Saitama 338-8570, Japan
| | - Suresh Panthee
- RIKEN Center for Sustainable Resource Science, Chemical Biology Research Group, Saitama 351-0198 and
| | - Teruo Hayashi
- RIKEN Center for Sustainable Resource Science, Chemical Biology Research Group, Saitama 351-0198 and
| | - Takeshi Shimizu
- RIKEN Center for Sustainable Resource Science, Chemical Biology Research Group, Saitama 351-0198 and
| | - Toshihiko Nogawa
- RIKEN Center for Sustainable Resource Science, Chemical Biology Research Group, Saitama 351-0198 and
| | - Hiroyuki Osada
- RIKEN Center for Sustainable Resource Science, Chemical Biology Research Group, Saitama 351-0198 and; the Graduate School of Science and Engineering, Saitama University, Saitama 338-8570, Japan.
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44
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Li S, Li Y, Lu C, Zhang J, Zhu J, Wang H, Shen Y. Activating a Cryptic Ansamycin Biosynthetic Gene Cluster To Produce Three New Naphthalenic Octaketide Ansamycins with n-Pentyl and n-Butyl Side Chains. Org Lett 2015; 17:3706-9. [PMID: 26167742 DOI: 10.1021/acs.orglett.5b01686] [Citation(s) in RCA: 38] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/16/2023]
Abstract
Genome mining is a rational approach to discovering new natural products. The genome sequence analysis of Streptomyces sp. LZ35 revealed the presence of a putative ansamycin gene cluster (nam). Constitutive overexpression of the pathway-specific transcriptional regulatory gene nam1 successfully activated the nam gene cluster, and three novel naphthalenic octaketide ansamycins were discovered with unprecedented n-pentylmalonyl-CoA or n-butylmalonyl-CoA extender units. This study represents the first example of discovering novel ansamycin scaffolds via activation of a cryptic gene cluster.
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Affiliation(s)
- Shanren Li
- †Key Laboratory of Chemical Biology (Ministry of Education), School of Pharmaceutical Sciences, Shandong University, Jinan, Shandong 250012, P. R. China
| | - Yaoyao Li
- †Key Laboratory of Chemical Biology (Ministry of Education), School of Pharmaceutical Sciences, Shandong University, Jinan, Shandong 250012, P. R. China
| | - Chunhua Lu
- †Key Laboratory of Chemical Biology (Ministry of Education), School of Pharmaceutical Sciences, Shandong University, Jinan, Shandong 250012, P. R. China
| | - Juanli Zhang
- †Key Laboratory of Chemical Biology (Ministry of Education), School of Pharmaceutical Sciences, Shandong University, Jinan, Shandong 250012, P. R. China
| | - Jing Zhu
- ‡State Key Laboratory of Microbial Technology, School of Life Sciences, Shandong University, Jinan, Shandong 250100, P. R. China
| | - Haoxin Wang
- ‡State Key Laboratory of Microbial Technology, School of Life Sciences, Shandong University, Jinan, Shandong 250100, P. R. China
| | - Yuemao Shen
- †Key Laboratory of Chemical Biology (Ministry of Education), School of Pharmaceutical Sciences, Shandong University, Jinan, Shandong 250012, P. R. China.,‡State Key Laboratory of Microbial Technology, School of Life Sciences, Shandong University, Jinan, Shandong 250100, P. R. China
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45
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Hertweck C. Decoding and reprogramming complex polyketide assembly lines: prospects for synthetic biology. Trends Biochem Sci 2015; 40:189-99. [PMID: 25757401 DOI: 10.1016/j.tibs.2015.02.001] [Citation(s) in RCA: 68] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/06/2015] [Revised: 02/11/2015] [Accepted: 02/11/2015] [Indexed: 12/12/2022]
Abstract
Bacterial modular type I polyketide synthases (PKSs) represent giant megasynthases that produce a vast number of complex polyketides, many of which are pharmaceutically relevant. This review highlights recent advances in elucidating the mechanism of bacterial type I PKSs and associated enzymes, and outlines the ramifications of this knowledge for synthetic biology approaches to expand structural diversity. New insights into biosynthetic codes and structures of thiotemplate systems pave the way to rational bioengineering strategies. Through advances in genome mining, DNA recombination technologies, and biochemical analyses, the toolbox of non-canonical polyketide-modifying enzymes has been greatly enlarged. In addition to various chain-branching and chain-fusing enzymes, an increasing set of scaffold modifying biocatalysts is now available for synthetically hard-to-emulate reactions.
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Affiliation(s)
- Christian Hertweck
- Department of Biomolecular Chemistry, Leibniz Institute for Natural Product Research and Infection Biology (HKI), Beutenbergstr. 11a, 07745 Jena, Germany; Chair of Natural Product Chemistry, Friedrich Schiller University, Jena, Germany.
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46
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An enzymatic [4+2] cyclization cascade creates the pentacyclic core of pyrroindomycins. Nat Chem Biol 2015; 11:259-65. [DOI: 10.1038/nchembio.1769] [Citation(s) in RCA: 104] [Impact Index Per Article: 11.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2014] [Accepted: 02/04/2015] [Indexed: 01/16/2023]
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47
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Matsuda Y, Iwabuchi T, Wakimoto T, Awakawa T, Abe I. Uncovering the Unusual D-Ring Construction in Terretonin Biosynthesis by Collaboration of a Multifunctional Cytochrome P450 and a Unique Isomerase. J Am Chem Soc 2015; 137:3393-401. [DOI: 10.1021/jacs.5b00570] [Citation(s) in RCA: 89] [Impact Index Per Article: 9.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Yudai Matsuda
- Graduate
School of Pharmaceutical
Sciences, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-0033, Japan
| | - Taiki Iwabuchi
- Graduate
School of Pharmaceutical
Sciences, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-0033, Japan
| | - Toshiyuki Wakimoto
- Graduate
School of Pharmaceutical
Sciences, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-0033, Japan
| | - Takayoshi Awakawa
- Graduate
School of Pharmaceutical
Sciences, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-0033, Japan
| | - Ikuro Abe
- Graduate
School of Pharmaceutical
Sciences, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-0033, Japan
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48
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Chen YP, Liu Q, Gao H, Lin HP, Tian HY, Hong K, Li J, Jiang RW, Yao XS, Tang JS. Streptospirodienoic acids A and B, 6,6-spiroketal polyketides from Streptomyces sp. RSC Adv 2014. [DOI: 10.1039/c4ra10672e] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
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49
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Takahashi S, Nagano S, Nogawa T, Kanoh N, Uramoto M, Kawatani M, Shimizu T, Miyazawa T, Shiro Y, Osada H. Structure-function analyses of cytochrome P450revI involved in reveromycin A biosynthesis and evaluation of the biological activity of its substrate, reveromycin T. J Biol Chem 2014; 289:32446-58. [PMID: 25258320 DOI: 10.1074/jbc.m114.598391] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Numerous cytochrome P450s are involved in secondary metabolite biosynthesis. The biosynthetic gene cluster for reveromycin A (RM-A), which is a promising lead compound with anti-osteoclastic activity, also includes a P450 gene, revI. To understand the roles of P450revI, we comprehensively characterized the enzyme by genetic, kinetic, and structural studies. The revI gene disruptants (ΔrevI) resulted in accumulation of reveromycin T (RM-T), and revI gene complementation restored RM-A production, indicating that the physiological substrate of P450revI is RM-T. Indeed, the purified P450revI catalyzed the C18-hydroxylation of RM-T more efficiently than the other RM derivatives tested. Moreover, the 1.4 Å resolution co-crystal structure of P450revI with RM-T revealed that the substrate binds the enzyme with a folded compact conformation for C18-hydroxylation. To address the structure-enzyme activity relationship, site-directed mutagenesis was performed in P450revI. R190A and R81A mutations, which abolished salt bridge formation with C1 and C24 carboxyl groups of RM-T, respectively, resulted in significant loss of enzyme activity. The interaction between Arg(190) and the C1 carboxyl group of RM-T elucidated why P450revI was unable to catalyze both RM-T 1-methyl ester and RM-T 1-ethyl ester. Moreover, the accumulation of RM-T in ΔrevI mutants enabled us to characterize its biological activity. Our results show that RM-T had stronger anticancer activity and isoleucyl-tRNA synthetase inhibition than RM-A. However, RM-T showed much less anti-osteoclastic activity than RM-A, indicating that hemisuccinate moiety is important for the activity. Structure-based P450revI engineering for novel hydroxylation and subsequent hemisuccinylation will help facilitate the development of RM derivatives with anti-osteoclast activity.
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Affiliation(s)
- Shunji Takahashi
- From the Chemical Biology Group, RIKEN Center for Sustainable Resource Science, Saitama 351-0198, Japan, the Antibiotics Laboratory, RIKEN, Saitama 351-0198, Japan,
| | - Shingo Nagano
- the Department of Chemistry and Biotechnology, Graduate School of Engineering, Tottori University, Tottori 680-8582, Japan, the Biometal Science Laboratory, RIKEN SPring-8 Center, 1-1-1 Kouto, Sayo, Hyogo 679-5148, Japan, and
| | - Toshihiko Nogawa
- From the Chemical Biology Group, RIKEN Center for Sustainable Resource Science, Saitama 351-0198, Japan
| | - Naoki Kanoh
- the Graduate School of Pharmaceutical Sciences, Tohoku University, Aobayama, Sendai 980-8578, Japan
| | | | | | | | | | - Yoshitsugu Shiro
- the Biometal Science Laboratory, RIKEN SPring-8 Center, 1-1-1 Kouto, Sayo, Hyogo 679-5148, Japan, and
| | - Hiroyuki Osada
- From the Chemical Biology Group, RIKEN Center for Sustainable Resource Science, Saitama 351-0198, Japan, the Antibiotics Laboratory, RIKEN, Saitama 351-0198, Japan
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50
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Luhavaya H, Williams SR, Hong H, Gonzaga de Oliveira L, Leadlay PF. Site-specific modification of the anticancer and antituberculosis polyether salinomycin by biosynthetic engineering. Chembiochem 2014; 15:2081-5. [PMID: 25155178 PMCID: PMC4515104 DOI: 10.1002/cbic.201402300] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2014] [Indexed: 11/23/2022]
Abstract
The complex bis-spiroacetal polyether ionophore salinomycin has been identified as a uniquely selective agent against cancer stem cells and is also strikingly effective in an animal model of latent tuberculosis. The basis for these important activities is unknown. We show here that deletion of the salE gene abolishes salinomycin production and yields two new analogues, in both of which the C18C19 cis double bond is replaced by a hydroxy group stereospecifically located at C19, but which differ from each other in the configuration of the bis-spiroacetal. These results identify SalE as a novel dehydratase and demonstrate that biosynthetic engineering can be used to redirect the reaction cascade of oxidative cyclization to yield new salinomycin analogues for use in mechanism-of-action studies.
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Affiliation(s)
- Hanna Luhavaya
- Department of Biochemistry, University of Cambridge80 Tennis Court Road, Cambridge CB2 1GA (UK)
| | - Simon R Williams
- University Chemical Laboratory, University of CambridgeLensfield Road, Cambridge CB2 1EW (UK)
| | - Hui Hong
- Department of Biochemistry, University of Cambridge80 Tennis Court Road, Cambridge CB2 1GA (UK)
| | - Luciana Gonzaga de Oliveira
- Department of Organic Chemistry, University of Campinas, UNICAMP, Cidade Universitária Zeferino Vaz s/nP.O. Box 6154, 13083-970, Campinas, SP (Brazil)
| | - Peter F Leadlay
- Department of Biochemistry, University of Cambridge80 Tennis Court Road, Cambridge CB2 1GA (UK)
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