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Heo KT, Lee B, Hwang GJ, Park B, Jang JP, Hwang BY, Jang JH, Hong YS. A unique dual acyltransferase system shared in the polyketide chain initiation of kidamycinone and rubiflavinone biosynthesis. Front Microbiol 2023; 14:1274358. [PMID: 38029143 PMCID: PMC10646177 DOI: 10.3389/fmicb.2023.1274358] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2023] [Accepted: 10/04/2023] [Indexed: 12/01/2023] Open
Abstract
The pluramycin family of natural products has diverse substituents at the C2 position, which are closely related to their biological activity. Therefore, it is important to understand the biosynthesis of C2 substituents. In this study, we describe the biosynthesis of C2 moieties in Streptomyces sp. W2061, which produces kidamycin and rubiflavinone C-1, containing anthrapyran aglycones. Sequence analysis of the loading module (Kid13) of the PKS responsible for the synthesis of these anthrapyran aglycones is useful for confirming the incorporation of atypical primer units into the corresponding products. Kid13 is a ketosynthase-like decarboxylase (KSQ)-type loading module with unusual dual acyltransferase (AT) domains (AT1-1 and AT1-2). The AT1-2 domain primarily loads ethylmalonyl-CoA and malonyl-CoA for rubiflavinone and kidamycinone and rubiflavinone, respectively; however, the AT1-1 domain contributed to the functioning of the AT1-2 domain to efficiently load ethylmalonyl-CoA for rubiflavinone. We found that the dual AT system was involved in the production of kidamycinone, an aglycone of kidamycin, and rubiflavinone C-1 by other shared biosynthetic genes in Streptomyces sp. W2061. This study broadens our understanding of the incorporation of atypical primer units into polyketide products.
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Affiliation(s)
- Kyung Taek Heo
- Chemical Biology Research Center, Korea Research Institute of Bioscience and Biotechnology (KRIBB), Cheongju-si, Republic of Korea
| | - Byeongsan Lee
- Chemical Biology Research Center, Korea Research Institute of Bioscience and Biotechnology (KRIBB), Cheongju-si, Republic of Korea
- College of Pharmacy, Chungbuk National University, Cheongju-si, Republic of Korea
| | - Gwi Ja Hwang
- Chemical Biology Research Center, Korea Research Institute of Bioscience and Biotechnology (KRIBB), Cheongju-si, Republic of Korea
| | - Beomcheol Park
- Chemical Biology Research Center, Korea Research Institute of Bioscience and Biotechnology (KRIBB), Cheongju-si, Republic of Korea
- College of Pharmacy, Chungbuk National University, Cheongju-si, Republic of Korea
| | - Jun-Pil Jang
- Chemical Biology Research Center, Korea Research Institute of Bioscience and Biotechnology (KRIBB), Cheongju-si, Republic of Korea
| | - Bang Yeon Hwang
- College of Pharmacy, Chungbuk National University, Cheongju-si, Republic of Korea
| | - Jae-Hyuk Jang
- Chemical Biology Research Center, Korea Research Institute of Bioscience and Biotechnology (KRIBB), Cheongju-si, Republic of Korea
| | - Young-Soo Hong
- Chemical Biology Research Center, Korea Research Institute of Bioscience and Biotechnology (KRIBB), Cheongju-si, Republic of Korea
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2
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Zhan J, Yuan J, Liu J, Zhang F, Yu F, Wang Y. Metabolomics analysis of mycelial exudates provides insights into fungal antagonists of Armillaria. Mycology 2023; 14:264-274. [PMID: 37583453 PMCID: PMC10424624 DOI: 10.1080/21501203.2023.2238753] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2023] [Accepted: 07/15/2023] [Indexed: 08/17/2023] Open
Abstract
The genus Armillaria has high edible and medical values, with zones of antagonism often occurring when different species are paired in culture on agar media, while the antagonism-induced metabolic alteration remains unclear. Here, the metabolome of mycelial exudates of two Chinese Armillaria biological species, C and G, co-cultured or cultured separately was analysed to discover the candidate biomarkers and the key metabolic pathways involved in Armillaria antagonists. A total of 2,377 metabolites were identified, mainly organic acids and derivatives, lipids and lipid-like molecules, and organoheterocyclic compounds. There were 248 and 142 differentially expressed metabolites between group C-G and C, C-G, and G, respectively, and fourteen common differentially expressed metabolites including malate, uracil, Leu-Gln-Arg, etc. Metabolic pathways like TCA cycle and pyrimidine metabolism were significantly affected by C-G co-culture. Additionally, 156 new metabolites (largely organic acids and derivatives) including 32 potential antifungal compounds, primarily enriched into biosynthesis of secondary metabolites pathways were identified in C-G co-culture mode. We concluded that malate and uracil could be used as the candidate biomarkers, and TCA cycle and pyrimidine metabolism were the key metabolic pathways involved in Armillaria antagonists. The metabolic changes revealed in this study provide insights into the mechanisms underlying fungal antagonists.
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Affiliation(s)
| | | | - Jianwei Liu
- The Germplasm Bank of Wild Species, Yunnan Key Laboratory for Fungal Diversity and Green Development, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, China
| | - Fengming Zhang
- The Germplasm Bank of Wild Species, Yunnan Key Laboratory for Fungal Diversity and Green Development, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, China
| | - Fuqiang Yu
- The Germplasm Bank of Wild Species, Yunnan Key Laboratory for Fungal Diversity and Green Development, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, China
| | - Yanliang Wang
- The Germplasm Bank of Wild Species, Yunnan Key Laboratory for Fungal Diversity and Green Development, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, China
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3
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Heo KT, Lee B, Jang JH, Hong YS. Elucidation of the di-c-glycosylation steps during biosynthesis of the antitumor antibiotic, kidamycin. Front Bioeng Biotechnol 2022; 10:985696. [PMID: 36091425 PMCID: PMC9452638 DOI: 10.3389/fbioe.2022.985696] [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: 07/04/2022] [Accepted: 07/21/2022] [Indexed: 11/24/2022] Open
Abstract
Kidamycins belong to the pluramycin family of antitumor antibiotics that contain di-C-glycosylated angucycline. Owing to its interesting biological activity, several synthetic derivatives of kidamycins are currently being developed. However, the synthesis of these complex structural compounds with unusual C-glycosylated residues is difficult. In the kidamycin-producing Streptomyces sp. W2061 strain, the genes encoding the biosynthetic enzymes responsible for the structural features of kidamycin were identified. Two glycosyltransferase-coding genes, kid7 and kid21, were found in the kidamycin biosynthetic gene cluster (BGC). Gene inactivation studies revealed that the subsequent glycosylation steps occurred in a sequential manner, in which Kid7 first attached N,N-dimethylvancosamine to the C10 position of angucycline aglycone, following which Kid21 transferred an anglosamine moiety to C8 of the C10-glycosylated angucycline. Therefore, this is the first report to reveal the sequential biosynthetic steps of the unique C-glycosylated amino-deoxyhexoses of kidamycin. Additionally, we confirmed that all three methyltransferases (Kid4, Kid9, and Kid24) present in this BGC were involved in the biosynthesis of these amino-deoxyhexoses, N,N-dimethylvancosamine and anglosamine. Aglycone compounds and the mono-C-glycosylated compound obtained in this process will be used as substrates for the development of synthetic derivatives in the future.
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Affiliation(s)
- Kyung Taek Heo
- Chemical Biology Research Center, Korea Research Institute of Bioscience and Biotechnology, Chungbuk, South Korea
- Department of Bio-Molecular Science, KRIBB School of Bioscience, University of Science and Technology(UST), Daejeon, South Korea
| | - Byeongsan Lee
- Chemical Biology Research Center, Korea Research Institute of Bioscience and Biotechnology, Chungbuk, South Korea
| | - Jae-Hyuk Jang
- Chemical Biology Research Center, Korea Research Institute of Bioscience and Biotechnology, Chungbuk, South Korea
- Department of Bio-Molecular Science, KRIBB School of Bioscience, University of Science and Technology(UST), Daejeon, South Korea
- *Correspondence: Jae-Hyuk Jang, ; Young-Soo Hong,
| | - Young-Soo Hong
- Chemical Biology Research Center, Korea Research Institute of Bioscience and Biotechnology, Chungbuk, South Korea
- Department of Bio-Molecular Science, KRIBB School of Bioscience, University of Science and Technology(UST), Daejeon, South Korea
- *Correspondence: Jae-Hyuk Jang, ; Young-Soo Hong,
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4
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Molecular Basis for Polyketide Ketoreductase-Substrate Interactions. Int J Mol Sci 2020; 21:ijms21207562. [PMID: 33066287 PMCID: PMC7588967 DOI: 10.3390/ijms21207562] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2020] [Revised: 10/11/2020] [Accepted: 10/12/2020] [Indexed: 11/16/2022] Open
Abstract
Polyketides are a large class of structurally and functionally diverse natural products with important bioactivities. Many polyketides are synthesized by reducing type II polyketide synthases (PKSs), containing transiently interacting standalone enzymes. During synthesis, ketoreductase (KR) catalyzes regiospecific carbonyl to hydroxyl reduction, determining the product outcome, yet little is known about what drives specific KR-substrate interactions. In this study, computational approaches were used to explore KR-substrate interactions based on previously solved apo and mimic cocrystal structures. We found five key factors guiding KR-substrate binding. First, two major substrate binding motifs were identified. Second, substrate length is the key determinant of substrate binding position. Third, two key residues in chain length specificity were confirmed. Fourth, phosphorylation of substrates is critical for binding. Finally, packing/hydrophobic effects primarily determine the binding stability. The molecular bases revealed here will help further engineering of type II PKSs and directed biosynthesis of new polyketides.
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Shellmycin A-D, Novel Bioactive Tetrahydroanthra-γ-Pyrone Antibiotics from Marine Streptomyces sp. Shell-016. Mar Drugs 2020; 18:md18010058. [PMID: 31963176 PMCID: PMC7024178 DOI: 10.3390/md18010058] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2019] [Revised: 01/07/2020] [Accepted: 01/12/2020] [Indexed: 12/11/2022] Open
Abstract
Four novel bioactive tetrahydroanthra-γ-pyrone compounds, shellmycin A-D (1-4), were isolated from the marine Streptomyces sp. shell-016 derived from a shell sediment sample collected from Binzhou Shell Dike Island and Wetland National Nature Reserve, China. The structures of these four compounds were established by interpretation of 1D and 2D NMR and HR-MS data, in which the absolute configuration of 1 was confirmed by single crystal X-ray diffraction, and compound 3 and 4 are a pair of stereoisomers. Compound 1-4 exhibited cytotoxic activity against five cancer cell lines with the IC50 value from 0.69 μM to 26.3 μM. Based on their structure-activity relationship, the putative biosynthetic pathways of these four compounds were also discussed.
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Lv Q, Fan Y, Tao G, Fu P, Zhai J, Ye B, Zhu W. Sekgranaticin, a SEK34b-Granaticin Hybrid Polyketide from Streptomyces sp. 166. J Org Chem 2019; 84:9087-9092. [PMID: 31273973 DOI: 10.1021/acs.joc.9b01022] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/13/2023]
Abstract
Sekgranaticin (1), a novel hybrid polyketide with a complex 6/6/6/6/6/6/6 7-ring system, was isolated together with granaticins A (2) and B (3) and methyl granaticinate (4) from the culture broth of Streptomyces sp. 166#. Its structure was elucidated by spectroscopic analysis. The absolute configuration was determined on the basis of the calculated 13C NMR and electronic circular dichroism data. Compounds 1-4 exhibited potent cytotoxicity against cancer cell lines MCF-7, A549, P6C, and HCT-116 with IC50 values of 0.02-6.77 μM. The biosynthetic pathway of sekgranaticin (1) was proposed.
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Affiliation(s)
- Qianqian Lv
- Key Laboratory of Marine Drugs, Ministry of Education of China, School of Medicine and Pharmacy , Ocean University of China , Qingdao 266003 , China
| | - Yaqin Fan
- Key Laboratory of Marine Drugs, Ministry of Education of China, School of Medicine and Pharmacy , Ocean University of China , Qingdao 266003 , China
| | - Ganzheng Tao
- School of Life Science and Technology , China Pharmaceutical University , Nanjing 210009 , China
| | - Peng Fu
- Key Laboratory of Marine Drugs, Ministry of Education of China, School of Medicine and Pharmacy , Ocean University of China , Qingdao 266003 , China.,Open Studio for Druggability Research of Marine Natural Products, Laboratory for Marine Drugs and Bioproducts , Pilot National Laboratory for Marine Science and Technology (Qingdao) , Qingdao 266003 , China
| | - Jingxin Zhai
- School of Life Science and Technology , China Pharmaceutical University , Nanjing 210009 , China
| | - Boping Ye
- School of Life Science and Technology , China Pharmaceutical University , Nanjing 210009 , China
| | - Weiming Zhu
- Key Laboratory of Marine Drugs, Ministry of Education of China, School of Medicine and Pharmacy , Ocean University of China , Qingdao 266003 , China.,Open Studio for Druggability Research of Marine Natural Products, Laboratory for Marine Drugs and Bioproducts , Pilot National Laboratory for Marine Science and Technology (Qingdao) , Qingdao 266003 , China
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7
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Biosynthesis of Polyketides in Streptomyces. Microorganisms 2019; 7:microorganisms7050124. [PMID: 31064143 PMCID: PMC6560455 DOI: 10.3390/microorganisms7050124] [Citation(s) in RCA: 66] [Impact Index Per Article: 13.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2019] [Revised: 04/24/2019] [Accepted: 04/27/2019] [Indexed: 12/12/2022] Open
Abstract
Polyketides are a large group of secondary metabolites that have notable variety in their structure and function. Polyketides exhibit a wide range of bioactivities such as antibacterial, antifungal, anticancer, antiviral, immune-suppressing, anti-cholesterol, and anti-inflammatory activity. Naturally, they are found in bacteria, fungi, plants, protists, insects, mollusks, and sponges. Streptomyces is a genus of Gram-positive bacteria that has a filamentous form like fungi. This genus is best known as one of the polyketides producers. Some examples of polyketides produced by Streptomyces are rapamycin, oleandomycin, actinorhodin, daunorubicin, and caprazamycin. Biosynthesis of polyketides involves a group of enzyme activities called polyketide synthases (PKSs). There are three types of PKSs (type I, type II, and type III) in Streptomyces responsible for producing polyketides. This paper focuses on the biosynthesis of polyketides in Streptomyces with three structurally-different types of PKSs.
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Nofiani R, Philmus B, Nindita Y, Mahmud T. 3-Ketoacyl-ACP synthase (KAS) III homologues and their roles in natural product biosynthesis. MEDCHEMCOMM 2019; 10:1517-1530. [PMID: 31673313 DOI: 10.1039/c9md00162j] [Citation(s) in RCA: 27] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/15/2019] [Accepted: 04/29/2019] [Indexed: 11/21/2022]
Abstract
The 3-ketoacyl-ACP synthase (KAS) III proteins are one of the most abundant enzymes in nature, as they are involved in the biosynthesis of fatty acids and natural products. KAS III enzymes catalyse a carbon-carbon bond formation reaction that involves the α-carbon of a thioester and the carbonyl carbon of another thioester. In addition to the typical KAS III enzymes involved in fatty acid and polyketide biosynthesis, there are proteins homologous to KAS III enzymes that catalyse reactions that are different from that of the traditional KAS III enzymes. Those include enzymes that are responsible for a head-to-head condensation reaction, the formation of acetoacetyl-CoA in mevalonate biosynthesis, tailoring processes via C-O bond formation or esterification, as well as amide formation. This review article highlights the diverse reactions catalysed by this class of enzymes and their role in natural product biosynthesis.
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Affiliation(s)
- Risa Nofiani
- Department of Pharmaceutical Sciences , Oregon State University , Corvallis , OR 97333 , USA . .,Department of Chemistry , Universitas Tanjungpura , Pontianak , Indonesia
| | - Benjamin Philmus
- Department of Pharmaceutical Sciences , Oregon State University , Corvallis , OR 97333 , USA .
| | - Yosi Nindita
- Department of Pharmaceutical Sciences , Oregon State University , Corvallis , OR 97333 , USA .
| | - Taifo Mahmud
- Department of Pharmaceutical Sciences , Oregon State University , Corvallis , OR 97333 , USA .
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9
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Dholakiya RN, Kumar R, Mishra A, Mody KH, Jha B. Antibacterial and Antioxidant Activities of Novel Actinobacteria Strain Isolated from Gulf of Khambhat, Gujarat. Front Microbiol 2017; 8:2420. [PMID: 29270160 PMCID: PMC5725476 DOI: 10.3389/fmicb.2017.02420] [Citation(s) in RCA: 35] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2017] [Accepted: 11/22/2017] [Indexed: 02/02/2023] Open
Abstract
Bacterial secondary metabolites possess a wide range of biologically active compounds including antibacterial and antioxidants. In this study, a Gram-positive novel marine Actinobacteria was isolated from sea sediment which showed 84% 16S rRNA gene sequence (KT588655) similarity with Streptomyces variabilis (EU841661) and designated as Streptomyces variabilis RD-5. The genus Streptomyces is considered as a promising source of bioactive secondary metabolites. The isolated novel bacterial strain was characterized by antibacterial characteristics and antioxidant activities. The BIOLOG based analysis suggested that S. variabilis RD-5 utilized a wide range of substrates compared to the reference strain. The result is further supported by statistical analysis such as AWCD (average well color development), heat-map and PCA (principal component analysis). The whole cell fatty acid profiling showed the dominance of iso/anteiso branched C15–C17 long chain fatty acids. The identified strain S. variabilis RD-5 exhibited a broad spectrum of antibacterial activities for the Gram-negative bacteria (Escherichia coli NCIM 2065, Shigella boydii NCIM, Klebsiella pneumoniae, Enterobacter cloacae, Pseudomonas sp. NCIM 2200 and Salmonella enteritidis NCIM), and Gram-positive bacteria (Bacillus subtilis NCIM 2920 and Staphylococcus aureus MTCC 96). Extract of S. variabilis strain RD-5 showed 82.86 and 89% of 2,2-diphenyl-1-picrylhydrazyl (DPPH) free radical scavenging and metal chelating activity, respectively, at 5.0 mg/mL. While H2O2 scavenging activity was 74.5% at 0.05 mg/mL concentration. Furthermore, polyketide synthases (PKSs types I and II), an enzyme complex that produces polyketides, the encoding gene(s) detected in the strain RD-5 which may probably involve for the synthesis of antibacterial compound(s). In conclusion, a novel bacterial strain of Actinobacteria, isolated from the unexplored sea sediment of Alang, Gulf of Khambhat (Gujarat), India showed promising antibacterial activities. However, fractionation and further characterization of active compounds from S. variabilis RD-5 are needed for their optimum utilization toward antibacterial purposes.
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Affiliation(s)
- Riddhi N Dholakiya
- Marine Biotechnology and Ecology Division, CSIR-Central Salt and Marine Chemicals Research Institute, Bhavnagar, India
| | - Raghawendra Kumar
- Marine Biotechnology and Ecology Division, CSIR-Central Salt and Marine Chemicals Research Institute, Bhavnagar, India
| | - Avinash Mishra
- Marine Biotechnology and Ecology Division, CSIR-Central Salt and Marine Chemicals Research Institute, Bhavnagar, India
| | - Kalpana H Mody
- Marine Biotechnology and Ecology Division, CSIR-Central Salt and Marine Chemicals Research Institute, Bhavnagar, India
| | - Bhavanath Jha
- Marine Biotechnology and Ecology Division, CSIR-Central Salt and Marine Chemicals Research Institute, Bhavnagar, India
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Katsuyama Y, Sone K, Satou R, Izumikawa M, Takagi M, Fujie M, Satoh N, Shin-ya K, Ohnishi Y. Involvement of the Baeyer-Villiger Monooxygenase IfnQ in the Biosynthesis of Isofuranonaphthoquinone Scaffold of JBIR-76 and -77. Chembiochem 2016; 17:1021-8. [DOI: 10.1002/cbic.201600095] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2016] [Indexed: 11/11/2022]
Affiliation(s)
- Yohei Katsuyama
- Department of Biotechnology; Graduate School of Agricultural and Life Sciences; The University of Tokyo; 1-1-1 Yayoi Bunkyo-ku Tokyo 113-8657 Japan
| | - Kaoru Sone
- Department of Biotechnology; Graduate School of Agricultural and Life Sciences; The University of Tokyo; 1-1-1 Yayoi Bunkyo-ku Tokyo 113-8657 Japan
| | - Ryutaro Satou
- Department of Biotechnology; Graduate School of Agricultural and Life Sciences; The University of Tokyo; 1-1-1 Yayoi Bunkyo-ku Tokyo 113-8657 Japan
| | - Miho Izumikawa
- Japan Biological Informatics Consortium (JBIC); 2-4-7 Aomi Koto-ku Tokyo 135-0064 Japan
| | - Motoki Takagi
- Japan Biological Informatics Consortium (JBIC); 2-4-7 Aomi Koto-ku Tokyo 135-0064 Japan
| | - Manabu Fujie
- Okinawa Institute of Science and Technology Graduate University; 1919-1 Tancha Onna-son Kunigami-gun Okinawa 904-0495 Japan
| | - Noriyuki Satoh
- Okinawa Institute of Science and Technology Graduate University; 1919-1 Tancha Onna-son Kunigami-gun Okinawa 904-0495 Japan
| | - Kazuo Shin-ya
- National Institute of Advanced Industrial Science and Technology (AIST); 2-4-7 Aomi Koto-ku Tokyo 135-0064 Japan
| | - Yasuo Ohnishi
- Department of Biotechnology; Graduate School of Agricultural and Life Sciences; The University of Tokyo; 1-1-1 Yayoi Bunkyo-ku Tokyo 113-8657 Japan
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Jackson DR, Tu SS, Nguyen M, Barajas JF, Schaub AJ, Krug D, Pistorius D, Luo R, Müller R, Tsai SC. Structural Insights into Anthranilate Priming during Type II Polyketide Biosynthesis. ACS Chem Biol 2016; 11:95-103. [PMID: 26473393 DOI: 10.1021/acschembio.5b00500] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
The incorporation of nonacetate starter units during type II polyketide biosynthesis helps diversify natural products. Currently, there are few enzymatic strategies for the incorporation of nonacetate starter units in type II polyketide synthase (PKS) pathways. Here we report the crystal structure of AuaEII, the anthranilate:CoA ligase responsible for the generation of anthraniloyl-CoA, which is used as a starter unit by a type II PKS in aurachin biosynthesis. We present structural and protein sequence comparisons to other aryl:CoA ligases. We also compare the AuaEII crystal structure to a model of a CoA ligase homologue, AuaE, which is present in the same gene cluster. AuaE is predicted to have the same fold as AuaEII, but instead of CoA ligation, AuaE catalyzes acyl transfer of anthranilate from anthraniloyl-CoA to the acyl carrier protein (ACP). Together, this work provides insight into the molecular basis for starter unit selection of anthranilate in type II PKS biosynthesis.
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Affiliation(s)
| | | | | | | | | | - Daniel Krug
- Department
of Microbial Natural Products, Helmholtz-Institute for Pharmaceutical
Research Saarland (HIPS), Helmholtz Centre for Infection Research
(HZI) and Pharmaceutical Biotechnology, Saarland University, Campus C2 3, 66123 Saarbrücken, Germany
| | - Dominik Pistorius
- Department
of Microbial Natural Products, Helmholtz-Institute for Pharmaceutical
Research Saarland (HIPS), Helmholtz Centre for Infection Research
(HZI) and Pharmaceutical Biotechnology, Saarland University, Campus C2 3, 66123 Saarbrücken, Germany
| | | | - Rolf Müller
- Department
of Microbial Natural Products, Helmholtz-Institute for Pharmaceutical
Research Saarland (HIPS), Helmholtz Centre for Infection Research
(HZI) and Pharmaceutical Biotechnology, Saarland University, Campus C2 3, 66123 Saarbrücken, Germany
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12
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Prabpai S, Kongsaeree P. Crystal structure of 1-(2,4-dihy-droxy-6-methyl-phen-yl)ethanone. Acta Crystallogr E Crystallogr Commun 2015; 71:o612-3. [PMID: 26396824 PMCID: PMC4571424 DOI: 10.1107/s2056989015013468] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2015] [Accepted: 07/14/2015] [Indexed: 11/10/2022]
Abstract
The title compound, C9H10O3, is a bioactive secondary metabolite, isolated from the endophytic fungus Nodulisporium sp. The compound exhibits an intra-molecular O-H⋯O hydrogen bond between the phenolic H atom and the carbonyl O atom of the adjacent acetyl group. In the crystal, mol-ecules are linked by hydrogen bonds involving the 4-phenolic H atom and a symmetry-related carbonyl O atom of a neighboring mol-ecule, resulting in extended supra-molecular chains along the a-axis direction. Aromatic π-π stacking inter-actions between the nearly parallel benzene rings of adjacent chains [centroid-centroid distance = 3.7478 (8) Å] further stabilize the three-dimensional supra-molecular framework.
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Affiliation(s)
- Samran Prabpai
- Department of Chemistry, and Center for Excellence in Protein Structure and Function, Faculty of Science, Mahidol University, Bangkok 10400, Thailand
| | - Palangpon Kongsaeree
- Department of Chemistry, and Center for Excellence in Protein Structure and Function, Faculty of Science, Mahidol University, Bangkok 10400, Thailand
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13
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Pathway and protein engineering approaches to produce novel and commodity small molecules. Curr Opin Biotechnol 2013; 24:1137-43. [DOI: 10.1016/j.copbio.2013.02.019] [Citation(s) in RCA: 56] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2013] [Revised: 02/07/2013] [Accepted: 02/20/2013] [Indexed: 11/19/2022]
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14
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Fitzgerald JT, Charkoudian LK, Watts KR, Khosla C. Analysis and refactoring of the A-74528 biosynthetic pathway. J Am Chem Soc 2013; 135:3752-5. [PMID: 23442197 DOI: 10.1021/ja311579s] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
A-74528 is a C30 polyketide natural product that functions as an inhibitor of 2',5'-oligoadenylate phosphodiesterase (2'-PDE), a key regulatory enzyme of the interferon pathway. Modulation of 2'-PDE represents a unique therapeutic approach for regulating viral infections. The gene cluster responsible for biosynthesis of A-74528 yields minute amounts of this natural product together with considerably larger quantities of a structurally dissimilar C30 cytotoxic agent, fredericamycin. Through construction and analysis of a series of knockout mutants, we identified the genes necessary for A-74528 biosynthesis. Remarkably, the formation of six stereocenters and the regiospecific formation of six rings in A-74528 appear to be catalyzed by only two tailoring enzymes, a cyclase and an oxygenase, in addition to the core polyketide synthase. The inferred pathway was genetically refactored in a heterologous host, Streptomyces coelicolor CH999, to produce 3 mg/L A-74528 in the absence of fredericamycin.
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Affiliation(s)
- Jay T Fitzgerald
- Department of Chemistry, Stanford University, Stanford, California 94305, USA
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15
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Kwon SJ, Mora-Pale M, Lee MY, Dordick JS. Expanding nature's small molecule diversity via in vitro biosynthetic pathway engineering. Curr Opin Chem Biol 2012; 16:186-95. [DOI: 10.1016/j.cbpa.2012.02.001] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2011] [Revised: 02/01/2012] [Accepted: 02/01/2012] [Indexed: 12/15/2022]
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Javidpour P, Das A, Khosla C, Tsai SC. Structural and biochemical studies of the hedamycin type II polyketide ketoreductase (HedKR): molecular basis of stereo- and regiospecificities. Biochemistry 2011; 50:7426-39. [PMID: 21776967 DOI: 10.1021/bi2006866] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Bacterial aromatic polyketides that include many antibiotic and antitumor therapeutics are biosynthesized by the type II polyketide synthase (PKS), which consists of 5-10 stand-alone enzymatic domains. Hedamycin, an antitumor antibiotic polyketide, is uniquely primed with a hexadienyl group generated by a type I PKS followed by coupling to a downstream type II PKS to biosynthesize a 24-carbon polyketide, whose C9 position is reduced by hedamycin type II ketoreductase (hedKR). HedKR is homologous to the actinorhodin KR (actKR), for which we have conducted extensive structural studies previously. How hedKR can accommodate a longer polyketide substrate than the actKR, and the molecular basis of its regio- and stereospecificities, is not well understood. Here we present a detailed study of hedKR that sheds light on its specificity. Sequence alignment of KRs predicts that hedKR is less active than actKR, with significant differences in substrate/inhibitor recognition. In vitro and in vivo assays of hedKR confirmed this hypothesis. The hedKR crystal structure further provides the molecular basis for the observed differences between hedKR and actKR in the recognition of substrates and inhibitors. Instead of the 94-PGG-96 motif observed in actKR, hedKR has the 92-NGG-94 motif, leading to S-dominant stereospecificity, whose molecular basis can be explained by the crystal structure. Together with mutations, assay results, docking simulations, and the hedKR crystal structure, a model for the observed regio- and stereospecificities is presented herein that elucidates how different type II KRs recognize substrates with different chain lengths, yet precisely reduce only the C9-carbonyl group. The molecular features of hedKR important for regio- and stereospecificities can potentially be applied to biosynthesize new polyketides via protein engineering that rationally controls polyketide ketoreduction.
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Affiliation(s)
- Pouya Javidpour
- Department of Molecular Biology and Biochemistry, University of California, Irvine, Irvine, California 92697, United States
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Wang P, Gao X, Chooi YH, Deng Z, Tang Y. Genetic characterization of enzymes involved in the priming steps of oxytetracycline biosynthesis in Streptomyces rimosus. Microbiology (Reading) 2011; 157:2401-2409. [DOI: 10.1099/mic.0.048439-0] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Tetracyclines are clinically important aromatic polyketides whose biosynthesis is catalysed by bacterial type II polyketide synthases (PKSs). Tetracyclines are biosynthesized starting with an amide-containing malonamate starter unit and the resulting C-2 carboxyamide is critical for the antibiotic activities. In this work, we genetically verified that an amidotransferase, OxyD, and a thiolase, OxyP, are involved in the biosynthesis and incorporation of the starter unit. First, two mutations, R248T and D268N, were found to be present in OxyD* encoded in Streptomyces rimosus ATCC 13224, a strain that produces the acetate-primed 2-acetyl-2-decarboxyamido-oxytetracycline (ADOTC) instead of the malonamate-primed oxytetracycline (OTC). Homology modelling suggested that in particular D268N may inactivate OxyD. Complementation of S. rimosus ATCC 13224 with wild-type OxyD restored OTC biosynthesis, thereby confirming the essential role of OxyD in the synthesis of the amide starter unit. Second, using a series of knockout and complementation approaches, we demonstrated that OxyP is most likely involved in maintaining fidelity of the amide-priming process via hydrolysis of the competing acetate priming starter units. While the inactivation of OxyP does not eliminate OTC biosynthesis, the ratio of acetate-primed ADOTC to malonamate-primed OTC is significantly increased. This suggests that OxyP plays an ancillary role in OTC biosynthesis and is important for minimizing the levels of ADOTC, a shunt product that has much weaker antibiotic activities than OTC.
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Affiliation(s)
- Peng Wang
- Department of Chemical and Biomolecular Engineering, University of California, Los Angeles, USA
- Laboratory of Microbial Metabolism and School of Life Sciences and Biotechnology, Shanghai Jiaotong University, Shanghai 200030, China
| | - Xue Gao
- Department of Chemical and Biomolecular Engineering, University of California, Los Angeles, USA
| | - Yit-Heng Chooi
- Department of Chemical and Biomolecular Engineering, University of California, Los Angeles, USA
| | - Zixin Deng
- Laboratory of Microbial Metabolism and School of Life Sciences and Biotechnology, Shanghai Jiaotong University, Shanghai 200030, China
| | - Yi Tang
- Department of Chemistry and Biochemistry, University of California, Los Angeles, USA
- Department of Chemical and Biomolecular Engineering, University of California, Los Angeles, USA
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Kalaitzis JA, Cheng Q, Meluzzi D, Xiang L, Izumikawa M, Dorrestein PC, Moore BS. Policing starter unit selection of the enterocin type II polyketide synthase by the type II thioesterase EncL. Bioorg Med Chem 2011; 19:6633-8. [PMID: 21531566 DOI: 10.1016/j.bmc.2011.04.024] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2011] [Revised: 04/05/2011] [Accepted: 04/11/2011] [Indexed: 11/18/2022]
Abstract
Enterocin is an atypical type II polyketide synthase (PKS) product from the marine actinomycete 'Streptomyces maritimus'. The enterocin biosynthesis gene cluster (enc) codes for proteins involved in the assembly and attachment of the rare benzoate primer that initiates polyketide assembly with the addition of seven malonate molecules and culminates in a Favorskii-like rearrangement of the linear poly-β-ketone to give its distinctive non-aromatic, caged core structure. Fundamental to enterocin biosynthesis, which utilizes a single acyl carrier protein (ACP), EncC, for both priming with benzoate and elongating with malonate, involves maintaining the correct balance of acyl-EncC substrates for efficient polyketide assembly. Here, we report the characterization of EncL as a type II thioesterase that functions to edit starter unit (mis)priming of EncC. We performed a series of in vivo mutational studies, heterologous expression experiments, in vitro reconstitution studies, and Fourier-transform mass spectrometry-monitored competitive enzyme assays that together support the proposed selective hydrolase activity of EncL toward misprimed acetyl-ACP over benzoyl-ACP to facilitate benzoyl priming of the enterocin PKS complex. While this system resembles the R1128 PKS that also utilizes an editing thioesterase (ZhuC) to purge acetate molecules from its initiation module ACP in favor of alkylacyl groups, the enterocin system is distinct in its usage of a single ACP for both priming and elongating reactions with different substrates.
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Affiliation(s)
- John A Kalaitzis
- Scripps Institution of Oceanography, University of California San Diego, La Jolla, CA 92093, USA
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Abstract
Oxytetracycline (OTC) is a broad-spectrum antibiotic that acts by inhibiting protein synthesis in bacteria. It is an important member of the bacterial aromatic polyketide family, which is a structurally diverse class of natural products. OTC is synthesized by a type II polyketide synthase that generates the poly-beta-ketone backbone through successive decarboxylative condensation of malonyl-CoA extender units, followed by modifications by cyclases, oxygenases, transferases, and additional tailoring enzymes. Genetic and biochemical studies have illuminated most of the steps involved in the biosynthesis of OTC, which is detailed here as a representative case study in type II polyketide biosynthesis.
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Affiliation(s)
- Lauren B. Pickens
- From the Department of Chemical and Biomolecular Engineering, University of California, Los Angeles, California 90095
| | - Yi Tang
- From the Department of Chemical and Biomolecular Engineering, University of California, Los Angeles, California 90095
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20
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Das A, Szu PH, Fitzgerald JT, Khosla C. Mechanism and engineering of polyketide chain initiation in fredericamycin biosynthesis. J Am Chem Soc 2010; 132:8831-3. [PMID: 20540492 PMCID: PMC2904946 DOI: 10.1021/ja102517q] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
The ability to incorporate atypical primer units through the use of dedicated initiation polyketide synthase (PKS) modules offers opportunities to expand the molecular diversity of polyketide natural products. Here we identify the initiation PKS module responsible for hexadienyl priming of the antibiotic fredericamycin and investigate its biochemical properties. We also exploit this PKS module for the design and in vivo biosynthesis of unusually primed analogues of a representative polyketide product, thereby emphasizing its utility to the metabolic engineer.
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Affiliation(s)
- Abhirup Das
- Department of Chemistry, Stanford University, Stanford, California 94305
| | - Ping-Hui Szu
- Department of Chemistry, Stanford University, Stanford, California 94305
| | - Jay T. Fitzgerald
- Department of Chemistry, Stanford University, Stanford, California 94305
| | - Chaitan Khosla
- Department of Chemistry, Stanford University, Stanford, California 94305
- Department of Chemical Engineering, Stanford University, Stanford, California 94305
- Department of Biochemistry, Stanford University, Stanford, California 94305
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21
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Zhou H, Li Y, Tang Y. Cyclization of aromatic polyketides from bacteria and fungi. Nat Prod Rep 2010; 27:839-68. [PMID: 20358042 DOI: 10.1039/b911518h] [Citation(s) in RCA: 102] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Affiliation(s)
- Hui Zhou
- Department of Chemical and Biomolecular Engineering, University of California, Los Angles, 420 Westwood Plaza, Los Angeles, CA 90095, USA
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