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Gong J, Yi JS, Cho HS, Shin CH, Won HJ, Cho BK, Noh M, Yoon YJ. Transcriptome profiles of Streptomyces clavuligerus strains producing different titers of clavulanic acid. Sci Data 2023; 10:804. [PMID: 37973966 PMCID: PMC10654394 DOI: 10.1038/s41597-023-02727-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2023] [Accepted: 11/07/2023] [Indexed: 11/19/2023] Open
Abstract
Streptomyces clavuligerus NRRL 3585 is a native producer of clavulanic acid (CA), a clinically used β-lactamase inhibitor, and is widely used as an industrial strain for the production of antibiotics. Selective random mutagenesis has successfully generated the improved CA-producing S. clavuligerus mutant strains as well as the strain with the loss of CA biosynthesis. To understand the molecular mechanisms associated with the improved CA-production potential, genome-scale RNA-sequencing-based transcriptional data were obtained for the wild-type S. clavuligerus strain and its three mutant strains. Total RNA samples for each strain were collected across four different growth stages, and all 32 sequencing data points exhibited an average Phred score of 36. The high-quality genome-scale transcriptional profile of S. clavuligerus strains with varied CA biosynthetic potential provides valuable insights and new opportunities for discovering efficient metabolic engineering strategies for the development of improved industrial strains.
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Affiliation(s)
- Junpyo Gong
- Natural Products Research Institute, College of Pharmacy, Seoul National University, Seoul, 08826, Republic of Korea
| | - Jeong Sang Yi
- Natural Products Research Institute, College of Pharmacy, Seoul National University, Seoul, 08826, Republic of Korea
| | - Hang Su Cho
- Natural Products Research Institute, College of Pharmacy, Seoul National University, Seoul, 08826, Republic of Korea
| | - Chang Hun Shin
- Research Institute of CKD BiO, Ansan, 15604, Republic of Korea
| | - Hyung-Jin Won
- Research Institute of CKD BiO, Ansan, 15604, Republic of Korea
| | - Byung-Kwan Cho
- Department of Biological Sciences and KI for the BioCentury, Korea Advanced Institute of Science and Technology, Daejeon, 34141, Republic of Korea
| | - Minsoo Noh
- Natural Products Research Institute, College of Pharmacy, Seoul National University, Seoul, 08826, Republic of Korea.
| | - Yeo Joon Yoon
- Natural Products Research Institute, College of Pharmacy, Seoul National University, Seoul, 08826, Republic of Korea.
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2
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Shin D, Byun WS, Kang S, Kang I, Bae ES, An JS, Im JH, Park J, Kim E, Ko K, Hwang S, Lee H, Kwon Y, Ko YJ, Hong S, Nam SJ, Kim SB, Fenical W, Yoon YJ, Cho JC, Lee SK, Oh DC. Targeted and Logical Discovery of Piperazic Acid-Bearing Natural Products Based on Genomic and Spectroscopic Signatures. J Am Chem Soc 2023; 145:19676-19690. [PMID: 37642383 DOI: 10.1021/jacs.3c04699] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 08/31/2023]
Abstract
A targeted and logical discovery method was devised for natural products containing piperazic acid (Piz), which is biosynthesized from ornithine by l-ornithine N-hydroxylase (KtzI) and N-N bond formation enzyme (KtzT). Genomic signature-based screening of a bacterial DNA library (2020 strains) using polymerase chain reaction (PCR) primers targeting ktzT identified 62 strains (3.1%). The PCR amplicons of KtzT-encoding genes were phylogenetically analyzed to classify the 23 clades into two monophyletic groups, I and II. Cultivating hit strains in media supplemented with 15NH4Cl and applying 1H-15N heteronuclear multiple bond correlation (HMBC) along with 1H-15N heteronuclear single quantum coherence (HSQC) and 1H-15N HSQC-total correlation spectroscopy (HSQC-TOCSY) NMR experiments detected the spectroscopic signatures of Piz and modified Piz. Chemical investigation of the hit strains prioritized by genomic and spectroscopic signatures led to the identification of a new azinothricin congener, polyoxyperuin B seco acid (1), previously reported chloptosin (2) in group I, depsidomycin D (3) incorporating two dehydropiperazic acids (Dpz), and lenziamides A and B (4 and 5), structurally novel 31-membered cyclic decapeptides in group II. By consolidating the phylogenetic and chemical analyses, clade-structure relationships were elucidated for 19 of the 23 clades. Lenziamide A (4) inhibited STAT3 activation and induced G2/M cell cycle arrest, apoptotic cell death, and tumor growth suppression in human colorectal cancer cells. Moreover, lenziamide A (4) resensitized 5-fluorouracil (5-FU) activity in both in vitro cell cultures and the in vivo 5-FU-resistant tumor xenograft mouse model. This work demonstrates that the genomic and spectroscopic signature-based searches provide an efficient and general strategy for new bioactive natural products containing specific structural motifs.
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Affiliation(s)
- Daniel Shin
- Natural Products Research Institute, College of Pharmacy, Seoul National University, Seoul 08826, Republic of Korea
| | - Woong Sub Byun
- Natural Products Research Institute, College of Pharmacy, Seoul National University, Seoul 08826, Republic of Korea
| | - Sangwook Kang
- Natural Products Research Institute, College of Pharmacy, Seoul National University, Seoul 08826, Republic of Korea
| | - Ilnam Kang
- Department of Biological Sciences, Inha University, Incheon 22212, Republic of Korea
| | - Eun Seo Bae
- Natural Products Research Institute, College of Pharmacy, Seoul National University, Seoul 08826, Republic of Korea
| | - Joon Soo An
- Natural Products Research Institute, College of Pharmacy, Seoul National University, Seoul 08826, Republic of Korea
| | - Ji Hyeon Im
- Natural Products Research Institute, College of Pharmacy, Seoul National University, Seoul 08826, Republic of Korea
| | - Jiyoon Park
- Natural Products Research Institute, College of Pharmacy, Seoul National University, Seoul 08826, Republic of Korea
| | - Eunji Kim
- Natural Products Research Institute, College of Pharmacy, Seoul National University, Seoul 08826, Republic of Korea
| | - Keebeom Ko
- Natural Products Research Institute, College of Pharmacy, Seoul National University, Seoul 08826, Republic of Korea
| | - Sunghoon Hwang
- Natural Products Research Institute, College of Pharmacy, Seoul National University, Seoul 08826, Republic of Korea
| | - Honghui Lee
- Natural Products Research Institute and Research Institute of Pharmaceutical Sciences, College of Pharmacy, Seoul National University, Seoul 08826, Republic of Korea
| | - Yun Kwon
- Research Institute of Pharmaceutical Science, College of Pharmacy, Kyungpook National University, Daegu 41566, Republic of Korea
| | - Yoon-Joo Ko
- Laboratory of Nuclear Magnetic Resonance, National Center for Inter-University Research Facilities (NCIRF), Seoul National University, Seoul 08826, Republic of Korea
| | - Suckchang Hong
- Natural Products Research Institute and Research Institute of Pharmaceutical Sciences, College of Pharmacy, Seoul National University, Seoul 08826, Republic of Korea
| | - Sang-Jip Nam
- Department of Chemistry and Nanoscience, Ewha Womans University, Seoul 03760, Republic of Korea
| | - Seung Bum Kim
- Department of Microbiology and Molecular Biology, College of Bioscience and Biotechnology, Chungnam National University, Daejeon 34134, Republic of Korea
| | - William Fenical
- Center for Marine Biotechnology and Biomedicine, Scripps Institution of Oceanography and Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California, San Diego, La Jolla, California 92093, United States
| | - Yeo Joon Yoon
- Natural Products Research Institute, College of Pharmacy, Seoul National University, Seoul 08826, Republic of Korea
- MolGenBio Co., Ltd., Seoul 08826, Republic of Korea
| | - Jang-Cheon Cho
- Department of Biological Sciences, Inha University, Incheon 22212, Republic of Korea
| | - Sang Kook Lee
- Natural Products Research Institute, College of Pharmacy, Seoul National University, Seoul 08826, Republic of Korea
| | - Dong-Chan Oh
- Natural Products Research Institute, College of Pharmacy, Seoul National University, Seoul 08826, Republic of Korea
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3
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Kumar P, Nalli Y, Singh S, Wakchaure PD, Gor R, Ghadge VA, Kim E, Ramalingam S, Azger Dusthackeer VN, Yoon YJ, Ganguly B, Shinde PB. Dactylides A-C, three new bioactive 22-membered macrolides produced by Dactylosporangium aurantiacum. J Antibiot (Tokyo) 2023; 76:503-510. [PMID: 37208457 DOI: 10.1038/s41429-023-00632-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/27/2022] [Revised: 04/15/2023] [Accepted: 05/02/2023] [Indexed: 05/21/2023]
Abstract
Three new 22-membered polyol macrolides, dactylides A-C (1-3), were isolated from Dactylosporangium aurantiacum ATCC 23491 employing repeated chromatographic separations, and their structures were established based on detailed analysis of NMR and MS data. The relative configurations at the stereocenters were established via vicinal 1H-1H coupling constants, NOE correlations, and by application of Kishi's universal NMR database. In order to get insights into the biosynthetic pathway of 1-3, the genome sequence of the producer strain D. aurantiacum was obtained and the putative biosynthetic gene cluster encoding their biosynthesis was identified through bioinformatic analysis using antiSMASH. Compounds 1-3 showed significant in-vitro antimycobacterial and cytotoxic activity.
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Affiliation(s)
- Pankaj Kumar
- Natural Products & Green Chemistry Division, CSIR-Central Salt and Marine Chemicals Research Institute (CSIR-CSMCRI), Council of Scientific and Industrial Research (CSIR), Bhavnagar, Gujarat, 364002, India
- Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, 201002, India
| | - Yedukondalu Nalli
- Natural Products & Green Chemistry Division, CSIR-Central Salt and Marine Chemicals Research Institute (CSIR-CSMCRI), Council of Scientific and Industrial Research (CSIR), Bhavnagar, Gujarat, 364002, India
| | - Sanju Singh
- Natural Products & Green Chemistry Division, CSIR-Central Salt and Marine Chemicals Research Institute (CSIR-CSMCRI), Council of Scientific and Industrial Research (CSIR), Bhavnagar, Gujarat, 364002, India
- Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, 201002, India
| | - Padmaja D Wakchaure
- Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, 201002, India
- Computation and Simulation Unit, Analytical and Environmental Science Division and Centralized Instrument Facility, CSIR-Central Salt and Marine Chemicals Research Institute, Bhavnagar, Gujarat, 364002, India
| | - Ravi Gor
- Department of Genetic Engineering, School of Bio-Engineering, SRM Institute of Science and Technology, Kattankulathur, Tamil Nadu, 603203, India
| | - Vishal A Ghadge
- Natural Products & Green Chemistry Division, CSIR-Central Salt and Marine Chemicals Research Institute (CSIR-CSMCRI), Council of Scientific and Industrial Research (CSIR), Bhavnagar, Gujarat, 364002, India
- Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, 201002, India
| | - Eunji Kim
- Natural Products Research Institute, College of Pharmacy, Seoul National University, Seoul, 08826, Republic of Korea
| | - Satish Ramalingam
- Department of Genetic Engineering, School of Bio-Engineering, SRM Institute of Science and Technology, Kattankulathur, Tamil Nadu, 603203, India
| | - V N Azger Dusthackeer
- Department of Bacteriology, National Institute for Research in Tuberculosis, ICMR, Sathyamoorty road, Chetpet, Chennai, 600031, Tamil Nadu, India
| | - Yeo Joon Yoon
- Natural Products Research Institute, College of Pharmacy, Seoul National University, Seoul, 08826, Republic of Korea
| | - Bishwajit Ganguly
- Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, 201002, India
- Computation and Simulation Unit, Analytical and Environmental Science Division and Centralized Instrument Facility, CSIR-Central Salt and Marine Chemicals Research Institute, Bhavnagar, Gujarat, 364002, India
| | - Pramod B Shinde
- Natural Products & Green Chemistry Division, CSIR-Central Salt and Marine Chemicals Research Institute (CSIR-CSMCRI), Council of Scientific and Industrial Research (CSIR), Bhavnagar, Gujarat, 364002, India.
- Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, 201002, India.
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4
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Shin YH, Im JH, Kang I, Kim E, Jang SC, Cho E, Shin D, Hwang S, Du YE, Huynh TH, Ko K, Ko YJ, Nam SJ, Awakawa T, Lee J, Hong S, Abe I, Moore BS, Fenical W, Yoon YJ, Cho JC, Lee SK, Oh KB, Oh DC. Genomic and Spectroscopic Signature-Based Discovery of Natural Macrolactams. J Am Chem Soc 2023; 145:1886-1896. [PMID: 36634356 DOI: 10.1021/jacs.2c11527] [Citation(s) in RCA: 8] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/14/2023]
Abstract
The logical and effective discovery of macrolactams, structurally unique natural molecules with diverse biological activities, has been limited by a lack of targeted search methods. Herein, a targeted discovery method for natural macrolactams was devised by coupling genomic signature-based PCR screening of a bacterial DNA library with spectroscopic signature-based early identification of macrolactams. DNA library screening facilitated the efficient selection of 43 potential macrolactam-producing strains (3.6% of 1,188 strains screened). The PCR amplicons of the amine-deprotecting enzyme-coding genes were analyzed to predict the macrolactam type (α-methyl, α-alkyl, or β-methyl) produced by the hit strains. 1H-15N HSQC-TOCSY NMR analysis of 15N-labeled culture extracts enabled macrolactam detection and structural type assignment without any purification steps. This method identified a high-titer Micromonospora strain producing salinilactam (1), a previously reported α-methyl macrolactam, and two Streptomyces strains producing new α-alkyl and β-methyl macrolactams. Subsequent purification and spectroscopic analysis led to the structural revision of 1 and the discovery of muanlactam (2), an α-alkyl macrolactam with diene amide and tetraene chromophores, and concolactam (3), a β-methyl macrolactam with a [16,6,6]-tricyclic skeleton. Detailed genomic analysis of the strains producing 1-3 identified putative biosynthetic gene clusters and pathways. Compound 2 displayed significant cytotoxicity against various cancer cell lines (IC50 = 1.58 μM against HCT116), whereas 3 showed inhibitory activity against Staphylococcus aureus sortase A. This genomic and spectroscopic signature-based method provides an efficient search strategy for new natural macrolactams and will be generally applicable for the discovery of nitrogen-bearing natural products.
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Affiliation(s)
- Yern-Hyerk Shin
- Natural Products Research Institute, College of Pharmacy, Seoul National University, Seoul 08826, Republic of Korea
| | - Ji Hyeon Im
- Natural Products Research Institute, College of Pharmacy, Seoul National University, Seoul 08826, Republic of Korea
| | - Ilnam Kang
- Department of Biological Sciences, Inha University, Incheon 22212, Republic of Korea
| | - Eunji Kim
- Natural Products Research Institute, College of Pharmacy, Seoul National University, Seoul 08826, Republic of Korea
| | - Sung Chul Jang
- Natural Products Research Institute, College of Pharmacy, Seoul National University, Seoul 08826, Republic of Korea
| | - Eunji Cho
- Department of Agricultural Biotechnology, College of Agriculture & Life Sciences, Seoul National University, Seoul 08826, Republic of Korea
| | - Daniel Shin
- Natural Products Research Institute, College of Pharmacy, Seoul National University, Seoul 08826, Republic of Korea
| | - Sunghoon Hwang
- Natural Products Research Institute, College of Pharmacy, Seoul National University, Seoul 08826, Republic of Korea
| | - Young Eun Du
- Natural Products Research Institute, College of Pharmacy, Seoul National University, Seoul 08826, Republic of Korea
| | - Thanh-Hau Huynh
- Natural Products Research Institute, College of Pharmacy, Seoul National University, Seoul 08826, Republic of Korea
| | - Keebeom Ko
- Natural Products Research Institute, College of Pharmacy, Seoul National University, Seoul 08826, Republic of Korea
| | - Yoon-Joo Ko
- Laboratory of Nuclear Magnetic Resonance, National Center of Inter-University Research Facilities (NCIRF), Seoul National University, Seoul 08826, Republic of Korea
| | - Sang-Jip Nam
- Department of Chemistry and Nanoscience, Ewha Womans University, Seoul 03760, Republic of Korea
| | - Takayoshi Awakawa
- Graduate School of Pharmaceutical Sciences, The University of Tokyo, Tokyo 113-0033, Japan.,RIKEN Center for Sustainable Resource Science, Wako, Saitama 351-0198, Japan
| | - Jeeyeon Lee
- Research Institute of Pharmaceutical Sciences, College of Pharmacy, Seoul National University, Seoul 08826, Republic of Korea
| | - Suckchang Hong
- Research Institute of Pharmaceutical Sciences, College of Pharmacy, Seoul National University, Seoul 08826, Republic of Korea
| | - Ikuro Abe
- Graduate School of Pharmaceutical Sciences, The University of Tokyo, Tokyo 113-0033, Japan
| | - Bradley S Moore
- Center for Marine Biotechnology and Biomedicine, Scripps Institution of Oceanography and Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California, San Diego, La Jolla, California 92093, United States
| | - William Fenical
- Center for Marine Biotechnology and Biomedicine, Scripps Institution of Oceanography and Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California, San Diego, La Jolla, California 92093, United States
| | - Yeo Joon Yoon
- Natural Products Research Institute, College of Pharmacy, Seoul National University, Seoul 08826, Republic of Korea.,MolGenBio Co., Ltd., Seoul 08826, Republic of Korea
| | - Jang-Cheon Cho
- Department of Biological Sciences, Inha University, Incheon 22212, Republic of Korea
| | - Sang Kook Lee
- Natural Products Research Institute, College of Pharmacy, Seoul National University, Seoul 08826, Republic of Korea
| | - Ki-Bong Oh
- Department of Agricultural Biotechnology, College of Agriculture & Life Sciences, Seoul National University, Seoul 08826, Republic of Korea
| | - Dong-Chan Oh
- Natural Products Research Institute, College of Pharmacy, Seoul National University, Seoul 08826, Republic of Korea
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5
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Yi JS, Kim JM, Ban YH, Yoon YJ. Modular polyketide synthase-derived insecticidal agents: from biosynthesis and metabolic engineering to combinatorial biosynthesis for their production. Nat Prod Rep 2023; 40:972-987. [PMID: 36691749 DOI: 10.1039/d2np00078d] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/25/2023]
Abstract
Covering: up to 2022Polyketides derived from actinomycetes are a valuable source of eco-friendly biochemical insecticides. The development of new insecticides is urgently required, as the number of insects resistant to more than one drug is rapidly increasing. Moreover, significant enhancement of the production of such biochemical insecticides is required for economical production. There has been considerable improvement in polyketide insecticidal agent production and development of new insecticides. However, most commercially important biochemical insecticides are synthesized by modular type I polyketide synthases (PKSs), and their structural complexities make chemical modification challenging. A detailed understanding of the biosynthetic mechanisms of potent polyketide insecticides and the structure-activity relationships of their analogs will provide insight into the comprehensive design of new insecticides with improved efficacies. Further metabolic engineering and combinatorial biosynthesis efforts, reinvigorated by synthetic biology, can eventually produce designed analogs in large quantities. This highlight reviews the biosynthesis of representative insecticides produced by modular type I PKSs, such as avermectin, spinosyn, and spectinabilin, and their insecticidal properties. Metabolic engineering and combinatorial biosynthetic strategies for the development of high-yield strains and analogs with insecticidal activities are emphasized, proposing a way to develop a next-generation insecticide.
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Affiliation(s)
- Jeong Sang Yi
- Natural Products Research Institute, College of Pharmacy, Seoul National University, Seoul, 08826, Republic of Korea.
| | - Jung Min Kim
- Natural Products Research Institute, College of Pharmacy, Seoul National University, Seoul, 08826, Republic of Korea.
| | - Yeon Hee Ban
- College of Biomedical Science, Kangwon National University, Chuncheon, 24341, Republic of Korea.
| | - Yeo Joon Yoon
- Natural Products Research Institute, College of Pharmacy, Seoul National University, Seoul, 08826, Republic of Korea.
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6
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Lee NJ, Kang W, Kwon Y, Oh JW, Jung H, Seo M, Seol Y, Wi JB, Ban YH, Yoon YJ, Park JW. Chemo-enzymatic Synthesis of Pseudo-trisaccharide Aminoglycoside Antibiotics with Enhanced Nonsense Read-through Inducer Activity. ChemMedChem 2023; 18:e202200497. [PMID: 36259357 DOI: 10.1002/cmdc.202200497] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2022] [Revised: 10/18/2022] [Indexed: 01/24/2023]
Abstract
Aminoglycosides (AGs) are broad-spectrum antibiotics used to treat bacterial infections. Over the last two decades, studies have reported the potential of AGs in the treatment of genetic disorders caused by nonsense mutations, owing to their ability to induce the ribosomes to read through these mutations and produce a full-length protein. However, the principal limitation in the clinical application of AGs arises from their high toxicity, including nephrotoxicity and ototoxicity. In this study, five novel pseudo-trisaccharide analogs were synthesized by chemo-enzymatic synthesis by acid hydrolysis of commercially available AGs, followed by an enzymatic reaction using recombinant substrate-flexible KanM2 glycosyltransferase. The relationships between their structures and biological activities, including the antibacterial, nephrotoxic, and nonsense readthrough inducer (NRI) activities, were investigated. The absence of 1-N-acylation, 3',4'-dideoxygenation, and post-glycosyl transfer modifications on the third sugar moiety of AGs diminishes their antibacterial activities. The 3',4'-dihydroxy and 6'-hydroxy moieties regulate the in vitro nephrotoxicity of AGs in mammalian cell lines. The 3',4'-dihydroxy and 6'-methyl scaffolds are indispensable for the ex vivo NRI activity of AGs. Based on the alleviated in vitro antibacterial properties and nephrotoxicity, and the highest ex vivo NRI activity among the five compounds, a kanamycin analog (6'-methyl-3''-deamino-3''-hydroxykanamycin C) was selected as a novel AG hit for further studies on human genetic disorders caused by premature transcriptional termination.
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Affiliation(s)
- Na Joon Lee
- Department of Integrated Biomedical and Life Sciences, Korea University, 02841, Seoul (Republic of, Korea
| | - Woongshin Kang
- Transdisciplinary Major in Learning Health Systems, Department of Integrated Biomedical and Life Sciences, Korea University, 02841, Seoul (Republic of, Korea
| | - Younghae Kwon
- Transdisciplinary Major in Learning Health Systems, Department of Integrated Biomedical and Life Sciences, Korea University, 02841, Seoul (Republic of, Korea
| | - Jae Wook Oh
- Transdisciplinary Major in Learning Health Systems, Department of Integrated Biomedical and Life Sciences, Korea University, 02841, Seoul (Republic of, Korea
| | - Hogwuan Jung
- Transdisciplinary Major in Learning Health Systems, Department of Integrated Biomedical and Life Sciences, Korea University, 02841, Seoul (Republic of, Korea
| | - Minsuk Seo
- Transdisciplinary Major in Learning Health Systems, Department of Integrated Biomedical and Life Sciences, Korea University, 02841, Seoul (Republic of, Korea
| | - Yurin Seol
- Transdisciplinary Major in Learning Health Systems, Department of Integrated Biomedical and Life Sciences, Korea University, 02841, Seoul (Republic of, Korea
| | - Jae Bok Wi
- Department of Integrated Biomedical and Life Sciences, Korea University, 02841, Seoul (Republic of, Korea
| | - Yeon Hee Ban
- College of Pharmacy, Natural Products Research Institute, Seoul National University, 08826, Seoul (Republic of, Korea
| | - Yeo Joon Yoon
- College of Pharmacy, Natural Products Research Institute, Seoul National University, 08826, Seoul (Republic of, Korea
| | - Je Won Park
- Department of Integrated Biomedical and Life Sciences, Korea University, 02841, Seoul (Republic of, Korea.,School of Biosystems and Biomedical Sciences, Korea University, 02841, Seoul (Republic of, Korea
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7
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Im JH, Shin D, Ban YH, Byun WS, Bae ES, Lee D, Du YE, Cui J, Kwon Y, Nam SJ, Cha S, Lee SK, Yoon YJ, Oh DC. Targeted Discovery of an Enediyne-Derived Cycloaromatized Compound, Jejucarboside A, from a Marine Actinomycete. Org Lett 2022; 24:7188-7193. [PMID: 36165456 DOI: 10.1021/acs.orglett.2c02934] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
A genomic and spectroscopic signature-based search revealed a cycloaromatized enediyne, jejucarboside A (1), from a marine actinomycete strain. The structure of 1 was determined as a new cyclopenta[a]indene glycoside bearing carbonate functionality by nuclear magnetic resonance, high-resolution mass spectrometry (MS), MS/MS, infrared spectroscopy, and a modified Mosher's method. An iterative enediyne synthase pathway has been proposed for the putative biosynthesis of 1 by genomic analysis. Jejucarboside A exhibited cytotoxicity against the HCT116 colon carcinoma cells.
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Affiliation(s)
- Ji Hyeon Im
- Natural Products Research Institute, College of Pharmacy, Seoul National University, Seoul 08826, Republic of Korea
| | - Daniel Shin
- Natural Products Research Institute, College of Pharmacy, Seoul National University, Seoul 08826, Republic of Korea
| | - Yeon Hee Ban
- Department of Molecular Bioscience, College of Biomedical Science, Kangwon National University, Chuncheon 24341, Republic of Korea
| | - Woong Sub Byun
- Natural Products Research Institute, College of Pharmacy, Seoul National University, Seoul 08826, Republic of Korea
| | - Eun Seo Bae
- Natural Products Research Institute, College of Pharmacy, Seoul National University, Seoul 08826, Republic of Korea
| | - Donghoon Lee
- Department of Chemistry, Dongguk University, Seoul 04620, Republic of Korea
| | - Young Eun Du
- Natural Products Research Institute, College of Pharmacy, Seoul National University, Seoul 08826, Republic of Korea
| | - Jinsheng Cui
- Natural Products Research Institute, College of Pharmacy, Seoul National University, Seoul 08826, Republic of Korea
| | - Yun Kwon
- Research Institute of Pharmaceutical Science, College of Pharmacy, Kyungpook National University, Daegu 41566, Republic of Korea
| | - Sang-Jip Nam
- Department of Chemistry and Nanoscience, Ewha Womans University, Seoul 03760, Republic of Korea
| | - Sangwon Cha
- Department of Chemistry, Dongguk University, Seoul 04620, Republic of Korea
| | - Sang Kook Lee
- Natural Products Research Institute, College of Pharmacy, Seoul National University, Seoul 08826, Republic of Korea
| | - Yeo Joon Yoon
- Natural Products Research Institute, College of Pharmacy, Seoul National University, Seoul 08826, Republic of Korea
| | - Dong-Chan Oh
- Natural Products Research Institute, College of Pharmacy, Seoul National University, Seoul 08826, Republic of Korea
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8
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Kim MS, Bae M, Song MC, Hwang S, Oh DC, Yoon YJ. Cyclodimerization of Mohangamide A by Thioesterase Domain Is Directed by Substrates. Org Lett 2022; 24:4444-4448. [PMID: 35699427 DOI: 10.1021/acs.orglett.2c01670] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Mohangamide A is a pseudo-dimeric nonribosomal peptide biosynthesized along with its monomer, WS9326A, and is expected to be formed by the head-to-tail cyclodimerization of linear WS9326A and another identical peptide chain with a different acyl side chain. In vitro experiments with the N-acetylcysteamine thioesters of the corresponding monomeric intermediates and thioesterase domains of Streptomyces sp. SNM55 and S. calvus showed that this cyclodimerization reaction is directed by the substrate structures and occurs only with both linear intermediates.
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Affiliation(s)
- Myoun-Su Kim
- Natural Products Research Institute, College of Pharmacy, Seoul National University, Seoul 08826, Republic of Korea
| | - Munhyung Bae
- College of Pharmacy, Gachon University, Incheon 21936, Republic of Korea
| | - Myoung Chong Song
- Natural Products Research Institute, College of Pharmacy, Seoul National University, Seoul 08826, Republic of Korea
| | - Sunghoon Hwang
- Natural Products Research Institute, College of Pharmacy, Seoul National University, Seoul 08826, Republic of Korea
| | - Dong-Chan Oh
- Natural Products Research Institute, College of Pharmacy, Seoul National University, Seoul 08826, Republic of Korea
| | - Yeo Joon Yoon
- Natural Products Research Institute, College of Pharmacy, Seoul National University, Seoul 08826, Republic of Korea
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9
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Cui J, Kim E, Moon DH, Kim TH, Kang I, Lim Y, Shin D, Hwang S, Du YE, Song MC, Bae M, Cho JC, Jang J, Lee SK, Yoon YJ, Oh DC. Taeanamides A and B, Nonribosomal Lipo-Decapeptides Isolated from an Intertidal-Mudflat-Derived Streptomyces sp. Mar Drugs 2022; 20:md20060400. [PMID: 35736203 PMCID: PMC9229766 DOI: 10.3390/md20060400] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2022] [Revised: 06/10/2022] [Accepted: 06/13/2022] [Indexed: 12/04/2022] Open
Abstract
Two new lipo-decapeptides, namely taeanamides A and B (1 and 2), were discovered from the Gram-positive bacterium Streptomyces sp. AMD43, which was isolated from a mudflat sample from Anmyeondo, Korea. The exact molecular masses of 1 and 2 were revealed by high-resolution mass spectrometry, and the planar structures of 1 and 2 were elucidated using NMR spectroscopy. The absolute configurations of 1 and 2 were determined using a combined analysis of 1H-1H coupling constants and ROESY correlations, the advanced Marfey’s method, and bioinformatics. The putative nonribosomal peptide synthetase pathway for the taeanamides was identified by analyzing the full genome sequence data of Streptomyces sp. AMD43. We also found that taeanamide A exhibited mild anti-tuberculosis bioactivity, whereas taeanamide B showed significant bioactivity against several cancer cell lines.
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Affiliation(s)
- Jinsheng Cui
- Natural Products Research Institute, College of Pharmacy, Seoul National University, Seoul 08826, Korea; (J.C.); (E.K.); (D.H.M.); (D.S.); (S.H.); (Y.E.D.); (M.C.S.); (S.K.L.)
| | - Eunji Kim
- Natural Products Research Institute, College of Pharmacy, Seoul National University, Seoul 08826, Korea; (J.C.); (E.K.); (D.H.M.); (D.S.); (S.H.); (Y.E.D.); (M.C.S.); (S.K.L.)
| | - Dong Hyun Moon
- Natural Products Research Institute, College of Pharmacy, Seoul National University, Seoul 08826, Korea; (J.C.); (E.K.); (D.H.M.); (D.S.); (S.H.); (Y.E.D.); (M.C.S.); (S.K.L.)
| | - Tae Ho Kim
- Molecular Mechanism of Antibiotics, Division of Life Science, Department of Bio & Medical Big Data (BK4 Program), Research Institute of Life Science, Gyeongsang National University, Jinju 52828, Korea; (T.H.K.); (J.J.)
| | - Ilnam Kang
- Department of Biological Sciences, Inha University, Incheon 22212, Korea; (I.K.); (Y.L.); (J.-C.C.)
| | - Yeonjung Lim
- Department of Biological Sciences, Inha University, Incheon 22212, Korea; (I.K.); (Y.L.); (J.-C.C.)
| | - Daniel Shin
- Natural Products Research Institute, College of Pharmacy, Seoul National University, Seoul 08826, Korea; (J.C.); (E.K.); (D.H.M.); (D.S.); (S.H.); (Y.E.D.); (M.C.S.); (S.K.L.)
| | - Sunghoon Hwang
- Natural Products Research Institute, College of Pharmacy, Seoul National University, Seoul 08826, Korea; (J.C.); (E.K.); (D.H.M.); (D.S.); (S.H.); (Y.E.D.); (M.C.S.); (S.K.L.)
| | - Young Eun Du
- Natural Products Research Institute, College of Pharmacy, Seoul National University, Seoul 08826, Korea; (J.C.); (E.K.); (D.H.M.); (D.S.); (S.H.); (Y.E.D.); (M.C.S.); (S.K.L.)
| | - Myoung Chong Song
- Natural Products Research Institute, College of Pharmacy, Seoul National University, Seoul 08826, Korea; (J.C.); (E.K.); (D.H.M.); (D.S.); (S.H.); (Y.E.D.); (M.C.S.); (S.K.L.)
| | - Munhyung Bae
- College of Pharmacy, Gachon University, Incheon 21936, Korea;
| | - Jang-Cheon Cho
- Department of Biological Sciences, Inha University, Incheon 22212, Korea; (I.K.); (Y.L.); (J.-C.C.)
| | - Jichan Jang
- Molecular Mechanism of Antibiotics, Division of Life Science, Department of Bio & Medical Big Data (BK4 Program), Research Institute of Life Science, Gyeongsang National University, Jinju 52828, Korea; (T.H.K.); (J.J.)
| | - Sang Kook Lee
- Natural Products Research Institute, College of Pharmacy, Seoul National University, Seoul 08826, Korea; (J.C.); (E.K.); (D.H.M.); (D.S.); (S.H.); (Y.E.D.); (M.C.S.); (S.K.L.)
| | - Yeo Joon Yoon
- Natural Products Research Institute, College of Pharmacy, Seoul National University, Seoul 08826, Korea; (J.C.); (E.K.); (D.H.M.); (D.S.); (S.H.); (Y.E.D.); (M.C.S.); (S.K.L.)
- Correspondence: (Y.J.Y.); (D.-C.O.); Tel.: +82-2-880-2379 (Y.J.Y.); +82-2-880-2491 (D.-C.O.); Fax: +82-2-762-8322 (D.-C.O.)
| | - Dong-Chan Oh
- Natural Products Research Institute, College of Pharmacy, Seoul National University, Seoul 08826, Korea; (J.C.); (E.K.); (D.H.M.); (D.S.); (S.H.); (Y.E.D.); (M.C.S.); (S.K.L.)
- Correspondence: (Y.J.Y.); (D.-C.O.); Tel.: +82-2-880-2379 (Y.J.Y.); +82-2-880-2491 (D.-C.O.); Fax: +82-2-762-8322 (D.-C.O.)
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10
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An JS, Kim MS, Han J, Jang SC, Im JH, Cui J, Lee Y, Nam SJ, Shin J, Lee SK, Yoon YJ, Oh DC. Nyuzenamide C, an Antiangiogenic Epoxy Cinnamic Acid-Containing Bicyclic Peptide from a Riverine Streptomyces sp. J Nat Prod 2022; 85:804-814. [PMID: 35294831 DOI: 10.1021/acs.jnatprod.1c00837] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/28/2023]
Abstract
A new nonribosomal peptide, nyuzenamide C (1), was discovered from riverine sediment-derived Streptomyces sp. DM14. Comprehensive analysis of the spectroscopic data of nyuzenamide C (1) revealed that 1 has a bicyclic backbone composed of six common amino acid residues (Asn, Leu, Pro, Gly, Val, and Thr) and four nonproteinogenic amino acid units, including hydroxyglycine, β-hydroxyphenylalanine, p-hydroxyphenylglycine, and 3,β-dihydroxytyrosine, along with 1,2-epoxypropyl cinnamic acid. The absolute configuration of 1 was proposed by J-based configuration analysis, the advanced Marfey's method, quantum mechanics-based DP4 calculations, and bioinformatic analysis of its nonribosomal peptide synthetase biosynthetic gene cluster. Nyuzenamide C (1) displayed antiangiogenic activity in human umbilical vein endothelial cells and induced quinone reductase in murine Hepa-1c1c7 cells.
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Affiliation(s)
- Joon Soo An
- Natural Products Research Institute, College of Pharmacy, Seoul National University, Seoul 08826, Republic of Korea
| | - Myoun-Su Kim
- Natural Products Research Institute, College of Pharmacy, Seoul National University, Seoul 08826, Republic of Korea
| | - Jaeho Han
- Natural Products Research Institute, College of Pharmacy, Seoul National University, Seoul 08826, Republic of Korea
| | - Sung Chul Jang
- Natural Products Research Institute, College of Pharmacy, Seoul National University, Seoul 08826, Republic of Korea
| | - Ji Hyeon Im
- Natural Products Research Institute, College of Pharmacy, Seoul National University, Seoul 08826, Republic of Korea
| | - Jinsheng Cui
- Natural Products Research Institute, College of Pharmacy, Seoul National University, Seoul 08826, Republic of Korea
| | - Yeonjin Lee
- Natural Products Research Institute, College of Pharmacy, Seoul National University, Seoul 08826, Republic of Korea
| | - Sang-Jip Nam
- Department of Chemistry and Nanoscience, Ewha Womans University, Seoul 03760, Republic of Korea
| | - Jongheon Shin
- Natural Products Research Institute, College of Pharmacy, Seoul National University, Seoul 08826, Republic of Korea
| | - Sang Kook Lee
- Natural Products Research Institute, College of Pharmacy, Seoul National University, Seoul 08826, Republic of Korea
| | - Yeo Joon Yoon
- Natural Products Research Institute, College of Pharmacy, Seoul National University, Seoul 08826, Republic of Korea
| | - Dong-Chan Oh
- Natural Products Research Institute, College of Pharmacy, Seoul National University, Seoul 08826, Republic of Korea
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11
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Ban YH, Song MC, Jeong JH, Kwun MS, Kim CR, Ryu HS, Kim E, Park JW, Lee DG, Yoon YJ. Microbial Enzymatic Synthesis of Amikacin Analogs With Antibacterial Activity Against Multidrug-Resistant Pathogens. Front Microbiol 2021; 12:725916. [PMID: 34512603 PMCID: PMC8430323 DOI: 10.3389/fmicb.2021.725916] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2021] [Accepted: 08/09/2021] [Indexed: 12/02/2022] Open
Abstract
With the constant emergence of multidrug-resistant gram-negative bacteria, interest in the development of new aminoglycoside (AG) antibiotics for clinical use has increased. The regioselective modification of AG scaffolds could be an efficient approach for the development of new antibiotics with improved therapeutic potency. We enzymatically synthesized three amikacin analogs containing structural modifications in the amino groups and evaluated their antibacterial activity and cytotoxicity. Among them, 6′-N-acyl-3″-N-methylated analogs showed improved antibacterial activity against the multidrug-resistant gram-negative bacteria tested, while exhibiting reduced in vitro nephrotoxicity compared to amikacin. This study demonstrated that the modifications of the 6′-amino group as well as the 3″-amino group have noteworthy advantages for circumventing the AG-resistance mechanism. The regiospecific enzymatic modification could be exploited to develop novel antibacterial agents with improved pharmacological potential.
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Affiliation(s)
- Yeon Hee Ban
- College of Pharmacy, Natural Products Research Institute, Seoul National University, Seoul, South Korea
| | - Myoung Chong Song
- College of Pharmacy, Natural Products Research Institute, Seoul National University, Seoul, South Korea
| | - Joong Ho Jeong
- College of Pharmacy, Natural Products Research Institute, Seoul National University, Seoul, South Korea
| | - Min Seok Kwun
- School of Life Sciences, BK21 FOUR KNU Creative BioResearch Group, College of Natural Sciences, Kyungpook National University, Daegu, South Korea
| | - Chang Rae Kim
- Department of Integrated Biomedical and Life Sciences, Korea University, Seoul, South Korea
| | - Hwi So Ryu
- Department of Integrated Biomedical and Life Sciences, Korea University, Seoul, South Korea
| | - Eunji Kim
- College of Pharmacy, Natural Products Research Institute, Seoul National University, Seoul, South Korea
| | - Je Won Park
- Department of Integrated Biomedical and Life Sciences, Korea University, Seoul, South Korea
| | - Dong Gun Lee
- School of Life Sciences, BK21 FOUR KNU Creative BioResearch Group, College of Natural Sciences, Kyungpook National University, Daegu, South Korea
| | - Yeo Joon Yoon
- College of Pharmacy, Natural Products Research Institute, Seoul National University, Seoul, South Korea
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12
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Kim M, Bae M, Jung Y, Kim JM, Hwang S, Song MC, Ban YH, Bae ES, Hong S, Lee SK, Cha S, Oh D, Yoon YJ. Inside Cover: Unprecedented Noncanonical Features of the Nonlinear Nonribosomal Peptide Synthetase Assembly Line for WS9326A Biosynthesis (Angew. Chem. Int. Ed. 36/2021). Angew Chem Int Ed Engl 2021. [DOI: 10.1002/anie.202107803] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
Affiliation(s)
- Myoun‐Su Kim
- Natural Products Research Institute College of Pharmacy Seoul National University 1 Gwanak-ro, Gwanak-gu Seoul 08826 Republic of Korea
| | - Munhyung Bae
- Natural Products Research Institute College of Pharmacy Seoul National University 1 Gwanak-ro, Gwanak-gu Seoul 08826 Republic of Korea
| | - Ye‐Eun Jung
- Department of Chemistry and Nanoscience Ewha Womans University 52 Ewhayeodae-gil, Seodaemun-gu Seoul 03760 Republic of Korea
| | - Jung Min Kim
- Natural Products Research Institute College of Pharmacy Seoul National University 1 Gwanak-ro, Gwanak-gu Seoul 08826 Republic of Korea
| | - Sunghoon Hwang
- Natural Products Research Institute College of Pharmacy Seoul National University 1 Gwanak-ro, Gwanak-gu Seoul 08826 Republic of Korea
| | - Myoung Chong Song
- Natural Products Research Institute College of Pharmacy Seoul National University 1 Gwanak-ro, Gwanak-gu Seoul 08826 Republic of Korea
| | - Yeon Hee Ban
- Natural Products Research Institute College of Pharmacy Seoul National University 1 Gwanak-ro, Gwanak-gu Seoul 08826 Republic of Korea
| | - Eun Seo Bae
- Natural Products Research Institute College of Pharmacy Seoul National University 1 Gwanak-ro, Gwanak-gu Seoul 08826 Republic of Korea
| | - Suckchang Hong
- Research Institute of Pharmaceutical Sciences College of Pharmacy Seoul National University 1 Gwanak-ro, Gwanak-gu Seoul 08826 Republic of Korea
| | - Sang Kook Lee
- Natural Products Research Institute College of Pharmacy Seoul National University 1 Gwanak-ro, Gwanak-gu Seoul 08826 Republic of Korea
| | - Sun‐Shin Cha
- Department of Chemistry and Nanoscience Ewha Womans University 52 Ewhayeodae-gil, Seodaemun-gu Seoul 03760 Republic of Korea
| | - Dong‐Chan Oh
- Natural Products Research Institute College of Pharmacy Seoul National University 1 Gwanak-ro, Gwanak-gu Seoul 08826 Republic of Korea
| | - Yeo Joon Yoon
- Natural Products Research Institute College of Pharmacy Seoul National University 1 Gwanak-ro, Gwanak-gu Seoul 08826 Republic of Korea
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13
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Kim M, Bae M, Jung Y, Kim JM, Hwang S, Song MC, Ban YH, Bae ES, Hong S, Lee SK, Cha S, Oh D, Yoon YJ. Unprecedented Noncanonical Features of the Nonlinear Nonribosomal Peptide Synthetase Assembly Line for WS9326A Biosynthesis. Angew Chem Int Ed Engl 2021. [DOI: 10.1002/ange.202103872] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Affiliation(s)
- Myoun‐Su Kim
- Natural Products Research Institute College of Pharmacy Seoul National University 1 Gwanak-ro, Gwanak-gu Seoul 08826 Republic of Korea
| | - Munhyung Bae
- Natural Products Research Institute College of Pharmacy Seoul National University 1 Gwanak-ro, Gwanak-gu Seoul 08826 Republic of Korea
| | - Ye‐Eun Jung
- Department of Chemistry and Nanoscience Ewha Womans University 52 Ewhayeodae-gil, Seodaemun-gu Seoul 03760 Republic of Korea
| | - Jung Min Kim
- Natural Products Research Institute College of Pharmacy Seoul National University 1 Gwanak-ro, Gwanak-gu Seoul 08826 Republic of Korea
| | - Sunghoon Hwang
- Natural Products Research Institute College of Pharmacy Seoul National University 1 Gwanak-ro, Gwanak-gu Seoul 08826 Republic of Korea
| | - Myoung Chong Song
- Natural Products Research Institute College of Pharmacy Seoul National University 1 Gwanak-ro, Gwanak-gu Seoul 08826 Republic of Korea
| | - Yeon Hee Ban
- Natural Products Research Institute College of Pharmacy Seoul National University 1 Gwanak-ro, Gwanak-gu Seoul 08826 Republic of Korea
| | - Eun Seo Bae
- Natural Products Research Institute College of Pharmacy Seoul National University 1 Gwanak-ro, Gwanak-gu Seoul 08826 Republic of Korea
| | - Suckchang Hong
- Research Institute of Pharmaceutical Sciences College of Pharmacy Seoul National University 1 Gwanak-ro, Gwanak-gu Seoul 08826 Republic of Korea
| | - Sang Kook Lee
- Natural Products Research Institute College of Pharmacy Seoul National University 1 Gwanak-ro, Gwanak-gu Seoul 08826 Republic of Korea
| | - Sun‐Shin Cha
- Department of Chemistry and Nanoscience Ewha Womans University 52 Ewhayeodae-gil, Seodaemun-gu Seoul 03760 Republic of Korea
| | - Dong‐Chan Oh
- Natural Products Research Institute College of Pharmacy Seoul National University 1 Gwanak-ro, Gwanak-gu Seoul 08826 Republic of Korea
| | - Yeo Joon Yoon
- Natural Products Research Institute College of Pharmacy Seoul National University 1 Gwanak-ro, Gwanak-gu Seoul 08826 Republic of Korea
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14
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Kim M, Bae M, Jung Y, Kim JM, Hwang S, Song MC, Ban YH, Bae ES, Hong S, Lee SK, Cha S, Oh D, Yoon YJ. Innentitelbild: Unprecedented Noncanonical Features of the Nonlinear Nonribosomal Peptide Synthetase Assembly Line for WS9326A Biosynthesis (Angew. Chem. 36/2021). Angew Chem Int Ed Engl 2021. [DOI: 10.1002/ange.202107803] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Affiliation(s)
- Myoun‐Su Kim
- Natural Products Research Institute College of Pharmacy Seoul National University 1 Gwanak-ro, Gwanak-gu Seoul 08826 Republic of Korea
| | - Munhyung Bae
- Natural Products Research Institute College of Pharmacy Seoul National University 1 Gwanak-ro, Gwanak-gu Seoul 08826 Republic of Korea
| | - Ye‐Eun Jung
- Department of Chemistry and Nanoscience Ewha Womans University 52 Ewhayeodae-gil, Seodaemun-gu Seoul 03760 Republic of Korea
| | - Jung Min Kim
- Natural Products Research Institute College of Pharmacy Seoul National University 1 Gwanak-ro, Gwanak-gu Seoul 08826 Republic of Korea
| | - Sunghoon Hwang
- Natural Products Research Institute College of Pharmacy Seoul National University 1 Gwanak-ro, Gwanak-gu Seoul 08826 Republic of Korea
| | - Myoung Chong Song
- Natural Products Research Institute College of Pharmacy Seoul National University 1 Gwanak-ro, Gwanak-gu Seoul 08826 Republic of Korea
| | - Yeon Hee Ban
- Natural Products Research Institute College of Pharmacy Seoul National University 1 Gwanak-ro, Gwanak-gu Seoul 08826 Republic of Korea
| | - Eun Seo Bae
- Natural Products Research Institute College of Pharmacy Seoul National University 1 Gwanak-ro, Gwanak-gu Seoul 08826 Republic of Korea
| | - Suckchang Hong
- Research Institute of Pharmaceutical Sciences College of Pharmacy Seoul National University 1 Gwanak-ro, Gwanak-gu Seoul 08826 Republic of Korea
| | - Sang Kook Lee
- Natural Products Research Institute College of Pharmacy Seoul National University 1 Gwanak-ro, Gwanak-gu Seoul 08826 Republic of Korea
| | - Sun‐Shin Cha
- Department of Chemistry and Nanoscience Ewha Womans University 52 Ewhayeodae-gil, Seodaemun-gu Seoul 03760 Republic of Korea
| | - Dong‐Chan Oh
- Natural Products Research Institute College of Pharmacy Seoul National University 1 Gwanak-ro, Gwanak-gu Seoul 08826 Republic of Korea
| | - Yeo Joon Yoon
- Natural Products Research Institute College of Pharmacy Seoul National University 1 Gwanak-ro, Gwanak-gu Seoul 08826 Republic of Korea
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15
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Kim M, Bae M, Jung Y, Kim JM, Hwang S, Song MC, Ban YH, Bae ES, Hong S, Lee SK, Cha S, Oh D, Yoon YJ. Unprecedented Noncanonical Features of the Nonlinear Nonribosomal Peptide Synthetase Assembly Line for WS9326A Biosynthesis. Angew Chem Int Ed Engl 2021; 60:19766-19773. [DOI: 10.1002/anie.202103872] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2021] [Revised: 05/04/2021] [Indexed: 12/21/2022]
Affiliation(s)
- Myoun‐Su Kim
- Natural Products Research Institute College of Pharmacy Seoul National University 1 Gwanak-ro, Gwanak-gu Seoul 08826 Republic of Korea
| | - Munhyung Bae
- Natural Products Research Institute College of Pharmacy Seoul National University 1 Gwanak-ro, Gwanak-gu Seoul 08826 Republic of Korea
| | - Ye‐Eun Jung
- Department of Chemistry and Nanoscience Ewha Womans University 52 Ewhayeodae-gil, Seodaemun-gu Seoul 03760 Republic of Korea
| | - Jung Min Kim
- Natural Products Research Institute College of Pharmacy Seoul National University 1 Gwanak-ro, Gwanak-gu Seoul 08826 Republic of Korea
| | - Sunghoon Hwang
- Natural Products Research Institute College of Pharmacy Seoul National University 1 Gwanak-ro, Gwanak-gu Seoul 08826 Republic of Korea
| | - Myoung Chong Song
- Natural Products Research Institute College of Pharmacy Seoul National University 1 Gwanak-ro, Gwanak-gu Seoul 08826 Republic of Korea
| | - Yeon Hee Ban
- Natural Products Research Institute College of Pharmacy Seoul National University 1 Gwanak-ro, Gwanak-gu Seoul 08826 Republic of Korea
| | - Eun Seo Bae
- Natural Products Research Institute College of Pharmacy Seoul National University 1 Gwanak-ro, Gwanak-gu Seoul 08826 Republic of Korea
| | - Suckchang Hong
- Research Institute of Pharmaceutical Sciences College of Pharmacy Seoul National University 1 Gwanak-ro, Gwanak-gu Seoul 08826 Republic of Korea
| | - Sang Kook Lee
- Natural Products Research Institute College of Pharmacy Seoul National University 1 Gwanak-ro, Gwanak-gu Seoul 08826 Republic of Korea
| | - Sun‐Shin Cha
- Department of Chemistry and Nanoscience Ewha Womans University 52 Ewhayeodae-gil, Seodaemun-gu Seoul 03760 Republic of Korea
| | - Dong‐Chan Oh
- Natural Products Research Institute College of Pharmacy Seoul National University 1 Gwanak-ro, Gwanak-gu Seoul 08826 Republic of Korea
| | - Yeo Joon Yoon
- Natural Products Research Institute College of Pharmacy Seoul National University 1 Gwanak-ro, Gwanak-gu Seoul 08826 Republic of Korea
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16
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Shin YH, Ban YH, Shin J, Park IW, Yoon S, Ko K, Shin J, Nam SJ, Winter JM, Kim Y, Yoon YJ, Oh DC. Azetidine-Bearing Non-Ribosomal Peptides, Bonnevillamides D and E, Isolated from a Carrion Beetle-Associated Actinomycete. J Org Chem 2021; 86:11149-11159. [PMID: 33979513 DOI: 10.1021/acs.joc.1c00360] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Two new nonribosomal peptides, bonnevillamides D and E (1 and 2), have been discovered in Streptomyces sp. UTZ13 isolated from the carrion beetle, Nicrophorus concolor. Combinational analysis of the UV, MS, and NMR spectroscopic data revealed that their planar structures were comprised of dichlorinated linear peptides containing nonproteinogenic amino acid residues, such as 4-methylazetidinecarboxylic acid and 4-O-acetyl-5-methylproline. The configurations of bonnevillamides D and E (1 and 2) were determined based on ROESY correlations, the advanced Marfey's method, phenylglycine methyl ester derivatization, molecular modeling, and circular dichroism spectroscopy. The nonribosomal peptide synthetase biosynthetic pathway of bonnevillamides D and E has been proposed using bioinformatic analysis of the whole-genome sequence data of Streptomyces sp. UTZ13. Their biological activity toward the aggregation of amyloid-β, which is one of the key pathogenic proteins in Alzheimer's disease, was evaluated using a thioflavin T assay and gel electrophoresis. Bonnevillamides D and E reversed the fibril formation by inducing the monomerization of amyloid-β aggregates.
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Affiliation(s)
- Yern-Hyerk Shin
- Natural Products Research Institute, College of Pharmacy, Seoul National University, 1 Gwanak-ro, Gwanak-gu, Seoul 08826, Republic of Korea
| | - Yeon Hee Ban
- Natural Products Research Institute, College of Pharmacy, Seoul National University, 1 Gwanak-ro, Gwanak-gu, Seoul 08826, Republic of Korea
| | - Jisu Shin
- Department of Pharmacy, Yonsei Institute of Pharmaceutical Sciences, and Department of Integrative Biotechnology and Translational Medicine, Yonsei University, 85 Songdogwahak-ro, Yeonsu-gu, Incheon 21983, Republic of Korea
| | - In Wook Park
- Department of Pharmacy, Yonsei Institute of Pharmaceutical Sciences, and Department of Integrative Biotechnology and Translational Medicine, Yonsei University, 85 Songdogwahak-ro, Yeonsu-gu, Incheon 21983, Republic of Korea
| | - Soljee Yoon
- Department of Pharmacy, Yonsei Institute of Pharmaceutical Sciences, and Department of Integrative Biotechnology and Translational Medicine, Yonsei University, 85 Songdogwahak-ro, Yeonsu-gu, Incheon 21983, Republic of Korea
| | - Keebeom Ko
- Natural Products Research Institute, College of Pharmacy, Seoul National University, 1 Gwanak-ro, Gwanak-gu, Seoul 08826, Republic of Korea
| | - Jongheon Shin
- Natural Products Research Institute, College of Pharmacy, Seoul National University, 1 Gwanak-ro, Gwanak-gu, Seoul 08826, Republic of Korea
| | - Sang-Jip Nam
- Department of Chemistry and Nanoscience, Ewha Womans University, Seoul 03760, Republic of Korea
| | - Jaclyn M Winter
- Department of Medicinal Chemistry, University of Utah, Salt Lake City, Utah 84112, United States
| | - YoungSoo Kim
- Department of Pharmacy, Yonsei Institute of Pharmaceutical Sciences, and Department of Integrative Biotechnology and Translational Medicine, Yonsei University, 85 Songdogwahak-ro, Yeonsu-gu, Incheon 21983, Republic of Korea
| | - Yeo Joon Yoon
- Natural Products Research Institute, College of Pharmacy, Seoul National University, 1 Gwanak-ro, Gwanak-gu, Seoul 08826, Republic of Korea
| | - Dong-Chan Oh
- Natural Products Research Institute, College of Pharmacy, Seoul National University, 1 Gwanak-ro, Gwanak-gu, Seoul 08826, Republic of Korea
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17
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Jung JA, Lee HJ, Song MC, Hwangbo A, Beom JY, Lee SJ, Park DJ, Oh JH, Ha SJ, Cheong E, Yoon YJ. Correction to Biosynthesis of Nonimmunosuppressive ProlylFK506 Analogues with Neurite Outgrowth and Synaptogenic Activity. J Nat Prod 2021; 84:1422. [PMID: 33761258 DOI: 10.1021/acs.jnatprod.1c00161] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/12/2023]
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18
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An JS, Shin B, Kim TH, Hwang S, Shin YH, Cui J, Du YE, Yi J, Nam SJ, Hong S, Shin J, Jang J, Yoon YJ, Oh DC. Dumulmycin, an Antitubercular Bicyclic Macrolide from a Riverine Sediment-Derived Streptomyces sp. Org Lett 2021; 23:3359-3363. [DOI: 10.1021/acs.orglett.1c00847] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/30/2023]
Affiliation(s)
- Joon Soo An
- Natural Products Research Institute, College of Pharmacy, Seoul National University, Seoul 08826, Republic of Korea
| | - Bora Shin
- Natural Products Research Institute, College of Pharmacy, Seoul National University, Seoul 08826, Republic of Korea
| | - Tae Ho Kim
- Molecular Mechanism of Antibiotics, Division of Life Science, Division of Bio & Medical Big Data Department (BK4 Program), Research Institute of Life Science, Gyeongsang National University, Jinju, Gyeongnam 52828, Republic of Korea
| | - Sunghoon Hwang
- Natural Products Research Institute, College of Pharmacy, Seoul National University, Seoul 08826, Republic of Korea
| | - Yern-Hyerk Shin
- Natural Products Research Institute, College of Pharmacy, Seoul National University, Seoul 08826, Republic of Korea
| | - Jinsheng Cui
- Natural Products Research Institute, College of Pharmacy, Seoul National University, Seoul 08826, Republic of Korea
| | - Young Eun Du
- Natural Products Research Institute, College of Pharmacy, Seoul National University, Seoul 08826, Republic of Korea
| | - Jungwoo Yi
- Natural Products Research Institute, College of Pharmacy, Seoul National University, Seoul 08826, Republic of Korea
| | - Sang-Jip Nam
- Department of Chemistry and Nanoscience, Ewha Womans University, Seoul 03760, Republic of Korea
| | - Suckchang Hong
- Research Institute of Pharmaceutical Sciences, College of Pharmacy, Seoul National University, Seoul 08826, Republic of Korea
| | - Jongheon Shin
- Natural Products Research Institute, College of Pharmacy, Seoul National University, Seoul 08826, Republic of Korea
| | - Jichan Jang
- Molecular Mechanism of Antibiotics, Division of Life Science, Division of Bio & Medical Big Data Department (BK4 Program), Research Institute of Life Science, Gyeongsang National University, Jinju, Gyeongnam 52828, Republic of Korea
| | - Yeo Joon Yoon
- Natural Products Research Institute, College of Pharmacy, Seoul National University, Seoul 08826, Republic of Korea
| | - Dong-Chan Oh
- Natural Products Research Institute, College of Pharmacy, Seoul National University, Seoul 08826, Republic of Korea
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19
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Cho JM, Yoon YJ, Lee S, Kim D, Choi D, Kim J, Lim JY. Retroductal Delivery of Epidermal Growth Factor Protects Salivary Progenitors after Irradiation. J Dent Res 2021; 100:883-890. [PMID: 33754871 DOI: 10.1177/0022034521999298] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022] Open
Abstract
Salivary gland hypofunction after irradiation is associated with a deficit of epithelial stem/progenitors in salivary glands. Although epidermal growth factor (EGF) is known to stimulate the proliferation of epithelial cells, the therapeutic effect of EGF on salivary epithelial stem/progenitors remains undetermined. In this study, we administered EGF to submandibular glands (SMGs) via a retrograde route through the SMG excretory duct before fractionated irradiation and examined whether EGF could protect salivary epithelial progenitor cells from radiation and alleviate radiation-induced salivary hypofunction. EGF-treated mice exhibited greater body and gland weights at 12 wk after irradiation than untreated mice. The retroductal delivery of EGF improved salivary secretory function and increased salivary amylase activity in a dose-dependent manner. Histological examinations highlighted the amelioration of the loss of keratine-14+ (KRT14+) basal ductal and/or MIST1+ acinar cells, as well as induction of fibrosis, following irradiation in EGF-treated mice. An additional in vitro experiment using a salivary gland organoid irradiation model indicated that the radioprotective effects of EGF promoted the growth and inhibited the apoptotic cell death of salivary epithelial cells. Our results suggest that retroductal delivery of EGF may be a promising therapeutic option for preventing radiation-induced salivary gland hypofunction.
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Affiliation(s)
- J M Cho
- Department of Otorhinolaryngology, Yonsei University College of Medicine, Seoul, Republic of Korea
| | - Y J Yoon
- Department of Otorhinolaryngology, Yonsei University College of Medicine, Seoul, Republic of Korea
| | - S Lee
- Department of Otorhinolaryngology, Yonsei University College of Medicine, Seoul, Republic of Korea
| | - D Kim
- Department of Otorhinolaryngology, Yonsei University College of Medicine, Seoul, Republic of Korea
| | - D Choi
- Department of Otorhinolaryngology, Yonsei University College of Medicine, Seoul, Republic of Korea
| | - J Kim
- Department of Otorhinolaryngology, Yonsei University College of Medicine, Seoul, Republic of Korea
| | - J Y Lim
- Department of Otorhinolaryngology, Yonsei University College of Medicine, Seoul, Republic of Korea
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20
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Kim E, Du YE, Ban YH, Shin YH, Oh DC, Yoon YJ. Enhanced Ohmyungsamycin A Production via Adenylation Domain Engineering and Optimization of Culture Conditions. Front Microbiol 2021; 12:626881. [PMID: 33679647 PMCID: PMC7925391 DOI: 10.3389/fmicb.2021.626881] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2020] [Accepted: 01/26/2021] [Indexed: 11/13/2022] Open
Abstract
Ohmyungsamycins (OMSs) A and B are cyclic depsipeptides produced by marine Streptomyces strains, which are synthesized by a non-ribosomal peptide synthetase. Notably, OMS A exhibits more potent activity against Mycobacterium tuberculosis and human cancer cells than OMS B. The substrate promiscuous adenylation (A) domain in the second module of OMS synthetase recruits either L-Val or L-Ile to synthesize OMSs A and B, respectively. Engineering of the substrate-coding residues of this A domain increased OMS A production by 1.2-fold, coupled with a drastic decrease in OMS B production. Furthermore, the culture conditions (sea salt concentration, inoculum size, and the supply of amino acids to serve as building blocks for OMS) were optimized for OMS production in the wild-type strain. Finally, cultivation of the A2-domain-engineered strain under the optimized culture conditions resulted in up to 3.8-fold increases in OMS A yields and an 8.4-fold decrease in OMS B production compared to the wild-type strain under the initial culture conditions.
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Affiliation(s)
- Eunji Kim
- Natural Products Research Institute, College of Pharmacy, Seoul National University, Seoul, South Korea
| | - Young Eun Du
- Natural Products Research Institute, College of Pharmacy, Seoul National University, Seoul, South Korea
| | - Yeon Hee Ban
- Natural Products Research Institute, College of Pharmacy, Seoul National University, Seoul, South Korea
| | - Yern-Hyerk Shin
- Natural Products Research Institute, College of Pharmacy, Seoul National University, Seoul, South Korea
| | - Dong-Chan Oh
- Natural Products Research Institute, College of Pharmacy, Seoul National University, Seoul, South Korea
| | - Yeo Joon Yoon
- Natural Products Research Institute, College of Pharmacy, Seoul National University, Seoul, South Korea
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21
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Baek S, Utomo JC, Lee JY, Dalal K, Yoon YJ, Ro DK. The yeast platform engineered for synthetic gRNA-landing pads enables multiple gene integrations by a single gRNA/Cas9 system. Metab Eng 2021; 64:111-121. [PMID: 33549837 DOI: 10.1016/j.ymben.2021.01.011] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2020] [Revised: 12/28/2020] [Accepted: 01/30/2021] [Indexed: 12/25/2022]
Abstract
Saccharomyces cerevisiae is a versatile microbial platform to build synthetic metabolic pathways for production of diverse chemicals. To expedite the construction of complex metabolic pathways by multiplex CRISPR-Cas9 genome-edit, eight desirable intergenic loci, located adjacent to highly expressed genes selected from top 100 expressers, were identified and fully characterized for three criteria after integrating green fluorescent protein (GFP) gene - CRISPR-mediated GFP integration efficiency, expression competency assessed by levels of GFP fluorescence, and assessing growth rates of GFP integrated strains. Five best performing intergenic loci were selected to build a multiplex CRISPR platform, and a synthetic 23-bp DNA comprised of 20-bp synthetic DNA with a protospacer adjacent motif (PAM) was integrated into the five loci using CRISPR-Cas9 in a sequential manner. This process resulted in five different yeast strains harbouring 1-5 synthetic gRNA-binding sites in their genomes. Using these pre-engineered yeast strains, simultaneous integrations of 2-, 3-, 4-, or 5-genes to the targeted loci were demonstrated with efficiencies from 85% to 98% using beet pigment betalain (3-gene pathway), hygromycin and geneticin resistance markers. Integrations of the multiple, foreign genes in the targeted loci with 100% precision were validated by genotyping. Finally, we further developed the strain to have 6th synthetic gRNA-binding site, and the resulting yeast strain was used to generate a yeast strain producing a sesquiterpene lactone, kauniolide by simultaneous 6-gene integrations. This study demonstrates the effectiveness of a single gRNA-mediated CRISPR platform to build complex metabolic pathways in yeast.
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Affiliation(s)
- Sihyun Baek
- Department of Biological Sciences, University of Calgary, Calgary, AB, T2N1N4, Canada
| | | | - Ji Young Lee
- Department of Chemistry and Nanoscience, Ewha Womans University, Seoul, 03760, Republic of Korea
| | - Kunal Dalal
- Department of Biological Sciences, University of Calgary, Calgary, AB, T2N1N4, Canada
| | - Yeo Joon Yoon
- Natural Products Research Institute, College of Pharmacy, Seoul National University, Seoul, 08826, Republic of Korea
| | - Dae-Kyun Ro
- Department of Biological Sciences, University of Calgary, Calgary, AB, T2N1N4, Canada.
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22
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Shin YH, Ban YH, Kim TH, Bae ES, Shin J, Lee SK, Jang J, Yoon YJ, Oh DC. Structures and Biosynthetic Pathway of Coprisamides C and D, 2-Alkenylcinnamic Acid-Containing Peptides from the Gut Bacterium of the Carrion Beetle Silpha perforata. J Nat Prod 2021; 84:239-246. [PMID: 33497210 DOI: 10.1021/acs.jnatprod.0c00864] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/12/2023]
Abstract
Coprisamides C and D (1 and 2) were isolated from a gut bacterium, Micromonospora sp. UTJ3, of the carrion beetle Silpha perforata. Based on the combined analysis of UV, MS, and NMR spectral data, the planar structures of 1 and 2 were elucidated to be unreported derivatives of coprisamides A and B, cyclic depsipeptides bearing a 2-alkenylcinnamic acid unit and the unusual amino acids β-methylaspartic acid and 2,3-diaminopropanoic acid. The absolute configuration of 1 was determined using the advanced Marfey's method, phenylglycine methyl ester derivatization, and J-based configuration analysis. The biosynthetic gene clusters for the coprisamides were investigated based on genomic data from coprisamide-producing strains Micromonospora sp. UTJ3 and Streptomyces sp. SNU533. Coprisamide C (1) was active against the Mycobacterium tuberculosis mc2 6230 strain.
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Affiliation(s)
- Yern-Hyerk Shin
- Natural Products Research Institute, College of Pharmacy, Seoul National University, 1 Gwanak-ro, Gwanak-gu, Seoul 08826, Republic of Korea
| | - Yeon Hee Ban
- Natural Products Research Institute, College of Pharmacy, Seoul National University, 1 Gwanak-ro, Gwanak-gu, Seoul 08826, Republic of Korea
| | - Tae Ho Kim
- Molecular Mechanism of Antibiotics, Division of Life Science, Research Institute of Life Science, Gyeongsang National University, Jinju 52828, Republic of Korea
- Division of Applied Life Science (BK21plus Program), Gyeongsang National University, Jinju 52828, Republic of Korea
| | - Eun Seo Bae
- Natural Products Research Institute, College of Pharmacy, Seoul National University, 1 Gwanak-ro, Gwanak-gu, Seoul 08826, Republic of Korea
| | - Jongheon Shin
- Natural Products Research Institute, College of Pharmacy, Seoul National University, 1 Gwanak-ro, Gwanak-gu, Seoul 08826, Republic of Korea
| | - Sang Kook Lee
- Natural Products Research Institute, College of Pharmacy, Seoul National University, 1 Gwanak-ro, Gwanak-gu, Seoul 08826, Republic of Korea
| | - Jichan Jang
- Molecular Mechanism of Antibiotics, Division of Life Science, Research Institute of Life Science, Gyeongsang National University, Jinju 52828, Republic of Korea
| | - Yeo Joon Yoon
- Natural Products Research Institute, College of Pharmacy, Seoul National University, 1 Gwanak-ro, Gwanak-gu, Seoul 08826, Republic of Korea
| | - Dong-Chan Oh
- Natural Products Research Institute, College of Pharmacy, Seoul National University, 1 Gwanak-ro, Gwanak-gu, Seoul 08826, Republic of Korea
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23
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Jung JA, Lee HJ, Song MC, Hwangbo A, Beom JY, Lee SJ, Park DJ, Oh JH, Ha SJ, Cheong E, Yoon YJ. Biosynthesis of Nonimmunosuppressive ProlylFK506 Analogues with Neurite Outgrowth and Synaptogenic Activity. J Nat Prod 2021; 84:195-203. [PMID: 33534559 DOI: 10.1021/acs.jnatprod.0c00767] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/12/2023]
Abstract
Separating the immunosuppressive activity of FK506 (1) from its neurotrophic activity is required to develop FK506 analogues as drugs for the treatment of neuronal diseases. Two new FK506 analogues, 9-deoxo-36,37-dihydro-prolylFK506 (2) and 9-deoxo-31-O-demethyl-36,37-dihydro-prolylFK506 (3) containing a proline moiety instead of the pipecolate ring at C-1 and modifications at the C-9/C-31 and C-36-C-37 positions, respectively, were biosynthesized, and their biological activities were evaluated. The proline substitution in 9-deoxo-36,37-dihydroFK506 and 9-deoxo-31-O-demethyl-36,37-dihydroFK506 reduced immunosuppressive activity by more than 120-fold, as previously observed. Compared with FK506 (1), 2 and 3 exhibited ∼1.2 × 105- and 2.2 × 105-fold reductions in immunosuppressive activity, respectively, whereas they retained almost identical neurite outgrowth activity. Furthermore, these compounds significantly increased the strength of synaptic transmission, confirming that replacement of the pipecolate ring with a proline is critical to reduce the strong immunosuppressive activity of FK506 (1) while enhancing its neurotrophic activity.
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Affiliation(s)
- Jin A Jung
- Department of Chemistry and Nanoscience, Ewha Womans University, Seoul 03760, Republic of Korea
| | - Heon Joo Lee
- Department of Biotechnology, College of Life Science and Biotechnology, Yonsei University, Seoul 03722, Republic of Korea
| | - Myoung Chong Song
- Natural Products Research Institute, College of Pharmacy, Seoul National University, Seoul 08826, Republic of Korea
| | - Areum Hwangbo
- Department of Biotechnology, College of Life Science and Biotechnology, Yonsei University, Seoul 03722, Republic of Korea
| | - Ji Yoon Beom
- Department of Chemistry and Nanoscience, Ewha Womans University, Seoul 03760, Republic of Korea
| | - Soo Jung Lee
- Department of Biotechnology, College of Life Science and Biotechnology, Yonsei University, Seoul 03722, Republic of Korea
| | - Dong Jin Park
- Department of Biochemistry, College of Life Science and Biotechnology, Yonsei University, Seoul 03722, Republic of Korea
| | - Ji Hoon Oh
- Department of Biochemistry, College of Life Science and Biotechnology, Yonsei University, Seoul 03722, Republic of Korea
| | - Sang-Jun Ha
- Department of Biochemistry, College of Life Science and Biotechnology, Yonsei University, Seoul 03722, Republic of Korea
| | - Eunji Cheong
- Department of Biotechnology, College of Life Science and Biotechnology, Yonsei University, Seoul 03722, Republic of Korea
| | - Yeo Joon Yoon
- Natural Products Research Institute, College of Pharmacy, Seoul National University, Seoul 08826, Republic of Korea
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24
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Shin CH, Cho HS, Won HJ, Kwon HJ, Kim CW, Yoon YJ. Enhanced production of clavulanic acid by improving glycerol utilization using reporter-guided mutagenesis of an industrial Streptomyces clavuligerus strain. J Ind Microbiol Biotechnol 2021; 48:6119913. [PMID: 33693777 PMCID: PMC9113135 DOI: 10.1093/jimb/kuab004] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2020] [Accepted: 01/22/2021] [Indexed: 11/13/2022]
Abstract
Abstract
Clavulanic acid (CA) produced by Streptomyces clavuligerus is a clinically important β-lactamase inhibitor. It is known that glycerol utilization can significantly improve cell growth and CA production of S. clavuligerus. We found that the industrial CA-producing S. clavuligerus strain OR generated by random mutagenesis consumes less glycerol than the wild-type strain; we then developed a mutant strain in which the glycerol utilization operon is overexpressed, as compared to the parent OR strain, through iterative random mutagenesis and reporter-guided selection. The CA production of the resulting S. clavuligerus ORUN strain was increased by approximately 31.3% (5.21 ± 0.26 g/l) in a flask culture and 17.4% (6.11 ± 0.36 g/l) in a fermenter culture, as compared to that of the starting OR strain. These results confirmed the important role of glycerol utilization in CA production and demonstrated that reporter-guided mutant selection is an efficient method for further improvement of randomly mutagenized industrial strains.
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Affiliation(s)
- Chang-Hun Shin
- Department of Biotechnology, College of Life Sciences and Biotechnology, Korea University, Seoul 02841, Republic of Korea
| | - Hang Su Cho
- Department of Biotechnology, College of Life Science and Biotechnology, Yonsei University, Seoul 03722, Republic of Korea
| | - Hyung-Jin Won
- Fermentation Technology Team, Research Institute of CKD Bio, Ansan 15604, Republic of Korea
| | - Ho Jeong Kwon
- Department of Biotechnology, College of Life Science and Biotechnology, Yonsei University, Seoul 03722, Republic of Korea
| | - Chan-Wha Kim
- Department of Biotechnology, College of Life Sciences and Biotechnology, Korea University, Seoul 02841, Republic of Korea
| | - Yeo Joon Yoon
- Natural Products Research Institute, College of Pharmacy, Seoul National University, Seoul 08826, Republic of Korea
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25
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Lee N, Hwang S, Kim W, Lee Y, Kim JH, Cho S, Kim HU, Yoon YJ, Oh MK, Palsson BO, Cho BK. Systems and synthetic biology to elucidate secondary metabolite biosynthetic gene clusters encoded in Streptomyces genomes. Nat Prod Rep 2021; 38:1330-1361. [PMID: 33393961 DOI: 10.1039/d0np00071j] [Citation(s) in RCA: 27] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Covering: 2010 to 2020 Over the last few decades, Streptomyces have been extensively investigated for their ability to produce diverse bioactive secondary metabolites. Recent advances in Streptomyces research have been largely supported by improvements in high-throughput technology 'omics'. From genomics, numerous secondary metabolite biosynthetic gene clusters were predicted, increasing their genomic potential for novel bioactive compound discovery. Additional omics, including transcriptomics, translatomics, interactomics, proteomics and metabolomics, have been applied to obtain a system-level understanding spanning entire bioprocesses of Streptomyces, revealing highly interconnected and multi-layered regulatory networks for secondary metabolism. The comprehensive understanding derived from this systematic information accelerates the rational engineering of Streptomyces to enhance secondary metabolite production, integrated with the exploitation of the highly efficient 'Design-Build-Test-Learn' cycle in synthetic biology. In this review, we describe the current status of omics applications in Streptomyces research to better understand the organism and exploit its genetic potential for higher production of valuable secondary metabolites and novel secondary metabolite discovery.
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Affiliation(s)
- Namil Lee
- Department of Biological Sciences, Korea Advanced Institute of Science and Technology, Daejeon 34141, Republic of Korea. and Innovative Biomaterials Centre, KI for the BioCentury, Korea Advanced Institute of Science and Technology, Daejeon 34141, Republic of Korea
| | - Soonkyu Hwang
- Department of Biological Sciences, Korea Advanced Institute of Science and Technology, Daejeon 34141, Republic of Korea. and Innovative Biomaterials Centre, KI for the BioCentury, Korea Advanced Institute of Science and Technology, Daejeon 34141, Republic of Korea
| | - Woori Kim
- Department of Biological Sciences, Korea Advanced Institute of Science and Technology, Daejeon 34141, Republic of Korea. and Innovative Biomaterials Centre, KI for the BioCentury, Korea Advanced Institute of Science and Technology, Daejeon 34141, Republic of Korea
| | - Yongjae Lee
- Department of Biological Sciences, Korea Advanced Institute of Science and Technology, Daejeon 34141, Republic of Korea. and Innovative Biomaterials Centre, KI for the BioCentury, Korea Advanced Institute of Science and Technology, Daejeon 34141, Republic of Korea
| | - Ji Hun Kim
- Department of Biological Sciences, Korea Advanced Institute of Science and Technology, Daejeon 34141, Republic of Korea. and Innovative Biomaterials Centre, KI for the BioCentury, Korea Advanced Institute of Science and Technology, Daejeon 34141, Republic of Korea
| | - Suhyung Cho
- Department of Biological Sciences, Korea Advanced Institute of Science and Technology, Daejeon 34141, Republic of Korea. and Innovative Biomaterials Centre, KI for the BioCentury, Korea Advanced Institute of Science and Technology, Daejeon 34141, Republic of Korea
| | - Hyun Uk Kim
- Department of Chemical and Biomolecular Engineering, Korea Advanced Institute of Science and Technology, Daejeon 34141, Republic of Korea
| | - Yeo Joon Yoon
- College of Pharmacy, Seoul National University, Seoul 08826, Republic of Korea.
| | - Min-Kyu Oh
- Department of Chemical and Biological Engineering, Korea University, Seoul 02841, Republic of Korea.
| | - Bernhard O Palsson
- Department of Bioengineering, University of California San Diego, La Jolla, CA 92093, USA. and Department of Pediatrics, University of California San Diego, La Jolla, CA 92093, USA and Novo Nordisk Foundation Centre for Biosustainability, Technical University of Denmark, Lyngby, 2800, Denmark
| | - Byung-Kwan Cho
- Department of Biological Sciences, Korea Advanced Institute of Science and Technology, Daejeon 34141, Republic of Korea. and Innovative Biomaterials Centre, KI for the BioCentury, Korea Advanced Institute of Science and Technology, Daejeon 34141, Republic of Korea and Novo Nordisk Foundation Centre for Biosustainability, Technical University of Denmark, Lyngby, 2800, Denmark
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26
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An JS, Lee JY, Kim E, Ahn H, Jang YJ, Shin B, Hwang S, Shin J, Yoon YJ, Lee SK, Oh DC. Formicolides A and B, Antioxidative and Antiangiogenic 20-Membered Macrolides from a Wood Ant Gut Bacterium. J Nat Prod 2020; 83:2776-2784. [PMID: 32892623 DOI: 10.1021/acs.jnatprod.0c00772] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/11/2023]
Abstract
Two new macrolides, formicolides A (1) and B (2), were isolated from Streptomyces sp. BA01, a gut bacterial strain of the wood ant (Formica yessensis). Their 20-membered macrocyclic lactone structures were established using NMR and mass spectrometric data. The relative configurations of the formicolides were determined by J-based configuration analysis utilizing ROESY, HETLOC, and HECADE NMR spectroscopic data. Genomic and bioinformatics analysis of the bacterial strain enabled us to identify the type-I polyketide synthase pathway employing a trans-acyltransferase system. The absolute configurations of 1 and 2 are proposed based on detailed analysis of the sequences of the ketoreductases in the modular gene cluster and statistical comparative analysis of the experimental NMR chemical shifts and quantum mechanical calculations. Formicolides A and B (1 and 2) induced quinone reductase activity in murine Hepa-1c1c7 cells and antiangiogenic activity by suppression of tube formation in human umbilical vein endothelial cells.
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Affiliation(s)
- Joon Soo An
- Natural Products Research Institute, College of Pharmacy, Seoul National University, Seoul 08826, Republic of Korea
| | - Ji Yun Lee
- Natural Products Research Institute, College of Pharmacy, Seoul National University, Seoul 08826, Republic of Korea
| | - Eunji Kim
- Natural Products Research Institute, College of Pharmacy, Seoul National University, Seoul 08826, Republic of Korea
| | - Hyungju Ahn
- Natural Products Research Institute, College of Pharmacy, Seoul National University, Seoul 08826, Republic of Korea
| | - Yong-Joon Jang
- Natura Center of Life and Environment, Seoul 08826, Republic of Korea
| | - Bora Shin
- Natural Products Research Institute, College of Pharmacy, Seoul National University, Seoul 08826, Republic of Korea
| | - Sunghoon Hwang
- Natural Products Research Institute, College of Pharmacy, Seoul National University, Seoul 08826, Republic of Korea
| | - Jongheon Shin
- Natural Products Research Institute, College of Pharmacy, Seoul National University, Seoul 08826, Republic of Korea
| | - Yeo Joon Yoon
- Natural Products Research Institute, College of Pharmacy, Seoul National University, Seoul 08826, Republic of Korea
| | - Sang Kook Lee
- Natural Products Research Institute, College of Pharmacy, Seoul National University, Seoul 08826, Republic of Korea
| | - Dong-Chan Oh
- Natural Products Research Institute, College of Pharmacy, Seoul National University, Seoul 08826, Republic of Korea
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27
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Moon K, Cui J, Kim E, Riandi ES, Park SH, Byun WS, Kal Y, Park JY, Hwang S, Shin D, Sun J, Oh KB, Cha S, Shin J, Lee SK, Yoon YJ, Oh DC. Structures and Biosynthetic Pathway of Pulvomycins B–D: 22-Membered Macrolides from an Estuarine Streptomyces sp. Org Lett 2020; 22:5358-5362. [DOI: 10.1021/acs.orglett.0c01249] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Kyuho Moon
- Natural Products Research Institute, College of Pharmacy, Seoul National University, Seoul 08826, Republic of Korea
- College of Pharmacy, Chonnam National University, Gwangju 61186, Republic of Korea
| | - Jinsheng Cui
- Natural Products Research Institute, College of Pharmacy, Seoul National University, Seoul 08826, Republic of Korea
| | - Eunji Kim
- Natural Products Research Institute, College of Pharmacy, Seoul National University, Seoul 08826, Republic of Korea
| | - Evan Setiawan Riandi
- Natural Products Research Institute, College of Pharmacy, Seoul National University, Seoul 08826, Republic of Korea
| | - So Hyun Park
- Natural Products Research Institute, College of Pharmacy, Seoul National University, Seoul 08826, Republic of Korea
| | - Woong Sub Byun
- Natural Products Research Institute, College of Pharmacy, Seoul National University, Seoul 08826, Republic of Korea
| | - Youngju Kal
- Department of Chemistry, Dongguk University, Seoul 04620, Republic of Korea
| | - Jun Young Park
- Department of Chemistry, Dongguk University, Seoul 04620, Republic of Korea
| | - Sunghoon Hwang
- Natural Products Research Institute, College of Pharmacy, Seoul National University, Seoul 08826, Republic of Korea
| | - Daniel Shin
- Natural Products Research Institute, College of Pharmacy, Seoul National University, Seoul 08826, Republic of Korea
| | - Jeongyoon Sun
- Department of Agricultural Biotechnology, College of Agriculture & Life Sciences, Seoul National University, Seoul 08826, Republic of Korea
| | - Ki-Bong Oh
- Department of Agricultural Biotechnology, College of Agriculture & Life Sciences, Seoul National University, Seoul 08826, Republic of Korea
| | - Sangwon Cha
- Department of Chemistry, Dongguk University, Seoul 04620, Republic of Korea
| | - Jongheon Shin
- Natural Products Research Institute, College of Pharmacy, Seoul National University, Seoul 08826, Republic of Korea
| | - Sang Kook Lee
- Natural Products Research Institute, College of Pharmacy, Seoul National University, Seoul 08826, Republic of Korea
| | - Yeo Joon Yoon
- Natural Products Research Institute, College of Pharmacy, Seoul National University, Seoul 08826, Republic of Korea
| | - Dong-Chan Oh
- Natural Products Research Institute, College of Pharmacy, Seoul National University, Seoul 08826, Republic of Korea
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28
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Ban YH, Song MC, Hwang JY, Shin HL, Kim HJ, Hong SK, Lee NJ, Park JW, Cha SS, Liu HW, Yoon YJ. Publisher Correction: Complete reconstitution of the diverse pathways of gentamicin B biosynthesis. Nat Chem Biol 2020; 16:810. [DOI: 10.1038/s41589-020-0577-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
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29
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Abstract
Tripartilactam (1) is a natural macrocyclic lactam originally reported to have a unique [18,8,4]-tricyclic framework. However, the validity of this structure has been contested since niizalactam C (2), bearing a [18,6,6]-tricyclic skeleton, was proposed as an alternative structure in 2015. In the present study, a comprehensive reinvestigation of NMR spectroscopic data and a 13C-13C COSY NMR experiment identified direct 13C-13C coupling, thus leading to the unequivocal revision of the structure of tripartilactam as niizalactam C (2). In addition, whole-genome sequencing analysis of the tripartilactam-producing bacterial strain and subsequent bioinformatics and mutagenesis analyses identified its biosynthetic pathway, which probably utilizes one of the type I polyketide synthase (PKS) modules iteratively during its biosynthesis and exhibits spontaneous [4+2] cycloaddition from the precursor compound, sceliphrolactam, in the post-PKS process.
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Affiliation(s)
- Sunghoon Hwang
- Natural Products Research Institute, College of Pharmacy, Seoul National University, Seoul 08826, Republic of Korea
| | - Eunji Kim
- Department of Chemistry and Nanoscience, Ewha Womans University, Seoul 03760, Republic of Korea
| | - Jeeyeon Lee
- College of Pharmacy, Seoul National University, Seoul 08826, Republic of Korea
| | - Jongheon Shin
- Natural Products Research Institute, College of Pharmacy, Seoul National University, Seoul 08826, Republic of Korea
| | - Yeo Joon Yoon
- Department of Chemistry and Nanoscience, Ewha Womans University, Seoul 03760, Republic of Korea
| | - Dong-Chan Oh
- Natural Products Research Institute, College of Pharmacy, Seoul National University, Seoul 08826, Republic of Korea
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Shin YH, Kang S, Byun WS, Jeon CW, Chung B, Beom JY, Hong S, Lee J, Shin J, Kwak YS, Lee SK, Oh KB, Yoon YJ, Oh DC. Absolute Configuration and Antibiotic Activity of Piceamycin. J Nat Prod 2020; 83:277-285. [PMID: 32073848 DOI: 10.1021/acs.jnatprod.9b00678] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/10/2023]
Abstract
The cultivation of a Streptomyces sp. SD53 strain isolated from the gut of the silkworm Bombyx mori produced two macrolactam natural products, piceamycin (1) and bombyxamycin C (2). The planar structures of 1 and 2 were identified by a combination of NMR, MS, and UV spectroscopic analyses. The absolute configurations were assigned based on chemical and chromatographic methods as well as ECD calculations. A new chromatography-based experimental method for determining the configurations of stereogenic centers β to nitrogen atoms in macrolactams was established and successfully applied in this report. These compounds exhibited significant bioactivities against the silkworm entomopathogen Bacillus thuringiensis and various human pathogens as well as human cancer cell lines. In particular, piceamycin potently inhibited Salmonella enterica and Proteus hauseri with MIC values of 0.083 μg/mL and 0.025 μg/mL, respectively. The biosynthetic pathway involved in the formation of the cyclopentenone moiety in piceamycin is discussed.
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Affiliation(s)
- Yern-Hyerk Shin
- Natural Products Research Institute, College of Pharmacy , Seoul National University , 1 Gwanak-ro , Gwanak-gu , Seoul 08826 , Republic of Korea
| | - Saeyeon Kang
- Department of Agricultural Biotechnology, College of Agriculture & Life Sciences , Seoul National University , 1 Gwanak-ro , Gwanak-gu , Seoul 08826 , Republic of Korea
| | - Woong Sub Byun
- Natural Products Research Institute, College of Pharmacy , Seoul National University , 1 Gwanak-ro , Gwanak-gu , Seoul 08826 , Republic of Korea
| | - Chang-Wook Jeon
- Department of Plant Medicine and IALS , Gyeongsang National University , 501 Jinju-daero , Jinju , Gyeongsang Nam-do 52828 , Republic of Korea
| | - Beomkoo Chung
- Department of Agricultural Biotechnology, College of Agriculture & Life Sciences , Seoul National University , 1 Gwanak-ro , Gwanak-gu , Seoul 08826 , Republic of Korea
| | - Ji Yoon Beom
- Department of Chemistry and Nanoscience , Ewha Womans University , Seoul 03760 , Republic of Korea
| | - Suckchang Hong
- College of Pharmacy , Seoul National University , 1 Gwanak-ro , Gwanak-gu , Seoul 08826 , Republic of Korea
| | - Jeeyeon Lee
- College of Pharmacy , Seoul National University , 1 Gwanak-ro , Gwanak-gu , Seoul 08826 , Republic of Korea
| | - Jongheon Shin
- Natural Products Research Institute, College of Pharmacy , Seoul National University , 1 Gwanak-ro , Gwanak-gu , Seoul 08826 , Republic of Korea
| | - Youn-Sig Kwak
- Department of Plant Medicine and IALS , Gyeongsang National University , 501 Jinju-daero , Jinju , Gyeongsang Nam-do 52828 , Republic of Korea
| | - Sang Kook Lee
- Natural Products Research Institute, College of Pharmacy , Seoul National University , 1 Gwanak-ro , Gwanak-gu , Seoul 08826 , Republic of Korea
| | - Ki-Bong Oh
- Department of Agricultural Biotechnology, College of Agriculture & Life Sciences , Seoul National University , 1 Gwanak-ro , Gwanak-gu , Seoul 08826 , Republic of Korea
| | - Yeo Joon Yoon
- Department of Chemistry and Nanoscience , Ewha Womans University , Seoul 03760 , Republic of Korea
| | - Dong-Chan Oh
- Natural Products Research Institute, College of Pharmacy , Seoul National University , 1 Gwanak-ro , Gwanak-gu , Seoul 08826 , Republic of Korea
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Abstract
FK506, also known as tacrolimus, is a clinically important immunosuppressant drug and has promising therapeutic potentials owing to its antifungal, neuroprotective, and neuroregenerative activities. To generate various FK506 derivatives, the structure of FK506 has been modified by chemical methods or biosynthetic pathway engineering. Herein, we describe the mode of the antifungal action of FK506 and the structure-activity relationship of FK506 derivatives in the context of immunosuppressive and antifungal activities. In addition, we discuss the neurotrophic mechanism of FK506 known to date, along with the neurotrophic FK506 derivatives with significantly reduced immunosuppressive activity. This review suggests the possibility to generate novel FK506 derivatives as antifungal as well as neuroregenerative/neuroprotective agents.
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Affiliation(s)
- Jin A Jung
- Department of Chemistry and Nanoscience, Ewha Womans University, Seoul 03760, Republic of Korea
| | - Yeo Joon Yoon
- Department of Chemistry and Nanoscience, Ewha Womans University, Seoul 03760, Republic of Korea,Corresponding author Phone: +82-2-3277-4082 Fax: +82-2-3277-3419 E-mail:
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32
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Ban YH, Song MC, Park JW, Yoon YJ. Minor components of aminoglycosides: recent advances in their biosynthesis and therapeutic potential. Nat Prod Rep 2020; 37:301-311. [DOI: 10.1039/c9np00041k] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]
Abstract
This Highlight covers the recent advances in the biosynthetic pathways of aminoglycosides including their minor components, together with the therapeutic potential for minor aminoglycoside components and semi-synthetic aminoglycosides.
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Affiliation(s)
- Yeon Hee Ban
- Department of Chemistry and Nanoscience
- Ewha Womans University
- Seoul 03760
- Republic of Korea
| | - Myoung Chong Song
- Department of Chemistry and Nanoscience
- Ewha Womans University
- Seoul 03760
- Republic of Korea
| | - Je Won Park
- School of Biosystems and Biomedical Sciences
- Korea University
- Seoul 02841
- Republic of Korea
| | - Yeo Joon Yoon
- Department of Chemistry and Nanoscience
- Ewha Womans University
- Seoul 03760
- Republic of Korea
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33
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Beom JY, Jung JA, Lee KT, Hwangbo A, Song MC, Lee Y, Lee SJ, Oh JH, Ha SJ, Nam SJ, Cheong E, Bahn YS, Yoon YJ. Biosynthesis of Nonimmunosuppressive FK506 Analogues with Antifungal Activity. J Nat Prod 2019; 82:2078-2086. [PMID: 31321978 DOI: 10.1021/acs.jnatprod.9b00144] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/10/2023]
Abstract
A reduction in the strong immunosuppressive activity of FK506 (1) is essential for developing this compound as an antifungal agent. Seven new FK506 analogues modified at both the FK506-binding protein 12- and the calcineurin-binding regions were biosynthesized. 9-DeoxoFK520 (7) exhibited a >900-fold reduction in the in vitro immunosuppressive activity but maintained significant antifungal activity, indicating that the C-9 and C-21 positions are critical for separation of immunosuppressive and antifungal activities. 7 exhibited robust synergistic antifungal activity with fluconazole. FK506 (1) is a 23-membered macrolide produced by several Streptomyces species and is used as an immunosuppressive drug to prevent the rejection of transplanted organs. FK506 has also exhibited antifungal, neuroprotective, and neuroregenerative activities. In humans, FK506 binds to FK506-binding protein (FKBP) 12, and the resulting FKBP12-FK506 complex interacts with a Ca2+-calmodulin-dependent phosphatase, calcineurin (CaN). Inactivation of CaN by forming the FKBP12-FK506-CaN ternary complex prevents the activation of nuclear factor of activated T cells (NF-AT), inhibiting the production of interleukin-2 and subsequent T-cell proliferation. This CaN signaling pathway also plays a critical role in the growth and pathogenesis of major fungal pathogens such as Cryptococcus neoformans, Candida albicans, and Aspergillus fumigatus. Therefore, the synthesis of FK506 analogues that can discriminate human FKBP12/CaN from its fungal counterparts may separate antifungal activity from the immunosuppressive activity, thereby allowing the development of a novel antifungal agent.
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Affiliation(s)
- Ji Yoon Beom
- Department of Chemistry and Nanoscience , Ewha Womans University , Seoul 03760 , Republic of Korea
| | - Jin A Jung
- Department of Chemistry and Nanoscience , Ewha Womans University , Seoul 03760 , Republic of Korea
| | - Kyung-Tae Lee
- Department of Biotechnology, College of Life Science and Biotechnology , Yonsei University , Seoul 03722 , Republic of Korea
| | - Areum Hwangbo
- Department of Biotechnology, College of Life Science and Biotechnology , Yonsei University , Seoul 03722 , Republic of Korea
| | - Myoung Chong Song
- Department of Chemistry and Nanoscience , Ewha Womans University , Seoul 03760 , Republic of Korea
| | - Yeonseon Lee
- Department of Biotechnology, College of Life Science and Biotechnology , Yonsei University , Seoul 03722 , Republic of Korea
| | - Soo Jung Lee
- Department of Biotechnology, College of Life Science and Biotechnology , Yonsei University , Seoul 03722 , Republic of Korea
| | - Ji Hoon Oh
- Department of Biochemistry, College of Life Science and Biotechnology , Yonsei University , Seoul 03722 , Republic of Korea
| | - Sang-Jun Ha
- Department of Biochemistry, College of Life Science and Biotechnology , Yonsei University , Seoul 03722 , Republic of Korea
| | - Sang-Jip Nam
- Department of Chemistry and Nanoscience , Ewha Womans University , Seoul 03760 , Republic of Korea
| | - Eunji Cheong
- Department of Biotechnology, College of Life Science and Biotechnology , Yonsei University , Seoul 03722 , Republic of Korea
| | - Yong-Sun Bahn
- Department of Biotechnology, College of Life Science and Biotechnology , Yonsei University , Seoul 03722 , Republic of Korea
| | - Yeo Joon Yoon
- Department of Chemistry and Nanoscience , Ewha Womans University , Seoul 03760 , Republic of Korea
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Pham JV, Yilma MA, Feliz A, Majid MT, Maffetone N, Walker JR, Kim E, Cho HJ, Reynolds JM, Song MC, Park SR, Yoon YJ. A Review of the Microbial Production of Bioactive Natural Products and Biologics. Front Microbiol 2019; 10:1404. [PMID: 31281299 PMCID: PMC6596283 DOI: 10.3389/fmicb.2019.01404] [Citation(s) in RCA: 217] [Impact Index Per Article: 43.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2019] [Accepted: 06/04/2019] [Indexed: 12/24/2022] Open
Abstract
A variety of organisms, such as bacteria, fungi, and plants, produce secondary metabolites, also known as natural products. Natural products have been a prolific source and an inspiration for numerous medical agents with widely divergent chemical structures and biological activities, including antimicrobial, immunosuppressive, anticancer, and anti-inflammatory activities, many of which have been developed as treatments and have potential therapeutic applications for human diseases. Aside from natural products, the recent development of recombinant DNA technology has sparked the development of a wide array of biopharmaceutical products, such as recombinant proteins, offering significant advances in treating a broad spectrum of medical illnesses and conditions. Herein, we will introduce the structures and diverse biological activities of natural products and recombinant proteins that have been exploited as valuable molecules in medicine, agriculture and insect control. In addition, we will explore past and ongoing efforts along with achievements in the development of robust and promising microorganisms as cell factories to produce biologically active molecules. Furthermore, we will review multi-disciplinary and comprehensive engineering approaches directed at improving yields of microbial production of natural products and proteins and generating novel molecules. Throughout this article, we will suggest ways in which microbial-derived biologically active molecular entities and their analogs could continue to inspire the development of new therapeutic agents in academia and industry.
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Affiliation(s)
- Janette V. Pham
- Geisinger Commonwealth School of Medicine, Scranton, PA, United States
- Baruch S. Blumberg Institute, Doylestown, PA, United States
| | - Mariamawit A. Yilma
- Geisinger Commonwealth School of Medicine, Scranton, PA, United States
- Baruch S. Blumberg Institute, Doylestown, PA, United States
| | - Adriana Feliz
- Geisinger Commonwealth School of Medicine, Scranton, PA, United States
- Baruch S. Blumberg Institute, Doylestown, PA, United States
| | - Murtadha T. Majid
- Geisinger Commonwealth School of Medicine, Scranton, PA, United States
- Baruch S. Blumberg Institute, Doylestown, PA, United States
| | - Nicholas Maffetone
- Geisinger Commonwealth School of Medicine, Scranton, PA, United States
- Baruch S. Blumberg Institute, Doylestown, PA, United States
| | - Jorge R. Walker
- Geisinger Commonwealth School of Medicine, Scranton, PA, United States
- Baruch S. Blumberg Institute, Doylestown, PA, United States
| | - Eunji Kim
- Department of Chemistry and Nanoscience, Ewha Womans University, Seoul, South Korea
| | - Hyo Je Cho
- School of Life Sciences and Biotechnology, Kyungpook National University, Daegu, South Korea
| | - Jared M. Reynolds
- Geisinger Commonwealth School of Medicine, Scranton, PA, United States
- Baruch S. Blumberg Institute, Doylestown, PA, United States
| | - Myoung Chong Song
- Department of Chemistry and Nanoscience, Ewha Womans University, Seoul, South Korea
| | - Sung Ryeol Park
- Geisinger Commonwealth School of Medicine, Scranton, PA, United States
- Baruch S. Blumberg Institute, Doylestown, PA, United States
- Natural Products Discovery Institute, Doylestown, PA, United States
| | - Yeo Joon Yoon
- Department of Chemistry and Nanoscience, Ewha Womans University, Seoul, South Korea
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Bae M, An JS, Bae ES, Oh J, Park SH, Lim Y, Ban YH, Kwon Y, Cho JC, Yoon YJ, Lee SK, Shin J, Oh DC. Donghaesulfins A and B, Dimeric Benz[a]anthracene Thioethers from Volcanic Island Derived Streptomyces sp. Org Lett 2019; 21:3635-3639. [DOI: 10.1021/acs.orglett.9b01057] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Munhyung Bae
- Natural Products Research Institute, College of Pharmacy, Seoul National University, Seoul 08826, Republic of Korea
| | - Joon Soo An
- Natural Products Research Institute, College of Pharmacy, Seoul National University, Seoul 08826, Republic of Korea
| | - Eun Seo Bae
- Natural Products Research Institute, College of Pharmacy, Seoul National University, Seoul 08826, Republic of Korea
| | - Jedo Oh
- Natural Products Research Institute, College of Pharmacy, Seoul National University, Seoul 08826, Republic of Korea
| | - So Hyun Park
- Natural Products Research Institute, College of Pharmacy, Seoul National University, Seoul 08826, Republic of Korea
| | - Yeonjung Lim
- Department of Biological Sciences, Inha University, Incheon 22212, Republic of Korea
| | - Yeon Hee Ban
- Department of Chemistry and Nanoscience, Ewha Womans University, Seoul 03760, Republic of Korea
| | - Yun Kwon
- Natural Products Research Institute, College of Pharmacy, Seoul National University, Seoul 08826, Republic of Korea
| | - Jang-Cheon Cho
- Department of Biological Sciences, Inha University, Incheon 22212, Republic of Korea
| | - Yeo Joon Yoon
- Department of Chemistry and Nanoscience, Ewha Womans University, Seoul 03760, Republic of Korea
| | - Sang Kook Lee
- Natural Products Research Institute, College of Pharmacy, Seoul National University, Seoul 08826, Republic of Korea
| | - Jongheon Shin
- Natural Products Research Institute, College of Pharmacy, Seoul National University, Seoul 08826, Republic of Korea
| | - Dong-Chan Oh
- Natural Products Research Institute, College of Pharmacy, Seoul National University, Seoul 08826, Republic of Korea
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Hong SH, Ban YH, Byun WS, Kim D, Jang YJ, An JS, Shin B, Lee SK, Shin J, Yoon YJ, Oh DC. Camporidines A and B: Antimetastatic and Anti-inflammatory Polyketide Alkaloids from a Gut Bacterium of Camponotus kiusiuensis. J Nat Prod 2019; 82:903-910. [PMID: 30912943 DOI: 10.1021/acs.jnatprod.8b01000] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/09/2023]
Abstract
Chemical studies of gut bacteria of the carpenter ant Camponotus kiusiuensis led to the discovery of two new alkaloids, camporidines A and B (1 and 2), from Streptomyces sp. STA1. The structures of 1 and 2 were established as new polyketide alkaloids bearing a piperidine-cyclopentene-epoxide 6/5/3 tricyclic system based on NMR spectroscopic and mass spectrometric analysis. The relative configurations of the camporidines were determined by their 1H-1H NOESY/ROESY and 1D NOE NMR correlations. The experimental ECD spectra of 1 and 2 were compared with their calculated ECD spectra to assign their absolute configurations. Camporidine A (1) displayed antimetastatic activity by suppression of cell invasion against the metastatic breast cancer cell line MDA-MB-231 and showed an anti-inflammatory effect by suppressing nitric oxide production induced by lipopolysaccharide. In addition, the putative biosynthetic gene cluster of the camporidines was identified, and the biosynthetic pathway of the camporidines was proposed based on bioinformatic analysis of the full genome of Streptomyces sp. STA1. Camporidines A and B (1 and 2) could be biosynthesized by a modular type I PKS containing an acyl transferase domain that accepts an unusual extender unit, which becomes the (C1'-C6') hexyl side chain. The post-PKS modification enzymes were predicted to perform an amination and an oxidation along with spontaneous Schiff base formation and generate the unique piperidine-cyclopentene-epoxide 6/5/3 tricyclic framework.
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Affiliation(s)
- Seong-Heon Hong
- Natural Products Research Institute, College of Pharmacy , Seoul National University , Seoul 08826 , Republic of Korea
| | - Yeon Hee Ban
- Department of Chemistry and Nanoscience , Ewha Womans University , Seoul 03760 , Republic of Korea
| | - Woong Sub Byun
- Natural Products Research Institute, College of Pharmacy , Seoul National University , Seoul 08826 , Republic of Korea
| | - Donghwa Kim
- Natural Products Research Institute, College of Pharmacy , Seoul National University , Seoul 08826 , Republic of Korea
| | - Yong-Joon Jang
- Natura Academia Research Center , Seoul 08826 , Republic of Korea
| | - Joon Soo An
- Natural Products Research Institute, College of Pharmacy , Seoul National University , Seoul 08826 , Republic of Korea
| | - Bora Shin
- Natural Products Research Institute, College of Pharmacy , Seoul National University , Seoul 08826 , Republic of Korea
| | - Sang Kook Lee
- Natural Products Research Institute, College of Pharmacy , Seoul National University , Seoul 08826 , Republic of Korea
| | - Jongheon Shin
- Natural Products Research Institute, College of Pharmacy , Seoul National University , Seoul 08826 , Republic of Korea
| | - Yeo Joon Yoon
- Department of Chemistry and Nanoscience , Ewha Womans University , Seoul 03760 , Republic of Korea
| | - Dong-Chan Oh
- Natural Products Research Institute, College of Pharmacy , Seoul National University , Seoul 08826 , Republic of Korea
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Shin YH, Beom JY, Chung B, Shin Y, Byun WS, Moon K, Bae M, Lee SK, Oh KB, Shin J, Yoon YJ, Oh DC. Bombyxamycins A and B, Cytotoxic Macrocyclic Lactams from an Intestinal Bacterium of the Silkworm Bombyx mori. Org Lett 2019; 21:1804-1808. [DOI: 10.1021/acs.orglett.9b00384] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/01/2023]
Affiliation(s)
- Yern-Hyerk Shin
- Natural Products Research Institute, College of Pharmacy, Seoul National University, Seoul 08826, Republic of Korea
| | - Ji Yoon Beom
- Department of Chemistry and Nanoscience, Ewha Womans University, Seoul 03760, Republic of Korea
| | - Beomkoo Chung
- Department of Agricultural Biotechnology, College of Agriculture & Life Sciences, Seoul National University, Seoul 08826, Republic of Korea
| | - Yoonho Shin
- Natural Products Research Institute, College of Pharmacy, Seoul National University, Seoul 08826, Republic of Korea
| | - Woong Sub Byun
- Natural Products Research Institute, College of Pharmacy, Seoul National University, Seoul 08826, Republic of Korea
| | - Kyuho Moon
- Natural Products Research Institute, College of Pharmacy, Seoul National University, Seoul 08826, Republic of Korea
| | - Munhyung Bae
- Natural Products Research Institute, College of Pharmacy, Seoul National University, Seoul 08826, Republic of Korea
| | - Sang Kook Lee
- Natural Products Research Institute, College of Pharmacy, Seoul National University, Seoul 08826, Republic of Korea
| | - Ki-Bong Oh
- Department of Agricultural Biotechnology, College of Agriculture & Life Sciences, Seoul National University, Seoul 08826, Republic of Korea
| | - Jongheon Shin
- Natural Products Research Institute, College of Pharmacy, Seoul National University, Seoul 08826, Republic of Korea
| | - Yeo Joon Yoon
- Department of Chemistry and Nanoscience, Ewha Womans University, Seoul 03760, Republic of Korea
| | - Dong-Chan Oh
- Natural Products Research Institute, College of Pharmacy, Seoul National University, Seoul 08826, Republic of Korea
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Park JW, Yoon YJ. Recent advances in the discovery and combinatorial biosynthesis of microbial 14-membered macrolides and macrolactones. J Ind Microbiol Biotechnol 2018; 46:445-458. [PMID: 30415291 DOI: 10.1007/s10295-018-2095-4] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2018] [Accepted: 10/19/2018] [Indexed: 01/05/2023]
Abstract
Macrolides, especially 14-membered macrolides, are a valuable group of antibiotics that originate from various microorganisms. In addition to their antibacterial activity, newly discovered 14-membered macrolides exhibit other therapeutic potentials, such as anti-proliferative and anti-protistal activities. Combinatorial biosynthetic approaches will allow us to create structurally diversified macrolide analogs, which are especially important during the emerging post-antibiotic era. This review focuses on recent advances in the discovery of new 14-membered macrolides (also including macrolactones) from microorganisms and the current status of combinatorial biosynthetic approaches, including polyketide synthase (PKS) and post-PKS tailoring pathways, and metabolic engineering for improved production together with heterologous production of 14-membered macrolides.
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Affiliation(s)
- Je Won Park
- School of Biosystem and Biomedical Science, Korea University, Seoul, 02841, Republic of Korea
| | - Yeo Joon Yoon
- Department of Chemistry and Nanoscience, Ewha Womans University, Seoul, 03760, Republic of Korea.
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39
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Lim JH, Hwang HH, Lee NJ, Lee JW, Seo EG, Son HB, Kim HJ, Yoon YJ, Park JW. Enhanced Biosynthesis of 2-Deoxy- scyllo-inosose in Metabolically Engineered Bacillus subtilis Recombinants. Front Microbiol 2018; 9:2333. [PMID: 30319595 PMCID: PMC6170601 DOI: 10.3389/fmicb.2018.02333] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/04/2018] [Accepted: 09/11/2018] [Indexed: 11/19/2022] Open
Abstract
2-Deoxy-scyllo-inosose (DOI) has been a valuable starting natural product for the manufacture of pharmaceuticals or chemical engineering resources such as pyranose catechol. DOI synthase, which uses glucose-6-phosphate (Glc6P) as a substrate for DOI biosynthesis, is indispensably involved in the initial stage of the biosynthesis of 2-deoxystreptamine-containing aminoglycoside antibiotics including butirosin, gentamicin, kanamycin, and tobramycin. A number of metabolically engineered recombinant strains of Bacillus subtilis were constructed here; either one or both genes pgi and pgcA that encode Glc6p isomerase and phosphoglucomutase, respectively, was (or were) disrupted in the sugar metabolic pathway of the host. After that, three different DOI synthase–encoding genes, which were artificially synthesized according to the codon preference of the B. subtilis host, were separately introduced into the engineered recombinants. The expression of a natural btrC gene, encoding DOI synthase in butirosin-producing B. circulans, in the heterologous host B. subtilis (BSDOI-2) generated approximately 2.3 g/L DOI, whereas expression of an artificially codon-optimized tobC gene, derived from tobramycin-producing Streptomyces tenebrarius, into the recombinant of B. subtilis (BSDOI-15) in which both genes pgi and pgcA are disrupted significantly enhanced the DOI titer: up to 37.2 g/L. Fed-batch fermentation by the BSDOI-15 recombinant using glycerol and glucose as a dual carbon source yielded the highest DOI titer (38.0 g/L). The development of engineered microbial cell factories empowered through convergence of metabolic engineering and synthetic biology should enable mass production of DOI. Thus, strain BSDOI-15 will surely be a useful contributor to the industrial manufacturing of various kinds of DOI-based pharmaceuticals and fine chemicals.
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Affiliation(s)
- Joo Hyun Lim
- Department of Integrated Biomedical and Life Sciences, Graduate School, Korea University, Seoul, South Korea
| | - Hyun Ha Hwang
- Department of Integrated Biomedical and Life Sciences, Graduate School, Korea University, Seoul, South Korea
| | - Na Joon Lee
- Department of Integrated Biomedical and Life Sciences, Graduate School, Korea University, Seoul, South Korea
| | - Jae Woo Lee
- Department of Integrated Biomedical and Life Sciences, Graduate School, Korea University, Seoul, South Korea
| | - Eun Gyo Seo
- Department of Integrated Biomedical and Life Sciences, Graduate School, Korea University, Seoul, South Korea
| | - Hye Bin Son
- Department of Integrated Biomedical and Life Sciences, Graduate School, Korea University, Seoul, South Korea
| | - Hye Ji Kim
- Department of Integrated Biomedical and Life Sciences, Graduate School, Korea University, Seoul, South Korea
| | - Yeo Joon Yoon
- Department of Chemistry and Nanoscience, Ewha Womans University, Seoul, South Korea
| | - Je Won Park
- Department of Integrated Biomedical and Life Sciences, Graduate School, Korea University, Seoul, South Korea.,School of Biosystem and Biomedical Science, Korea University, Seoul, South Korea
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40
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Kwon Y, Byun WS, Kim BY, Song MC, Bae M, Yoon YJ, Shin J, Lee SK, Oh DC. Depsidomycins B and C: New Cyclic Peptides from a Ginseng Farm Soil-Derived Actinomycete. Molecules 2018; 23:molecules23061266. [PMID: 29799492 PMCID: PMC6099933 DOI: 10.3390/molecules23061266] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2018] [Revised: 05/19/2018] [Accepted: 05/24/2018] [Indexed: 12/13/2022] Open
Abstract
LC/MS-based chemical profiling of a ginseng farm soil-derived actinomycete strain, Streptomyces sp. BYK1371, enabled the discovery of two new cyclic heptapeptides, depsidomycins B and C (1 and 2), each containing two piperazic acid units and a formyl group at their N-terminus. The structures of 1 and 2 were elucidated by a combination of spectroscopic and chemical analyses. These new compounds were determined to possess d-leucine, d-threonine, d-valine, and S-piperazic acid based on the advanced Marfey's method and a GITC (2,3,4,6-tetra-O-acetyl-β-d-glucopyranosyl isothiocyanate) derivatization of their hydrolysates, followed by LC/MS analysis. Depsidomycins B and C displayed significant antimetastatic activities against metastatic breast cancer cells (MDA-MB-231).
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Affiliation(s)
- Yun Kwon
- Natural Products Research Institute, College of Pharmacy, Seoul National University, Seoul 08826, Republic of Korea.
| | - Woong Sub Byun
- Natural Products Research Institute, College of Pharmacy, Seoul National University, Seoul 08826, Republic of Korea.
| | - Byung-Yong Kim
- ChunLab, Inc., JW TOWER, Seocho-gu, Seoul 06725, Republic of Korea.
| | - Myoung Chong Song
- Department of Chemistry and Nanoscience, Ewha Womans University, Seoul 03760, Republic of Korea.
| | - Munhyung Bae
- Natural Products Research Institute, College of Pharmacy, Seoul National University, Seoul 08826, Republic of Korea.
| | - Yeo Joon Yoon
- Department of Chemistry and Nanoscience, Ewha Womans University, Seoul 03760, Republic of Korea.
| | - Jongheon Shin
- Natural Products Research Institute, College of Pharmacy, Seoul National University, Seoul 08826, Republic of Korea.
| | - Sang Kook Lee
- Natural Products Research Institute, College of Pharmacy, Seoul National University, Seoul 08826, Republic of Korea.
| | - Dong-Chan Oh
- Natural Products Research Institute, College of Pharmacy, Seoul National University, Seoul 08826, Republic of Korea.
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An YJ, Rowland SE, Na JH, Spigolon D, Hong SK, Yoon YJ, Lee JH, Robb FT, Cha SS. Structural and mechanistic characterization of an archaeal-like chaperonin from a thermophilic bacterium. Nat Commun 2017; 8:827. [PMID: 29018216 PMCID: PMC5635000 DOI: 10.1038/s41467-017-00980-z] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2017] [Accepted: 08/08/2017] [Indexed: 11/13/2022] Open
Abstract
The chaperonins (CPNs) are megadalton sized hollow complexes with two cavities that open and close to encapsulate non-native proteins. CPNs are assigned to two sequence-related groups that have distinct allosteric mechanisms. In Group I CPNs a detachable co-chaperone, GroES, closes the chambers whereas in Group II a built-in lid closes the chambers. Group I CPNs have a bacterial ancestry, whereas Group II CPNs are archaeal in origin. Here we describe open and closed crystal structures representing a new phylogenetic branch of CPNs. These Group III CPNs are divergent in sequence and structure from extant CPNs, but are closed by a built-in lid like Group II CPNs. A nucleotide-sensing loop, present in both Group I and Group II CPNs, is notably absent. We identified inter-ring pivot joints that articulate during ring closure. These Group III CPNs likely represent a relic from the ancestral CPN that formed distinct bacterial and archaeal branches. Chaperonins (CPNs) are ATP-dependent protein-folding machines. Here the authors present the open and closed crystal structures of a Group III CPN from the thermophilic bacterium Carboxydothermus hydrogenoformans, discuss its mechanism and structurally compare it with Group I and II CPNs.
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Affiliation(s)
- Young Jun An
- Marine Biotechnology Research Center, Korea Institute of Ocean Science and Technology, Ansan, 15627, Republic of Korea
| | - Sara E Rowland
- Department of Microbiology and Immunology, University of Maryland, Baltimore, MD, 21201, USA.,Institute of Marine and Environmental Technology, Baltimore, MD, 21201, USA
| | - Jung-Hyun Na
- Department of Chemistry & Nanoscience, Ewha Womans University, Seoul, 03760, Republic of Korea
| | - Dario Spigolon
- Department of Microbiology and Immunology, University of Maryland, Baltimore, MD, 21201, USA.,Institute of Marine and Environmental Technology, Baltimore, MD, 21201, USA
| | - Seung Kon Hong
- Department of Chemistry & Nanoscience, Ewha Womans University, Seoul, 03760, Republic of Korea
| | - Yeo Joon Yoon
- Department of Chemistry & Nanoscience, Ewha Womans University, Seoul, 03760, Republic of Korea
| | - Jung-Hyun Lee
- Marine Biotechnology Research Center, Korea Institute of Ocean Science and Technology, Ansan, 15627, Republic of Korea
| | - Frank T Robb
- Department of Microbiology and Immunology, University of Maryland, Baltimore, MD, 21201, USA. .,Institute of Marine and Environmental Technology, Baltimore, MD, 21201, USA.
| | - Sun-Shin Cha
- Department of Chemistry & Nanoscience, Ewha Womans University, Seoul, 03760, Republic of Korea.
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Lee KJ, Jung JS, Mo YM, Yoon YJ, Kim SI. Isolation of Antagonistic Microbes for Biological Control of Ginseng Root Rot. Am J Transl Res 2017. [DOI: 10.1055/s-0037-1608502] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
Affiliation(s)
- KJ Lee
- Ginseng & Medicinal Plants Research Institute, Gangwon Agricultural Research & Extension Services, Cheorwon, Korea, Republic of (South)
| | - JS Jung
- Ginseng & Medicinal Plants Research Institute, Gangwon Agricultural Research & Extension Services, Cheorwon, Korea, Republic of (South)
| | - YM Mo
- Ginseng & Medicinal Plants Research Institute, Gangwon Agricultural Research & Extension Services, Cheorwon, Korea, Republic of (South)
| | - YJ Yoon
- Ginseng & Medicinal Plants Research Institute, Gangwon Agricultural Research & Extension Services, Cheorwon, Korea, Republic of (South)
| | - SI Kim
- Ginseng & Medicinal Plants Research Institute, Gangwon Agricultural Research & Extension Services, Cheorwon, Korea, Republic of (South)
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Yoon YJ, Jeong HN, Jung JS, Lee KJ, Mo YM, Kim SI. Growth characteristics and yield of ginseng (Panax ginseng C.A. Meyer) by irrigation set point in rain shelter house. Am J Transl Res 2017. [DOI: 10.1055/s-0037-1608503] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
Affiliation(s)
- YJ Yoon
- Ginseng & Medicinal Plants Research Institute, Gangwon Agricultural Research & Extension Services, Cheorwon, Korea, Republic of (South)
| | - HN Jeong
- Ginseng & Medicinal Plants Research Institute, Gangwon Agricultural Research & Extension Services, Cheorwon, Korea, Republic of (South)
| | - JS Jung
- Ginseng & Medicinal Plants Research Institute, Gangwon Agricultural Research & Extension Services, Cheorwon, Korea, Republic of (South)
| | - KJ Lee
- Ginseng & Medicinal Plants Research Institute, Gangwon Agricultural Research & Extension Services, Cheorwon, Korea, Republic of (South)
| | - YM Mo
- Ginseng & Medicinal Plants Research Institute, Gangwon Agricultural Research & Extension Services, Cheorwon, Korea, Republic of (South)
| | - SI Kim
- Ginseng & Medicinal Plants Research Institute, Gangwon Agricultural Research & Extension Services, Cheorwon, Korea, Republic of (South)
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Le TC, Yim CY, Park S, Katila N, Yang I, Song MC, Yoon YJ, Choi DY, Choi H, Nam SJ, Fenical W. Lodopyridones B and C from a marine sediment-derived bacterium Saccharomonospora sp. Bioorg Med Chem Lett 2017; 27:3123-3126. [DOI: 10.1016/j.bmcl.2017.05.035] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2017] [Revised: 05/09/2017] [Accepted: 05/11/2017] [Indexed: 11/30/2022]
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Kim E, Song MC, Kim MS, Beom JY, Jung JA, Cho HS, Yoon YJ. One-Pot Combinatorial Biosynthesis of Glycosylated Anthracyclines by Cocultivation of Streptomyces Strains Producing Aglycones and Nucleotide Deoxysugars. ACS Comb Sci 2017; 19:262-270. [PMID: 28191923 DOI: 10.1021/acscombsci.6b00194] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/05/2023]
Abstract
Anthracyclines, such as doxorubicin, are effective anticancer drugs composed of a tetracyclic polyketide aglycone and one or more deoxysugar moieties, which play a critical role in their biological activity. A facile one-pot combinatorial biosynthetic system was developed for the generation of a range of glycosylated derivatives of anthracyclines. Cocultivation of Streptomyces venezuelae mutants producing two anthracycline aglycones with eight different nucleotide deoxysugar-producing S. venezuelae mutants that coexpress a substrate-flexible glycosyltransferase led to the generation of 16 aklavinone or ε-rhodomycinone glycosides containing diverse deoxysugar moieties, seven of which are new. This demonstrates the potential of the one-pot combinatorial biosynthetic system based on cocultivation as a facile biological tool capable of combining diverse aglycones and deoxysugars to generate structurally diverse polyketides carrying engineered sugars for drug discovery and development.
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Affiliation(s)
- Eunji Kim
- Department of Chemistry and
Nanoscience, Ewha Womans University, Seoul, Republic of Korea
| | - Myoung Chong Song
- Department of Chemistry and
Nanoscience, Ewha Womans University, Seoul, Republic of Korea
| | - Myoun Su Kim
- Department of Chemistry and
Nanoscience, Ewha Womans University, Seoul, Republic of Korea
| | - Ji Yoon Beom
- Department of Chemistry and
Nanoscience, Ewha Womans University, Seoul, Republic of Korea
| | - Jin A Jung
- Department of Chemistry and
Nanoscience, Ewha Womans University, Seoul, Republic of Korea
| | - Hang Soo Cho
- Department of Chemistry and
Nanoscience, Ewha Womans University, Seoul, Republic of Korea
| | - Yeo Joon Yoon
- Department of Chemistry and
Nanoscience, Ewha Womans University, Seoul, Republic of Korea
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46
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Park JW, Ban YH, Nam SJ, Cha SS, Yoon YJ. Biosynthetic pathways of aminoglycosides and their engineering. Curr Opin Biotechnol 2017; 48:33-41. [PMID: 28365471 DOI: 10.1016/j.copbio.2017.03.019] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2017] [Revised: 02/27/2017] [Accepted: 03/15/2017] [Indexed: 11/30/2022]
Abstract
Despite decades long clinical usage, aminoglycosides still remain a valuable pharmaceutical source for fighting Gram-negative bacterial pathogens, and their newly identified bioactivities are also renewing interest in this old class of antibiotics. As Nature's gift, some aminoglycosides possess natural defensive structural elements that can circumvent drug resistance mechanisms. Thus, a detailed understanding of aminoglycoside biosynthesis will enable us to apply Nature's biosynthetic strategy towards expanding structural diversity in order to produce novel and more robust aminoglycoside analogs. The engineered biosynthesis of novel aminoglycosides is required not only to develop effective therapeutics against the emerging 'superbugs' but also to reinvigorate antibiotic lead discovery in readiness for the emerging post-antibiotic era.
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Affiliation(s)
- Je Won Park
- School of Biosystem and Biomedical Science, Korea University, Seoul 02841, Republic of Korea
| | - Yeon Hee Ban
- Department of Chemistry and Nanoscience, Ewha Womans University, Seoul 03760, Republic of Korea
| | - Sang-Jip Nam
- Department of Chemistry and Nanoscience, Ewha Womans University, Seoul 03760, Republic of Korea
| | - Sun-Shin Cha
- Department of Chemistry and Nanoscience, Ewha Womans University, Seoul 03760, Republic of Korea
| | - Yeo Joon Yoon
- Department of Chemistry and Nanoscience, Ewha Womans University, Seoul 03760, Republic of Korea.
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47
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Hoang NH, Huong NL, Kim B, Sohng JK, Yoon YJ, Park JW. Istamycin aminoglycosides profiling and their characterization in Streptomyces tenjimariensis ATCC 31603 culture using high-performance liquid chromatography with tandem mass spectrometry. J Sep Sci 2016; 39:4712-4722. [PMID: 27778478 DOI: 10.1002/jssc.201600925] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/20/2016] [Revised: 10/12/2016] [Accepted: 10/22/2016] [Indexed: 11/08/2022]
Abstract
A high-performance liquid chromatography with electrospray ionization ion trap tandem mass spectrometry method was developed and validated for the robust profiling and characterization of biosynthetic congeners in the 2-deoxy-aminocyclitol istamycin pathway, from the fermentation broth of Streptomyces tenjimariensis ATCC 31603. Gradient elution on an Acquity CSH C18 column was performed with a gradient of 5 mM aqueous pentafluoropropionic acid and 50% acetonitrile. Sixteen natural istamycin congeners were profiled and quantified in descending order; istamycin A, istamycin B, istamycin A0 , istamycin B0 , istamycin B1 , istamycin A1 , istamycin C, istamycin A2 , istamycin C1 , istamycin C0 , istamycin X0 , istamycin A3 , istamycin Y0 , istamycin B3 , and istamycin FU-10 plus istamycin AP. In addition, a total of five sets of 1- or 3-epimeric pairs were chromatographically separated using a macrocyclic glycopeptide-bonded chiral column. The lower limit of quantification of istamycin-A present in S. tenjimariensis fermentation was estimated to be 2.2 ng/mL. The simultaneous identification of a wide range of 2-deoxy-aminocyclitol-type istamycin profiles from bacterial fermentation was determined for the first time by employing high-performance liquid chromatography with tandem mass spectrometry analysis and the separation of istamycin epimers.
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Affiliation(s)
- Nguyen Huu Hoang
- Department of Biotechnology Convergent Pharmaceutical Engineering, SunMoon University, Chungnam, Republic of Korea
| | - Nguyen Lan Huong
- Department of Biotechnology Convergent Pharmaceutical Engineering, SunMoon University, Chungnam, Republic of Korea
| | - Byul Kim
- School of Biosystem and Biomedical Science, Korea University, Seoul, Republic of Korea
| | - Jae Kyung Sohng
- Department of Biotechnology Convergent Pharmaceutical Engineering, SunMoon University, Chungnam, Republic of Korea
| | - Yeo Joon Yoon
- Department of Chemistry and Nano Sciences, Ewha Womans University, Seoul, Republic of Korea
| | - Je Won Park
- School of Biosystem and Biomedical Science, Korea University, Seoul, Republic of Korea
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Abstract
PikD is a widely known pathway-specific regulator for controlling pikromycin production in Streptomyces venezuelae ATCC 15439, which is a representative of the large ATP-binding regulator of the LuxR family (LAL) in Streptomyces sp. RapH and FkbN also belong to the LAL family of transcriptional regulators, which show greatest homology with the ATP-binding motif and helix-turn-helix DNA-binding motif of PikD. Overexpression of pikD and heterologous expression of rapH and fkbN led to enhanced production of pikromycin by approximately 1.8-, 1.6-, and 1.6-fold in S. venezuelae, respectively. Cross-complementation of rapH and fkbN in the pikD deletion mutant (ΔpikD) restored pikromycin and derived macrolactone production. Overall, these results show that heterologous expression of rapH and fkbN leads to the overproduction of pikromycin and its congeners from the pikromycin biosynthetic pathway in S. venezuelae, and they have the same functionality as the pathwayspecific transcriptional activator for the pikromycin biosynthetic pathway in the ΔpikD strain. These results also show extensive "cross-communication" between pathway-specific regulators of streptomycetes and suggest revision of the current paradigm for pathwayspecific versus global regulation of secondary metabolism in Streptomyces species.
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Affiliation(s)
- SangJoon Mo
- Clinical Trial Institute, Biosafety and Validation Center, Dankook University, Choenan 31116, Republic of Korea
| | - Yeo Joon Yoon
- Department of Chemistry and Nano Science, Ewha Womans University, Seoul 03760, Republic of Korea
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Yoo YJ, Kim H, Park SR, Yoon YJ. An overview of rapamycin: from discovery to future perspectives. J Ind Microbiol Biotechnol 2016; 44:537-553. [PMID: 27613310 DOI: 10.1007/s10295-016-1834-7] [Citation(s) in RCA: 65] [Impact Index Per Article: 8.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2016] [Accepted: 08/22/2016] [Indexed: 12/17/2022]
Abstract
Rapamycin is an immunosuppressive metabolite produced from several actinomycete species. Besides its immunosuppressive activity, rapamycin and its analogs have additional therapeutic potentials, including antifungal, antitumor, neuroprotective/neuroregenerative, and lifespan extension activities. The core structure of rapamycin is derived from (4R,5R)-4,5-dihydrocyclohex-1-ene-carboxylic acid that is extended by polyketide synthase. The resulting linear polyketide chain is cyclized by incorporating pipecolate and further decorated by post-PKS modification enzymes. Herein, we review the discovery and biological activities of rapamycin as well as its mechanism of action, mechanistic target, biosynthesis, and regulation. In addition, we introduce the many efforts directed at enhancing the production of rapamycin and generating diverse analogs and also explore future perspectives in rapamycin research. This review will also emphasize the remarkable pilot studies on the biosynthesis and production improvement of rapamycin by Dr. Demain, one of the world's distinguished scientists in industrial microbiology and biotechnology.
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Affiliation(s)
- Young Ji Yoo
- Department of Chemistry and Nanoscience, Ewha Womans University, Seoul, 120-750, Republic of Korea
| | - Hanseong Kim
- Department of Biological Chemistry, University of Michigan, Ann Arbor, MI, 48109, USA
| | - Sung Ryeol Park
- Natural Products Discovery Institute, The Baruch S. Blumberg Institute, Hepatitis B Foundation, Doylestown, PA, 18902, USA.
| | - Yeo Joon Yoon
- Department of Chemistry and Nanoscience, Ewha Womans University, Seoul, 120-750, Republic of Korea.
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50
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Kim E, Song MC, Kim MS, Beom JY, Lee EY, Kim DM, Nam SJ, Yoon YJ. Characterization of the Two Methylation Steps Involved in the Biosynthesis of Mycinose in Tylosin. J Nat Prod 2016; 79:2014-2021. [PMID: 27453999 DOI: 10.1021/acs.jnatprod.6b00267] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/06/2023]
Abstract
The S-adenosyl-l-methionine-dependent O-methyltransferases TylE and TylF catalyze the last two methylation reactions in the tylosin biosynthetic pathway of Streptomyces fradiae. It has long been known that the TylE-catalyzed C2‴-O-methylation of the 6-deoxy-d-allose bound to demethylmacrocin or demethyllactenocin precedes the TylF-catalyzed C3‴-O-methylation of the d-javose (C2‴-O-methylated 6-deoxy-d-allose) attached to macrocin or lactenocin. This study reveals the unexpected substrate promiscuity of TylE and TylF responsible for the biosynthesis of d-mycinose (C3‴-O-methylated d-javose) in tylosin through the identification of a new minor intermediate 2‴-O-demethyldesmycosin (2; 3‴-methyl-demethyllactenocin), which lacks a 2‴-O-methyl group on the mycinose moiety of desmycosin, along with 2‴-O-demethyltylosin (1; 3‴-methyl-demethylmacrocin) that was previously detected from the S. fradiae mutant containing a mutation in the tylE gene. These results unveil the unique substrate flexibility of TylE and TylF and demonstrate their potential for the engineered biosynthesis of novel glycosylated macrolide derivatives.
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Affiliation(s)
- Eunji Kim
- Department of Chemistry and Nanoscience, Ewha Womans University , Seoul 03760, Republic of Korea
| | - Myoung Chong Song
- Department of Chemistry and Nanoscience, Ewha Womans University , Seoul 03760, Republic of Korea
| | - Myoun Su Kim
- Department of Chemistry and Nanoscience, Ewha Womans University , Seoul 03760, Republic of Korea
| | - Ji Yoon Beom
- Department of Chemistry and Nanoscience, Ewha Womans University , Seoul 03760, Republic of Korea
| | - Eun Yeol Lee
- Department of Chemical Engineering, Kyung Hee University , Gyeonggi-do 17104, Republic of Korea
| | - Dong-Myung Kim
- Department of Chemical Engineering and Applied Chemistry, Chungnam National University , Daejeon 34134, Republic of Korea
| | - Sang-Jip Nam
- Department of Chemistry and Nanoscience, Ewha Womans University , Seoul 03760, Republic of Korea
| | - Yeo Joon Yoon
- Department of Chemistry and Nanoscience, Ewha Womans University , Seoul 03760, Republic of Korea
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