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A Abdelhakim I, Futamura Y, Asami Y, Hanaki H, Kito N, Masuda S, Shibata A, Muranaka A, Koshino H, Shirasu K, Osada H, Ishikawa J, Takahashi S. Expression of Syo_1.56 SARP Regulator Unveils Potent Elasnin Derivatives with Antibacterial Activity. JOURNAL OF NATURAL PRODUCTS 2024; 87:1459-1470. [PMID: 38652684 DOI: 10.1021/acs.jnatprod.4c00259] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/25/2024]
Abstract
Actinomycetes are prolific producers of natural products, particularly antibiotics. However, a significant proportion of its biosynthetic gene clusters (BGCs) remain silent under typical laboratory conditions. This limits the effectiveness of conventional isolation methods for the discovery of novel natural products. Genetic interventions targeting the activation of silent gene clusters are necessary to address this challenge. Streptomyces antibiotic regulatory proteins (SARPs) act as cluster-specific activators and can be used to target silent BGCs for the discovery of new antibiotics. In this study, the expression of a previously uncharacterized SARP protein, Syo_1.56, in Streptomyces sp. RK18-A0406 significantly enhanced the production of known antimycins and led to the discovery of 12 elasnins (1-12), 10 of which were novel. The absolute stereochemistry of elasnin A1 was assigned for the first time to be 6S. Unexpectedly, Syo_1.56 seems to function as a pleiotropic rather than cluster-specific SARP regulator, with the capability of co-regulating two distinct biosynthetic pathways, simultaneously. All isolated elasnins were active against wild-type and methicillin-resistant Staphylococcus aureus with IC50 values of 0.5-20 μg/mL, some of which (elasnins A1, B2, and C1 and proelasnins A1, and C1) demonstrated moderate to strong antimalarial activities against Plasmodium falciparum 3D7. Elasnins A1, B3, and C1 also showed in vitro inhibition of the metallo-β-lactamase responsible for the development of highly antibiotic-resistant bacterial strains.
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Affiliation(s)
- Islam A Abdelhakim
- Natural Product Biosynthesis Research Unit, RIKEN CSRS, Wako, Saitama 351-0198, Japan
- Department of Pharmacognosy, Faculty of Pharmacy, Assiut University, Assiut 71515, Egypt
| | - Yushi Futamura
- Chemical Resource Development Research Unit and Drug Discovery Chemical Bank Unit, RIKEN CSRS, Wako, Saitama 351-0198, Japan
| | - Yukihiro Asami
- O̅mura Satoshi Memorial Institute, Kitasato University, Tokyo 108-8641, Japan
| | - Hideaki Hanaki
- O̅mura Satoshi Memorial Institute, Kitasato University, Tokyo 108-8641, Japan
| | - Naoko Kito
- Natural Product Biosynthesis Research Unit, RIKEN CSRS, Wako, Saitama 351-0198, Japan
| | - Sachiko Masuda
- Plant Immunity Research Group, RIKEN CSRS, Yokohama 230-0045, Japan
| | - Arisa Shibata
- Plant Immunity Research Group, RIKEN CSRS, Yokohama 230-0045, Japan
| | - Atsuya Muranaka
- Molecular Structure Characterization Unit, RIKEN CSRS, Wako, Saitama 351-0198, Japan
| | - Hiroyuki Koshino
- Molecular Structure Characterization Unit, RIKEN CSRS, Wako, Saitama 351-0198, Japan
| | - Ken Shirasu
- Plant Immunity Research Group, RIKEN CSRS, Yokohama 230-0045, Japan
| | - Hiroyuki Osada
- Chemical Resource Development Research Unit and Drug Discovery Chemical Bank Unit, RIKEN CSRS, Wako, Saitama 351-0198, Japan
| | - Jun Ishikawa
- National Institute of Infectious Diseases, Tokyo, 162-8640, Japan
| | - Shunji Takahashi
- Natural Product Biosynthesis Research Unit, RIKEN CSRS, Wako, Saitama 351-0198, Japan
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Takahashi S. Studies on Streptomyces sp. SN-593: reveromycin biosynthesis, β-carboline biomediator activating LuxR family regulator, and construction of terpenoid biosynthetic platform. J Antibiot (Tokyo) 2022; 75:432-444. [PMID: 35778609 DOI: 10.1038/s41429-022-00539-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2022] [Revised: 06/08/2022] [Accepted: 06/09/2022] [Indexed: 11/09/2022]
Abstract
Streptomyces represents an important reservoir for biologically active natural products. Understanding the biosynthetic mechanism and the mode of gene expression is important for enhanced metabolite production and evaluation of biological activities. This review provides an overview of biosynthetic studies investigating reveromycin and β-carboline biomediators that enhanced the production of reveromycin in Streptomyces sp. SN-593 through activation of the LuxR family regulator. Furthermore, based on the optimal expression of a pathway specific regulator controlling the mevalonate pathway gene cluster, Streptomyces sp. SN-593 was developed as a platform for terpenoid compounds mass production.
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Affiliation(s)
- Shunji Takahashi
- Natural Product Biosynthesis Research Unit, RIKEN Centre for Sustainable Resource Science, 2-1 Hirosawa, Wako, Saitama, 351-0198, Japan.
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A Abdelhakim I, Bin Mahmud F, Motoyama T, Futamura Y, Takahashi S, Osada H. Dihydrolucilactaene, a Potent Antimalarial Compound from Fusarium sp. RK97-94. JOURNAL OF NATURAL PRODUCTS 2022; 85:63-69. [PMID: 34949088 DOI: 10.1021/acs.jnatprod.1c00677] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/14/2023]
Abstract
A recently discovered secondary metabolism regulator, NPD938, was used to alter the secondary metabolite profile in Fusarium sp. RK97-94. Three lucilactaene analogues were detected via UPLC-ESI-MS analysis in NPD938-treated culture. The three metabolites were successfully purified and identified as dihydroNG391 (1), dihydrolucilactaene (2), and 13α-hydroxylucilactaene (3) via extensive spectroscopic analyses. DihydroNG391 (1) exhibited weak in vitro antimalarial activity (IC50 = 62 μM). In contrast, dihydrolucilactaene (2) and 13α-hydroxylucilactaene (3) showed very potent antimalarial activity (IC50 = 0.0015 and 0.68 μM, respectively). These findings provide insight into the structure-activity relationship of lucilactaene and its analogues as antimalarial lead compounds.
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Affiliation(s)
- Islam A Abdelhakim
- Graduate School of Science and Engineering, Saitama University, Sakura, Saitama 338-8570, Japan
- Department of Pharmacognosy, Faculty of Pharmacy, Assiut University, Assiut 71515, Egypt
- Chemical Biology Research Group, RIKEN CSRS, Wako, Saitama 351-0198, Japan
- Natural Product Biosynthesis Research Unit, RIKEN CSRS, Wako, Saitama 351-0198, Japan
| | - Fauze Bin Mahmud
- Chemical Biology Research Group, RIKEN CSRS, Wako, Saitama 351-0198, Japan
- Institute for Research in Molecular Medicine, Universiti Sains Malaysia, Penang 11800, Malaysia
- Faculty of Science and Natural Resources, Universiti Malaysia Sabah, Sabah 88400, Malaysia
| | - Takayuki Motoyama
- Chemical Biology Research Group, RIKEN CSRS, Wako, Saitama 351-0198, Japan
| | - Yushi Futamura
- Chemical Biology Research Group, RIKEN CSRS, Wako, Saitama 351-0198, Japan
| | - Shunji Takahashi
- Natural Product Biosynthesis Research Unit, RIKEN CSRS, Wako, Saitama 351-0198, Japan
| | - Hiroyuki Osada
- Chemical Biology Research Group, RIKEN CSRS, Wako, Saitama 351-0198, Japan
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Covington BC, Xu F, Seyedsayamdost MR. A Natural Product Chemist's Guide to Unlocking Silent Biosynthetic Gene Clusters. Annu Rev Biochem 2021; 90:763-788. [PMID: 33848426 PMCID: PMC9148385 DOI: 10.1146/annurev-biochem-081420-102432] [Citation(s) in RCA: 54] [Impact Index Per Article: 18.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
Microbial natural products have provided an important source of therapeutic leads and motivated research and innovation in diverse scientific disciplines. In recent years, it has become evident that bacteria harbor a large, hidden reservoir of potential natural products in the form of silent or cryptic biosynthetic gene clusters (BGCs). These can be readily identified in microbial genome sequences but do not give rise to detectable levels of a natural product. Herein, we provide a useful organizational framework for the various methods that have been implemented for interrogating silent BGCs. We divide all available approaches into four categories. The first three are endogenous strategies that utilize the native host in conjunction with classical genetics, chemical genetics, or different culture modalities. The last category comprises expression of the entire BGC in a heterologous host. For each category, we describe the rationale, recent applications, and associated advantages and limitations.
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Affiliation(s)
- Brett C Covington
- Department of Chemistry, Princeton University, Princeton, New Jersey 08544, USA; ,
| | - Fei Xu
- Institute of Pharmaceutical Biotechnology and Department of Gastroenterology of the Second Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou 310058, China;
| | - Mohammad R Seyedsayamdost
- Department of Chemistry, Princeton University, Princeton, New Jersey 08544, USA; ,
- Department of Molecular Biology, Princeton University, New Jersey 08544, USA
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Rawa MSA, Nogawa T, Okano A, Futamura Y, Nakamura T, Wahab HA, Osada H. A new peptaibol, RK-026A, from the soil fungus Trichoderma sp. RK10-F026 by culture condition-dependent screening. Biosci Biotechnol Biochem 2021; 85:69-76. [DOI: 10.1093/bbb/zbaa051] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2020] [Accepted: 09/30/2020] [Indexed: 12/28/2022]
Abstract
Abstract
A new peptaibol, RK-026A (1) was isolated from a fungus, Trichoderma sp. RK10-F026, along with atroviridin B (2), alamethicin II (3), and polysporin B (4) as a cytotoxic compound, which was selected by principal component analysis of the MS data from 5 different culture conditions. The structure of 1 was determined as a new atroviridin B derivative containing Glu at the 18th residue instead of Gln by NMR and HR-MS analyses including the investigation of detailed MS/MS fragmentations. 1 showed cytotoxicity toward K562 leukemia cells at an IC50 value of 4.1 µm.
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Affiliation(s)
- Mira Syahfriena Amir Rawa
- Chemical Biology Research Group, RIKEN Center for Sustainable Resource Science, Wako, Saitama, Japan
- School of Pharmaceutical Sciences, Universiti Sains Malaysia, Minden, Penang, Malaysia
| | - Toshihiko Nogawa
- Chemical Biology Research Group, RIKEN Center for Sustainable Resource Science, Wako, Saitama, Japan
| | - Akiko Okano
- Chemical Biology Research Group, RIKEN Center for Sustainable Resource Science, Wako, Saitama, Japan
| | - Yushi Futamura
- Chemical Biology Research Group, RIKEN Center for Sustainable Resource Science, Wako, Saitama, Japan
| | - Takemichi Nakamura
- Molecular Structure Characterization Unit, RIKEN Center for Sustainable Resource Science, Wako, Saitama, Japan
| | - Habibah A Wahab
- School of Pharmaceutical Sciences, Universiti Sains Malaysia, Minden, Penang, Malaysia
| | - Hiroyuki Osada
- Chemical Biology Research Group, RIKEN Center for Sustainable Resource Science, Wako, Saitama, Japan
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Panthee S, Kito N, Hayashi T, Shimizu T, Ishikawa J, Hamamoto H, Osada H, Takahashi S. β-carboline chemical signals induce reveromycin production through a LuxR family regulator in Streptomyces sp. SN-593. Sci Rep 2020; 10:10230. [PMID: 32576869 PMCID: PMC7311520 DOI: 10.1038/s41598-020-66974-y] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2019] [Accepted: 05/27/2020] [Indexed: 12/21/2022] Open
Abstract
Actinomycetes bacteria produce diverse bioactive molecules that are useful as drug seeds. To improve their yield, researchers often optimize the fermentation medium. However, exactly how the extracellular chemicals present in the medium activate secondary metabolite gene clusters remains unresolved. BR-1, a β-carboline compound, was recently identified as a chemical signal that enhanced reveromycin A production in Streptomyces sp. SN-593. Here we show that BR-1 specifically bound to the transcriptional regulator protein RevU in the reveromycin A biosynthetic gene cluster, and enhanced RevU binding to its promoter. RevU belongs to the LuxR family regulator that is widely found in bacteria. Interestingly, BR-1 and its derivatives also enhanced the production of secondary metabolites in other Streptomyces species. Although LuxR-N-acyl homoserine lactone systems have been characterized in Gram-negative bacteria, we revealed LuxR-β-carboline system in Streptomyces sp. SN-593 for the production of secondary metabolites. This study might aid in understanding hidden chemical communication by β-carbolines.
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Affiliation(s)
- Suresh Panthee
- RIKEN Center for Sustainable Resource Science, Natural Product Biosynthesis Research Unit, Wako, Hirosawa 2-1, 351-0198, Saitama, Japan.,Teikyo University Institute of Medical Mycology, Otsuka 359, Hachioji, Tokyo, Japan
| | - Naoko Kito
- RIKEN Center for Sustainable Resource Science, Natural Product Biosynthesis Research Unit, Wako, Hirosawa 2-1, 351-0198, Saitama, Japan
| | - Teruo Hayashi
- RIKEN Center for Sustainable Resource Science, Chemical Biology Research Group, Wako, Hirosawa 2-1, 351-0198, Saitama, Japan
| | - Takeshi Shimizu
- RIKEN Center for Sustainable Resource Science, Chemical Biology Research Group, Wako, Hirosawa 2-1, 351-0198, Saitama, Japan
| | - Jun Ishikawa
- Department of Bioactive Molecules, National Institute of Infectious Diseases, Toyama 1-23-1, Shinjuku, Tokyo, 162-8640, Japan
| | - Hiroshi Hamamoto
- Teikyo University Institute of Medical Mycology, Otsuka 359, Hachioji, Tokyo, Japan
| | - Hiroyuki Osada
- RIKEN Center for Sustainable Resource Science, Chemical Biology Research Group, Wako, Hirosawa 2-1, 351-0198, Saitama, Japan.
| | - Shunji Takahashi
- RIKEN Center for Sustainable Resource Science, Natural Product Biosynthesis Research Unit, Wako, Hirosawa 2-1, 351-0198, Saitama, Japan.
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