51
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Kramer GJ, Pimentel-Elardo S, Nodwell JR. Dual-PKS Cluster for Biosynthesis of a Light-Induced Secondary Metabolite Found from Genome Sequencing of Hyphodiscus hymeniophilus Fungus. Chembiochem 2020; 21:2116-2120. [PMID: 32314858 PMCID: PMC7496686 DOI: 10.1002/cbic.201900689] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2019] [Revised: 03/17/2020] [Indexed: 11/15/2022]
Abstract
Filamentous fungi are known producers of important secondary metabolites. In spite of this, the majority of these organisms have not been studied at the genome level, leaving many of the bioactive molecules they produce undiscovered. In this study, we explore the secondary metabolite potential of an understudied fungus, Hyphodiscus hymeniophilus. By sequencing and assembling the first genome from this genus, we show that this fungus has genes for at least 20 natural products and that many of these products are likely novel. One of these metabolites is identified: a new, red-pigmented member of the azaphilone class, hyphodiscorubrin. We show that this metabolite is only produced when the fungus is grown in the light. Furthermore, the biosynthetic gene cluster of hyphodiscorubrin is identified though homology to other known azaphilone producing clusters.
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Affiliation(s)
- Glenna J Kramer
- Department of Biochemistry, University of Toronto, MaRS Centre, West Tower, 661 University Avenue, Toronto, ON, M5G 1M1, Canada
| | - Sheila Pimentel-Elardo
- Department of Biochemistry, University of Toronto, MaRS Centre, West Tower, 661 University Avenue, Toronto, ON, M5G 1M1, Canada
| | - Justin R Nodwell
- Department of Biochemistry, University of Toronto, MaRS Centre, West Tower, 661 University Avenue, Toronto, ON, M5G 1M1, Canada
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52
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Huang L, Wang SL, Xu YL, Yu HF, Zhan ZJ, Shan WG, Wang JW, Ying YM. Induced Production of Tremulane Sesquiterpenoids in Bjerkandera adusta by Chemical Epigenetic Modification. Chem Nat Compd 2020. [DOI: 10.1007/s10600-020-03140-w] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
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53
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Lin Z, Nielsen J, Liu Z. Bioprospecting Through Cloning of Whole Natural Product Biosynthetic Gene Clusters. Front Bioeng Biotechnol 2020; 8:526. [PMID: 32582659 PMCID: PMC7290108 DOI: 10.3389/fbioe.2020.00526] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2020] [Accepted: 05/04/2020] [Indexed: 12/24/2022] Open
Abstract
Since the discovery of penicillin, natural products and their derivatives have been a valuable resource for drug discovery. With recent development of genome mining approaches in the post-genome era, a great number of natural product biosynthetic gene clusters (BGCs) have been identified and these can potentially be exploited for the discovery of novel natural products that can find application as pharmaceuticals. Since many BGCs are silent or do not express in native hosts under laboratory conditions, heterologous expression of BGCs in genetically tractable hosts becomes an attractive route to activate these BGCs to discover the corresponding products. Here, we highlight recent achievements in cloning and discovery of natural product biosynthetic pathways via intact BGC capturing, and discuss the prospects of high-throughput and multiplexed cloning of rational-designed gene clusters in the future.
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Affiliation(s)
- Zhenquan Lin
- Beijing Advanced Innovation Center for Soft Matter Science and Engineering, College of Life Science and Technology, Beijing University of Chemical Technology, Beijing, China
| | - Jens Nielsen
- Beijing Advanced Innovation Center for Soft Matter Science and Engineering, College of Life Science and Technology, Beijing University of Chemical Technology, Beijing, China.,Department of Biology and Biological Engineering, Chalmers University of Technology, Gothenburg, Sweden.,Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Lyngby, Denmark.,BioInnovation Institute, Copenhagen, Denmark
| | - Zihe Liu
- Beijing Advanced Innovation Center for Soft Matter Science and Engineering, College of Life Science and Technology, Beijing University of Chemical Technology, Beijing, China
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54
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Núñez-Montero K, Quezada-Solís D, Khalil ZG, Capon RJ, Andreote FD, Barrientos L. Genomic and Metabolomic Analysis of Antarctic Bacteria Revealed Culture and Elicitation Conditions for the Production of Antimicrobial Compounds. Biomolecules 2020; 10:E673. [PMID: 32349314 PMCID: PMC7277857 DOI: 10.3390/biom10050673] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2020] [Revised: 04/15/2020] [Accepted: 04/21/2020] [Indexed: 01/08/2023] Open
Abstract
Concern about finding new antibiotics against drug-resistant pathogens is increasing every year. Antarctic bacteria have been proposed as an unexplored source of bioactive metabolites; however, most biosynthetic gene clusters (BGCs) producing secondary metabolites remain silent under common culture conditions. Our work aimed to characterize elicitation conditions for the production of antibacterial secondary metabolites from 34 Antarctic bacterial strains based on MS/MS metabolomics and genome mining approaches. Bacterial strains were cultivated under different nutrient and elicitation conditions, including the addition of lipopolysaccharide (LPS), sodium nitroprusside (SNP), and coculture. Metabolomes were obtained by HPLC-QTOF-MS/MS and analyzed through molecular networking. Antibacterial activity was determined, and seven strains were selected for genome sequencing and analysis. Biosynthesis pathways were activated by all the elicitation treatments, which varies among strains and dependents of culture media. Increased antibacterial activity was observed for a few strains and addition of LPS was related with inhibition of Gram-negative pathogens. Antibiotic BGCs were found for all selected strains and the expressions of putative actinomycin, carotenoids, and bacillibactin were characterized by comparison of genomic and metabolomic data. This work established the use of promising new elicitors for bioprospection of Antarctic bacteria and highlights the importance of new "-omics" comparative approaches for drug discovery.
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Affiliation(s)
- Kattia Núñez-Montero
- Laboratory of Molecular Applied Biology, Center of Excellence in Translational Medicine, Universidad de La Frontera, Avenida Alemania 0458, Temuco 4810296, Chile; (K.N.-M.); (D.Q.-S.)
- Scientific and Technological Bioresource Nucleus (BIOREN), Universidad de La Frontera, Temuco 4811230, Chile
- Biotechnology Investigation Center, Department of Biology, Instituto Tecnológico de Costa Rica, Cartago 159-7050, Costa Rica
| | - Damián Quezada-Solís
- Laboratory of Molecular Applied Biology, Center of Excellence in Translational Medicine, Universidad de La Frontera, Avenida Alemania 0458, Temuco 4810296, Chile; (K.N.-M.); (D.Q.-S.)
| | - Zeinab G. Khalil
- Institute for Molecular Bioscience, The University of Queensland, St Lucia, QLD 4072, Australia; (Z.G.K.); (R.J.C.)
| | - Robert J. Capon
- Institute for Molecular Bioscience, The University of Queensland, St Lucia, QLD 4072, Australia; (Z.G.K.); (R.J.C.)
| | - Fernando D. Andreote
- Department of Soil Science, “Luiz de Queiroz” College of Agriculture, University of São Paulo, Piracicaba, SP 13418-900, Brazil;
| | - Leticia Barrientos
- Laboratory of Molecular Applied Biology, Center of Excellence in Translational Medicine, Universidad de La Frontera, Avenida Alemania 0458, Temuco 4810296, Chile; (K.N.-M.); (D.Q.-S.)
- Scientific and Technological Bioresource Nucleus (BIOREN), Universidad de La Frontera, Temuco 4811230, Chile
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55
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Song Z, Ma Z, Bechthold A, Yu X. Effects of addition of elicitors on rimocidin biosynthesis in Streptomyces rimosus M527. Appl Microbiol Biotechnol 2020; 104:4445-4455. [PMID: 32221690 DOI: 10.1007/s00253-020-10565-4] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2020] [Revised: 03/10/2020] [Accepted: 03/20/2020] [Indexed: 01/25/2023]
Abstract
The polyene macrolide rimocidin, produced by Streptomyces rimosus M527, is highly effective against a broad range of fungal plant pathogens, but at low yields. Elicitation is an effective method of stimulating the yield of bioactive secondary metabolites. In this study, the biomass and filtrate of a culture broth of Escherichia coli JM109, Bacillus subtilis WB600, Saccharomyces cerevisiae, and Fusarium oxysporum f. sp. cucumerinum were employed as elicitors to promote rimocidin production in S. rimosus M527. Adding culture broth and biomass of S. cerevisiae (A3) and F. oxysporum f. sp. cucumerinum (B4) resulted in an increase of rimocidin production by 51.2% and 68.3% respectively compared with the production under normal conditions in 5-l fermentor. In addition, quantitative RT-PCR analysis revealed that the transcriptions of ten genes (rimA to rimK) located in the gene cluster involved in rimocidin biosynthesis in A3 or B4 elicitation experimental group were all higher than those of a control group. Using a β-glucuronidase (GUS) reporter system, GUS enzyme activity assay, and Western blot analysis, we discovered that elicitation of A3 or B4 increased protein synthesis in S. rimosus M527. These results demonstrate that the addition of elicitors is a useful approach to improve rimocidin production.Key Points • An effective strategy for enhancing rimocidin production in S. rimosus M527 is demonstrated. • Overproduction of rimocidin is a result of higher expressed structural genes followed by an increase in protein synthesis.
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Affiliation(s)
- Zhangqing Song
- Zhejiang Provincial Key Laboratory of Biometrology and Inspection & Quarantine, College of Life Sciences, China Jiliang University, Xueyuan Street, Xiasha Higher Education District, Hangzhou, 310018, Zhejiang Province, People's Republic of China
| | - Zheng Ma
- Zhejiang Provincial Key Laboratory of Biometrology and Inspection & Quarantine, College of Life Sciences, China Jiliang University, Xueyuan Street, Xiasha Higher Education District, Hangzhou, 310018, Zhejiang Province, People's Republic of China.
| | - Andreas Bechthold
- Institute for Pharmaceutical Sciences, Pharmaceutical Biology and Biotechnology, University of Freiburg, 79104, Freiburg, Germany
| | - Xiaoping Yu
- Zhejiang Provincial Key Laboratory of Biometrology and Inspection & Quarantine, College of Life Sciences, China Jiliang University, Xueyuan Street, Xiasha Higher Education District, Hangzhou, 310018, Zhejiang Province, People's Republic of China
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56
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Epigenetic modulation of secondary metabolite profiles in Aspergillus calidoustus and Aspergillus westerdijkiae through histone deacetylase (HDAC) inhibition by vorinostat. J Antibiot (Tokyo) 2020; 73:410-413. [DOI: 10.1038/s41429-020-0286-5] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2019] [Revised: 01/10/2020] [Accepted: 01/28/2020] [Indexed: 12/20/2022]
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57
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Ying YM, Li L, Yu HF, Xu YL, Huang L, Mao W, Tong CP, Zhang ZD, Zhan ZJ, Zhang Y. Induced production of a new polyketide in Penicillium sp. HS-11 by chemical epigenetic manipulation. Nat Prod Res 2020; 35:3446-3451. [PMID: 31899961 DOI: 10.1080/14786419.2019.1709190] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/25/2022]
Abstract
Chemical investigation into the culture broth of the plant endophyte Penicillium sp. HS-11 in the modified Martin's medium supplemented with subemylanilide hydroxamic acid (SAHA), a well-known histone deacetylase (HDACs) inhibitor, led to the isolation and identification of two induced products 4-epipenicillone B (1) and (R)-(+)-chrysogine (2). 4-epipenicillone B (1) was obtained as a new compound whose structure was elucidated by comprehensive spectroscopic methods including 1 D/2D NMR, HRESMS, and quantum chemistry calculations including DFT GIAO 13C NMR and ECD calculation. Acquisition of 4-epipenicillone B (1) enriched the chemical diversities of fungal natural products possessing a tricyclo [5.3.1.03,8] undecane skeleton. The cytotoxic activity of 1 was also evaluated.
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Affiliation(s)
- You-Min Ying
- College of Pharmaceutical Science, Zhejiang University of Technology, Hangzhou, P. R. China
| | - Ling Li
- College of Pharmaceutical Science, Zhejiang University of Technology, Hangzhou, P. R. China
| | - Hang-Fei Yu
- College of Pharmaceutical Science, Zhejiang University of Technology, Hangzhou, P. R. China
| | - Yi-Lian Xu
- College of Pharmaceutical Science, Zhejiang University of Technology, Hangzhou, P. R. China
| | - Lu Huang
- College of Pharmaceutical Science, Zhejiang University of Technology, Hangzhou, P. R. China.,Department of Quality Management, Hangzhou Zhongmeihuadong China Pharmaceutical Co., Ltd, Hangzhou, P. R. China
| | - Wei Mao
- Department of Quality Management, Hangzhou Zhongmeihuadong China Pharmaceutical Co., Ltd, Hangzhou, P. R. China
| | - Cui-Ping Tong
- Department of Quality Management, Hangzhou Zhongmeihuadong China Pharmaceutical Co., Ltd, Hangzhou, P. R. China
| | - Zhi-Dong Zhang
- Xinjiang Laboratory of Special Environmental Microbiology, Institute of Microbiology, Xinjiang Academy of Agricultural Sciences, Urumqi, Xinjiang, P. R. China
| | - Zha-Jun Zhan
- College of Pharmaceutical Science, Zhejiang University of Technology, Hangzhou, P. R. China
| | - Yun Zhang
- Department of Quality Management, Hangzhou Zhongmeihuadong China Pharmaceutical Co., Ltd, Hangzhou, P. R. China
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58
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Hutchings MI, Truman AW, Wilkinson B. Antibiotics: past, present and future. Curr Opin Microbiol 2019; 51:72-80. [PMID: 31733401 DOI: 10.1016/j.mib.2019.10.008] [Citation(s) in RCA: 816] [Impact Index Per Article: 163.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2019] [Accepted: 10/18/2019] [Indexed: 12/12/2022]
Abstract
The first antibiotic, salvarsan, was deployed in 1910. In just over 100 years antibiotics have drastically changed modern medicine and extended the average human lifespan by 23 years. The discovery of penicillin in 1928 started the golden age of natural product antibiotic discovery that peaked in the mid-1950s. Since then, a gradual decline in antibiotic discovery and development and the evolution of drug resistance in many human pathogens has led to the current antimicrobial resistance crisis. Here we give an overview of the history of antibiotic discovery, the major classes of antibiotics and where they come from. We argue that the future of antibiotic discovery looks bright as new technologies such as genome mining and editing are deployed to discover new natural products with diverse bioactivities. We also report on the current state of antibiotic development, with 45 drugs currently going through the clinical trials pipeline, including several new classes with novel modes of action that are in phase 3 clinical trials. Overall, there are promising signs for antibiotic discovery, but changes in financial models are required to translate scientific advances into clinically approved antibiotics.
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Affiliation(s)
- Matthew I Hutchings
- School of Biological Sciences, University of East Anglia, Norwich Research Park, Norwich, NR4 7TJ, UK.
| | - Andrew W Truman
- Department of Molecular Microbiology, John Innes Centre, Norwich Research Park, Norwich, NR4 7UH, UK.
| | - Barrie Wilkinson
- Department of Molecular Microbiology, John Innes Centre, Norwich Research Park, Norwich, NR4 7UH, UK.
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59
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Niu G, Li W. Next-Generation Drug Discovery to Combat Antimicrobial Resistance. Trends Biochem Sci 2019; 44:961-972. [PMID: 31256981 DOI: 10.1016/j.tibs.2019.05.005] [Citation(s) in RCA: 36] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2019] [Revised: 05/30/2019] [Accepted: 05/31/2019] [Indexed: 12/16/2022]
Abstract
The widespread emergence of antibiotic-resistant pathogens poses a severe threat to public health. This problem becomes even worse with a coincident decline in the supply of new antibiotics. Conventional bioactivity-guided natural product discovery has failed to meet the urgent need for new antibiotics, largely due to limited resources and high rediscovery rates. Recent advances in cultivation techniques, analytical technologies, and genomics-based approaches have greatly expanded our access to previously underexploited microbial sources. These strategies will enable us to access new reservoirs of microorganisms and unleash their chemical potentials, thus opening new opportunities for the discovery of next-generation drugs to address the growing concerns of antimicrobial resistance.
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Affiliation(s)
- Guoqing Niu
- Biotechnology Research Center, Southwest University, Chongqing 400715, China; Chongqing Key Laboratory of Plant Resource Conservation and Germplasm Innovation, Southwest University, Chongqing 400715, China; State Cultivation Base of Crop Stress Biology for Southern Mountainous Land, Academy of Agricultural Sciences, Southwest University, Chongqing 400715, China.
| | - Wenli Li
- Key Laboratory of Marine Drugs, Ministry of Education of China, School of Medicine and Pharmacy, Ocean University of China, Qingdao 266003, China; Laboratory for Marine Drugs and Bioproducts, Qingdao National Laboratory for Marine Science and Technology, Qingdao 266237, China.
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