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Zou Y, Shi J, Sun JL, Li LY, Yan ZY, Guo ZK, Jiao RH. Maduraflavacins A-E, Unusual Phenyl Polyene Metabolites Produced by a Rare Marine-Derived Actinomadura sp. JOURNAL OF NATURAL PRODUCTS 2024. [PMID: 39318040 DOI: 10.1021/acs.jnatprod.4c00836] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 09/26/2024]
Abstract
Phenyl polyenes comprise a small family of bacterial natural products with broad and potent bioactivities, primarily found in actinobacteria. Here we report the discovery of five new phenyl polyene metabolites, maduraflavacins A-E (1-5), from a rare, marine-derived actinobacteria strain Actinomadura glauciflava NA03286. The structures of these natural products were determined by NMR spectroscopy, HRESIMS, LC-MS/MS, and chemical derivatization. All of these new maduraflavacins feature methyl substitutions at the polyene side chain, and maduraflavacins A-C (1-3) possessed a 1-N-β-d-glucosamine-(3 → 1)-O-β-d-glucopyranosyl-(3 → 1)-O-β-d-glucopyranosyl-(6 → 1)-O-β-d-glucopyranoside tetrasaccharide moiety via an amido linkage with a phenyl polyene skeleton. Compounds 1 and 2 showed weak antibacterial activities against the Gram-positive bacteria Staphylococcus aureus Sau 16339 and Micrococcus luteus, respectively.
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Affiliation(s)
- Yan Zou
- State Key Laboratory of Pharmaceutical Biotechnology, Institute of Functional Biomolecules, Chemistry and Biomedicine Innovation Center (ChemBIC), School of Life Sciences, Nanjing University, Nanjing 210023, China
| | - Jing Shi
- State Key Laboratory of Pharmaceutical Biotechnology, Institute of Functional Biomolecules, Chemistry and Biomedicine Innovation Center (ChemBIC), School of Life Sciences, Nanjing University, Nanjing 210023, China
| | - Jia Lin Sun
- State Key Laboratory of Pharmaceutical Biotechnology, Institute of Functional Biomolecules, Chemistry and Biomedicine Innovation Center (ChemBIC), School of Life Sciences, Nanjing University, Nanjing 210023, China
| | - Ling Yu Li
- State Key Laboratory of Pharmaceutical Biotechnology, Institute of Functional Biomolecules, Chemistry and Biomedicine Innovation Center (ChemBIC), School of Life Sciences, Nanjing University, Nanjing 210023, China
| | - Zhang Yuan Yan
- State Key Laboratory of Pharmaceutical Biotechnology, Institute of Functional Biomolecules, Chemistry and Biomedicine Innovation Center (ChemBIC), School of Life Sciences, Nanjing University, Nanjing 210023, China
| | - Zhi Kai Guo
- Hainan Key Laboratory of Tropical Microbe Resources, Institute of Tropical Bioscience and Biotechnology, Chinese Academy of Tropical Agricultural Sciences & Key Laboratory for Biology and Genetic Resources of Tropical Crops of Hainan Province, Hainan Institute for Tropical Agricultural Resources, Haikou 571101, China
| | - Rui Hua Jiao
- State Key Laboratory of Pharmaceutical Biotechnology, Institute of Functional Biomolecules, Chemistry and Biomedicine Innovation Center (ChemBIC), School of Life Sciences, Nanjing University, Nanjing 210023, China
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Rong X, Zhang L, He W, Guo Z, Lv H, Bai J, Yu L, Zhang L, Zhang T. Exploration of diverse secondary metabolites from Penicillium brasilianum by co-culturing with Armillaria mellea. Appl Microbiol Biotechnol 2024; 108:462. [PMID: 39264460 PMCID: PMC11393291 DOI: 10.1007/s00253-024-13282-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2024] [Revised: 08/07/2024] [Accepted: 08/14/2024] [Indexed: 09/13/2024]
Abstract
Bioinformatic analysis revealed that the genomes of ubiquitous Penicillium spp. might carry dozens of biosynthetic gene clusters (BGCs), yet many clusters have remained uncharacterized. In this study, a detailed investigation of co-culture fermentation including the basidiomycete Armillaria mellea CPCC 400891 and the P. brasilianum CGMCC 3.4402 enabled the isolation of five new compounds including two bisabolene-type sesquiterpenes (arpenibisabolanes A and B), two carotane-type sesquiterpenes (arpenicarotanes A and B), and one polyketide (arpenichorismite A) along with seven known compounds. The assignments of their structures were deduced by the extensive analyses of detailed spectroscopic data, electronic circular dichroism spectra, together with delimitation of the biogenesis. Most new compounds were not detected in monocultures under the same fermentation conditions. Arpenibisabolane A represents the first example of a 6/5-fused bicyclic bisabolene. The bioassay of these five new compounds exhibited no cytotoxic activities in vitro against three human cancer cell lines (A549, MCF-7, and HepG2). Moreover, sequence alignments and bioinformatic analysis to other metabolic pathways, two BGCs including Pb-bis and Pb-car, responsible for generating sesquiterpenoids from co-culture were identified, respectively. Furthermore, based on the chemical structures and deduced gene functions of the two clusters, a hypothetic metabolic pathway for biosynthesizing induced sesquiterpenoids was proposed. These results demonstrated that the co-culture approach would facilitate bioprospecting for new metabolites even from the well-studied microbes. Our findings would provide opportunities for further understanding of the biosynthesis of intriguing sesquiterpenoids via metabolic engineering strategies. KEY POINTS: • Penicillium and Armillaria co-culture facilitates the production of diverse secondary metabolites • Arpenibisabolane A represents the first example of 6/5-fused bicyclic bisabolenes • A hypothetic metabolic pathway for biosynthesizing induced sesquiterpenoids was proposed.
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Affiliation(s)
- Xiaoting Rong
- Institute of Medicinal Biotechnology, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, 100050, China
| | - Lihua Zhang
- National Key Laboratory of Chinese Medicine Modernization, State Key Laboratory of Component-Based Chinese Medicine, Institute of Traditional Chinese Medicine, Tianjin University of Traditional Chinese Medicine, Tianjin, 301617, China
| | - Wenni He
- Institute of Medicinal Biotechnology, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, 100050, China
| | - Zhe Guo
- Institute of Medicinal Biotechnology, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, 100050, China
| | - Hui Lv
- Institute of Medicinal Biotechnology, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, 100050, China
| | - Jinglin Bai
- Institute of Medicinal Biotechnology, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, 100050, China
| | - Liyan Yu
- Institute of Medicinal Biotechnology, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, 100050, China.
| | - Lixin Zhang
- State Key Laboratory of Bioreactor Engineering, East China University of Science & Technology, Shanghai, 200237, China.
| | - Tao Zhang
- Institute of Medicinal Biotechnology, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, 100050, China.
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Karimian S, Farahmandzad N, Mohammadipanah F. Manipulation and epigenetic control of silent biosynthetic pathways in actinobacteria. World J Microbiol Biotechnol 2024; 40:65. [PMID: 38191749 DOI: 10.1007/s11274-023-03861-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2023] [Accepted: 11/29/2023] [Indexed: 01/10/2024]
Abstract
Most biosynthetic gene clusters (BGCs) of Actinobacteria are either silent or expressed less than the detectable level. The non-genetic approaches including biological interactions, chemical agents, and physical stresses that can be used to awaken silenced pathways are compared in this paper. These non-genetic induction strategies often need screening approaches, including one strain many compounds (OSMAC), reporter-guided mutant selection, and high throughput elicitor screening (HiTES) have been developed. Different types of genetic manipulations applied in the induction of cryptic BGCs of Actinobacteria can be categorized as genome-wide pleiotropic and targeted approaches like manipulation of global regulatory systems, modulation of regulatory genes, ribosome and engineering of RNA polymerase or phosphopantheteine transferases. Targeted approaches including genome editing by CRISPR, mutation in transcription factors and modification of BGCs promoters, inactivation of the highly expressed biosynthetic pathways, deleting the suppressors or awakening the activators, heterologous expression, or refactoring of gene clusters can be applied for activation of pathways which are predicted to synthesize new bioactive structures in genome mining studies of Acinobacteria. In this review, the challenges and advantages of employing these approaches in induction of Actinobacteria BGCs are discussed. Further, novel natural products needed as drug for pharmaceutical industry or as biofertilizers in agricultural industry can be discovered even from known species of Actinobactera by the innovative approaches of metabolite biosynthesis elicitation.
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Affiliation(s)
- Sanaz Karimian
- Department of Biotechnology, Faculty of Biological Science, Alzahra University, Tehran, Iran
| | - Navid Farahmandzad
- Department of Biosystems Engineering, Auburn university, Auburn, AL 36849, USA
- Pharmaceutical Biotechnology Lab, School of Biology and Center of Excellence in Phylogeny of Living Organisms, College of Science, University of Tehran, Tehran, 14155-6455, Iran
| | - Fatemeh Mohammadipanah
- Pharmaceutical Biotechnology Lab, School of Biology and Center of Excellence in Phylogeny of Living Organisms, College of Science, University of Tehran, Tehran, 14155-6455, Iran.
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Santamaría RI, Martínez-Carrasco A, Tormo JR, Martín J, Genilloud O, Reyes F, Díaz M. Interactions of Different Streptomyces Species and Myxococcus xanthus Affect Myxococcus Development and Induce the Production of DK-Xanthenes. Int J Mol Sci 2023; 24:15659. [PMID: 37958645 PMCID: PMC10649082 DOI: 10.3390/ijms242115659] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2023] [Revised: 10/19/2023] [Accepted: 10/24/2023] [Indexed: 11/15/2023] Open
Abstract
The co-culturing of microorganisms is a well-known strategy to study microbial interactions in the laboratory. This approach facilitates the identification of new signals and molecules produced by one species that affects other species' behavior. In this work, we have studied the effects of the interaction of nine Streptomyces species (S. albidoflavus, S. ambofaciens, S. argillaceus, S. griseus, S. lividans, S. olivaceus, S. parvulus, S. peucetius, and S. rochei) with the predator bacteria Myxococcus xanthus, five of which (S. albidoflavus, S. griseus, S. lividans, S. olivaceus, and S. argillaceus) induce mound formation of M. xanthus on complex media (Casitone Yeast extract (CYE) and Casitone tris (CTT); media on which M. xanthus does not form these aggregates under normal culture conditions. An in-depth study on S. griseus-M. xanthus interactions (the Streptomyces strain producing the strongest effect) has allowed the identification of two siderophores produced by S. griseus, demethylenenocardamine and nocardamine, responsible for this grouping effect over M. xanthus. Experiments using pure commercial nocardamine and different concentrations of FeSO4 show that iron depletion is responsible for the behavior of M. xanthus. Additionally, it was found that molecules, smaller than 3 kDa, produced by S. peucetius can induce the production of DK-xanthenes by M. xanthus.
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Affiliation(s)
- Ramón I. Santamaría
- Instituto de Biología Funcional y Genómica (IBFG), Departamento de Microbiología y Genética, Consejo Superior de Investigaciones Científicas (CSIC), Universidad de Salamanca, C/Zacarías González, nº 2, 37007 Salamanca, Spain;
| | - Ana Martínez-Carrasco
- Instituto de Biología Funcional y Genómica (IBFG), Departamento de Microbiología y Genética, Consejo Superior de Investigaciones Científicas (CSIC), Universidad de Salamanca, C/Zacarías González, nº 2, 37007 Salamanca, Spain;
| | - José R. Tormo
- Fundación MEDINA, Centro de Excelencia en Investigación de Medicamentos Innovadores en Andalucía, Avda. del Conocimiento 34, 18016 Granada, Spain; (J.R.T.); (J.M.); (O.G.); (F.R.)
| | - Jesús Martín
- Fundación MEDINA, Centro de Excelencia en Investigación de Medicamentos Innovadores en Andalucía, Avda. del Conocimiento 34, 18016 Granada, Spain; (J.R.T.); (J.M.); (O.G.); (F.R.)
| | - Olga Genilloud
- Fundación MEDINA, Centro de Excelencia en Investigación de Medicamentos Innovadores en Andalucía, Avda. del Conocimiento 34, 18016 Granada, Spain; (J.R.T.); (J.M.); (O.G.); (F.R.)
| | - Fernando Reyes
- Fundación MEDINA, Centro de Excelencia en Investigación de Medicamentos Innovadores en Andalucía, Avda. del Conocimiento 34, 18016 Granada, Spain; (J.R.T.); (J.M.); (O.G.); (F.R.)
| | - Margarita Díaz
- Instituto de Biología Funcional y Genómica (IBFG), Departamento de Microbiología y Genética, Consejo Superior de Investigaciones Científicas (CSIC), Universidad de Salamanca, C/Zacarías González, nº 2, 37007 Salamanca, Spain;
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Liu W, Li E, Liu L, Tian F, Luo X, Cai Y, Wang J, Jin X. Antifungal activity of compounds from Gordonia sp. WA8-44 isolated from the gut of Periplaneta americana and molecular docking studies. Heliyon 2023; 9:e17777. [PMID: 37539250 PMCID: PMC10395128 DOI: 10.1016/j.heliyon.2023.e17777] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2023] [Revised: 06/13/2023] [Accepted: 06/28/2023] [Indexed: 08/05/2023] Open
Abstract
Invasive fungal infections are on the rise, leading to a continuous demand for antifungal antibiotics. Rare actinomycetes have been shown to contain a variety of interesting compounds worth exploring. In this study, 15 strains of rare actinobacterium Gordonia were isolated from the gut of Periplaneta americana and screened for their anti-fungal activity against four human pathogenic fungi. Strain WA8-44 was found to exhibit significant anti-fungal activity and was selected for bioactive compound production, separation, purification, and characterization. Three anti-fungal compounds, Collismycin A, Actinomycin D, and Actinomycin X2, were isolated from the fermentation broth of Gordonia strain WA8-44. Of these, Collismycin A was isolated and purified from the secondary metabolites of Gordonia for the first time, and its anti-filamentous fungi activity was firstly identified in this study. Molecular docking was carried out to determine their hypothetical binding affinities against nine target proteins of Candida albicans. Chitin Synthase 2 was found to be the most preferred antimicrobial protein target for Collismycin A, while 1,3-Beta-Glucanase was the most preferred anti-fungal protein target for Actinomycin D and Actinomycin X2. ADMET prediction revealed that Collismycin A has favorable oral bioavailability and little toxicity, making it a potential candidate for development as an orally active medication.
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Affiliation(s)
- Wenbin Liu
- Guangdong Provincial Key Laboratory of Pharmaceutical Bioactive Substances, Guangdong Pharmaceutical University, Guangzhou 510006, PR China
- School of Basic Medical Sciences, Guangdong Pharmaceutical University, Guangzhou 510006, PR China
| | - Ertong Li
- Guangdong Provincial Key Laboratory of Pharmaceutical Bioactive Substances, Guangdong Pharmaceutical University, Guangzhou 510006, PR China
- School of Basic Medical Sciences, Guangdong Pharmaceutical University, Guangzhou 510006, PR China
| | - Lingyan Liu
- School of Pharmacy, Xi'an Medical College, Xi'an 710300, PR China
| | - Fangyuan Tian
- Guangdong Provincial Key Laboratory of Pharmaceutical Bioactive Substances, Guangdong Pharmaceutical University, Guangzhou 510006, PR China
- School of Basic Medical Sciences, Guangdong Pharmaceutical University, Guangzhou 510006, PR China
| | - Xiongming Luo
- Guangdong Provincial Key Laboratory of Pharmaceutical Bioactive Substances, Guangdong Pharmaceutical University, Guangzhou 510006, PR China
- School of Basic Medical Sciences, Guangdong Pharmaceutical University, Guangzhou 510006, PR China
| | - Yanqu Cai
- Guangdong Provincial Key Laboratory of Pharmaceutical Bioactive Substances, Guangdong Pharmaceutical University, Guangzhou 510006, PR China
- School of Basic Medical Sciences, Guangdong Pharmaceutical University, Guangzhou 510006, PR China
| | - Jie Wang
- Guangdong Provincial Key Laboratory of Pharmaceutical Bioactive Substances, Guangdong Pharmaceutical University, Guangzhou 510006, PR China
- School of Basic Medical Sciences, Guangdong Pharmaceutical University, Guangzhou 510006, PR China
| | - Xiaobao Jin
- Guangdong Provincial Key Laboratory of Pharmaceutical Bioactive Substances, Guangdong Pharmaceutical University, Guangzhou 510006, PR China
- School of Basic Medical Sciences, Guangdong Pharmaceutical University, Guangzhou 510006, PR China
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6
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El-Hawary SS, Hassan MHA, Hudhud AO, Abdelmohsen UR, Mohammed R. Elicitation for activation of the actinomycete genome's cryptic secondary metabolite gene clusters. RSC Adv 2023; 13:5778-5795. [PMID: 36816076 PMCID: PMC9932869 DOI: 10.1039/d2ra08222e] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/25/2022] [Accepted: 01/28/2023] [Indexed: 02/18/2023] Open
Abstract
This review summarizes the recent advances in the elicitation approaches used to activate the actinomycete genome's cryptic secondary metabolite gene clusters and shows the diversity of natural products obtained by various elicitation methods up to June 2022, such as co-cultivation of actinomycetes with actinomycetes, other non-actinomycete bacteria, fungi, cell-derived components, and/or algae. Chemical elicitation and molecular elicitation as transcription factor decoys, engineering regulatory genes, the promoter replacement strategy, global regulatory genes, and reporter-guided mutant selection were also reported. For researchers interested in this field, this review serves as a valuable resource for the latest studies and references.
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Affiliation(s)
- Seham S El-Hawary
- Department of Pharmacognosy, Faculty of Pharmacy, Cairo University Cairo Egypt
| | - Marwa H A Hassan
- Department of Pharmacognosy, Faculty of Pharmacy, Beni-Suef University Beni-Suef 62511 Egypt
| | - Ahmed O Hudhud
- Department of Pharmacognosy, Faculty of Pharmacy, Merit University Sohag 82511 Egypt
| | - Usama Ramadan Abdelmohsen
- Department of Pharmacognosy, Faculty of Pharmacy, Minia University Minia 61519 Egypt
- Department of Pharmacognosy, Faculty of Pharmacy, Deraya University New Minia 61111 Egypt
| | - Rabab Mohammed
- Department of Pharmacognosy, Faculty of Pharmacy, Beni-Suef University Beni-Suef 62511 Egypt
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Sánchez-Suárez J, Díaz L, Coy-Barrera E, Villamil L. Specialized Metabolism of Gordonia Genus: An Integrated Survey on Chemodiversity Combined with a Comparative Genomics-Based Analysis. BIOTECH 2022; 11:53. [PMID: 36412754 PMCID: PMC9680422 DOI: 10.3390/biotech11040053] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/03/2022] [Revised: 11/07/2022] [Accepted: 11/08/2022] [Indexed: 11/23/2022] Open
Abstract
Members of the phylum Actinomycetota (formerly Actinobacteria) have historically been the most prolific providers of small bioactive molecules. Although the genus Streptomyces is the best-known member for this issue, other genera, such as Gordonia, have shown interesting potential in their specialized metabolism. Thus, we combined herein the result of a comprehensive literature survey on metabolites derived from Gordonia strains with a comparative genomic analysis to examine the potential of the specialized metabolism of the genus Gordonia. Thirty Gordonia-derived compounds of different classes were gathered (i.e., alkaloids, amides, phenylpropanoids, and terpenoids), exhibiting antimicrobial and cytotoxic activities, and several were also isolated from Streptomyces (e.g., actinomycin, nocardamin, diolmycin A1). With the genome data, we estimated an open pan-genome of 57,901 genes, most of them being part of the cloud genome. Regarding the BGCs content, 531 clusters were found, including Terpenes, RiPP-like, and NRPS clusters as the most frequent clusters. Our findings demonstrated that Gordonia is a poorly studied genus in terms of its specialized metabolism production and potential applications. Nevertheless, given their BGCs content, Gordonia spp. are a valuable biological resource that could expand the chemical spectrum of the phylum Actinomycetota, involving novel BGCs for inspiring innovative outlines for synthetic biology and further use in biotechnological initiatives. Therefore, further studies and more efforts should be made to explore different environments and evaluate other bioactivities.
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Affiliation(s)
- Jeysson Sánchez-Suárez
- Doctoral Program in Biosciences, School of Engineering, Universidad de La Sabana, Chía 250001, Colombia
- Bioprospecting Research Group, School of Engineering, Universidad de La Sabana, Chía 250001, Colombia
| | - Luis Díaz
- Doctoral Program in Biosciences, School of Engineering, Universidad de La Sabana, Chía 250001, Colombia
- Bioprospecting Research Group, School of Engineering, Universidad de La Sabana, Chía 250001, Colombia
| | - Ericsson Coy-Barrera
- Bioorganic Chemistry Laboratory, Universidad Militar Nueva Granada, Cajicá 250247, Colombia
| | - Luisa Villamil
- Doctoral Program in Biosciences, School of Engineering, Universidad de La Sabana, Chía 250001, Colombia
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Li J, Zhang L, Yao G, Zhu L, Lin J, Wang C, Du B, Ding Y, Mei X. Synergistic effect of co-culture rhizosphere Streptomyces: A promising strategy to enhance antimicrobial activity and plant growth-promoting function. Front Microbiol 2022; 13:976484. [PMID: 36033877 PMCID: PMC9403869 DOI: 10.3389/fmicb.2022.976484] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2022] [Accepted: 07/21/2022] [Indexed: 11/13/2022] Open
Abstract
Rhizosphere Streptomyces is one of the important types of rhizosphere microorganisms that plays an important role in promoting plant growth and controlling plant diseases to maintain agricultural ecosystem balance and green ecological agriculture development as beneficial bacteria. Microbial co-culture simulates the complex biocommunity in nature, which has more advantages than the monoculture with a synergistic effect. As the key signal mediums of microorganisms, plants, and their interactions, microbial metabolites are of great significance in revealing their functional mechanism. In this study, two potential plant growth-promoting rhizobacteria, Streptomyces albireticuli MDJK11, and Streptomyces alboflavus MDJK44, were selected to explore the effects of co-culture and monoculture on plant growth promotion and disease prevention, and the metabolic material basis was analyzed by metabonomics. Results showed that Streptomyces MDJK11, MDJK44 monoculture, and co-culture condition all showed good growth promoting and antimicrobial effects. Moreover, as compared to the monoculture, the co-culture showed the advantage of a synergistic enhancement effect. LC-MS-based metabonomics analysis showed the metabolic material bases of Streptomyces for plant growth promotion and disease prevention were mainly plant hormone and antibiotics and the co-culture condition could significantly stimulate the production of plant hormone promoters and macrolide, cyclic peptide, and aminoglycoside antibiotics. The study proved that the co-cultures of S. albireticuli MDJK11 and S. alboflavus MDJK44 have great potential in crop growth promotion and disease prevention.
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Affiliation(s)
- Jing Li
- State Key Laboratory of Crop Biology, College of Agronomy, Shandong Agricultural University, Tai’an, China
| | - Lin Zhang
- State Key Laboratory of Crop Biology, College of Agronomy, Shandong Agricultural University, Tai’an, China
| | - Gan Yao
- College of life sciences, Shandong Agricultural University, Tai’an, China
| | - Lixiang Zhu
- State Key Laboratory of Crop Biology, College of Agronomy, Shandong Agricultural University, Tai’an, China
| | - Jingling Lin
- State Key Laboratory of Crop Biology, College of Agronomy, Shandong Agricultural University, Tai’an, China
| | - Chengqiang Wang
- College of life sciences, Shandong Agricultural University, Tai’an, China
| | - Binghai Du
- College of life sciences, Shandong Agricultural University, Tai’an, China
| | - Yanqin Ding
- College of life sciences, Shandong Agricultural University, Tai’an, China
- *Correspondence: Yanqin Ding,
| | - Xiangui Mei
- State Key Laboratory of Crop Biology, College of Agronomy, Shandong Agricultural University, Tai’an, China
- Xiangui Mei,
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Streptomyces: Still the Biggest Producer of New Natural Secondary Metabolites, a Current Perspective. MICROBIOLOGY RESEARCH 2022. [DOI: 10.3390/microbiolres13030031] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022] Open
Abstract
There is a real consensus that new antibiotics are urgently needed and are the best chance for combating antibiotic resistance. The phylum Actinobacteria is one of the main producers of new antibiotics, with a recent paradigm shift whereby rare actinomycetes have been increasingly targeted as a source of new secondary metabolites for the discovery of new antibiotics. However, this review shows that the genus Streptomyces is still the largest current producer of new and innovative secondary metabolites. Between January 2015 and December 2020, a significantly high number of novel Streptomyces spp. have been isolated from different environments, including extreme environments, symbionts, terrestrial soils, sediments and also from marine environments, mainly from marine invertebrates and marine sediments. This review highlights 135 new species of Streptomyces during this 6-year period with 108 new species of Streptomyces from the terrestrial environment and 27 new species from marine sources. A brief summary of the different pre-treatment methods used for the successful isolation of some of the new species of Streptomyces is also discussed, as well as the biological activities of the isolated secondary metabolites. A total of 279 new secondary metabolites have been recorded from 121 species of Streptomyces which exhibit diverse biological activity. The greatest number of new secondary metabolites originated from the terrestrial-sourced Streptomyces spp.
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Huynh TH, Lee J, Moon DH, Nguyen TQ, Son S, Hwang S, Du YE, Cui J, Jang JH, Nam SJ, Shin J, Jang J, Lee SK, Oh KB, Oh DC. Gwanakosides A and B, 6-Deoxy-α-l-talopyranose-Bearing Aromatic Metabolites from a Streptomyces sp. and Coculture with Pandoraea sp. JOURNAL OF NATURAL PRODUCTS 2022; 85:83-90. [PMID: 34931849 DOI: 10.1021/acs.jnatprod.1c00703] [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
Single-strain cultivation of a mountain soil-derived Streptomyces sp. GA02 and its coculture with Pandoraea sp. GA02N produced two aromatic products, gwanakosides A and B (1 and 2, respectively). Their spectroscopic analysis revealed that 1 is a new dichlorinated naphthalene glycoside and 2 is a pentacyclic aromatic glycoside. The assignment of the two chlorine atoms in 1 was confirmed by the analysis of its band-selective CLIP-HSQMBC spectrum. The sugars in the gwanakosides were identified as 6-deoxy-α-l-talopyranose based on 1H-1H coupling constants, Rotating frame Overhauser enhancement spectroscopy (ROESY) NMR correlations, and chemical derivatization followed by spectroscopic and chromatographic analyses. The absolute configuration of 2, whose production was enhanced approximately 100-fold in coculture, was proposed based on a quantum mechanics-based chemical shift analysis method, DP4 calculations, and the chemically determined configuration of 6-deoxy-α-l-talopyranose. Gwanakoside A displayed inhibitory activity against pathogenic bacteria, including Staphylococcus aureus (MIC = 8 μg/mL) and Mycobacterium tuberculosis (MIC50 = 15 μg/mL), and antiproliferative activity against several human cancer cell lines (IC50 = 5.6-19.4 μM).
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Affiliation(s)
- Thanh-Hau Huynh
- Natural Products Research Institute, College of Pharmacy, Seoul National University, 1 Gwanak-ro, Gwanak-gu, Seoul 08826, Republic of Korea
| | - Jayho Lee
- Department of Agricultural Biotechnology, College of Agriculture and Life Sciences, Seoul National University, 1 Gwanak-ro, Gwanak-gu, Seoul 08826, Republic of Korea
| | - Dong Hyun Moon
- Natural Products Research Institute, College of Pharmacy, Seoul National University, 1 Gwanak-ro, Gwanak-gu, Seoul 08826, Republic of Korea
| | - Thanh Quang Nguyen
- 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 52828, Republic of Korea
| | - Sangkeun Son
- Anticancer Agent Research Center, Korea Research Institute of Bioscience and Biotechnology, Cheongju 28116, 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
| | - Young Eun Du
- Natural Products Research Institute, College of Pharmacy, Seoul National University, 1 Gwanak-ro, Gwanak-gu, Seoul 08826, Republic of Korea
| | - Jinsheng Cui
- Natural Products Research Institute, College of Pharmacy, Seoul National University, 1 Gwanak-ro, Gwanak-gu, Seoul 08826, Republic of Korea
| | - Jae-Hyuk Jang
- Anticancer Agent Research Center, Korea Research Institute of Bioscience and Biotechnology, Cheongju 28116, 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, 1 Gwanak-ro, Gwanak-gu, 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 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 and Life Sciences, 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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11
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Boruta T. A bioprocess perspective on the production of secondary metabolites by Streptomyces in submerged co-cultures. World J Microbiol Biotechnol 2021; 37:171. [PMID: 34490503 PMCID: PMC8421279 DOI: 10.1007/s11274-021-03141-z] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2021] [Accepted: 08/31/2021] [Indexed: 12/17/2022]
Abstract
Filamentous microorganisms are potent sources of bioactive secondary metabolites, the molecules formed in response to complex environmental signals. The chemical diversity encoded in microbial genomes is only partially revealed by following the standard microbiological approaches. Mimicking the natural stimuli through laboratory co-cultivation is one of the most effective methods of awakening the formation of high-value metabolic products. Whereas the biosynthetic outcomes of co-cultures are reviewed extensively, the bioprocess aspects of such efforts are often overlooked. The aim of the present review is to discuss the submerged co-cultivation strategies used for triggering and enhancing secondary metabolites production in Streptomyces, a heavily investigated bacterial genus exhibiting an impressive repertoire of secondary metabolites, including a vast array of antibiotics. The previously published studies on influencing the biosynthetic capabilities of Streptomyces through co-cultivation are comparatively analyzed in the bioprocess perspective, mainly with the focus on the approaches of co-culture initiation, the experimental setup, the design of experimental controls and the ways of influencing the outcomes of co-cultivation processes. These topics are discussed in the general context of secondary metabolites production in submerged microbial co-cultures by referring to the Streptomyces-related studies as illustrative examples.
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Affiliation(s)
- Tomasz Boruta
- Department of Bioprocess Engineering, Faculty of Process and Environmental Engineering, Lodz University of Technology, ul. Wolczanska 213, 90-924, Lodz, Poland.
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12
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Kim JH, Lee N, Hwang S, Kim W, Lee Y, Cho S, Palsson BO, Cho BK. Discovery of novel secondary metabolites encoded in actinomycete genomes through coculture. J Ind Microbiol Biotechnol 2021; 48:6119915. [PMID: 33825906 PMCID: PMC9113425 DOI: 10.1093/jimb/kuaa001] [Citation(s) in RCA: 24] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2020] [Accepted: 11/02/2020] [Indexed: 01/23/2023]
Abstract
Actinomycetes are a rich source of bioactive natural products important for novel drug leads. Recent genome mining approaches have revealed an enormous number of secondary metabolite biosynthetic gene clusters (smBGCs) in actinomycetes. However, under standard laboratory culture conditions, many smBGCs are silent or cryptic. To activate these dormant smBGCs, several approaches, including culture-based or genetic engineering-based strategies, have been developed. Above all, coculture is a promising approach to induce novel secondary metabolite production from actinomycetes by mimicking an ecological habitat where cryptic smBGCs may be activated. In this review, we introduce coculture studies that aim to expand the chemical diversity of actinomycetes, by categorizing the cases by the type of coculture partner. Furthermore, we discuss the current challenges that need to be overcome to support the elicitation of novel bioactive compounds from actinomycetes.
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Affiliation(s)
- Ji Hun Kim
- Department of Biological Sciences and KI for the BioCentury, Korea Advanced Institute of Science and Technology, Daejeon 34141, Republic of Korea
| | - Namil Lee
- Department of Biological Sciences and KI for the BioCentury, Korea Advanced Institute of Science and Technology, Daejeon 34141, Republic of Korea
| | - Soonkyu Hwang
- Department of Biological Sciences and KI for the BioCentury, Korea Advanced Institute of Science and Technology, Daejeon 34141, Republic of Korea
| | - Woori Kim
- Department of Biological Sciences and KI for the BioCentury, Korea Advanced Institute of Science and Technology, Daejeon 34141, Republic of Korea
| | - Yongjae Lee
- Department of Biological Sciences and KI for the BioCentury, Korea Advanced Institute of Science and Technology, Daejeon 34141, Republic of Korea
| | - Suhyung Cho
- Department of Biological Sciences and KI for the BioCentury, Korea Advanced Institute of Science and Technology, Daejeon 34141, Republic of Korea
| | - Bernhard O Palsson
- Department of Bioengineering, University of California, San Diego, La Jolla, CA 92093, USA.,Department of Pediatrics, University of California, San Diego, La Jolla, CA 92093, USA.,Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, 2800 Lyngby, Denmark
| | - Byung-Kwan Cho
- Department of Biological Sciences and KI for the BioCentury, Korea Advanced Institute of Science and Technology, Daejeon 34141, Republic of Korea.,Intelligent Synthetic Biology Center, Daejeon 34141, Republic of Korea
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13
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Tenorio-Salgado S, Castelán-Sánchez HG, Dávila-Ramos S, Huerta-Saquero A, Rodríguez-Morales S, Merino-Pérez E, Roa de la Fuente LF, Solis-Pereira SE, Pérez-Rueda E, Lizama-Uc G. Metagenomic analysis and antimicrobial activity of two fermented milk kefir samples. Microbiologyopen 2021; 10:e1183. [PMID: 33970536 PMCID: PMC8103080 DOI: 10.1002/mbo3.1183] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2021] [Revised: 03/22/2021] [Accepted: 03/23/2021] [Indexed: 11/09/2022] Open
Abstract
In recent years, the fermented milk product kefir has been intensively studied because of its health benefits. Here, we evaluated the microbial consortia of two kefir samples, from Escarcega, Campeche, and Campeche (México). We considered a functional comparison between both samples, including fungal and bacterial inhibition; second, we applied shotgun metagenomics to assess the structure and functional diversity of the communities of microorganisms. These two samples exhibited antagonisms against bacterial and fungal pathogens. Bioactive polyketides and nonribosomal peptides were identified by LC‐HRMS analysis. We also observed a high bacterial diversity and an abundance of Actinobacteria in both kefir samples, and a greater abundance of Saccharomyces species in kefir of Escarcega than in the Campeche kefir. When the prophage compositions were evaluated, the Campeche sample showed a higher diversity of prophage sequences. In Escarcega, we observed a prevalence of prophage families that infect Enterobacteria and Lactobacillus. The sequences associated with secondary metabolites, such as plipastatin, fengycin, and bacillaene, and also bacteriocins like helveticin and zoocin, were also found in different proportions, with greater diversity in the Escarcega sample. The analyses described in this work open the opportunity to understand the microbial diversity in kefir samples from two distant localities.
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Affiliation(s)
| | - Hugo G Castelán-Sánchez
- Centro de Investigación en Dinámica Celular, Universidad Autónoma del Estado de Morelos, Cuernavaca, México
| | - Sonia Dávila-Ramos
- Centro de Investigación en Dinámica Celular, Universidad Autónoma del Estado de Morelos, Cuernavaca, México
| | | | | | - Enrique Merino-Pérez
- Departamento de Microbiologia, Instituto de Biotecnologıa, Universidad Nacional Autonoma de Mexico, Cuernavaca, México
| | - Luis Fernando Roa de la Fuente
- Centro de Investigación de Ciencia y Tecnología Aplicada de Tabasco, Universidad Juárez Autónoma de Tabasco, Tabasco, México
| | | | - Ernesto Pérez-Rueda
- Instituto de Investigaciones en Matemáticas Aplicadas y en Sistemas, UNAM, Unidad Académica Yucatán, Mérida, México
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14
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Utilizing cross-species co-cultures for discovery of novel natural products. Curr Opin Biotechnol 2021; 69:252-262. [PMID: 33647849 DOI: 10.1016/j.copbio.2021.01.023] [Citation(s) in RCA: 19] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2020] [Revised: 01/12/2021] [Accepted: 01/24/2021] [Indexed: 12/11/2022]
Abstract
Discovery of new natural products, especially those with high biological activities and application values, is of great research significance. However, conventional methods based on the cultivation of microbial mono-cultures can hardly satisfy the increasing need of novel natural product generation. Recently, the development of co-cultures composed of different species has emerged as an effective approach for mining novel natural products. Inspired by microbial communities in nature, these co-culture systems create favorable environmental conditions to promote interactions between co-culture members for activating the natural product biosynthesis that is hard to induce otherwise. A large variety of novel natural products have been identified using this robust approach. This review summarizes the recent achievements of using cross-species co-cultures for natural products discovery and discusses the existing challenges and future directions.
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15
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Arora D, Gupta P, Jaglan S, Roullier C, Grovel O, Bertrand S. Expanding the chemical diversity through microorganisms co-culture: Current status and outlook. Biotechnol Adv 2020; 40:107521. [PMID: 31953204 DOI: 10.1016/j.biotechadv.2020.107521] [Citation(s) in RCA: 63] [Impact Index Per Article: 15.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2019] [Revised: 11/29/2019] [Accepted: 01/13/2020] [Indexed: 12/17/2022]
Abstract
Natural products (NPs) are considered as a cornerstone for the generation of bioactive leads in drug discovery programs. However, one of the major limitations of NP drug discovery program is "rediscovery" of known compounds, thereby hindering the rate of drug discovery efficiency. Therefore, in recent years, to overcome these limitations, a great deal of attention has been drawn towards understanding the role of microorganisms' co-culture in inducing novel chemical entities. Such induction could be related to activation of genes which might be silent or expressed at very low levels (below detection limit) in pure-strain cultures under normal laboratory conditions. In this review, chemical diversity of compounds isolated from microbial co-cultures, is discussed. For this purpose, chemodiversity has been represented as a chemical-structure network based on the "Tanimoto Structural Similarity Index". This highlights the huge structural diversity induced by microbial co-culture. In addition, the current trends in microbial co-culture research are highlighted. Finally, the current challenges (1 - induction monitoring, 2 - reproducibility, 3 - growth time effect and 4 - up-scaling for isolation purposes) are discussed. The information in this review will support researchers to design microbial co-culture strategies for future research efforts. In addition, guidelines for co-culture induction reporting are also provided to strengthen future reporting in this NP field.
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Affiliation(s)
- Divya Arora
- Microbial Biotechnology Division, CSIR-Indian Institute of Integrative Medicine, Jammu 180001, India; Academy of Scientific and Innovative Research (AcSIR), Jammu Campus, Jammu 180001, India; Groupe Mer, Molécules, Santé-EA 2160, Faculté des Sciences pharmaceutiques et biologiques, Université de Nantes, 9 rue Bias, BP 53508, F-44035 Nantes Cedex 01, France
| | - Prasoon Gupta
- Natural Product Chemistry Division, CSIR-Indian Institute of Integrative Medicine, Jammu 180001, India; Academy of Scientific and Innovative Research (AcSIR), Jammu Campus, Jammu 180001, India
| | - Sundeep Jaglan
- Microbial Biotechnology Division, CSIR-Indian Institute of Integrative Medicine, Jammu 180001, India; Academy of Scientific and Innovative Research (AcSIR), Jammu Campus, Jammu 180001, India
| | - Catherine Roullier
- Groupe Mer, Molécules, Santé-EA 2160, Faculté des Sciences pharmaceutiques et biologiques, Université de Nantes, 9 rue Bias, BP 53508, F-44035 Nantes Cedex 01, France
| | - Olivier Grovel
- Groupe Mer, Molécules, Santé-EA 2160, Faculté des Sciences pharmaceutiques et biologiques, Université de Nantes, 9 rue Bias, BP 53508, F-44035 Nantes Cedex 01, France
| | - Samuel Bertrand
- Groupe Mer, Molécules, Santé-EA 2160, Faculté des Sciences pharmaceutiques et biologiques, Université de Nantes, 9 rue Bias, BP 53508, F-44035 Nantes Cedex 01, France.
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16
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Pan R, Bai X, Chen J, Zhang H, Wang H. Exploring Structural Diversity of Microbe Secondary Metabolites Using OSMAC Strategy: A Literature Review. Front Microbiol 2019; 10:294. [PMID: 30863377 PMCID: PMC6399155 DOI: 10.3389/fmicb.2019.00294] [Citation(s) in RCA: 134] [Impact Index Per Article: 26.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2018] [Accepted: 02/04/2019] [Indexed: 12/27/2022] Open
Abstract
Microbial secondary metabolites (MSMs) have played and continue to play a highly significant role in the drug discovery and development process. Genetically, MSM chemical structures are biologically synthesized by microbial gene clusters. Recently, however, the speed of new bioactive MSM discovery has been slowing down due to consistent employment of conventional cultivation and isolation procedure. In order to alleviate this challenge, a number of new approaches have been developed. The strategy of one strain many compounds (OSMAC) has been shown as a simple and powerful tool that can activate many silent biogenetic gene clusters in microorganisms to make more natural products. This review highlights important and successful examples using OSMAC approaches, which covers changing medium composition and cultivation status, co-cultivation with other strain(s), adding enzyme inhibitor(s) and MSM biosynthetic precursor(s). Available evidences had shown that variation of cultivation condition is the most effective way to produce more MSMs and facilitate the discovery of new therapeutic agents.
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Affiliation(s)
- Rui Pan
- School of Pharmaceutical Sciences, Zhejiang University of Technology, Hangzhou, China
| | - Xuelian Bai
- College of Life and Environmental Sciences, Hangzhou Normal University, Hangzhou, China
| | - Jianwei Chen
- School of Pharmaceutical Sciences, Zhejiang University of Technology, Hangzhou, China
| | - Huawei Zhang
- School of Pharmaceutical Sciences, Zhejiang University of Technology, Hangzhou, China
| | - Hong Wang
- School of Pharmaceutical Sciences, Zhejiang University of Technology, Hangzhou, China
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17
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Activation of silent biosynthetic pathways and discovery of novel secondary metabolites in actinomycetes by co-culture with mycolic acid-containing bacteria. J Ind Microbiol Biotechnol 2018; 46:363-374. [PMID: 30488365 DOI: 10.1007/s10295-018-2100-y] [Citation(s) in RCA: 43] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2018] [Accepted: 10/26/2018] [Indexed: 01/25/2023]
Abstract
Bacterial secondary metabolites (SM) are rich sources of drug leads, and in particular, numerous metabolites have been isolated from actinomycetes. It was revealed by recent genome sequence projects that actinomycetes harbor much more secondary metabolite-biosynthetic gene clusters (SM-BGCs) than previously expected. Nevertheless, large parts of SM-BGCs in actinomycetes are dormant and cryptic under the standard culture conditions. Therefore, a widely applicable methodology for cryptic SM-BGC activation is required to obtain novel SM. Recently, it was discovered that co-culturing with mycolic-acid-containing bacteria (MACB) widely activated cryptic SM-BGCs in actinomycetes. This "combined-culture" methodology (co-culture methodology using MACB as the partner of actinomycetes) is easily applicable for a broad range of actinomycetes, and indeed, 33 novel SM have been successfully obtained from 12 actinomycetes so far. In this review, the development, application, and mechanistic analysis of the combined-culture method were summarized.
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